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Sample records for california niche modeling

  1. Spatial analysis of plague in California: niche modeling predictions of the current distribution and potential response to climate change

    Directory of Open Access Journals (Sweden)

    Tucker James R

    2009-06-01

    Full Text Available Abstract Background Plague, caused by the bacterium Yersinia pestis, is a public and wildlife health concern in California and the western United States. This study explores the spatial characteristics of positive plague samples in California and tests Maxent, a machine-learning method that can be used to develop niche-based models from presence-only data, for mapping the potential distribution of plague foci. Maxent models were constructed using geocoded seroprevalence data from surveillance of California ground squirrels (Spermophilus beecheyi as case points and Worldclim bioclimatic data as predictor variables, and compared and validated using area under the receiver operating curve (AUC statistics. Additionally, model results were compared to locations of positive and negative coyote (Canis latrans samples, in order to determine the correlation between Maxent model predictions and areas of plague risk as determined via wild carnivore surveillance. Results Models of plague activity in California ground squirrels, based on recent climate conditions, accurately identified case locations (AUC of 0.913 to 0.948 and were significantly correlated with coyote samples. The final models were used to identify potential plague risk areas based on an ensemble of six future climate scenarios. These models suggest that by 2050, climate conditions may reduce plague risk in the southern parts of California and increase risk along the northern coast and Sierras. Conclusion Because different modeling approaches can yield substantially different results, care should be taken when interpreting future model predictions. Nonetheless, niche modeling can be a useful tool for exploring and mapping the potential response of plague activity to climate change. The final models in this study were used to identify potential plague risk areas based on an ensemble of six future climate scenarios, which can help public managers decide where to allocate surveillance resources

  2. A Niche Width Model of Optimal Specialization

    NARCIS (Netherlands)

    Bruggeman, Jeroen; Ó Nualláin, Breanndán

    2000-01-01

    Niche width theory, a part of organizational ecology, predicts whether “specialist” or “generalist” forms of organizations have higher “fitness,” in a continually changing environment. To this end, niche width theory uses a mathematical model borrowed from biology. In this paper, we first loosen th

  3. The probabilistic niche model reveals substantial variation in the niche structure of empirical food webs.

    Science.gov (United States)

    Williams, Richard J; Purves, Drew W

    2011-09-01

    The structure of food webs, complex networks of interspecies feeding interactions, plays a crucial role in ecosystem resilience and function, and understanding food web structure remains a central problem in ecology. Previous studies have shown that key features of empirical food webs can be reproduced by low-dimensional "niche" models. Here we examine the form and variability of food web niche structure by fitting a probabilistic niche model to 37 empirical food webs, a much larger number of food webs than used in previous studies. The model relaxes previous assumptions about parameter distributions and hierarchy and returns parameter estimates for each species in each web. The model significantly outperforms previous niche model variants and also performs well for several webs where a body-size-based niche model performs poorly, implying that traits other than body size are important in structuring these webs' niche space. Parameter estimates frequently violate previous models' assumptions: in 19 of 37 webs, parameter values are not significantly hierarchical, 32 of 37 webs have nonuniform niche value distributions, and 15 of 37 webs lack a correlation between niche width and niche position. Extending the model to a two-dimensional niche space yields networks with a mixture of one- and two-dimensional niches and provides a significantly better fit for webs with a large number of species and links. These results confirm that food webs are strongly niche-structured but reveal substantial variation in the form of the niche structuring, a result with fundamental implications for ecosystem resilience and function.

  4. Evaluating correlative and mechanistic niche models for assessing the risk of pest establishment

    Science.gov (United States)

    Ecological niche modeling was used to assess the risk of establishment of western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), in sweet cherry, Prunus avium (L.) L., in the commercial cherry-growing areas of California. We integrated species occurrence records and spatial...

  5. The probabilistic niche model reveals the niche structure and role of body size in a complex food web.

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    Richard J Williams

    Full Text Available The niche model has been widely used to model the structure of complex food webs, and yet the ecological meaning of the single niche dimension has not been explored. In the niche model, each species has three traits, niche position, diet position and feeding range. Here, a new probabilistic niche model, which allows the maximum likelihood set of trait values to be estimated for each species, is applied to the food web of the Benguela fishery. We also developed the allometric niche model, in which body size is used as the niche dimension. About 80% of the links in the empirical data are predicted by the probabilistic niche model, a significant improvement over recent models. As in the niche model, species are uniformly distributed on the niche axis. Feeding ranges are exponentially distributed, but diet positions are not uniformly distributed below the predator. Species traits are strongly correlated with body size, but the allometric niche model performs significantly worse than the probabilistic niche model. The best-fit parameter set provides a significantly better model of the structure of the Benguela food web than was previously available. The methodology allows the identification of a number of taxa that stand out as outliers either in the model's poor performance at predicting their predators or prey or in their parameter values. While important, body size alone does not explain the structure of the one-dimensional niche.

  6. GIS-based niche modeling for mapping species' habitat.

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    Rotenberry, John T; Preston, Kristine L; Knick, Steven T

    2006-06-01

    Ecological "niche modeling" using presence-only locality data and large-scale environmental variables provides a powerful tool for identifying and mapping suitable habitat for species over large spatial extents. We describe a niche modeling approach that identifies a minimum (rather than an optimum) set of basic habitat requirements for a species, based on the assumption that constant environmental relationships in a species' distribution (i.e., variables that maintain a consistent value where the species occurs) are most likely to be associated with limiting factors. Environmental variables that take on a wide range of values where a species occurs are less informative because they do not limit a species' distribution, at least over the range of variation sampled. This approach is operationalized by partitioning Mahalanobis D2 (standardized difference between values of a set of environmental variables for any point and mean values for those same variables calculated from all points at which a species was detected) into independent components. The smallest of these components represents the linear combination of variables with minimum variance; increasingly larger components represent larger variances and are increasingly less limiting. We illustrate this approach using the California Gnatcatcher (Polioptila californica Brewster) and provide SAS code to implement it.

  7. GIS-based niche modeling for mapping species' habitats

    Science.gov (United States)

    Rotenberry, J.T.; Preston, K.L.; Knick, S.

    2006-01-01

    Ecological a??niche modelinga?? using presence-only locality data and large-scale environmental variables provides a powerful tool for identifying and mapping suitable habitat for species over large spatial extents. We describe a niche modeling approach that identifies a minimum (rather than an optimum) set of basic habitat requirements for a species, based on the assumption that constant environmental relationships in a species' distribution (i.e., variables that maintain a consistent value where the species occurs) are most likely to be associated with limiting factors. Environmental variables that take on a wide range of values where a species occurs are less informative because they do not limit a species' distribution, at least over the range of variation sampled. This approach is operationalized by partitioning Mahalanobis D2 (standardized difference between values of a set of environmental variables for any point and mean values for those same variables calculated from all points at which a species was detected) into independent components. The smallest of these components represents the linear combination of variables with minimum variance; increasingly larger components represent larger variances and are increasingly less limiting. We illustrate this approach using the California Gnatcatcher (Polioptila californica Brewster) and provide SAS code to implement it.

  8. Ecological niche modeling and its applications in biodiversity conservation

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    Gengping Zhu

    2013-01-01

    Full Text Available Based on the environmental variables that associated with species’ occurrence records, ecological niche modeling (ENM seeks to characterize environmental conditions suitable for a particular species and then identify where suitable environmental habitats are distributed in the space. Recently, ENM has been used increasingly in biological invasion, conservation biology, biological responses toclimate change, disease spatial transmission, and variety aspects of ecology and evolutionary biology research. However, the theoretical background of these applications is generally poorly understood, leading to artifactual conclusions in some studies (e.g. niche differentiation during species’ invasion. In this paper we discuss the relationship between niche and geographic distribution and introduce the theoretical basis of ENM, along with relationships between the niche and ENM. Abiotic/biotic, historical and dispersal factors are three key elements that determine species’ geographic distributions at different scales. By using environmental variables derived from distributional records, ENM is based on observations that already include effects of biotic interactions, therefore ENM is used to characterize somewhere between the realized niche and potential niche, not the fundamental niche. Grinnellian and Eltonian niches are both manifested in ENM calibration, depending on the types of variables used to fit model, the natural spatial scale at which they can be measured, and the dispersal of individuals throughout the environment. Applications of ENM in understanding ecological requirements of species, discovery of new species or populations, nature reserve design, predicting potential invasion, modeling biological responses to climate change, niche conservatism, and pecies delimitation are discussed in this paper.

  9. Modeling dynamics of mutants in heterogeneous stem cell niche

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    Shahriyari, L.; Mahdipour-Shirayeh, A.

    2017-02-01

    Studying the stem cell (SC) niche architecture is a crucial step for investigating the process of oncogenesis and obtaining an effective stem cell therapy for various cancers. Recently, it has been observed that there are two groups of SCs in the SC niche collaborating with each other to maintain tissue homeostasis: border stem cells (BSCs), which are responsible in controlling the number of non-stem cells as well as stem cells, and central stem cells (CeSCs), which regulate the SC niche. Here, we develop a bi-compartmental stochastic model for the SC niche to study the spread of mutants within the niche. The analytic calculations and numeric simulations, which are in perfect agreement, reveal that in order to delay the spread of mutants in the SC niche, a small but non-zero number of SC proliferations must occur in the CeSC compartment. Moreover, the migration of BSCs to CeSCs delays the spread of mutants. Furthermore, the fixation probability of mutants in the SC niche is independent of types of SC division as long as all SCs do not divide fully asymmetrically. Additionally, the progeny of CeSCs have a much higher chance than the progeny of BSCs to take over the entire niche.

  10. Advances and Limitations of Disease Biogeography Using Ecological Niche Modeling.

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    Escobar, Luis E; Craft, Meggan E

    2016-01-01

    Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks.

  11. Advances and Limitations of Disease Biogeography Using Ecological Niche Modeling

    Science.gov (United States)

    Escobar, Luis E.; Craft, Meggan E.

    2016-01-01

    Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks. PMID:27547199

  12. Advances and Limitations of Disease Biogeography Using Ecological Niche Modeling

    Directory of Open Access Journals (Sweden)

    Luis E Escobar

    2016-08-01

    Full Text Available Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches can fail to generate robust study designs, generating incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables, identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks.

  13. Introducing BioSARN - an ecological niche model refinement tool.

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    Heap, Marshall J

    2016-08-01

    Environmental niche modeling outputs a biological species' potential distribution. Further work is needed to arrive at a species' realized distribution. The Biological Species Approximate Realized Niche (BioSARN) application provides the ecological modeler with a toolset to refine Environmental niche models (ENMs). These tools include soil and land class filtering, niche area quantification and novelties like enhanced temporal corridor definition, and output to a high spatial resolution land class model. BioSARN is exemplified with a study on Fraser fir, a tree species with strong land class and edaphic correlations. Soil and land class filtering caused the potential distribution area to decline 17%. Enhanced temporal corridor definition permitted distinction of current, continuing, and future niches, and thus niche change and movement. Tile quantification analysis provided further corroboration of these trends. BioSARN does not substitute other established ENM methods. Rather, it allows the experimenter to work with their preferred ENM, refining it using their knowledge and experience. Output from lower spatial resolution ENMs to a high spatial resolution land class model is a pseudo high-resolution result. Still, it maybe the best that can be achieved until wide range high spatial resolution environmental data and accurate high precision species occurrence data become generally available.

  14. Ecological Niche Modelling of Bank Voles in Western Europe

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    Sara Amirpour Haredasht

    2013-01-01

    Full Text Available The bank vole (Myodes glareolus is the natural host of Puumala virus (PUUV in vast areas of Europe. PUUV is one of the hantaviruses which are transmitted to humans by infected rodents. PUUV causes a general mild form of hemorrhagic fever with renal syndrome (HFRS called nephropathia epidemica (NE. Vector-borne and zoonotic diseases generally display clear spatial patterns due to different space-dependent factors. Land cover influences disease transmission by controlling both the spatial distribution of vectors or hosts, as well as by facilitating the human contact with them. In this study the use of ecological niche modelling (ENM for predicting the geographical distribution of bank vole population on the basis of spatial climate information is tested. The Genetic Algorithm for Rule-set Prediction (GARP is used to model the ecological niche of bank voles in Western Europe. The meteorological data, land cover types and geo-referenced points representing the locations of the bank voles (latitude/longitude in the study area are used as the primary model input value. The predictive accuracy of the bank vole ecologic niche model was significant (training accuracy of 86%. The output of the GARP models based on the 50% subsets of points used for testing the model showed an accuracy of 75%. Compared with random models, the probability of such high predictivity was low (χ2 tests, p < 10−6. As such, the GARP models were predictive and the used ecologic niche model indeed indicates the ecologic requirements of bank voles. This approach successfully identified the areas of infection risk across the study area. The result suggests that the niche modelling approach can be implemented in a next step towards the development of new tools for monitoring the bank vole’s population.

  15. Models of cultural niche construction with selection and assortative mating.

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    Creanza, Nicole; Fogarty, Laurel; Feldman, Marcus W

    2012-01-01

    Niche construction is a process through which organisms modify their environment and, as a result, alter the selection pressures on themselves and other species. In cultural niche construction, one or more cultural traits can influence the evolution of other cultural or biological traits by affecting the social environment in which the latter traits may evolve. Cultural niche construction may include either gene-culture or culture-culture interactions. Here we develop a model of this process and suggest some applications of this model. We examine the interactions between cultural transmission, selection, and assorting, paying particular attention to the complexities that arise when selection and assorting are both present, in which case stable polymorphisms of all cultural phenotypes are possible. We compare our model to a recent model for the joint evolution of religion and fertility and discuss other potential applications of cultural niche construction theory, including the evolution and maintenance of large-scale human conflict and the relationship between sex ratio bias and marriage customs. The evolutionary framework we introduce begins to address complexities that arise in the quantitative analysis of multiple interacting cultural traits.

  16. Models of cultural niche construction with selection and assortative mating.

    Directory of Open Access Journals (Sweden)

    Nicole Creanza

    Full Text Available Niche construction is a process through which organisms modify their environment and, as a result, alter the selection pressures on themselves and other species. In cultural niche construction, one or more cultural traits can influence the evolution of other cultural or biological traits by affecting the social environment in which the latter traits may evolve. Cultural niche construction may include either gene-culture or culture-culture interactions. Here we develop a model of this process and suggest some applications of this model. We examine the interactions between cultural transmission, selection, and assorting, paying particular attention to the complexities that arise when selection and assorting are both present, in which case stable polymorphisms of all cultural phenotypes are possible. We compare our model to a recent model for the joint evolution of religion and fertility and discuss other potential applications of cultural niche construction theory, including the evolution and maintenance of large-scale human conflict and the relationship between sex ratio bias and marriage customs. The evolutionary framework we introduce begins to address complexities that arise in the quantitative analysis of multiple interacting cultural traits.

  17. Niche variability and its consequences for species distribution modeling.

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    Matt J Michel

    Full Text Available When species distribution models (SDMs are used to predict how a species will respond to environmental change, an important assumption is that the environmental niche of the species is conserved over evolutionary time-scales. Empirical studies conducted at ecological time-scales, however, demonstrate that the niche of some species can vary in response to environmental change. We use habitat and locality data of five species of stream fishes collected across seasons to examine the effects of niche variability on the accuracy of projections from Maxent, a popular SDM. We then compare these predictions to those from an alternate method of creating SDM projections in which a transformation of the environmental data to similar scales is applied. The niche of each species varied to some degree in response to seasonal variation in environmental variables, with most species shifting habitat use in response to changes in canopy cover or flow rate. SDMs constructed from the original environmental data accurately predicted the occurrences of one species across all seasons and a subset of seasons for two other species. A similar result was found for SDMs constructed from the transformed environmental data. However, the transformed SDMs produced better models in ten of the 14 total SDMs, as judged by ratios of mean probability values at known presences to mean probability values at all other locations. Niche variability should be an important consideration when using SDMs to predict future distributions of species because of its prevalence among natural populations. The framework we present here may potentially improve these predictions by accounting for such variability.

  18. Niche models tell half the story

    DEFF Research Database (Denmark)

    Swab, Rebecca Marie; Regan, Helen M.; Keith, David A.;

    2012-01-01

    functions representing a suite of average fire return intervals. We compared scenarios with a variety of hypothetical patches, a patch framework based upon current habitat suitability and one with dynamic habitat suitability based on climate change scenarios A1FI and A2. Results  Leucopogon setiger...... threat when habitat reductions were predicted. Incorporating life-history traits into habitat suitability models by linking species distribution models with population models allowed for the population-level evaluation of multiple stressors that affect population dynamics and habitat, ultimately...... was found to be sensitive to fire frequency, with shorter intervals reducing expected minimum abundances (EMAs). Spatial decoupling of fires across the landscape reduced the vulnerability of the species to shortened fire frequencies. Shifting habitat, while reducing EMAs, was less of a threat to the species...

  19. Maximum Entropy-Based Ecological Niche Model and Bio-Climatic Determinants of Lone Star Tick (Amblyomma americanum) Niche.

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    Raghavan, Ram K; Goodin, Douglas G; Hanzlicek, Gregg A; Zolnerowich, Gregory; Dryden, Michael W; Anderson, Gary A; Ganta, Roman R

    2016-03-01

    The potential distribution of Amblyomma americanum ticks in Kansas was modeled using maximum entropy (MaxEnt) approaches based on museum and field-collected species occurrence data. Various bioclimatic variables were used in the model as potentially influential factors affecting the A. americanum niche. Following reduction of dimensionality among predictor variables using principal components analysis, which revealed that the first two principal axes explain over 87% of the variance, the model indicated that suitable conditions for this medically important tick species cover a larger area in Kansas than currently believed. Soil moisture, temperature, and precipitation were highly correlated with the first two principal components and were influential factors in the A. americanum ecological niche. Assuming that the niche estimated in this study covers the occupied distribution, which needs to be further confirmed by systematic surveys, human exposure to this known disease vector may be considerably under-appreciated in the state.

  20. Framework for analyzing ecological trait-based models in multidimensional niche spaces

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    Biancalani, Tommaso; DeVille, Lee; Goldenfeld, Nigel

    2015-05-01

    We develop a theoretical framework for analyzing ecological models with a multidimensional niche space. Our approach relies on the fact that ecological niches are described by sequences of symbols, which allows us to include multiple phenotypic traits. Ecological drivers, such as competitive exclusion, are modeled by introducing the Hamming distance between two sequences. We show that a suitable transform diagonalizes the community interaction matrix of these models, making it possible to predict the conditions for niche differentiation and, close to the instability onset, the asymptotically long time population distributions of niches. We exemplify our method using the Lotka-Volterra equations with an exponential competition kernel.

  1. A mechanistic niche model for measuring species' distributional responses to seasonal temperature gradients.

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    William B Monahan

    Full Text Available Niche theory is central to understanding how species respond geographically to climate change. It defines a species' realized niche in a biological community, its fundamental niche as determined by physiology, and its potential niche--the fundamental niche in a given environment or geographic space. However, most predictions of the effects of climate change on species' distributions are limited to correlative models of the realized niche, which assume that species are in distributional equilibrium with respect to the variables or gradients included in the model. Here, I present a mechanistic niche model that measures species' responses to major seasonal temperature gradients that interact with the physiology of the organism. I then use lethal physiological temperatures to parameterize the model for bird species in North and South America and show that most focal bird species are not in direct physiological equilibrium with the gradients. Results also show that most focal bird species possess broad thermal tolerances encompassing novel climates that could become available with climate change. I conclude with discussion of how mechanistic niche models may be used to (i gain insights into the processes that cause species to respond to climate change and (ii build more accurate correlative distribution models in birds and other species.

  2. Improved Predictions of the Geographic Distribution of Invasive Plants Using Climatic Niche Models.

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    Ramírez-Albores, Jorge E; Bustamante, Ramiro O; Badano, Ernesto I

    2016-01-01

    Climatic niche models for invasive plants are usually constructed with occurrence records taken from literature and collections. Because these data neither discriminate among life-cycle stages of plants (adult or juvenile) nor the origin of individuals (naturally established or man-planted), the resulting models may mispredict the distribution ranges of these species. We propose that more accurate predictions could be obtained by modelling climatic niches with data of naturally established individuals, particularly with occurrence records of juvenile plants because this would restrict the predictions of models to those sites where climatic conditions allow the recruitment of the species. To test this proposal, we focused on the Peruvian peppertree (Schinus molle), a South American species that has largely invaded Mexico. Three climatic niche models were constructed for this species using high-resolution dataset gathered in the field. The first model included all occurrence records, irrespective of the life-cycle stage or origin of peppertrees (generalized niche model). The second model only included occurrence records of naturally established mature individuals (adult niche model), while the third model was constructed with occurrence records of naturally established juvenile plants (regeneration niche model). When models were compared, the generalized climatic niche model predicted the presence of peppertrees in sites located farther beyond the climatic thresholds that naturally established individuals can tolerate, suggesting that human activities influence the distribution of this invasive species. The adult and regeneration climatic niche models concurred in their predictions about the distribution of peppertrees, suggesting that naturally established adult trees only occur in sites where climatic conditions allow the recruitment of juvenile stages. These results support the proposal that climatic niches of invasive plants should be modelled with data of

  3. Improved Predictions of the Geographic Distribution of Invasive Plants Using Climatic Niche Models.

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    Jorge E Ramírez-Albores

    Full Text Available Climatic niche models for invasive plants are usually constructed with occurrence records taken from literature and collections. Because these data neither discriminate among life-cycle stages of plants (adult or juvenile nor the origin of individuals (naturally established or man-planted, the resulting models may mispredict the distribution ranges of these species. We propose that more accurate predictions could be obtained by modelling climatic niches with data of naturally established individuals, particularly with occurrence records of juvenile plants because this would restrict the predictions of models to those sites where climatic conditions allow the recruitment of the species. To test this proposal, we focused on the Peruvian peppertree (Schinus molle, a South American species that has largely invaded Mexico. Three climatic niche models were constructed for this species using high-resolution dataset gathered in the field. The first model included all occurrence records, irrespective of the life-cycle stage or origin of peppertrees (generalized niche model. The second model only included occurrence records of naturally established mature individuals (adult niche model, while the third model was constructed with occurrence records of naturally established juvenile plants (regeneration niche model. When models were compared, the generalized climatic niche model predicted the presence of peppertrees in sites located farther beyond the climatic thresholds that naturally established individuals can tolerate, suggesting that human activities influence the distribution of this invasive species. The adult and regeneration climatic niche models concurred in their predictions about the distribution of peppertrees, suggesting that naturally established adult trees only occur in sites where climatic conditions allow the recruitment of juvenile stages. These results support the proposal that climatic niches of invasive plants should be modelled with

  4. Improved Predictions of the Geographic Distribution of Invasive Plants Using Climatic Niche Models

    Science.gov (United States)

    Ramírez-Albores, Jorge E.; Bustamante, Ramiro O.

    2016-01-01

    Climatic niche models for invasive plants are usually constructed with occurrence records taken from literature and collections. Because these data neither discriminate among life-cycle stages of plants (adult or juvenile) nor the origin of individuals (naturally established or man-planted), the resulting models may mispredict the distribution ranges of these species. We propose that more accurate predictions could be obtained by modelling climatic niches with data of naturally established individuals, particularly with occurrence records of juvenile plants because this would restrict the predictions of models to those sites where climatic conditions allow the recruitment of the species. To test this proposal, we focused on the Peruvian peppertree (Schinus molle), a South American species that has largely invaded Mexico. Three climatic niche models were constructed for this species using high-resolution dataset gathered in the field. The first model included all occurrence records, irrespective of the life-cycle stage or origin of peppertrees (generalized niche model). The second model only included occurrence records of naturally established mature individuals (adult niche model), while the third model was constructed with occurrence records of naturally established juvenile plants (regeneration niche model). When models were compared, the generalized climatic niche model predicted the presence of peppertrees in sites located farther beyond the climatic thresholds that naturally established individuals can tolerate, suggesting that human activities influence the distribution of this invasive species. The adult and regeneration climatic niche models concurred in their predictions about the distribution of peppertrees, suggesting that naturally established adult trees only occur in sites where climatic conditions allow the recruitment of juvenile stages. These results support the proposal that climatic niches of invasive plants should be modelled with data of

  5. To predict the niche, model colonization and extinction

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    Yackulic, Charles B.; Nichols, James D.; Reid, Janice; Der, Ricky

    2015-01-01

    Ecologists frequently try to predict the future geographic distributions of species. Most studies assume that the current distribution of a species reflects its environmental requirements (i.e., the species' niche). However, the current distributions of many species are unlikely to be at equilibrium with the current distribution of environmental conditions, both because of ongoing invasions and because the distribution of suitable environmental conditions is always changing. This mismatch between the equilibrium assumptions inherent in many analyses and the disequilibrium conditions in the real world leads to inaccurate predictions of species' geographic distributions and suggests the need for theory and analytical tools that avoid equilibrium assumptions. Here, we develop a general theory of environmental associations during periods of transient dynamics. We show that time-invariant relationships between environmental conditions and rates of local colonization and extinction can produce substantial temporal variation in occupancy–environment relationships. We then estimate occupancy–environment relationships during three avian invasions. Changes in occupancy–environment relationships over time differ among species but are predicted by dynamic occupancy models. Since estimates of the occupancy–environment relationships themselves are frequently poor predictors of future occupancy patterns, research should increasingly focus on characterizing how rates of local colonization and extinction vary with environmental conditions.

  6. EVOLUTIONARY DYNAMIC MODEL OF POPULATION WITH NICHE CONSTRUCTION AND ITS APPLICATION RESEARCH

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Based on the theories and approaches in biomechanics, the mechanism and pattern of niche construction were discussed systematically. Through establishing the spatial pattern of niche and its measuring-fitness formula, and the dynamic system models of single- and two-population with niche construction, including corresponding theoretical analysis and numerical simulation on their evolutionary dynamics of population and the mechanism of competitive coexistence, the co-evolutionary relationship between organisms and their environments was revealed. The results indicate that population dynamics is governed by positive feedback between primary ecological factors and resource content.Niche construction generates an evolutionary effect in system by influencing the fitness of population. A threshold effect exists in single population dynamic system. In dynamic system of two competitive populations, niche construction can lead to alternative competitive consequences, which may be a potential mechanism to explain the competitive coexistence of species.

  7. Evaluating how species niche modelling is affected by partial distributions with an empirical case

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    Carretero, Miguel A.; Sillero, Neftalí

    2016-11-01

    Ecological niche models (ENMs) will successfully identify a species' ecological niche, provided that important assumptions are fulfilled, namely environment equilibrium and niche equality across the distribution. Violations may seriously affect ENM reliability, leading to erroneous biogeographic conclusions and inappropriate conservation prioritisation. We evaluate the robustness of ENMs against incomplete knowledge of distribution with a real example, the threatened Iberian lizard Podarcis carbonelli, whose distribution was gradually discovered over a long time period. We used several ENM methods for presence-only data (Maxent, ENFA, Bioclim, and Domain) to infer the realised ecological niche at two spatial resolutions (1 km and 200 m). The distribution data were split into four partial datasets corresponding to separate subranges: Central System (CS); Viseu-Aveiro (VA); Atlantic coast (AC); and Doñana (DO). We then accumulated the datasets following the species discovery sequence: CS + VA, CS + VA + AC, and CS + VA + AC + DO. Niche equivalence and similarity between partial models were compared using Ecospat. ENMs were strongly affected by the violation of niche equilibrium; only the VA subrange forecasts the complete species range. ENMs were also sensitive to the violation of niche equality: only VA models were similar to the Iberian model, altitude being the most important variable followed by annual precipitation, maximum temperature in July, and annual radiation. When the ENMs were applied only to the first subrange discovered (CS), only the VA area was predicted, while the other subranges might have remained unknown, thus compromising conservation strategies. As assumptions of niche equilibrium and equality were violated, likely owing to the species' ecological multimodality, the models generated were biased and of limited predictive value. ENMs are useful tools in biogeography and conservation, but only if their basal assumptions are achieved. Partial

  8. Global and niche ecosystem in a simple dynamical model

    Energy Technology Data Exchange (ETDEWEB)

    Sertorio, L. [Turin Univ., Turin (Italy). Dipt. di Fisica Teorica; Tinetti, G. [Istituto Nazionale di Fisica Nucleare, Turin (Italy)

    2000-12-01

    In this paper it is adopted the viewpoint that the living ecosystem can be described by a dynamical system, where the variables are the populations of the various species. It is discussed the assumptions which justify the reduction of the number of variables to only three, according to the hierarchy herbs, herbivores, carnivores. In this way the dynamics takes into account a basic physical constraints, namely the global energy chain, where the input is the solar flux. This system is dissipative and stable. The next question is whether the global dynamics may contain a niche. It is tried to define the concept of niche as a subsystem having a self-contained cycle. It is chosen a Lotka-Volterra subsystem as the simplest realization of such a cycle. Moreover it is analyzed which assumptions must be made and which conditions must be satisfied for the appearance of a Lotka-Volterra subsystem within the global energy chain. Then it is showed that while the complex global ecosystem is strong, namely is able to adapt itself to variations of the driving term, the niche is fragile.

  9. Diversity and Habitat Niche Modeling of Candidate Archaeal Phylum Aigarchaeota

    Science.gov (United States)

    Alba, T. W.; Goertz, G.; Williams, A. J.; Cole, J. K.; Murugapiran, S. K.; Dodsworth, J. A.; Hedlund, B. P.

    2013-12-01

    ';Aigarchaeota' (formerly known as pSL4 and Hot Water Crenarchaeotic Group I (HWCGI)) is a candidate phylum of Archaea known only by 16S rRNA gene fragments from cultivation-independent microbial surveys and a single composite genome from Candidatus ';Caldiarchaeum subterraneum', an inhabitant of a subterranean gold mine in Japan. Sequences reported in various publications are found exclusively in geothermal settings, but a comprehensive assessment has not yet been performed. We mined public databases for 16S rRNA gene sequences related to known ';Aigarchaeota' and used a combination of approaches to rigorously define the phylogenetic boundaries of the phylum. The analyses supported the proposed relationship between ';Aigarchaeota', Thaumarchaeota, Crenarchaeota, and Korarchaeota in the so-called 'TACK superphylum' and identified ~200 16S rRNA genes and gene fragments belonging to ';Aigarchaeota', including those recovered from terrestrial geothermal systems on several continents (North America, Asia, Africa, Europe, and Oceania) and marine geothermal and subsurface samples in both the Atlantic and Pacific. ';Aigarchaeota' belonged to at least three family- to order-level groups and at least seven genus-level groups. All genus-level groups were recovered from geographically distant locations, suggesting a global distribution within amenable habitats. ';Aigarchaeota'-specific primers for the polymerase chain reaction (PCR) amplification of 16S rRNA genes were designed using SP-Designer and reviewed using the Ribosomal Database Project Probe Match tool. The primers will be used to determine the presence and abundance of ';Aigarchaeota' in a wide variety of samples from terrestrial geothermal systems in the western U.S. and Asia. These phylogenetic data, along with a large geochemical database, will be analyzed using multivariate statistics to develop biogeographic and habitat niche models for ';Aigarchaeota'. This study offers the first coherent view of the

  10. A framework for analyzing ecological trait-based models in multi-dimensional niche spaces

    OpenAIRE

    Biancalani, Tommaso; DeVille, Lee; Goldenfeld, Nigel

    2014-01-01

    We develop an theoretical approach for predicting biodiversity in multi-dimensional niche spaces, arising due to ecological drivers such as competitive exclusion. The novelty of our approach relies on the fact that ecological niches are described by sequences of strings, which allows us to describe multiple traits. We define the mathematical framework for analyzing pattern forming instabilities in these models, showing surprisingly that the analytic linear theory predicts the asymptotically l...

  11. Quantifying inter- and intra-population niche variability using hierarchical bayesian stable isotope mixing models.

    Science.gov (United States)

    Semmens, Brice X; Ward, Eric J; Moore, Jonathan W; Darimont, Chris T

    2009-07-09

    Variability in resource use defines the width of a trophic niche occupied by a population. Intra-population variability in resource use may occur across hierarchical levels of population structure from individuals to subpopulations. Understanding how levels of population organization contribute to population niche width is critical to ecology and evolution. Here we describe a hierarchical stable isotope mixing model that can simultaneously estimate both the prey composition of a consumer diet and the diet variability among individuals and across levels of population organization. By explicitly estimating variance components for multiple scales, the model can deconstruct the niche width of a consumer population into relevant levels of population structure. We apply this new approach to stable isotope data from a population of gray wolves from coastal British Columbia, and show support for extensive intra-population niche variability among individuals, social groups, and geographically isolated subpopulations. The analytic method we describe improves mixing models by accounting for diet variability, and improves isotope niche width analysis by quantitatively assessing the contribution of levels of organization to the niche width of a population.

  12. Place prioritization for biodiversity content using species ecological niche modeling

    Directory of Open Access Journals (Sweden)

    Víctor Sánchez-Cordero

    2005-01-01

    Full Text Available Place prioritization for biodiversity representation is essential for conservation planning, particularly in megadiverse countries where high deforestation threatens biodiversity. Given the collecting biases and uneven sampling of biological inventories, there is a need to develop robust models of species’ distributions. By modeling species’ ecological niches using point occurrence data and digitized environmental feature maps, we can predict potential and extant distributions of species in untransformed landscapes, as well as in those transformed by vegetation change (including deforestation. Such distributional predictions provide a framework for use of species as biodiversity surrogates in place prioritization procedures such as those based on rarity and complementarity. Beyond biodiversity conservation, these predictions can also be used for place prioritization for ecological restoration under current conditions and under future scenarios of habitat change (e.g., deforestation scenarios. To illustrate these points, we (1 predict distributions under current and future deforestation scenarios for the Mexican endemic mammal Dipodomys phillipsii, and show how areas for restoration may be selected; and (2 propose conservation areas by combining nonvolant mammal distributional predictions as biodiversity surrogates with place prioritization procedures, to connect decreed natural protected areas in a region holding exceptional biodiversity: the Transvolcanic Belt in central Mexico. La selección de áreas prioritarias de conservación es fundamental en la planeación sistemática de la conservación, particularmente en países de mega-diversidad, en donde la alta deforestación es una de las amenazas a la biodiversidad. Debido a los sesgos taxonómicos y geográficos de colecta de los inventarios biológicos, es indispensable generar modelos robustos de distribución de especies. Al modelar el nicho ecológico de especies usando localidades de

  13. Ecological niche modeling of sympatric krill predators around Marguerite Bay, Western Antarctic Peninsula

    Science.gov (United States)

    Friedlaender, Ari S.; Johnston, David W.; Fraser, William R.; Burns, Jennifer; Halpin, Patrick N.; Costa, Daniel P.

    2011-07-01

    Adélie penguins ( Pygoscelis adeliae), carabeater seals ( Lobodon carcinophagus), humpback ( Megaptera novaeangliae), and minke whales ( Balaenoptera bonaernsis) are found in the waters surrounding the Western Antarctic Peninsula. Each species relies primarily on Antarctic krill ( Euphausia superba) and has physiological constraints and foraging behaviors that dictate their ecological niches. Understanding the degree of ecological overlap between sympatric krill predators is critical to understanding and predicting the impacts on climate-driven changes to the Antarctic marine ecosystem. To explore ecological relationships amongst sympatric krill predators, we developed ecological niche models using a maximum entropy modeling approach (Maxent) that allows the integration of data collected by a variety of means (e.g. satellite-based locations and visual observations). We created spatially explicit probability distributions for the four krill predators in fall 2001 and 2002 in conjunction with a suite of environmental variables. We find areas within Marguerite Bay with high krill predator occurrence rates or biological hot spots. We find the modeled ecological niches for Adélie penguins and crabeater seals may be affected by their physiological needs to haul-out on substrate. Thus, their distributions may be less dictated by proximity to prey and more so by physical features that over time provide adequate access to prey. Humpback and minke whales, being fully marine and having greater energetic demands, occupy ecological niches more directly proximate to prey. We also find evidence to suggest that the amount of overlap between modeled niches is relatively low, even for species with similar energetic requirements. In a rapidly changing and variable environment, our modeling work shows little indication that krill predators maintain similar ecological niches across years around Marguerite Bay. Given the amount of variability in the marine environment around the

  14. Robustness and accuracy of Maxent niche modelling for Lactuca species distributions in light of collecting expeditions

    NARCIS (Netherlands)

    Cobben, M.M.P.; Treuren, van R.; Castaneda-Alvarez, N.P.; Khoury, C.K.; Kik, C.; Hintum, van T.J.L.

    2015-01-01

    Niche modelling software can be used to assess the probability of detecting a population of a plant species at a certain location. In this study, we used the distribution of the wild relatives of lettuce (Lactuca spp.) to investigate the applicability of Maxent species distribution models for collec

  15. Mineral Controls on Microbial Niche Space in Subsurface Serpentinites of the Coast Range Ophiolite, Northern California

    Science.gov (United States)

    Cardace, D.; Carnevale, D.; Schrenk, M. O.; Twing, K. I.; McCollom, T. M.; Hoehler, T. M.

    2012-12-01

    Serpentinites on Earth are excellent candidate environments for the origin of life and continue to serve as an outstanding model system for study of modern selection pressures (such as gradients in temperature, pressure, aqueous geochemistry, oxidation-reduction potential) on microbial communities. Recent coring (August 2011) in the Coast Range Ophiolite near Lower Lake, CA resulted in the establishment of two sets of reference continental serpentinite cores (to 30 and 42 m depth, respectively) and the installation of eight monitoring wells drawing from different depths. Six of these wells plumb serpentinizing waters, with characteristic high pH (up to 12.5), high calcium loads (10-200 ppm), and methane concentrations that are at or near one-atmosphere saturation, while hydrogen levels are orders of magnitude lower than is typically observed in other similar systems. Low hydrogen levels are cryptic; they may reflect consumption by microbial communities or possibly a pressure- or temperature-related solubility response. Two reference wells provide access to quasi-parallel, shallower groundwater flow regimes with near neutral pH values and surface-related major element and organic acid inventories. Many environmental parameters pertinent to microbiological communities active in serpentinites (such as dissolved hydrogen, methane, and other gas concentrations, redox status, ambient pH, and ionic strength) are largely controlled by host rock mineralogy and, thus, the temperature and progress of serpentinization. Since iron partitioning between co-existing minerals in serpentinites is strongly linked to the evolution of hydrogen (McCollom and Bach, 2009), we report here on mineralogy, bulk geochemistry, and selected mineral chemistry data for the serpentinite cores in order to constrain the production of hydrogen, the dominant bioenergetic driving force in this land-based deep biosphere setting. Parallel microbiological analyses of the same drill cores have shown the

  16. A niche model to predict Microcystis bloom decline in Chaohu Lake, China

    Institute of Scientific and Technical Information of China (English)

    WANG Zhicong; LI Zhongjie; LI Dunhai

    2012-01-01

    Cyanobacterial blooms occur frequently in lakes due to eutrophication.Although a number of models have been proposed to forecast algal blooms,a good and applicable method is still lacking.This study explored a simple and effective mathematical-ecological model to evaluate the growth status and predict the population dynamics of Microcystis blooms.In this study,phytoplankton were collected and identified from 8 sampling sites in Chaohu Lake every month from July to October,2010.The niche breadth and niche overlap of common species were calculated using standard equations,and the potential relative growth rates of Microcystis were calculated as a weighted-value of niche overlap.In July,the potential relative growth rate was 2.79 (a.u.,arbitrary units) but then rapidly declined in the following months to -3.99 a.u.in September.A significant correlation (R=0.998,P<0.01) was found in the model between the net-increase in biomass of Microcystis in the field and the predicted values calculated by the niche model,we concluded that the niche model is suitable for forecasting the dynamics of Microcystis blooms.Redundancy analysis indicated that decreases in water temperature,dissolved oxygen and total dissolved phosphorus might be major factors underlying bloom decline.Based on the theory of community succession being caused by resource competition,the growth and decline of blooms can be predicted from a community structure.This may provide a basis for early warning and control of algal blooms.

  17. Malaria in Africa: vector species' niche models and relative risk maps.

    Directory of Open Access Journals (Sweden)

    Alexander Moffett

    Full Text Available A central theoretical goal of epidemiology is the construction of spatial models of disease prevalence and risk, including maps for the potential spread of infectious disease. We provide three continent-wide maps representing the relative risk of malaria in Africa based on ecological niche models of vector species and risk analysis at a spatial resolution of 1 arc-minute (9 185 275 cells of approximately 4 sq km. Using a maximum entropy method we construct niche models for 10 malaria vector species based on species occurrence records since 1980, 19 climatic variables, altitude, and land cover data (in 14 classes. For seven vectors (Anopheles coustani, A. funestus, A. melas, A. merus, A. moucheti, A. nili, and A. paludis these are the first published niche models. We predict that Central Africa has poor habitat for both A. arabiensis and A. gambiae, and that A. quadriannulatus and A. arabiensis have restricted habitats in Southern Africa as claimed by field experts in criticism of previous models. The results of the niche models are incorporated into three relative risk models which assume different ecological interactions between vector species. The "additive" model assumes no interaction; the "minimax" model assumes maximum relative risk due to any vector in a cell; and the "competitive exclusion" model assumes the relative risk that arises from the most suitable vector for a cell. All models include variable anthrophilicity of vectors and spatial variation in human population density. Relative risk maps are produced from these models. All models predict that human population density is the critical factor determining malaria risk. Our method of constructing relative risk maps is equally general. We discuss the limits of the relative risk maps reported here, and the additional data that are required for their improvement. The protocol developed here can be used for any other vector-borne disease.

  18. Ecological Niche Modeling of Potential West Nile Virus Vector Mosquito Species in Iowa

    OpenAIRE

    2010-01-01

    Ecological niche modeling (ENM) algorithms, Maximum Entropy Species Distribution Modeling (Maxent) and Genetic Algorithm for Rule-set Prediction (GARP), were used to develop models in Iowa for three species of mosquito — two significant, extant West Nile virus (WNV) vectors (Culex pipiens L and Culex tarsalis Coquillett (Diptera: Culicidae)), and the nuisance mosquito, Aedes vexans Meigen (Diptera: Culicidae), a potential WNV bridge vector. Occurrence data for the three mosquito species from ...

  19. Integrating life stages into ecological niche models: a case study on tiger beetles.

    Directory of Open Access Journals (Sweden)

    Angela Taboada

    Full Text Available Detailed understanding of a species' natural history and environmental needs across spatial scales is a primary requisite for effective conservation planning, particularly for species with complex life cycles in which different life stages occupy different niches and respond to the environment at different scales. However, niche models applied to conservation often neglect early life stages and are mostly performed at broad spatial scales. Using the endangered heath tiger beetle (Cicindela sylvatica as a model species, we relate presence/absence and abundance data of locally dispersing adults and sedentary larvae to abiotic and biotic variables measured in a multiscale approach within the geographic extent relevant to active conservation management. At the scale of hundreds of meters, fine-grained abiotic conditions (i.e., vegetation structure are fundamental determinants of the occurrence of both life stages, whereas the effect of biotic factors is mostly contained in the abiotic signature. The combination of dense heath vegetation and bare ground areas is thus the first requirement for the species' preservation, provided that accessibility to the suitable habitat is ensured. At a smaller scale (centimetres, the influence of abiotic factors on larval occurrence becomes negligible, suggesting the existence of important additional variables acting within larval proximity. Sustained significant correlations between neighbouring larvae in the models provide an indication of the potential impact of neighbourhood crowding on the larval niche within a few centimetres. Since the species spends the majority of its life cycle in the larval stage, it is essential to consider the hierarchical abiotic and biotic processes affecting the larvae when designing practical conservation guidelines for the species. This underlines the necessity for a more critical evaluation of the consequences of disregarding niche variation between life stages when estimating

  20. Coevolutionary motion and swarming in a niche space model of ecological species interactions

    Science.gov (United States)

    Dommar, C. J.; Ryabov, A.; Blasius, B.

    2008-04-01

    Organisms are involved in coevolutionary relationships with their competitors, predators, preys and parasites. In this context, we present a simple model for the co-evolution of species in a common niche space, where the fitness of each species is defined via the network of interactions with all other species. In our model, the sign and type of the pairwise interactions (being either beneficial, harmful or neutral) is given by a pre-determined community matrix, while the interaction strength depends on the niche-overlap, i.e. the pairwise distances between species in niche space. The evolutionary process drives the species toward the places with the higher local fitness along the fitness gradient. This gives rise to a dynamic fitness landscape, since the evolutionary motion of a single species can change the landscape of the others (known as the Red Queen Principle). In the simplest case of only two-species we observe either a convergence/divergence equilibrium or a coevolutionary arms race. For a larger number of species our analysis concentrates on an antisymmetric interaction matrix, where we observe a large range of dynamic behaviour, from oscillations, quasiperiodic to chaotic dynamics. In dependence of the value of a first integral of motion we observe either quasiperiodic motion around a central region in niche space or unbounded movement, characterised by chaotic scattering of species pairs. Finally, in a linear food-chain we observe complex swarming behaviour in which the swarm moves as a whole only if the chain consists of an even number of species. Our results could be an important contribution to evolutionary niche theory.

  1. Using Ecological Niche Modeling for Biodiversity Conservation Guidance in the Western Podillya (Ukraine: Reptiles

    Directory of Open Access Journals (Sweden)

    Tytar V.

    2015-12-01

    Full Text Available Using Ecological Niche Modeling for Biodiversity Conservation Guidance in the Western Podillya (Ukraine: Reptiles. Tytar, V., Sobolenko, L., Nekrasova, O. Mezhzherin, S. - Maximum entropy niche modeling was employed as a tool to assess potential habitat suitability for 10 reptile species and to map their potential distribution in the Western Podillya (Ukraine. We used climate, topography and human impact (assessed by the Human Footprint as predictor variables. “Isothermality”, “temperature seasonality” and the “mean temperature of coldest month” were three most important factors in predicting habitat suitability and distribution. A profound contribution to the modeling has been displayed by the Human Footprint, meaning that human infrastructure may benefit reptile species. Areas have been distinguished that in the first place should be of interest to biodiversity conservationists targeting reptiles and maps summarizing predicted habitat suitability and species richness were produced for guiding conservation efforts.

  2. The fate of the Arctic seaweed Fucus distichus under climate change: an ecological niche modeling approach.

    Science.gov (United States)

    Jueterbock, Alexander; Smolina, Irina; Coyer, James A; Hoarau, Galice

    2016-03-01

    Rising temperatures are predicted to melt all perennial ice cover in the Arctic by the end of this century, thus opening up suitable habitat for temperate and subarctic species. Canopy-forming seaweeds provide an ideal system to predict the potential impact of climate-change on rocky-shore ecosystems, given their direct dependence on temperature and their key role in the ecological system. Our primary objective was to predict the climate-change induced range-shift of Fucus distichus, the dominant canopy-forming macroalga in the Arctic and subarctic rocky intertidal. More specifically, we asked: which Arctic/subarctic and cold-temperate shores of the northern hemisphere will display the greatest distributional change of F. distichus and how will this affect niche overlap with seaweeds from temperate regions? We used the program MAXENT to develop correlative ecological niche models with dominant range-limiting factors and 169 occurrence records. Using three climate-change scenarios, we projected habitat suitability of F. distichus - and its niche overlap with three dominant temperate macroalgae - until year 2200. Maximum sea surface temperature was identified as the most important factor in limiting the fundamental niche of F. distichus. Rising temperatures were predicted to have low impact on the species' southern distribution limits, but to shift its northern distribution limits poleward into the high Arctic. In cold-temperate to subarctic regions, new areas of niche overlap were predicted between F. distichus and intertidal macroalgae immigrating from the south. While climate-change threatens intertidal seaweeds in warm-temperate regions, seaweed meadows will likely flourish in the Arctic intertidal. Although this enriches biodiversity and opens up new seaweed-harvesting grounds, it will also trigger unpredictable changes in the structure and functioning of the Arctic intertidal ecosystem.

  3. Potential Distribution of Chagas Disease Vectors (Hemiptera, Reduviidae, Triatominae) in Colombia, Based on Ecological Niche Modeling

    Science.gov (United States)

    Suárez-Escudero, Laura C.; González-Caro, Sebastián

    2016-01-01

    Ecological niche modeling of Triatominae bugs allow us to establish the local risk of transmission of the parasite Trypanosoma cruzi, which causes Chagas disease. This information could help to guide health authority recommendations on infection monitoring, prevention, and control. In this study, we estimated the geographic distribution of triatomine species in Colombia and identified the relationship between landscape structure and climatic factors influencing their occurrence. A total of 2451 records of 4 triatomine species (Panstrongylus geniculatus, Rhodnius pallescens, R. prolixus, and Triatoma maculata) were analyzed. The variables that provided more information to explain the ecologic niche of these vectors were related to precipitation, altitude, and temperature. We found that the species with the broadest potential geographic distribution were P. geniculatus, R. pallescens, and R. prolixus. In general, the models predicted the highest occurrence probability of these vectors in the eastern slope of the Eastern Cordillera, the southern region of the Magdalena valley, and the Sierra Nevada of Santa Marta. PMID:28115946

  4. Why not use niche modelling for computing risk of wildfires ignition and spreading?

    Directory of Open Access Journals (Sweden)

    Alessandro Ferrarini

    2012-12-01

    Full Text Available A forest fire can be a true ecological calamity, regardless of whether it is caused by natural forces or human actions. Although it is impossible to control nature, it is possible to map wildfire risk zones, and thence minimize the frequency of wildfires and prevent damages. Wildfire risk zones are locations where a fire is likely to start, and from where it can spread to other areas. Predictions of wildfires ignitions are critical aspects of biodiversity conservation and management, and they are only possible when a reliable fire risk zone map is available. I suggest in this paper that wildfire ignition risk computed from points of past wildfires obeys the same conceptual and mathematical rules of niche models commonly applied to points of sampled plants or animals. Therefore, niche modeling can also be an inductive approach for an effective and inexpensive computation of wildfires ignition and spreading likelihood.

  5. Locating Pleistocene Refugia: Comparing Phylogeographic and Ecological Niche Model Predictions

    Science.gov (United States)

    2007-07-01

    research groups [21,42–46], support the idea that the bioclimatic variables used in our ENM predictions (see Materials and Methods) are of importance to the...calibrating the downscaled LGM climate data to actual observed climate conditions. ENMs were based on the 19 bioclimatic variables in the WorldClim...phylogenetics and bioclimatic modeling. Systematic Biology 55: 785–802. 34. Graham CH, Ron SR, Santos JC, Schneider CJ, Moritz C (2004) Integrating

  6. Modeling Gas Dynamics in California Sea Lions

    Science.gov (United States)

    2015-09-30

    predicted and observed values. The model will be used to investigate specific scenarios where marine mammals could be particularly prone to...specific parameter estimates for California sea lions, which was tested in this fiscal year; Aim 2) Compare estimated and measured arterial and venous PO2...In addition, the existing model’s compliance estimate for upper airways was from a terrestrial mammal , whereas we can now use data for California

  7. Modeling the impact of climate change on wild Piper nigrum (Black Pepper) in Western Ghats, India using ecological niche models.

    Science.gov (United States)

    Sen, Sandeep; Gode, Ameya; Ramanujam, Srirama; Ravikanth, G; Aravind, N A

    2016-11-01

    The center of diversity of Piper nigrum L. (Black Pepper), one of the highly valued spice crops is reported to be from India. Black pepper is naturally distributed in India in the Western Ghats biodiversity hotspot and is the only known existing source of its wild germplasm in the world. We used ecological niche models to predict the potential distribution of wild P. nigrum in the present and two future climate change scenarios viz (A1B) and (A2A) for the year 2080. Three topographic and nine uncorrelated bioclim variables were used to develop the niche models. The environmental variables influencing the distribution of wild P. nigrum across different climate change scenarios were identified. We also assessed the direction and magnitude of the niche centroid shift and the change in niche breadth to estimate the impact of projected climate change on the distribution of P. nigrum. The study shows a niche centroid shift in the future climate scenarios. Both the projected future climate scenarios predicted a reduction in the habitat of P. nigrum in Southern Western Ghats, which harbors many wild accessions of P. nigrum. Our results highlight the impact of future climate change on P. nigrum and provide useful information for designing sound germplasm conservation strategies for P. nigrum.

  8. Using environmental niche models to test the 'everything is everywhere' hypothesis for Badhamia.

    Science.gov (United States)

    Aguilar, María; Fiore-Donno, Anna-Maria; Lado, Carlos; Cavalier-Smith, Thomas

    2014-04-01

    It is often discussed whether the biogeography of free-living protists is better explained by the 'everything is everywhere'(EiE) hypothesis, which postulates that only ecology drives their distribution, or by the alternative hypothesis of 'moderate endemicity' in which geographic barriers can limit their dispersal. To formally test this, it would be necessary not only to find organisms restricted to a geographical area but also to check for their presence in any other place with a similar ecology. We propose the use of environmental niche models to generate and test null EiE distributions. Here we have analysed the distribution of 18S rDNA variants (ribotypes) of the myxomycete Badhamia melanospora (belonging to the protozoan phylum Amoebozoa) using 125 specimens from 91 localities. Two geographically structured groups of ribotypes congruent with slight morphological differences in the spores can be distinguished. One group comprises all populations from Argentina and Chile, and the other is formed by populations from North America together with human-introduced populations from other parts of the world. Environmental climatic niche models constructed separately for the two groups have significant differences, but show several overlapping areas. However, only specimens from one group were found in an intensively surveyed area in South America where both niche models overlap. It can be concluded that everything is not everywhere for B. melanospora. This taxon constitutes a complex formed by at least two cryptic species that probably diverged allopatrically in North and South America.

  9. Using environmental niche models to test the ‘everything is everywhere' hypothesis for Badhamia

    Science.gov (United States)

    Aguilar, María; Fiore-Donno, Anna-Maria; Lado, Carlos; Cavalier-Smith, Thomas

    2014-01-01

    It is often discussed whether the biogeography of free-living protists is better explained by the ‘everything is everywhere'(EiE) hypothesis, which postulates that only ecology drives their distribution, or by the alternative hypothesis of ‘moderate endemicity' in which geographic barriers can limit their dispersal. To formally test this, it would be necessary not only to find organisms restricted to a geographical area but also to check for their presence in any other place with a similar ecology. We propose the use of environmental niche models to generate and test null EiE distributions. Here we have analysed the distribution of 18S rDNA variants (ribotypes) of the myxomycete Badhamia melanospora (belonging to the protozoan phylum Amoebozoa) using 125 specimens from 91 localities. Two geographically structured groups of ribotypes congruent with slight morphological differences in the spores can be distinguished. One group comprises all populations from Argentina and Chile, and the other is formed by populations from North America together with human-introduced populations from other parts of the world. Environmental climatic niche models constructed separately for the two groups have significant differences, but show several overlapping areas. However, only specimens from one group were found in an intensively surveyed area in South America where both niche models overlap. It can be concluded that everything is not everywhere for B. melanospora. This taxon constitutes a complex formed by at least two cryptic species that probably diverged allopatrically in North and South America. PMID:24132078

  10. Mapping the potential risk of mycetoma infection in Sudan and South Sudan using ecological niche modeling.

    Science.gov (United States)

    Samy, Abdallah M; van de Sande, Wendy W J; Fahal, Ahmed Hassan; Peterson, A Townsend

    2014-10-01

    In 2013, the World Health Organization (WHO) recognized mycetoma as one of the neglected tropical conditions due to the efforts of the mycetoma consortium. This same consortium formulated knowledge gaps that require further research. One of these gaps was that very few data are available on the epidemiology and transmission cycle of the causative agents. Previous work suggested a soil-borne or Acacia thorn-prick-mediated origin of mycetoma infections, but no studies have investigated effects of soil type and Acacia geographic distribution on mycetoma case distributions. Here, we map risk of mycetoma infection across Sudan and South Sudan using ecological niche modeling (ENM). For this study, records of mycetoma cases were obtained from the scientific literature and GIDEON; Acacia records were obtained from the Global Biodiversity Information Facility. We developed ENMs based on digital GIS data layers summarizing soil characteristics, land-surface temperature, and greenness indices to provide a rich picture of environmental variation across Sudan and South Sudan. ENMs were calibrated in known endemic districts and transferred countrywide; model results suggested that risk is greatest in an east-west belt across central Sudan. Visualizing ENMs in environmental dimensions, mycetoma occurs under diverse environmental conditions. We compared niches of mycetoma and Acacia trees, and could not reject the null hypothesis of niche similarity. This study revealed contributions of different environmental factors to mycetoma infection risk, identified suitable environments and regions for transmission, signaled a potential mycetoma-Acacia association, and provided steps towards a robust risk map for the disease.

  11. Geological 3D model of the investigation niche in ONKALO, Olkiluoto, southwestern Finland

    Energy Technology Data Exchange (ETDEWEB)

    Koittola, N.

    2014-07-15

    The main goal of this Master of Science Thesis was to create a geological 3D-model of the investigation niche 3 and its surroundings. The model were created for the needs of the rock mechanical back analysis. This study is a part of Posiva's regional studies for characterization of the bedrock. Totally 4 models were created: lithological model, foliation model, fracture model, and physical rock property model. Besides the modeling, there was also made a study of the migmatite structures in the niche. Used geological and geophysical methods were drill core loggings, tunnel mapping, ground penetration radar, mise-a-la-masse and drill hole geophysics. Four rock types exist at the niche area: veined gneiss, pegmatite granite, diatexitic gneiss and quartz gneiss. The lithological units were modeled primary with the drill core loggings, tunnel mapping and ground penetrating radar. The major lithological units followed the main foliation direction (south dipping). So the continuations were fairly easy to model in the walls and roof, where the data was lacking. Foliation and fractures were modeled as discs, with mid-points at the measurement points of the structure. There were two main foliation directions 164/46 and 62/39. Fractures were more scattered but three fracture sets can be separated: 156/34, 270/85 and 342/83. The first set is mainly from the drill core loggings, second and third from tunnel mapping. Used methods in foliation model were drill core loggings, tunnel mapping and drill hole geophysics. In fracture model used data was from drill core loggings, tunnel mapping, mise-a-la-masse measurements and drill core geophysic. Four anomalous zones were detected with the drill hole geophysics. Three of these zones were associated with intensely fractured zones and one was connected to exceptionally high mica content in the gneiss. Rocks of Olkiluoto are divided into gneisses and magmatic rocks in the geological mapping. Actually almost all Olkiluoto

  12. Ecological niche models reveal the importance of climate variability for the biogeography of protosteloid amoebae.

    Science.gov (United States)

    Aguilar, María; Lado, Carlos

    2012-08-01

    Habitat availability and environmental preferences of species are among the most important factors in determining the success of dispersal processes and therefore in shaping the distribution of protists. We explored the differences in fundamental niches and potential distributions of an ecological guild of slime moulds-protosteloid amoebae-in the Iberian Peninsula. A large set of samples collected in a north-east to south-west transect of approximately 1000 km along the peninsula was used to test the hypothesis that, together with the existence of suitable microhabitats, climate conditions may determine the probability of survival of species. Although protosteloid amoebae share similar morphologies and life history strategies, canonical correspondence analyses showed that they have varied ecological optima, and that climate conditions have an important effect in niche differentiation. Maxent environmental niche models provided consistent predictions of the probability of presence of the species based on climate data, and they were used to generate maps of potential distribution in an 'everything is everywhere' scenario. The most important climatic factors were, in both analyses, variables that measure changes in conditions throughout the year, confirming that the alternation of fruiting bodies, cysts and amoeboid stages in the life cycles of protosteloid amoebae constitutes an advantage for surviving in a changing environment. Microhabitat affinity seems to be influenced by climatic conditions, which suggests that the micro-environment may vary at a local scale and change together with the external climate at a larger scale.

  13. Ecological Niche Modeling for the Prediction of the Geographic Distribution of Cutaneous Leishmaniasis in Tunisia.

    Science.gov (United States)

    Chalghaf, Bilel; Chlif, Sadok; Mayala, Benjamin; Ghawar, Wissem; Bettaieb, Jihène; Harrabi, Myriam; Benie, Goze Bertin; Michael, Edwin; Salah, Afif Ben

    2016-04-01

    Cutaneous leishmaniasis is a very complex disease involving multiple factors that limit its emergence and spatial distribution. Prediction of cutaneous leishmaniasis epidemics in Tunisia remains difficult because most of the epidemiological tools used so far are descriptive in nature and mainly focus on a time dimension. The purpose of this work is to predict the potential geographic distribution of Phlebotomus papatasi and zoonotic cutaneous leishmaniasis caused by Leishmania major in Tunisia using Grinnellian ecological niche modeling. We attempted to assess the importance of environmental factors influencing the potential distribution of P. papatasi and cutaneous leishmaniasis caused by L. major. Vectors were trapped in central Tunisia during the transmission season using CDC light traps (John W. Hock Co., Gainesville, FL). A global positioning system was used to record the geographical coordinates of vector occurrence points and households tested positive for cutaneous leishmaniasis caused by L. major. Nine environmental layers were used as predictor variables to model the P. papatasi geographical distribution and five variables were used to model the L. major potential distribution. Ecological niche modeling was used to relate known species' occurrence points to values of environmental factors for these same points to predict the presence of the species in unsampled regions based on the value of the predictor variables. Rainfall and temperature contributed the most as predictors for sand flies and human case distributions. Ecological niche modeling anticipated the current distribution of P. papatasi with the highest suitability for species occurrence in the central and southeastern part of Tunisian. Furthermore, our study demonstrated that governorates of Gafsa, Sidi Bouzid, and Kairouan are at highest epidemic risk.

  14. Ecological niche model to predict the potential distribution of phytoplankton in the Aguamilpa Dam, Nayarit. Mexico

    Directory of Open Access Journals (Sweden)

    Humberto Macias-Cuellar

    2010-12-01

    Full Text Available Phytoplankton species are an important basis of the food web for various systems such as pelagic, coastal and lake. Due to their photosynthetic capacity, this community is sensitive to changes in light availability, temperature, nutrient concentrations, herbivores consumption, parasitism and competition. Therefore, they show a high spatial and temporal variability related to environmental changes both natural and anthropogenic. However, as any taxonomic group, phytoplankton species have environmental thresholds, ecological niches that define their distribution. This study was located in Aguamilpa Dam, an artificial aquatic reservoir which started operations in 1994 for electric energy production. In this system the potential distribution of the phytoplankton was evaluated, where the highest species richness and restricted distribution areas were identified. Potential distribution models based on ecological niche definition were generated using ArcMap 9.2® with Maxent (Maximun Entropy Method. The development of distribution maps was carried out using Digital Elevation Models in cells of 100 m x 100 m (1 ha, based on nine physico-chemical and biological water parameters monitored in the reservoir. The highest species richness areas were found in the Huaynamota river tributary and at the station called La Confluencia, while the less abundance areas were found in the Santiago river tributary during warm and cold dry seasons with a great abundance of cyanophyta. During the rainfall season, the Huaynamota river tributary diversity areas were extended and the presence of some dominant species of cyanophyta were indentified. These species can be associated with trophic processes related to anthropogenic pollutants in the reservoir. This study illustrates the potential application of niche modeling approach in aquatic ecosystems.

  15. Global thermal niche models of two European grasses show high invasion risks in Antarctica.

    Science.gov (United States)

    Pertierra, Luis R; Aragón, Pedro; Shaw, Justine D; Bergstrom, Dana M; Terauds, Aleks; Olalla-Tárraga, Miguel Ángel

    2016-12-14

    The two non-native grasses that have established long-term populations in Antarctica (Poa pratensis and Poa annua) were studied from a global multidimensional thermal niche perspective to address the biological invasion risk to Antarctica. These two species exhibit contrasting introduction histories and reproductive strategies and represent two referential case studies of biological invasion processes. We used a multistep process with a range of species distribution modelling techniques (ecological niche factor analysis, multidimensional envelopes, distance/entropy algorithms) together with a suite of thermoclimatic variables, to characterize the potential ranges of these species. Their native bioclimatic thermal envelopes in Eurasia, together with the different naturalized populations across continents, were compared next. The potential niche of P. pratensis was wider at the cold extremes; however, P. annua life history attributes enable it to be a more successful colonizer. We observe that particularly cold summers are a key aspect of the unique Antarctic environment. In consequence, ruderals such as P. annua can quickly expand under such harsh conditions, whereas the more stress-tolerant P. pratensis endures and persist through steady growth. Compiled data on human pressure at the Antarctic Peninsula allowed us to provide site-specific biosecurity risk indicators. We conclude that several areas across the region are vulnerable to invasions from these and other similar species. This can only be visualized in species distribution models (SDMs) when accounting for founder populations that reveal nonanalogous conditions. Results reinforce the need for strict management practices to minimize introductions. Furthermore, our novel set of temperature-based bioclimatic GIS layers for ice-free terrestrial Antarctica provide a mechanism for regional and global species distribution models to be built for other potentially invasive species.

  16. Integrated Hydrosystem Modeling of the California Basin

    Science.gov (United States)

    Davison, J. H.; Hwang, H. T.; Sudicky, E. A.; Mallia, D.; Lin, J. C.

    2015-12-01

    The Western United States is facing one of the worst droughts on record. Climate change projections predict warmer temperatures, higher evapotranspiration rates, and no foreseeable increase in precipitation. California, in particular, has supplemented their decreased surface water supplies by mining deep groundwater. However, this supply of groundwater is limited, especially with reduced recharge. These combined factors place California's water-demanding society at dire risk. In an effort to quantify California's risks, we present a fully integrated water cycle model that captures the dynamics of the subsurface, land surface, and atmospheric domains over the entire California basin. Our water cycle model combines HydroGeoSphere (HGS), a 3-D control-volume finite element model that accommodates variably-saturated subsurface and surface water flow with evapotranspiration processes to the Weather Research and Forecasting (WRF) model, a 3-D finite difference nonhydrostatic mesoscale atmospheric simulator. The two-way coupling within our model, referred to as HGS-WRF, tightly integrates the water cycling processes by passing precipitation and potential evapotranspiration data from WRF to HGS, while exchanging actual evapotranspiration and soil saturation data from HGS to WRF. Furthermore, HGS-WRF implements a flexible coupling method that allows each model to use a unique mesh while maintaining mass conservation within and between domains. Our simulation replicated field measured evapotranspiration fluxes and showed a strong correlation between the soil saturation (depth to groundwater table) and latent heat fluxes. Altogether, the HGS-WRF California basin model is currently the most complete water resource simulation framework as it combines groundwater, surface water, the unsaturated zone, and the atmosphere into one coupled system.

  17. Reversible neural stem cell niche dysfunction in a model of multiple sclerosis

    DEFF Research Database (Denmark)

    Rasmussen, Stine; Imitola, Jaime; Ayuso-Sacido, Angel;

    2011-01-01

    OBJECTIVE: The subventricular zone (SVZ) of the brain constitutes a niche for neural stem and progenitor cells that can initiate repair after central nervous system (CNS) injury. In a relapsing-remitting model of experimental autoimmune encephalomyelitis (EAE), the neural stem cells (NSCs) become...... with minocycline, an inhibitor of microglia activation, increases stem cell proliferation in both naive and EAE animals. Minocycline treatment decreases cortical and periventricular pathology in the chronic phase of EAE, improving the proliferation of Sox2 stem cells and NG2 oligodendrocyte precursors cells...

  18. Mapping the potential risk of mycetoma infection in Sudan and South Sudan using ecological niche modeling.

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    Abdallah M Samy

    2014-10-01

    Full Text Available In 2013, the World Health Organization (WHO recognized mycetoma as one of the neglected tropical conditions due to the efforts of the mycetoma consortium. This same consortium formulated knowledge gaps that require further research. One of these gaps was that very few data are available on the epidemiology and transmission cycle of the causative agents. Previous work suggested a soil-borne or Acacia thorn-prick-mediated origin of mycetoma infections, but no studies have investigated effects of soil type and Acacia geographic distribution on mycetoma case distributions. Here, we map risk of mycetoma infection across Sudan and South Sudan using ecological niche modeling (ENM. For this study, records of mycetoma cases were obtained from the scientific literature and GIDEON; Acacia records were obtained from the Global Biodiversity Information Facility. We developed ENMs based on digital GIS data layers summarizing soil characteristics, land-surface temperature, and greenness indices to provide a rich picture of environmental variation across Sudan and South Sudan. ENMs were calibrated in known endemic districts and transferred countrywide; model results suggested that risk is greatest in an east-west belt across central Sudan. Visualizing ENMs in environmental dimensions, mycetoma occurs under diverse environmental conditions. We compared niches of mycetoma and Acacia trees, and could not reject the null hypothesis of niche similarity. This study revealed contributions of different environmental factors to mycetoma infection risk, identified suitable environments and regions for transmission, signaled a potential mycetoma-Acacia association, and provided steps towards a robust risk map for the disease.

  19. Complexity in models of cultural niche construction with selection and homophily.

    Science.gov (United States)

    Creanza, Nicole; Feldman, Marcus W

    2014-07-22

    Niche construction is the process by which organisms can alter the ecological environment for themselves, their descendants, and other species. As a result of niche construction, differences in selection pressures may be inherited across generations. Homophily, the tendency of like phenotypes to mate or preferentially associate, influences the evolutionary dynamics of these systems. Here we develop a model that includes selection and homophily as independent culturally transmitted traits that influence the fitness and mate choice determined by another focal cultural trait. We study the joint dynamics of a focal set of beliefs, a behavior that can differentially influence the fitness of those with certain beliefs, and a preference for partnering based on similar beliefs. Cultural transmission, selection, and homophily interact to produce complex evolutionary dynamics, including oscillations, stable polymorphisms of all cultural phenotypes, and simultaneous stability of oscillation and fixation, which have not previously been observed in models of cultural evolution or gene-culture interactions. We discuss applications of this model to the interaction of beliefs and behaviors regarding education, contraception, and animal domestication.

  20. Trends and biases in global scientific literature about ecological niche models.

    Science.gov (United States)

    Vaz, U L; Cunha, H F; Nabout, J C

    2015-11-01

    Recently, ecological niche models have been employed to investigate the potential geographical distribution of species. However, it is necessary to analyze the vast number of publications on this topic to understand the trends and biases of research using ecological niche models (ENMs). Therefore, this study aims to investigate trends in the scientific literature regarding studies on ENMs. For the quantitative analysis of the literature on ENMs, we performed a search in the Thomson ISI (Web of Science) database between 1991 and 2013. The search identified 3042 papers containing preselected keywords in either the title or abstract. The results showed that the number of papers has increased over the years (r=0.77, Pplants (402 papers, or 28.36% of the total). There was no relationship between the modeling method used and the taxonomic group studied (χ2=4.8, P=0.15). Finally, the wide availability of biological, environmental and computational resources has elicited the broad use of tools for ENMs. Despite the conceptual discussions of the ENMs, this method is currently the most effective way to evaluate the potential geographical distribution of species, and to predict the distribution under different environmental conditions (i.e., future or past scenarios).

  1. Modeling pre-metastatic lymphvascular niche in the mouse ear sponge assay

    Science.gov (United States)

    García-Caballero, Melissa; Van de Velde, Maureen; Blacher, Silvia; Lambert, Vincent; Balsat, Cédric; Erpicum, Charlotte; Durré, Tania; Kridelka, Frédéric; Noel, Agnès

    2017-01-01

    Lymphangiogenesis, the formation of new lymphatic vessels, occurs in primary tumors and in draining lymph nodes leading to pre-metastatic niche formation. Reliable in vivo models are becoming instrumental for investigating alterations occurring in lymph nodes before tumor cell arrival. In this study, we demonstrate that B16F10 melanoma cell encapsulation in a biomaterial, and implantation in the mouse ear, prevents their rapid lymphatic spread observed when cells are directly injected in the ear. Vascular remodeling in lymph nodes was detected two weeks after sponge implantation, while their colonization by tumor cells occurred two weeks later. In this model, a huge lymphangiogenic response was induced in primary tumors and in pre-metastatic and metastatic lymph nodes. In control lymph nodes, lymphatic vessels were confined to the cortex. In contrast, an enlargement and expansion of lymphatic vessels towards paracortical and medullar areas occurred in pre-metastatic lymph nodes. We designed an original computerized-assisted quantification method to examine the lymphatic vessel structure and the spatial distribution. This new reliable and accurate model is suitable for in vivo studies of lymphangiogenesis, holds promise for unraveling the mechanisms underlying lymphatic metastases and pre-metastatic niche formation in lymph nodes, and will provide new tools for drug testing. PMID:28128294

  2. Predicted Distribution of Visceral Leishmaniasis Vectors (Diptera: Psychodidae; Phlebotominae) in Iran: A Niche Model Study.

    Science.gov (United States)

    Hanafi-Bojd, A A; Rassi, Y; Yaghoobi-Ershadi, M R; Haghdoost, A A; Akhavan, A A; Charrahy, Z; Karimi, A

    2015-12-01

    Visceral leishmaniasis (VL) is an important vector-borne disease in Iran. Till now, Leishmania infantum has been detected from five species of sand flies in the country including Phlebotomus kandelakii, Phlebotomus major s.l., Phlebotomus perfiliewi, Phlebotomus alexandri and Phlebotomus tobbi. Also, Phlebotomus keshishiani was found to be infected with Leishmania parasites. This study aimed at predicting the probable niches and distribution of vectors of visceral leishmaniasis in Iran. Data on spatial distribution studies of sand flies were obtained from Iranian database on sand flies. Sample points were included in data from faunistic studies on sand flies conducted during 1995-2013. MaxEnt software was used to predict the appropriate ecological niches for given species, using climatic and topographical data. Distribution maps were prepared and classified in ArcGIS to find main ecological niches of the vectors and hot spots for VL transmission in Iran. Phlebotomus kandelakii, Ph. major s.l. and Ph. alexandri seem to have played a more important role in VL transmission in Iran, so this study focuses on them. Representations of MaxEnt model for probability of distribution of the studied sand flies showed high contribution of climatological and topographical variables to predict the potential distribution of three vector species. Isothermality was found to be an environmental variable with the highest gain when used in isolation for Ph. kandelakii and Ph. major s.l., while for Ph. alexandri, the most effective variable was precipitation of the coldest quarter. The results of this study present the first prediction on distribution of sand fly vectors of VL in Iran. The predicted distributions were matched with the disease-endemic areas in the country, while it was found that there were some unaffected areas with the potential transmission. More comprehensive studies are recommended on the ecology and vector competence of VL vectors in the country.

  3. How to catch a parasite: Parasite Niche Modeler (PaNic) meets Fishbase

    Science.gov (United States)

    Strona, Giovanni; Lafferty, Kevin D.

    2012-01-01

    Parasite Niche Modeler (PaNic) is a free online software tool that suggests potential hosts for fish parasites. For a particular parasite species from the major helminth groups (Acanthocephala, Cestoda, Monogenea, Nematoda, Trematoda), PaNic takes data from known hosts (maximum body length, growth rate, life span, age at first maturity, trophic level, phylogeny, and biogeography) and hypothesizes similar fish species that might serve as hosts to that parasite. Users can give varying weights to host attributes and create custom models. In addition to suggesting plausible hosts (with varying degrees of confidence), the models indicate known host species that appear to be outliers in comparison to other known hosts. These unique features make PaNic an innovative tool for addressing both theoretical and applied questions in fish parasitology. PaNic can be accessed at .

  4. Modeling of Iranian Cheetah Habitat using Ecological Niche Factor Analysis (Case Study: Dare Anjir Wildlife Refuge

    Directory of Open Access Journals (Sweden)

    N. Zamani

    2016-03-01

    Full Text Available Evaluation of habitat sustainability indexes is essential in wildlife management and conservation of rare species. Suitable habitats are required in wildlife managements and conservation also, they increase reproduction and survival rate of species. In this study in order to mapping habitat sustainability and recognizing habitat requirements of Iranian Cheetah (Acinonyx jubatus venaticus, field data from Dare Anjir  wildlife refuge were collected since autumn 2009 until summer 2011. Ecological Niche Factor Analysis approach has been used to develop habitat suitability model. In this method primary maps of  habitat variables including elevation, slope, aspect, vegetation cover, distance from water sources and environmental monitoring stations have been produced by Idrisi and Biomapper software and imported in Biomapper. The output scores obtained from the analysis showed that Iranian cheetah tends to mountain areas where has more topographical features for camouflage in order to hunting, and northern aspects which have more humidity, denser vegetation cover and more preys . Our result showed that the Iranian cheetah has medium niche width and prefer marginal habitats.

  5. Ecological Niche Modeling of Risk Factors for H7N9 Human Infection in China

    Directory of Open Access Journals (Sweden)

    Min Xu

    2016-06-01

    Full Text Available China was attacked by a serious influenza A (H7N9 virus in 2013. The first human infection case was confirmed in Shanghai City and soon spread across most of eastern China. Using the methods of Geographic Information Systems (GIS and ecological niche modeling (ENM, this research quantitatively analyzed the relationships between the H7N9 occurrence and the main environmental factors, including meteorological variables, human population density, bird migratory routes, wetland distribution, and live poultry farms, markets, and processing factories. Based on these relationships the probability of the presence of H7N9 was predicted. Results indicated that the distribution of live poultry processing factories, farms, and human population density were the top three most important determinants of the H7N9 human infection. The relative contributions to the model of live poultry processing factories, farms and human population density were 39.9%, 17.7% and 17.7%, respectively, while the maximum temperature of the warmest month and mean relative humidity had nearly no contribution to the model. The paper has developed an ecological niche model (ENM that predicts the spatial distribution of H7N9 cases in China using environmental variables. The area under the curve (AUC values of the model were greater than 0.9 (0.992 for the training samples and 0.961 for the test data. The findings indicated that most of the high risk areas were distributed in the Yangtze River Delta. These findings have important significance for the Chinese government to enhance the environmental surveillance at multiple human poultry interfaces in the high risk area.

  6. A privileged intraphagocyte niche is responsible for disseminated infection of Staphylococcus aureus in a zebrafish model.

    Science.gov (United States)

    Prajsnar, Tomasz K; Hamilton, Ruth; Garcia-Lara, Jorge; McVicker, Gareth; Williams, Alexander; Boots, Michael; Foster, Simon J; Renshaw, Stephen A

    2012-10-01

    The innate immune system is the primary defence against the versatile pathogen, Staphylococcus aureus. How this organism is able to avoid immune killing and cause infections is poorly understood. Using an established larval zebrafish infection model, we have shown that overwhelming infection is due to subversion of phagocytes by staphylococci, allowing bacteria to evade killing and found foci of disease. Larval zebrafish coinfected with two S. aureus strains carrying different fluorescent reporter gene fusions (but otherwise isogenic) had bacterial lesions, at the time of host death, containing predominantly one strain. Quantitative data using two marked strains revealed that the strain ratios, during overwhelming infection, were often skewed towards the extremes, with one strain predominating. Infection with passaged bacterial clones revealed the phenomenon not to bedue to adventitious mutations acquired by the pathogen. After infection of the host, all bacteria are internalized by phagocytes and the skewing of population ratios is absolutely dependent on the presence of phagocytes. Mathematical modelling of pathogen population dynamics revealed the data patterns are consistent with the hypothesis that a small number of infected phagocytes serve as an intracellular reservoir for S. aureus, which upon release leads to disseminated infection. Strategies to specifically alter neutrophil/macrophage numbers were used to map the potential subpopulation of phagocytes acting as a pathogen reservoir, revealing neutrophils as the likely 'niche'. Subsequently in a murine sepsis model, S. aureus abscesses in kidneys were also found to be predominantly clonal, therefore likely founded by an individual cell, suggesting a potential mechanism analogous to the zebrafish model with few protected niches. These findings add credence to the argument that S. aureus control regimes should recognize both the intracellular as well as extracellular facets of the S. aureus life

  7. Assessing the potential for establishment of western cherry fruit fly using ecological niche modeling.

    Science.gov (United States)

    Kumar, Sunil; Neven, Lisa G; Yee, Wee L

    2014-06-01

    Sweet cherries, Prunus avium (L.) L., grown in the western United States are exported to many countries around the world. Some of these countries have enforced strict quarantine rules and trade restrictions owing to concerns about the potential establishment and subsequent spread of western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), a major quarantine pest of sweet cherry. We used 1) niche models (CLIMEX and MaxEnt) to map the climatic suitability, 2) North Carolina State University-Animal and Plant Health Inspection Service Plant Pest Forecasting System to examine chilling requirement, and 3) host distribution and availability to assess the potential for establishment of R. indifferens in areas of western North America where it currently does not exist and eight current or potential fresh sweet cherry markets: Colombia, India, Indonesia, Malaysia, Taiwan, Thailand, Venezuela, and Vietnam. Results from niche models conformed well to the current distribution of R. indifferens in western North America. MaxEnt and CLIMEX models had high performance and predicted climatic suitability in some of the countries (e.g., Andean range in Colombia and Venezuela, northern and northeastern India, central Taiwan, and parts of Vietnam). However, our results showed no potential for establishment of R. indifferens in Colombia, Indonesia, Malaysia, Taiwan, Thailand, Venezuela, and Vietnam when the optimal chilling requirement to break diapause (minimum temperature < or = 3 degree C for at least 15 wk) was used as the criterion for whether establishment can occur. Furthermore, these countries have no host plant species available for R. indifferens. Our results can be used to make scientifically informed international trade decisions and negotiations by policy makers.

  8. Ecological Niche Modeling of main reservoir hosts of zoonotic cutaneous leishmaniasis in Iran.

    Science.gov (United States)

    Gholamrezaei, Mostafa; Mohebali, Mehdi; Hanafi-Bojd, Ahmad Ali; Sedaghat, Mohammad Mehdi; Shirzadi, Mohammad Reza

    2016-08-01

    Zoonotic cutaneous leishmaniasis (ZCL), caused by Leishmania major, is a common zoonotic vector-borne disease in Iran. Close contact with infected reservoir hosts increases the probability of transmission of Leishmania parasite infections to susceptible humans. Four gerbil species (Rodentia: Gerbillidae) serve as the main reservoir hosts for ZCL in different endemic foci of Iran. These species include Rhombomys opimus, Meriones libycus, Meriones hurrianae and Tatera indica; while notable infection has been reported in Nesokia indica as well. The purpose of this study is to model the distribution of these reservoirs to identify the risk areas of ZCL. A data bank was developed including all published data during the period of 1970-2015. Maximum entropy model was used to find the most appropriate ecological niches for each species. The areas under curve obtained were 0.961, 0.927, 0.922, 0.997 and 0.899, instead of 1, for training test in R. opimus, M. libycus, T. indica, M. hurrianae and N. indica, respectively. The environmental variable with the highest gain when used in isolation was slope for R. opimus and N. indica, annual mean temperature for M. libycus, and seasonal precipitation for T. indica and M. hurrianae. Summation of presence probabilities for three main species, i.e., R. opimus, M. libycus and T. indica revealed favorable ecological niches in wide areas of 16 provinces. This is the first study to predict the distribution of ZCL reservoir hosts in Iran. Climatology and topography variables had high contributions toward the prediction of potential distribution of the main reservoir species; therefore, as climate changes, the models should be updated periodically with novel data, and the results should be used in disease-monitoring programs.

  9. Long-term homeostasis and wound healing in an in vitro epithelial stem cell niche model

    Science.gov (United States)

    Miyashita, Hideyuki; Niwano, Hiroko; Yoshida, Satoru; Hatou, Shin; Inagaki, Emi; Tsubota, Kazuo; Shimmura, Shigeto

    2017-01-01

    Cultures of epithelial cells are limited by the proliferative capacity of primary cells and cell senescence. Herein we show that primary human epithelial cell sheets cultured without dermal equivalents maintained homeostasis in vitro for at least 1 year. Transparency of these sheets enabled live observation of pigmented melanocytes and Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) labeled epithelial cells during wound healing. Cell turn over and KRT15 expression pattern stabilized within 3 months, when KRT15 bright clusters often associated with niche-like melanocytes became apparent. EdU labels were retained in a subset of epithelial cells and melanocytes after 6 months chasing, suggesting their slow cell cycling property. FUCCI-labeling demonstrated robust cell migration and proliferation following wounding. Transparency and long-term (1 year) homeostasis of this model will be a powerful tool for the study of wound healing and cell linage tracing. PMID:28233843

  10. Using Ecological Niche Modeling For Biodiversity Conservation Guidance In The Western Podillya (Ukraine: Amphibians

    Directory of Open Access Journals (Sweden)

    Tytar V.

    2015-04-01

    Full Text Available Maximum entropy niche modeling was employed as a tool to assess potential habitat suitability for 13 amphibian species and to map their potential distribution in the Western Podillya (Ukraine. The predictor variables used were of climate, topography and human impact (assessed by the Human Footprint. The “mean temperature of coldest quarter” and “isothermality” were two of the most important factors in predicting habitat suitability and distribution. Another profound contribution has been displayed by the Human Footprint, meaning that human infrastructure may benefit amphibians, a phenomenon that perhaps is much more widespread than thought. Areas have been distinguished that in the first place should be of interest to nature conservationists targeting amphibians (exemplified by Bombina variegata and a map summarizing species richness was produced.

  11. Estimating niche width using stable isotopes in the face of habitat variability: a modelling case study in the marine environment.

    Science.gov (United States)

    Cummings, David O; Buhl, Jerome; Lee, Raymond W; Simpson, Stephen J; Holmes, Sebastian P

    2012-01-01

    Distributions of stable isotopes have been used to infer an organism's trophic niche width, the 'isotopic niche', and examine resource partitioning. Spatial variation in the isotopic composition of prey may however confound the interpretation of isotopic signatures especially when foragers exploit resources across numerous locations. In this study the isotopic compositions from marine assemblages are modelled to determine the role of variation in the signature of prey items and the effect of dietary breadth and foraging strategies on predator signatures. Outputs from the models reveal that isotopic niche widths can be greater for populations of dietary specialists rather than for generalists, which contravenes what is generally accepted in the literature. When a range of different mixing models are applied to determine if the conversion from δ to p-space can be used to improve model accuracy, predator signature variation is increased rather than model precision. Furthermore the mixing models applied failed to correctly identify dietary specialists and/or to accurately estimate diet contributions that may identify resource partitioning. The results presented illustrate the need to collect sufficiently large sample sizes, in excess of what is collected under most current studies, across the complete distribution of a species and its prey, before attempts to use stable isotopes to make inferences about niche width can be made.

  12. Estimating niche width using stable isotopes in the face of habitat variability: a modelling case study in the marine environment.

    Directory of Open Access Journals (Sweden)

    David O Cummings

    Full Text Available Distributions of stable isotopes have been used to infer an organism's trophic niche width, the 'isotopic niche', and examine resource partitioning. Spatial variation in the isotopic composition of prey may however confound the interpretation of isotopic signatures especially when foragers exploit resources across numerous locations. In this study the isotopic compositions from marine assemblages are modelled to determine the role of variation in the signature of prey items and the effect of dietary breadth and foraging strategies on predator signatures. Outputs from the models reveal that isotopic niche widths can be greater for populations of dietary specialists rather than for generalists, which contravenes what is generally accepted in the literature. When a range of different mixing models are applied to determine if the conversion from δ to p-space can be used to improve model accuracy, predator signature variation is increased rather than model precision. Furthermore the mixing models applied failed to correctly identify dietary specialists and/or to accurately estimate diet contributions that may identify resource partitioning. The results presented illustrate the need to collect sufficiently large sample sizes, in excess of what is collected under most current studies, across the complete distribution of a species and its prey, before attempts to use stable isotopes to make inferences about niche width can be made.

  13. Modelling species invasions using thermal and trophic niche dynamics under climate change

    Directory of Open Access Journals (Sweden)

    Simone eLibralato

    2015-05-01

    Full Text Available Changing marine temperatures modify the distributional ranges of natural populations, but the success of invasion of new areas depends on local physical and ecological conditions. We explore the invasion by thermophilic species and their ecosystem effects by simulating a sea surface temperature increase using a trophodynamic model for the northern Adriatic Sea (NAS, in which thermal and trophic niches are explicitly represented for each thermophilic non-indigenous species and native species. The NAS acts as a cul-de-sac for local species, preventing a further poleward migration as a response to temperature rise. In this situation, model results showed that effects of warming and invasion produced complex, non-linear changes on biomasses but never resulted in a complete overturn of a group of native species and/or a bloom of invasive ones. Despite this, the diversity index stabilizes at increased values after simulating invasion, possibly indicating that in such enclosed systems the establishment of invasive species could represent enrichment in ecosystem structure. In addition, the absence of complete species substitution clearly showed the contribution of resident species towards increasing the resilience, i.e. the capability of the system to cope with invasion without changing substantially. Contrasting scenarios highlighted that changes in ecosystem primary production and species adaptation had secondary effects in ecosystem structure, while results for scenarios with different exploitation levels indicated that fishing can destabilize community structure in these change contexts, e.g. reducing community resilience. The results confirmed the importance of an ecological niche approach to analyze possible effects of invasion and highlighted the complexity of dynamics linked to temperature-driven species invasion’, in terms of both the predicted strength of impacts and the direction of biomass change.

  14. Ecological niche modelling of Rift Valley fever virus vectors in Baringo, Kenya

    Directory of Open Access Journals (Sweden)

    Alfred O. Ochieng

    2016-11-01

    Full Text Available Background: Rift Valley fever (RVF is a vector-borne zoonotic disease that has an impact on human health and animal productivity. Here, we explore the use of vector presence modelling to predict the distribution of RVF vector species under climate change scenario to demonstrate the potential for geographic spread of Rift Valley fever virus (RVFV. Objectives: To evaluate the effect of climate change on RVF vector distribution in Baringo County, Kenya, with an aim of developing a risk map for spatial prediction of RVF outbreaks. Methodology: The study used data on vector presence and ecological niche modelling (MaxEnt algorithm to predict the effect of climatic change on habitat suitability and the spatial distribution of RVF vectors in Baringo County. Data on species occurrence were obtained from longitudinal sampling of adult mosquitoes and larvae in the study area. We used present (2000 and future (2050 Bioclim climate databases to model the vector distribution. Results: Model results predicted potential suitable areas with high success rates for Culex quinquefasciatus, Culex univitattus, Mansonia africana, and Mansonia uniformis. Under the present climatic conditions, the lowlands were found to be highly suitable for all the species. Future climatic conditions indicate an increase in the spatial distribution of Cx. quinquefasciatus and M. africana. Model performance was statistically significant. Conclusion: Soil types, precipitation in the driest quarter, precipitation seasonality, and isothermality showed the highest predictive potential for the four species.

  15. The use of ecological niche modeling to infer potential risk areas of snakebite in the Mexican state of Veracruz.

    Directory of Open Access Journals (Sweden)

    Carlos Yañez-Arenas

    Full Text Available Many authors have claimed that snakebite risk is associated with human population density, human activities, and snake behavior. Here we analyzed whether environmental suitability of vipers can be used as an indicator of snakebite risk. We tested several hypotheses to explain snakebite incidence, through the construction of models incorporating both environmental suitability and socioeconomic variables in Veracruz, Mexico.Ecological niche modeling (ENM was used to estimate potential geographic and ecological distributions of nine viper species' in Veracruz. We calculated the distance to the species' niche centroid (DNC; this distance may be associated with a prediction of abundance. We found significant inverse relationships between snakebites and DNCs of common vipers (Crotalus simus and Bothrops asper, explaining respectively 15% and almost 35% of variation in snakebite incidence. Additionally, DNCs for these two vipers, in combination with marginalization of human populations, accounted for 76% of variation in incidence.Our results suggest that niche modeling and niche-centroid distance approaches can be used to mapping distributions of environmental suitability for venomous snakes; combining this ecological information with socioeconomic factors may help with inferring potential risk areas for snakebites, since hospital data are often biased (especially when incidences are low.

  16. Predicting geographic distributions of Phacellodomus species (Aves: Furnariidae in South America based on ecological niche modeling

    Directory of Open Access Journals (Sweden)

    Maria da Salete Gurgel Costa

    2014-08-01

    Full Text Available Phacellodomus Reichenbach, 1853, comprises nine species of Furnariids that occur in South America in open and generally dry areas. This study estimated the geographic distributions of Phacellodomus species in South America by ecological niche modeling. Applying maximum entropy method, models were produced for eight species based on six climatic variables and 949 occurrence records. Since highest climatic suitability for Phacellodomus species has been estimated in open and dry areas, the Amazon rainforest areas are not very suitable for these species. Annual precipitation and minimum temperature of the coldest month are the variables that most influence the models. Phacellodomus species occurred in 35 ecoregions of South America. Chaco and Uruguayan savannas were the ecoregions with the highest number of species. Despite the overall connection of Phacellodomus species with dry areas, species such as P. ruber, P. rufifrons, P. ferrugineigula and P. erythrophthalmus occurred in wet forests and wetland ecoregions.

  17. Potential distribution of Mexican primates: modeling the ecological niche with the maximum entropy algorithm.

    Science.gov (United States)

    Vidal-García, Francisca; Serio-Silva, Juan Carlos

    2011-07-01

    We developed a potential distribution model for the tropical rain forest species of primates of southern Mexico: the black howler monkey (Alouatta pigra), the mantled howler monkey (Alouatta palliata), and the spider monkey (Ateles geoffroyi). To do so, we applied the maximum entropy algorithm from the ecological niche modeling program MaxEnt. For each species, we used occurrence records from scientific collections, and published and unpublished sources, and we also used the 19 environmental coverage variables related to precipitation and temperature from WorldClim to develop the models. The predicted distribution of A. pigra was strongly associated with the mean temperature of the warmest quarter (23.6%), whereas the potential distributions of A. palliata and A. geoffroyi were strongly associated with precipitation during the coldest quarter (52.2 and 34.3% respectively). The potential distribution of A. geoffroyi is broader than that of the Alouatta spp. The areas with the greatest probability of presence of A. pigra and A. palliata are strongly associated with riparian vegetation, whereas the presence of A. geoffroyi is more strongly associated with the presence of rain forest. Our most significant contribution is the identification of areas with a high probability of the presence of these primate species, which is information that can be applied to planning future studies and then establishing criteria for the creation of areas to primate conservation in Mexico.

  18. Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant model Arabidopsis arenosa.

    Science.gov (United States)

    Kolář, Filip; Fuxová, Gabriela; Záveská, Eliška; Nagano, Atsushi J; Hyklová, Lucie; Lučanová, Magdalena; Kudoh, Hiroshi; Marhold, Karol

    2016-08-01

    Quaternary climatic oscillations profoundly impacted temperate biodiversity. For many diverse yet undersampled areas, however, the consequences of this impact are still poorly known. In Europe, particular uncertainty surrounds the role of Balkans, a major hotspot of European diversity, in postglacial recolonization of more northerly areas, and the Carpathians, a debatable candidate for a northern 'cryptic' glacial refugium. Using genome-wide SNPs and microsatellites, we examined how the interplay of historical processes and niche shifts structured genetic diversity of diploid Arabidopsis arenosa, a little-known member of the plant model genus that occupies a wide niche range from sea level to alpine peaks across eastern temperate Europe. While the northern Balkans hosted one isolated endemic lineage, most of the genetic diversity was concentrated further north in the Pannonian Basin and the Carpathians, where it likely survived the last glaciation in northern refugia. Finally, a distinct postglacial environment in northern Europe was colonized by populations of admixed origin from the two Carpathian lineages. Niche differentiation along altitude-related bioclimatic gradients was the main trend in the phylogeny of A. arenosa. The most prominent niche shifts, however, characterized genetically only slightly divergent populations that expanded into narrowly defined alpine and northern coastal postglacial environments. Our study highlights the role of eastern central European mountains not only as refugia for unique temperate diversity but also sources for postglacial expansion into novel high-altitude and high-latitude niches. Knowledge of distinct genetic substructure of diploid A. arenosa also opens new opportunities for follow-up studies of this emerging model of evolutionary biology.

  19. Indirect Energy Flows in Niche Model Food Webs: Effects of Size and Connectance.

    Directory of Open Access Journals (Sweden)

    Jane Shevtsov

    Full Text Available Indirect interactions between species have long been of interest to ecologists. One such interaction type takes place when energy or materials flow via one or more intermediate species between two species with a direct predator-prey relationship. Previous work has shown that, although each such flow is small, their great number makes them important in ecosystems. A new network analysis method, dynamic environ approximation, was used to quantify the fraction of energy flowing from prey to predator over paths of length greater than 1 (flow indirectness or FI in a commonly studied food web model. Web structure was created using the niche model and dynamics followed the Yodzis-Innes model. The effect of food web size (10 to 40 species and connectance (0.1 to 0.48 on FI was examined. For each of 250 model realizations run for each pair of size and connectance values, the FI of every predator-prey interaction in the model was computed and then averaged over the whole network. A classification and regression tree (CART analysis was then used to find the best predictors of FI. The mean FI of the model food webs is 0.092, with a standard deviation of 0.0279. It tends to increase with system size but peaks at intermediate connectance levels. Of 27 potential predictor variables, only five (mean path length, dominant eigenvalue of the adjacency matrix, connectance, mean trophic level and fraction of species belonging to intermediate trophic levels were selected by the CART algorithm as best accounting for variation in the data; mean path length and the dominant eigenvalue of the adjacency matrix were dominant.

  20. Predicting the Plant Root-Associated Ecological Niche of 21 Pseudomonas Species Using Machine Learning and Metabolic Modeling

    OpenAIRE

    Chien, Jennifer; Larsen, Peter

    2017-01-01

    Plants rarely occur in isolated systems. Bacteria can inhabit either the endosphere, the region inside the plant root, or the rhizosphere, the soil region just outside the plant root. Our goal is to understand if using genomic data and media dependent metabolic model information is better for training machine learning of predicting bacterial ecological niche than media independent models or pure genome based species trees. We considered three machine learning techniques: support vector machin...

  1. San Diego, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The San Diego, California Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

  2. Monterey, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Monterey, California Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

  3. Distribution and Conservation of Davilla (Dilleniaceae in Brazilian Atlantic Forest Using Ecological Niche Modeling

    Directory of Open Access Journals (Sweden)

    Ismael Martins Pereira

    2014-01-01

    Full Text Available We have modeled the ecological niche for 12 plant species belonging to the genus Davilla (Dilleniaceae which occur in the Atlantic Forest of Brazil. This group includes endemic species lianas threatened by extinction and is therefore a useful indicator for forest areas requiring conservation. The aims are to compare the distribution and richness of species within the protected areas, assessing the degree of protection and gap analysis of reserves for this group. We used the Maxent algorithm with environmental and occurrence data, and produced geographic distribution maps. The results show that high species richness occurs in forest and coastal forest of Espírito Santo to Bahia states. The endemic species comprise D. flexuosa, D. macrocarpa, D. flexuosa, D. grandifolia, and D. sessilifolia. In the Atlantic Forest of southeastern Brazil, the following endemic species occur: D. tintinnabulata and D. glaziovii, with this latter species being included in the “red list” due habitat loss and predatory extractivism. The indicators of species richness in the coastal region of Bahia correspond with floristic inventories that point to this area having a high biodiversity. Although this region has several protected areas, there are gaps in reserves, which, combined with anthropogenic threats and fragmentation, have caused several problems for biodiversity.

  4. Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution.

    Directory of Open Access Journals (Sweden)

    Tábita Hünemeier

    Full Text Available Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905 to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the F(ST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.

  5. Character displacement and the evolution of niche complementarity in a model biofilm community.

    Science.gov (United States)

    Ellis, Crystal N; Traverse, Charles C; Mayo-Smith, Leslie; Buskirk, Sean W; Cooper, Vaughn S

    2015-02-01

    Colonization of vacant environments may catalyze adaptive diversification and be followed by competition within the nascent community. How these interactions ultimately stabilize and affect productivity are central problems in evolutionary ecology. Diversity can emerge by character displacement, in which selection favors phenotypes that exploit an alternative resource and reduce competition, or by facilitation, in which organisms change the environment and enable different genotypes or species to become established. We previously developed a model of long-term experimental evolution in which bacteria attach to a plastic bead, form a biofilm, and disperse to a new bead. Here, we focus on the evolution of coexisting mutants within a population of Burkholderia cenocepacia and how their interactions affected productivity. Adaptive mutants initially competed for space, but later competition declined, consistent with character displacement and the predicted effects of the evolved mutations. The community reached a stable equilibrium as each ecotype evolved to inhabit distinct, complementary regions of the biofilm. Interactions among ecotypes ultimately became facilitative and enhanced mixed productivity. Observing the succession of genotypes within niches illuminated changing selective forces within the community, including a fundamental role for genotypes producing small colony variants that underpin chronic infections caused by B. cenocepacia.

  6. Tracking a medically important spider: climate change, ecological niche modeling, and the brown recluse (Loxosceles reclusa.

    Directory of Open Access Journals (Sweden)

    Erin E Saupe

    Full Text Available Most spiders use venom to paralyze their prey and are commonly feared for their potential to cause injury to humans. In North America, one species in particular, Loxosceles reclusa (brown recluse spider, Sicariidae, causes the majority of necrotic wounds induced by the Araneae. However, its distributional limitations are poorly understood and, as a result, medical professionals routinely misdiagnose brown recluse bites outside endemic areas, confusing putative spider bites for other serious conditions. To address the issue of brown recluse distribution, we employ ecological niche modeling to investigate the present and future distributional potential of this species. We delineate range boundaries and demonstrate that under future climate change scenarios, the spider's distribution may expand northward, invading previously unaffected regions of the USA. At present, the spider's range is centered in the USA, from Kansas east to Kentucky and from southern Iowa south to Louisiana. Newly influenced areas may include parts of Nebraska, Minnesota, Wisconsin, Michigan, South Dakota, Ohio, and Pennsylvania. These results illustrate a potential negative consequence of climate change on humans and will aid medical professionals in proper bite identification/treatment, potentially reducing bite misdiagnoses.

  7. Evolutionary Responses to a Constructed Niche: Ancient Mesoamericans as a Model of Gene-Culture Coevolution

    Science.gov (United States)

    Hünemeier, Tábita; Amorim, Carlos Eduardo Guerra; Azevedo, Soledad; Contini, Veronica; Acuña-Alonzo, Víctor; Rothhammer, Francisco; Dugoujon, Jean-Michel; Mazières, Stephane; Barrantes, Ramiro; Villarreal-Molina, María Teresa; Paixão-Côrtes, Vanessa Rodrigues; Salzano, Francisco M.; Canizales-Quinteros, Samuel; Ruiz-Linares, Andres; Bortolini, Maria Cátira

    2012-01-01

    Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the FST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele. PMID:22768049

  8. Quercus suber range dynamics by ecological niche modelling: from the Last Interglacial to present time

    Science.gov (United States)

    Vessella, Federico; Simeone, Marco Cosimo; Schirone, Bartolomeo

    2015-07-01

    Ecological Niche Modelling (ENM) is widely used to depict species potential occurrence according to environmental variables under different climatic scenarios. We tested the ENM approach to infer past range dynamics of cork oak, a keystone species of the Mediterranean Biome, from 130 ka to the present time. Hindcasting implications would deal with a better species risk assessment and conservation management for the future. We modelled present and past occurrence of cork oak using seven ENM algorithms, starting from 63,733 spatially unique presence points at 30 arc-second resolution. Fourteen environmental variables were used and four time slices were considered (Last Interglacial, Last Glacial Maximum, mid-Holocene and present time). A threshold-independent evaluation of the goodness-of-fit of the models was evaluated by means of ROC curve and fossil or historical evidences were used to validate the results. Four weighted average maps depicted the dynamics of area suitability for cork oak in the last 130 ka. The derived species autoecology allowed its long-term occurrence in the Mediterranean without striking range reduction or shifting. Fossil and historical post-processing validation support the modelled past spatial extension and a neglected species presence at Levantine until the recent time. Despite the severe climatic oscillation since the Last Glacial Maximum, cork oak potential distribution area experienced limited range changes, confirming its strong link with the Mediterranean Basin. The ecological amplitude of Quercus suber could be therefore adopted as a reference to trace the Mediterranean bioclimate area. A better knowledge of the past events of Mediterranean vegetation, a wider range of study species and environmental determinants are essential to inform us about its current state, its sensitivity to human impact and the potential responses to future changes.

  9. Predicting the current and future potential distributions of lymphatic filariasis in Africa using maximum entropy ecological niche modelling.

    Science.gov (United States)

    Slater, Hannah; Michael, Edwin

    2012-01-01

    Modelling the spatial distributions of human parasite species is crucial to understanding the environmental determinants of infection as well as for guiding the planning of control programmes. Here, we use ecological niche modelling to map the current potential distribution of the macroparasitic disease, lymphatic filariasis (LF), in Africa, and to estimate how future changes in climate and population could affect its spread and burden across the continent. We used 508 community-specific infection presence data collated from the published literature in conjunction with five predictive environmental/climatic and demographic variables, and a maximum entropy niche modelling method to construct the first ecological niche maps describing potential distribution and burden of LF in Africa. We also ran the best-fit model against climate projections made by the HADCM3 and CCCMA models for 2050 under A2a and B2a scenarios to simulate the likely distribution of LF under future climate and population changes. We predict a broad geographic distribution of LF in Africa extending from the west to the east across the middle region of the continent, with high probabilities of occurrence in the Western Africa compared to large areas of medium probability interspersed with smaller areas of high probability in Central and Eastern Africa and in Madagascar. We uncovered complex relationships between predictor ecological niche variables and the probability of LF occurrence. We show for the first time that predicted climate change and population growth will expand both the range and risk of LF infection (and ultimately disease) in an endemic region. We estimate that populations at risk to LF may range from 543 and 804 million currently, and that this could rise to between 1.65 to 1.86 billion in the future depending on the climate scenario used and thresholds applied to signify infection presence.

  10. Predicting the current and future potential distributions of lymphatic filariasis in Africa using maximum entropy ecological niche modelling.

    Directory of Open Access Journals (Sweden)

    Hannah Slater

    Full Text Available Modelling the spatial distributions of human parasite species is crucial to understanding the environmental determinants of infection as well as for guiding the planning of control programmes. Here, we use ecological niche modelling to map the current potential distribution of the macroparasitic disease, lymphatic filariasis (LF, in Africa, and to estimate how future changes in climate and population could affect its spread and burden across the continent. We used 508 community-specific infection presence data collated from the published literature in conjunction with five predictive environmental/climatic and demographic variables, and a maximum entropy niche modelling method to construct the first ecological niche maps describing potential distribution and burden of LF in Africa. We also ran the best-fit model against climate projections made by the HADCM3 and CCCMA models for 2050 under A2a and B2a scenarios to simulate the likely distribution of LF under future climate and population changes. We predict a broad geographic distribution of LF in Africa extending from the west to the east across the middle region of the continent, with high probabilities of occurrence in the Western Africa compared to large areas of medium probability interspersed with smaller areas of high probability in Central and Eastern Africa and in Madagascar. We uncovered complex relationships between predictor ecological niche variables and the probability of LF occurrence. We show for the first time that predicted climate change and population growth will expand both the range and risk of LF infection (and ultimately disease in an endemic region. We estimate that populations at risk to LF may range from 543 and 804 million currently, and that this could rise to between 1.65 to 1.86 billion in the future depending on the climate scenario used and thresholds applied to signify infection presence.

  11. Body size and the small branch niche: using marsupial ontogeny to model primate locomotor evolution.

    Science.gov (United States)

    Shapiro, Liza J; Young, Jesse W; VandeBerg, John L

    2014-03-01

    Recently proposed ancestral locomotor and morphological 'stages' leading to the evolution of primates have emphasized small body size, and a transition from a clawed non-grasping stage, to a clawed, grasping stage with clawless opposable hallux, to a fully-nailed primate with grasping extremities. This evolutionary transition was presumably associated with frequent use of the small branch niche. To model elements of these evolutionary transitions, we investigate how body size, substrate size, substrate orientation and grasping morphology interact to influence quadrupedal kinematics within and between ontogenetic samples of two small-bodied marsupials, one arboreal (Petaurus breviceps) and the other mainly terrestrial (Monodelphis domestica). Longitudinal morphometric and kinematic data were collected from four juvenile P. breviceps (33-75 g) and two juvenile M. domestica (18-95 g) walking across poles of three diameters (2.5, 1.0, and 0.5 cm) and three orientations (horizontal, 30° incline, 30° decline). The two species responded similarly to some substrate conditions, but diverged in response to others. Kinematic divergence between the two species reflects Monodelphis' relatively shorter digits, reduced grasping ability and greater need for stabilizing mechanisms on narrow substrates. At a given relative body size or pole orientation, Monodelphis used higher limb duty factors, more limbs in support per stride, lower limb phases, and in some conditions, faster speeds compared with Petaurus. Interspecific differences were the least distinct on declined poles, highlighting the particular challenge of this substrate condition, even for arboreally adapted species. Small-bodied, arboreal primate ancestors would likely have employed the kinematic mechanisms common to our model taxa, but those with enhanced grasping adaptations would most likely not have required the increased level of stabilizing mechanisms exhibited by Monodelphis. Thus, using these two species

  12. Plant stem cell niches.

    Science.gov (United States)

    Aichinger, Ernst; Kornet, Noortje; Friedrich, Thomas; Laux, Thomas

    2012-01-01

    Multicellular organisms possess pluripotent stem cells to form new organs, replenish the daily loss of cells, or regenerate organs after injury. Stem cells are maintained in specific environments, the stem cell niches, that provide signals to block differentiation. In plants, stem cell niches are situated in the shoot, root, and vascular meristems-self-perpetuating units of organ formation. Plants' lifelong activity-which, as in the case of trees, can extend over more than a thousand years-requires that a robust regulatory network keep the balance between pluripotent stem cells and differentiating descendants. In this review, we focus on current models in plant stem cell research elaborated during the past two decades, mainly in the model plant Arabidopsis thaliana. We address the roles of mobile signals on transcriptional modules involved in balancing cell fates. In addition, we discuss shared features of and differences between the distinct stem cell niches of Arabidopsis.

  13. Niche explosion.

    Science.gov (United States)

    Normark, Benjamin B; Johnson, Norman A

    2011-05-01

    The following syndrome of features occurs in several groups of phytophagous insects: (1) wingless females, (2) dispersal by larvae, (3) woody hosts, (4) extreme polyphagy, (5) high abundance, resulting in status as economic pests, (6) invasiveness, and (7) obligate parthenogenesis in some populations. If extreme polyphagy is defined as feeding on 20 or more families of hostplants, this syndrome is found convergently in several species of bagworm moths, tussock moths, root weevils, and 5 families of scale insects. We hypothesize that extreme polyphagy in these taxa results from "niche explosion", a positive feedback loop connecting large population size to broad host range. The niche explosion has a demographic component (sometimes called the "amplification effect" in studies of pathogens) as well as a population-genetic component, due mainly to the increased effectiveness of natural selection in larger populations. The frequent origins of parthenogenesis in extreme polyphages are, in our interpretation, a consequence of this increased effectiveness of natural selection and consequent reduced importance of sexuality. The niche explosion hypothesis makes detailed predictions about the comparative genomics and population genetics of extreme polyphages and related specialists. It has a number of potentially important implications, including an explanation for the lack of observed trade-offs between generalists and specialists, a re-interpretation of the ecological correlates of parthenogenesis, and a general expectation that Malthusian population explosions may be amplified by Darwinian effects.

  14. Ecological niche modelling and nDNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Oliver Hawlitschek

    Full Text Available BACKGROUND: DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data. METHODOLOGY/PRINCIPAL FINDINGS: The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n. CONCLUSION/SIGNIFICANCE: In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species.

  15. Crescent City, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Crescent City, California Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST)...

  16. Los Angeles, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Los Angeles, California Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST)...

  17. Santa Barbara, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Santa Barbara, California Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST)...

  18. Santa Monica, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Santa Monica, California Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST)...

  19. Point Reyes, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Point Reyes, California Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST)...

  20. Using remote sensing, ecological niche modeling, and Geographic Information Systems for Rift Valley fever risk assessment in the United States

    Science.gov (United States)

    Tedrow, Christine Atkins

    The primary goal in this study was to explore remote sensing, ecological niche modeling, and Geographic Information Systems (GIS) as aids in predicting candidate Rift Valley fever (RVF) competent vector abundance and distribution in Virginia, and as means of estimating where risk of establishment in mosquitoes and risk of transmission to human populations would be greatest in Virginia. A second goal in this study was to determine whether the remotely-sensed Normalized Difference Vegetation Index (NDVI) can be used as a proxy variable of local conditions for the development of mosquitoes to predict mosquito species distribution and abundance in Virginia. As part of this study, a mosquito surveillance database was compiled to archive the historical patterns of mosquito species abundance in Virginia. In addition, linkages between mosquito density and local environmental and climatic patterns were spatially and temporally examined. The present study affirms the potential role of remote sensing imagery for species distribution prediction, and it demonstrates that ecological niche modeling is a valuable predictive tool to analyze the distributions of populations. The MaxEnt ecological niche modeling program was used to model predicted ranges for potential RVF competent vectors in Virginia. The MaxEnt model was shown to be robust, and the candidate RVF competent vector predicted distribution map is presented. The Normalized Difference Vegetation Index (NDVI) was found to be the most useful environmental-climatic variable to predict mosquito species distribution and abundance in Virginia. However, these results indicate that a more robust prediction is obtained by including other environmental-climatic factors correlated to mosquito densities (e.g., temperature, precipitation, elevation) with NDVI. The present study demonstrates that remote sensing and GIS can be used with ecological niche and risk modeling methods to estimate risk of virus establishment in mosquitoes and

  1. Ecological niche modeling of coastal dune plants and future potential distribution in response to climate change and sea level rise.

    Science.gov (United States)

    Mendoza-González, Gabriela; Martínez, M Luisa; Rojas-Soto, Octavio R; Vázquez, Gabriela; Gallego-Fernández, Juan B

    2013-08-01

    Climate change (CC) and sea level rise (SLR) are phenomena that could have severe impacts on the distribution of coastal dune vegetation. To explore this we modeled the climatic niches of six coastal dunes plant species that grow along the shoreline of the Gulf of Mexico and the Yucatan Peninsula, and projected climatic niches to future potential distributions based on two CC scenarios and SLR projections. Our analyses suggest that distribution of coastal plants will be severely limited, and more so in the case of local endemics (Chamaecrista chamaecristoides, Palafoxia lindenii, Cakile edentula). The possibilities of inland migration to the potential 'new shoreline' will be limited by human infrastructure and ecosystem alteration that will lead to a 'coastal squeeze' of the coastal habitats. Finally, we identified areas as future potential refuges for the six species in central Gulf of Mexico, and northern Yucatán Peninsula especially under CC and SLR scenarios.

  2. Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions

    Directory of Open Access Journals (Sweden)

    Alberto Muñoz

    2016-10-01

    Full Text Available Ecological Niche Models (ENMs are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models. Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species and taxonomy (amphibians and reptiles. Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural

  3. Climatic niche conservatism and biogeographical non-equilibrium in Eschscholzia californica (Papaveraceae), an invasive plant in the Chilean Mediterranean region.

    Science.gov (United States)

    Peña-Gómez, Francisco T; Guerrero, Pablo C; Bizama, Gustavo; Duarte, Milén; Bustamante, Ramiro O

    2014-01-01

    Species climate requirements are useful for predicting their geographic distribution. It is often assumed that the niche requirements for invasive plants are conserved during invasion, especially when the invaded regions share similar climate conditions. California and central Chile have a remarkable degree of convergence in their vegetation structure, and a similar Mediterranean climate. Such similarities make these geographic areas an interesting natural experiment for testing climatic niche dynamics and the equilibrium of invasive species in a new environment. We tested to see if the climatic niche of Eschscholzia californica is conserved in the invaded range (central Chile), and we assessed whether the invasion process has reached a biogeographical equilibrium, i.e., occupy all the suitable geographic locations that have suitable conditions under native niche requirements. We compared the climatic niche in the native and invaded ranges as well as the projected potential geographic distribution in the invaded range. In order to compare climatic niches, we conducted a Principal Component Analysis (PCA) and Species Distribution Models (SDMs), to estimate E. californica's potential geographic distribution. We also used SDMs to predict altitudinal distribution limits in central Chile. Our results indicated that the climatic niche occupied by E. californica in the invaded range is firmly conserved, occupying a subset of the native climatic niche but leaving a substantial fraction of it unfilled. Comparisons of projected SDMs for central Chile indicate a similarity, yet the projection from native range predicted a larger geographic distribution in central Chile compared to the prediction of the model constructed for central Chile. The projected niche occupancy profile from California predicted a higher mean elevation than that projected from central Chile. We concluded that the invasion process of E. californica in central Chile is consistent with climatic niche

  4. Climatic niche conservatism and biogeographical non-equilibrium in Eschscholzia californica (Papaveraceae, an invasive plant in the Chilean Mediterranean region.

    Directory of Open Access Journals (Sweden)

    Francisco T Peña-Gómez

    Full Text Available Species climate requirements are useful for predicting their geographic distribution. It is often assumed that the niche requirements for invasive plants are conserved during invasion, especially when the invaded regions share similar climate conditions. California and central Chile have a remarkable degree of convergence in their vegetation structure, and a similar Mediterranean climate. Such similarities make these geographic areas an interesting natural experiment for testing climatic niche dynamics and the equilibrium of invasive species in a new environment. We tested to see if the climatic niche of Eschscholzia californica is conserved in the invaded range (central Chile, and we assessed whether the invasion process has reached a biogeographical equilibrium, i.e., occupy all the suitable geographic locations that have suitable conditions under native niche requirements. We compared the climatic niche in the native and invaded ranges as well as the projected potential geographic distribution in the invaded range. In order to compare climatic niches, we conducted a Principal Component Analysis (PCA and Species Distribution Models (SDMs, to estimate E. californica's potential geographic distribution. We also used SDMs to predict altitudinal distribution limits in central Chile. Our results indicated that the climatic niche occupied by E. californica in the invaded range is firmly conserved, occupying a subset of the native climatic niche but leaving a substantial fraction of it unfilled. Comparisons of projected SDMs for central Chile indicate a similarity, yet the projection from native range predicted a larger geographic distribution in central Chile compared to the prediction of the model constructed for central Chile. The projected niche occupancy profile from California predicted a higher mean elevation than that projected from central Chile. We concluded that the invasion process of E. californica in central Chile is consistent with

  5. California Basin Characterization Model Downscaled Climate and Hydrology

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The California Basin Characterization Model (CA-BCM 2014) dataset provides historical and projected climate and hydrologic surfaces for the region that encompasses...

  6. High resolution niche models of malaria vectors in northern Tanzania: a new capacity to predict malaria risk?

    Directory of Open Access Journals (Sweden)

    Manisha A Kulkarni

    Full Text Available BACKGROUND: Malaria transmission rates in Africa can vary dramatically over the space of a few kilometres. This spatial heterogeneity reflects variation in vector mosquito habitat and presents an important obstacle to the efficient allocation of malaria control resources. Malaria control is further complicated by combinations of vector species that respond differently to control interventions. Recent modelling innovations make it possible to predict vector distributions and extrapolate malaria risk continentally, but these risk mapping efforts have not yet bridged the spatial gap to guide on-the-ground control efforts. METHODOLOGY/PRINCIPAL FINDINGS: We used Maximum Entropy with purpose-built, high resolution land cover data and other environmental factors to model the spatial distributions of the three dominant malaria vector species in a 94,000 km(2 region of east Africa. Remotely sensed land cover was necessary in each vector's niche model. Seasonality of precipitation and maximum annual temperature also contributed to niche models for Anopheles arabiensis and An. funestus s.l. (AUC 0.989 and 0.991, respectively, but cold season precipitation and elevation were important for An. gambiae s.s. (AUC 0.997. Although these niche models appear highly accurate, the critical test is whether they improve predictions of malaria prevalence in human populations. Vector habitat within 1.5 km of community-based malaria prevalence measurements interacts with elevation to substantially improve predictions of Plasmodium falciparum prevalence in children. The inclusion of the mechanistic link between malaria prevalence and vector habitat greatly improves the precision and accuracy of prevalence predictions (r(2 = 0.83 including vector habitat, or r(2 = 0.50 without vector habitat. Predictions including vector habitat are unbiased (observations vs. model predictions of prevalence: slope = 1.02. Using this model, we generate a high resolution map of predicted

  7. Land Suitability Modeling using a Geographic Socio-Environmental Niche-Based Approach: A Case Study from Northeastern Thailand.

    Science.gov (United States)

    Heumann, Benjamin W; Walsh, Stephen J; Verdery, Ashton M; McDaniel, Phillip M; Rindfuss, Ronald R

    2013-01-01

    Understanding the pattern-process relations of land use/land cover change is an important area of research that provides key insights into human-environment interactions. The suitability or likelihood of occurrence of land use such as agricultural crop types across a human-managed landscape is a central consideration. Recent advances in niche-based, geographic species distribution modeling (SDM) offer a novel approach to understanding land suitability and land use decisions. SDM links species presence-location data with geospatial information and uses machine learning algorithms to develop non-linear and discontinuous species-environment relationships. Here, we apply the MaxEnt (Maximum Entropy) model for land suitability modeling by adapting niche theory to a human-managed landscape. In this article, we use data from an agricultural district in Northeastern Thailand as a case study for examining the relationships between the natural, built, and social environments and the likelihood of crop choice for the commonly grown crops that occur in the Nang Rong District - cassava, heavy rice, and jasmine rice, as well as an emerging crop, fruit trees. Our results indicate that while the natural environment (e.g., elevation and soils) is often the dominant factor in crop likelihood, the likelihood is also influenced by household characteristics, such as household assets and conditions of the neighborhood or built environment. Furthermore, the shape of the land use-environment curves illustrates the non-continuous and non-linear nature of these relationships. This approach demonstrates a novel method of understanding non-linear relationships between land and people. The article concludes with a proposed method for integrating the niche-based rules of land use allocation into a dynamic land use model that can address both allocation and quantity of agricultural crops.

  8. Combining physiological threshold knowledge to species distribution models is key to improving forecasts of the future niche for macroalgae.

    Science.gov (United States)

    Martínez, Brezo; Arenas, Francisco; Trilla, Alba; Viejo, Rosa M; Carreño, Francisco

    2015-04-01

    Species distribution models (SDM) are a useful tool for predicting species range shifts in response to global warming. However, they do not explore the mechanisms underlying biological processes, making it difficult to predict shifts outside the environmental gradient where the model was trained. In this study, we combine correlative SDMs and knowledge on physiological limits to provide more robust predictions. The thermal thresholds obtained in growth and survival experiments were used as proxies of the fundamental niches of two foundational marine macrophytes. The geographic projections of these species' distributions obtained using these thresholds and existing SDMs were similar in areas where the species are either absent-rare or frequent and where their potential and realized niches match, reaching consensus predictions. The cold-temperate foundational seaweed Himanthalia elongata was predicted to become extinct at its southern limit in northern Spain in response to global warming, whereas the occupancy of southern-lusitanic Bifurcaria bifurcata was expected to increase. Combined approaches such as this one may also highlight geographic areas where models disagree potentially due to biotic factors. Physiological thresholds alone tended to over-predict species prevalence, as they cannot identify absences in climatic conditions within the species' range of physiological tolerance or at the optima. Although SDMs tended to have higher sensitivity than threshold models, they may include regressions that do not reflect causal mechanisms, constraining their predictive power. We present a simple example of how combining correlative and mechanistic knowledge provides a rapid way to gain insight into a species' niche resulting in consistent predictions and highlighting potential sources of uncertainty in forecasted responses to climate change.

  9. Comparative phylogeography and niche modeling for three species complexes of SE China (Paradoxornisspp., Pycnonotus spp.,Spizixos spp.)

    Institute of Scientific and Technical Information of China (English)

    Luke B KLICKA; Luke C CAMPILLO; Joseph D MANTHEY; Yanhua QU

    2015-01-01

    Contrasting multiple organisms with similar contemporary distributions, researchers can identify shared evolutionary patterns and provide historical context for community composition. We used three species complexes with overlapping distribu-tions in Southeastern China and surrounding islands to explore the phylogeographic history of the region. Despite similar geo-graphic distributions, genetic data revealed few congruent patterns, but all complexes displayed genetic divergence for Taiwanese populations. Additionally, niche modeling and divergence dating did not find support for diversification associated with the Last Glacial Maximum [Current Zoology 61 (5): 943–950 , 2015].

  10. Redefining the Australian Anthrax Belt: Modeling the Ecological Niche and Predicting the Geographic Distribution of Bacillus anthracis.

    Directory of Open Access Journals (Sweden)

    Alassane S Barro

    2016-06-01

    Full Text Available The ecology and distribution of B. anthracis in Australia is not well understood, despite the continued occurrence of anthrax outbreaks in the eastern states of the country. Efforts to estimate the spatial extent of the risk of disease have been limited to a qualitative definition of an anthrax belt extending from southeast Queensland through the centre of New South Wales and into northern Victoria. This definition of the anthrax belt does not consider the role of environmental conditions in the distribution of B. anthracis. Here, we used the genetic algorithm for rule-set prediction model system (GARP, historical anthrax outbreaks and environmental data to model the ecological niche of B. anthracis and predict its potential geographic distribution in Australia. Our models reveal the niche of B. anthracis in Australia is characterized by a narrow range of ecological conditions concentrated in two disjunct corridors. The most dominant corridor, used to redefine a new anthrax belt, parallels the Eastern Highlands and runs from north Victoria to central east Queensland through the centre of New South Wales. This study has redefined the anthrax belt in eastern Australia and provides insights about the ecological factors that limit the distribution of B. anthracis at the continental scale for Australia. The geographic distributions identified can help inform anthrax surveillance strategies by public and veterinary health agencies.

  11. Predicting geographic and ecological distributions of triatomine species in the southern Mexican state of Puebla using ecological niche modeling.

    Science.gov (United States)

    Sandoval-Ruiz, C A; Zumaquero-Rios, J L; Rojas-Soto, O R

    2008-05-01

    We analyzed the geographic distribution using ecological niche modeling of three species of triatomines distributed in the Mexican state of Puebla. Punctual records were gathered for a period of 5 yr of fieldwork sampling. We used the genetic algorithm for rule-set production (GARP) to achieve the potential distribution of the ecological niche of triatomines. The models showed that Triatoma barberi and Meccus pallidipennis are sympatric and widely distributed in the central-southern part of the state, whereas T. dimidata is restricted to the northern mountains of the state with no overlapping among other species, M. bassolsae was not modeled because of the scarce number of locality records. We highlighted the warm and dry conditions in southern Puebla as important potential areas for triatomine presence. Finally, we correlated the species potential presence with the human population at risk of acquiring Chagas disease by vector-borne transmission; it is showed that M. pallidipennis presents the highest values of both ecological and poverty risk scenarios representing the main potential vector in the state.

  12. Oral Lactobacilli and Dental Caries: A Model for Niche Adaptation in Humans.

    Science.gov (United States)

    Caufield, P W; Schön, C N; Saraithong, P; Li, Y; Argimón, S

    2015-09-01

    Lactobacilli have been associated with dental caries for over a century. Here, we review the pertinent literature along with findings from our own study to formulate a working hypothesis about the natural history and role of lactobacilli. Unlike most indigenous microbes that stably colonize a host, lactobacilli appear to be planktonic, opportunistic settlers that can gather and multiply only in certain restrictive niches of the host, at least within the oral cavity. We postulate that the following essential requirements are necessary for sustained colonization of lactobacilli in humans: 1) a stagnant, retentive niche that is mostly anaerobic; 2) a low pH milieu; and 3) ready access to carbohydrates. Three sites on the human body meet these specifications: caries lesions, the stomach, and the vagina. Only a handful of Lactobacillus species is found in caries lesions, but they are largely absent in caries-free children. Lactobacilli present in caries lesions represent both a major contributor to caries progression and a major reservoir to the gastrointestinal (GI) tract. We extend the assertion from other investigators that lactobacilli found in the GI tract originate in the oral cavity by proposing that lactobacilli in the oral cavity arise from caries lesions. This, in turn, leads us to reflect on the health implications of the lactobacilli in the mouth and downstream GI and to ponder whether these or any of the Lactobacillus species are truly indigenous to the human GI tract or the oral cavity.

  13. Modelling Niche Differentiation of Co-Existing, Elusive and Morphologically Similar Species: A Case Study of Four Macaque Species in Nakai-Nam Theun National Protected Area, Laos.

    Science.gov (United States)

    Coudrat, Camille N Z; Nekaris, K Anne-Isola

    2013-01-30

    Species misidentification often occurs when dealing with co-existing and morphologically similar species such as macaques, making the study of their ecology challenging. To overcome this issue, we use reliable occurrence data from camera-trap images and transect survey data to model their respective ecological niche and potential distribution locally in Nakai-Nam Theun National Protected Area (NNT NPA), central-Eastern Laos. We investigate niche differentiation of morphologically similar species using four sympatric macaque species in NNT NPA, as our model species: rhesus Macaca mulatta (Taxonomic Serial Number, TSN 180099), Northern pig-tailed M. leonina (TSN not listed); Assamese M. assamensis (TSN 573018) and stump-tailed M. arctoides (TSN 573017). We examine the implications for their conservation. We obtained occurrence data of macaque species from systematic 2006-2011 camera-trapping surveys and 2011-2012 transect surveys and model their niche and potential distribution with MaxEnt software using 25 environmental and topographic variables. The respective suitable habitat predicted for each species reveals niche segregation between the four species with a gradual geographical distribution following an environmental gradient within the study area. Camera-trapping positioned at many locations can increase elusive-species records with a relatively reduced and more systematic sampling effort and provide reliable species occurrence data. These can be used for environmental niche modelling to study niche segregation of morphologically similar species in areas where their distribution remains uncertain. Examining unresolved species' niches and potential distributions can have crucial implications for future research and species' management and conservation even in the most remote regions and for the least-known species.

  14. Modelling Niche Differentiation of Co-Existing, Elusive and Morphologically Similar Species: A Case Study of Four Macaque Species in Nakai-Nam Theun National Protected Area, Laos

    Directory of Open Access Journals (Sweden)

    Camille N. Z. Coudrat

    2013-01-01

    Full Text Available Species misidentification often occurs when dealing with co-existing and morphologically similar species such as macaques, making the study of their ecology challenging. To overcome this issue, we use reliable occurrence data from camera-trap images and transect survey data to model their respective ecological niche and potential distribution locally in Nakai-Nam Theun National Protected Area (NNT NPA, central-Eastern Laos. We investigate niche differentiation of morphologically similar species using four sympatric macaque species in NNT NPA, as our model species: rhesus Macaca mulatta (Taxonomic Serial Number, TSN 180099, Northern pig-tailed M. leonina (TSN not listed; Assamese M. assamensis (TSN 573018 and stump-tailed M. arctoides (TSN 573017. We examine the implications for their conservation. We obtained occurrence data of macaque species from systematic 2006–2011 camera-trapping surveys and 2011–2012 transect surveys and model their niche and potential distribution with MaxEnt software using 25 environmental and topographic variables. The respective suitable habitat predicted for each species reveals niche segregation between the four species with a gradual geographical distribution following an environmental gradient within the study area. Camera-trapping positioned at many locations can increase elusive-species records with a relatively reduced and more systematic sampling effort and provide reliable species occurrence data. These can be used for environmental niche modelling to study niche segregation of morphologically similar species in areas where their distribution remains uncertain. Examining unresolved species' niches and potential distributions can have crucial implications for future research and species' management and conservation even in the most remote regions and for the least-known species.

  15. Range wide molecular data and niche modeling revealed the Pleistocene history of a global invader (Halyomorpha halys)

    Science.gov (United States)

    Zhu, Geng-Ping; Ye, Zhen; Du, Juan; Zhang, Dan-Li; Zhen, Ya-hui; Zheng, Chen-guang; Zhao, Li; Li, Min; Bu, Wen-Jun

    2016-01-01

    Invasive species’ Pleistocene history contains much information on its present population structure, dispersability and adaptability. In this study, the Pleistocene history of a global invasive pest (Brown Marmorated Stink Bug BMSB, Halyomorpha halys) was unveiled using the coupled approach of phylogeography and ecological niche modelling. Rangewide molecular data suggests that the Taiwan and other native populations had diverged in mid-Pleistocene. In mainland China, the native BMSB did not experience population contraction and divergence during last glacial, but persisted in interconnected populations. Combined Bayesian Skyline Plot (BSP) and niche modelling revealed a rapid expansion occurred during the transition of Last Inter Glacial (LIG) to Last Glacial Maximum (LGM). High genetic diversity and multi-reticular haplotypes network exist in the original sources populations of BMSB invasion in northern China. They were speculated to be colonized from the central China, with many derived haplotypes evolved to adapt the novel environment. The ENM future prediction suggest that BMSB may expand northward to higher latitudes in the US and Europe, because of its high invasive ability, together with the available suitable climate space there. PMID:26996353

  16. Ecological niche modelling of potential West Nile virus vector mosquito species and their geographical association with equine epizootics in Italy.

    Science.gov (United States)

    Mughini-Gras, Lapo; Mulatti, Paolo; Severini, Francesco; Boccolini, Daniela; Romi, Roberto; Bongiorno, Gioia; Khoury, Cristina; Bianchi, Riccardo; Montarsi, Fabrizio; Patregnani, Tommaso; Bonfanti, Lebana; Rezza, Giovanni; Capelli, Gioia; Busani, Luca

    2014-01-01

    In Italy, West Nile virus (WNV) equine outbreaks have occurred annually since 2008. Characterizing WNV vector habitat requirements allows for the identification of areas at risk of viral amplification and transmission. Maxent-based ecological niche models were developed using literature records of 13 potential WNV Italian vector mosquito species to predict their habitat suitability range and to investigate possible geographical associations with WNV equine outbreak occurrence in Italy from 2008 to 2010. The contribution of different environmental variables to the niche models was also assessed. Suitable habitats for Culex pipiens, Aedes albopictus, and Anopheles maculipennis were widely distributed; Culex modestus, Ochlerotatus geniculatus, Ochlerotatus caspius, Coquillettidia richiardii, Aedes vexans, and Anopheles plumbeus were concentrated in north-central Italy; Aedes cinereus, Culex theileri, Ochlerotatus dorsalis, and Culiseta longiareolata were restricted to coastal/southern areas. Elevation, temperature, and precipitation variables showed the highest predictive power. Host population and landscape variables provided minor contributions. WNV equine outbreaks had a significantly higher probability to occur in habitats suitable for Cx. modestus and Cx. pipiens, providing circumstantial evidence that the potential distribution of these two species coincides geographically with the observed distribution of the disease in equines.

  17. Climate-driven diversification and Pleistocene refugia in Philippine birds: evidence from phylogeographic structure and paleoenvironmental niche modeling.

    Science.gov (United States)

    Hosner, Peter A; Sánchez-González, Luis A; Peterson, A Townsend; Moyle, Robert G

    2014-09-01

    Avian diversification in oceanic archipelagos is largely attributed to isolation across marine barriers. During glacial maxima, lowered sea levels resulted in repeated land connections between islands joined by shallow seas. Consequently, such islands are not expected to show endemism. However, if climate fluctuations simultaneously caused shifts in suitable environmental conditions, limiting populations to refugia, then occurrence on and dispersal across periodic land bridges are not tenable. To assess the degree to which paleoclimate barriers, rather than marine barriers, drove avian diversification in the Philippine Archipelago, we produced ecological niche models for current-day, glacial maxima, and interglacial climate scenarios to infer potential Pleistocene distributions and paleoclimate barriers. We then tested marine and paleoclimate barriers for correspondence to geographic patterns of population divergence, inferred from DNA sequences from eight codistributed bird species. In all species, deep-water channels corresponded to zones of genetic differentiation, but six species exhibited deeper divergence associated with a periodic land bridge in the southern Philippines. Ecological niche models for these species identified a common paleoclimate barrier that coincided with deep genetic structure among populations. Although dry land connections joined southern Philippine islands during low sea level stands, unfavorable environmental conditions limited populations within landmasses, resulting in long-term isolation and genetic differentiation. These results highlight the complex nature of diversification in archipelagos: marine barriers, changes in connectivity due to sea level change, and climate-induced refugia acted in concert to produce great species diversity and endemism in the Philippines.

  18. Chick embryo xenograft model reveals a novel perineural niche for human adipose-derived stromal cells

    Directory of Open Access Journals (Sweden)

    Ingrid R. Cordeiro

    2015-09-01

    Full Text Available Human adipose-derived stromal cells (hADSC are a heterogeneous cell population that contains adult multipotent stem cells. Although it is well established that hADSC have skeletal potential in vivo in adult organisms, in vitro assays suggest further differentiation capacity, such as into glia. Thus, we propose that grafting hADSC into the embryo can provide them with a much more instructive microenvironment, allowing the human cells to adopt diverse fates or niches. Here, hADSC spheroids were grafted into either the presumptive presomitic mesoderm or the first branchial arch (BA1 regions of chick embryos. Cells were identified without previous manipulations via human-specific Alu probes, which allows efficient long-term tracing of heterogeneous primary cultures. When grafted into the trunk, in contrast to previous studies, hADSC were not found in chondrogenic or osteogenic territories up to E8. Surprisingly, 82.5% of the hADSC were associated with HNK1+ tissues, such as peripheral nerves. Human skin fibroblasts showed a smaller tropism for nerves. In line with other studies, hADSC also adopted perivascular locations. When grafted into the presumptive BA1, 74.6% of the cells were in the outflow tract, the final goal of cardiac neural crest cells, and were also associated with peripheral nerves. This is the first study showing that hADSC could adopt a perineural niche in vivo and were able to recognize cues for neural crest cell migration of the host. Therefore, we propose that xenografts of human cells into chick embryos can reveal novel behaviors of heterogeneous cell populations, such as response to migration cues.

  19. The Multidimensional Nutritional Niche.

    Science.gov (United States)

    Machovsky-Capuska, Gabriel E; Senior, Alistair M; Simpson, Stephen J; Raubenheimer, David

    2016-05-01

    The dietary generalist-specialist distinction plays a pivotal role in theoretical and applied ecology, conservation, invasion biology, and evolution and yet the concept remains poorly characterised. Diets, which are commonly used to define niche breadth, are almost exclusively considered in terms of foods, with little regard for the mixtures of nutrients and other compounds they contain. We use nutritional geometry (NG) to integrate nutrition with food-level approaches to the dietary niche and illustrate the application of our framework in the important context of invasion biology. We use an example that involves a model with four hypothetical nonexclusive scenarios. We additionally show how this approach can provide fresh theoretical insight into the ways nutrition and food choices impact trait evolution and trophic interactions.

  20. A mathematical model of cancer stem cell driven tumor initiation: implications of niche size and loss of homeostatic regulatory mechanisms.

    Directory of Open Access Journals (Sweden)

    Sara N Gentry

    Full Text Available Hierarchical organized tissue structures, with stem cell driven cell differentiation, are critical to the homeostatic maintenance of most tissues, and this underlying cellular architecture is potentially a critical player in the development of a many cancers. Here, we develop a mathematical model of mutation acquisition to investigate how deregulation of the mechanisms preserving stem cell homeostasis contributes to tumor initiation. A novel feature of the model is the inclusion of both extrinsic and intrinsic chemical signaling and interaction with the niche to control stem cell self-renewal. We use the model to simulate the effects of a variety of types and sequences of mutations and then compare and contrast all mutation pathways in order to determine which ones generate cancer cells fastest. The model predicts that the sequence in which mutations occur significantly affects the pace of tumorigenesis. In addition, tumor composition varies for different mutation pathways, so that some sequences generate tumors that are dominated by cancerous cells with all possible mutations, while others are primarily comprised of cells that more closely resemble normal cells with only one or two mutations. We are also able to show that, under certain circumstances, healthy stem cells diminish due to the displacement by mutated cells that have a competitive advantage in the niche. Finally, in the event that all homeostatic regulation is lost, exponential growth of the cancer population occurs in addition to the depletion of normal cells. This model helps to advance our understanding of how mutation acquisition affects mechanisms that influence cell-fate decisions and leads to the initiation of cancers.

  1. Using niche-based modelling to assess the impact of climate change on tree functional diversity in Europe

    DEFF Research Database (Denmark)

    Thuiller, Wilfried; Lavorel, Sandra; Sykes, Martin T.;

    2006-01-01

    Rapid anthropogenic climate change is already affecting species distributions and ecosystem functioning worldwide. We applied niche-based models to analyse the impact of climate change on tree species and functional diversity in Europe. Present-day climate was used to predict the distributions...... role in the future of different European regions. Temperate areas were projected to lose both species richness and functional diversity due to the loss of broadleaved deciduous trees. These were projected to migrate to boreal forests, thereby increasing their species richness and functional diversity....... Atlantic areas provided an intermediate case, with a predicted reduction in the numbers of species and occasional predicted gains in functional diversity. This resulted from a loss in species within the broadleaved deciduous FT, but overall maintenance of the group. Our results illustrate the fact...

  2. Potential for spread of the white-nose fungus (Pseudogymnoascus destructans) in the Americas: use of Maxent and NicheA to assure strict model transference.

    Science.gov (United States)

    Escobar, Luis E; Lira-Noriega, Andrés; Medina-Vogel, Gonzalo; Townsend Peterson, A

    2014-11-01

    Emerging infectious diseases can present serious threats to wildlife, even to the point of causing extinction. Whitenose fungus (Pseudogymnoascus destructans) is causing an epizootic in bats that is expanding rapidly, both geographically and taxonomically. Little is known of the ecology and distributional potential of this intercontinental pathogen. We address this gap via ecological niche models that characterise coarse resolution niche differences between fungus populations on different continents, identifying areas potentially vulnerable to infection in South America. Here we explore a novel approach to identifying areas of potential distribution across novel geographic regions that avoids perilious extrapolation into novel environments. European and North American fungus populations show differential use of environmental space, but rather than niche differentiation, we find that changes are best attributed to climatic differences between the two continents. Suitable areas for spread of the pathogen were identified across southern South America; however caution should be taken to avoid underestimating the potential for spread of this pathogen in South America.

  3. Climatic suitability of Aedes albopictus in Europe referring to climate change projections: comparison of mechanistic and correlative niche modelling approaches.

    Science.gov (United States)

    Fischer, D; Thomas, S M; Neteler, M; Tjaden, N B; Beierkuhnlein, C

    2014-02-13

    The Asian tiger mosquito, Aedes albopictus, is capable of transmitting a broad range of viruses to humans. Since its introduction at the end of the 20th century, it has become well established in large parts of southern Europe. As future expansion as a result of climate change can be expected, determining the current and projected future climatic suitability of this invasive mosquito in Europe is of interest. Several studies have tried to detect the potential habitats for this species, but differing data sources and modelling approaches must be considered when interpreting the findings. Here, various modelling methodologies are compared with special emphasis on model set-up and study design. Basic approaches and model algorithms for the projection of spatio-temporal trends within the 21st century differ substantially. Applied methods range from mechanistic models (e.g. overlay of climatic constraints based on geographic information systems or rather process-based approaches) to correlative niche models. We conclude that spatial characteristics such as introduction gateways and dispersal pathways need to be considered. Laboratory experiments addressing the climatic constraints of the mosquito are required for improved modelling results. However, the main source of uncertainty remains the insufficient knowledge about the species' ability to adapt to novel environments.

  4. A Model Program for Dental Assisting Education in California.

    Science.gov (United States)

    California State Dept. of Education, Sacramento. Bureau of Industrial Education.

    Intended to provide assistance for developing new programs and improving existing ones, the guide was constructed by dental assisting instructors and other professional participants in a 196 5 workshop conference. Elements of the model program were derived from a statistical analysis of California junior colleg e programs in dental assisting and…

  5. From California dreaming to California data: Challenging historic models for landfill CH4 emissions

    Directory of Open Access Journals (Sweden)

    Kurt Spokas

    2015-06-01

    Full Text Available Abstract Improved quantification of diverse CH4 sources at the urban scale is needed to guide local GHG mitigation strategies in the Anthropocene. Herein, we focus on landfill CH4 emissions in California, challenging the current IPCC methodology which focuses on a climate dependency for landfill CH4 generation (methanogenesis, but does not explicitly consider climate or soil dependencies for emissions. Relying on a comprehensive California landfill database, a field-validated process-based model for landfill CH4 emissions (CALMIM, and select field measurements at 10 California sites with a variety of methods, we support the contrary position: Limited climate dependency for methanogenesis, but strong climate dependency for landfill CH4 emissions. Contrary to the historic IPCC empirical model for methanogenesis with kinetic constants related to climate, we demonstrate a simpler and more robust linear empirical relationship (r2 = 0.85; n=128 between waste mass and landfill biogas recovery [126 × 10-6 Nm3 CH4 hr-1 Mgwaste-1]. More interestingly, there are no statistically significant relationships with climate, site age, or status (open/closed for landfill biogas recovery. The current IPCC methodology does not consider soil or climate drivers for gaseous transport or seasonal methanotrophy in different cover soils. On the other hand, we illustrate strong climate and soil dependencies for landfill emissions—e.g., average intermediate cover emissions below 20 g CH4 m-2 d-1 when the site’s mean annual precipitation is >500 mm y-1. Thereby, for the California landfill CH4 inventory, the highest-emitting sites shift from landfills containing the largest mass of waste to sites dominated by intermediate cover types having a reduced rate of soil CH4 oxidation during the annual cycle. These differences have profound implications for developing more realistic, science-based urban and regional scale GHG inventories for landfill CH4 while reducing

  6. Spatial distributions of niche-constructing populations

    Directory of Open Access Journals (Sweden)

    Xiaozhuo Han

    2015-12-01

    Full Text Available Niche construction theory regards organisms not only as the object of natural selection but also an active subject that can change their own selective pressure through eco-evolutionary feedbacks. Through reviewing the existing works on the theoretical models of niche construction, here we present the progress made on how niche construction influences genetic structure of spatially structured populations and the spatial-temporal dynamics of metapopulations, with special focuses on mathematical models and simulation methods. The majority of results confirmed that niche construction can significantly alter the evolutionary trajectories of structured populations. Organism-environmental interactions induced by niche construction can have profound influence on the dynamics, competition and diversity of metapopulations. It can affect fine-scale spatially distribution of species and spatial heterogeneity of the environment. We further propose a few research directions with potentials, such as applying adaptive dynamics or spatial game theory to explore the effect of niche construction on phenotypic evolution and diversification.

  7. Species delimitation in the continental forms of the genus Epicrates (Serpentes, Boidae integrating phylogenetics and environmental niche models.

    Directory of Open Access Journals (Sweden)

    Paula C Rivera

    Full Text Available Until recently, the genus Epicrates (Boidae presented only one continental species, Epicrates cenchria, distributed in Central and South America, but after a taxonomic revision using morphologic characters five species were recognized: E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi. We analyzed two independent data sets, environmental niche models and phylogeny based on molecular information, to explore species delimitation in the continental species of this genus. Our results indicated that the environmental requirements of the species are different; therefore there are not evidences of ecological interchangeability among them. There is a clear correlation between species distributions and the major biogeographic regions of Central and South America. Their overall distribution reveals that allopatry or parapatry is the general pattern. These evidences suggest that habitat isolation prevents or limits gene exchange among them. The phylogenetic reconstruction showed that the continental Epicrates are monophyletic, being E. alvarezi the sister species for the remaining two clades: E. crassus-E. assisi, and E. maurus-E. cenchria. The clade grouping the continental Epicrates is the sister taxon of the genus Eunectes and not of the Caribbean Epicrates clade, indicating that the genus is paraphyletic. There is a non-consistent pattern in niche evolution among continental Epicrates. On the contrary, a high variation and abrupt shifts in environmental variables are shown when ancestral character states were reconstructed on the sequence-based tree. The degree of genetic and ecological divergence among continental Epicrates and the phylogenetic analyses support the elevation to full species of E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi.

  8. Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche

    Directory of Open Access Journals (Sweden)

    Alvarez-Buylla Elena R

    2010-10-01

    Full Text Available Abstract Background Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner. Results We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks. Conclusions These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not

  9. Life History Traits and Niche Instability Impact Accuracy and Temporal Transferability for Historically Calibrated Distribution Models of North American Birds.

    Science.gov (United States)

    Wogan, Guinevere O U

    2016-01-01

    A primary assumption of environmental niche models (ENMs) is that models are both accurate and transferable across geography or time; however, recent work has shown that models may be accurate but not highly transferable. While some of this is due to modeling technique, individual species ecologies may also underlie this phenomenon. Life history traits certainly influence the accuracy of predictive ENMs, but their impact on model transferability is less understood. This study investigated how life history traits influence the predictive accuracy and transferability of ENMs using historically calibrated models for birds. In this study I used historical occurrence and climate data (1950-1990s) to build models for a sample of birds, and then projected them forward to the 'future' (1960-1990s). The models were then validated against models generated from occurrence data at that 'future' time. Internal and external validation metrics, as well as metrics assessing transferability, and Generalized Linear Models were used to identify life history traits that were significant predictors of accuracy and transferability. This study found that the predictive ability of ENMs differs with regard to life history characteristics such as range, migration, and habitat, and that the rarity versus commonness of a species affects the predicted stability and overlap and hence the transferability of projected models. Projected ENMs with both high accuracy and transferability scores, still sometimes suffered from over- or under- predicted species ranges. Life history traits certainly influenced the accuracy of predictive ENMs for birds, but while aspects of geographic range impact model transferability, the mechanisms underlying this are less understood.

  10. A co-culture model of the hippocampal neurogenic niche reveals differential effects of astrocytes, endothelial cells and pericytes on proliferation and differentiation of adult murine precursor cells

    Directory of Open Access Journals (Sweden)

    Fanny Ehret

    2015-11-01

    Full Text Available The niche concept of stem cell biology proposes a functional unit between the precursor cells and their local microenvironment, to which several cell types might contribute by cell–cell contacts, extracellular matrix, and humoral factors. We here established three co-culture models (with cell types separated by membrane for both adherent monolayers and neurospheres to address the potential influence of different niche cell types in the neurogenic zone of the adult hippocampus of mice. Astrocytes and endothelial cells enhanced precursor cell proliferation and neurosphere formation. Endothelial factors also led to a prolonged increase in proliferation after growth factor withdrawal, which otherwise induces differentiation. All niche cell types enhanced cell survival in monolayer cultures, endothelial cells also stimulated neuronal differentiation. A parallel trend elicited by astrocytes did not reach conventional statistical significance. Pericytes had variable effects here. We did not observe changes in differentiation in neurosphere co-cultures. In summary, our data indicate that in precursor cell culture protocols survival could be improved by adding as yet unknown factors physiologically contributed by astrocytes and endothelial cells. Our findings also underscore the complexity of the niche and the differential impact of factors from the different sources on distinct aspects of neuronal development. With the help of the models presented here, identification of these factors and their specific biological activity can now be initiated.

  11. Assessing the Global Risk of Establishment of Cydia pomonella (Lepidoptera: Tortricidae) using CLIMEX and MaxEnt Niche Models.

    Science.gov (United States)

    Kumar, Sunil; Neven, Lisa G; Zhu, Hongyu; Zhang, Runzhi

    2015-08-01

    Accurate assessment of insect pest establishment risk is needed by national plant protection organizations to negotiate international trade of horticultural commodities that can potentially carry the pests and result in inadvertent introductions in the importing countries. We used mechanistic and correlative niche models to quantify and map the global patterns of the potential for establishment of codling moth (Cydia pomonella L.), a major pest of apples, peaches, pears, and other pome and stone fruits, and a quarantine pest in countries where it currently does not occur. The mechanistic model CLIMEX was calibrated using species-specific physiological tolerance thresholds, whereas the correlative model MaxEnt used species occurrences and climatic spatial data. Projected potential distribution from both models conformed well to the current known distribution of codling moth. None of the models predicted suitable environmental conditions in countries located between 20°N and 20°S potentially because of shorter photoperiod, and lack of chilling requirement (<60 d at ≤10°C) in these areas for codling moth to break diapause. Models predicted suitable conditions in South Korea and Japan where codling moth currently does not occur but where its preferred host species (i.e., apple) is present. Average annual temperature and latitude were the main environmental variables associated with codling moth distribution at global level. The predictive models developed in this study present the global risk of establishment of codling moth, and can be used for monitoring potential introductions of codling moth in different countries and by policy makers and trade negotiators in making science-based decisions.

  12. Reconstitution of bone-like matrix in osteogenically differentiated mesenchymal stem cell–collagen constructs: A three-dimensional in vitro model to study hematopoietic stem cell niche

    Directory of Open Access Journals (Sweden)

    WY Lai

    2013-10-01

    Full Text Available Mesenchymal stem/stromal cells (MSCs and osteoblasts are important niche cells for hematopoietic stem cells (HSCs in bone marrow osteoblastic niche. Here, we aim to partially reconstitute the bone marrow HSC niche in vitro using collagen microencapsulation for investigation of the interactions between HSCs and MSCs. Mouse MSCs (mMSCs microencapsulated in collagen were osteogenically differentiated to derive a bone-like matrix consisting of osteocalcin, osteopontin, and calcium deposits and secreted bone morphogenic protein 2 (BMP2. Decellularized bone-like matrix was seeded with fluorescence-labeled human MSCs and HSCs. Comparing with pure collagen scaffold, significantly more HSCs and HSC–MSC pairs per unit area were found in the decellularized bone-like matrix. Moreover, incubation with excess neutralizing antibody of BMP2 resulted in a significantly higher number of HSC per unit area than that without in the decellularized matrix. This work suggests that the osteogenic differentiated MSC–collagen microsphere is a valuable three-dimensional in vitro model to elucidate cell–cell and cell–matrix interactions in HSC niche.

  13. Central California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  14. Eureka, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  15. Monterey, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  16. Santa Barbara, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  17. Arena Cove, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  18. Crescent City, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  19. San Diego, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  20. Santa Monica, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  1. Fort Bragg, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  2. Using environmental niche modeling to find suitable habitats for the Hard-ground Barasingha in Madhya Pradesh, India

    Directory of Open Access Journals (Sweden)

    C. P. Singh

    2015-09-01

    Full Text Available The subspecies of Swamp Deer, the Hard-ground Barasingha (Rucervus duvaucelii branderi Pocock, is presently found only in Kanha Tiger Reserve (KTR in Madhya Pradesh, India. This subspecies is highly vulnerable to extinction, and reintroduction in suitable sites is the need of the hour.  Environmental niche models (GARP, SVM, ED, CSM aimed at providing a detailed prediction of species distribution by relating presence of species to 19 bioclimatic indices were developed, using swamp deer occurrence records in KTR. The predictions were appropriately weighted with the prevailing LU/LC classes to identify suitable habitats in Madhya Pradesh, India. The result shows that the southern region of Madhya Pradesh is suitable for the sustenance of Barasingha with varying degrees of habitability. Vicarious validation shows that most of these forest areas were the same as that of historical records dating back to 50 years. However, land use maps can help identify areas where this subspecies can be reintroduced. 

  3. Pre-rain green-up is ubiquitous across southern tropical Africa: implications for temporal niche separation and model representation.

    Science.gov (United States)

    Ryan, Casey M; Williams, Mathew; Grace, John; Woollen, Emily; Lehmann, Caroline E R

    2017-01-01

    Tree phenology mediates land-atmosphere mass and energy exchange and is a determinant of ecosystem structure and function. In the dry tropics, including African savannas, many trees grow new leaves during the dry season - weeks or months before the rains typically start. This syndrome of pre-rain green-up has long been recognized at small scales, but the high spatial and interspecific variability in leaf phenology has precluded regional generalizations. We used remote sensing data to show that this precocious phenology is ubiquitous across the woodlands and savannas of southern tropical Africa. In 70% of the study area, green-up preceded rain onset by > 20 d (42% > 40 d). All the main vegetation formations exhibited pre-rain green-up, by as much as 53 ± 18 d (in the wet miombo). Green-up showed low interannual variability (SD between years = 11 d), and high spatial variability (> 100 d). These results are consistent with a high degree of local phenological adaptation, and an insolation trigger of green-up. Tree-tree competition and niche separation may explain the ubiquity of this precocious phenology. The ubiquity of pre-rain green-up described here challenges existing model representations and suggests resistance (but not necessarily resilience) to the delay in rain onset predicted under climate change.

  4. Atlantis model outputs - Developing end-to-end models of the California Current Large Marine Ecosystem

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web...

  5. Model outputs - Developing end-to-end models of the Gulf of California

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the northern Gulf of California, linking oceanography, biogeochemistry, food web...

  6. Genetic differentiation in two widespread, open-forest bird species of Southeast Asia (Copsychus saularis andMegalaima haemacephala):Insights from ecological niche modeling

    Institute of Scientific and Technical Information of China (English)

    Haw Chuan LIM; Fasheng ZOU; Frederick H SHELDON

    2015-01-01

    Ecological niche modeling has emerged as an useful tool in the investigation of the phylogeographic histories of spe-cies or communities in a region. The high biodiversity (oftentimes cryptic), and complex geography and geological history of Southeast Asia particularly call for multipronged approaches in phylogeographic investigations. Past studies have focused on taxa that are associated with lowland rainforests, which is the dominant natural vegetation type. Here, we combine published phylo-genetic data, ecological niche modeling and paleo-climate models to reveal potential drivers of divergence in two open-forest bird species, the oriental magpie-robinCopsychus saularis and Coppersmith barbetMegalaima haemacephala. In spite of broad overlap in current distributions, there are subtle differences in their climatic niches, which result in different responses to past climatic changes. ForC. saularis, both Last Glacial Maximum climate models indicated that the entire Sundaland was climati-cally suitable, while phylogenetic analyses found divergent eastern and western Sundaland lineages. We thus postulate that this genetic divergence was a result of past separations of coastal habitats into eastern and western portions due to the emergence of Sunda shelf as sea-level fell. The current separation of morphological subspecies in Borneo is maintained by low climatic suita-bility (high annual rainfall) in certain regions. The extirpation ofM. haemacephala from Borneo and southern Malay Peninsula might have been driven by unsuitable conditions (high temperature seasonality) in central Sundaland and/or the lack of open woodlands. Our study shows that ecological niche modeling adds a powerful dimension to our attempt to understand lineage evolution in space [Current Zoology 61 (5): 922–934, 2015].

  7. Ecological niche model of Phlebotomus perniciosus, the main vector of canine leishmaniasis in north-eastern Italy.

    Science.gov (United States)

    Signorini, Manuela; Cassini, Rudi; Drigo, Michele; Frangipane di Regalbono, Antonio; Pietrobelli, Mario; Montarsi, Fabrizio; Stensgaard, Anna-Sofie

    2014-11-01

    With respect to the epidemiology of leishmaniasis, it is crucial to take into account the ecoclimatic and environmental characteristics that influence the distribution patterns of the vector sand fly species. It is also important to consider the possible impact of on-going climate changes on the emergence of this disease. In order to map the potential distribution of Phlebotomus perniciosus, the main vector species of canine leishmaniasis in north-eastern Italy, geographical information systems tools, ecological niche models (ENM) and remotely sensed environmental data were applied for a retrospective analysis of an entomological survey conducted in north-eastern Italy over 12 years. Sand fly trapping was conducted from 2001 to 2012 in 175 sites in the provinces of Veneto, Friuli-Venezia Giulia and Trentino-Alto Adige. We developed a predictive model of potential distribution of P. perniciosus using the maximum entropy algorithm software, based on seasonal normalized difference vegetation index, day and night land surface temperature, the Corine land cover 2006, a digital elevation model (GTOPO30) and climate layers obtained from the WorldClim database. The MaxEnt prediction found the more suitable habitat for P. perniciosus to be hilly areas (100-300 m above the mean sea level) characterised by temperate climate during the winter and summer seasons, high winter vegetation cover and moderate rainfall during the activity season of vector sand fly. ENM provided a greater understanding of the geographical distribution and ecological requirements of P. perniciosus in the study area, which can be applied for the development of future surveillance strategies.

  8. Ecological niche model of Phlebotomus perniciosus, the main vector of canine leishmaniasis in north-eastern Italy

    Directory of Open Access Journals (Sweden)

    Manuela Signorini

    2014-11-01

    Full Text Available With respect to the epidemiology of leishmaniasis, it is crucial to take into account the ecoclimatic and environ- mental characteristics that influence the distribution patterns of the vector sand fly species. It is also important to consider the possible impact of on-going climate changes on the emergence of this disease. In order to map the potential distribu- tion of Phlebotomus perniciosus, the main vector species of canine leishmaniasis in north-eastern Italy, geographical information systems tools, ecological niche models (ENM and remotely sensed environmental data were applied for a retrospective analysis of an entomological survey conducted in north-eastern Italy over 12 years. Sand fly trapping was conducted from 2001 to 2012 in 175 sites in the provinces of Veneto, Friuli-Venezia Giulia and Trentino-Alto Adige. We developed a predictive model of potential distribution of P. perniciosus using the maximum entropy algorithm software, based on seasonal normalized difference vegetation index, day and night land surface temperature, the Corine land cover 2006, a digital elevation model (GTOPO30 and climate layers obtained from the WorldClim database. The MaxEnt pre- diction found the more suitable habitat for P. perniciosus to be hilly areas (100-300 m above the mean sea level charac- terised by temperate climate during the winter and summer seasons, high winter vegetation cover and moderate rainfall during the activity season of vector sand fly. ENM provided a greater understanding of the geographical distribution and ecological requirements of P. perniciosus in the study area, which can be applied for the development of future surveil- lance strategies.

  9. Ecological niche of plant pathogens

    Directory of Open Access Journals (Sweden)

    Ecaterina Fodor

    2011-02-01

    Full Text Available Disease ecology is a new approach to the understanding of the spread and dynamics of pathogens in natural and man-made environments. Defining and describing the ecological niche of the pathogens is one of the major tasks for ecological theory, as well as for practitioners preoccupied with the control and forecasting of established and emerging diseases. Niche theory has been periodically revised, not including in an explicit way the pathogens. However, many progresses have been achieved in niche modeling of disease spread, but few attempts were made to construct a theoretical frame for the ecological niche of pathogens. The paper is a review of the knowledge accumulated during last decades in the niche theory of pathogens and proposes an ecological approach in research. It quest for new control methods in what concerns forest plant pathogens, with a special emphasis on fungi like organisms of the genus Phytophthora. Species of Phytophthora are the most successful plant pathogens of the moment, affecting forest and agricultural systems worldwide, many of them being invasive alien organisms in many ecosystems. The hyperspace of their ecological niche is defined by hosts, environment and human interference, as main axes. To select most important variables within the hyperspace, is important for the understanding of the complex role of pathogens in the ecosystems as well as for control programs. Biotic relationships within ecosystem of host-pathogen couple are depicted by ecological network and specific metrics attached to this. The star shaped network is characterized by few high degree nodes, by short path lengths and relatively low connectivity, premises for a rapid disturbance spread.

  10. Reconciling phylogeography and ecological niche models for New Zealand beetles looking beyond glacial refugia

    DEFF Research Database (Denmark)

    Marske, Katharine Ann; Leschen, Richard; Buckley, Thomas

    2011-01-01

    Mitochondrial DNA (cox1) sequence data and recently developed coalescent phylogeography models were used to construct geo-spatial histories for the New Zealand fungus beetles Epistranus lawsoni and Pristoderus bakewelli (Zopheridae). These methods utilize continuous-time Markov chains and Bayesian...

  11. The potential distribution of Phlebotomus papatasi (Diptera: Psychodidae) in Libya based on ecological niche model.

    Science.gov (United States)

    Abdel-Dayem, M S; Annajar, B B; Hanafi, H A; Obenauer, P J

    2012-05-01

    The increased cases of cutaneous leishmaniasis vectored by Phlebotomus papatasi (Scopoli) in Libya have driven considerable effort to develop a predictive model for the potential geographical distribution of this disease. We collected adult P. papatasi from 17 sites in Musrata and Yefern regions of Libya using four different attraction traps. Our trap results and literature records describing the distribution of P. papatasi were incorporated into a MaxEnt algorithm prediction model that used 22 environmental variables. The model showed a high performance (AUC = 0.992 and 0.990 for training and test data, respectively). High suitability for P. papatasi was predicted to be largely confined to the coast at altitudes Libya may find this information useful in their efforts to control zoonotic cutaneous leishmaniasis. Existing records are strongly biased toward a few geographical regions, and therefore, further sand fly collections are warranted that should include documentation of such factors as soil texture and humidity, land cover, and normalized difference vegetation index (NDVI) data to increase the model's predictive power.

  12. Ecological niche models for four native cockroach species (Blattaria: Blattellidae: Ectobiinae) in the Netherlands

    NARCIS (Netherlands)

    Ciliberti, P.; Jong, de H.; Schouten, M.A.; Verweij, P.A.; Heitmans, W.R.B.

    2009-01-01

    This paper aims at modelling the spatial distribution of the cockroach species Capraiellus panzeri, Ectobius lapponicus, Ectobius pallidus and Ectobius sylvestris within the Netherlands and comparing the habitat preferences of these species. Maxent was used to calculate habitat suitability and to id

  13. Ecological niche models for four native cockroach species (Blattaria: Blattellidae:Ectobiinae) in the Netherlands

    NARCIS (Netherlands)

    Ciliberti, P.; de Jong, Herman; Schouten, M.A.; Verweij, P.A.; Heitmans, W.R.B.

    2009-01-01

    This paper aims at modelling the spatial distribution of the cockroach species Capraiellus panzeri, Ectobius lapponicus, Ectobius pallidus and Ectobius sylvestris within the Netherlands and comparing the habitat preferences of these species. Maxent was used to calculate habitat suitability and to id

  14. Use of ecological niche modeling as a tool for predicting the potential distribution of Microcystis sp (cyanobacteria in the Aguamilpa Dam, Nayarit, Mexico

    Directory of Open Access Journals (Sweden)

    Enrique Martinez-Meyer

    2012-04-01

    Full Text Available Ecological niche modeling is an important tool to evaluate the spatial distribution of terrestrial species, however, its applicability has been little explored in the aquatic environment. Microcystis sp., a species of cyanobacteria, is widely recognized for its ability to produce a group of toxins known as microcystins, which can cause death of animals as fish, birds and mammals depending on the amount of toxin absorbed. Like any taxonomic group, cyanobacteria has environmental thresholds, therefore, a suitable ecological niche will define their distribution. This study was conducted in Aguamilpa Hydroelectric Reservoir, an artificial ecosystem that started operations in 1994. In this system we evaluated the potential distribution of Microcystis sp., by generating a prediction model based on the concept of ecological niche MAXENT, using a Digital Elevation Model in cells of 100 m x 100 m (1 ha spatial resolution and monitoring eleven physicochemical and biological variables and nutrients in water. The distribution maps were developed using ArcMap 9.2®. The results indicated that Microcystis sp., is distributed mainly in the upper tributary basin (Huaynamota basin during the dry season. There was less chance to find cyanobacteria in the entire system during the cold dry season, while during the warm dry season cyanobacteria was recognized at the confluence of two rivers. During the rainfall season there were no reports of cyanobacteria presence. This species is often associated with arising trophic processes of anthropogenic origin; therefore, attention is required in specific areas that have been identified in this work to improve Aguamilpa’s watershed management and restoration. It was also recognized the importance of phosphorus and nitrogen interaction, which determines the distribution of Microcystis sp., in the Aguamilpa Reservoir. The results of this study demonstrated that ecological niche modeling was a suitable tool to assess the

  15. Modelling the ecological niche of hookworm in Brazil based on climate.

    Science.gov (United States)

    Mudenda, Ntombi B; Malone, John B; Kearney, Michael T; Mischler, Paula D; Nieto, Prixia del Mar; McCarroll, Jennifer C; Vounatsou, Penelope

    2012-09-01

    The distribution of hookworm in schistosomiasis-endemic areas in Brazil was mapped based on climate suitability. Known biological requirements of hookworm were fitted to data in a monthly long-term normal climate grid (18 x 18 km) using geographical information systems. Hookworm risk models were produced using the growing degree day (GDD) water budget (WB) concept. A moisture-adjusted model (MA-GDD) was developed based on accumulation of monthly temperatures above a base temperature of 15 °C (below which there is no lifecycle progression of Necator americanus) conditional on concurrent monthly values (rain/potential, evapotranspiration) of over 0.4. A second model, designated the gradient index, was calculated based on the monthly accumulation of the product of GDD and monthly WB values (GDD x WB). Both parameters had a significant positive correlation to hookworm prevalence. In the northeastern part of Brazil (the Caatinga), low hookworm prevalence was due to low soil moisture content, while the low prevalence in southern Brazil was related to low mean monthly temperatures. Both environmental temperature and soil moisture content were found to be important parameters for predicting the prevalence of N. americanus.

  16. Modelling the ecological niche of hookworm in Brazil based on climate

    Directory of Open Access Journals (Sweden)

    Ntombi B. Mudenda

    2012-09-01

    Full Text Available The distribution of hookworm in schistosomiasis-endemic areas in Brazil was mapped based on climate suitability. Known biological requirements of hookworm were fitted to data in a monthly long-term normal climate grid (18 x 18 km using geographical information systems. Hookworm risk models were produced using the growing degree day (GDD water budget (WB concept. A moisture-adjusted model (MA-GDD was developed based on accumulation of monthly temperatures above a base temperature of 15 °C (below which there is no lifecycle progression of Necator americanus conditional on concurrent monthly values (rain/potential, evapotranspiration of over 0.4. A second model, designated the gradient index, was calculated based on the monthly accumulation of the product of GDD and monthly WB values (GDD x WB. Both parameters had a significant positive correlation to hookworm prevalence. In the northeastern part of Brazil (the Caatinga, low hookworm prevalence was due to low soil moisture content, while the low prevalence in southern Brazil was related to low mean monthly temperatures. Both environmental temperature and soil moisture content were found to be important parameters for predicting the prevalence of N. americanus.

  17. Phlebotominae of epidemiological importance in cutaneous leishmaniasis in northwestern Argentina: risk maps and ecological niche models.

    Science.gov (United States)

    Quintana, M; Salomón, O; Guerra, R; De Grosso, M Lizarralde; Fuenzalida, A

    2013-03-01

    In Argentina, 58.2% out of the 8126 Cutaneous Leishmaniasis (CL) incident cases accumulated from 1954 to 2006 were reported in the provinces of Salta and Jujuy. The aim of this study was to develop an exploratory risk map and a potential distribution map of the vector, in order to offer recommendations for CL prevention. A total of 12 079 Phlebotominae (Diptera: Psychodidae) belonging to the species Lutzomyia neivai (Pinto), Lu. migonei (França), Lu. cortelezzii (Brèthes), Lu. shannoni (Dyar), Lu. quinquefer (Dyar) and Brumptomyia spp. (França & Parrot) were captured. Potential distribution models were created for two species, Lu. neivai (incriminated vector of Leishmania braziliensis) and Lu. migonei, associated with domestic animals in Argentina and that in turn could be involved as a link between zoonotic transmission cycles and anthropozoonotic. The Maximum Entropy Modeling System (MaxEnt) was used. The Jackknife test was performed, and the 'rainfall of the driest month' was the variable that best generalized the models. Accuracy was evaluated by the area under the curve (AUC) and validated by the Cohen's kappa index. This approximation provides a new analytical resource of high potential for the prevention of the disease, in order to allocate resources properly and to develop the most suitable strategies for action.

  18. Refugia, colonization and diversification of an arid-adapted bird: coincident patterns between genetic data and ecological niche modelling.

    Science.gov (United States)

    Barrientos, Rafael; Kvist, Laura; Barbosa, Andrés; Valera, Francisco; Khoury, Fares; Varela, Sara; Moreno, Eulalia

    2014-02-01

    Phylogeographical studies are common in boreal and temperate species from the Palaearctic, but scarce in arid-adapted species. We used nuclear and mitochondrial markers to investigate phylogeography and to estimate chronology of colonization events of the trumpeter finch Bucanetes githagineus, an arid-adapted bird. We used 271 samples from 16 populations, most of which were fresh samples but including some museum specimens. Microsatellite data showed no clear grouping according to the sampling locations. Microsatellite and mitochondrial data showed the clearest differentiation between Maghreb and Canary Islands and between Maghreb and Western Sahara. Mitochondrial data suggest differentiation between different Maghreb populations and among Maghreb and Near East populations, between Iberian Peninsula and Canary Islands, as well as between Western Sahara and Maghreb. Our coalescence analyses indicate that the trumpeter finch colonized North Africa during the humid Marine Isotope Stage 5 (MIS5) period of the Sahara region 125 000 years ago. We constructed an ecological niche model (ENM) to estimate the geographical distribution of climatically suitable habitats for the trumpeter finch. We tested whether changes in the species range in relation to glacial-interglacial cycles could be responsible for observed patterns of genetic diversity and structure. Modelling results matched with those from genetic data as the species' potential range increases in interglacial scenarios (in the present climatic scenario and during MIS5) and decreases in glacial climates (during the last glacial maximum, LGM, 21 000 years ago). Our results suggest that the trumpeter finch responded to Pleistocene climatic changes by expanding and contracting its range.

  19. Prevalence, Distribution, and Development of an Ecological Niche Model of Dermacentor variabilis Ticks Positive for Rickettsia montanensis.

    Science.gov (United States)

    St John, Heidi K; Adams, Melissa L; Masuoka, Penny M; Flyer-Adams, Johanna G; Jiang, Ju; Rozmajzl, Patrick J; Stromdahl, Ellen Y; Richards, Allen L

    2016-04-01

    Rickettsia montanensis has long been considered a nonpathogenic member of the spotted fever group rickettsiae. However, the infection potential of R. montanensis is being revisited in light of its recent association with a case of human infection in the United States and the possibility that additional cases may have been misdiagnosed as Rocky Mountain spotted fever. To this end, DNA was extracted from American dog ticks (Dermacentor variabilis) removed from Department of Defense (DoD) personnel and their dependents at DoD medical treatment facilities (MTFs) during 2002-2012 (n = 4792). These 4792 samples were analyzed for the presence of R. montanensis (n =  36; 2.84%) and all vector DNA was confirmed to be of D. variabilis origin using a novel Dermacentor genus-specific quantitative real-time polymerase chain reaction procedure, Derm, and a novel Dermacentor species multilocus sequence typing assay. To assess the risk of R. montanensis infection, the positive and negative samples were geographically mapped utilizing MTF site locations. Tick localities were imported into a geographical information systems (GIS) program, ArcGIS, for mapping and analysis. The ecological niche modeling (ENM) program, Maxent, was used to estimate the probability of tick presence in eastern United States using locations of both R. montanensis-positive and -negative ticks, climate, and elevation data. The ENM for R. montanensis-positive D. variabilis estimated high probabilities of the positive ticks occurring in two main areas, including the northern Midwest and mid-Atlantic portions of the northeastern regions of United States, whereas the R. montanensis-negative D. variabilis tick model showed a wider estimated range. The results suggest that R. montanensis-positive and -negative D. variabilis have different ranges where humans may be at risk and are influenced by similar and different factors.

  20. A privileged intraphagocyte niche is responsible for disseminated infection of Staphylococcus aureus in a zebrafish model

    OpenAIRE

    Prajsnar, T. K.; Hamilton, R.; Garcia-Lara, J.; McVicker, G.; Williams, A; Boots, M.; Foster, S J; Renshaw, S. A.

    2012-01-01

    The innate immune system is the primary defence\\ud against the versatile pathogen, Staphylococcus\\ud aureus. How this organism is able to avoid immune\\ud killing and cause infections is poorly understood.\\ud Using an established larval zebrafish infection\\ud model, we have shown that overwhelming infection\\ud is due to subversion of phagocytes by staphylococci,\\ud allowing bacteria to evade killing and found foci\\ud of disease. Larval zebrafish coinfected with two\\ud S. aureus strains carryin...

  1. Market positioning: the shifting effects of niche overlap

    NARCIS (Netherlands)

    Bruggeman, J.; Grunow, D.; Leenders, M.A.A.M.; Vermeulen, I.; Kuilman, J.G.

    2012-01-01

    Organizational ecology models of market dynamics emphasize the competition-inducing role of inter-organizational niche overlap—targeting similar market niches increases competitive pressure and thus reduces organizations’ fitness. Recent studies, however, have suggested that moderate niche overlap m

  2. Ecological niches of open ocean phytoplankton taxa

    DEFF Research Database (Denmark)

    Brun, Philipp Georg; Vogt, Meike; Payne, Mark;

    2015-01-01

    We characterize the realized ecological niches of 133 phytoplankton taxa in the open ocean based on observations from the MAREDAT initiative and a statistical species distribution model (MaxEnt). The models find that the physical conditions (mixed layer depth, temperature, light) govern large...... conditions in the open ocean. Our estimates of the realized niches roughly match the predictions of Reynolds' C-S-R model for the global ocean, namely that taxa classified as nutrient stress tolerant have niches at lower nutrient and higher irradiance conditions than light stress tolerant taxa. Yet...

  3. Modelling suitable estuarine habitats for Zostera noltii , using Ecological Niche Factor Analysis and Bathymetric LiDAR

    Science.gov (United States)

    Valle, Mireia; Borja, Ángel; Chust, Guillem; Galparsoro, Ibon; Garmendia, Joxe Mikel

    2011-08-01

    Predicting species distribution and habitat suitability is of considerable use in supporting the implementation of environmental legislation, protection and conservation of marine waters and ecosystem-based management. As other seagrasses, Zostera noltii has declined worldwide, mainly due to human pressures, such as eutrophication and habitat loss. In the case of the Basque Country (northern Spain), the species is present only in 3 out of 12 estuaries. From the literature, it is known that at least 6 of these estuaries were formerly vegetated by this seagrass. Consequently, efforts to monitor and restore (potential) habitats have been enhanced. Therefore, we aim: (i) to determine the main environmental variables explaining Zostera noltii distribution, within the Basque estuaries based upon the Oka estuary; (ii) to model habitat suitability for this species, as a wider applicable management-decision tool for seagrass restoration; and (iii) to assess the applicability and predicted accuracy of the model by using internal and external validation methods. For this purpose, Ecological Niche Factor Analysis (ENFA) has been used to model habitat suitability, based upon topographical variables, obtained from bathymetric Light Detection And Ranging (LiDAR); sediment characteristics variables; and hydrodynamic variables. The results obtained from the ecological factors of the ENFA (Marginality: 1.00; Specialization: 2.59) indicate that the species habitat differs considerably from the mean environmental conditions over the study area; likewise, that the species is restrictive in the selection of the range of conditions within which it dwells. The main environmental variables relating to the species distribution, in order of importance, are: mean grain size; redox potential; intertidal height; sediment sorting; slope of intertidal flat; percentage of gravels; and percentage of organic matter content. The model has a high predicted accuracy (Boyce index: 0.92). Model

  4. Selecting a Conservation Surrogate Species for Small Fragmented Habitats Using Ecological Niche Modelling

    Directory of Open Access Journals (Sweden)

    K. Anne-Isola Nekaris

    2015-01-01

    Full Text Available Flagship species are traditionally large, charismatic animals used to rally conservation efforts. Accepted flagship definitions suggest they need only fulfil a strategic role, unlike umbrella species that are used to shelter cohabitant taxa. The criteria used to select both flagship and umbrella species may not stand up in the face of dramatic forest loss, where remaining fragments may only contain species that do not suit either set of criteria. The Cinderella species concept covers aesthetically pleasing and overlooked species that fulfil the criteria of flagships or umbrellas. Such species are also more likely to occur in fragmented habitats. We tested Cinderella criteria on mammals in the fragmented forests of the Sri Lankan Wet Zone. We selected taxa that fulfilled both strategic and ecological roles. We created a shortlist of ten species, and from a survey of local perceptions highlighted two finalists. We tested these for umbrella characteristics against the original shortlist, utilizing Maximum Entropy (MaxEnt modelling, and analysed distribution overlap using ArcGIS. The criteria highlighted Loris tardigradus tardigradus and Prionailurus viverrinus as finalists, with the former having highest flagship potential. We suggest Cinderella species can be effective conservation surrogates especially in habitats where traditional flagship species have been extirpated.

  5. Potential for spread of the white-nose fungus (Pseudogymnoascus destructans in the Americas: use of Maxent and NicheA to assure strict model transference

    Directory of Open Access Journals (Sweden)

    Luis E. Escobar

    2014-11-01

    Full Text Available Emerging infectious diseases can present serious threats to wildlife, even to the point of causing extinction. White- nose fungus (Pseudogymnoascus destructans is causing an epizootic in bats that is expanding rapidly, both geographically and taxonomically. Little is known of the ecology and distributional potential of this intercontinental pathogen. We address this gap via ecological niche models that characterise coarse resolution niche differences between fungus populations on dif- ferent continents, identifying areas potentially vulnerable to infection in South America. Here we explore a novel approach to identifying areas of potential distribution across novel geographic regions that avoids perilious extrapolation into novel environments. European and North American fungus populations show differential use of environmental space, but rather than niche differentiation, we find that changes are best attributed to climatic differences between the two continents. Suitable areas for spread of the pathogen were identified across southern South America; however caution should be taken to avoid underestimating the potential for spread of this pathogen in South America.

  6. Climate change and risk of leishmaniasis in north america: predictions from ecological niche models of vector and reservoir species.

    Directory of Open Access Journals (Sweden)

    Camila González

    Full Text Available BACKGROUND: Climate change is increasingly being implicated in species' range shifts throughout the world, including those of important vector and reservoir species for infectious diseases. In North America (México, United States, and Canada, leishmaniasis is a vector-borne disease that is autochthonous in México and Texas and has begun to expand its range northward. Further expansion to the north may be facilitated by climate change as more habitat becomes suitable for vector and reservoir species for leishmaniasis. METHODS AND FINDINGS: The analysis began with the construction of ecological niche models using a maximum entropy algorithm for the distribution of two sand fly vector species (Lutzomyia anthophora and L. diabolica, three confirmed rodent reservoir species (Neotoma albigula, N. floridana, and N. micropus, and one potential rodent reservoir species (N. mexicana for leishmaniasis in northern México and the United States. As input, these models used species' occurrence records with topographic and climatic parameters as explanatory variables. Models were tested for their ability to predict correctly both a specified fraction of occurrence points set aside for this purpose and occurrence points from an independently derived data set. These models were refined to obtain predicted species' geographical distributions under increasingly strict assumptions about the ability of a species to disperse to suitable habitat and to persist in it, as modulated by its ecological suitability. Models successful at predictions were fitted to the extreme A2 and relatively conservative B2 projected climate scenarios for 2020, 2050, and 2080 using publicly available interpolated climate data from the Third Intergovernmental Panel on Climate Change Assessment Report. Further analyses included estimation of the projected human population that could potentially be exposed to leishmaniasis in 2020, 2050, and 2080 under the A2 and B2 scenarios. All confirmed

  7. Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning.

    Directory of Open Access Journals (Sweden)

    Robin L Miller-Coleman

    Full Text Available Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes. PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7-8.5 at concentrations up to 6.6×10(6 16S rRNA gene copies g(-1 wet sediment. In Yellowstone National Park (YNP, Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB, Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C

  8. Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning.

    Science.gov (United States)

    Miller-Coleman, Robin L; Dodsworth, Jeremy A; Ross, Christian A; Shock, Everett L; Williams, Amanda J; Hartnett, Hilairy E; McDonald, Austin I; Havig, Jeff R; Hedlund, Brian P

    2012-01-01

    Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7-8.5 at concentrations up to 6.6×10(6) 16S rRNA gene copies g(-1) wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to

  9. Climatic niche divergence or conservatism? Environmental niches and range limits in ecologically similar damselflies.

    Science.gov (United States)

    Wellenreuther, Maren; Larson, Keith W; Svensson, Erik I

    2012-06-01

    The factors that determine species' range limits are of central interest to biologists. One particularly interesting group comprises odonates (dragonflies and damselflies), which show large differences in secondary sexual traits and respond quickly to climatic factors, but often have minor interspecific niche differences, challenging models of niche-based species coexistence. We quantified the environmental niches at two geographic scales to understand the ecological causes of northern range limits and the coexistence of two congeneric damselflies (Calopteryx splendens and C. virgo). Using environmental niche modeling, we quantified niche divergence first across the whole geographic range in Fennoscandia, and second only in the sympatric part of this range. We found evidence for interspecific divergence along the environmental axes of temperature and precipitation across the northern range in Fennoscandia, suggesting that adaptation to colder and wetter climate might have allowed C. virgo to expand farther north than C. splendens. However, in the sympatric zone in southern Fennoscandia we found only negligible and nonsignificant niche differences. Minor niche differences in sympatry lead to frequent encounters and intense interspecific sexual interactions at the local scale of populations. Nevertheless, niche differences across Fennoscandia suggest that species differences in physiological tolerances limit range expansions northward, and that current and future climate could have large effects on the distributional ranges of these and ecologically similar insects.

  10. California Reservoir Drought Sensitivity and Exhaustion Risk Using Statistical Graphical Models

    OpenAIRE

    Taeb, Armeen; Reager, John T.; Turmon, Michael; Chandrasekaran, Venkat

    2016-01-01

    The ongoing California drought has highlighted the potential vulnerability of state water management infrastructure to multi-year dry intervals. Due to the high complexity of the network, dynamic storage changes across the California reservoir system have been difficult to model using either conventional statistical or physical approaches. Here, we analyze the interactions of monthly volumes in a network of 55 large California reservoirs, over a period of 136 months from 2004 to 2015, and we ...

  11. The role of public policies in reducing smoking prevalence in California: results from the California tobacco policy simulation model.

    Science.gov (United States)

    Levy, David T; Hyland, Andrew; Higbee, Cheryl; Remer, Lillian; Compton, Christine

    2007-07-01

    Tobacco control policies are examined utilizing a simulation model for California, the state with the longest running comprehensive program. We assess the impact of the California Tobacco Control Program (CTCP) and surrounding price changes on smoking prevalence and smoking-attributable deaths. Modeling begins in 1988 and progresses chronologically to 2004, and considers four types of policies (taxes, mass media, clean air laws, and youth access policies) independently and as a package. The model is validated against existing smoking prevalence estimates. The difference in trends between predicted smoking rates from the model and other commonly used estimates of smoking prevalence for the overall period were generally small. The model also predicted some important changes in trend, which occurred with changes in policy. The California SimSmoke model estimates that tobacco control policies reduced smoking rates in California by an additional 25% relative to the level that they would have been if policies were kept at their 1988 level. By 2004, the model attributes 59% of the reduction to price increases, 28% of the overall effect to media policies, 11% to clean air laws, and only a small percent to youth access policies. The model estimates that over 5000 lives will be saved in the year 2010 alone as a result of the CTCP and industry-initiated price increases, and that over 50,000 lives were saved over the period 1988-2010. Tobacco control policies implemented as comprehensive tobacco control strategies have significantly impacted smoking rates. Further tax increases should lead to additional lives saved, and additional policies may result in further impacts on smoking rates, and consequently on smoking-attributable health outcomes in the population.

  12. Relaxed random walk model coupled with ecological niche modeling unravel the dispersal dynamics of a Neotropical savanna tree species in the deeper Quaternary

    Directory of Open Access Journals (Sweden)

    Rosane Garcia Collevatti

    2015-08-01

    Full Text Available Understanding the dispersal routes of Neotropical savanna tree species is an essential step to unravel the effects of past climate change on genetic patterns, species distribution and population demography. Here we reconstruct the demographic history and dispersal dynamics of the Neotropical savanna tree species Tabebuia aurea to understand the effects of Quaternary climate change on its current spatial patterns of genetic diversity. We sampled 285 individuals from 21 populations throughout Brazilian savannas and sequenced all individuals for three chloroplast intergenic spacers and ITS nrDNA. We analyzed data using a multi-model inference framework by coupling the relaxed random walk model, ecological niche modeling (ENM and statistical phylogeography. The most recent common ancestor of T. aurea lineages dated from ~4.0 ± 2.5 Ma. Tabebuia aurea lineages cyclically dispersed from the West towards the Central-West Brazil, and from the Southeast towards the East and Northeast Brazil, following the paleodistribution dynamics shown by the ENMs through the last glacial cycle. A historical refugium through time may have allowed dispersal of lineages among populations of Central Brazil, overlapping with population expansion during interglacial periods and the diversification of new lineages. Range and population expansion through the Quaternary were, respectively, the most frequent prediction from ENMs and the most likely demographic scenario from coalescent simulations. Consistent phylogeographic patterns among multiple modeling inferences indicate a promising approach, allowing us to understand how cyclical climate changes through the Quaternary drove complex population dynamics and the current patterns of species distribution and genetic diversity.

  13. Ecological Niche Modelling Predicts Southward Expansion of Lutzomyia (Nyssomyia) flaviscutellata (Diptera: Psychodidae: Phlebotominae), Vector of Leishmania (Leishmania) amazonensis in South America, under Climate Change

    Science.gov (United States)

    Carvalho, Bruno M.; Ready, Paul D.

    2015-01-01

    Vector borne diseases are susceptible to climate change because distributions and densities of many vectors are climate driven. The Amazon region is endemic for cutaneous leishmaniasis and is predicted to be severely impacted by climate change. Recent records suggest that the distributions of Lutzomyia (Nyssomyia) flaviscutellata and the parasite it transmits, Leishmania (Leishmania) amazonensis, are expanding southward, possibly due to climate change, and sometimes associated with new human infection cases. We define the vector’s climatic niche and explore future projections under climate change scenarios. Vector occurrence records were compiled from the literature, museum collections and Brazilian Health Departments. Six bioclimatic variables were used as predictors in six ecological niche model algorithms (BIOCLIM, DOMAIN, MaxEnt, GARP, logistic regression and Random Forest). Projections for 2050 used 17 general circulation models in two greenhouse gas representative concentration pathways: “stabilization” and “high increase”. Ensemble models and consensus maps were produced by overlapping binary predictions. Final model outputs showed good performance and significance. The use of species absence data substantially improved model performance. Currently, L. flaviscutellata is widely distributed in the Amazon region, with records in the Atlantic Forest and savannah regions of Central Brazil. Future projections indicate expansion of the climatically suitable area for the vector in both scenarios, towards higher latitudes and elevations. L. flaviscutellata is likely to find increasingly suitable conditions for its expansion into areas where human population size and density are much larger than they are in its current locations. If environmental conditions change as predicted, the range of the vector is likely to expand to southeastern and central-southern Brazil, eastern Paraguay and further into the Amazonian areas of Bolivia, Peru, Ecuador, Colombia and

  14. Ecological Niche Modelling Predicts Southward Expansion of Lutzomyia (Nyssomyia flaviscutellata (Diptera: Psychodidae: Phlebotominae, Vector of Leishmania (Leishmania amazonensis in South America, under Climate Change.

    Directory of Open Access Journals (Sweden)

    Bruno M Carvalho

    Full Text Available Vector borne diseases are susceptible to climate change because distributions and densities of many vectors are climate driven. The Amazon region is endemic for cutaneous leishmaniasis and is predicted to be severely impacted by climate change. Recent records suggest that the distributions of Lutzomyia (Nyssomyia flaviscutellata and the parasite it transmits, Leishmania (Leishmania amazonensis, are expanding southward, possibly due to climate change, and sometimes associated with new human infection cases. We define the vector's climatic niche and explore future projections under climate change scenarios. Vector occurrence records were compiled from the literature, museum collections and Brazilian Health Departments. Six bioclimatic variables were used as predictors in six ecological niche model algorithms (BIOCLIM, DOMAIN, MaxEnt, GARP, logistic regression and Random Forest. Projections for 2050 used 17 general circulation models in two greenhouse gas representative concentration pathways: "stabilization" and "high increase". Ensemble models and consensus maps were produced by overlapping binary predictions. Final model outputs showed good performance and significance. The use of species absence data substantially improved model performance. Currently, L. flaviscutellata is widely distributed in the Amazon region, with records in the Atlantic Forest and savannah regions of Central Brazil. Future projections indicate expansion of the climatically suitable area for the vector in both scenarios, towards higher latitudes and elevations. L. flaviscutellata is likely to find increasingly suitable conditions for its expansion into areas where human population size and density are much larger than they are in its current locations. If environmental conditions change as predicted, the range of the vector is likely to expand to southeastern and central-southern Brazil, eastern Paraguay and further into the Amazonian areas of Bolivia, Peru, Ecuador

  15. Ecological Niche Modelling Predicts Southward Expansion of Lutzomyia (Nyssomyia) flaviscutellata (Diptera: Psychodidae: Phlebotominae), Vector of Leishmania (Leishmania) amazonensis in South America, under Climate Change.

    Science.gov (United States)

    Carvalho, Bruno M; Rangel, Elizabeth F; Ready, Paul D; Vale, Mariana M

    2015-01-01

    Vector borne diseases are susceptible to climate change because distributions and densities of many vectors are climate driven. The Amazon region is endemic for cutaneous leishmaniasis and is predicted to be severely impacted by climate change. Recent records suggest that the distributions of Lutzomyia (Nyssomyia) flaviscutellata and the parasite it transmits, Leishmania (Leishmania) amazonensis, are expanding southward, possibly due to climate change, and sometimes associated with new human infection cases. We define the vector's climatic niche and explore future projections under climate change scenarios. Vector occurrence records were compiled from the literature, museum collections and Brazilian Health Departments. Six bioclimatic variables were used as predictors in six ecological niche model algorithms (BIOCLIM, DOMAIN, MaxEnt, GARP, logistic regression and Random Forest). Projections for 2050 used 17 general circulation models in two greenhouse gas representative concentration pathways: "stabilization" and "high increase". Ensemble models and consensus maps were produced by overlapping binary predictions. Final model outputs showed good performance and significance. The use of species absence data substantially improved model performance. Currently, L. flaviscutellata is widely distributed in the Amazon region, with records in the Atlantic Forest and savannah regions of Central Brazil. Future projections indicate expansion of the climatically suitable area for the vector in both scenarios, towards higher latitudes and elevations. L. flaviscutellata is likely to find increasingly suitable conditions for its expansion into areas where human population size and density are much larger than they are in its current locations. If environmental conditions change as predicted, the range of the vector is likely to expand to southeastern and central-southern Brazil, eastern Paraguay and further into the Amazonian areas of Bolivia, Peru, Ecuador, Colombia and Venezuela

  16. Combining a climatic niche model of an invasive fungus with its host species distributions to identify risks to natural assets: Puccinia psidii Sensu Lato in Australia.

    Directory of Open Access Journals (Sweden)

    Darren J Kriticos

    Full Text Available Puccinia psidii sensu lato (s.l. is an invasive rust fungus threatening a wide range of plant species in the family Myrtaceae. Originating from Central and South America, it has invaded mainland USA and Hawai'i, parts of Asia and Australia. We used CLIMEX to develop a semi-mechanistic global climatic niche model based on new data on the distribution and biology of P. psidii s.l. The model was validated using independent distribution data from recently invaded areas in Australia, China and Japan. We combined this model with distribution data of its potential Myrtaceae host plant species present in Australia to identify areas and ecosystems most at risk. Myrtaceaeous species richness, threatened Myrtaceae and eucalypt plantations within the climatically suitable envelope for P. psidii s.l in Australia were mapped. Globally the model identifies climatically suitable areas for P. psidii s.l. throughout the wet tropics and sub-tropics where moist conditions with moderate temperatures prevail, and also into some cool regions with a mild Mediterranean climate. In Australia, the map of species richness of Myrtaceae within the P. psidii s.l. climatic envelope shows areas where epidemics are hypothetically more likely to be frequent and severe. These hotspots for epidemics are along the eastern coast of New South Wales, including the Sydney Basin, in the Brisbane and Cairns areas in Queensland, and in the coastal region from the south of Bunbury to Esperance in Western Australia. This new climatic niche model for P. psidii s.l. indicates a higher degree of cold tolerance; and hence a potential range that extends into higher altitudes and latitudes than has been indicated previously. The methods demonstrated here provide some insight into the impacts an invasive species might have within its climatically suited range, and can help inform biosecurity policies regarding the management of its spread and protection of valued threatened assets.

  17. Evolution of pollination niches in a generalist plant clade.

    Science.gov (United States)

    Gómez, José María; Perfectti, Francisco; Abdelaziz, Mohamed; Lorite, Juan; Muñoz-Pajares, Antonio Jesús; Valverde, Javier

    2015-01-01

    It is widely assumed that floral diversification occurs by adaptive shifts between pollination niches. In contrast to specialized flowers, identifying pollination niches of generalist flowers is a challenge. Consequently, how generalist pollination niches evolve is largely unknown. We apply tools from network theory and comparative methods to investigate the evolution of pollination niches among generalist species belonging to the genus Erysimum. These species have similar flowers. We found that the studied species may be grouped in several multidimensional niches separated not by a shift of pollinators, but instead by quantitative variation in the relative abundance of pollinator functional groups. These pollination niches did not vary in generalization degree; we did not find any evolutionary trend toward specialization within the studied clade. Furthermore, the evolution of pollination niche fitted to a Brownian motion model without phylogenetic signal, and was characterized by frequent events of niche convergences and divergences. We presume that the evolution of Erysimum pollination niches has occurred mostly by recurrent shifts between slightly different generalized pollinator assemblages varying spatially as a mosaic and without any change in specialization degree. Most changes in pollination niches do not prompt floral divergence, a reason why adaptation to pollinators is uncommon in generalist plants.

  18. A seamless, high-resolution, coastal digital elevation model (DEM) for Southern California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A seamless, three-meter digital elevation model (DEM) was constructed for the entire Southern California coastal zone, extending 473 km from Point Conception to the...

  19. Digital elevation model of Little Holland Tract, Sacramento-San Joaquin Delta, California, 2015

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This product is a digital elevation model (DEM) for the Little Holland Tract in the Sacramento-San Joaquin River Delta, California based on U.S. Geological Survey...

  20. Digital Elevation Model of Little Holland Tract, Sacramento-San Joaquin Delta, California, 2015

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This product is a digital elevation model (DEM) for the Little Holland Tract in the Sacramento-San Joaquin River Delta, California based on U.S. Geological Survey...

  1. Physical oceanography - Developing end-to-end models of the California Current Large Marine Ecosystem

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web...

  2. Ecological niche transferability using invasive species as a case study.

    Directory of Open Access Journals (Sweden)

    Miguel Fernández

    Full Text Available Species distribution modeling is widely applied to predict invasive species distributions and species range shifts under climate change. Accurate predictions depend upon meeting the assumption that ecological niches are conserved, i.e., spatially or temporally transferable. Here we present a multi-taxon comparative analysis of niche conservatism using biological invasion events well documented in natural history museum collections. Our goal is to assess spatial transferability of the climatic niche of a range of noxious terrestrial invasive species using two complementary approaches. First we compare species' native versus invasive ranges in environmental space using two distinct methods, Principal Components Analysis and Mahalanobis distance. Second we compare species' native versus invaded ranges in geographic space as estimated using the species distribution modeling technique Maxent and the comparative index Hellinger's I. We find that species exhibit a range of responses, from almost complete transferability, in which the invaded niches completely overlap with the native niches, to a complete dissociation between native and invaded ranges. Intermediate responses included expansion of dimension attributable to either temperature or precipitation derived variables, as well as niche expansion in multiple dimensions. We conclude that the ecological niche in the native range is generally a poor predictor of invaded range and, by analogy, the ecological niche may be a poor predictor of range shifts under climate change. We suggest that assessing dimensions of niche transferability prior to standard species distribution modeling may improve the understanding of species' dynamics in the invaded range.

  3. Unveiling the factors shaping the distribution of widely distributed alpine vertebrates, using multi-scale ecological niche modelling of the bat Plecotus macrobullaris.

    Science.gov (United States)

    Alberdi, Antton; Aizpurua, Ostaizka; Aihartza, Joxerra; Garin, Inazio

    2014-01-01

    Several alpine vertebrates share a distribution pattern that extends across the South-western Palearctic but is limited to the main mountain massifs. Although they are usually regarded as cold-adapted species, the range of many alpine vertebrates also includes relatively warm areas, suggesting that factors beyond climatic conditions may be driving their distribution. In this work we first recognize the species belonging to the mentioned biogeographic group and, based on the environmental niche analysis of Plecotus macrobullaris, we identify and characterize the environmental factors constraining their ranges. Distribution overlap analysis of 504 European vertebrates was done using the Sorensen Similarity Index, and we identified four birds and one mammal that share the distribution with P. macrobullaris. We generated 135 environmental niche models including different variable combinations and regularization values for P. macrobullaris at two different scales and resolutions. After selecting the best models, we observed that topographic variables outperformed climatic predictors, and the abruptness of the landscape showed better predictive ability than elevation. The best explanatory climatic variable was mean summer temperature, which showed that P. macrobullaris is able to cope with mean temperature ranges spanning up to 16°C. The models showed that the distribution of P. macrobullaris is mainly shaped by topographic factors that provide rock-abundant and open-space habitats rather than climatic determinants, and that the species is not a cold-adapted, but rather a cold-tolerant eurithermic organism. P. macrobullaris shares its distribution pattern as well as several ecological features with five other alpine vertebrates, suggesting that the conclusions obtained from this study might be extensible to them. We concluded that rock-dwelling and open-space foraging vertebrates with broad temperature tolerance are the best candidates to show wide alpine distribution

  4. Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling

    Science.gov (United States)

    Pauwels, Maxime; Pasierbinski, Andrzej; Przedpelska-Wasowicz, Ewa M.; Babst-Kostecka, Alicja A.; Saumitou-Laprade, Pierre; Rostanski, Adam

    2016-01-01

    The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest. PMID:26835186

  5. Phylogeographic analysis and environmental niche modeling of widespread shrub Rhododendron simsii in China reveals multiple glacial refugia during the last glacial maximum

    Institute of Scientific and Technical Information of China (English)

    Yong LI; Hai-Fei YAN; Xue-Jun GE

    2012-01-01

    The phylogeography of common and widespread species can help us to understand the history of local flora and vegetation.Here,we study the semi-evergreen shrub Rhododendron simsii Planch.,which is found in most areas of current evergreen broad leaved forest in China.Two noncoding chloroplast DNA (cpDNA) regions(rpl20-rps12 and trnL-F) and three amplified fragment length polymorphism (AFLP) primer sets (E-AAC/M-CTA,E-AGC/M-CTA and E-AGG/M-CAT) were used to examine the phylogeographic pattern in relation to past (last glacial maximum) and present distributions based on ecological niche modeling.The cpDNA data revealed four phylogeographic groups (East,South,West,and North groups) corresponding to geographic regions.Molecular dating suggests that lineage diversification within species likely occurred during the mid-to-late Pleistocene.In contrast,the four main cpDNA phylogeographic groups were not supported by the AFLP dataset.The highest likelihood of the AFLP data was obtained when samples were clustered into three groups (K =3).However,these groupings did not correspond to separate geographic regions supported by cpDNA data.Both mismatch distribution analysis and environmental niche modeling (ENM) indicated that multiple glacial refugia were maintained across the range of Rhododendron simsii during the last glacial maximum,contrary to the previous hypothesis that subtropical broad leaved evergreen forests were forced to retreat southward as far as 25°N.The discordance between the patterns revealed by cpDNA and AFLP data indicate that localized postglacial range expansions may facilitate extensive gene flow between the major glacial refugia.

  6. Estimating Policy-Driven Greenhouse Gas Emissions Trajectories in California: The California Greenhouse Gas Inventory Spreadsheet (GHGIS) Model

    Energy Technology Data Exchange (ETDEWEB)

    Greenblatt, Jeffery B.

    2013-10-10

    A California Greenhouse Gas Inventory Spreadsheet (GHGIS) model was developed to explore the impact of combinations of state policies on state greenhouse gas (GHG) and regional criteria pollutant emissions. The model included representations of all GHG- emitting sectors of the California economy (including those outside the energy sector, such as high global warming potential gases, waste treatment, agriculture and forestry) in varying degrees of detail, and was carefully calibrated using available data and projections from multiple state agencies and other sources. Starting from basic drivers such as population, numbers of households, gross state product, numbers of vehicles, etc., the model calculated energy demands by type (various types of liquid and gaseous hydrocarbon fuels, electricity and hydrogen), and finally calculated emissions of GHGs and three criteria pollutants: reactive organic gases (ROG), nitrogen oxides (NOx), and fine (2.5 ?m) particulate matter (PM2.5). Calculations were generally statewide, but in some sectors, criteria pollutants were also calculated for two regional air basins: the South Coast Air Basin (SCAB) and the San Joaquin Valley (SJV). Three scenarios were developed that attempt to model: (1) all committed policies, (2) additional, uncommitted policy targets and (3) potential technology and market futures. Each scenario received extensive input from state energy planning agencies, in particular the California Air Resources Board. Results indicate that all three scenarios are able to meet the 2020 statewide GHG targets, and by 2030, statewide GHG emissions range from between 208 and 396 MtCO2/yr. However, none of the scenarios are able to meet the 2050 GHG target of 85 MtCO2/yr, with emissions ranging from 188 to 444 MtCO2/yr, so additional policies will need to be developed for California to meet this stringent future target. A full sensitivity study of major scenario assumptions was also performed. In terms of criteria pollutants

  7. Gulf of California species and catch spatial distributions and historical time series - Developing end-to-end models of the Gulf of California

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the northern Gulf of California, linking oceanography, biogeochemistry, food web...

  8. Multiple Landslide-Hazard Scenarios Modeled for the Oakland-Berkeley Area, Northern California

    Science.gov (United States)

    Pike, Richard J.; Graymer, Russell W.

    2008-01-01

    With the exception of Los Angeles, perhaps no urban area in the United States is more at risk from landsliding, triggered by either precipitation or earthquake, than the San Francisco Bay region of northern California. By January each year, seasonal winter storms usually bring moisture levels of San Francisco Bay region hillsides to the point of saturation, after which additional heavy rainfall may induce landslides of various types and levels of severity. In addition, movement at any time along one of several active faults in the area may generate an earthquake large enough to trigger landslides. The danger to life and property rises each year as local populations continue to expand and more hillsides are graded for development of residential housing and its supporting infrastructure. The chapters in the text consist of: *Introduction by Russell W. Graymer *Chapter 1 Rainfall Thresholds for Landslide Activity, San Francisco Bay Region, Northern California by Raymond C. Wilson *Chapter 2 Susceptibility to Deep-Seated Landsliding Modeled for the Oakland-Berkeley Area, Northern California by Richard J. Pike and Steven Sobieszczyk *Chapter 3 Susceptibility to Shallow Landsliding Modeled for the Oakland-Berkeley Area, Northern California by Kevin M. Schmidt and Steven Sobieszczyk *Chapter 4 Landslide Hazard Modeled for the Cities of Oakland, Piedmont, and Berkeley, Northern California, from a M=7.1 Scenario Earthquake on the Hayward Fault Zone by Scott B. Miles and David K. Keefer *Chapter 5 Synthesis of Landslide-Hazard Scenarios Modeled for the Oakland-Berkeley Area, Northern California by Richard J. Pike The plates consist of: *Plate 1 Susceptibility to Deep-Seated Landsliding Modeled for the Oakland-Berkeley Area, Northern California by Richard J. Pike, Russell W. Graymer, Sebastian Roberts, Naomi B. Kalman, and Steven Sobieszczyk *Plate 2 Susceptibility to Shallow Landsliding Modeled for the Oakland-Berkeley Area, Northern California by Kevin M. Schmidt and Steven

  9. Niche Formation in the Mashup Ecosystem

    Directory of Open Access Journals (Sweden)

    Michael Weiss

    2013-05-01

    Full Text Available Mashups enable end-users to "mix and match" data and services available on the web to create applications. Their creation is supported by a complex ecosystem of i data providers who offer open APIs to users, ii users who combine APIs into mashups, and iii platforms, such as the ProgrammableWeb or Mashape, that facilitate the construction and publication of mashups. In this article, we argue that the evolution of the mashup ecosystem can be explained in terms of ecosystem niches anchored around hub or keystone APIs. The members of a niche are focused on an area of specialization (e.g., mapping applications and contribute their knowledge to the value proposition of the ecosystem as a whole. To demonstrate the formation of niches in the mashup ecosystem, we model groups of related mashups as species, and we reconstruct the evolution of mashup species through phylogenetic analysis.

  10. Environmental Niche Modelling of Phlebotomine Sand Flies and Cutaneous Leishmaniasis Identifies Lutzomyia intermedia as the Main Vector Species in Southeastern Brazil

    Science.gov (United States)

    Meneguzzi, Viviane Coutinho; dos Santos, Claudiney Biral; Leite, Gustavo Rocha; Fux, Blima; Falqueto, Aloísio

    2016-01-01

    Cutaneous leishmaniasis (CL) is caused by a protozoan of the genus Leishmania and is transmitted by sand flies. The state of Espírito Santo (ES), an endemic area in southeast Brazil, has shown a considerably high prevalence in recent decades. Environmental niche modelling (ENM) is a useful tool for predicting potential disease risk. In this study, ENM was applied to sand fly species and CL cases in ES to identify the principal vector and risk areas of the disease. Sand flies were collected in 466 rural localities between 1997 and 2013 using active and passive capture. Insects were identified to the species level, and the localities were georeferenced. Twenty-one bioclimatic variables were selected from WorldClim. Maxent was used to construct models projecting the potential distribution for five Lutzomyia species and CL cases. ENMTools was used to overlap the species and the CL case models. The Kruskal–Wallis test was performed, adopting a 5% significance level. Approximately 250,000 specimens were captured, belonging to 43 species. The area under the curve (AUC) was considered acceptable for all models. The slope was considered relevant to the construction of the models for all the species identified. The overlay test identified Lutzomyia intermedia as the main vector of CL in southeast Brazil. ENM tools enable an analysis of the association among environmental variables, vector distributions and CL cases, which can be used to support epidemiologic and entomological vigilance actions to control the expansion of CL in vulnerable areas. PMID:27783641

  11. How many studies are necessary to compare niche-based models for geographic distributions? Inductive reasoning may fail at the end.

    Science.gov (United States)

    Terribile, L C; Diniz-Filho, J A F; De Marco jr, P

    2010-05-01

    The use of ecological niche models (ENM) to generate potential geographic distributions of species has rapidly increased in ecology, conservation and evolutionary biology. Many methods are available and the most used are Maximum Entropy Method (MAXENT) and the Genetic Algorithm for Rule Set Production (GARP). Recent studies have shown that MAXENT perform better than GARP. Here we used the statistics methods of ROC - AUC (area under the Receiver Operating Characteristics curve) and bootstrap to evaluate the performance of GARP and MAXENT in generate potential distribution models for 39 species of New World coral snakes. We found that values of AUC for GARP ranged from 0.923 to 0.999, whereas those for MAXENT ranged from 0.877 to 0.999. On the whole, the differences in AUC were very small, but for 10 species GARP outperformed MAXENT. Means and standard deviations for 100 bootstrapped samples with sample sizes ranging from 3 to 30 species did not show any trends towards deviations from a zero difference in AUC values of GARP minus AUC values of MAXENT. Ours results suggest that further studies are still necessary to establish under which circumstances the statistical performance of the methods vary. However, it is also important to consider the possibility that this empirical inductive reasoning may fail in the end, because we almost certainly could not establish all potential scenarios generating variation in the relative performance of models.

  12. How many studies are necessary to compare niche-based models for geographic distributions? Inductive reasoning may fail at the end

    Directory of Open Access Journals (Sweden)

    LC Terribile

    Full Text Available The use of ecological niche models (ENM to generate potential geographic distributions of species has rapidly increased in ecology, conservation and evolutionary biology. Many methods are available and the most used are Maximum Entropy Method (MAXENT and the Genetic Algorithm for Rule Set Production (GARP. Recent studies have shown that MAXENT perform better than GARP. Here we used the statistics methods of ROC - AUC (area under the Receiver Operating Characteristics curve and bootstrap to evaluate the performance of GARP and MAXENT in generate potential distribution models for 39 species of New World coral snakes. We found that values of AUC for GARP ranged from 0.923 to 0.999, whereas those for MAXENT ranged from 0.877 to 0.999. On the whole, the differences in AUC were very small, but for 10 species GARP outperformed MAXENT. Means and standard deviations for 100 bootstrapped samples with sample sizes ranging from 3 to 30 species did not show any trends towards deviations from a zero difference in AUC values of GARP minus AUC values of MAXENT. Ours results suggest that further studies are still necessary to establish under which circumstances the statistical performance of the methods vary. However, it is also important to consider the possibility that this empirical inductive reasoning may fail in the end, because we almost certainly could not establish all potential scenarios generating variation in the relative performance of models.

  13. Model and observed statistics of California earthquakes parameters

    Directory of Open Access Journals (Sweden)

    R. CONSOLE

    1977-06-01

    Full Text Available RIASSUNTO - 11 modello proposto da Caputo per la statistica dei parametri
    dei terremoti in una zona sismica viene confrontato con i dati disponibili per
    la California. Tali dati provengono dal lavoro di Thatcher e Hanks e da quelli
    di Tucker e Brune. In essi sono riportate le serie di parametri M,M0 , l e / p
    osservati sperimentalmente. Per entrambe le serie di parametri vengono calcolate
    le distribuzioni statistiche e i risultali sono confrontati fra loro per mezzo delle
    relazioni imposte dalla teoria. I risultati, compatibilmente con le incertezze
    sperimentali e la scarsezza dei campioni adoperati, sembrano confermare la
    teoria e permettono di valutare la distribuzione per i parametri delle faglie che
    danno origine ai terremoti nella California.

  14. Data Assimilation and Model Simulations in the California Current

    Science.gov (United States)

    2016-06-07

    regions in order to improve our scientific understanding of the structure and dynamics of such regions. OBJECTIVES The broad objective of this research...analysis, and to apply the method to several quasi-synoptic hydrographic data sets from the California Current and the Alboran Sea. WORK COMPLETED During...5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Naval Postgraduate School,Department of Meteorology (MR/Hy),589 Dyer Rd

  15. Circumbinary Habitability Niches

    CERN Document Server

    Mason, Paul A; Cuartas-Restrepo, Pablo A; Clark, Joni M

    2014-01-01

    Binaries could provide the best niches for life in the galaxy. Though counterintuitive, this assertion follows directly from stellar tidal interaction theory and the evolution of lower mass stars. There is strong evidence that chromospheric activity of rapidly rotating young stars may be high enough to cause mass loss from atmospheres of potentially habitable planets. The removal of atmospheric water is most critical. Tidal breaking in binaries could help reduce magnetic dynamo action and thereby chromospheric activity in favor of life. We call this the Binary Habitability Mechanism (BHM), that we suggest allows for water retention at levels comparable to or better than Earth. We discuss novel advantages that life may exploit, in these cases, and suggest that life may even thrive on some circumbinary planets. We find that while many binaries do not benefit from BHM, high quality niches do exist for various combinations of stars between 0.55 and 1.0 solar masses. For a given pair of stellar masses, BHM operate...

  16. Genetic diversity and ecological niche modelling of wild barley: refugia, large-scale post-LGM range expansion and limited mid-future climate threats?

    Directory of Open Access Journals (Sweden)

    Joanne Russell

    Full Text Available Describing genetic diversity in wild barley (Hordeum vulgare ssp. spontaneum in geographic and environmental space in the context of current, past and potential future climates is important for conservation and for breeding the domesticated crop (Hordeum vulgare ssp. vulgare. Spatial genetic diversity in wild barley was revealed by both nuclear- (2,505 SNP, 24 nSSR and chloroplast-derived (5 cpSSR markers in 256 widely-sampled geo-referenced accessions. Results were compared with MaxEnt-modelled geographic distributions under current, past (Last Glacial Maximum, LGM and mid-term future (anthropogenic scenario A2, the 2080s climates. Comparisons suggest large-scale post-LGM range expansion in Central Asia and relatively small, but statistically significant, reductions in range-wide genetic diversity under future climate. Our analyses support the utility of ecological niche modelling for locating genetic diversity hotspots and determine priority geographic areas for wild barley conservation under anthropogenic climate change. Similar research on other cereal crop progenitors could play an important role in tailoring conservation and crop improvement strategies to support future human food security.

  17. A 3-D Geodynamic Model of Strain Partitioning in Southern California

    Science.gov (United States)

    Ye, J.; Liu, M.; Lin, F.

    2012-12-01

    In southern California, strain resulting from the relative motion between the Pacific and the North American plates is partitioned in a complex system of transcurrent, transcompressional, and transtensional faults. High-precision GPS measurements in this region have enabled kinematic modeling of the present-day strain partitioning between major faults in southern California. However, geodynamic models are needed to understand the cause of strain partitioning and to determine strain in regions where faults are blind or diffuse. We have developed a regional-scale geodynamic model of strain partitioning in southern California. This 3-D viscoelasto-plastic finite element model incorporates first-order fault geometry of the major active faults in the region. The model domain includes an elastoplastic upper crust on top of a viscoelastic lower lithospheric layer. Deformation is driven by the relative motion between the Pacific and the North American plates, imposed as a displacement boundary condition. Plastic deformation both within the fault zones and in the unfaulted surrounding crust is calculated. Our results show that the Big Bend of the San Andreas Fault, and other geometric complexity of faults in southern California, plays a major role in strain partitioning. The observed variations of strain portioning in southern California can be explained by the geometric configuration of fault systems relative to the relative plate motion, without appealing to basal traction of a flowing lower lithosphere. The model predicts concentrated plastic strain under the reverse fault systems in the Transverse Ranges and the young and diffuse faults in the Eastern California Shear Zone across the Mojave Desert, where a number damaging earthquakes occurred in the past decades.

  18. Why CMIP5 models projected precipitation changes over California are uncertain

    Science.gov (United States)

    Polade, S. D.; Gershunov, A.; Pierce, D. W.; Cayan, D. R.; Dettinger, M. D.

    2014-12-01

    Future planning for adaptation to and mitigation of the impacts of anthropogenic climatic changes depends mainly on the robustness of climate-model projections. California is one of the global regions where CMIP5 models projections for end-of-century precipitation changes are most uncertain. However, over other mediterranean-climate regions the same models robustly project drier futures. Here we investigate wintertime precipitation projections by the end of the century from 30 CMIP5 models over the five global mediterranean regions (California, South America, the Mediterranean basin, South Africa, and Australia) to disentangle the causes of uncertainty in projections over California. Our findings reveal that the projections of increases in wintertime precipitation over California by two thirds of the models are mainly driven by a comparably weaker increase in the frequency of dry days and a stronger increase in the frequency of heavy precipitation events (99th percentile) along with an increase in the intensity of moderate precipitating events (50-75th percentile) compared to the other mediterranean regions. California is projected to have 5-7 dry days and one more once in year heavy precipitation events in ensemble mean per year. The significant increases in the frequency of heavy events and weak increase in dry days' frequency are mostly attributed to the intensification of the north Pacific low-pressure system along with the strengthening of the sub tropical jet stream. The uniqueness of California's circulation change compared to other mediterranean regions is partially due to the modulation of the large-scale circulation by the low frequency Pacific climate variability.

  19. Geographical parthenogenesis: General purpose genotypes and frozen niche variation

    DEFF Research Database (Denmark)

    Vrijenhoek, Robert C.; Parker, Dave

    2009-01-01

    hypotheses concerning the evolution of niche breadth in asexual species - the "general-purpose genotype" (GPG) and "frozen niche-variation" (FNV) models. The two models are often portrayed as mutually exclusive, respectively viewing clonal lineages as generalists versus specialists. Nonetheless......, and sometimes generalist and specialist traits (e.g., physiological tolerance, microspatial preference, seasonal abundance, food habits, etc.) are found together in an asexual organism. Ultimately, persistent natural clones should be viewed as microspecies in ecological models that consider spatial and temporal...

  20. Activity response to climate seasonality in species with fossorial habits: a niche modeling approach using the lowland burrowing treefrog (Smilisca fodiens).

    Science.gov (United States)

    Encarnación-Luévano, Alondra; Rojas-Soto, Octavio R; Sigala-Rodríguez, J Jesús

    2013-01-01

    The importance of climatic conditions in shaping the geographic distribution of amphibian species is mainly associated to their high sensitivity to environmental conditions. How they cope with climate gradients through behavioral adaptations throughout their distribution is an important issue due to the ecological and evolutionary implications for population viability. Given their low dispersal abilities, the response to seasonal climate changes may not be migration, but behavioral and physiological adaptations. Here we tested whether shifts in climatic seasonality can predict the temporal variation of surface activity of the fossorial Lowland Burrowing Treefrog (Smilisca fodiens) across its geographical distribution. We employed Ecological Niche Modeling (ENM) to perform a monthly analysis of spatial variation of suitable climatic conditions (defined by the July conditions, the month of greatest activity), and then evaluated the geographical correspondence of monthly projections with the occurrence data per month. We found that the species activity, based on the species' occurrence data, corresponds with the latitudinal variation of suitable climatic conditions. Due to the behavioral response of this fossorial frog to seasonal climate variation, we suggest that precipitation and temperature have played a major role in the definition of geographical and temporal distribution patterns, as well as in shaping behavioral adaptations to local climatic conditions. This highlights the influence of macroclimate on shaping activity patterns and the important role of fossorials habits to meet the environmental requirements necessary for survival.

  1. Activity response to climate seasonality in species with fossorial habits: a niche modeling approach using the lowland burrowing treefrog (Smilisca fodiens.

    Directory of Open Access Journals (Sweden)

    Alondra Encarnación-Luévano

    Full Text Available The importance of climatic conditions in shaping the geographic distribution of amphibian species is mainly associated to their high sensitivity to environmental conditions. How they cope with climate gradients through behavioral adaptations throughout their distribution is an important issue due to the ecological and evolutionary implications for population viability. Given their low dispersal abilities, the response to seasonal climate changes may not be migration, but behavioral and physiological adaptations. Here we tested whether shifts in climatic seasonality can predict the temporal variation of surface activity of the fossorial Lowland Burrowing Treefrog (Smilisca fodiens across its geographical distribution. We employed Ecological Niche Modeling (ENM to perform a monthly analysis of spatial variation of suitable climatic conditions (defined by the July conditions, the month of greatest activity, and then evaluated the geographical correspondence of monthly projections with the occurrence data per month. We found that the species activity, based on the species' occurrence data, corresponds with the latitudinal variation of suitable climatic conditions. Due to the behavioral response of this fossorial frog to seasonal climate variation, we suggest that precipitation and temperature have played a major role in the definition of geographical and temporal distribution patterns, as well as in shaping behavioral adaptations to local climatic conditions. This highlights the influence of macroclimate on shaping activity patterns and the important role of fossorials habits to meet the environmental requirements necessary for survival.

  2. Arteriolar niches maintain haematopoietic stem cell quiescence.

    Science.gov (United States)

    Kunisaki, Yuya; Bruns, Ingmar; Scheiermann, Christoph; Ahmed, Jalal; Pinho, Sandra; Zhang, Dachuan; Mizoguchi, Toshihide; Wei, Qiaozhi; Lucas, Daniel; Ito, Keisuke; Mar, Jessica C; Bergman, Aviv; Frenette, Paul S

    2013-10-31

    Cell cycle quiescence is a critical feature contributing to haematopoietic stem cell (HSC) maintenance. Although various candidate stromal cells have been identified as potential HSC niches, the spatial localization of quiescent HSCs in the bone marrow remains unclear. Here, using a novel approach that combines whole-mount confocal immunofluorescence imaging techniques and computational modelling to analyse significant three-dimensional associations in the mouse bone marrow among vascular structures, stromal cells and HSCs, we show that quiescent HSCs associate specifically with small arterioles that are preferentially found in endosteal bone marrow. These arterioles are ensheathed exclusively by rare NG2 (also known as CSPG4)(+) pericytes, distinct from sinusoid-associated leptin receptor (LEPR)(+) cells. Pharmacological or genetic activation of the HSC cell cycle alters the distribution of HSCs from NG2(+) periarteriolar niches to LEPR(+) perisinusoidal niches. Conditional depletion of NG2(+) cells induces HSC cycling and reduces functional long-term repopulating HSCs in the bone marrow. These results thus indicate that arteriolar niches are indispensable for maintaining HSC quiescence.

  3. Arteriolar niches maintain haematopoietic stem cell quiescence

    Science.gov (United States)

    Kunisaki, Yuya; Bruns, Ingmar; Scheiermann, Christoph; Ahmed, Jalal; Pinho, Sandra; Zhang, Dachuan; Mizoguchi, Toshihide; Wei, Qiaozhi; Lucas, Daniel; Ito, Keisuke; Mar, Jessica C.; Bergman, Aviv; Frenette, Paul S.

    2013-01-01

    Cell cycle quiescence is a critical feature contributing to haematopoietic stem cell (HSC) maintenance. Although various candidate stromal cells have been identified as potential HSC niches, the spatial localization of quiescent HSCs in the bone marrow (BM) remains unclear. Here, using a novel approach that combines whole-mount confocal immunofluorescence imaging techniques and computational modelling to analyse significant tridimensional associations among vascular structures, stromal cells and HSCs, we show that quiescent HSCs associate specifically with small arterioles that are preferentially found in endosteal BM. These arterioles are ensheathed exclusively by rare NG2+ pericytes, distinct from sinusoid-associated LepR+ cells. Pharmacological or genetic activation of HSC cell cycle alters the distribution of HSCs from NG2+ peri-arteriolar niches to LepR+ peri-sinusoidal niches. Conditional depletion of NG2+ cells induces HSC cycling and reduces functional long-term repopulating HSCs in BM. These results thus indicate that arteriolar niches are indispensable to maintain HSC quiescence. PMID:24107994

  4. Predicting the potential environmental suitability for Theileria orientalis transmission in New Zealand cattle using maximum entropy niche modelling.

    Science.gov (United States)

    Lawrence, K E; Summers, S R; Heath, A C G; McFadden, A M J; Pulford, D J; Pomroy, W E

    2016-07-15

    The tick-borne haemoparasite Theileria orientalis is the most important infectious cause of anaemia in New Zealand cattle. Since 2012 a previously unrecorded type, T. orientalis type 2 (Ikeda), has been associated with disease outbreaks of anaemia, lethargy, jaundice and deaths on over 1000 New Zealand cattle farms, with most of the affected farms found in the upper North Island. The aim of this study was to model the relative environmental suitability for T. orientalis transmission throughout New Zealand, to predict the proportion of cattle farms potentially suitable for active T. orientalis infection by region, island and the whole of New Zealand and to estimate the average relative environmental suitability per farm by region, island and the whole of New Zealand. The relative environmental suitability for T. orientalis transmission was estimated using the Maxent (maximum entropy) modelling program. The Maxent model predicted that 99% of North Island cattle farms (n=36,257), 64% South Island cattle farms (n=15,542) and 89% of New Zealand cattle farms overall (n=51,799) could potentially be suitable for T. orientalis transmission. The average relative environmental suitability of T. orientalis transmission at the farm level was 0.34 in the North Island, 0.02 in the South Island and 0.24 overall. The study showed that the potential spatial distribution of T. orientalis environmental suitability was much greater than presumed in the early part of the Theileria associated bovine anaemia (TABA) epidemic. Maximum entropy offers a computer efficient method of modelling the probability of habitat suitability for an arthropod vectored disease. This model could help estimate the boundaries of the endemically stable and endemically unstable areas for T. orientalis transmission within New Zealand and be of considerable value in informing practitioner and farmer biosecurity decisions in these respective areas.

  5. High Resolution Niche Models of Malaria Vectors in Northern Tanzania: A New Capacity to Predict Malaria Risk?

    OpenAIRE

    Kulkarni, Manisha A; Desrochers, Rachelle E; Kerr, Jeremy T.

    2010-01-01

    Background Malaria transmission rates in Africa can vary dramatically over the space of a few kilometres. This spatial heterogeneity reflects variation in vector mosquito habitat and presents an important obstacle to the efficient allocation of malaria control resources. Malaria control is further complicated by combinations of vector species that respond differently to control interventions. Recent modelling innovations make it possible to predict vector distributions and extrapolate malaria...

  6. Predicting the past distribution of species climatic niches

    DEFF Research Database (Denmark)

    Nogues, David Bravo

    2009-01-01

    Predicting past distributions of species climatic niches, hindcasting, by using climate envelope models (CEMs) is emerging as an exciting research area. CEMs are used to examine veiled evolutionary questions about extinctions, locations of past refugia and migration pathways, or to propose...... the theoretical assumptions behind niche modelling and using inadequate methods for hindcasting CEMs may well entail a cascade of errors and naïve ecological and evolutionary inferences. We should also push integrative research lines linking macroecology, physiology, population biology, palaeontology...

  7. Predicting the current potential and future world wide distribution of the onion maggot, Delia antiqua using maximum entropy ecological niche modeling

    Science.gov (United States)

    Feng, Jinian

    2017-01-01

    Climate change will markedly impact biology, population ecology, and spatial distribution patterns of insect pests because of the influence of future greenhouse effects on insect development and population dynamics. Onion maggot, Delia antiqua, larvae are subterranean pests with limited mobility, that directly feed on bulbs of Allium sp. and render them completely unmarketable. Modeling the spatial distribution of such a widespread and damaging pest is crucial not only to identify current potentially suitable climactic areas but also to predict where the pest is likely to spread in the future so that appropriate monitoring and management programs can be developed. In this study, Maximum Entropy Niche Modeling was used to estimate the current potential distribution of D. antiqua and to predict the future distribution of this species in 2030, 2050, 2070 and 2080 by using emission scenario (A2) with 7 climate variables. The results of this study show that currently highly suitable habitats for D.antiqua occur throughout most of East Asia, some regions of North America, Western Europe, and Western Asian countries near the Caspian sea and Black Sea. In the future, we predict an even broader distribution of this pest spread more extensively throughout Asia, North America and Europe, particularly in most of European countries, Central regions of United States and much of East Asia. Our present day and future predictions can enhance strategic planning of agricultural organizations by identifying regions that will need to develop Integrated Pest Management programs to manage the onion maggot. The distribution forecasts will also help governments to optimize economic investments in management programs for this pest by identifying regions that are or will become less suitable for current and future infestations. PMID:28158259

  8. Phylogeography of Thlaspi arvense (Brassicaceae in China Inferred from Chloroplast and Nuclear DNA Sequences and Ecological Niche Modeling

    Directory of Open Access Journals (Sweden)

    Miao An

    2015-06-01

    Full Text Available Thlaspi arvense is a well-known annual farmland weed with worldwide distribution, which can be found from sea level to above 4000 m high on the Qinghai-Tibetan Plateau (QTP. In this paper, a phylogeographic history of T. arvense including 19 populations from China was inferred by using three chloroplast (cp DNA segments (trnL-trnF, rpl32-trnL and rps16 and one nuclear (n DNA segment (Fe-regulated transporter-like protein, ZIP. A total of 11 chloroplast haplotypes and six nuclear alleles were identified, and haplotypes unique to the QTP were recognized (C4, C5, C7 and N4. On the basis of molecular dating, haplotypes C4, C5 and C7 have separated from others around 1.58 Ma for cpDNA, which corresponds to the QTP uplift. In addition, this article suggests that the T. arvense populations in China are a mixture of diverged subpopulations as inferred by hT/vT test (hT ≤ vT, cpDNA and positive Tajima’s D values (1.87, 0.05 < p < 0.10 for cpDNA and 3.37, p < 0.01 for nDNA. Multimodality mismatch distribution curves and a relatively large shared area of suitable environmental conditions between the Last Glacial Maximum (LGM as well as the present time recognized by MaxEnt software reject the sudden expansion population model.

  9. The pitfalls of niche marketing.

    Science.gov (United States)

    Raynor, M E

    1992-01-01

    Corporate marketers have jumped on the micromarketing bandwagon, but many have discovered that the path to profits contains a number of potholes. This article details three companies' niche marketing mistakes; the author suggests how to avoid them.

  10. Exploring climate niches of ponderosa pine (Pinus ponderosa Douglas ex Lawson) haplotypes in the western United States: Implications for evolutionary history and conservation

    Science.gov (United States)

    Shinneman, Douglas; Means, Robert E.; Potter, Kevin M.; Hipkins, Valerie D.

    2016-01-01

    Ponderosa pine (Pinus ponderosa Douglas ex Lawson) occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. ponderosa) and Rocky Mountain (P. p. var. scopulorum) varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM), ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P. p. vars. ponderosa and scopulorum, respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated with

  11. Exploring Climate Niches of Ponderosa Pine (Pinus ponderosa Douglas ex Lawson Haplotypes in the Western United States: Implications for Evolutionary History and Conservation.

    Directory of Open Access Journals (Sweden)

    Douglas J Shinneman

    Full Text Available Ponderosa pine (Pinus ponderosa Douglas ex Lawson occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. ponderosa and Rocky Mountain (P. p. var. scopulorum varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM, ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P. p. vars. ponderosa and scopulorum, respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated

  12. Exploring Climate Niches of Ponderosa Pine (Pinus ponderosa Douglas ex Lawson) Haplotypes in the Western United States: Implications for Evolutionary History and Conservation.

    Science.gov (United States)

    Shinneman, Douglas J; Means, Robert E; Potter, Kevin M; Hipkins, Valerie D

    2016-01-01

    Ponderosa pine (Pinus ponderosa Douglas ex Lawson) occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. ponderosa) and Rocky Mountain (P. p. var. scopulorum) varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM), ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P. p. vars. ponderosa and scopulorum, respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated with discrete

  13. Profound climatic effects on two East Asian black-throated tits (Ave: Aegithalidae, revealed by ecological niche models and phylogeographic analysis.

    Directory of Open Access Journals (Sweden)

    Chuanyin Dai

    Full Text Available Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis-concinnus with the combined analysis of phylogeography and Ecological Niche Models (ENMs. We sequenced three mitochondrial DNA markers from 32 populations (203 individuals and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG, last glacial maximum (LGM and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis-concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory.

  14. Circum-Mediterranean phylogeography of a bat coupled with past environmental niche modeling: A new paradigm for the recolonization of Europe?

    Science.gov (United States)

    Bilgin, Raşit; Gürün, Kanat; Rebelo, Hugo; Puechmaille, Sebastien J; Maracı, Öncü; Presetnik, Primoz; Benda, Petr; Hulva, Pavel; Ibáñez, Carlos; Hamidovic, Daniela; Fressel, Norma; Horáček, Ivan; Karataş, Ayşegül; Karataş, Ahmet; Allegrini, Benjamin; Georgiakakis, Panagiotis; Gazaryan, Suren; Nagy, Zoltan L; Abi-Said, Mounir; Lučan, Radek K; Bartonička, Tomáš; Nicolaou, Haris; Scaravelli, Dino; Karapandža, Branko; Uhrin, Marcel; Paunović, Milan; Juste, Javier

    2016-06-01

    The isolation of populations in the Iberian, Italian and Balkan peninsulas during the ice ages define four main paradigms that explain much of the known distribution of intraspecific genetic diversity in Europe. In this study we investigated the phylogeography of a wide-spread bat species, the bent-winged bat, Miniopterus schreibersii around the Mediterranean basin and in the Caucasus. Environmental Niche Modeling (ENM) analysis was applied to predict both the current distribution of the species and its distribution during the last glacial maximum (LGM). The combination of genetics and ENM results suggest that the populations of M. schreibersii in Europe, the Caucasus and Anatolia went extinct during the LGM, and the refugium for the species was a relatively small area to the east of the Levantine Sea, corresponding to the Mediterranean coasts of present-day Syria, Lebanon, Israel, and northeastern and northwestern Egypt. Subsequently the species first repopulated Anatolia, diversified there, and afterwards expanded into the Caucasus, continental Europe and North Africa after the end of the LGM. The fossil record in Iberia and the ENM results indicate continuous presence of Miniopterus in this peninsula that most probably was related to the Maghrebian lineage during the LGM, which did not persist afterwards. Using our results combined with similar findings in previous studies, we propose a new paradigm explaining the general distribution of genetic diversity in Europe involving the recolonization of the continent, with the main contribution from refugial populations in Anatolia and the Middle East. The study shows how genetics and ENM approaches can complement each other in providing a more detailed picture of intraspecific evolution.

  15. A discrete stage-structured model of California newt population dynamics during a period of drought.

    Science.gov (United States)

    Jones, Marjorie T; Milligan, William R; Kats, Lee B; Vandergon, Thomas L; Honeycutt, Rodney L; Fisher, Robert N; Davis, Courtney L; Lucas, Timothy A

    2017-02-07

    We introduce a mathematical model for studying the population dynamics under drought of the California newt (Taricha torosa), a species of special concern in the state of California. Since 2012, California has experienced a record-setting drought, and multiple studies predict drought conditions currently underway will persist and even increase in severity. Recent declines and local extinctions of California newt populations in Santa Monica Mountain streams motivate our study of the impact of drought on newt population sizes. Although newts are terrestrial salamanders, they migrate to streams each spring to breed and lay eggs. Since egg and larval stages occur in water, a precipitation deficit due to drought conditions reduces the space for newt egg-laying and the necessary habitat for larval development. To mathematically forecast newt population dynamics, we develop a nonlinear system of discrete equations that includes demographic parameters such as survival rates for newt life stages and egg production, which depend on habitat availability and rainfall. We estimate these demographic parameters using 15 years of stream survey data collected from Cold Creek in Los Angeles County, California, and our model captures the observed decline of the parameterized Cold Creek newt population. Based upon data analysis, we predict how the number of available newt egg-laying sites varies with annual precipitation. Our model allows us to make predictions about how the length and severity of drought can affect the likelihood of persistence and the time to critical endangerment of a local newt population. We predict that sustained severe drought will critically endanger the newt population but that the newt population can rebound if a drought is sufficiently short.

  16. Learning and colonization of new niches: a first step toward speciation.

    Science.gov (United States)

    Beltman, Joost B; Haccou, Patsy; ten Cate, Carel

    2004-01-01

    Learning processes potentially play a role in speciation but are often ignored in speciation models. Learning may, for instance, play a role when a new niche is being colonized, because the learning of niche features may cause niche-specific assortative mating and a tendency to produce young in this niche. Several animal species learn about their environmental features that may be important in finding or attracting mates. We use a gene-culture coevolutionary model to look into the effect of such learning on the colonization of new niches and on the genetic divergence between groups using different niches, which are steps necessary in achieving speciation. We assume that density is regulated separately in each of the two niches and that the viability of an individual depends on its genotype as well as on which niche it exploits. Our results show that genetic adaptation to the new niche is enhanced by a high female fecundity and a low viability selection against heterozygotes. Furthermore, when initial colonization (without genetic adaptation) fails, genetic divergence is more difficult when the mating preference is stronger. In contrast, when colonization without genetic adaptation is successful, a stronger mating preference makes genetic divergence easier. An increase in the number of egg-laying mistakes by females can have a positive or negative effect on the success of genetic adaptation depending on other parameters. We show that genetic divergence can be prevented by a niche shift, which can occur only if viabilities in the two niches are asymmetrical.

  17. Evidence of climatic niche shift during biological invasion

    DEFF Research Database (Denmark)

    Broennimann, O.; Treier, Urs; Müller-Schärer, H.;

    2007-01-01

    Niche-based models calibrated in the native range by relating species observations to climatic variables are commonly used to predict the potential spatial extent of species' invasion. This climate matching approach relies on the assumption that invasive species conserve their climatic niche in t...... of introduction and establishment of newly or not-yet-introduced neophytes, but may not predict the full extent of invasions....

  18. Impacts of WRF Physics and Measurement Uncertainty on California Wintertime Model Wet Bias

    Energy Technology Data Exchange (ETDEWEB)

    Chin, H S; Caldwell, P M; Bader, D C

    2009-07-22

    The Weather and Research Forecast (WRF) model version 3.0.1 is used to explore California wintertime model wet bias. In this study, two wintertime storms are selected from each of four major types of large-scale conditions; Pineapple Express, El Nino, La Nina, and synoptic cyclones. We test the impacts of several model configurations on precipitation bias through comparison with three sets of gridded surface observations; one from the National Oceanographic and Atmospheric Administration, and two variations from the University of Washington (without and with long-term trend adjustment; UW1 and UW2, respectively). To simplify validation, California is divided into 4 regions (Coast, Central Valley, Mountains, and Southern California). Simulations are driven by North American Regional Reanalysis data to minimize large-scale forcing error. Control simulations are conducted with 12-km grid spacing (low resolution) but additional experiments are performed at 2-km (high) resolution to evaluate the robustness of microphysics and cumulus parameterizations to resolution changes. We find that the choice of validation dataset has a significant impact on the model wet bias, and the forecast skill of model precipitation depends strongly on geographic location and storm type. Simulations with right physics options agree better with UW1 observations. In 12-km resolution simulations, the Lin microphysics and the Kain-Fritsch cumulus scheme have better forecast skill in the coastal region while Goddard, Thompson, and Morrison microphysics, and the Grell-Devenyi cumulus scheme perform better in the rest of California. The effect of planetary boundary layer, soil-layer, and radiation physics on model precipitation is weaker than that of microphysics and cumulus processes for short- to medium-range low-resolution simulations. Comparison of 2-km and 12-km resolution runs suggests a need for improvement of cumulus schemes, and supports the use of microphysics schemes in coarser

  19. Niching method using clustering crowding

    Institute of Scientific and Technical Information of China (English)

    GUO Guan-qi; GUI Wei-hua; WU Min; YU Shou-yi

    2005-01-01

    This study analyzes drift phenomena of deterministic crowding and probabilistic crowding by using equivalence class model and expectation proportion equations. It is proved that the replacement errors of deterministic crowding cause the population converging to a single individual, thus resulting in premature stagnation or losing optional optima. And probabilistic crowding can maintain equilibrium multiple subpopulations as the population size is adequate large. An improved niching method using clustering crowding is proposed. By analyzing topology of fitness landscape using hill valley function and extending the search space for similarity analysis, clustering crowding determines the locality of search space more accurately, thus greatly decreasing replacement errors of crowding. The integration of deterministic and probabilistic replacement increases the capacity of both parallel local hill climbing and maintaining multiple subpopulations. The experimental results optimizing various multimodal functions show that,the performances of clustering crowding, such as the number of effective peaks maintained, average peak ratio and global optimum ratio are uniformly superior to those of the evolutionary algorithms using fitness sharing, simple deterministic crowding and probabilistic crowding.

  20. Niche conservatism and the future potential range of Epipactis helleborine (Orchidaceae.

    Directory of Open Access Journals (Sweden)

    Marta Kolanowska

    Full Text Available The aim of the present study was to evaluate the current distribution of suitable niches for the invasive orchid species, Epipactis helleborine, and to estimate the possibility of its further expansion. Moreover, niche modeling tools were used to explain its rapid expansion in North America and to test the niche conservatism of the species. The maximum entropy method was used to create models of the suitable niche distribution. A database of E. helleborine localities was prepared based on the examination of herbarium specimens, information from electronic databases as well as data gathered during field works. The differences between the niches occupied by native and invasive populations were evaluated using the niche overlap and niche identity test indexes. Moreover, the coverage of the most suitable habitats for the species was measured for three future scenarios as well as for the present time model. Populations of E. helleborine occupy North American west coast habitats very similar to those preferred by native, Eurasian populations, while the expansion in the east coast is related to the niche shift. The created models of suitable niche distribution indicate that the species does not realize its potential niche in the native range. The total surface of the habitats potentially available for E. helleborine will decrease in all climate change scenarios created for 2080.

  1. Crime Trend Prediction Using Regression Models for Salinas, California

    Science.gov (United States)

    2012-06-01

    supervision  Lack of positive adult male role models  Multi-generational gang families  Lack of effective teacher/ student attachments with at-risk...to many police departments adopting crime analysis techniques, finally concluding in the creation of the International Association of Crime Analysts...Model Goodness-of-fit for a Poisson model is measured using the residual deviance instead of R2 or the residual standard error used in linear

  2. Nearshore waves in southern California: hindcast, and modeled historical and 21st-century projected time series

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Abstract: This data release presents modeled time series of nearshore waves along the southern California coast, from Point Conception to the Mexican border,...

  3. Mammalian niche conservation through deep time.

    Directory of Open Access Journals (Sweden)

    Larisa R G DeSantis

    Full Text Available Climate change alters species distributions, causing plants and animals to move north or to higher elevations with current warming. Bioclimatic models predict species distributions based on extant realized niches and assume niche conservation. Here, we evaluate if proxies for niches (i.e., range areas are conserved at the family level through deep time, from the Eocene to the Pleistocene. We analyze the occurrence of all mammalian families in the continental USA, calculating range area, percent range area occupied, range area rank, and range polygon centroids during each epoch. Percent range area occupied significantly increases from the Oligocene to the Miocene and again from the Pliocene to the Pleistocene; however, mammalian families maintain statistical concordance between rank orders across time. Families with greater taxonomic diversity occupy a greater percent of available range area during each epoch and net changes in taxonomic diversity are significantly positively related to changes in percent range area occupied from the Eocene to the Pleistocene. Furthermore, gains and losses in generic and species diversity are remarkably consistent with ~2.3 species gained per generic increase. Centroids demonstrate southeastern shifts from the Eocene through the Pleistocene that may correspond to major environmental events and/or climate changes during the Cenozoic. These results demonstrate range conservation at the family level and support the idea that niche conservation at higher taxonomic levels operates over deep time and may be controlled by life history traits. Furthermore, families containing megafauna and/or terminal Pleistocene extinction victims do not incur significantly greater declines in range area rank than families containing only smaller taxa and/or only survivors, from the Pliocene to Pleistocene. Collectively, these data evince the resilience of families to climate and/or environmental change in deep time, the absence of

  4. 基于生态位模型的高标准基本农田建设适宜性评价%Suitability evaluation on high quality capital farmland consolidation based on niche-fitness model

    Institute of Scientific and Technical Information of China (English)

    赵素霞; 牛海鹏; 张捍卫; 张合兵; 张小虎

    2016-01-01

    It is China's significant strategic move to carry out rural land consolidation and construct high quality capital farmland on a large scale, which ensures stable yields despite drought or excessive rain. However, the construction project of high quality capital farmland is currently with the lack of scientific instruction in line with local conditions in respect of project site selection and design approach. An empirical research was conducted in Xinzheng City to study suitability evaluation and obstacle indicators of high quality capital farmland. Based on the theory of ecological niche and the construction target of high-quality capital farmland, this paper proposed the very concept of high quality capital farmland niche, and established the index system from the different aspects of natural resource endowment, infrastructure, sustainability of high quality capital farmland and its space stability. Thirteen indicators were selected during the evaluation. Then this paper built the niche-fitness evaluation model. Throughout the evaluation model as well as the matching degree between the actual niche and the first-rate niche, 4 levels were divided to pinpoint the niche of the high quality capital farmland in different regions. The farmland in the first level areas was high quality capital farmland; the farmland in the second level areas needed to be improved; the farmland in the third level needed to be comprehensively renovated; and the farmland in the fourth level was not appropriate for exploitation. This paper clarified the niche of the high quality capital farmland in different regions, took the first-rate niche as the sole criterion to establish the diagnosis model of obstacle indicators, analyzed the restricted degree and diversity of the obstacle indicators, clarified the priority and orientation on capital farmland construction in different regions, and sought countermeasures and valid paths. The results were as follows: 1) 14017.72 hm2 farmland was high

  5. Re-examining "temporal niche".

    Science.gov (United States)

    Smarr, Benjamin L; Schwartz, Michael D; Wotus, Cheryl; de la Iglesia, Horacio O

    2013-07-01

    The circadian system temporally organizes physiology and behavior throughout the 24-h day. At the core of this organization lies a network of multiple circadian oscillators located within the central nervous system as well as in virtually every peripheral organ. These oscillators define a 24-h temporal landscape of mutually interacting circadian rhythms that is known as the temporal niche of a species. This temporal niche is constituted by the collective phases of all biological rhythms emerging from this multi-oscillatory system. We review evidence showing that under different environmental conditions, this system can adopt different harmonic configurations. Thus, the classic chronobiological approach of searching for "the" circadian phase of an animal-typically by studying circadian rhythms of locomotor activity-represents a narrow look into the circadian system of an animal. We propose that the study of hormonal rhythms may lead to a more insightful assessment of a species' temporal niche.

  6. U.S. Coastal Relief Model - Southern California Version 2

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NGDC's U.S. Coastal Relief Model (CRM) provides a comprehensive view of the U.S. coastal zone integrating offshore bathymetry with land topography into a seamless...

  7. U.S. Coastal Relief Model - Southern California

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NGDC's U.S. Coastal Relief Model (CRM) provides the first comprehensive view of the U.S. coastal zone integrating offshore bathymetry with land topography into a...

  8. San Francisco Bay, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  9. Port San Luis, California Coastal Digital Elevation Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Geophysical Data Center (NGDC) is building high-resolution digital elevation models (DEMs) for select U.S. coastal regions. These integrated...

  10. Fire risk in San Diego County, California: A weighted Bayesian model approach

    Science.gov (United States)

    Kolden, Crystal A.; Weigel, Timothy J.

    2007-01-01

    Fire risk models are widely utilized to mitigate wildfire hazards, but models are often based on expert opinions of less understood fire-ignition and spread processes. In this study, we used an empirically derived weights-of-evidence model to assess what factors produce fire ignitions east of San Diego, California. We created and validated a dynamic model of fire-ignition risk based on land characteristics and existing fire-ignition history data, and predicted ignition risk for a future urbanization scenario. We then combined our empirical ignition-risk model with a fuzzy fire behavior-risk model developed by wildfire experts to create a hybrid model of overall fire risk. We found that roads influence fire ignitions and that future growth will increase risk in new rural development areas. We conclude that empirically derived risk models and hybrid models offer an alternative method to assess current and future fire risk based on management actions.

  11. Multivariate Statistical Models for Predicting Sediment Yields from Southern California Watersheds

    Science.gov (United States)

    Gartner, Joseph E.; Cannon, Susan H.; Helsel, Dennis R.; Bandurraga, Mark

    2009-01-01

    Debris-retention basins in Southern California are frequently used to protect communities and infrastructure from the hazards of flooding and debris flow. Empirical models that predict sediment yields are used to determine the size of the basins. Such models have been developed using analyses of records of the amount of material removed from debris retention basins, associated rainfall amounts, measures of watershed characteristics, and wildfire extent and history. In this study we used multiple linear regression methods to develop two updated empirical models to predict sediment yields for watersheds located in Southern California. The models are based on both new and existing measures of volume of sediment removed from debris retention basins, measures of watershed morphology, and characterization of burn severity distributions for watersheds located in Ventura, Los Angeles, and San Bernardino Counties. The first model presented reflects conditions in watersheds located throughout the Transverse Ranges of Southern California and is based on volumes of sediment measured following single storm events with known rainfall conditions. The second model presented is specific to conditions in Ventura County watersheds and was developed using volumes of sediment measured following multiple storm events. To relate sediment volumes to triggering storm rainfall, a rainfall threshold was developed to identify storms likely to have caused sediment deposition. A measured volume of sediment deposited by numerous storms was parsed among the threshold-exceeding storms based on relative storm rainfall totals. The predictive strength of the two models developed here, and of previously-published models, was evaluated using a test dataset consisting of 65 volumes of sediment yields measured in Southern California. The evaluation indicated that the model developed using information from single storm events in the Transverse Ranges best predicted sediment yields for watersheds in San

  12. Water-resources optimization model for Santa Barbara, California

    Science.gov (United States)

    Nishikawa, T.

    1998-01-01

    A simulation-optimization model has been developed for the optimal management of the city of Santa Barbara's water resources during a drought. The model, which links groundwater simulation with linear programming, has a planning horizon of 5 years. The objective is to minimize the cost of water supply subject to: water demand constraints, hydraulic head constraints to control seawater intrusion, and water capacity constraints. The decision variables are montly water deliveries from surface water and groundwater. The state variables are hydraulic heads. The drought of 1947-51 is the city's worst drought on record, and simulated surface-water supplies for this period were used as a basis for testing optimal management of current water resources under drought conditions. The simulation-optimization model was applied using three reservoir operation rules. In addition, the model's sensitivity to demand, carry over [the storage of water in one year for use in the later year(s)], head constraints, and capacity constraints was tested.

  13. Global climate niche estimates for bioenergy crops and invasive species of agronomic origin: potential problems and opportunities.

    Directory of Open Access Journals (Sweden)

    Jacob N Barney

    Full Text Available The global push towards a more biomass-based energy sector is ramping up efforts to adopt regionally appropriate high-yielding crops. As potential bioenergy crops are being moved around the world an assessment of the climatic suitability would be a prudent first step in identifying suitable areas of productivity and risk. Additionally, this assessment also provides a necessary step in evaluating the invasive potential of bioenergy crops, which present a possible negative externality to the bioeconomy. Therefore, we provide the first global climate niche assessment for the major graminaceous (9, herbaceous (3, and woody (4 bioenergy crops. Additionally, we contrast these with climate niche assessments for North American invasive species that were originally introduced for agronomic purposes as examples of well-intentioned introductions gone awry. With few exceptions (e.g., Saccharum officinarum, Pennisetum purpureum, the bioenergy crops exhibit broad climatic tolerance, which allows tremendous flexibility in choosing crops, especially in areas with high summer rainfall and long growing seasons (e.g., southeastern US, Amazon Basin, eastern Australia. Unsurprisingly, the invasive species of agronomic origin have very similar global climate niche profiles as the proposed bioenergy crops, also demonstrating broad climatic tolerance. The ecoregional evaluation of bioenergy crops and known invasive species demonstrates tremendous overlap at both high (EI≥30 and moderate (EI≥20 climate suitability. The southern and western US ecoregions support the greatest number of invasive species of agronomic origin, especially the Southeastern USA Plains, Mixed Woods Plains, and Mediterranean California. Many regions of the world have a suitable climate for several bioenergy crops allowing selection of agro-ecoregionally appropriate crops. This model knowingly ignores the complex biotic interactions and edaphic conditions, but provides a robust assessment of

  14. Modeling the Dynamic Water Resource Needs of California's Coastal Watersheds

    Science.gov (United States)

    Alford, C.

    2009-12-01

    Many watersheds face formidable water supply challenges when it comes to managing water availability to meet diverse water supply and ecosystem management objectives. California’s central coast watersheds are no exception, and both the scarcity of water resources during drier water years and mandates to establish minimum instream flows for salmon habitat have prompted interests in reassessing water management strategies for several of these watersheds. Conventional supply-oriented hydrologic models, however, are not adequate to fully investigate and describe the reciprocal implications of surface water demands for human use and the maintenance of instream flows for salmon habitat that vary both temporally and spatially within a watershed. In an effort to address this issue I developed a coastal watershed management model based on the San Gregorio watershed utilizing the Water Evaluation and Planning (WEAP) system, which permits demand-side prioritization at a time step interval and spatial resolution that captures functional supply and demand relationships. Physiographic input data such as soil type, land cover, elevation, habitat, and water demand sites were extrapolated at a sub-basin level in a GIS. Time-series climate data were collected and processed utilizing the Berkeley Water Center Data Cube at daily time steps for the period 1952 through September 2009. Recent synoptic flow measurements taken at seven tributary sites during the 2009 water year, water depth measured by pressure transducers at six sites within the watershed from September 2005 through September 2009, and daily gauge records from temporary gauges installed in 1981 were used to assess the hydrologic patterns of sub-basins and supplement historic USGS gauge flow records. Empirical functions were used to describe evapotranspiration, surface runoff, sub-surface runoff, and deep percolation. Initial model simulations carried out under both dry and wet water year scenarios were able to capture

  15. Modeling Nonresident Seabird Foraging Distributions to Inform Ocean Zoning in Central California.

    Science.gov (United States)

    Studwell, Anna J; Hines, Ellen; Elliott, Meredith L; Howar, Julie; Holzman, Barbara; Nur, Nadav; Jahncke, Jaime

    2017-01-01

    Seabird aggregations at sea have been shown to be associated with concentrations of prey. Previous research identified Central California as a highly used foraging area for seabirds, with locally breeding seabirds foraging close to their colonies on Southeast Farallon Island. Herein, we focus on nonresident (i.e. non-locally breeding) seabird species off of Central California. We hypothesized that high-use foraging areas for nonresident seabirds would be influenced by oceanographic and bathymetric factors and that spatial and temporal distributions would be similar within planktivorous and generalist foraging guilds but would differ between them. With data collected by the Applied California Current Ecosystem Studies (ACCESS) partnership during cruises between April and October from 2004-2013, we developed generalized linear models to identify high-use foraging areas for each of six nonresident seabird species. The four generalist species are Phoebastria nigripes (black-footed albatross), Ardenna griseus (sooty shearwater), Ardenna creatopus (pink-footed shearwater), and Fulmarus glacialis (northern fulmar). The two planktivorous species are Phalaropus lobatus (red-necked phalarope) and Phalaropus fulicarius (red phalarope). Sea surface temperature was significant for generalist species and sea surface salinity was important for planktivorous species. The distance to the 200-m isobath was significant in five of six models, Pacific Decadal Oscillation with a 3-month lag in four models, and sea surface fluorescence, the distance to Cordell Bank, and depth in three models. We did not find statistically significant differences between distributions of individual seabird species within a foraging guild or between guilds, with the exception of the sooty shearwater. Model results for a multi-use seabird foraging area highlighted the continental shelf break, particularly within the vicinity of Cordell Bank, as the highest use areas as did Marxan prioritization. Our

  16. Using seabird habitat modeling to inform marine spatial planning in central California's National Marine Sanctuaries.

    Science.gov (United States)

    McGowan, Jennifer; Hines, Ellen; Elliott, Meredith; Howar, Julie; Dransfield, Andrea; Nur, Nadav; Jahncke, Jaime

    2013-01-01

    Understanding seabird habitat preferences is critical to future wildlife conservation and threat mitigation in California. The objective of this study was to investigate drivers of seabird habitat selection within the Gulf of the Farallones and Cordell Bank National Marine Sanctuaries to identify areas for targeted conservation planning. We used seabird abundance data collected by the Applied California Current Ecosystem Studies Program (ACCESS) from 2004-2011. We used zero-inflated negative binomial regression to model species abundance and distribution as a function of near surface ocean water properties, distances to geographic features and oceanographic climate indices to identify patterns in foraging habitat selection. We evaluated seasonal, inter-annual and species-specific variability of at-sea distributions for the five most abundant seabirds nesting on the Farallon Islands: western gull (Larus occidentalis), common murre (Uria aalge), Cassin's auklet (Ptychorampus aleuticus), rhinoceros auklet (Cerorhinca monocerata) and Brandt's cormorant (Phalacrocorax penicillatus). The waters in the vicinity of Cordell Bank and the continental shelf east of the Farallon Islands emerged as persistent and highly selected foraging areas across all species. Further, we conducted a spatial prioritization exercise to optimize seabird conservation areas with and without considering impacts of current human activities. We explored three conservation scenarios where 10, 30 and 50 percent of highly selected, species-specific foraging areas would be conserved. We compared and contrasted results in relation to existing marine protected areas (MPAs) and the future alternative energy footprint identified by the California Ocean Uses Atlas. Our results show that the majority of highly selected seabird habitat lies outside of state MPAs where threats from shipping, oil spills, and offshore energy development remain. This analysis accentuates the need for innovative marine spatial

  17. Using seabird habitat modeling to inform marine spatial planning in central California's National Marine Sanctuaries.

    Directory of Open Access Journals (Sweden)

    Jennifer McGowan

    Full Text Available Understanding seabird habitat preferences is critical to future wildlife conservation and threat mitigation in California. The objective of this study was to investigate drivers of seabird habitat selection within the Gulf of the Farallones and Cordell Bank National Marine Sanctuaries to identify areas for targeted conservation planning. We used seabird abundance data collected by the Applied California Current Ecosystem Studies Program (ACCESS from 2004-2011. We used zero-inflated negative binomial regression to model species abundance and distribution as a function of near surface ocean water properties, distances to geographic features and oceanographic climate indices to identify patterns in foraging habitat selection. We evaluated seasonal, inter-annual and species-specific variability of at-sea distributions for the five most abundant seabirds nesting on the Farallon Islands: western gull (Larus occidentalis, common murre (Uria aalge, Cassin's auklet (Ptychorampus aleuticus, rhinoceros auklet (Cerorhinca monocerata and Brandt's cormorant (Phalacrocorax penicillatus. The waters in the vicinity of Cordell Bank and the continental shelf east of the Farallon Islands emerged as persistent and highly selected foraging areas across all species. Further, we conducted a spatial prioritization exercise to optimize seabird conservation areas with and without considering impacts of current human activities. We explored three conservation scenarios where 10, 30 and 50 percent of highly selected, species-specific foraging areas would be conserved. We compared and contrasted results in relation to existing marine protected areas (MPAs and the future alternative energy footprint identified by the California Ocean Uses Atlas. Our results show that the majority of highly selected seabird habitat lies outside of state MPAs where threats from shipping, oil spills, and offshore energy development remain. This analysis accentuates the need for innovative marine

  18. Tectonoestratigraphic and Thermal Models of the Tiburon and Wagner Basins, northern Gulf of California Rift System

    Science.gov (United States)

    Contreras, J.; Ramirez Zerpa, N. A.; Negrete-Aranda, R.

    2014-12-01

    The northern Gulf of California Rift System consist sofa series faults that accommodate both normal and strike-slip motion. The faults formed a series of half-greens filled with more than 7 km of siliciclastic suc­cessions. Here, we present tectonostratigraphic and heat flow models for the Tiburón basin, in the southern part of the system, and the Wag­ner basin in the north. The models are constrained by two-dimensional seis­mic lines and by two deep boreholes drilled by PEMEX­-PEP. Analysis of the seismic lines and models' results show that: (i) subsidence of the basins is controlled by high-angle normal faults and by flow of the lower crust, (ii) basins share a common history, and (iii) there are significant differences in the way brittle strain was partitioned in the basins, a feature frequently observed in rift basins. On one hand, the bounding faults of the Tiburón basin have a nested geometry and became active following a west-to-east sequence of activation. The Tiburon half-graben was formed by two pulses of fault activity. One took place during the protogulf extensional phase in the Miocene and the other during the opening of Gulf of California in the Pleistocene. On the other hand, the Wagner basin is the result of two fault generations. During the late-to middle Miocene, the west-dipping Cerro Prieto and San Felipe faults formed a domino array. Then, during the Pleistocene the Consag and Wagner faults dissected the hanging-wall of the Cerro Prieto fault forming the modern Wagner basin. Thermal modeling of the deep borehole temperatures suggests that the heat flow in these basins in the order of 110 mW/m2 which is in agreement with superficial heat flow measurements in the northern Gulf of California Rift System.

  19. Photochemical modeling in California with two chemical mechanisms: model intercomparison and response to emission reductions.

    Science.gov (United States)

    Cai, Chenxia; Kelly, James T; Avise, Jeremy C; Kaduwela, Ajith P; Stockwell, William R

    2011-05-01

    An updated version of the Statewide Air Pollution Research Center (SAPRC) chemical mechanism (SAPRC07C) was implemented into the Community Multiscale Air Quality (CMAQ) version 4.6. CMAQ simulations using SAPRC07C and the previously released version, SAPRC99, were performed and compared for an episode during July-August, 2000. Ozone (O3) predictions of the SAPRC07C simulation are generally lower than those of the SAPRC99 simulation in the key areas of central and southern California, especially in areas where modeled concentrations are greater than the federal 8-hr O3 standard of 75 parts per billion (ppb) and/or when the volatile organic compound (VOC)/nitrogen oxides (NOx) ratio is less than 13. The relative changes of ozone production efficiency (OPE) against the VOC/NOx ratio at 46 sites indicate that the OPE is reduced in SAPRC07C compared with SAPRC99 at most sites by as much as approximately 22%. The SAPRC99 and SAPRC07C mechanisms respond similarly to 20% reductions in anthropogenic VOC emissions. The response of the mechanisms to 20% NOx emissions reductions can be grouped into three cases. In case 1, in which both mechanisms show a decrease in daily maximum 8-hr O3 concentration with decreasing NOx emissions, the O3 decrease in SAPRC07C is smaller. In case 2, in which both mechanisms show an increase in O3 with decreasing NOx emissions, the O3 increase is larger in SAPRC07C. In case 3, SAPRC07C simulates an increase in O3 in response to reduced NOx emissions whereas SAPRC99 simulates a decrease in O3 for the same region. As a result, the areas where NOx controls would be disbeneficial are spatially expanded in SAPRC07C. Although the results presented here are valuable for understanding differences in predictions and model response for SAPRC99 and SAPRC07C, the study did not evaluate the impact of mechanism differences in the context of the U.S. Environmental Protection Agency's guidance for using numerical models in demonstrating air quality attainment

  20. Probabilistic Modeling for Risk Assessment of California Ground Water Contamination by Pesticides

    Science.gov (United States)

    Clayton, M.; Troiano, J.; Spurlock, F.

    2007-12-01

    The California Department of Pesticide Regulation (DPR) is responsible for the registration of pesticides in California. DPR's Environmental Monitoring Branch evaluates the potential for pesticide active ingredients to move to ground water under legal agricultural use conditions. Previous evaluations were primarily based on threshold values for specific persistence and mobility properties of pesticides as prescribed in the California Pesticide Contamination Prevention Act of 1985. Two limitations identified with that process were the univariate nature where interactions of the properties were not accounted for, and the inability to accommodate multiple values of a physical-chemical property. We addressed these limitations by developing a probabilistic modeling method based on prediction of potential well water concentrations. A mechanistic pesticide transport model, LEACHM, is used to simulate sorption, degradation and transport of a candidate pesticide through the root zone. A second empirical model component then simulates pesticide degradation and transport through the vadose zone to a receiving ground water aquifer. Finally, degradation during transport in the aquifer to the well screen is included in calculating final potential well concentrations. Using Monte Carlo techniques, numerous LEACHM simulations are conducted using random samples of the organic carbon normalized soil adsorption coefficients (Koc) and soil dissipation half-life values derived from terrestrial field dissipation (TFD) studies. Koc and TFD values are obtained from gamma distributions fitted to pooled data from agricultural-use pesticides detected in California ground water: atrazine, simazine, diuron, bromacil, hexazinone, and norflurazon. The distribution of predicted well water concentrations for these pesticides is in good agreement with concentrations measured in domestic wells in coarse, leaching vulnerable soils of Fresno and Tulure Counties. The leaching potential of a new

  1. A Seamless, High-Resolution, Coastal Digital Elevation Model (DEM) for Southern California

    Science.gov (United States)

    Barnard, Patrick L.; Hoover, Daniel

    2010-01-01

    A seamless, 3-meter digital elevation model (DEM) was constructed for the entire Southern California coastal zone, extending 473 km from Point Conception to the Mexican border. The goal was to integrate the most recent, high-resolution datasets available (for example, Light Detection and Ranging (Lidar) topography, multibeam and single beam sonar bathymetry, and Interferometric Synthetic Aperture Radar (IfSAR) topography) into a continuous surface from at least the 20-m isobath to the 20-m elevation contour. This dataset was produced to provide critical boundary conditions (bathymetry and topography) for a modeling effort designed to predict the impacts of severe winter storms on the Southern California coast (Barnard and others, 2009). The hazards model, run in real-time or with prescribed scenarios, incorporates atmospheric information (wind and pressure fields) with a suite of state-of-the-art physical process models (tide, surge, and wave) to enable detailed prediction of water levels, run-up, wave heights, and currents. Research-grade predictions of coastal flooding, inundation, erosion, and cliff failure are also included. The DEM was constructed to define the general shape of nearshore, beach and cliff surfaces as accurately as possible, with less emphasis on the detailed variations in elevation inland of the coast and on bathymetry inside harbors. As a result this DEM should not be used for navigation purposes.

  2. Spatially explicit West Nile virus risk modeling in Santa Clara County, California.

    Science.gov (United States)

    Konrad, Sarah K; Miller, Scott N; Reeves, Will K; Tietze, Noor S

    2009-06-01

    A geographic information system model designed to identify regions at risk for West Nile virus (WNV) transmission was calibrated and tested with data collected in Santa Clara County, California. American Crows that died from WNV infection in 2005 provided spatial and temporal ground truth. When the model was run with parameters based on Culex tarsalis infected with the NY99 genotype of the virus, it underestimated WNV occurrence in Santa Clara Co. The parameters were calibrated to fit the field data by reducing the number of degree-days necessary to reach the mosquito's extrinsic incubation period from 109 to 76. The calibration raised model efficiency from 61% to 92% accuracy, and the model performed well the following year in Santa Clara Co.

  3. Beyond carbon and nitrogen: guidelines for estimating three-dimensional isotopic niche space.

    Science.gov (United States)

    Rossman, Sam; Ostrom, Peggy H; Gordon, Forrest; Zipkin, Elise F

    2016-04-01

    Isotopic niche has typically been characterized through carbon and nitrogen ratios and most modeling approaches are limited to two dimensions. Yet, other stable isotopes can provide additional power to resolve questions associated with foraging, migration, dispersal and variations in resource use. The ellipse niche model was recently generalized to n-dimensions. We present an analogous methodology which incorporates variation across three stable dimensions to estimate the significant features of a population's isotopic niche space including: 1) niche volume (referred to as standard ellipsoid volume, SEV), 2) relative centroid location (CL), 3) shape and 4) area of overlap between multiple ellipsoids and 5) distance between two CLs. We conducted a simulation study showing the accuracy and precision of three dimensional niche models across a range of values. Importantly, the model correctly identifies differences in SEV and CL among populations, even with small sample sizes and in cases where the absolute values cannot precisely be recovered. We use these results to provide guidelines for sample size in conducting multivariate isotopic niche modeling. We demonstrate the utility of our approach with a case study of three bottlenose dolphin populations which appear to possess largely overlapping niches when analyzed with only carbon and nitrogen isotopes. Upon inclusion of sulfur, we see that the three dolphin ecotypes are in fact segregated on the basis of salinity and find the stable isotope niche of inshore bottlenose dolphins significantly larger than coastal and offshore populations.

  4. Step back! Niche dynamics in cave-dwelling predators

    Science.gov (United States)

    Mammola, Stefano; Piano, Elena; Isaia, Marco

    2016-08-01

    The geometry of the Hutchinson's hypervolume derives from multiple selective pressures defined, on one hand, by the physiological tolerance of the species, and on the other, by intra- and interspecific competition. The quantification of these evolutionary forces is essential for the understanding of the coexistence of predators in light of competitive exclusion dynamics. We address this topic by investigating the ecological niche of two medium-sized troglophile spiders (Meta menardi and Pimoa graphitica). Over one year, we surveyed several populations in four subterranean sites in the Western Italian Alps, monitoring monthly their spatial and temporal dynamics and the associated physical and ecological variables. We assessed competition between the two species by means of multi regression techniques and by evaluating the intersection between their multidimensional hypervolumes. We detected a remarkable overlap between the microclimatic and trophic niche of M. menardi and P. graphitica, however, the former -being larger in size- resulted the best competitor in proximity of the cave entrance, causing the latter to readjust its spatial niche towards the inner part, where prey availability is scarcer ("step back effect"). In parallel to the slight variations in the subterranean microclimatic condition, the niche of the two species was also found to be seasonal dependent, varying over the year. With this work, we aim at providing new insights about the relationships among predators, demonstrating that energy-poor environments such as caves maintain the potential for diversification of predators via niche differentiation and serve as useful models for theoretical ecological studies.

  5. Analyzing Source Apportioned Methane in Northern California During DISCOVER-AQ-CA Using Airborne Measurements and Model Simulations

    Science.gov (United States)

    Johnson, Matthew S.

    2014-01-01

    This study analyzes source apportioned methane (CH4) emissions and atmospheric concentrations in northern California during the Discover-AQ-CA field campaign using airborne measurement data and model simulations. Source apportioned CH4 emissions from the Emissions Database for Global Atmospheric Research (EDGAR) version 4.2 were applied in the 3-D chemical transport model GEOS-Chem and analyzed using airborne measurements taken as part of the Alpha Jet Atmospheric eXperiment over the San Francisco Bay Area (SFBA) and northern San Joaquin Valley (SJV). During the time period of the Discover-AQ-CA field campaign EDGAR inventory CH4 emissions were 5.30 Gg/day (Gg 1.0 109 grams) (equating to 1.9 103 Gg/yr) for all of California. According to EDGAR, the SFBA and northern SJV region contributes 30 of total emissions from California. Source apportionment analysis during this study shows that CH4 concentrations over this area of northern California are largely influenced by global emissions from wetlands and local/global emissions from gas and oil production and distribution, waste treatment processes, and livestock management. Model simulations, using EDGAR emissions, suggest that the model under-estimates CH4 concentrations in northern California (average normalized mean bias (NMB) -5 and linear regression slope 0.25). The largest negative biases in the model were calculated on days when hot spots of local emission sources were measured and atmospheric CH4 concentrations reached values 3.0 parts per million (model NMB -10). Sensitivity emission studies conducted during this research suggest that local emissions of CH4 from livestock management processes are likely the primary source of the negative model bias. These results indicate that a variety, and larger quantity, of measurement data needs to be obtained and additional research is necessary to better quantify source apportioned CH4 emissions in California and further the understanding of the physical processes

  6. Regional three-dimensional seismic velocity model of the crust and uppermost mantle of northern California

    Science.gov (United States)

    Thurber, C.; Zhang, H.; Brocher, T.; Langenheim, V.

    2009-01-01

    We present a three-dimensional (3D) tomographic model of the P wave velocity (Vp) structure of northern California. We employed a regional-scale double-difference tomography algorithm that incorporates a finite-difference travel time calculator and spatial smoothing constraints. Arrival times from earthquakes and travel times from controlled-source explosions, recorded at network and/or temporary stations, were inverted for Vp on a 3D grid with horizontal node spacing of 10 to 20 km and vertical node spacing of 3 to 8 km. Our model provides an unprecedented, comprehensive view of the regional-scale structure of northern California, putting many previously identified features into a broader regional context and improving the resolution of a number of them and revealing a number of new features, especially in the middle and lower crust, that have never before been reported. Examples of the former include the complex subducting Gorda slab, a steep, deeply penetrating fault beneath the Sacramento River Delta, crustal low-velocity zones beneath Geysers-Clear Lake and Long Valley, and the high-velocity ophiolite body underlying the Great Valley. Examples of the latter include mid-crustal low-velocity zones beneath Mount Shasta and north of Lake Tahoe. Copyright 2009 by the American Geophysical Union.

  7. Integrated Modeling of Drought-Impacted Areas using Remote Sensing and Microenvironmental Data in California

    Science.gov (United States)

    Rao, M.; Silber-coats, Z.; Lawrence, F.

    2015-12-01

    California's ongoing drought condition shriveled not just the agricultural sector, but also the natural resources sector including forestry, wildlife, and fisheries. As future predictions of drought and fire severity become more real in California, there is an increased awareness to pursue innovative and cost-effective solutions that are based on silvicultural treatments and controlled burns to improve forest health and reduce the risk of high-severity wildfires. The main goal of this study is to develop a GIS map of the drought-impacted region of northern and central California using remote sensing data for the summer period of 2014. Specifically, Landsat/NAIP imagery will be analyzed using a combination of object-oriented classification and spectral indices such as the Modified Perpendicular Drought Index (MPDI). This spectral index basically scales the line perpendicular to the soil line defined in the Red-NIR feature space in conjunction with added information about vegetative fraction derived using NDVI. The resulting output will be correlated with USGS-produced estimates of climatic water deficit (CWD) data to characterize the severity of the drought. The CWD is simulated based on hydrological tool, Basin Characterization Model (BCM) that ingests historical climate data in conjunction with soils, topography, and geological data to predict other monthly hydrological outputs including runoff, recharge, and snowpack. In addition to field data, data collected by state agencies including USFS, calforests.org will be used in the classification and accuracy assessment procedures. Visual assessment using high-resolution imagery such as NAIP will be used to further refine the spatial maps. The drought severity maps produced will greatly facilitate site-specific planning efforts aimed at implementing resource management decisions.

  8. Low-flow transport models for conservative and sorbed solutes; Uvas Creek, near Morgan Hill, California

    Science.gov (United States)

    Jackman, A.P.; Walters, R.A.; Kennedy, V.C.

    1984-01-01

    Models describing low-flow transport of conservative (nonreactive) and reactive solutes, which adsorb on the streambed, are developed and tested. Temporary storage within the bed plays an important role in solute movement. Three different models of bed-storage processes are developed for conservative solutes. One model assumes the bed is a well-mixed, nondiffusing, nonreacting zone. Solute flux into the bed is then proportional to the difference between stream and bed-solute concentrations. A second model assumes that solute is transported within the bed by a vertical diffusion process. The bed-solute concentration, which matches the stream concentration at the interface, varies with depth in the bed according to Fick 's law. A third model assumes convection in the downstream direction occurs in certain parts of the bed, while the mechanism of the first model functions elsewhere. Storage of absorbing species is assumed to occur by equilibrium adsorption within streambed particles. Uptake rate is described by an intraparticle diffusion process. Model equations were solved using finite element numerical methods. Models were calibrated using data from a 24-hour injection of conservative chloride and adsorptive Sr ions at Uvas Creek near Morgan Hill, California. All models predict well except for some overestimation by the adsorption model during dieaway. (USGS)

  9. Phylogenetic conservatism of environmental niches in mammals.

    Science.gov (United States)

    Cooper, Natalie; Freckleton, Rob P; Jetz, Walter

    2011-08-01

    Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter, σ(2), to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.

  10. Reconstructing ecological niches and geographic distributions of caribou ( Rangifer tarandus) and red deer ( Cervus elaphus) during the Last Glacial Maximum

    Science.gov (United States)

    Banks, William E.; d'Errico, Francesco; Peterson, A. Townsend; Kageyama, Masa; Colombeau, Guillaume

    2008-12-01

    A variety of approaches have been used to reconstruct glacial distributions of species, identify their environmental characteristics, and understand their influence on subsequent population expansions. Traditional methods, however, provide only rough estimates of past distributions, and are often unable to identify the ecological and geographic processes that shaped them. Recently, ecological niche modeling (ENM) methodologies have been applied to these questions in an effort to overcome such limitations. We apply ENM to the European faunal record of the Last Glacial Maximum (LGM) to reconstruct ecological niches and potential ranges for caribou ( Rangifer tarandus) and red deer ( Cervus elaphus), and evaluate whether their LGM distributions resulted from tracking the geographic footprint of their ecological niches (niche conservatism) or if ecological niche shifts between the LGM and present might be implicated. Results indicate that the LGM geographic ranges of both species represent distributions characterized by niche conservatism, expressed through geographic contraction of the geographic footprints of their respective ecological niches.

  11. Construction of 3-D geologic framework and textural models for Cuyama Valley groundwater basin, California

    Science.gov (United States)

    Sweetkind, Donald S.; Faunt, Claudia C.; Hanson, Randall T.

    2013-01-01

    Groundwater is the sole source of water supply in Cuyama Valley, a rural agricultural area in Santa Barbara County, California, in the southeasternmost part of the Coast Ranges of California. Continued groundwater withdrawals and associated water-resource management concerns have prompted an evaluation of the hydrogeology and water availability for the Cuyama Valley groundwater basin by the U.S. Geological Survey, in cooperation with the Water Agency Division of the Santa Barbara County Department of Public Works. As a part of the overall groundwater evaluation, this report documents the construction of a digital three-dimensional geologic framework model of the groundwater basin suitable for use within a numerical hydrologic-flow model. The report also includes an analysis of the spatial variability of lithology and grain size, which forms the geologic basis for estimating aquifer hydraulic properties. The geologic framework was constructed as a digital representation of the interpreted geometry and thickness of the principal stratigraphic units within the Cuyama Valley groundwater basin, which include younger alluvium, older alluvium, and the Morales Formation, and underlying consolidated bedrock. The framework model was constructed by creating gridded surfaces representing the altitude of the top of each stratigraphic unit from various input data, including lithologic and electric logs from oil and gas wells and water wells, cross sections, and geologic maps. Sediment grain-size data were analyzed in both two and three dimensions to help define textural variations in the Cuyama Valley groundwater basin and identify areas with similar geologic materials that potentially have fairly uniform hydraulic properties. Sediment grain size was used to construct three-dimensional textural models that employed simple interpolation between drill holes and two-dimensional textural models for each stratigraphic unit that incorporated spatial structure of the textural data.

  12. Climatic niche evolution in New World monkeys (Platyrrhini.

    Directory of Open Access Journals (Sweden)

    Andressa Duran

    Full Text Available Despite considerable interest in recent years on species distribution modeling and phylogenetic niche conservatism, little is known about the way in which climatic niches change over evolutionary time. This knowledge is of major importance to understand the mechanisms underlying limits of species distributions, as well as to infer how different lineages might be affected by anthropogenic climate change. In this study we investigate the tempo and mode climatic niche evolution in New World monkeys (Platyrrhini. Climatic conditions found throughout the distribution of 140 primate species were investigated using a principal component analysis, which indicated that mean temperature (particularly during the winter is the most important climatic correlate of platyrrhine geographical distributions, accounting for nearly half of the interspecific variation in climatic niches. The effects of precipitation were associated with the second principal component, particularly with respect to the dry season. When models of trait evolution were fit to scores on each of the principal component axes, significant phylogenetic signal was detected for PC1 scores, but not for PC2 scores. Interestingly, although all platyrrhine families occupied comparable regions of climatic space, some aotid species such as Aotus lemurinus, A. jorgehernandezi, and A. miconax show highly distinctive climatic niches associated with drier conditions (high PC2 scores. This shift might have been made possible by their nocturnal habits, which could serve as an exaptation that allow them to be less constrained by humidity during the night. These results underscore the usefulness of investigating explicitly the tempo and mode of climatic niche evolution and its role in determining species distributions.

  13. Climatic niche evolution in New World monkeys (Platyrrhini).

    Science.gov (United States)

    Duran, Andressa; Meyer, Andreas L S; Pie, Marcio R

    2013-01-01

    Despite considerable interest in recent years on species distribution modeling and phylogenetic niche conservatism, little is known about the way in which climatic niches change over evolutionary time. This knowledge is of major importance to understand the mechanisms underlying limits of species distributions, as well as to infer how different lineages might be affected by anthropogenic climate change. In this study we investigate the tempo and mode climatic niche evolution in New World monkeys (Platyrrhini). Climatic conditions found throughout the distribution of 140 primate species were investigated using a principal component analysis, which indicated that mean temperature (particularly during the winter) is the most important climatic correlate of platyrrhine geographical distributions, accounting for nearly half of the interspecific variation in climatic niches. The effects of precipitation were associated with the second principal component, particularly with respect to the dry season. When models of trait evolution were fit to scores on each of the principal component axes, significant phylogenetic signal was detected for PC1 scores, but not for PC2 scores. Interestingly, although all platyrrhine families occupied comparable regions of climatic space, some aotid species such as Aotus lemurinus, A. jorgehernandezi, and A. miconax show highly distinctive climatic niches associated with drier conditions (high PC2 scores). This shift might have been made possible by their nocturnal habits, which could serve as an exaptation that allow them to be less constrained by humidity during the night. These results underscore the usefulness of investigating explicitly the tempo and mode of climatic niche evolution and its role in determining species distributions.

  14. Results of the Regional Earthquake Likelihood Models (RELM) test of earthquake forecasts in California.

    Science.gov (United States)

    Lee, Ya-Ting; Turcotte, Donald L; Holliday, James R; Sachs, Michael K; Rundle, John B; Chen, Chien-Chih; Tiampo, Kristy F

    2011-10-04

    The Regional Earthquake Likelihood Models (RELM) test of earthquake forecasts in California was the first competitive evaluation of forecasts of future earthquake occurrence. Participants submitted expected probabilities of occurrence of M ≥ 4.95 earthquakes in 0.1° × 0.1° cells for the period 1 January 1, 2006, to December 31, 2010. Probabilities were submitted for 7,682 cells in California and adjacent regions. During this period, 31 M ≥ 4.95 earthquakes occurred in the test region. These earthquakes occurred in 22 test cells. This seismic activity was dominated by earthquakes associated with the M = 7.2, April 4, 2010, El Mayor-Cucapah earthquake in northern Mexico. This earthquake occurred in the test region, and 16 of the other 30 earthquakes in the test region could be associated with it. Nine complete forecasts were submitted by six participants. In this paper, we present the forecasts in a way that allows the reader to evaluate which forecast is the most "successful" in terms of the locations of future earthquakes. We conclude that the RELM test was a success and suggest ways in which the results can be used to improve future forecasts.

  15. California Tiger Salamander Range - CWHR [ds588

    Data.gov (United States)

    California Department of Resources — Vector datasets of CWHR range maps are one component of California Wildlife Habitat Relationships (CWHR), a comprehensive information system and predictive model for...

  16. Supply Chain Development: Insights from Strategic Niche Management

    Science.gov (United States)

    Caniels, Marjolein C. J.; Romijn, Henny A.

    2008-01-01

    Purpose: The purpose of this paper is to contribute to the study of supply chain design from the perspective of complex dynamic systems. Unlike extant studies that use formal simulation modelling and associated methodologies rooted in the physical sciences, it adopts a framework rooted in the social sciences, strategic niche management, which…

  17. Using Adjoint Methods to Improve 3-D Velocity Models of Southern California

    Science.gov (United States)

    Liu, Q.; Tape, C.; Maggi, A.; Tromp, J.

    2006-12-01

    We use adjoint methods popular in climate and ocean dynamics to calculate Fréchet derivatives for tomographic inversions in southern California. The Fréchet derivative of an objective function χ(m), where m denotes the Earth model, may be written in the generic form δχ=int Km(x) δln m(x) d3x, where δln m=δ m/m denotes the relative model perturbation. For illustrative purposes, we construct the 3-D finite-frequency banana-doughnut kernel Km, corresponding to the misfit of a single traveltime measurement, by simultaneously computing the 'adjoint' wave field s† forward in time and reconstructing the regular wave field s backward in time. The adjoint wave field is produced by using the time-reversed velocity at the receiver as a fictitious source, while the regular wave field is reconstructed on the fly by propagating the last frame of the wave field saved by a previous forward simulation backward in time. The approach is based upon the spectral-element method, and only two simulations are needed to produce density, shear-wave, and compressional-wave sensitivity kernels. This method is applied to the SCEC southern California velocity model. Various density, shear-wave, and compressional-wave sensitivity kernels are presented for different phases in the seismograms. We also generate 'event' kernels for Pnl, S and surface waves, which are the Fréchet kernels of misfit functions that measure the P, S or surface wave traveltime residuals at all the receivers simultaneously for one particular event. Effectively, an event kernel is a sum of weighted Fréchet kernels, with weights determined by the associated traveltime anomalies. By the nature of the 3-D simulation, every event kernel is also computed based upon just two simulations, i.e., its construction costs the same amount of computation time as an individual banana-doughnut kernel. One can think of the sum of the event kernels for all available earthquakes, called the 'misfit' kernel, as a graphical

  18. The regulatory niche of intestinal stem cells.

    Science.gov (United States)

    Sailaja, Badi Sri; He, Xi C; Li, Linheng

    2016-09-01

    The niche constitutes a unique category of cells that support the microenvironment for the maintenance and self-renewal of stem cells. Intestinal stem cells reside at the base of the crypt, which contains adjacent epithelial cells, stromal cells and smooth muscle cells, and soluble and cell-associated growth and differentiation factors. We summarize here recent advances in our understanding of the crucial role of the niche in regulating stem cells. The stem cell niche maintains a balance among quiescence, proliferation and regeneration of intestinal stem cells after injury. Mesenchymal cells, Paneth cells, immune cells, endothelial cells and neural cells are important regulatory components that secrete niche ligands, growth factors and cytokines. Intestinal homeostasis is regulated by niche signalling pathways, specifically Wnt, bone morphogenetic protein, Notch and epidermal growth factor. These insights into the regulatory stem cell niche during homeostasis and post-injury regeneration offer the potential to accelerate development of therapies for intestine-related disorders.

  19. 2nd Sandia Fracture Challenge Summit: Sandia California's Modeling Approach

    Energy Technology Data Exchange (ETDEWEB)

    Karlson, Kyle N. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Brown, Arthur [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Foulk, James W. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2015-02-01

    Team Sandia California (Team H) used the Sandia code SIERRA Solid Mechanics: Implicit (SIERRA SM) to model the SFC2 challenge problem. SIERRA SM is a Lagrangian, three-dimensional, implicit code for the analysis of solids and structures. It contains a versatile library of continuum and structural elements, and an extensive library of material models. For all SFC2 related simulations, our team used Q1P0, 8 node hexahedral elements with element side lengths on the order 0.175 mm in failure regions. To model crack initiation and failure, element death removed elements from the simulation according to a continuum damage model. SIERRA SM’s implicit dynamics, implemented with an HHT time integration scheme for numerical damping [1], was used to model the unstable failure modes of the models. We chose SIERRA SM’s isotropic Elasto Viscoplastic material model for our simulations because it contains most of the physics required to accurately model the SFC2 challenge problem such as the flexibility to include temperature and rate dependence for a material.

  20. An individual-based model of the krill Euphausia pacifica in the California Current

    Science.gov (United States)

    Dorman, Jeffrey G.; Sydeman, William J.; Bograd, Steven J.; Powell, Thomas M.

    2015-11-01

    Euphausia pacifica is an abundant and important prey resource for numerous predators of the California Current and elsewhere in the North Pacific. We developed an individual-based model (IBM) for E. pacifica to study its bioenergetics (growth, stage development, reproduction, and mortality) under constant/ideal conditions as well as under varying ocean conditions and food resources. To model E. pacifica under varying conditions, we coupled the IBM to an oceanographic-ecosystem model over the period 2000-2008 (9 years). Model results under constant/ideal food conditions compare favorably with experimental studies conducted under food unlimited conditions. Under more realistic variable oceanographic conditions, mean growth rates over the continental shelf were positive only when individuals migrated diurnally to the depth of maximum phytoplankton layer during nighttime feeding. Our model only used phytoplankton as prey and coastal growth rates were lower than expected (0.01 mm d-1), suggesting that a diverse prey base (zooplankton, protists, marine snow) may be required to facilitate growth and survival of modeled E. pacifica in the coastal environment. This coupled IBM-ROMS modeling framework and its parameters provides a tool for understanding the biology and ecology of E. pacifica and could be developed to further the understanding of climatic effects on this key prey species and enhance an ecosystem approach to fisheries and wildlife management in this region.

  1. Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae).

    Science.gov (United States)

    Seeholzer, Glenn F; Claramunt, Santiago; Brumfield, Robb T

    2017-03-01

    Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic-niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic-niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic-niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic-niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined.

  2. Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae)

    Science.gov (United States)

    Gómez, Camila; Tenorio, Elkin A.; Montoya, Paola; Cadena, Carlos Daniel

    2016-01-01

    Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour. PMID:26865303

  3. Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae).

    Science.gov (United States)

    Gómez, Camila; Tenorio, Elkin A; Montoya, Paola; Cadena, Carlos Daniel

    2016-02-10

    Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour.

  4. Modeling future water demand in California from developed and agricultural land uses

    Science.gov (United States)

    Wilson, T. S.; Sleeter, B. M.; Cameron, D. R.

    2015-12-01

    Municipal and urban land-use intensification in coming decades will place increasing pressure on water resources in California. The state is currently experiencing one of the most extreme droughts on record. This coupled with earlier spring snowmelt and projected future climate warming will increasingly constrain already limited water supplies. The development of spatially explicit models of future land use driven by empirical, historical land use change data allow exploration of plausible LULC-related water demand futures and potential mitigation strategies. We utilized the Land Use and Carbon Scenario Simulator (LUCAS) state-and-transition simulation model to project spatially explicit (1 km) future developed and agricultural land use from 2012 to 2062 and estimated the associated water use for California's Mediterranean ecoregions. We modeled 100 Monte Carlo simulations to better characterize and project historical land-use change variability. Under current efficiency rates, total water demand was projected to increase 15.1% by 2062, driven primarily by increases in urbanization and shifts to more water intensive crops. Developed land use was projected to increase by 89.8%-97.2% and result in an average 85.9% increase in municipal water use, while agricultural water use was projected to decline by approximately 3.9%, driven by decreases in row crops and increases in woody cropland. In order for water demand in 2062 to balance to current demand levels, the currently mandated 25% reduction in urban water use must remain in place in conjunction with a near 7% reduction in agricultural water use. Scenarios of land-use related water demand are useful for visualizing alternative futures, examining potential management approaches, and enabling better informed resource management decisions.

  5. California Bioregions

    Data.gov (United States)

    California Department of Resources — California regions developed by the Inter-agency Natural Areas Coordinating Committee (INACC) were digitized from a 1:1,200,000 California Department of Fish and...

  6. A Kinematic Fault Network Model of Crustal Deformation for California and Its Application to the Seismic Hazard Analysis

    Science.gov (United States)

    Zeng, Y.; Shen, Z.; Harmsen, S.; Petersen, M. D.

    2010-12-01

    We invert GPS observations to determine the slip rates on major faults in California based on a kinematic fault model of crustal deformation with geological slip rate constraints. Assuming an elastic half-space, we interpret secular surface deformation using a kinematic fault network model with each fault segment slipping beneath a locking depth. This model simulates both block-like deformation and elastic strain accumulation within each bounding block. Each fault segment is linked to its adjacent elements with slip continuity imposed at fault nodes or intersections. The GPS observations across California and its neighbors are obtained from the SCEC WGCEP project of California Crustal Motion Map version 1.0 and SCEC Crustal Motion Map 4.0. Our fault models are based on the SCEC UCERF 2.0 fault database, a previous southern California block model by Shen and Jackson, and the San Francisco Bay area block model by d’Alessio et al. Our inversion shows a slip rate ranging from 20 to 26 mm/yr for the northern San Andreas from the Santa Cruz Mountain to the Peninsula segment. Slip rates vary from 8 to 14 mm/yr along the Hayward to the Maacama segment, and from 17 to 6 mm/yr along the central Calaveras to West Napa. For the central California creeping section, we find a depth dependent slip rate with an average slip rate of 23 mm/yr across the upper 5 km and 30 mm/yr underneath. Slip rates range from 30 mm/yr along the Parkfield and central California creeping section of the San Andres to an average of 6 mm/yr on the San Bernardino Mountain segment. On the southern San Andreas, slip rates vary from 21 to 30 mm/yr from the Cochella Valley to the Imperial Valley, and from 7 to 16 mm/yr along the San Jacinto segments. The shortening rate across the greater Los Angeles region is consistent with the regional tectonics and crustal thickening in the area. We are now in the process of applying the result to seismic hazard evaluation. Overall the geodetic and geological derived

  7. CoSMoS (Coastal Storm Modeling System) Southern California v3.0 Phase 2 storm-hazard projections

    Science.gov (United States)

    Barnard, Patrick; Erikson, Li; O'Neill, Andrea; Foxgrover, Amy; Herdman, Liv

    2017-01-01

    The Coastal Storm Modeling System (CoSMoS) makes detailed predictions (meter-scale) over large geographic scales (100s of kilometers) of storm-induced coastal flooding and erosion for both current and future SLR scenarios, as well as long-term shoreline change and cliff retreat.  Resulting projections for future climate scenarios (sea-level rise and storms) provide emergency responders and coastal planners with critical storm-hazards information that can be used to increase public safety, mitigate physical damages, and more effectively manage and allocate resources within complex coastal settings. Several versions of CoSMoS have been implemented for areas of the California coast, including Southern California, Central California, and San Francisco Bay, and further versions will be incorporated as additional regions and improvements are developed.

  8. Physiochemical Evidence of Faulting Processes and Modeling of Fluid in Evolving Fault Systems in Southern California

    Energy Technology Data Exchange (ETDEWEB)

    Boles, James [Professor

    2013-05-24

    Our study targets recent (Plio-Pleistocene) faults and young (Tertiary) petroleum fields in southern California. Faults include the Refugio Fault in the Transverse Ranges, the Ellwood Fault in the Santa Barbara Channel, and most recently the Newport- Inglewood in the Los Angeles Basin. Subsurface core and tubing scale samples, outcrop samples, well logs, reservoir properties, pore pressures, fluid compositions, and published structural-seismic sections have been used to characterize the tectonic/diagenetic history of the faults. As part of the effort to understand the diagenetic processes within these fault zones, we have studied analogous processes of rapid carbonate precipitation (scaling) in petroleum reservoir tubing and manmade tunnels. From this, we have identified geochemical signatures in carbonate that characterize rapid CO2 degassing. These data provide constraints for finite element models that predict fluid pressures, multiphase flow patterns, rates and patterns of deformation, subsurface temperatures and heat flow, and geochemistry associated with large fault systems.

  9. Integrated modeling and field study of potential mechanisms forinduced seismicity at The Geysers Goethermal Field, California

    Energy Technology Data Exchange (ETDEWEB)

    Rutqvist, Jonny; Majer, Ernie; Oldenburg, Curt; Peterson, John; Vasco, Don

    2006-06-07

    In this paper, we present progress made in a study aimed atincreasing the understanding of the relative contributions of differentmechanisms that may be causing the seismicity occurring at The Geysersgeothermal field, California. The approach we take is to integrate: (1)coupled reservoir geomechanical numerical modeling, (2) data fromrecently upgraded and expanded NCPA/Calpine/LBNL seismic arrays, and (3)tens of years of archival InSAR data from monthly satellite passes. Wehave conducted a coupled reservoir geomechanical analysis to studypotential mechanisms induced by steam production. Our simulation resultscorroborate co-locations of hypocenter field observations of inducedseismicity and their correlation with steam production as reported in theliterature. Seismic and InSAR data are being collected and processed foruse in constraining the coupled reservoir geomechanicalmodel.

  10. Predicting the distribution of a parasite using the ecological niche model, GARP Predicción de la distribución de un parásito usando el modelo de nicho ecológico, GARP

    Directory of Open Access Journals (Sweden)

    Terry R. Haverkost

    2010-12-01

    Full Text Available The ecological niche of a parasite exists only at the nexus of certain abiotic and biotic conditions suitable for both the definitive and intermediate hosts. However, the life cycles of most parasites are not known, or are poorly known, and using known ranges of hosts to find endemic parasitic infections has been difficult. However, with ecological niche modeling, we can create potential range maps using known localities of infection. Testing the validity of such maps requires knowledge of the localities of other parasites with common history. Here, we find that the ecological niche of a tapeworm parasite of voles, Paranoplocephala macrocephala (Cestoda: Anoplocephalidae, allows prediction of the presence (in ecological and geographic space of 19 related parasite species from 3 genera in 23 different hosts throughout the Nearctic. These results give credence to the idea that this group shares similar life cycle requirements despite phylogenetic distance. This work further validates ecological niche modeling as a means by which to predict occurrence of parasites when not all facets of the life cycle are confirmed. Such inductive methods create the opportunity for deducing potential reservoir or intermediate hosts, and complementing studies of parasite biodiversity and community ecology.El nicho ecológico de un parásito existe sólo cuando coinciden condiciones abióticas y bióticas necesarias para los hospederos definitivos e intermediarios. No obstante, los ciclos de vida de la mayoría de los parásitos son poco conocidos; el usar áreas de distribución de hospederos para encontrar áreas endémicas de parasitismo ha resultado difícil. Con el modelado de nicho, se pueden producir mapas del área de distribución potencial con base en sitios conocidos de presencia. Para probar la validez de estos mapas, se requiere el conocimiento de sitios de presencia de otros parásitos relacionados. En este estudio, encontramos que el nicho ecol

  11. The accuracy of matrix population model projections for coniferous trees in the Sierra Nevada, California

    Science.gov (United States)

    van Mantgem, P.J.; Stephenson, N.L.

    2005-01-01

    1 We assess the use of simple, size-based matrix population models for projecting population trends for six coniferous tree species in the Sierra Nevada, California. We used demographic data from 16 673 trees in 15 permanent plots to create 17 separate time-invariant, density-independent population projection models, and determined differences between trends projected from initial surveys with a 5-year interval and observed data during two subsequent 5-year time steps. 2 We detected departures from the assumptions of the matrix modelling approach in terms of strong growth autocorrelations. We also found evidence of observation errors for measurements of tree growth and, to a more limited degree, recruitment. Loglinear analysis provided evidence of significant temporal variation in demographic rates for only two of the 17 populations. 3 Total population sizes were strongly predicted by model projections, although population dynamics were dominated by carryover from the previous 5-year time step (i.e. there were few cases of recruitment or death). Fractional changes to overall population sizes were less well predicted. Compared with a null model and a simple demographic model lacking size structure, matrix model projections were better able to predict total population sizes, although the differences were not statistically significant. Matrix model projections were also able to predict short-term rates of survival, growth and recruitment. Mortality frequencies were not well predicted. 4 Our results suggest that simple size-structured models can accurately project future short-term changes for some tree populations. However, not all populations were well predicted and these simple models would probably become more inaccurate over longer projection intervals. The predictive ability of these models would also be limited by disturbance or other events that destabilize demographic rates. ?? 2005 British Ecological Society.

  12. Quantifying the stability of planktic foraminiferal physical niches between the Holocene and Last Glacial Maximum

    Science.gov (United States)

    Waterson, A. M.; Edgar, K. M.; Schmidt, D. N.; Valdes, P. J.

    2017-01-01

    The application of transfer functions on fossil assemblages to reconstruct past environments is fundamentally based on the assumption of stable environmental niches in both space and time. We quantitatively test this assumption for six dominant planktic foraminiferal species (Globigerinoides ruber (pink), G. ruber (white), Trilobatus sacculifer, Truncorotalia truncatulinoides, Globigerina bulloides, and Neogloboquadrina pachyderma) by contrasting reconstructions of species realized and optimum distributions in the modern and during the Last Glacial Maximum (LGM) using an ecological niche model (ENM; MaxEnt) and ordination framework. Global ecological niche models calibrated in the modern ocean have high predictive performance when projected to the LGM for subpolar and polar species, indicating that the environmental niches of these taxa are largely stable at the global scale across this interval. In contrast, ENMs had much poorer predictive performance for the optimal niche of tropical-dwelling species, T. sacculifer and G. ruber (pink). This finding is supported by independent metrics of niche margin change, suggesting that niche stability in environmental space was greatest for (sub)polar species, with greatest expansion of the niche observed for tropical species. We find that globally calibrated ENMs showed good predictions of species occurrences globally, whereas models calibrated in either the Pacific or Atlantic Oceans only and then projected globally performed less well for T. sacculifer. Our results support the assumption of environmental niche stability over the last 21,000 years for most of our focal planktic foraminiferal species and, thus, the application of transfer function techniques for palaeoenvironmental reconstruction during this interval. However, the lower observed niche stability for (sub)tropical taxa T. sacculifer and G. ruber (pink) suggests that (sub)tropical temperatures could be underestimated in the glacial ocean with the strongest

  13. Identification of hepatic niche harboring human acute lymphoblastic leukemic cells via the SDF-1/CXCR4 axis.

    Directory of Open Access Journals (Sweden)

    Itaru Kato

    Full Text Available In acute lymphoblastic leukemia (ALL patients, the bone marrow niche is widely known to be an important element of treatment response and relapse. Furthermore, a characteristic liver pathology observed in ALL patients implies that the hepatic microenvironment provides an extramedullary niche for leukemic cells. However, it remains unclear whether the liver actually provides a specific niche. The mechanism underlying this pathology is also poorly understood. Here, to answer these questions, we reconstituted the histopathology of leukemic liver by using patients-derived primary ALL cells into NOD/SCID/Yc (null mice. The liver pathology in this model was similar to that observed in the patients. By using this model, we clearly demonstrated that bile duct epithelial cells form a hepatic niche that supports infiltration and proliferation of ALL cells in the liver. Furthermore, we showed that functions of the niche are maintained by the SDF-1/CXCR4 axis, proposing a novel therapeutic approach targeting the extramedullary niche by inhibition of the SDF-1/CXCR4 axis. In conclusion, we demonstrated that the liver dissemination of leukemia is not due to nonselective infiltration, but rather systematic invasion and proliferation of leukemic cells in hepatic niche. Although the contribution of SDF-1/CXCR4 axis is reported in some cancer cells or leukemic niches such as bone marrow, we demonstrated that this axis works even in the extramedullary niche of leukemic cells. Our findings form the basis for therapeutic approaches that target the extramedullary niche by inhibiting the SDF-1/CXCR4 axis.

  14. Trophic niche shifts driven by phytoplankton in sandy beach ecosystems

    Science.gov (United States)

    Bergamino, Leandro; Martínez, Ana; Han, Eunah; Lercari, Diego; Defeo, Omar

    2016-10-01

    Stable isotopes (δ13C and δ15N) together with chlorophyll a and densities of surf diatoms were used to analyze changes in trophic niches of species in two sandy beaches of Uruguay with contrasting morphodynamics (i.e. dissipative vs. reflective). Consumers and food sources were collected over four seasons, including sediment organic matter (SOM), suspended particulate organic matter (POM) and the surf zone diatom Asterionellopsis guyunusae. Circular statistics and a Bayesian isotope mixing model were used to quantify food web differences between beaches. Consumers changed their trophic niche between beaches in the same direction of the food web space towards higher reliance on surf diatoms in the dissipative beach. Mixing models indicated that A. guyunusae was the primary nutrition source for suspension feeders in the dissipative beach, explaining their change in dietary niche compared to the reflective beach where the proportional contribution of surf diatoms was low. The high C/N ratios in A. guyunusae indicated its high nutritional value and N content, and may help to explain the high assimilation by suspension feeders at the dissipative beach. Furthermore, density of A. guyunusae was higher in the dissipative than in the reflective beach, and cell density was positively correlated with chlorophyll a only in the dissipative beach. Therefore, surf diatoms are important drivers in the dynamics of sandy beach food webs, determining the trophic niche space and productivity. Our study provides valuable insights on shifting foraging behavior by beach fauna in response to changes in resource availability.

  15. NICHE: The Non-Imaging CHErenkov Array

    CERN Document Server

    Bergman, Douglas

    2012-01-01

    The accurate measurement of the Cosmic Ray (CR) nuclear composition around and above the Knee (~ 10^15.5 eV) has been difficult due to uncertainties inherent to the measurement techniques and/or dependence on hadronic Monte Carlo simulation models required to interpret the data. Measurement of the Cherenkov air shower signal, calibrated with air fluorescence measurements, offers a methodology to provide an accurate measurement of the nuclear composition evolution over a large energy range. NICHE will use an array of widely-spaced, non-imaging Cherenkov counters to measure the amplitude and time-spread of the air shower Cherenkov signal to extract CR nuclear composition measurements and to cross-calibrate the Cherenkov energy and composition measurements with TA/TALE fluorescence and surface detector measurements.

  16. Occupy the Financial Niche: Saturation and Crisis

    Science.gov (United States)

    Purica, Ionut

    The model presented is one theoretical approach within a broader research program that could verify the nonlinear conjectures made, such that to quantify and predict potential discontinuous behaviour. In this case, the crisis behaviour associated with financial funds reallocation among various credit instruments, described as memes with the sense of Dawkins, is shown to be of discontinuous nature stemming from a logistic penetration in the behaviour niche. Actually the logistic penetration is typical in creating cyclic behaviour of economic structures as shown by Marchetti and others from IIASA. A Fokker-Planck equation description results in a stationary solution having a bifurcation like solution with evolution trajectories on a `cusp' type catastrophe that may describe discontinuous decision behaviour.

  17. Shifting Niches for Community Structure Detection

    DEFF Research Database (Denmark)

    Grappiolo, Corrado; Togelius, Julian; Yannakakis, Georgios N.

    2013-01-01

    in complete networks, this approach seems to scale badly due to solutions with the wrong number of communities dominating the population. The new algorithm is based on a niching model, where separate compartments of the population contain candidate solutions with different numbers of communities. We......We present a new evolutionary algorithm for com- munity structure detection in both undirected and unweighted (sparse) graphs and fully connected weighted digraphs (complete networks). Previous investigations have found that, although evolutionary computation can identify community structure...... experimentally compare the new algorithm to the well-known algorithms of Pizzuti and Tasgin, and find that we outperform those algorithms for sparse graphs under some conditions, and drastically outperform them on complete networks under all tested conditions....

  18. Hybrid apomicts trapped in the ecological niches of their sexual ancestors.

    Science.gov (United States)

    Mau, Martin; Lovell, John T; Corral, José M; Kiefer, Christiane; Koch, Marcus A; Aliyu, Olawale M; Sharbel, Timothy F

    2015-05-01

    Asexual reproduction is expected to reduce the adaptive potential to novel or changing environmental conditions, restricting or altering the ecological niche of asexual lineages. Asexual lineages of plants and animals are typically polyploid, an attribute that may influence their genetic variation, plasticity, adaptive potential, and niche breadth. The genus Boechera (Brassicaceae) represents an ideal model to test the relative ecological and biogeographic impacts of reproductive mode and ploidy because it is composed of diploid sexual and both diploid and polyploid asexual (i.e., apomictic) lineages. Here, we demonstrate a strong association between a transcriptionally conserved allele and apomictic seed formation. We then use this allele as a proxy apomixis marker in 1,649 accessions to demonstrate that apomixis is likely to be a common feature across the Boechera phylogeny. Phylogeographic analyses of these data demonstrate (i) species-specific niche differentiation in sexuals, (ii) extensive niche conservation between differing reproductive modes of the same species, (iii) ploidy-specific niche differentiation within and among species, and (iv) occasional niche drift between apomicts and their sexual ancestors. We conclude that ploidy is a substantially stronger and more common driver of niche divergence within and across Boechera species although variation in both traits may not necessarily lead to niche evolution on the species scale.

  19. Evidence for large-scale effects of competition: niche displacement in Canada lynx and bobcat.

    Science.gov (United States)

    Peers, Michael J L; Thornton, Daniel H; Murray, Dennis L

    2013-12-22

    Determining the patterns, causes and consequences of character displacement is central to our understanding of competition in ecological communities. However, the majority of competition research has occurred over small spatial extents or focused on fine-scale differences in morphology or behaviour. The effects of competition on broad-scale distribution and niche characteristics of species remain poorly understood but critically important. Using range-wide species distribution models, we evaluated whether Canada lynx (Lynx canadensis) or bobcat (Lynx rufus) were displaced in regions of sympatry. Consistent with our prediction, we found that lynx niches were less similar to those of bobcat in areas of sympatry versus allopatry, with a stronger reliance on snow cover driving lynx niche divergence in the sympatric zone. By contrast, bobcat increased niche breadth in zones of sympatry, and bobcat niches were equally similar to those of lynx in zones of sympatry and allopatry. These findings suggest that competitively disadvantaged species avoid competition at large scales by restricting their niche to highly suitable conditions, while superior competitors expand the diversity of environments used. Our results indicate that competition can manifest within climatic niche space across species' ranges, highlighting the importance of biotic interactions occurring at large spatial scales on niche dynamics.

  20. A fault-based model for crustal deformation, fault slip-rates and off-fault strain rate in California

    Science.gov (United States)

    Zeng, Yuehua; Shen, Zheng-Kang

    2016-01-01

    We invert Global Positioning System (GPS) velocity data to estimate fault slip rates in California using a fault‐based crustal deformation model with geologic constraints. The model assumes buried elastic dislocations across the region using Uniform California Earthquake Rupture Forecast Version 3 (UCERF3) fault geometries. New GPS velocity and geologic slip‐rate data were compiled by the UCERF3 deformation working group. The result of least‐squares inversion shows that the San Andreas fault slips at 19–22  mm/yr along Santa Cruz to the North Coast, 25–28  mm/yr along the central California creeping segment to the Carrizo Plain, 20–22  mm/yr along the Mojave, and 20–24  mm/yr along the Coachella to the Imperial Valley. Modeled slip rates are 7–16  mm/yr lower than the preferred geologic rates from the central California creeping section to the San Bernardino North section. For the Bartlett Springs section, fault slip rates of 7–9  mm/yr fall within the geologic bounds but are twice the preferred geologic rates. For the central and eastern Garlock, inverted slip rates of 7.5 and 4.9  mm/yr, respectively, match closely with the geologic rates. For the western Garlock, however, our result suggests a low slip rate of 1.7  mm/yr. Along the eastern California shear zone and southern Walker Lane, our model shows a cumulative slip rate of 6.2–6.9  mm/yr across its east–west transects, which is ∼1  mm/yr increase of the geologic estimates. For the off‐coast faults of central California, from Hosgri to San Gregorio, fault slips are modeled at 1–5  mm/yr, similar to the lower geologic bounds. For the off‐fault deformation, the total moment rate amounts to 0.88×1019  N·m/yr, with fast straining regions found around the Mendocino triple junction, Transverse Ranges and Garlock fault zones, Landers and Brawley seismic zones, and farther south. The overall California moment rate is 2.76×1019

  1. Uniform California earthquake rupture forecast, version 3 (UCERF3): the time-independent model

    Science.gov (United States)

    Field, Edward H.; Biasi, Glenn P.; Bird, Peter; Dawson, Timothy E.; Felzer, Karen R.; Jackson, David D.; Johnson, Kaj M.; Jordan, Thomas H.; Madden, Christopher; Michael, Andrew J.; Milner, Kevin R.; Page, Morgan T.; Parsons, Thomas; Powers, Peter M.; Shaw, Bruce E.; Thatcher, Wayne R.; Weldon, Ray J.; Zeng, Yuehua; ,

    2013-01-01

    In this report we present the time-independent component of the Uniform California Earthquake Rupture Forecast, Version 3 (UCERF3), which provides authoritative estimates of the magnitude, location, and time-averaged frequency of potentially damaging earthquakes in California. The primary achievements have been to relax fault segmentation assumptions and to include multifault ruptures, both limitations of the previous model (UCERF2). The rates of all earthquakes are solved for simultaneously, and from a broader range of data, using a system-level "grand inversion" that is both conceptually simple and extensible. The inverse problem is large and underdetermined, so a range of models is sampled using an efficient simulated annealing algorithm. The approach is more derivative than prescriptive (for example, magnitude-frequency distributions are no longer assumed), so new analysis tools were developed for exploring solutions. Epistemic uncertainties were also accounted for using 1,440 alternative logic tree branches, necessitating access to supercomputers. The most influential uncertainties include alternative deformation models (fault slip rates), a new smoothed seismicity algorithm, alternative values for the total rate of M≥5 events, and different scaling relationships, virtually all of which are new. As a notable first, three deformation models are based on kinematically consistent inversions of geodetic and geologic data, also providing slip-rate constraints on faults previously excluded because of lack of geologic data. The grand inversion constitutes a system-level framework for testing hypotheses and balancing the influence of different experts. For example, we demonstrate serious challenges with the Gutenberg-Richter hypothesis for individual faults. UCERF3 is still an approximation of the system, however, and the range of models is limited (for example, constrained to stay close to UCERF2). Nevertheless, UCERF3 removes the apparent UCERF2 overprediction of

  2. Target Article with Commentaries: Developmental Niche Construction

    Science.gov (United States)

    Flynn, Emma G.; Laland, Kevin N.; Kendal, Rachel L.; Kendal, Jeremy R.

    2013-01-01

    Niche construction is the modification of components of the environment through an organism's activities. Humans modify their environments mainly through ontogenetic and cultural processes, and it is this reliance on learning, plasticity and culture that lends human niche construction a special potency. In this paper we aim to facilitate…

  3. Final Report: Natural State Models of The Geysers Geothermal System, Sonoma County, California

    Energy Technology Data Exchange (ETDEWEB)

    T. H. Brikowski; D. L. Norton; D. D. Blackwell

    2001-12-31

    Final project report of natural state modeling effort for The Geysers geothermal field, California. Initial models examined the liquid-dominated state of the system, based on geologic constraints and calibrated to match observed whole rock delta-O18 isotope alteration. These models demonstrated that the early system was of generally low permeability (around 10{sup -12} m{sup 2}), with good hydraulic connectivity at depth (along the intrusive contact) and an intact caprock. Later effort in the project was directed at development of a two-phase, supercritical flow simulation package (EOS1sc) to accompany the Tough2 flow simulator. Geysers models made using this package show that ''simmering'', or the transient migration of vapor bubbles through the hydrothermal system, is the dominant transition state as the system progresses to vapor-dominated. Such a system is highly variable in space and time, making the rock record more difficult to interpret, since pressure-temperature indicators likely reflect only local, short duration conditions.

  4. The Cell as the First Niche Construction.

    Science.gov (United States)

    Torday, John S

    2016-04-28

    Niche construction nominally describes how organisms can form their own environments, increasing their capacity to adapt to their surroundings. It is hypothesized that the formation of the first cell as 'internal' Niche Construction was the foundation for life, and that subsequent niche constructions were iterative exaptations of that event. The first instantation of niche construction has been faithfully adhered to by returning to the unicellular state, suggesting that the life cycle is zygote to zygote, not adult to adult as is commonly held. The consequent interactions between niche construction and epigenetic inheritance provide a highly robust, interactive, mechanistic way of thinking about evolution being determined by initial conditions rather than merely by chance mutation and selection. This novel perspective offers an opportunity to reappraise the processes involved in evolution mechanistically, allowing for scientifically testable hypotheses rather than relying on metaphors, dogma, teleology and tautology.

  5. The Cell as the First Niche Construction

    Directory of Open Access Journals (Sweden)

    John S. Torday

    2016-04-01

    Full Text Available Niche construction nominally describes how organisms can form their own environments, increasing their capacity to adapt to their surroundings. It is hypothesized that the formation of the first cell as ‘internal’ Niche Construction was the foundation for life, and that subsequent niche constructions were iterative exaptations of that event. The first instantation of niche construction has been faithfully adhered to by returning to the unicellular state, suggesting that the life cycle is zygote to zygote, not adult to adult as is commonly held. The consequent interactions between niche construction and epigenetic inheritance provide a highly robust, interactive, mechanistic way of thinking about evolution being determined by initial conditions rather than merely by chance mutation and selection. This novel perspective offers an opportunity to reappraise the processes involved in evolution mechanistically, allowing for scientifically testable hypotheses rather than relying on metaphors, dogma, teleology and tautology.

  6. Desert shrub responses to experimental modification of precipitation seasonality and soil depth: relationship to the two-layer model and ecohydrological niche

    Science.gov (United States)

    Germino, Matthew J.; Reinhardt, Keith

    2013-01-01

    1. Ecohydrological niches are important for understanding plant community responses to climate shifts, particularly in dry lands. According to the two-layer hypothesis, selective use of deep-soil water increases growth or persistence of woody species during warm and dry summer periods and thereby contributes to their coexistence with shallow-rooted herbs in dry ecosystems. The resource-pool hypothesis further suggests that shallow-soil water benefits growth of all plants while deep-soil water primarily enhances physiological maintenance and survival of woody species. Few studies have directly tested these by manipulating deep-soil water availability and observing the long-term outcomes. 2. We predicted that factors promoting infiltration and storage of water in deep soils, specifically greater winter precipitation and soil depth, would enhance Artemisia tridentata (big sagebrush) in cold, winter-wet/summer-dry desert. Sagebrush responses to 20 years of winter irrigation were compared to summer- or no irrigation, on plots having relatively deep or shallow soils (2 m vs. 1 m depths). 3. Winter irrigation increased sagebrush cover, and crown and canopy volumes, but not density (individuals/plot) compared to summer or no irrigation, on deep-soil plots. On shallow-soil plots, winter irrigation surprisingly decreased shrub cover and size, and summer irrigation had no effect. Furthermore, multiple regression suggested that the variations in growth were related (i) firstly to water in shallow soils (0-0.2 m) and secondly to deeper soils (> 1 m deep) and (ii) more by springtime than by midsummer soil water. Water-use efficiency increased considerably on shallow soils without irrigation and was lowest with winter irrigation. 4. Synthesis. Sagebrush was more responsive to the seasonal timing of precipitation than to total annual precipitation. Factors that enhanced deep-water storage (deeper soils plus more winter precipitation) led to increases in Artemisia tridentata that

  7. Niche as a determinant of word fate in online groups.

    Science.gov (United States)

    Altmann, Eduardo G; Pierrehumbert, Janet B; Motter, Adilson E

    2011-05-12

    Patterns of word use both reflect and influence a myriad of human activities and interactions. Like other entities that are reproduced and evolve, words rise or decline depending upon a complex interplay between their intrinsic properties and the environments in which they function. Using Internet discussion communities as model systems, we define the concept of a word niche as the relationship between the word and the characteristic features of the environments in which it is used. We develop a method to quantify two important aspects of the size of the word niche: the range of individuals using the word and the range of topics it is used to discuss. Controlling for word frequency, we show that these aspects of the word niche are strong determinants of changes in word frequency. Previous studies have already indicated that word frequency itself is a correlate of word success at historical time scales. Our analysis of changes in word frequencies over time reveals that the relative sizes of word niches are far more important than word frequencies in the dynamics of the entire vocabulary at shorter time scales, as the language adapts to new concepts and social groupings. We also distinguish endogenous versus exogenous factors as additional contributors to the fates of words, and demonstrate the force of this distinction in the rise of novel words. Our results indicate that short-term nonstationarity in word statistics is strongly driven by individual proclivities, including inclinations to provide novel information and to project a distinctive social identity.

  8. Niche as a determinant of word fate in online groups.

    Directory of Open Access Journals (Sweden)

    Eduardo G Altmann

    Full Text Available Patterns of word use both reflect and influence a myriad of human activities and interactions. Like other entities that are reproduced and evolve, words rise or decline depending upon a complex interplay between their intrinsic properties and the environments in which they function. Using Internet discussion communities as model systems, we define the concept of a word niche as the relationship between the word and the characteristic features of the environments in which it is used. We develop a method to quantify two important aspects of the size of the word niche: the range of individuals using the word and the range of topics it is used to discuss. Controlling for word frequency, we show that these aspects of the word niche are strong determinants of changes in word frequency. Previous studies have already indicated that word frequency itself is a correlate of word success at historical time scales. Our analysis of changes in word frequencies over time reveals that the relative sizes of word niches are far more important than word frequencies in the dynamics of the entire vocabulary at shorter time scales, as the language adapts to new concepts and social groupings. We also distinguish endogenous versus exogenous factors as additional contributors to the fates of words, and demonstrate the force of this distinction in the rise of novel words. Our results indicate that short-term nonstationarity in word statistics is strongly driven by individual proclivities, including inclinations to provide novel information and to project a distinctive social identity.

  9. A Comparison of Groundwater Storage Using GRACE Data, Groundwater Levels, and a Hydrological Model in Californias Central Valley

    Science.gov (United States)

    Kuss, Amber; Brandt, William; Randall, Joshua; Floyd, Bridget; Bourai, Abdelwahab; Newcomer, Michelle; Skiles, Joseph; Schmidt, Cindy

    2011-01-01

    The Gravity Recovery and Climate Experiment (GRACE) measures changes in total water storage (TWS) remotely, and may provide additional insight to the use of well-based data in California's agriculturally productive Central Valley region. Under current California law, well owners are not required to report groundwater extraction rates, making estimation of total groundwater extraction difficult. As a result, other groundwater change detection techniques may prove useful. From October 2002 to September 2009, GRACE was used to map changes in TWS for the three hydrological regions (the Sacramento River Basin, the San Joaquin River Basin, and the Tulare Lake Basin) encompassing the Central Valley aquifer. Net groundwater storage changes were calculated from the changes in TWS for each of the three hydrological regions and by incorporating estimates for additional components of the hydrological budget including precipitation, evapotranspiration, soil moisture, snow pack, and surface water storage. The calculated changes in groundwater storage were then compared to simulated values from the California Department of Water Resource's Central Valley Groundwater- Surface Water Simulation Model (C2VSIM) and their Water Data Library (WDL) Geographic Information System (GIS) change in storage tool. The results from the three methods were compared. Downscaling GRACE data into the 21 smaller Central Valley sub-regions included in C2VSIM was also evaluated. This work has the potential to improve California's groundwater resource management and use of existing hydrological models for the Central Valley.

  10. Application of the Telegraph Model to Coda Q Variations in Southern California

    Science.gov (United States)

    Davis, P. M.; Clayton, R. W.

    2006-12-01

    We examine data used to construct coda magnitude in southern California to estimate the spatial variation of coda Q and its dependence on frequency. Our analysis combined with independent borehole data (Abercrombie, 1995) suggests coda is mainly generated by multiple scattering in the upper few km of the crust where large impedance contrasts occur due to surface layering or fracturing. The ubiquitous observation that coda Q increases with frequency is explained as arising from multiple reverberations in the upper crust. We suggest that the telegraph model that has been successfully used to describe reflection seismogram multiples in the exploration industry may also apply to earthquakes. Under this model the apparent increase of Q with frequency is due to trapping of high frequency energy in the upper crust. This behavior is expected if the associated reflector series has an exponential autocorrelation function, a feature of the telegraph model. At lower frequencies trapping is less efficient. The combined effects give rise to an apparent absorption band that we suppose is superimposed on frequency-independent intrinsic attenuation. Maximum apparent attenuation occurs at wavelengths equal to the dimensions of the regions of upper crust that contain the scattering layers. At lower frequencies trapping is less effective and attenuation decreases as the longer wavelength waves sample the deeper crust and upper mantle where, due to over-burden pressures, acoustic impedance contrasts are less extreme.

  11. Not all renal stem cell niches are the same: anatomy of an evolution

    Directory of Open Access Journals (Sweden)

    Clara Gerosa

    2016-08-01

    Full Text Available The renal stem cell niche represents the most important structure of the developing kidney, responsible for nephrogenesis. Recently, some Authors have reported, at ultrastructural level, a previously unknown complexity of the architecture of renal stem cell niche in experimental models. This study was aimed at studying, at histological level, the anatomy of renal stem cell niches in the human fetal kidney. To this end, ten fetal kidneys, whose gestational ages ranged from 11 up to 24 weeks, were studied. H&E-stained sections were observed at high power. The study of the anatomy of renal stem cell niches in the human kidney revealed a previously unreported complexity: some niches appeared as a roundish arrangement of mesenchymal cells; others showed the initial phases of induction by ureteric buds; in other niches the process of mesenchymal epithelial transition was more evident; finally, in other stem cell niches the first signs of nephron origin were detectable. These findings suggest the existence of niches with different anatomy in the same kidney, indicating different stages of evolution even in adjacent niches. All stem cell niches were in strict contact with the capsular cells, suggesting a major role of the renal capsule in nephrogenesis. Finally, our study confirms the existence of a strict contact between the bud tip cells and the surrounding mesenchyme in the human developing kidney, giving a morphological support to the theory of intercellular channels allowing the passage of transcription factors from the epithelial to the mesenchymal stem/progenitors cells.Proceedings of the 2nd International Course on Perinatal Pathology (part of the 11th International Workshop on Neonatology · October 26th-31st, 2015 · Cagliari (Italy · October 31st, 2015 · Stem cells: present and future Guest Editors: Gavino Faa, Vassilios Fanos, Antonio Giordano

  12. Conclusions about niche expansion in introduced Impatiens walleriana populations depend on method of analysis.

    Directory of Open Access Journals (Sweden)

    Lisa Mandle

    Full Text Available Determining the degree to which climate niches are conserved across plant species' native and introduced ranges is valuable to developing successful strategies to limit the introduction and spread of invasive plants, and also has important ecological and evolutionary implications. Here, we test whether climate niches differ between native and introduced populations of Impatiens walleriana, globally one of the most popular horticultural species. We use approaches based on both raw climate data associated with occurrence points and ecological niche models (ENMs developed with Maxent. We include comparisons of climate niche breadth in both geographic and environmental spaces, taking into account differences in available habitats between the distributional areas. We find significant differences in climate envelopes between native and introduced populations when comparing raw climate variables, with introduced populations appearing to expand into wetter and cooler climates. However, analyses controlling for differences in available habitat in each region do not indicate expansion of climate niches. We therefore cannot reject the hypothesis that observed differences in climate envelopes reflect only the limited environments available within the species' native range in East Africa. Our results suggest that models built from only native range occurrence data will not provide an accurate prediction of the potential for invasiveness if applied to areas containing a greater range of environmental combinations, and that tests of niche expansion may overestimate shifts in climate niches if they do not control carefully for environmental differences between distributional areas.

  13. Why do niches develop in Caesarean uterine scars? Hypotheses on the aetiology of niche development.

    Science.gov (United States)

    Vervoort, A J M W; Uittenbogaard, L B; Hehenkamp, W J K; Brölmann, H A M; Mol, B W J; Huirne, J A F

    2015-12-01

    Caesarean section (CS) results in the occurrence of the phenomenon 'niche'. A 'niche' describes the presence of a hypoechoic area within the myometrium of the lower uterine segment, reflecting a discontinuation of the myometrium at the site of a previous CS. Using gel or saline instillation sonohysterography, a niche is identified in the scar in more than half of the women who had had a CS, most with the uterus closed in one single layer, without closure of the peritoneum. An incompletely healed scar is a long-term complication of the CS and is associated with more gynaecological symptoms than is commonly acknowledged. Approximately 30% of women with a niche report spotting at 6-12 months after their CS. Other reported symptoms in women with a niche are dysmenorrhoea, chronic pelvic pain and dyspareunia. Given the association between a niche and gynaecological symptoms, obstetric complications and potentially with subfertility, it is important to elucidate the aetiology of niche development after CS in order to develop preventive strategies. Based on current published data and our observations during sonographic, hysteroscopic and laparoscopic evaluations of niches we postulate some hypotheses on niche development. Possible factors that could play a role in niche development include a very low incision through cervical tissue, inadequate suturing technique during closure of the uterine scar, surgical interventions that increase adhesion formation or patient-related factors that impair wound healing or increase inflammation or adhesion formation.

  14. Modeling the effects of ship emissions on coastal air quality: A case study of southern California

    Science.gov (United States)

    Vutukuru, Satish; Dabdub, Donald

    2008-05-01

    Impact of emissions from ocean-going ships on ozone and particulate matter concentrations is quantified using UCI-CIT model for the South Coast Air Basin of California (SoCAB). The modeling domain encompasses Los Angeles and Long Beach ports and part of the Pacific Ocean that is traversed by ships to visit these ports. Impacts are assessed for a base year (2002) and a future year (2020) by analyzing results from simulations of a three-day summer episode. Contribution of ship emissions to peak 1-h and 8-h ozone concentrations is predicted to be up to 29 and 24 ppb, respectively, for the year 2002. Similarly, particulate nitrate and sulfate concentrations increase up to 12.8 and 1.7 μg m-3, respectively, in the basin when ship emissions are included. Maximum impacts are predicted to occur along the coasts of Ventura and Los Angeles and also at inland locations near Simi Valley. Future year simulations show substantial increase in impacts from ships due to expected growth in ship emissions. Ozone increases are as high as 59 ppb for land-based locations when estimates of ship emissions for 2020 are included. Similarly, particulate nitrate and sulfate increase up to 14 and 2.5 μg m-3. The results of this study show that control of ship emissions is important to mitigate air pollution.

  15. Final report on "Modeling Diurnal Variations of California Land Biosphere CO2 Fluxes"

    Energy Technology Data Exchange (ETDEWEB)

    Fung, Inez

    2014-07-28

    In Mediterranean climates, the season of water availability (winter) is out of phase with the season of light availability and atmospheric demand for moisture (summer). Multi-year half-hourly observations of sap flow velocities in 26 evergreen trees in a small watershed in Northern California show that different species of evergreen trees have different seasonalities of transpiration: Douglas-firs respond immediately to the first winter rain, while Pacific madrones have peak transpiration in the dry summer. Using these observations, we have derived species-specific parameterization of normalized sap flow velocities in terms of insolation, vapor pressure deficit and near-surface soil moisture. A simple 1-D boundary layer model showed that afternoon temperatures may be higher by 1 degree Celsius in an area with Douglas-firs than with Pacific madrones. The results point to the need to develop a new representation of subsurface moisture, in particular pools beneath the organic soil mantle and the vadose zone. Our ongoing and future work includes coupling our new parameterization of transpiration with new representation of sub-surface moisture in saprolite and weathered bedrock. The results will be implemented in a regional climate model to explore vegetation-climate feedbacks, especially in the dry season.

  16. A numerical test method of California bearing ratio on graded crushed rocks using particle flow modeling

    Directory of Open Access Journals (Sweden)

    Yingjun Jiang

    2015-04-01

    Full Text Available In order to better understand the mechanical properties of graded crushed rocks (GCRs and to optimize the relevant design, a numerical test method based on the particle flow modeling technique PFC2D is developed for the California bearing ratio (CBR test on GCRs. The effects of different testing conditions and micro-mechanical parameters used in the model on the CBR numerical results have been systematically studied. The reliability of the numerical technique is verified. The numerical results suggest that the influences of the loading rate and Poisson's ratio on the CBR numerical test results are not significant. As such, a loading rate of 1.0–3.0 mm/min, a piston diameter of 5 cm, a specimen height of 15 cm and a specimen diameter of 15 cm are adopted for the CBR numerical test. The numerical results reveal that the CBR values increase with the friction coefficient at the contact and shear modulus of the rocks, while the influence of Poisson's ratio on the CBR values is insignificant. The close agreement between the CBR numerical results and experimental results suggests that the numerical simulation of the CBR values is promising to help assess the mechanical properties of GCRs and to optimize the grading design. Besides, the numerical study can provide useful insights on the mesoscopic mechanism.

  17. Overview of the Uniform California Earthquake Rupture Forecast Version 3 (UCERF3) Time-Independent Model

    Science.gov (United States)

    Field, E. H.; Arrowsmith, R.; Biasi, G. P.; Bird, P.; Dawson, T. E.; Felzer, K. R.; Jackson, D. D.; Johnson, K. M.; Jordan, T. H.; Madugo, C. M.; Michael, A. J.; Milner, K. R.; Page, M. T.; Parsons, T.; Powers, P.; Shaw, B. E.; Thatcher, W. R.; Weldon, R. J.; Zeng, Y.

    2013-12-01

    We present the time-independent component of the Uniform California Earthquake Rupture Forecast, Version 3 (UCERF3), where the primary achievements have been to relax fault segmentation and include multi-fault ruptures, both limitations of UCERF2. The rates of all earthquakes are solved for simultaneously, and from a broader range of data, using a system-level 'grand inversion' that is both conceptually simple and extensible. The inverse problem is large and underdetermined, so a range of models is sampled using an efficient simulated annealing algorithm. The approach is more derivative than prescriptive (e.g., magnitude-frequency distributions are no longer assumed), so new analysis tools were developed for exploring solutions. Epistemic uncertainties were also accounted for using 1440 alternative logic tree branches, necessitating access to supercomputers. The most influential uncertainties include alternative deformation models (fault slip rates), a new smoothed seismicity algorithm, alternative values for the total rate of M≥5 events, and different scaling relationships, virtually all of which are new. As a notable first, three deformation models are based on kinematically consistent inversions of geodetic and geologic data, also providing slip-rate constraints on faults previously excluded due to lack of geologic data. The grand inversion constitutes a system-level framework for testing hypotheses and balancing the influence of different experts. For example, we demonstrate serious challenges with the Gutenberg-Richter hypothesis for individual faults. UCERF3 is still an approximation of the system, however, and the range of models is limited (e.g., constrained to stay close to UCERF2). Nevertheless, UCERF3 removes the apparent UCERF2 over-prediction of M6.5-7 earthquake rates, and also includes types of multi-fault ruptures seen in nature. While UCERF3 fits the data better than UCERF2 overall, there may be areas that warrant further site

  18. Calibration of numerical models for small debris flows in Yosemite Valley, California, USA

    Science.gov (United States)

    Bertolo, P.; Wieczorek, G.F.

    2005-01-01

    This study compares documented debris flow runout distances with numerical simulations in the Yosemite Valley of California, USA, where about 15% of historical events of slope instability can be classified as debris flows and debris slides (Wieczorek and Snyder, 2004). To model debris flows in the Yosemite Valley, we selected six streams with evidence of historical debris flows; three of the debris flow deposits have single channels, and the other three split their pattern in the fan area into two or more channels. From field observations all of the debris flows involved coarse material, with only very small clay content. We applied the one dimensional DAN (Dynamic ANalysis) model (Hungr, 1995) and the two-dimensional FLO2D model (O'Brien et al., 1993) to predict and compare the runout distance and the velocity of the debris flows observed in the study area. As a first step, we calibrated the parameters for the two softwares through the back analysis of three debris- flows channels using a trial-and-error procedure starting with values suggested in the literature. In the second step we applied the selected values to the other channels, in order to evaluate their predictive capabilities. After parameter calibration using three debris flows we obtained results similar to field observations We also obtained a good agreement between the two models for velocities. Both models are strongly influenced by topography: we used the 30 m cell size DTM available for the study area, that is probably not accurate enough for a highly detailed analysis, but it can be sufficient for a first screening. European Geosciences Union ?? 2005 Author(s). This work is licensed under a Creative Commons License.

  19. CyberShake: A Physics-Based Seismic Hazard Model for Southern California

    Science.gov (United States)

    Graves, R.; Jordan, T.H.; Callaghan, S.; Deelman, E.; Field, E.; Juve, G.; Kesselman, C.; Maechling, P.; Mehta, G.; Milner, K.; Okaya, D.; Small, P.; Vahi, K.

    2011-01-01

    CyberShake, as part of the Southern California Earthquake Center's (SCEC) Community Modeling Environment, is developing a methodology that explicitly incorporates deterministic source and wave propagation effects within seismic hazard calculations through the use of physics-based 3D ground motion simulations. To calculate a waveform-based seismic hazard estimate for a site of interest, we begin with Uniform California Earthquake Rupture Forecast, Version 2.0 (UCERF2.0) and identify all ruptures within 200 km of the site of interest. We convert the UCERF2.0 rupture definition into multiple rupture variations with differing hypocenter locations and slip distributions, resulting in about 415,000 rupture variations per site. Strain Green Tensors are calculated for the site of interest using the SCEC Community Velocity Model, Version 4 (CVM4), and then, using reciprocity, we calculate synthetic seismograms for each rupture variation. Peak intensity measures are then extracted from these synthetics and combined with the original rupture probabilities to produce probabilistic seismic hazard curves for the site. Being explicitly site-based, CyberShake directly samples the ground motion variability at that site over many earthquake cycles (i. e., rupture scenarios) and alleviates the need for the ergodic assumption that is implicitly included in traditional empirically based calculations. Thus far, we have simulated ruptures at over 200 sites in the Los Angeles region for ground shaking periods of 2 s and longer, providing the basis for the first generation CyberShake hazard maps. Our results indicate that the combination of rupture directivity and basin response effects can lead to an increase in the hazard level for some sites, relative to that given by a conventional Ground Motion Prediction Equation (GMPE). Additionally, and perhaps more importantly, we find that the physics-based hazard results are much more sensitive to the assumed magnitude-area relations and

  20. Dense Root Removal by Asymmetric Delamination in Sierra Nevada, California: Insights from Numerical Modeling

    Science.gov (United States)

    Valera, J.; Negredo, A. M.; Billen, M.

    2008-12-01

    Recent studies provide compelling evidence for an event of removal of lithospheric mantle in southern -and possibly central- Sierra Nevada (SN) mountains, California (Zandt et al., Nature, 431, 2004). A sequential history of foundering of the ultramafic root of the Sierra Nevada batholith, with a pronounced asymmetric flow, is proposed to explain a number of geophysical and geological observations, including a fast seismic velocity in the mantle located to the west of the SN crest, a gap in the Moho, recent subsidence and tilting of the Sierra Nevada, and a change in mineralogy of the xenolith population recorded at the surface. In the present study we focus on the quantitative evaluation of this conceptual model. We apply new thermo- mechanical algorithms, developed in MATLAB code, suitable to study the temporal evolution of laterally migrating lithospheric delamination. The motion equation, formulated in terms of the stream function, and the coupled thermal equation are solved applying finite difference techniques. Our physical modeling is shown to properly reproduce the first order features of the conceptual model for lithospheric delamination in the Sierra Nevada. We investigate the evolution of a dense ultramafic root, which brings about a Rayleigh-Taylor gravitational instability. Following our preliminary results, the presence of a fluid-weakened lithosphere, located just east of Sierra Nevada, is required to reproduce the asymmetric development of this instability, as previously proposed by Zandt et al. (2004). This weak rheology zone, which is modeled by means of a reduced viscosity, is shown to enable the ascent of asthenospheric material and westward propagation of delamination. Our predictions are also consistent with the previous inference of the V-shaped cone of crust being dragged down into the downwelling mantle (i.e., the Moho gap). Present results highlight that viscous drag is also likely responsible for present-day surface subsidence.

  1. Embryonic anti-aging niche.

    Science.gov (United States)

    Conboy, Irina M; Yousef, Hanadie; Conboy, Michael J

    2011-05-01

    Although functional organ stem cells persist in the old, tissue damage invariably overwhelms tissue repair, ultimately causing the demise of an organism. The poor performance of stem cells in an aged organ, such as skeletal muscle, is caused by the changes in regulatory pathways such as Notch, MAPK and TGF-β, where old differentiated tissue actually inhibits its own regeneration. This perspective analyzes the current literature on regulation of organ stem cells by their young versus old niches and suggests that determinants of healthy and prolonged life might be under a combinatorial control of cell cycle check point proteins and mitogens, which need to be tightly balanced in order to promote tissue regeneration without tumor formation. While responses of adult stem cells are regulated extrinsically and age-specifically, we put forward experimental evidence suggesting that embryonic cells have an intrinsic youthful barrier to aging and produce soluble pro-regenerative proteins that signal the MAPK pathway for rejuvenating myogenesis. Future identification of this activity will improve our understanding of embryonic versus adult regulation of tissue regeneration suggesting novel strategies for organ rejuvenation. Comprehensively, the current intersection of aging and stem cell science indicates that if the age-imposed decline in the regenerative capacity of stem cells was understood, the debilitating lack of organ maintenance in the old could be ameliorated and perhaps, even reversed.

  2. Current and future niche of North and Central American sand flies (Diptera: psychodidae) in climate change scenarios.

    Science.gov (United States)

    Moo-Llanes, David; Ibarra-Cerdeña, Carlos N; Rebollar-Téllez, Eduardo A; Ibáñez-Bernal, Sergio; González, Camila; Ramsey, Janine M

    2013-01-01

    Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i) potential change in niche breadth, ii) direction and magnitude of niche centroid shifts, iii) shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3), for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%), while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases.

  3. Current and future niche of North and Central American sand flies (Diptera: psychodidae in climate change scenarios.

    Directory of Open Access Journals (Sweden)

    David Moo-Llanes

    Full Text Available Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i potential change in niche breadth, ii direction and magnitude of niche centroid shifts, iii shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3, for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%, while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases.

  4. Current and Future Niche of North and Central American Sand Flies (Diptera: Psychodidae) in Climate Change Scenarios

    Science.gov (United States)

    Moo-Llanes, David; Ibarra-Cerdeña, Carlos N.; Rebollar-Téllez, Eduardo A.; Ibáñez-Bernal, Sergio; González, Camila; Ramsey, Janine M.

    2013-01-01

    Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i) potential change in niche breadth, ii) direction and magnitude of niche centroid shifts, iii) shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3), for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%), while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases. PMID:24069478

  5. 2013 NOAA Coastal California TopoBathy Merge Project Digital Elevation Model (DEM)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This project merged recently collected topographic, bathymetric, and acoustic elevation data along the entire California coastline from approximately the 10 meter...

  6. 2009-2011 CA Coastal California TopoBathy Merged Project Digital Elevation Model (DEM)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This project merged recently collected topographic, bathymetric, and acoustic elevation data along the entire California coastline from approximately the 10 meter...

  7. West Coast fish, mammal, bird life history and abunance parameters - Developing end-to-end models of the California Current Large Marine Ecosystem

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web...

  8. West Coast fish, mammal, and bird species diets - Developing end-to-end models of the California Current Large Marine Ecosystem

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web...

  9. Traffic jam functions in a branched pathway from Notch activation to niche cell fate.

    Science.gov (United States)

    Wingert, Lindsey; DiNardo, Stephen

    2015-07-01

    The niche directs key behaviors of its resident stem cells, and is thus crucial for tissue maintenance, repair and longevity. However, little is known about the genetic pathways that guide niche specification and development. The male germline stem cell niche in Drosophila houses two stem cell populations and is specified within the embryonic gonad, thus making it an excellent model for studying niche development. The hub cells that form the niche are specified early by Notch activation. Over the next few hours, these individual cells then cluster together and take up a defined position before expressing markers of hub cell differentiation. This timing suggests that there are other factors for niche development yet to be defined. Here, we have identified a role for the large Maf transcription factor Traffic jam (Tj) in hub cell specification downstream of Notch. Tj downregulation is the first detectable effect of Notch activation in hub cells. Furthermore, Tj depletion is sufficient to generate ectopic hub cells that can recruit stem cells. Surprisingly, ectopic niche cells in tj mutants remain dispersed in the absence of Notch activation. This led us to uncover a branched pathway downstream of Notch in which Bowl functions to direct hub cell assembly in parallel to Tj downregulation.

  10. Niche divergence builds the case for ecological speciation in skinks of the Plestiodon skiltonianus species complex

    Science.gov (United States)

    Wogan, Guinevere O.U.; Richmond, Jonathan Q.

    2015-01-01

    Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate-based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by-product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size-divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype–environment associations that further support the case for ecological speciation in these lizards.

  11. Estimating California ecosystem carbon change using process model and land cover disturbance data: 1951-2000

    Science.gov (United States)

    Liu, J.; Vogelmann, J.E.; Zhu, Z.; Key, C.H.; Sleeter, B.M.; Price, D.T.; Chen, J.M.; Cochrane, M.A.; Eidenshink, J.C.; Howard, S.M.; Bliss, N.B.; Jiang, H.

    2011-01-01

    Land use change, natural disturbance, and climate change directly alter ecosystem productivity and carbon stock level. The estimation of ecosystem carbon dynamics depends on the quality of land cover change data and the effectiveness of the ecosystem models that represent the vegetation growth processes and disturbance effects. We used the Integrated Biosphere Simulator (IBIS) and a set of 30- to 60-m resolution fire and land cover change data to examine the carbon changes of California's forests, shrublands, and grasslands. Simulation results indicate that during 1951-2000, the net primary productivity (NPP) increased by 7%, from 72.2 to 77.1TgCyr-1 (1 teragram=1012g), mainly due to CO2 fertilization, since the climate hardly changed during this period. Similarly, heterotrophic respiration increased by 5%, from 69.4 to 73.1TgCyr-1, mainly due to increased forest soil carbon and temperature. Net ecosystem production (NEP) was highly variable in the 50-year period but on average equalled 3.0TgCyr-1 (total of 149TgC). As with NEP, the net biome production (NBP) was also highly variable but averaged -0.55TgCyr-1 (total of -27.3TgC) because NBP in the 1980s was very low (-5.34TgCyr-1). During the study period, a total of 126Tg carbon were removed by logging and land use change, and 50Tg carbon were directly removed by wildland fires. For carbon pools, the estimated total living upper canopy (tree) biomass decreased from 928 to 834TgC, and the understory (including shrub and grass) biomass increased from 59 to 63TgC. Soil carbon and dead biomass carbon increased from 1136 to 1197TgC. Our analyses suggest that both natural and human processes have significant influence on the carbon change in California. During 1951-2000, climate interannual variability was the key driving force for the large interannual changes of ecosystem carbon source and sink at the state level, while logging and fire were the dominant driving forces for carbon balances in several specific

  12. CROSS DRIFT ALCOVE/NICHE UTILITIES ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    S. Goodin

    1999-07-08

    The purpose of this analysis is to provide the design basis and general arrangement requirements of the non-potable water, waste water, compressed air and ventilation (post excavation) utilities required in support of the Cross Drift alcoves and niches.

  13. 2010 bathymetric survey and digital elevation model of Corte Madera Bay, California

    Science.gov (United States)

    Foxgrover, Amy C.; Finlayson, David P.; Jaffe, Bruce E.; Takekawa, John Y.; Thorne, Karen M.; Spragens, Kyle A.

    2011-01-01

    A high-resolution bathymetric survey of Corte Madera Bay, California, was collected in early 2010 in support of a collaborative research project initiated by the San Francisco Bay Conservation and Development Commission and funded by the U.S. Environmental Protection Agency. The primary objective of the Innovative Wetland Adaptation in the Lower Corte Madera Creek Watershed Project is to develop shoreline adaptation strategies to future sea-level rise based upon sound science. Fundamental to this research was the development of an of an up-to-date, high-resolution digital elevation model (DEM) extending from the subtidal environment through the surrounding intertidal marsh. We provide bathymetric data collected by the U.S. Geological Survey and have merged the bathymetry with a 1-m resolution aerial lidar data set that was collected by the National Oceanic and Atmospheric Administration during the same time period to create a seamless, high-resolution DEM of Corte Madera Bay and the surrounding topography. The bathymetric and DEM surfaces are provided at both 1 m and 10 m resolutions formatted as both X, Y, Z text files and ESRI Arc ASCII files, which are accompanied by Federal Geographic Data Committee compliant metadata.

  14. California's Methane Budget derived from CalNex P-3 Aircraft Observations and the WRF-STILT Lagrangian Transport Model

    Science.gov (United States)

    Santoni, G. W.; Xiang, B.; Kort, E. A.; Daube, B.; Andrews, A. E.; Sweeney, C.; Wecht, K.; Peischl, J.; Ryerson, T. B.; Angevine, W. M.; Trainer, M.; Nehrkorn, T.; Eluszkiewicz, J.; Wofsy, S. C.

    2012-12-01

    We present constraints on California emission inventories of methane (CH4) using atmospheric observations from nine NOAA P-3 flights during the California Nexus (CalNex) campaign in May and June of 2010. Measurements were made using a quantum cascade laser spectrometer (QCLS) and a cavity ring-down spectrometer (CRDS) and calibrated to NOAA standards in-flight. Five flights sampled above the northern and southern central valley and an additional four flights probed the south coast air basin, quantifying emissions from the Los Angeles basin. The data show large (>100 ppb) CH4 enhancements associated with point and area sources such as cattle and manure management, landfills, wastewater treatment, gas production and distribution infrastructure, and rice agriculture. We compare aircraft observations to modeled CH4 distributions by accounting for a) transport using the Stochastic Time-Inverted Lagrangian Transport (STILT) model driven by Weather Research and Forecasting (WRF) meteorology, b) emissions from inventories such as EDGAR and ones constructed from California-specific state and county databases, each gridded to 0.1° x 0.1° resolution, and c) spatially and temporally evolving boundary conditions such as GEOS-Chem and a NOAA aircraft profile measurement derived curtain imposed at the edge of the WRF domain. After accounting for errors associated with transport, planetary boundary layer height, lateral boundary conditions, seasonality of emissions, and the spatial resolution of surface emission prior estimates, we find that the California Air Resources Board (CARB) CH4 budget is a factor of 1.64 too low. Using a Bayesian inversion to the flight data, we estimate California's CH4 budget to be 2.5 TgCH4/yr, with emissions from cattle and manure management, landfills, rice, and natural gas infrastructure, representing roughly 82%, 26%, 9% and 32% (sum = 149% with other sources accounting for the additional 15%) of the current CARB CH4 budget estimate of 1.52 TgCH4

  15. A-Priori Rupture Models for Northern California Type-A Faults

    Science.gov (United States)

    Wills, Chris J.; Weldon, Ray J.; Field, Edward H.

    2008-01-01

    This appendix describes how a-priori rupture models were developed for the northern California Type-A faults. As described in the main body of this report, and in Appendix G, ?a-priori? models represent an initial estimate of the rate of single and multi-segment surface ruptures on each fault. Whether or not a given model is moment balanced (i.e., satisfies section slip-rate data) depends on assumptions made regarding the average slip on each segment in each rupture (which in turn depends on the chosen magnitude-area relationship). Therefore, for a given set of assumptions, or branch on the logic tree, the methodology of the present Working Group (WGCEP-2007) is to find a final model that is as close as possible to the a-priori model, in the least squares sense, but that also satisfies slip rate and perhaps other data. This is analogous the WGCEP- 2002 approach of effectively voting on the relative rate of each possible rupture, and then finding the closest moment-balance model (under a more limiting set of assumptions than adopted by the present WGCEP, as described in detail in Appendix G). The 2002 Working Group Report (WCCEP, 2003, referred to here as WGCEP-2002), created segmented earthquake rupture forecast models for all faults in the region, including some that had been designated as Type B faults in the NSHMP, 1996, and one that had not previously been considered. The 2002 National Seismic Hazard Maps used the values from WGCEP-2002 for all the faults in the region, essentially treating all the listed faults as Type A faults. As discussed in Appendix A, the current WGCEP found that there are a number of faults with little or no data on slip-per-event, or dates of previous earthquakes. As a result, the WGCEP recommends that faults with minimal available earthquake recurrence data: the Greenville, Mount Diablo, San Gregorio, Monte Vista-Shannon and Concord-Green Valley be modeled as Type B faults to be consistent with similarly poorly-known faults statewide

  16. Developmental cues and persistent neurogenic potential within an in vitro neural niche

    Directory of Open Access Journals (Sweden)

    Fairchild Corinne L

    2010-01-01

    Full Text Available Abstract Background Neurogenesis, the production of neural cell-types from neural stem cells (NSCs, occurs during development as well as within select regions of the adult brain. NSCs in the adult subependymal zone (SEZ exist in a well-categorized niche microenvironment established by surrounding cells and their molecular products. The components of this niche maintain the NSCs and their definitive properties, including the ability to self-renew and multipotency (neuronal and glial differentiation. Results We describe a model in vitro NSC niche, derived from embryonic stem cells, that produces many of the cells and products of the developing subventricular zone (SVZ and adult SEZ NSC niche. We demonstrate a possible role for apoptosis and for components of the extracellular matrix in the maintenance of the NSC population within our niche cultures. We characterize expression of genes relevant to NSC self-renewal and the process of neurogenesis and compare these findings to gene expression produced by an established neural-induction protocol employing retinoic acid. Conclusions The in vitro NSC niche shows an identity that is distinct from the neurally induced embryonic cells that were used to derive it. Molecular and cellular components found in our in vitro NSC niche include NSCs, neural progeny, and ECM components and their receptors. Establishment of the in vitro NSC niche occurs in conjunction with apoptosis. Applications of this culture system range from studies of signaling events fundamental to niche formation and maintenance as well as development of unique NSC transplant platforms to treat disease or injury.

  17. Field Scale Groundwater Nitrate Loading Model for the Central Valley, California, 1945-Current

    Science.gov (United States)

    Harter, T.; Dzurella, K.; Bell, A.; Kourakos, G.

    2015-12-01

    Anthropogenic groundwater nitrate contamination in the Central Valley aquifer system, California, is widespread, with over 40% of domestic wells in some counties exceeding drinking water standards. Sources of groundwater nitrate include leaky municipal wastewater systems, municipal wastewater recharge, onsite wastewater treatment (septic) systems, atmospheric nitrogen deposition, animal farming, application of organic waste materials (sludge, biosolids, animal manure) to agricultural lands, and synthetic fertilizer. At the site or field scale, nitrogen inputs to the landscape are balanced by plant nitrogen uptake and harvest, atmospheric nitrogen losses, surface runoff of nitrogen, soil nitrogen storage changes, and leaching to groundwater. Irrigated agriculture is a dominant player in the Central Valley nitrogen cycle: The largest nitrogen fluxes are synthetic fertilizer and animal manure applications to cropland, crop nitrogen uptake, and groundwater nitrogen losses. We construct a historic field/parcel scale groundwater nitrogen loading model distinguishing urban and residential areas, individual animal farming areas, leaky wastewater lagoons, and approximately 50 different categories of agricultural crops. For non-agricultural landuses, groundwater nitrate loading is based on reported leaching values, animal population, and human population. For cropland, groundwater nitrate loading is computed from mass balance, taking into account diverse and historically changing management practices between different crops. Groundwater nitrate loading is estimated for 1945 to current. Significant increases in groundwater nitrate loading are associated with the expansion of synthetic fertilizer use in the 1950s to 1970s. Nitrate loading from synthetic fertilizer use has stagnated over the past 20 years due to improvements in nutrient use efficiency. However, an unbroken 60 year exponential increase in dairy production until the late 2000s has significantly impacted the

  18. A structural equation model analysis of postfire plant diversity in California shrublands

    Science.gov (United States)

    Grace, J.B.; Keeley, J.E.

    2006-01-01

    This study investigates patterns of plant diversity following wildfires in fire-prone shrublands of California, seeks to understand those patterns in terms of both local and landscape factors, and considers the implications for fire management. Ninety study sites were established following extensive wildfires in 1993, and 1000-m2 plots were used to sample a variety of parameters. Data on community responses were collected for five years following fire. Structural equation modeling (SEM) was used to relate plant species richness to plant abundance, fire severity, abiotic conditions, within-plot heterogeneity, stand age, and position in the landscape. Temporal dynamics of average richness response was also modeled. Richness was highest in the first year following fire, indicating postfire enhancement of diversity. A general decline in richness over time was detected, with year-to-year variation attributable to annual variations in precipitation. Peak richness in the landscape was found where (1) plant abundance was moderately high, (2) within-plot heterogeneity was high, (3) soils were moderately low in nitrogen, high in sand content, and with high rock cover, (4) fire severity was low, and (5) stands were young prior to fire. Many of these characteristics were correlated with position in the landscape and associated conditions. We infer from the SEM results that postfire richness in this system is strongly influenced by local conditions and that these conditions are, in turn, predictably related to landscape-level conditions. For example, we observed that older stands of shrubs were characterized by more severe fires, which were associated with a low recovery of plant cover and low richness. These results may have implications for the use of prescribed fire in this system if these findings extrapolate to prescribed burns as we would expect. ?? 2006 by the Ecological Society of America.

  19. More rapid shift to a benthic niche in larger Gadus morhua juveniles.

    Science.gov (United States)

    Ólafsdóttir, G Á; Gunnarsson, G S; Karlsson, H

    2015-08-01

    Trophic use by Atlantic cod Gadus morhua juveniles was examined early and late in the shift from pelagic to benthic habitats. Changes in the proportion of pelagic copepods, estimates of benthic prey indicated by isotope mixing models and stable-isotope values between sample periods suggested a gradual shift towards a benthic niche. Values of the trophic proxies, however, changed most markedly in the largest juvenile group, suggesting a more rapid trophic niche shift, and in turn competitive advantage, of larger juveniles.

  20. Stemness & Niche sans Frontiers – The Cancer Stem Cell myth

    Directory of Open Access Journals (Sweden)

    Editorial

    2014-04-01

    malignant and aggressive metastatic phenotype during their period of latency in the bone marrow [5]. Based on these findings, it is pessimistically fascinating to wonder how these cancer stem cells are able to maintain their stemness and tissue characteristic properties inspite of moving across environments where the niche characteristics might be drastically different from their site of origin. Also what is the factor that makes these cancer stem cells different from normal stem cells; is it a component in their cell or is it the niche that moulds itself to the tunes of the cancer stem cell, the charmer. The article by Kasai and colleagues in this issue is an article of high relevance, in which they propose the micro-environment as a ‘cancerous niche’ and they have discussed its role in the formation and maintenance of cancer stem cells based on recent experimental evidence of creating cancer stem cell models from induced pluripotent stem cells. Elaborate researches are warranted to study the nature of the cancer stem cells in conserving their ‘stemness’ and their ability to create a niche even at distant sites different from their tissues/organs of origin to endure their viability and propagation.

  1. Testing the niche apportionment hypothesis with parasite communities: is random assortment always the rule?

    Science.gov (United States)

    Muñoz, G; Mouillot, D; Poulin, R

    2006-05-01

    Niche apportionment models have only been applied once to parasite communities. Only the random assortment model (RA), which indicates that species abundances are independent from each other and that interspecific competition is unimportant, provided a good fit to 3 out of 6 parasite communities investigated. The generality of this result needs to be validated, however. In this study we apply 5 niche apportionment models to the parasite communities of 14 fish species from the Great Barrier Reef. We determined which model fitted the data when using either numerical abundance or biomass as an estimate of parasite abundance, and whether the fit of niche apportionment models depends on how the parasite community is defined (e.g. ecto, endoparasites or all parasites considered together). The RA model provided a good fit for the whole community of parasites in 7 fish species when using biovolume (as a surrogate of biomass) as a measure of species abundance. The RA model also fitted observed data when ecto- and endoparasites were considered separately, using abundance or biovolume, but less frequently. Variation in fish sizes among species was not associated with the probability of a model fitting the data. Total numerical abundance and biovolume of parasites were not related across host species, suggesting that they capture different aspects of abundance. Biovolume is not only a better measurement to use with niche-orientated models, it should also be the preferred descriptor to analyse parasite community structure in other contexts. Most of the biological assumptions behind the RA model, i.e. randomness in apportioning niche space, lack of interspecific competition, independence of abundance among different species, and species with variable niches in changeable environments, are in accordance with some previous findings on parasite communities. Thus, parasite communities may generally be unsaturated with species, with empty niches, and interspecific interactions may

  2. Common cancer in a wild animal: the California sea lion (Zalophus californianus) as an emerging model for carcinogenesis.

    Science.gov (United States)

    Browning, Helen M; Gulland, Frances M D; Hammond, John A; Colegrove, Kathleen M; Hall, Ailsa J

    2015-07-19

    Naturally occurring cancers in non-laboratory species have great potential in helping to decipher the often complex causes of neoplasia. Wild animal models could add substantially to our understanding of carcinogenesis, particularly of genetic and environmental interactions, but they are currently underutilized. Studying neoplasia in wild animals is difficult and especially challenging in marine mammals owing to their inaccessibility, lack of exposure history, and ethical, logistical and legal limits on experimentation. Despite this, California sea lions (Zalophus californianus) offer an opportunity to investigate risk factors for neoplasia development that have implications for terrestrial mammals and humans who share much of their environment and diet. A relatively accessible California sea lion population on the west coast of the USA has a high prevalence of urogenital carcinoma and is regularly sampled during veterinary care in wildlife rehabilitation centres. Collaborative studies have revealed that genotype, persistent organic pollutants and a herpesvirus are all associated with this cancer. This paper reviews research to date on the epidemiology and pathogenesis of urogenital carcinoma in this species, and presents the California sea lion as an important and currently underexploited wild animal model of carcinogenesis.

  3. Impact of boundary regions on the interior circulation of the California Current System in a regional modeling framework

    Science.gov (United States)

    Veneziani, M.; Edwards, C.; Moore, A.

    2008-12-01

    We use the Regional Ocean Modeling System (ROMS) to model the circulation of the California Current System (CCS) using ECCO-GODAE products to force the model at the open boundaries of the domain. We investigate the impact that lateral boundary forcing (and the boundary region in general) has on particular metrics of the interior circulation by adopting both an adjoint model and a traditional sensitivity approach. Adjoint methods are naturally suited to sensitivity studies as they provide the direct dependencies of circulation metrics on uncertainties of the model initial conditions, surface and lateral external forcing, and model parameters, but their results are only valid within the time scale during which the linearity assumption underlying adjoint models can be considered to hold. More traditional sensitivity studies must be conducted to investigate longer time scales. We describe the adjoint model results for two metrics that represent the upwelling processes of the Central California region and the mean sea level field of the coastal circulation, respectively. The spatial distribution of the adjoint sensitivity fields allows us to quantify the contribution of the boundary regions over a biweekly time scale. We investigate longer time scales by adopting two methods: 1) apply different ECCO products at the open boundaries and evaluate mean stratification changes in the CalCOFI coastal region; 2) release passive tracers at the boundaries and calculate ventilation time scales and pathways from the boundary areas to the CCS interior.

  4. Mapping the zoonotic niche of Ebola virus disease in Africa.

    Science.gov (United States)

    Pigott, David M; Golding, Nick; Mylne, Adrian; Huang, Zhi; Henry, Andrew J; Weiss, Daniel J; Brady, Oliver J; Kraemer, Moritz U G; Smith, David L; Moyes, Catherine L; Bhatt, Samir; Gething, Peter W; Horby, Peter W; Bogoch, Isaac I; Brownstein, John S; Mekaru, Sumiko R; Tatem, Andrew J; Khan, Kamran; Hay, Simon I

    2014-09-08

    Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976-2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.

  5. New kinematic models for Pacific-North America Motion from 3 Ma to Present, II: Evidence for a “Baja California Shear Zone”

    Science.gov (United States)

    Dixon, Timothy; Farina, Fred; DeMets, Charles; Suarez-Vidal, Francisco; Fletcher, John; Marquez-Azua, Bertha; Miller, Meghan; Sanchez, Osvaldo; Umhoefer, Paul

    2000-12-01

    We use new models for present-day Pacific-North America motion to evaluate the tectonics of offshore regions west of the Californias. Vandenburg in coastal Alta California moves at the Pacific plate velocity within uncertainties (˜1 mm/yr) after correcting for strain accumulation on the San Andreas and San Gregorio-Hosgri faults with a model that includes a viscoelastic lower crust. Modeled and measured velocities at coastal sites in Baja California south of the Agua Blanca fault, a region that most previous models consider Pacific plate, differ by 3-8 mm/yr, with coastal sites moving slower that the Pacific plate. We interpret these discrepancies in terms of strain accumulation on known on-shore faults, combined with right lateral slip at a rate of 3-4 mm/yr on additional faults offshore peninsular Baja California in the Pacific. Offshore seismicity, offset Quaternary features along the west coast of Baja California, and a discrepancy between the magnetically determined spreading rate in the Gulf Rise and the total plate rate from a geological model provide independent evidence for a “Baja California shear zone.”

  6. River and Reservoir Operations Model, Truckee River basin, California and Nevada, 1998

    Science.gov (United States)

    Berris, Steven N.; Hess, Glen W.; Bohman, Larry R.

    2001-01-01

    The demand for all uses of water in the Truckee River Basin, California and Nevada, commonly is greater than can be supplied. Storage reservoirs in the system have a maximum effective total capacity equivalent to less than two years of average river flows, so longer-term droughts can result in substantial water-supply shortages for irrigation and municipal users and may stress fish and wildlife ecosystems. Title II of Public Law (P.L.) 101-618, the Truckee?Carson?Pyramid Lake Water Rights Settlement Act of 1990, provides a foundation for negotiating and developing operating criteria, known as the Truckee River Operating Agreement (TROA), to balance interstate and interbasin allocation of water rights among the many interests competing for water from the Truckee River. In addition to TROA, the Truckee River Water Quality Settlement Agreement (WQSA), signed in 1996, provides for acquisition of water rights to resolve water-quality problems during low flows along the Truckee River in Nevada. Efficient execution of many of the planning, management, or environmental assessment requirements of TROA and WQSA will require detailed water-resources data coupled with sound analytical tools. Analytical modeling tools constructed and evaluated with such data could help assess effects of alternative operational scenarios related to reservoir and river operations, water-rights transfers, and changes in irrigation practices. The Truckee?Carson Program of the U.S. Geological Survey, to support U.S. Department of the Interior implementation of P.L. 101-618, is developing a modeling system to support efficient water-resources planning, management, and allocation. The daily operations model documented herein is a part of the modeling system that includes a database management program, a graphical user interface program, and a program with modules that simulate river/reservoir operations and a variety of hydrologic processes. The operations module is capable of simulating lake

  7. ARAC dispersion modeling of the August 1998 Tracy, California tire fire

    Energy Technology Data Exchange (ETDEWEB)

    Aluzzi, F J; Baskett, R L; Bowen, B M; Foster, C S; Pace, J C; Pobanz, B; Vogt, P J

    1998-08-28

    At about 4:30 pm PDT on Friday, August 7, 1998 a fire ignited the large tire disposal pit of Royster Tire Co. on Macarthur Drive about 5 km (3 miles) south of downtown Tracy, California. While providing on-scene mutual aid late Friday night, the LLNL Fire Department called and requested that the Atmospheric Release Advisory Capability (ARAC) make a plume forecast for Saturday. The response team in the field was interested in the forecasted location as well as an estimate of potential health effects on the following day. Not having any previous experience with tire fire source terms, ARAC assessors used a constant unit source rate (1 g/s) of particulate and produced plots showing only the location of the ground-level normalized time-integrated air concentrations from the smoke plume. Very early Saturday morning the assessors faxed plots of ground-level smoke air concentrations forecasted for Saturday from 6 am through 6 pm PDT to the Tracy Fire Emergency Operations Center. (As a part of standard procedure, before delivering the plots, the assessors notified ARAC's DOE sponsor.) Fortunately due to the intense heat from the fire, the dense black smoke immediately lofted into the air preventing high ground-level concentrations close to the tire dump. Later on Saturday morning ARAC forecasted a second set of plume integrated air concentrations for Sunday. By Monday the intensity of the fire lessened, and ARAC's support was no longer requested. Following ARAC's response, we made a third calculation on a large scale of the continuous smoke dispersion for 3 days after the fire. A newspaper photograph showed the plume initially rising toward the northeast and the upper part of the smoke cloud turning counterclockwise toward the north. Winds from ARAC's mesoscale prognostic model reproduced this plume structure, while data from the Friday afternoon sounding from Oakland did not. On the 250 km scale, using gridded wind outputs from our mesoscale forecast

  8. Climatic niche divergence and habitat suitability of eight alien invasive weeds in China under climate change.

    Science.gov (United States)

    Wan, Ji-Zhong; Wang, Chun-Jing; Tan, Jing-Fang; Yu, Fei-Hai

    2017-03-01

    Testing climatic niche divergence and modeling habitat suitability under conditions of climate change are important for developing strategies to limit the introduction and expansion of alien invasive weeds (AIWs) and providing important ecological and evolutionary insights. We assessed climatic niches in both native and invasive ranges as well as habitat suitability under climate change for eight representative Chinese AIWs from the American continent. We used climatic variables associated with occurrence records and developed ecological niche models with Maxent. Interestingly, the climatic niches of all eight AIWs diverged significantly between the native and invasive ranges (the American continent and China). Furthermore, the AIWs showed larger climatic niche breadths in the invasive ranges than in the native ranges. Our results suggest that climatic niche shifts between native and invasive ranges occurred. Thus, the occurrence records of both native and invasive regions must be considered when modeling and predicting the spatial distributions of AIWs under current and future climate scenarios. Owing to high habitat suitability, AIWs were more likely to expand into regions of low latitude, and future climate change was predicted to result in a shift in the AIWs in Qinghai and Tibet (regions of higher altitude) as well as Heilongjiang, Jilin, Liaoning, Inner Mongolia, and Gansu (regions of higher latitude). Our results suggest that we need measures to prevent and control AIW expansion at the country-wide level.

  9. Biodiversity influences plant productivity through niche-efficiency.

    Science.gov (United States)

    Liang, Jingjing; Zhou, Mo; Tobin, Patrick C; McGuire, A David; Reich, Peter B

    2015-05-05

    The loss of biodiversity is threatening ecosystem productivity and services worldwide, spurring efforts to quantify its effects on the functioning of natural ecosystems. Previous research has focused on the positive role of biodiversity on resource acquisition (i.e., niche complementarity), but a lack of study on resource utilization efficiency, a link between resource and productivity, has rendered it difficult to quantify the biodiversity-ecosystem functioning relationship. Here we demonstrate that biodiversity loss reduces plant productivity, other things held constant, through theory, empirical evidence, and simulations under gradually relaxed assumptions. We developed a theoretical model named niche-efficiency to integrate niche complementarity and a heretofore-ignored mechanism of diminishing marginal productivity in quantifying the effects of biodiversity loss on plant productivity. Based on niche-efficiency, we created a relative productivity metric and a productivity impact index (PII) to assist in biological conservation and resource management. Relative productivity provides a standardized measure of the influence of biodiversity on individual productivity, and PII is a functionally based taxonomic index to assess individual species' inherent value in maintaining current ecosystem productivity. Empirical evidence from the Alaska boreal forest suggests that every 1% reduction in overall plant diversity could render an average of 0.23% decline in individual tree productivity. Out of the 283 plant species of the region, we found that large woody plants generally have greater PII values than other species. This theoretical model would facilitate the integration of biological conservation in the international campaign against several pressing global issues involving energy use, climate change, and poverty.

  10. Importance of the temperature field and its uncertainties in modeling ductile deformation of the southern California lithosphere

    Science.gov (United States)

    Thatcher, W. R.; Chapman, D. S.; Williams, C. F.; Hearn, E. H.

    2015-12-01

    Temperature is arguably the most important parameter controlling ductile deformation in tectonically active regions. Laboratory measurements at lower crust and upper mantle conditions define the mechanisms controlling ductile deformation and constrain quantitative rules relating stress and strain rate. Exhumed ductily deformed rocks reveal the micromechanics of deformation, supplying ground truth that can be compared with lab results. However, even if the mechanism and ductile deformation rules are accepted at face value, strain rates are exquisitely dependent on temperature. Here we critically assess observational data relevant to constraining the southern California lithospheric temperature field. Our goal is to improve estimates of the 3D temperature field and its real uncertainties and apply them to regional deformation modeling. We use a phased approach to estimating geotherms, beginning with simple 1D steady state conductive models. We identify the most important parameters and disaggregate them, separately examining the effects of varying radiogenic heat source concentration, rock type, crust and lithosphere thickness and asthenosphere solidus. We assess geotherm uncertainties by assigning realistic error bounds on all input quantities, propagate these uncertainties by Monte Carlo sampling and determine probability density functions for the geotherm. We find that although other parameter uncertainties contribute, variability in heat sources produces the largest variation in model-predicted geotherms. Because heat production depends strongly on rock type, better characterization of crustal lithology using refined seismic imaging results now becoming available beneath southern California is likely to produce the largest improvements in thermal models. Nonetheless, substantial uncertainty will remain, arguing for adoption of one or a few standard thermal models as common starting points for regional deformation modeling in southern California and elsewhere.

  11. Niche-modulated and niche-modulating genes in bone marrow cells

    Science.gov (United States)

    Cohen, Y; Garach-Jehoshua, O; Bar-Chaim, A; Kornberg, A

    2012-01-01

    Bone marrow (BM) cells depend on their niche for growth and survival. However, the genes modulated by niche stimuli have not been discriminated yet. For this purpose, we investigated BM aspirations from patients with various hematological malignancies. Each aspirate was fractionated, and the various samples were fixed at different time points and analyzed by microarray. Identification of niche-modulated genes relied on sustained change in expression following loss of niche regulation. Compared with the reference (‘authentic') samples, which were fixed immediately following aspiration, the BM samples fixed after longer stay out-of-niche acquired numerous changes in gene-expression profile (GEP). The overall genes modulated included a common subset of functionally diverse genes displaying prompt and sustained ‘switch' in expression irrespective of the tumor type. Interestingly, the ‘switch' in GEP was reversible and turned ‘off-and-on' again in culture conditions, resuming cell–cell–matrix contact versus respread into suspension, respectively. Moreover, the resuming of contact prolonged the survival of tumor cells out-of-niche, and the regression of the ‘contactless switch' was followed by induction of a new set of genes, this time mainly encoding extracellular proteins including angiogenic factors and extracellular matrix proteins. Our data set, being unique in authentic expression design, uncovered niche-modulated and niche-modulating genes capable of controlling homing, expansion and angiogenesis. PMID:23241658

  12. Macro-Climatic Distribution Limits Show Both Niche Expansion and Niche Specialization among C4 Panicoids.

    Science.gov (United States)

    Aagesen, Lone; Biganzoli, Fernando; Bena, Julia; Godoy-Bürki, Ana C; Reinheimer, Renata; Zuloaga, Fernando O

    2016-01-01

    Grasses are ancestrally tropical understory species whose current dominance in warm open habitats is linked to the evolution of C4 photosynthesis. C4 grasses maintain high rates of photosynthesis in warm and water stressed environments, and the syndrome is considered to induce niche shifts into these habitats while adaptation to cold ones may be compromised. Global biogeographic analyses of C4 grasses have, however, concentrated on diversity patterns, while paying little attention to distributional limits. Using phylogenetic contrast analyses, we compared macro-climatic distribution limits among ~1300 grasses from the subfamily Panicoideae, which includes 4/5 of the known photosynthetic transitions in grasses. We explored whether evolution of C4 photosynthesis correlates with niche expansions, niche changes, or stasis at subfamily level and within the two tribes Paniceae and Paspaleae. We compared the climatic extremes of growing season temperatures, aridity, and mean temperatures of the coldest months. We found support for all the known biogeographic distribution patterns of C4 species, these patterns were, however, formed both by niche expansion and niche changes. The only ubiquitous response to a change in the photosynthetic pathway within Panicoideae was a niche expansion of the C4 species into regions with higher growing season temperatures, but without a withdrawal from the inherited climate niche. Other patterns varied among the tribes, as macro-climatic niche evolution in the American tribe Paspaleae differed from the pattern supported in the globally distributed tribe Paniceae and at family level.

  13. Food-web structure in low- and high-dimensional trophic niche spaces

    Science.gov (United States)

    Rossberg, Axel G.; Brännström, Åke; Dieckmann, Ulf

    2010-01-01

    A question central to modelling and, ultimately, managing food webs concerns the dimensionality of trophic niche space, that is, the number of independent traits relevant for determining consumer–resource links. Food-web topologies can often be interpreted by assuming resource traits to be specified by points along a line and each consumer's diet to be given by resources contained in an interval on this line. This phenomenon, called intervality, has been known for 30 years and is widely acknowledged to indicate that trophic niche space is close to one-dimensional. We show that the degrees of intervality observed in nature can be reproduced in arbitrary-dimensional trophic niche spaces, provided that the processes of evolutionary diversification and adaptation are taken into account. Contrary to expectations, intervality is least pronounced at intermediate dimensions and steadily improves towards lower- and higher-dimensional trophic niche spaces. PMID:20462875

  14. Channel responses to varying sediment input: A flume experiment modeled after Redwood Creek, California

    Science.gov (United States)

    Madej, M.A.; Sutherland, D.G.; Lisle, T.E.; Pryor, B.

    2009-01-01

    At the reach scale, a channel adjusts to sediment supply and flow through mutual interactions among channel form, bed particle size, and flow dynamics that govern river bed mobility. Sediment can impair the beneficial uses of a river, but the timescales for studying recovery following high sediment loading in the field setting make flume experiments appealing. We use a flume experiment, coupled with field measurements in a gravel-bed river, to explore sediment transport, storage, and mobility relations under various sediment supply conditions. Our flume experiment modeled adjustments of channel morphology, slope, and armoring in a gravel-bed channel. Under moderate sediment increases, channel bed elevation increased and sediment output increased, but channel planform remained similar to pre-feed conditions. During the following degradational cycle, most of the excess sediment was evacuated from the flume and the bed became armored. Under high sediment feed, channel bed elevation increased, the bed became smoother, mid-channel bars and bedload sheets formed, and water surface slope increased. Concurrently, output increased and became more poorly sorted. During the last degradational cycle, the channel became armored and channel incision ceased before all excess sediment was removed. Selective transport of finer material was evident throughout the aggradational cycles and became more pronounced during degradational cycles as the bed became armored. Our flume results of changes in bed elevation, sediment storage, channel morphology, and bed texture parallel those from field surveys of Redwood Creek, northern California, which has exhibited channel bed degradation for 30??years following a large aggradation event in the 1970s. The flume experiment suggested that channel recovery in terms of reestablishing a specific morphology may not occur, but the channel may return to a state of balancing sediment supply and transport capacity.

  15. Toxic volatile organic compounds in environmental tobacco smoke: Emission factors for modeling exposures of California populations

    Energy Technology Data Exchange (ETDEWEB)

    Daisey, J.M.; Mahanama, K.R.R.; Hodgson, A.T. [Lawrence Berkeley Lab., CA (United States)

    1994-10-01

    The primary objective of this study was to measure emission factors for selected toxic air contaminants in environmental tobacco smoke (ETS) using a room-sized environmental chamber. The emissions of 23 volatile organic compounds (VOCs), including, 1,3-butadiene, three aldehydes and two vapor-phase N-nitrosamines were determined for six commercial brands of cigarettes and reference cigarette 1R4F. The commercial brands were selected to represent 62.5% of the cigarettes smoked in California. For each brand, three cigarettes were machine smoked in the chamber. The experiments were conducted over four hours to investigate the effects of aging. Emission factors of the target compounds were also determined for sidestream smoke (SS). For almost all target compounds, the ETS emission factors were significantly higher than the corresponding SS values probably due to less favorable combustion conditions and wall losses in the SS apparatus. Where valid comparisons could be made, the ETS emission factors were generally in good agreement with the literature. Therefore, the ETS emission factors, rather than the SS values, are recommended for use in models to estimate population exposures from this source. The variabilities in the emission factors ({mu}g/cigarette) of the selected toxic air contaminants among brands, expressed as coefficients of variation, were 16 to 29%. Therefore, emissions among brands were Generally similar. Differences among brands were related to the smoked lengths of the cigarettes and the masses of consumed tobacco. Mentholation and whether a cigarette was classified as light or regular did not significantly affect emissions. Aging was determined not to be a significant factor for the target compounds. There were, however, deposition losses of the less volatile compounds to chamber surfaces.

  16. Modeling Land Application of Food-Processing Wastewater in the Central Valley, California

    Science.gov (United States)

    Rubin, Y.; Benito, P.; Miller, G.; McLaughlin, J.; Hou, Z.; Hermanowicz, S.; Mayer, U.

    2007-12-01

    California's Central Valley contains over 640 food-processing plants, serving a multi-billion dollar agricultural industry. These processors consume approximately 7.9 x 107 m3 of water per year. Approximately 80% of these processors discharge the resulting wastewater, which is typically high in organic matter, nitrogen, and salts, to land, and many of these use land application as a treatment method. Initial investigations revealed elevated salinity levels to be the most common form of groundwater degradation near land application sites, followed by concentrations of nitrogen compounds, namely ammonia and nitrate. Enforcement actions have been taken against multiple food processors, and the regulatory boards have begun to re-examine the land disposal permitting process. This paper summarizes a study that was commissioned in support of these actions. The study has multiple components which will be reviewed briefly, including: (1) characterization of the food-processing related waste stream; (2) fate and transport of the effluent waste stream in the unsaturated zone at the land application sites; (3) fate and transport of the effluent waste stream at the regional scale; (4) predictive uncertainty due to spatial variability and data scarcity at the land application sites and at the regional scale; (5) problem mitigation through off-site and in-situ actions; (6) long-term solutions. The emphasis of the talk will be placed on presenting and demonstrating a stochastic framework for modeling the transport and attenuation of these wastes in the vadose zone and in the saturated zone, and the related site characterization needs, as affected by site conditions, water table depth, waste water application rate, and waste constituent concentrations.

  17. Artificial hematopoietic stem cell niche: bioscaffolds to microfluidics to mathematical simulations.

    Science.gov (United States)

    Didwania, Maruti; Didwania, Anjani; Mehta, Geeta; Basak, Grzegorz W; Yasukawa, Satoshi; Takayama, Shuichi; de Necochea-Campion, Rosalia; Srivastava, Anand; Carrier, Ewa

    2011-01-01

    Due to the recent advancements in stem cell biology and engineering, scientists have been increasingly interested in creating in vitro niches for embryonic and adult stem cells, and, following induction and differentiation with the appropriate media, the production of large scale blood production. This artificially created niche for hematopoietic cells will be composed of three materials: the stem cells themselves, the scaffold surrounding the stem cell, and the media used to expand and differentiate the stem cells. This paper will examine the recent advancements in technology for each of these relating to the development of an artificial stem cell niche. Many key aspects of the artificial niche need to be improved on before we can scale up the engineered device for large scale blood production including more efficient methods of retrieval of the embroid bodies produced from the microfluidic channels. The current state of experimental methods such as these as well as relevant discoveries in related fields that could be applied to artificial niche technology is described in this paper. Furthermore, we present a mathematical model to describe cell expansion in the artificial hematopoietic stem cell niche in order to design and optimize a scaled-up bioreactor. The mathematical model describes the dynamics of expansion, and maintenance of homeostasis in the bioreactor.

  18. Remote Sensing-Based Detection and Spatial Pattern Analysis for Geo-Ecological Niche Modeling of Tillandsia SPP. In the Atacama, Chile

    Science.gov (United States)

    Wolf, N.; Siegmund, A.; del Río, C.; Osses, P.; García, J. L.

    2016-06-01

    In the coastal Atacama Desert in Northern Chile plant growth is constrained to so-called `fog oases' dominated by monospecific stands of the genus Tillandsia. Adapted to the hyperarid environmental conditions, these plants specialize on the foliar uptake of fog as main water and nutrient source. It is this characteristic that leads to distinctive macro- and micro-scale distribution patterns, reflecting complex geo-ecological gradients, mainly affected by the spatiotemporal occurrence of coastal fog respectively the South Pacific Stratocumulus clouds reaching inlands. The current work employs remote sensing, machine learning and spatial pattern/GIS analysis techniques to acquire detailed information on the presence and state of Tillandsia spp. in the Tarapacá region as a base to better understand the bioclimatic and topographic constraints determining the distribution patterns of Tillandsia spp. Spatial and spectral predictors extracted from WorldView-3 satellite data are used to map present Tillandsia vegetation in the Tarapaca region. Regression models on Vegetation Cover Fraction (VCF) are generated combining satellite-based as well as topographic variables and using aggregated high spatial resolution information on vegetation cover derived from UAV flight campaigns as a reference. The results are a first step towards mapping and modelling the topographic as well as bioclimatic factors explaining the spatial distribution patterns of Tillandsia fog oases in the Atacama, Chile.

  19. REMOTE SENSING-BASED DETECTION AND SPATIAL PATTERN ANALYSIS FOR GEO-ECOLOGICAL NICHE MODELING OF TILLANDSIA SPP. IN THE ATACAMA, CHILE

    Directory of Open Access Journals (Sweden)

    N. Wolf

    2016-06-01

    Full Text Available In the coastal Atacama Desert in Northern Chile plant growth is constrained to so-called ‘fog oases’ dominated by monospecific stands of the genus Tillandsia. Adapted to the hyperarid environmental conditions, these plants specialize on the foliar uptake of fog as main water and nutrient source. It is this characteristic that leads to distinctive macro- and micro-scale distribution patterns, reflecting complex geo-ecological gradients, mainly affected by the spatiotemporal occurrence of coastal fog respectively the South Pacific Stratocumulus clouds reaching inlands. The current work employs remote sensing, machine learning and spatial pattern/GIS analysis techniques to acquire detailed information on the presence and state of Tillandsia spp. in the Tarapacá region as a base to better understand the bioclimatic and topographic constraints determining the distribution patterns of Tillandsia spp. Spatial and spectral predictors extracted from WorldView-3 satellite data are used to map present Tillandsia vegetation in the Tarapaca region. Regression models on Vegetation Cover Fraction (VCF are generated combining satellite-based as well as topographic variables and using aggregated high spatial resolution information on vegetation cover derived from UAV flight campaigns as a reference. The results are a first step towards mapping and modelling the topographic as well as bioclimatic factors explaining the spatial distribution patterns of Tillandsia fog oases in the Atacama, Chile.

  20. Niche construction on Bali: the gods of the countryside.

    Science.gov (United States)

    Lansing, J Stephen; Fox, Karyn M

    2011-03-27

    Human niche construction encompasses both purely biological phenomena, such as the evolution of lactose tolerance, and dual inheritance theory, which investigates the transmission of cultural information. But does niche construction help to explain phenomena in which conscious intention also plays a role? The creation of the engineered landscape of Balinese rice terraces offers a test case. Population genetic analysis and archaeological evidence are used to investigate whether this phenomenon emerged historically from trial and error by generations of farmers, or alternatively was designed by Bali's rulers. In light of strong support for the former hypothesis, two models are developed to explore the emergence of functional structure at both local and global scales. As time goes forward and selected patterns of irrigation schedules are implemented, local variation in rice harvests influences future decisions by the farmers, creating a coupled human-natural system governed by feedback from the environment. This mathematical analysis received a measure of empirical support when government agricultural policies severed the local feedback channels, resulting in the almost instantaneous collapse of rice harvests. The historical process of niche construction may also have included an evolution of religious consciousness, reflected in the beliefs and practices of the water temple cult.

  1. Implications of irradiating the subventricular zone stem cell niche

    Directory of Open Access Journals (Sweden)

    Vivian Capilla-Gonzalez

    2016-03-01

    Full Text Available Radiation therapy is a standard treatment for brain tumor patients. However, it comes with side effects, such as neurological deficits. While likely multi-factorial, the effect may in part be associated with the impact of radiation on the neurogenic niches. In the adult mammalian brain, the neurogenic niches are localized in the subventricular zone (SVZ of the lateral ventricles and the dentate gyrus of the hippocampus, where the neural stem cells (NSCs reside. Several reports showed that radiation produces a drastic decrease in the proliferative capacity of these regions, which is related to functional decline. In particular, radiation to the SVZ led to a reduced long-term olfactory memory and a reduced capacity to respond to brain damage in animal models, as well as compromised tumor outcomes in patients. By contrast, other studies in humans suggested that increased radiation dose to the SVZ may be associated with longer progression-free survival in patients with high-grade glioma. In this review, we summarize the cellular and functional effects of irradiating the SVZ niche. In particular, we review the pros and cons of using radiation during brain tumor treatment, discussing the complex relationship between radiation dose to the SVZ and both tumor control and toxicity.

  2. Implications of irradiating the subventricular zone stem cell niche.

    Science.gov (United States)

    Capilla-Gonzalez, Vivian; Bonsu, Janice M; Redmond, Kristin J; Garcia-Verdugo, Jose Manuel; Quiñones-Hinojosa, Alfredo

    2016-03-01

    Radiation therapy is a standard treatment for brain tumor patients. However, it comes with side effects, such as neurological deficits. While likely multi-factorial, the effect may in part be associated with the impact of radiation on the neurogenic niches. In the adult mammalian brain, the neurogenic niches are localized in the subventricular zone (SVZ) of the lateral ventricles and the dentate gyrus of the hippocampus, where the neural stem cells (NSCs) reside. Several reports showed that radiation produces a drastic decrease in the proliferative capacity of these regions, which is related to functional decline. In particular, radiation to the SVZ led to a reduced long-term olfactory memory and a reduced capacity to respond to brain damage in animal models, as well as compromised tumor outcomes in patients. By contrast, other studies in humans suggested that increased radiation dose to the SVZ may be associated with longer progression-free survival in patients with high-grade glioma. In this review, we summarize the cellular and functional effects of irradiating the SVZ niche. In particular, we review the pros and cons of using radiation during brain tumor treatment, discussing the complex relationship between radiation dose to the SVZ and both tumor control and toxicity.

  3. Residual analysis methods for space--time point processes with applications to earthquake forecast models in California

    CERN Document Server

    Clements, Robert Alan; Schorlemmer, Danijel; 10.1214/11-AOAS487

    2012-01-01

    Modern, powerful techniques for the residual analysis of spatial-temporal point process models are reviewed and compared. These methods are applied to California earthquake forecast models used in the Collaboratory for the Study of Earthquake Predictability (CSEP). Assessments of these earthquake forecasting models have previously been performed using simple, low-power means such as the L-test and N-test. We instead propose residual methods based on rescaling, thinning, superposition, weighted K-functions and deviance residuals. Rescaled residuals can be useful for assessing the overall fit of a model, but as with thinning and superposition, rescaling is generally impractical when the conditional intensity $\\lambda$ is volatile. While residual thinning and superposition may be useful for identifying spatial locations where a model fits poorly, these methods have limited power when the modeled conditional intensity assumes extremely low or high values somewhere in the observation region, and this is commonly t...

  4. Large, high-intensity fire events in Southern California shrublands: Debunking the fine-grain age patch model

    Science.gov (United States)

    Keeley, J.E.; Zedler, P.H.

    2009-01-01

    We evaluate the fine-grain age patch model of fire regimes in southern California shrublands. Proponents contend that the historical condition was characterized by frequent small to moderate size, slow-moving smoldering fires, and that this regime has been disrupted by fire suppression activities that have caused unnatural fuel accumulation and anomalously large and catastrophic wildfires. A review of more than 100 19th-century newspaper reports reveals that large, high-intensity wildfires predate modern fire suppression policy, and extensive newspaper coverage plus first-hand accounts support the conclusion that the 1889 Santiago Canyon Fire was the largest fire in California history. Proponents of the fine-grain age patch model contend that even the very earliest 20th-century fires were the result of fire suppression disrupting natural fuel structure. We tested that hypothesis and found that, within the fire perimeters of two of the largest early fire events in 1919 and 1932, prior fire suppression activities were insufficient to have altered the natural fuel structure. Over the last 130 years there has been no significant change in the incidence of large fires greater than 10000 ha, consistent with the conclusion that fire suppression activities are not the cause of these fire events. Eight megafires (???50 000 ha) are recorded for the region, and half have occurred in the last five years. These burned through a mosaic of age classes, which raises doubts that accumulation of old age classes explains these events. Extreme drought is a plausible explanation for this recent rash of such events, and it is hypothesized that these are due to droughts that led to increased dead fine fuels that promoted the incidence of firebrands and spot fires. A major shortcoming of the fine-grain age patch model is that it requires age-dependent flammability of shrubland fuels, but seral stage chaparral is dominated by short-lived species that create a dense surface layer of fine

  5. Best Practices Models for Implementing, Sustaining, and Using Instructional School Gardens in California

    Science.gov (United States)

    Hazzard, Eric L.; Moreno, Elizabeth; Beall, Deborah L.; Zidenberg-Cherr, Sheri

    2011-01-01

    To ascertain best practices for schools implementing or sustaining instructional school gardens by interviewing key members in 10 schools with exemplary instructional school gardens programs in California. Practices of schools with exemplary instructional school gardens programs were analyzed by constant comparative analysis using qualitative data…

  6. Incorporating anthropogenic influences into fire probability models: Effects of development and climate change on fire activity in California

    Science.gov (United States)

    Mann, M.; Moritz, M.; Batllori, E.; Waller, E.; Krawchuk, M.; Berck, P.

    2014-12-01

    The costly interactions between humans and natural fire regimes throughout California demonstrate the need to understand the uncertainties surrounding wildfire, especially in the face of a changing climate and expanding human communities. Although a number of statistical and process-based wildfire models exist for California, there is enormous uncertainty about the location and number of future fires. Models estimate an increase in fire occurrence between nine and fifty-three percent by the end of the century. Our goal is to assess the role of uncertainty in climate and anthropogenic influences on the state's fire regime from 2000-2050. We develop an empirical model that integrates novel information about the distribution and characteristics of future plant communities without assuming a particular distribution, and improve on previous efforts by integrating dynamic estimates of population density at each forecast time step. Historically, we find that anthropogenic influences account for up to fifty percent of the total fire count, and that further housing development will incite or suppress additional fires according to their intensity. We also find that the total area burned is likely to increase but at a slower than historical rate. Previous findings of substantially increased numbers of fires may be tied to the assumption of static fuel loadings, and the use of proxy variables not relevant to plant community distributions. We also find considerable agreement between GFDL and PCM model A2 runs, with decreasing fire counts expected only in areas of coastal influence below San Francisco and above Los Angeles. Due to potential shifts in rainfall patterns, substantial uncertainty remains for the semiarid deserts of the inland south. The broad shifts of wildfire between California's climatic regions forecast in this study point to dramatic shifts in the pressures plant and human communities will face by midcentury. The information provided by this study reduces the

  7. Engineering the niche for stem cells.

    Science.gov (United States)

    Tan, Shawna; Barker, Nicholas

    2013-12-01

    Much has been made about the potential for stem cells in regenerative medicine but the reality is that the development of actual therapies has been slow. Adult stem cells rely heavily on the assortment of biochemical and biophysical elements that constitute the local microenvironment in which they exist. One goal of biomedicine is to create an artificial yet biofunctional niche to support multipotency, differentiation and proliferation. Such tools would facilitate more conclusive experimentation by biologists, pharmaceutical scientists and tissue engineers. While many bioengineering techniques and platforms are already in use, technological innovations now allow this to be done at a higher resolution and specificity. Ultimately, the multidisciplinary integration of engineering and biology will allow the niche to be generated at a scale that can be clinically exploited. Using the systems that constitute the intestinal, hematopoietic and epidermal tissues, this article summarizes the various approaches and tools currently employed to recreate stem cell niches and also explores recent advances in the field.

  8. California Red-Legged Frog Range - CWHR [ds587

    Data.gov (United States)

    California Department of Resources — Vector datasets of CWHR range maps are one component of California Wildlife Habitat Relationships (CWHR), a comprehensive information system and predictive model for...

  9. Stable isotope evidence for trophic niche partitioning in a South African savanna rodent community

    Institute of Scientific and Technical Information of China (English)

    Jacqueline CODRON; Kevin J DUFFY; Nico L AVENANT; Matt SPONHEIMER; Jennifer LEICHLITER; Oliver PAINE; Paul SANDBERG; Daryl CODRON

    2015-01-01

    Species’ partitioning of resources remains one of the most integral components for understanding community assem-bly. Analysis of stable carbon and nitrogen isotopes in animal tissues has the potential to help resolve patterns of partitioning be-cause these proxies represent the individual’s diet and trophic niche, respectively. Using free-ranging rodents in a southern Afri-can savanna as a model community, we find that syntopic species within habitats occupy distinct isotope niches. Moreover, spe-cies with strongly overlapping isotope niches did not overlap in their spatial distribution patterns, suggesting an underlying effect of competitive exclusion. Niche conservatism appears to characterize the behaviour of most species in our sample – with little or no observed changes across habitats – with the exception of one species,Mastomys coucha. This species displayed a generalist distribution, being found in similar abundances across a variety of habitats. This spatial pattern was coupled with a generalist isotope niche that shifted across habitats, likely in response to changes in species composition over the same spatial gradient. The case forM. coucha supports contentions that past competition effects played a significant evolutionary role in shaping community structures of today, including the absence of strong interspecific niche overlaps within particular habitats. Our study highlights the value of stable isotope approaches to help resolve key questions in community ecology, and moreover introduces novel ana-lytical approaches to quantifying isotope niche breadths and niche overlaps that are easily comparable with traditional metrices [Current Zoology 61 (3): 397–441, 2015].

  10. Niche conservatism of Eulophia alta, a trans-Atlantic orchid species

    Directory of Open Access Journals (Sweden)

    Marta Kolanowska

    2014-03-01

    Full Text Available The genus Eulophia embraces over 230 species distributed through the tropical and subtropical Africa, Asia, Australia and the Americas. In Neotropics it is represented by a sole species – E. alta. The aim of the presented study was to evaluate the difference between ecological niches occupied by American and African populations of this species based on the ecological niche modeling. The similarity between the glacial and present niches occupied by E. alta was calculated and the factors limiting the species occurrence were identified. Areas of seasonal tropical forest, tropical savanna and woodland served as refugia for the studied species during last glacial maximum and they were more widespread in Neotropics than in Africa. No significant niche shift after last glacial maximum was observed. The distribution of E. alta in its whole range is restricted mainly by temperature seasonality. The differences in the niches occupied by African and Neotropical populations of E. alta suggest preglacial disjunction of the species range and independent adaptation of both groups. Despite the significant range disjunction of E. alta the species is characterized by relatively high degree of niche conservatism.

  11. Social niche specialization under constraints: personality, social interactions and environmental heterogeneity.

    Science.gov (United States)

    Montiglio, Pierre-Olivier; Ferrari, Caterina; Réale, Denis

    2013-05-19

    Several personality traits are mainly expressed in a social context, and others, which are not restricted to a social context, can be affected by the social interactions with conspecifics. In this paper, we focus on the recently proposed hypothesis that social niche specialization (i.e. individuals in a population occupy different social roles) can explain the maintenance of individual differences in personality. We first present ecological and social niche specialization hypotheses. In particular, we show how niche specialization can be quantified and highlight the link between personality differences and social niche specialization. We then review some ecological factors (e.g. competition and environmental heterogeneity) and the social mechanisms (e.g. frequency-dependent, state-dependent and social awareness) that may be associated with the evolution of social niche specialization and personality differences. Finally, we present a conceptual model and methods to quantify the contribution of ecological factors and social mechanisms to the dynamics between personality and social roles. In doing so, we suggest a series of research objectives to help empirical advances in this research area. Throughout this paper, we highlight empirical studies of social niche specialization in mammals, where available.

  12. Classification and comparison of niche services for developing strategy of medical tourism in Asian countries.

    Science.gov (United States)

    Chen, Hung-chi; Kuo, Hsin-chih; Chung, Kuo-Piao; Chang, Sophia; Su, Syi; Yang, Ming-chin

    2010-01-01

    Medical tourism is a new trend in medical service. It is booming not only in Asian countries but also in European and South American countries. Worldwide competition of medical service is expected in the future, and niche service will be a "trademark" for the promotion of global medicine. Niche service also functions for market segmentation. Niche services are usually surgical procedures. A study was carried out to compare different strategies for developing medical tourism in Asian countries. The role of a niche service is evaluated in the initiation and further development of medical tourism for individual countries. From this study, a general classification was proposed in terms of treatment procedures. It can be used as a useful guideline for additional studies in medical tourism. Niche service plays the following roles in the development of medical tourism: (1) It attracts attention in the mass media and helps in subsequent promotion of business, (2) it exerts pressure on the hospital, which must improve the quality of health care provided in treating foreign patients, especially the niche services, and (3) it is a tool for setting up the business model. E-Da Hospital is an example for developing medical tourism in Taiwan. A side effect is that niche service brings additional foreign patients, which will contribute to the benefit of the hospital, but this leaves less room for treating domestic patients. A niche service is a means of introduction for entry into the market of medical tourism. How to create a successful story is important for the development of a niche service. When a good reputation has been established, the information provided on the Internet can last for a long time and can spread internationally to form a distinguished mark for further development. Niche services can be classified into 3 categories: (1) Low-risk procedures with large price differences and long stay after retirement; (2) high-risk procedures with less of a price difference

  13. Implications of the Regional Earthquake Likelihood Models test of earthquake forecasts in California

    Directory of Open Access Journals (Sweden)

    Michael Karl Sachs

    2012-09-01

    Full Text Available The Regional Earthquake Likelihood Models (RELM test was the first competitive comparison of prospective earthquake forecasts. The test was carried out over 5 years from 1 January 2006 to 31 December 2010 over a region that included all of California. The test area was divided into 7682 0.1°x0.1° spatial cells. Each submitted forecast gave the predicted numbers of earthquakes Nemi larger than M=4.95 in 0.1 magnitude bins for each cell. In this paper we present a method that separates the forecast of the number of test earthquakes from the forecast of their locations. We first obtain the number Nem of forecast earthquakes in magnitude bin m. We then determine the conditional probability λemi=Nemi/Nem that an earthquake in magnitude bin m will occur in cell i. The summation of λemi over all 7682 cells is unity. A random (no skill forecast gives equal values of λemi for all spatial cells and magnitude bins. The skill of a forecast, in terms of the location of the earthquakes, is measured by the success in assigning large values of λemi to the cells in which earthquakes occur and low values of λemi to the cells where earthquakes do not occur. Thirty-one test earthquakes occurred in 27 different combinations of spatial cells i and magnitude bins m, we had the highest value of λemi for that mi cell. We evaluate the performance of eleven submitted forecasts in two ways. First, we determine the number of mi cells for which the forecast λemi was the largest, the best forecast is the one with the highest number. Second, we determine the mean value of λemi for the 27 mi cells for each forecast. The best forecast has the highest mean value of λemi. The success of a forecast during the test period is dependent on the allocation of the probabilities λemi between the mi cells, since the sum over the mi cells is unity. We illustrate the forecast distributions of λemi and discuss their differences. We conclude that the RELM test was successful in

  14. Groundwater simulation and management models for the upper Klamath Basin, Oregon and California

    Science.gov (United States)

    Gannett, Marshall W.; Wagner, Brian J.; Lite, Kenneth E.

    2012-01-01

    The upper Klamath Basin encompasses about 8,000 square miles, extending from the Cascade Range east to the Basin and Range geologic province in south-central Oregon and northern California. The geography of the basin is dominated by forested volcanic uplands separated by broad interior basins. Most of the interior basins once held broad shallow lakes and extensive wetlands, but most of these areas have been drained or otherwise modified and are now cultivated. Major parts of the interior basins are managed as wildlife refuges, primarily for migratory waterfowl. The permeable volcanic bedrock of the upper Klamath Basin hosts a substantial regional groundwater system that provides much of the flow to major streams and lakes that, in turn, provide water for wildlife habitat and are the principal source of irrigation water for the basin's agricultural economy. Increased allocation of surface water for endangered species in the past decade has resulted in increased groundwater pumping and growing interest in the use of groundwater for irrigation. The potential effects of increased groundwater pumping on groundwater levels and discharge to springs and streams has caused concern among groundwater users, wildlife and Tribal interests, and State and Federal resource managers. To provide information on the potential impacts of increased groundwater development and to aid in the development of a groundwater management strategy, the U.S. Geological Survey, in collaboration with the Oregon Water Resources Department and the Bureau of Reclamation, has developed a groundwater model that can simulate the response of the hydrologic system to these new stresses. The groundwater model was developed using the U.S. Geological Survey MODFLOW finite-difference modeling code and calibrated using inverse methods to transient conditions from 1989 through 2004 with quarterly stress periods. Groundwater recharge and agricultural and municipal pumping are specified for each stress period. All

  15. Modeling spatial patterns of wildfire susceptibility in southern California: Applications of MODIS remote sensing data and mesoscale numerical weather models

    Science.gov (United States)

    Schneider, Philipp

    This dissertation investigates the potential of Moderate Resolution Imaging Spectroradiometer (MODIS) imagery and mesoscale numerical weather models for mapping wildfire susceptibility in general and for improving the Fire Potential Index (FPI) in southern California in particular. The dissertation explores the use of the Visible Atmospherically Resistant Index (VARI) from MODIS data for mapping relative greenness (RG) of vegetation and subsequently for computing the FPI. VARI-based RG was validated against in situ observations of live fuel moisture. The results indicate that VARI is superior to the previously used Normalized Difference Vegetation Index (NDVI) for computing RG. FPI computed using VARI-based RG was found to outperform the traditional FPI when validated against historical fire detections using logistic regression. The study further investigates the potential of using Multiple Endmember Spectral Mixture Analysis (MESMA) on MODIS data for estimating live and dead fractions of vegetation. MESMA fractions were compared against in situ measurements and fractions derived from data of a high-resolution, hyperspectral sensor. The results show that live and dead fractions obtained from MODIS using MESMA are well correlated with the reference data. Further, FPI computed using MESMA-based green vegetation fraction in lieu of RG was validated against historical fire occurrence data. MESMA-based FPI performs at a comparable level to the traditional NDVI-based FPI, but can do so using a single MODIS image rather than an extensive remote sensing time series as required for the RG approach. Finally this dissertation explores the potential of integrating gridded wind speed data obtained from the MM5 mesoscale numerical weather model in the FPI. A new fire susceptibility index, the Wind-Adjusted Fire Potential Index (WAFPI), was introduced. It modifies the FPI algorithm by integrating normalized wind speed. Validating WAFPI against historical wildfire events using

  16. Development of State Interindustry Models for Rocky Mountain Region and California

    Energy Technology Data Exchange (ETDEWEB)

    Sathaye, Jayant A.; Kunin, Leonard

    1976-02-01

    Interindustry tables have been developed for the eight Rocky Mountain States and California. These tables are based on the 367-order 1967 national interindustry table. The national matrix was expanded to 404 sectors by disaggregating the seven minerals industries to 44 industries. The state tables can be used for energy and other resource analysis. Regional impacts of alternate development strategies can be evaluated with their use. A general computer program has been developed to facilitate construction of state interindustry tables.

  17. Methodology for a Regional Tidal Model Evaluation, With Application to Central California

    Science.gov (United States)

    2009-01-01

    moorings off Pt Sur and the AOSN moorings; Gary Egbert and Lana Erofeeva (OSU) for | roviding tidal solutions for the West Coast; and Paul Martin...rotated into the ICON curvilinear coordinates according to Paul Martin’s scheme (personal comm.). The transport component orthogonal to the open... Ekman balance in the California Current. Journal of Geophysical Research 100. 18261-18269. Chereskin. T.K.. Morris. M.Y., Niiler, P.P., Kosro, P.M

  18. Ecology and the ratchet of events: climate variability, niche dimensions, and species distributions.

    Science.gov (United States)

    Jackson, Stephen T; Betancourt, Julio L; Booth, Robert K; Gray, Stephen T

    2009-11-17

    Climate change in the coming centuries will be characterized by interannual, decadal, and multidecadal fluctuations superimposed on anthropogenic trends. Predicting ecological and biogeographic responses to these changes constitutes an immense challenge for ecologists. Perspectives from climatic and ecological history indicate that responses will be laden with contingencies, resulting from episodic climatic events interacting with demographic and colonization events. This effect is compounded by the dependency of environmental sensitivity upon life-stage for many species. Climate variables often used in empirical niche models may become decoupled from the proximal variables that directly influence individuals and populations. Greater predictive capacity, and more-fundamental ecological and biogeographic understanding, will come from integration of correlational niche modeling with mechanistic niche modeling, dynamic ecological modeling, targeted experiments, and systematic observations of past and present patterns and dynamics.

  19. ECRB ALCOVE AND NICHE GROUND SUPPORT ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    J.W. Keifer

    1999-05-09

    The purpose of the analysis is to provide design bases for Enhanced Characterization of the Repository Block (ECRB) alcove and niche ground support drawings. The objective is to evaluate the ESF Alcove Ground Support Analysis (Ref 5.1) to determine if the calculations technically bound the ECRB alcoves and to address specific differences in the conditions and constraints.

  20. 3-D Velocity Model of the Coachella Valley, Southern California Based on Explosive Shots from the Salton Seismic Imaging Project

    Science.gov (United States)

    Persaud, P.; Stock, J. M.; Fuis, G. S.; Hole, J. A.; Goldman, M.; Scheirer, D. S.

    2014-12-01

    We have analyzed explosive shot data from the 2011 Salton Seismic Imaging Project (SSIP) across a 2-D seismic array and 5 profiles in the Coachella Valley to produce a 3-D P-wave velocity model that will be used in calculations of strong ground shaking. Accurate maps of seismicity and active faults rely both on detailed geological field mapping and a suitable velocity model to accurately locate earthquakes. Adjoint tomography of an older version of the SCEC 3-D velocity model shows that crustal heterogeneities strongly influence seismic wave propagation from moderate earthquakes (Tape et al., 2010). These authors improve the crustal model and subsequently simulate the details of ground motion at periods of 2 s and longer for hundreds of ray paths. Even with improvements such as the above, the current SCEC velocity model for the Salton Trough does not provide a match of the timing or waveforms of the horizontal S-wave motions, which Wei et al. (2013) interpret as caused by inaccuracies in the shallow velocity structure. They effectively demonstrate that the inclusion of shallow basin structure improves the fit in both travel times and waveforms. Our velocity model benefits from the inclusion of known location and times of a subset of 126 shots detonated over a 3-week period during the SSIP. This results in an improved velocity model particularly in the shallow crust. In addition, one of the main challenges in developing 3-D velocity models is an uneven stations-source distribution. To better overcome this challenge, we also include the first arrival times of the SSIP shots at the more widely spaced Southern California Seismic Network (SCSN) in our inversion, since the layout of the SSIP is complementary to the SCSN. References: Tape, C., et al., 2010, Seismic tomography of the Southern California crust based on spectral-element and adjoint methods: Geophysical Journal International, v. 180, no. 1, p. 433-462. Wei, S., et al., 2013, Complementary slip distributions

  1. Bone Marrow Vascular Niche: Home for Hematopoietic Stem Cells

    Directory of Open Access Journals (Sweden)

    Ningning He

    2014-01-01

    Full Text Available Though discovered later than osteoblastic niche, vascular niche has been regarded as an alternative indispensable niche operating regulation on hematopoietic stem cells (HSCs. As significant progresses gained on this type niche, it is gradually clear that the main work of vascular niche is undertaking to support hematopoiesis. However, compared to what have been defined in the mechanisms through which the osteoblastic niche regulates hematopoiesis, we know less in vascular niche. In this review, based on research data hitherto we will focus on component foundation and various functions of vascular niche that guarantee the normal hematopoiesis process within bone marrow microenvironments. And the possible pathways raised by various research results through which this environment undergoes its function will be discussed as well.

  2. California Air Basins

    Data.gov (United States)

    California Department of Resources — Air ResourcesCalifornia Air Resources BoardThe following datasets are from the California Air Resources Board: * arb_california_airbasins - California Air BasinsThe...

  3. Ecological niche models and patterns of richness and endemism of the southern Andean genus Eurymetopum (Coleoptera, Cleridae Modelos de nicho ecológico y patrones de riqueza y endemismo del género andino austral Eurymetopum (Coleoptera, Cleridae

    Directory of Open Access Journals (Sweden)

    Tania Escalante

    2009-01-01

    Full Text Available Eurymetopum is an Andean clerid genus with 22 species. We modeled the ecological niches of 19 species with Maxent and used them as potential distributional maps to identify patterns of richness and endemicity. All modeled species maps were overlapped in a single map in order to determine richness. We performed an optimality analysis with NDM/VNDM in a grid of 1º latitude-longitude in order to identify endemism. We found a highly rich area, located between 32º and 41º south latitude, where the richest pixels have 16 species. One area of endemism was identified, located in the Maule and Valdivian Forest biogeographic provinces, which extends also to the Santiago province of the Central Chilean subregion, and contains four endemic species (E. parallelum, E. prasinum, E. proteus, and E. viride, as well as 16 non-endemic species. The sympatry of these phylogenetically unrelated species might indicate ancient vicariance processes, followed by episodes of dispersal. Based on our results, we suggest a close relationship between these provinces, with the Maule representing a complex area.Eurymetopum es un género de cléridos andinos con 22 especies. Modelamos los nichos ecológicos de 19 especies con Maxent y los utilizamos como mapas de distribución potencial para identificar patrones de riqueza y endemismo. Todos los mapas de las especies se superpusieron en un mapa único para determinar la riqueza. Realizamos un análisis de optimalidad con NDM/VNDM en una cuadrícula de 1º de latitud-longitud para identificar el endemismo. Hallamos un área de mayor riqueza, localizada entre los 32º y 41º de latitud sur, donde los pixeles más ricos poseen 16 especies. Se identificó un área de endemismo en las provincias biogeográficas del Maule y el Bosque Valdiviano, la cual se extiende también a la provincia de Santiago de la subregión Chilena Central, y que contiene cuatro especies endémicas (E. parallelum, E. prasinum, E. proteus y E. viride, as

  4. Ten Niche Strategies To Commercialize New High-Tech Products

    NARCIS (Netherlands)

    Ortt, J.R.; Langley, D.J.; Pals, N.

    2013-01-01

    There are serious gaps in the scientific literature relating to niche strategies as a means for commercializing new high-tech products. In particular, there is no clarity about what types of niche strategies can be distinguished, or how a niche strategy can be selected to suit a certain ituation. In

  5. Niching genetic algorithms for optimization in electromagnetics - I. Fundamentals

    OpenAIRE

    Sareni, Bruno; Krähenbühl, Laurent; Nicolas, Alain

    1998-01-01

    Niching methods extend genetic algorithms and permit the investigation of multiple optimal solutions in the search space. In this paper, we review and discuss various strategies of niching for optimization in electromagnetics. Traditional mathematical problems and an electromagnetic benchmark are solved using niching genetic algorithms to show their interest in real world optimization.

  6. Functional traits, convergent evolution, and periodic tables of niches.

    Science.gov (United States)

    Winemiller, Kirk O; Fitzgerald, Daniel B; Bower, Luke M; Pianka, Eric R

    2015-08-01

    Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche 'dimensions', or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait-value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification.

  7. Helicobacter urease: Niche construction at the single molecule level

    Indian Academy of Sciences (India)

    Shahid Khan; Asim Karim; Shaheryar Iqbal

    2009-10-01

    The urease of the human pathogen, Helicobacter pylori, is essential for pathogenesis. The ammonia produced by the enzyme neutralizes stomach acid; thereby modifying its environment. The dodecameric enzyme complex has high affinity for its substrate, urea. We compared urease sequences and derivative 3D homology model structures from all published Helicobacter genomes and an equal number of genomes belonging to strains of another enteric bacterium, Escherichia coli. We found that the enzyme’s architecture adapts to fit its niche. This finding, coupled to a survey of other physiological features responsible for the bacterium’s acid resistance, suggests how it copes with pH changes caused by disease onset and progression.

  8. Population genetics and ecological niche of invasive Aedes albopictus in Mexico.

    Science.gov (United States)

    Pech-May, Angélica; Moo-Llanes, David A; Puerto-Avila, María Belem; Casas, Mauricio; Danis-Lozano, Rogelio; Ponce, Gustavo; Tun-Ku, Ezequiel; Pinto-Castillo, José Francisco; Villegas, Alejandro; Ibáñez-Piñon, Clemente R; González, Cassandra; Ramsey, Janine M

    2016-05-01

    The Asian tiger mosquito Aedes albopictus (Skuse), is one of the most invasive mosquito species worldwide. In Mexico it is now recorded in 12 states and represents a serious public health problem, given the recent introduction of Chikungunya on the southern border. The aim of this study was to analyze the population genetics of A. albopictus from all major recorded foci, and model its ecological niche. Niche similarity with that from its autochthonous distribution in Asia and other invaded countries were analyzed and its potential future expansion and potential human exposure in climate change scenarios measured. We analyzed 125 sequences of a 317 bp fragment of the cyt b gene from seven A. albopictus populations across Mexico. The samples belong to 25 haplotypes with moderate population structuring (Fst=0.081, pMexico. Both Neotropical and Nearctic regions are included in the Mexican niche model. Currently in Mexico, 38.6 million inhabitants are exposed to A. albopictus, which is expected to increase to 45.6 million by 2070. Genetic evidence supports collection information that A. albopictus was introduced to Mexico principally by land from the USA and Central and South America. Prevalent haplotypes from Mexico are shared with most invasive regions across the world, just as there was high niche similarity with both natural and invaded regions. The important overlap with the Asian niche model suggests a high potential for the species to disperse to sylvatic regions in Mexico.

  9. Testing alternative conceptual models of seawater intrusion in a coastal aquifer using computer simulation, southern California, USA

    Science.gov (United States)

    Nishikawa, T.

    1997-01-01

    Two alternative conceptual models of the physical processes controlling seawater intrusion in a coastal basin in California, USA, were tested to identify a likely principal pathway for seawater intrusion. The conceptual models were tested by using a two-dimensional, finite-element groundwater flow and transport model. This pathway was identified by the conceptual model that best replicated the historical data. The numerical model was applied in cross section to a submarine canyon that is a main avenue for seawater to enter the aquifer system underlying the study area. Both models are characterized by a heterogeneous, layered, water-bearing aquifer. However, the first model is characterized by flat-lying aquifer layers and by a high value of hydraulic conductivity in the basal aquifer layer, which is thought to be a principal conduit for seawater intrusion. The second model is characterized by offshore folding, which was modeled as a very nearshore outcrop, thereby providing a shorter path for seawater to intrude. General conclusions are that: 1) the aquifer system is best modeled as a flat, heterogeneous, layered system; 2) relatively thin basal layers with relatively high values of hydraulic conductivity are the principal pathways for seawater intrusion; and 3) continuous clay layers of low hydraulic conductivity play an important role in controlling the movement of seawater.

  10. The use of climatic niches in screening procedures for introduced species to evaluate risk of spread: a case with the American Eastern grey squirrel.

    Science.gov (United States)

    Di Febbraro, Mirko; Lurz, Peter W W; Genovesi, Piero; Maiorano, Luigi; Girardello, Marco; Bertolino, Sandro

    2013-01-01

    Species introduction represents one of the most serious threats for biodiversity. The realized climatic niche of an invasive species can be used to predict its potential distribution in new areas, providing a basis for screening procedures in the compilation of black and white lists to prevent new introductions. We tested this assertion by modeling the realized climatic niche of the Eastern grey squirrel Sciurus carolinensis. Maxent was used to develop three models: one considering only records from the native range (NRM), a second including records from native and invasive range (NIRM), a third calibrated with invasive occurrences and projected in the native range (RCM). Niche conservatism was tested considering both a niche equivalency and a niche similarity test. NRM failed to predict suitable parts of the currently invaded range in Europe, while RCM underestimated the suitability in the native range. NIRM accurately predicted both the native and invasive range. The niche equivalency hypothesis was rejected due to a significant difference between the grey squirrel's niche in native and invasive ranges. The niche similarity test yielded no significant results. Our analyses support the hypothesis of a shift in the species' climatic niche in the area of introductions. Species Distribution Models (SDMs) appear to be a useful tool in the compilation of black lists, allowing identifying areas vulnerable to invasions. We advise caution in the use of SDMs based only on the native range of a species for the compilation of white lists for other geographic areas, due to the significant risk of underestimating its potential invasive range.

  11. Molecular signatures of the primitive prostate stem cell niche reveal novel mesenchymal-epithelial signaling pathways.

    Directory of Open Access Journals (Sweden)

    Roy Blum

    Full Text Available BACKGROUND: Signals between stem cells and stroma are important in establishing the stem cell niche. However, very little is known about the regulation of any mammalian stem cell niche as pure isolates of stem cells and their adjacent mesenchyme are not readily available. The prostate offers a unique model to study signals between stem cells and their adjacent stroma as in the embryonic prostate stem cell niche, the urogenital sinus mesenchyme is easily separated from the epithelial stem cells. Here we investigate the distinctive molecular signals of these two stem cell compartments in a mammalian system. METHODOLOGY/PRINCIPAL FINDINGS: We isolated fetal murine urogenital sinus epithelium and urogenital sinus mesenchyme and determined their differentially expressed genes. To distinguish transcripts that are shared by other developing epithelial/mesenchymal compartments from those that pertain to the prostate stem cell niche, we also determined the global gene expression of epidermis and dermis of the same embryos. Our analysis indicates that several of the key transcriptional components that are predicted to be active in the embryonic prostate stem cell niche regulate processes such as self-renewal (e.g., E2f and Ap2, lipid metabolism (e.g., Srebp1 and cell migration (e.g., Areb6 and Rreb1. Several of the enriched promoter binding motifs are shared between the prostate epithelial/mesenchymal compartments and their epidermis/dermis counterparts, indicating their likely relevance in epithelial/mesenchymal signaling in primitive cellular compartments. Based on differential gene expression we also defined ligand-receptor interactions that may be part of the molecular interplay of the embryonic prostate stem cell niche. CONCLUSIONS/SIGNIFICANCE: We provide a comprehensive description of the transcriptional program of the major regulators that are likely to control the cellular interactions in the embryonic prostatic stem cell niche, many of which may

  12. Three-dimensional electrical resistivity model of the hydrothermal system in Long Valley Caldera, California, from magnetotellurics

    Science.gov (United States)

    Peacock, J. R.; Mangan, M. T.; McPhee, D.; Wannamaker, P. E.

    2016-08-01

    Though shallow flow of hydrothermal fluids in Long Valley Caldera, California, has been well studied, neither the hydrothermal source reservoir nor heat source has been well characterized. Here a grid of magnetotelluric data were collected around the Long Valley volcanic system and modeled in 3-D. The preferred electrical resistivity model suggests that the source reservoir is a narrow east-west elongated body 4 km below the west moat. The heat source could be a zone of 2-5% partial melt 8 km below Deer Mountain. Additionally, a collection of hypersaline fluids, not connected to the shallow hydrothermal system, is found 3 km below the medial graben, which could originate from a zone of 5-10% partial melt 8 km below the south moat. Below Mammoth Mountain is a 3 km thick isolated body containing fluids and gases originating from an 8 km deep zone of 5-10% basaltic partial melt.

  13. Ecological niche and geographic distribution of human monkeypox in Africa.

    Directory of Open Access Journals (Sweden)

    Rebecca S Levine

    Full Text Available Monkeypox virus, a zoonotic member of the genus Orthopoxviridae, can cause a severe, smallpox-like illness in humans. Monkeypox virus is thought to be endemic to forested areas of western and Central Africa. Considerably more is known about human monkeypox disease occurrence than about natural sylvatic cycles of this virus in non-human animal hosts. We use human monkeypox case data from Africa for 1970-2003 in an ecological niche modeling framework to construct predictive models of the ecological requirements and geographic distribution of monkeypox virus across West and Central Africa. Tests of internal predictive ability using different subsets of input data show the model to be highly robust and suggest that the distinct phylogenetic lineages of monkeypox in West Africa and Central Africa occupy similar ecological niches. High mean annual precipitation and low elevations were shown to be highly correlated with human monkeypox disease occurrence. The synthetic picture of the potential geographic distribution of human monkeypox in Africa resulting from this study should support ongoing epidemiologic and ecological studies, as well as help to guide public health intervention strategies to areas at highest risk for human monkeypox.

  14. Modeling Study of Cross-Shore Exchange Processes in the Southern California Bight Using QuikSCAT Winds

    Science.gov (United States)

    Song, Y.; Liu, W.; Tang, W.

    2002-12-01

    The South California Bight (SCB) forms a complex bathymetric region (islands, shallow banks, basin, and channels) extending from the coast to about 200 km offshore and from Point Conception to the tip of Baja California. Geographically the region is sheltered from the strong upwelling-favorable winds characteristic of the region north of Point Conception. However, recent QuikSCAT winds, for the first time, clearly reveal a persistent cyclonic eddy centered at Catalina Island within the Bight (Liu et al. 2001). Using a costal circulation model, we have investigated the oceanic response to the newly observed sea-surface winds. Two experiments are carried out to explore the individual roles of wind forcing and topography. The first experiment uses the COADS winds to determine the general circulation of the Bight. The second experiment uses the QuikSCAT winds to examine how the space-time variability of atmospheric forcing affects the frontal structure, circulation pattern, and cross-shore exchange of water masses. Comparisons of these two experiments allow us to identify the combined effect of winds and topography on the cross-shore exchange processes between the Bight and its adjacent waters.

  15. Two-dimensional magnetotelluric model of deep resistivity structure in the Bodie-Aurora district of California

    Science.gov (United States)

    Sampson, Jay A.

    2006-01-01

    Introduction: Magnetotelluric data were acquired during October 2001 by the U.S. Geological Survey (USGS) as part of a study to examine the structural nature of basins in the transition zone between the Sierra Nevada Mountains of California and the Basin and Range province of Nevada. Magnetotelluric (MT) geophysical studies assist the mapping of geologic structure and the inference of lithologic packages that are concealed beneath the Earth's surface. The Basin and Range province has a complicated geologic history, which includes extension and compression of the Earth's crust to form the basins and ranges that blanket much of Nevada. The basins and ranges in the vicinity of this study trend northeastward and are bounded by steeply dipping strike slip faults. Interestingly, deep east-west magnetic trends occur in the aeromagnetic data of this study area indicating that the northeast-trending basins and ranges represent only thin-skinned deformation at the surface with an underlying east-west structure. To investigate this issue, MT data were acquired at seven stations in eastern California, 20 km east of Mono Lake. The purpose of this report is to present a two-dimensional apparent resistivity model of the MT data acquired for this study.

  16. Study of the Logistics Enterprise Development Path based on Niche Theory

    Institute of Scientific and Technical Information of China (English)

    Sun Wenxia

    2013-01-01

    This paper refers evolutionary ecology of niche theory,analyzes logistics enterprises niche,as well as niche overlapping,niche separation,niche compression,niche expansionetc.And on this basis,this paper proposes,the development path of the logistics enterprise “co-operation,with in the horizontal,external vertical cooperation”,hoping advancing further of logisticsenterprises.

  17. A simulation-optimization model for water-resources management, Santa Barbara, California

    Science.gov (United States)

    Nishikawa, Tracy

    1998-01-01

    In times of drought, the local water supplies of the city of Santa Barbara, California, are insufficient to satisfy water demand. In response, the city has built a seawater desalination plant and gained access to imported water in 1997. Of primary concern to the city is delivering water from the various sources at a minimum cost while satisfying water demand and controlling seawater intrusion that might result from the overpumping of ground water. A simulation-optimization model has been developed for the optimal management of Santa Barbara?s water resources. The objective is to minimize the cost of water supply while satisfying various physical and institutional constraints such as meeting water demand, maintaining minimum hydraulic heads at selected sites, and not exceeding water-delivery or pumping capacities. The model is formulated as a linear programming problem with monthly management periods and a total planning horizon of 5 years. The decision variables are water deliveries from surface water (Gibraltar Reservoir, Cachuma Reservoir, Cachuma Reservoir cumulative annual carryover, Mission Tunnel, State Water Project, and desalinated seawater) and ground water (13 production wells). The state variables are hydraulic heads. Basic assumptions for all simulations are that (1) the cost of water varies with source but is fixed over time, and (2) only existing or planned city wells are considered; that is, the construction of new wells is not allowed. The drought of 1947?51 is Santa Barbara?s worst drought on record, and simulated surface-water supplies for this period were used as a basis for testing optimal management of current water resources under drought conditions. Assumptions that were made for this base case include a head constraint equal to sea level at the coastal nodes; Cachuma Reservoir carryover of 3,000 acre-feet per year, with a maximum carryover of 8,277 acre-feet; a maximum annual demand of 15,000 acre-feet; and average monthly capacities for the

  18. Testing the Consistency of Diffusion Modelling in Multiple Crystal Phases: A Case Study from the Bishop Tuff, California

    Science.gov (United States)

    Morgan, D. J.; Chamberlain, K. J.; Wilson, C. J. N.

    2014-12-01

    Diffusion modelling of elemental gradients across compositional zones within crystals is frequently used to investigate timescales of various magmatic processes. In most cases, however, only a single crystal phase is used for this modelling. The ~0.76 Ma Bishop Tuff (Long Valley, eastern California) in later parts of its eruptive sequence has zoned orthopyroxene, quartz and sanidine. It thus provides an unusual opportunity to compare the modelled timescales from each phase, and assess the limitations of single-phase diffusion modelling in lower-temperature, rhyolitic volcanic systems. The presence of a late-stage compositionally distinct melt (the 'bright-rim' melt) mixing into the lower parts of the Bishop magma chamber has been noted by many authors [e.g. Wark et al. 2007, Geology 35, 235; Roberge et al. 2013, CMP 165, 237; Chamberlain et al. 2014, J Petrol 55, 395] in later-erupted material discharged from vents along the northern ring fracture of the caldera. Here we present the results of 1D diffusion modelling of Ba and Sr in sanidine, Ti in quartz and Fe-Mg interdiffusion in orthopyroxene in samples from later-erupted ignimbrite packages in the tuff. Timescales from diffusion modelling of Fe-Mg interdiffusion in orthopyroxene are Bishop Tuff eruption. We highlight the importance of having a good understanding of the assumptions made and uncertainties in diffusion coefficients when undertaking such modelling, especially in examples where only one phase is available for diffusion modelling.

  19. Impacts of Future Climate Change on California Perennial Crop Yields: Model Projections with Climate and Crop Uncertainties

    Energy Technology Data Exchange (ETDEWEB)

    Lobell, D; Field, C; Cahill, K; Bonfils, C

    2006-01-10

    Most research on the agricultural impacts of climate change has focused on the major annual crops, yet perennial cropping systems are less adaptable and thus potentially more susceptible to damage. Improved assessments of yield responses to future climate are needed to prioritize adaptation strategies in the many regions where perennial crops are economically and culturally important. These impact assessments, in turn, must rely on climate and crop models that contain often poorly defined uncertainties. We evaluated the impact of climate change on six major perennial crops in California: wine grapes, almonds, table grapes, oranges, walnuts, and avocados. Outputs from multiple climate models were used to evaluate climate uncertainty, while multiple statistical crop models, derived by resampling historical databases, were used to address crop response uncertainties. We find that, despite these uncertainties, climate change in California is very likely to put downward pressure on yields of almonds, walnuts, avocados, and table grapes by 2050. Without CO{sub 2} fertilization or adaptation measures, projected losses range from 0 to >40% depending on the crop and the trajectory of climate change. Climate change uncertainty generally had a larger impact on projections than crop model uncertainty, although the latter was substantial for several crops. Opportunities for expansion into cooler regions are identified, but this adaptation would require substantial investments and may be limited by non-climatic constraints. Given the long time scales for growth and production of orchards and vineyards ({approx}30 years), climate change should be an important factor in selecting perennial varieties and deciding whether and where perennials should be planted.

  20. Novel Concordance Between Geographic, Environmental, and Genetic Structure in the Ecological Generalist Prickly Sculpin (Cottus asper) in California.

    Science.gov (United States)

    Baumsteiger, Jason; Kinziger, Andrew P; Aguilar, Andres

    2016-11-01

    Ecological generalists may contain a wealth of information concerning diversity, ecology, and geographic connectivity throughout their range. We explored these ideas in prickly sculpin (Cottus asper), a small generalist freshwater fish species where coastal forms have potentially undergone radiations into inland lacustrine and riverine environments. Using a 962bp cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity, divergence times, gene flow, and structure among populations at 43 locations throughout California. We then incorporated genetic and GIS data into ecological niche models to assess ecological conditions within identified groups. Though not reciprocally monophyletic, unique mtDNA haplotypes, microsatellite clustering, and measures of isolation by distance (Coastal: r = 0.960, P < 0.001; Inland: r = 0.277, P = 0.148) suggest 2 novel taxonomic groups, Coastal and Inland (constrained to Great Central Valley). Divergence estimates of 41-191 kya combined with the regional biogeographic history suggest geographic barriers are absent between groups since divergence, but ecological niche modeling revealed significant environmental differences (t = 10.84, P < 0.001). Introgressed individuals were also discovered between groups in an ecologically and geographically intermediate region. Population structure was limited, predominately found in tributaries of the San Joaquin basin in the Inland group. Overall, C. asper exhibited substantial genetic diversity, despite its ecological generality, reflecting California's historically unique and complex hydrology. More broadly, this study illustrates variable environments within the range of a generalist species may mask genetic divergences and should not be overlooked in biodiversity assessments.

  1. Doctoral education in a successful ecological niche

    DEFF Research Database (Denmark)

    Christensen, Mette Krogh; Lund, Ole

    2014-01-01

    explore the microclimate in an ecological niche of doctoral education. Based on a theoretical definition of microclimate as the emotional atmosphere that ties group members together and affects their actions, we conducted a case study that aimed to describe the key features of the microclimate...... in a successful ecological niche of doctoral education, and the ways in which the microclimate support the doctoral students’ learning. The methods we applied in the case study were based on short-term ethnographic fieldwork. The results reveal four key features of the emotional atmosphere in the microclimate...... successful doctoral education because it: 1) fleshes out the professional attitude that is necessary for becoming a successful researcher in the department, 2) shapes and adapts the doctoral students’ desires to grasp and identify with the department’s practices, and 3) provides the doctoral students...

  2. [Niche comparison of dominant entomopathogenic fungi in three forest ecosystems].

    Science.gov (United States)

    Chen, Ming-Jun; Huang, Bo; Li, Zeng-Zhi

    2011-05-01

    An investigation was made on the quantitative composition, niche width, and niche overlap of dominant entomopathogenic fungi in three different forest ecosystems, i.e., natural broad-leaved forest, natural secondary broad-leaved forest, and pure Masson' s pine plantation. In the three forest ecosystems, Beauveria bassiana was the first dominant species in natural secondary broad-leaved forest, the second in pure Masson's pine plantation, and the third in natural broad-leaved forest. B. bassiana had the broadest temporal niche width and nutritional niche width, whereas the dominant species Isaria cateinannulata, L. farinose, and I. tenuipes had much smaller niche widths. Meanwhile, B. bassiana had larger temporal niche overlaps but smaller nutritional niche overlaps with other dominant entomopathogenic fungi. It was suggested that in the three forest ecosystems, B. bassiana had the longest occurrence duration, widest host range, and strongest environmental adaptability.

  3. Niche Markets: Filling Gaps with Expertise, Ingenuity.

    Science.gov (United States)

    Kaldy, Joanne

    2015-08-01

    Niche markets present opportunities for pharmacists to expand their presence and increase the demand for their services. These practitioners have clinical skills that they can use to improve medication management, reduce medication-related problems and hospitalizations, and enhance the quality of life for patients in specialty areas such as menopause management and women's health, hospice and palliative care, and pediatric long-term care.

  4. Forests, Water, and the Atmosphere in Northern California: Insights from Sap-Flow Data Analysis and Numerical Atmospheric Model Simulations

    Science.gov (United States)

    Link, Percy Anne

    Evapotranspiration cools the land surface by consuming a large fraction of the net radiative energy at the surface. In forested regions, trees actively control the rate of transpiration by modulating stomatal conductance in response to environmental conditions, and species with different stomatal dynamics can affect the atmosphere in distinct ways. Using principal component analysis (PCA) and Markov chain Monte Carlo (MCMC) parameter estimation with direct, tree-level measurements of water use, we show that Douglas-firs ( Pseudotsuga menziesii), a common evergreen needleleaf tree species in the Northern California Coast Range, decrease their transpiration sharply in the summer dry season in response to a dry root zone; and in contrast, broadleaf evergreen tree species, especially Pacific madrones (Arbutus menziesii), transpire maximally in the summer dry season because their transpiration is much less sensitive to a dry root zone and increases continually in response to increasing atmospheric evaporative demand. We scale up these tree-level observations to construct a bottom-up estimate of regional transpiration, and we use these regional estimates along with atmospheric models, one simple and one comprehensive, to quantify the potential impact of species transpiration differences on regional summertime climate. The atmospheric models suggest that these species differences in transpiration could affect the well-mixed atmospheric boundary layer temperature and humidity by 1-1.5 degrees C and 1 g/kg, respectively, and near-surface temperature and humidity by 1.5-2.5 degrees C and 2-3 g/kg, respectively. We further investigate the sensitivity of California climate to evapotranspiration by estimating the sensitivity of wind energy forecasts at a California wind farm to regional-scale perturbations in soil moisture using a regional atmospheric model. These tests show that forecasts at this particular farm are most sensitive to soil moisture in the Central Valley, and

  5. Construction, calibration, and validation of the RBM10 water temperature model for the Trinity River, northern California

    Science.gov (United States)

    Jones, Edward C.; Perry, Russell W.; Risley, John C.; Som, Nicholas A.; Hetrick, Nicholas J.

    2016-03-31

    We constructed a one-dimensional daily averaged water-temperature model to simulate Trinity River temperatures for 1980–2013. The purpose of this model is to assess effects of water-management actions on water temperature and to provide water temperature inputs for a salmon population dynamics model. Simulated meteorological data, observed streamflow data, and observed water temperatures were used as model inputs to simulate a continuous 34-year time series of historical daily mean water temperature at eight locations along 112.2 river miles from Lewiston Dam near Weaverville, California, downstream to the Klamath River confluence. To demonstrate the utility of the model to inform management actions, we simulated three management alternatives to assess the effects of bypass flow augmentation in a drought year, 1994, and compared those results to the simulated historical baseline, referred to as the “No Action” alternative scenario. Augmentation flows from the Lewiston Dam bypass consist of temperature-controlled releases capable of cooling downstream water temperatures in hot times of the year, which can reduce the probability of disease outbreaks in fish populations. Outputs from the Trinity River water-temperature model were then used as inputs to an existing water-temperature model of the Klamath River to evaluate the effect of augmentation flow releases on water temperatures in the lower Klamath River. 

  6. Move two: establishing a niche

    Directory of Open Access Journals (Sweden)

    Wasima Shehzad

    2008-04-01

    Full Text Available The significant purpose of the author in the Introduction of a research article is to convince the reader about the importance of the work to be presented. To achieve this end, a convincing “niche” needs to be built by evaluating, rejecting or indicating gaps in previous related work. The purpose of “establishing a niche” is to emphasize the current research project presented by the author. The present paper investigates how Computer scientists use this obligatory step of “Create a Research Space” (CARS model (Swales & Feak, 1994 & 2004 to highlight their own research work. This paper not only compares the results with other similar studies but also presents an in-depth analysis of various types of gap statements used in Computer Science research article Introductions. The issue of cyclicity of this step and the linguistic indicators used for the establishment of “niche” (the gap statements are both discussed.

  7. Balance Trees Reveal Microbial Niche Differentiation.

    Science.gov (United States)

    Morton, James T; Sanders, Jon; Quinn, Robert A; McDonald, Daniel; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Navas-Molina, Jose A; Song, Se Jin; Metcalf, Jessica L; Hyde, Embriette R; Lladser, Manuel; Dorrestein, Pieter C; Knight, Rob

    2017-01-01

    Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss. Author Video: An author video summary of this article is available.

  8. Balance Trees Reveal Microbial Niche Differentiation

    Science.gov (United States)

    Morton, James T.; Sanders, Jon; Quinn, Robert A.; McDonald, Daniel; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Navas-Molina, Jose A.; Metcalf, Jessica L.; Hyde, Embriette R.; Lladser, Manuel; Dorrestein, Pieter C.

    2017-01-01

    ABSTRACT Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss. Author Video: An author video summary of this article is available. PMID:28144630

  9. Application of a new hydraulic conductivity model to simulate rapid groundwater fluctuations in the Eel River watershed in Northern California

    Science.gov (United States)

    Vrettas, M. D.; Fung, I. Y.

    2015-12-01

    High-frequency multi-year observations of the water table at several wells in the Angelo Coast Range Reserve in the Eel River Watershed in northern California show rapid fluctuations, where the water table, some 10-15 meters below the surface, rises by as much as 1 meter in a day or two after the first storms of the rain season. The observations highlight preferential flow through weathered bedrock, which can store as much as 30% of the moisture in the column ("rock moisture"). This rapid transfer of moisture and storage at depth could have a significant impact on ecosystem dynamics and the water and energy budgets of the atmosphere on various time scales. Despite its high importance, preferential flow through weather bedrock is not routinely captured in most climate models. This work presents a new hydraulic conductivity parameterization that captures the preferential flow, with straightforward implementation into current global climate models. The hydraulic conductivity is represented as a product of the effective saturation (normalized water content) and a background hydraulic conductivity Kbkg, drawn from a depth dependent lognormal distribution. A unique feature of the parameterization is that the variance of hydraulic conductivity is large when there is little rock moisture, and decreases with increasing saturation, mimicking flow through fractures. The new method is applied to seven wells locations on a steep (35 degrees) hill-slope in the Eel River watershed in Northern California, for the duration of six years and estimates of the model parameters are provided by assimilating, into Richards' equation, measurements of precipitation [mm] and water table depths [m] at 30-minute time intervals. The simulation results show that the new approach yields a good agreement of the rapid rise of the observed water table at the tested well locations. Furthermore, the water stored in the weathered bedrock is estimated to be in the range between 32% and 41%, which could

  10. Economic analysis of electronic waste recycling: modeling the cost and revenue of a materials recovery facility in California.

    Science.gov (United States)

    Kang, Hai-Yong; Schoenung, Julie M

    2006-03-01

    The objectives of this study are to identify the various techniques used for treating electronic waste (e-waste) at material recovery facilities (MRFs) in the state of California and to investigate the costs and revenue drivers for these techniques. The economics of a representative e-waste MRF are evaluated by using technical cost modeling (TCM). MRFs are a critical element in the infrastructure being developed within the e-waste recycling industry. At an MRF, collected e-waste can become marketable output products including resalable systems/components and recyclable materials such as plastics, metals, and glass. TCM has two main constituents, inputs and outputs. Inputs are process-related and economic variables, which are directly specified in each model. Inputs can be divided into two parts: inputs for cost estimation and for revenue estimation. Outputs are the results of modeling and consist of costs and revenues, distributed by unit operation, cost element, and revenue source. The results of the present analysis indicate that the largest cost driver for the operation of the defined California e-waste MRF is the materials cost (37% of total cost), which includes the cost to outsource the recycling of the cathode ray tubes (CRTs) (dollar 0.33/kg); the second largest cost driver is labor cost (28% of total cost without accounting for overhead). The other cost drivers are transportation, building, and equipment costs. The most costly unit operation is cathode ray tube glass recycling, and the next are sorting, collecting, and dismantling. The largest revenue source is the fee charged to the customer; metal recovery is the second largest revenue source.

  11. Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

    Science.gov (United States)

    Franklin, J.; Wejnert, K.E.; Hathaway, S.A.; Rochester, C.J.; Fisher, R.N.

    2009-01-01

    Aim: Several studies have found that more accurate predictive models of species' occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species' survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location: Coastal southern California, USA. Methods: Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver-operating characteristic (ROC) plot based on twofold cross-validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results: Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions: Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the

  12. Development of a Statistical Model for Estimating Spatial and Temporal Ambient Ozone Patterns in the Sierra Nevada, California

    Directory of Open Access Journals (Sweden)

    Haiganoush K. Preisler

    2002-01-01

    Full Text Available Statistical approaches for modeling spatially and temporally explicit data are discussed for 79 passive sampler sites and 9 active monitors distributed across the Sierra Nevada, California. A generalized additive regression model was used to estimate spatial patterns and relationships between predicted ozone exposure and explanatory variables, and to predict exposure at nonmonitored sites. The fitted model was also used to estimate probability maps for season average ozone levels exceeding critical (or subcritical levels in the Sierra Nevada region. The explanatory variables — elevation, maximum daily temperature, and precipitation and ozone level at closest active monitor — were significant in the model. There was also a significant mostly east-west spatial trend. The between-site variability had the same magnitude as the error variability. This seems to indicate that there still exist important site features not captured by the variables used in the analysis and that may improve the accuracy of the predictive model in future studies. The fitted model using robust techniques had an overall R2 value of 0.58. The mean standard deviation for a predicted value was 6.68 ppb.

  13. Modeling and validation of a 3D velocity structure for the Santa Clara Valley, California, for seismic-wave simulations

    Science.gov (United States)

    Hartzell, S.; Harmsen, S.; Williams, R.A.; Carver, D.; Frankel, A.; Choy, G.; Liu, P.-C.; Jachens, R.C.; Brocher, T.M.; Wentworth, C.M.

    2006-01-01

    A 3D seismic velocity and attenuation model is developed for Santa Clara Valley, California, and its surrounding uplands to predict ground motions from scenario earthquakes. The model is developed using a variety of geologic and geophysical data. Our starting point is a 3D geologic model developed primarily from geologic mapping and gravity and magnetic surveys. An initial velocity model is constructed by using seismic velocities from boreholes, reflection/refraction lines, and spatial autocorrelation microtremor surveys. This model is further refined and the seismic attenuation is estimated through waveform modeling of weak motions from small local events and strong-ground motion from the 1989 Loma Prieta earthquake. Waveforms are calculated to an upper frequency of 1 Hz using a parallelized finite-difference code that utilizes two regions with a factor of 3 difference in grid spacing to reduce memory requirements. Cenozoic basins trap and strongly amplify ground motions. This effect is particularly strong in the Evergreen Basin on the northeastern side of the Santa Clara Valley, where the steeply dipping Silver Creek fault forms the southwestern boundary of the basin. In comparison, the Cupertino Basin on the southwestern side of the valley has a more moderate response, which is attributed to a greater age and velocity of the Cenozoic fill. Surface waves play a major role in the ground motion of sedimentary basins, and they are seen to strongly develop along the western margins of the Santa Clara Valley for our simulation of the Loma Prieta earthquake.

  14. District Allocation of Human Resources Utilizing the Evidence Based Model: A Study of One High Achieving School District in Southern California

    Science.gov (United States)

    Lane, Amber Marie

    2013-01-01

    This study applies the Gap Analysis Framework to understand the gaps that exist in human resource allocation of one Southern California school district. Once identified, gaps are closed with the reallocation of human resources, according to the Evidenced Based Model, requiring the re-purposing of core classroom teachers, specialists, special…

  15. Groundwater-flow and land-subsidence model of Antelope Valley, California

    Science.gov (United States)

    Siade, Adam J.; Nishikawa, Tracy; Rewis, Diane L.; Martin, Peter; Phillips, Steven P.

    2014-01-01

    Antelope Valley, California, is a topographically closed basin in the western part of the Mojave Desert, about 50 miles northeast of Los Angeles. The Antelope Valley groundwater basin is about 940 square miles and is separated from the northern part of Antelope Valley by faults and low-lying hills. Prior to 1972, groundwater provided more than 90 percent of the total water supply in the valley; since 1972, it has provided between 50 and 90 percent. Most groundwater pumping in the valley occurs in the Antelope Valley groundwater basin, which includes the rapidly growing cities of Lancaster and Palmdale. Groundwater-level declines of more than 270 feet in some parts of the groundwater basin have resulted in an increase in pumping lifts, reduced well efficiency, and land subsidence of more than 6 feet in some areas. Future urban growth and limits on the supply of imported water may increase reliance on groundwater.

  16. Natural Gas Variability In California: Environmental Impacts And Device Performance Combustion Modeling of Pollutant Emissions From a Residential Cooking Range

    Energy Technology Data Exchange (ETDEWEB)

    Tonse, S. R.; Singer, B. C.

    2011-07-01

    As part of a larger study of liquefied natural gas impacts on device performance and pollutant emissions for existing equipment in California, this report describes a cmoputer modeling study of a partially premixed flame issueing from a single cooktop burner port. The model consisted of a reactive computational fluid dynamics three-dimensional spatial grid and a 71-species chemical mechanism with propane combustion capability. Simulations were conducted with a simplified fuel mixture containing methane, ethane, and propane in proportions that yield properties similar to fuels distributed throughout much of California now and in recent years (baseline fuel), as well as with two variations of simulated liquefied natural gas blends. A variety of simulations were conducted with baseline fuel to explore the effect of several key parameters on pollutant formation and other flame characteristics. Simulations started with fuel and air issuing through the burner port, igniting, and continuing until the flame was steady with time. Conditions at this point were analyzed to understand fuel, secondary air and reaction product flows, regions of pollutant formation, and exhaust concentrations of carbon monoxide, nitric oxide and formaldehyde. A sensitivity study was conducted, varying the inflow parameters of this baseline gs about real-world operating conditions. Flame properties responded as expected from reactive flow theory. In the simulation, carbon monoxide levels were influenced more by the mixture's inflow velocity than by the gas-to-air ratio in the mixture issuing from the inflow port. Additional simulations were executed at two inflow conditions - high heat release and medium heat release - to examine the impact of replacing the baseline gas with two mixtures representative of liquefied natural gas. Flame properties and pollutant generation rates were very similar among the three fuel mixtures.

  17. Different Motile Behaviors of Human Hematopoietic Stem versus Progenitor Cells at the Osteoblastic Niche

    Directory of Open Access Journals (Sweden)

    Katie Foster

    2015-11-01

    Full Text Available Despite advances in our understanding of interactions between mouse hematopoietic stem cells (HSCs and their niche, little is known about communication between human HSCs and the microenvironment. Using a xenotransplantation model and intravital imaging, we demonstrate that human HSCs display distinct motile behaviors to their hematopoietic progenitor cell (HPC counterparts, and the same pattern can be found between mouse HSCs and HPCs. HSCs become significantly less motile after transplantation, while progenitor cells remain motile. We show that human HSCs take longer to find their niche than previously expected and suggest that the niche be defined as the position where HSCs stop moving. Intravital imaging is the only technique to determine where in the bone marrow stem cells stop moving, and future analyses should focus on the environment surrounding the HSC at this point.

  18. Extended evolution: A conceptual framework for integrating regulatory networks and niche construction.

    Science.gov (United States)

    Laubichler, Manfred D; Renn, Jürgen

    2015-11-01

    This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path-dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems.

  19. Requirements for plant coexistence through pollination niche partitioning.

    Science.gov (United States)

    Benadi, Gita

    2015-07-07

    Plant-pollinator interactions are often thought to have been a decisive factor in the diversification of flowering plants, but to be of little or no importance for the maintenance of existing plant diversity. In a recent opinion paper, Pauw (2013 Trends Ecol. Evol. 28, 30-37. (doi:10.1016/j.tree.2012.07.019)) challenged this view by proposing a mechanism of diversity maintenance based on pollination niche partitioning. In this article, I investigate under which conditions the mechanism suggested by Pauw can promote plant coexistence, using a mathematical model of plant and pollinator population dynamics. Numerical simulations show that this mechanism is most effective when the costs of searching for flowers are low, pollinator populations are strongly limited by resources other than pollen and nectar, and plant-pollinator interactions are sufficiently specialized. I review the empirical literature on these three requirements, discuss additional factors that may be important for diversity maintenance through pollination niche partitioning, and provide recommendations on how to detect this coexistence mechanism in natural plant communities.

  20. Evolution of lactase persistence: an example of human niche construction.

    Science.gov (United States)

    Gerbault, Pascale; Liebert, Anke; Itan, Yuval; Powell, Adam; Currat, Mathias; Burger, Joachim; Swallow, Dallas M; Thomas, Mark G

    2011-03-27

    Niche construction is the process by which organisms construct important components of their local environment in ways that introduce novel selection pressures. Lactase persistence is one of the clearest examples of niche construction in humans. Lactase is the enzyme responsible for the digestion of the milk sugar lactose and its production decreases after the weaning phase in most mammals, including most humans. Some humans, however, continue to produce lactase throughout adulthood, a trait known as lactase persistence. In European populations, a single mutation (-13910*T) explains the distribution of the phenotype, whereas several mutations are associated with it in Africa and the Middle East. Current estimates for the age of lactase persistence-associated alleles bracket those for the origins of animal domestication and the culturally transmitted practice of dairying. We report new data on the distribution of -13910*T and summarize genetic studies on the diversity of lactase persistence worldwide. We review relevant archaeological data and describe three simulation studies that have shed light on the evolution of this trait in Europe. These studies illustrate how genetic and archaeological information can be integrated to bring new insights to the origins and spread of lactase persistence. Finally, we discuss possible improvements to these models.

  1. A Guide for Using the Transient Ground-Water Flow Model of the Death Valley Regional Ground-Water Flow System, Nevada and California

    Energy Technology Data Exchange (ETDEWEB)

    Joan B. Blainey; Claudia C. Faunt, and Mary C. Hill

    2006-05-16

    This report is a guide for executing numerical simulations with the transient ground-water flow model of the Death Valley regional ground-water flow system, Nevada and California using the U.S. Geological Survey modular finite-difference ground-water flow model, MODFLOW-2000. Model inputs, including observations of hydraulic head, discharge, and boundary flows, are summarized. Modification of the DVRFS transient ground-water model is discussed for two common uses of the Death Valley regional ground-water flow system model: predictive pumping scenarios that extend beyond the end of the model simulation period (1998), and model simulations with only steady-state conditions.

  2. Evidence of niche shift and global invasion potential of the Tawny Crazy ant, Nylanderia fulva.

    Science.gov (United States)

    Kumar, Sunil; LeBrun, Edward G; Stohlgren, Thomas J; Stabach, Jared A; McDonald, Danny L; Oi, David H; LaPolla, John S

    2015-10-01

    Analysis of an invasive species' niche shift between native and introduced ranges, along with potential distribution maps, can provide valuable information about its invasive potential. The tawny crazy ant, Nylanderia fulva, is a rapidly emerging and economically important invasive species in the southern United States. It is originally from east-central South America and has also invaded Colombia and the Caribbean Islands. Our objectives were to generate a global potential distribution map for N. fulva, identify important climatic drivers associated with its current distribution, and test whether N. fulva's realized climatic niche has shifted across its invasive range. We used MaxEnt niche model to map the potential distribution of N. fulva using its native and invaded range occurrences and climatic variables. We used principal component analysis methods for investigating potential shifts in the realized climatic niche of N. fulva during invasion. We found strong evidence for a shift in the realized climatic niche of N. fulva across its invasive range. Our models predicted potentially suitable habitat for N. fulva in the United States and other parts of the world. Our analyses suggest that the majority of observed occurrences of N. fulva in the United States represent stabilizing populations. Mean diurnal range in temperature, degree days at ≥10°C, and precipitation of driest quarter were the most important variables associated with N. fulva distribution. The climatic niche expansion demonstrated in our study may suggest significant plasticity in the ability of N. fulva to survive in areas with diverse temperature ranges shown by its tolerance for environmental conditions in the southern United States, Caribbean Islands, and Colombia. The risk maps produced in this study can be useful in preventing N. fulva's future spread, and in managing and monitoring currently infested areas.

  3. Ecological Niche Divergence between Trapelus ruderatus (Olivier, 1807) and T. persicus (Blanford, 1881) (Sauria:Agamidae) in the Middle East

    Institute of Scientific and Technical Information of China (English)

    Omid MIRSHAMSI; etin ILGAZ; Yusuf KUMLUTA; Aziz AVCI

    2016-01-01

    Modeling the potential distribution areas for a given species is important in understanding the relationship between the actual distribution and the most suitable habitat for a species. In this study, we obtained all available records of Trapelus ruderatus and Trapelus persicus from museums, literature and fieldwork and used them with environmental layers in the Maximum Entropy algorithm to predict highly suitable habitat areas. The distribution model of T. ruderatus and T. persicus showed excellent performance for both models (T. ruderatus AUC = 0.964 ± 0.001 and T. persicus AUC= 0.996 ± 0.003), and predicted suitable regions in Iran, Turkey, Iraq and Syria. Niche overlap was measured between the two groups by ENMtools and 13% overlapped. We used a niche identity test to determine differences between the niches of the two species. Finally, by comparing our null hypothesis to the true niche overlap of the two species, we were able to reject our null hypothesis of no difference between the niches. Due to the sympatric distribution pattern of these species, we do not need a background test for niche divergence.

  4. Mercury- and silver-rich ferromanganese oxides, southern California Borderland: Deposit model and environmental implications

    Science.gov (United States)

    Hein, J.R.; Koschinsky, A.; McIntyre, B.R.

    2005-01-01

    Mercury- and silver-enriched ferromanganese oxide crusts were recovered at water depths of 1,750 tol,300 m from La Victoria knoll, located about 72 km off the coast of northern Baja California. No other ferromanganese precipitate found so far in the modern ocean basins is similarly enriched in Hg and Ag. The precipitates consist of submetallic gray, brecciated, Mn oxide layers overlain by brown earthy, laminated Fe-Mn oxide crusts. Both oxide types are rich in Hg (to 10 ppm) and Ag (to 5.5 ppm). The Mn-rich layers are composed of ??MnO2, with lesser amounts of 10A?? and 7A?? manganates, whereas the Mn phase in the Fe-Mn crusts is solely ??MnO2. The Fe phase in both layers is X-ray amorphous. Established criteria for distinguishing hydrothermal versus hydrogenetic crusts indicate that the Mn-rich layers are predominantly of low-temperature hydrothermal origin, whereas the Fe-Mn crusts are hydrogenetic, although there is some overlap in the source of chemical components in both types. La Victoria knoll is uplifted continental basement rock with basalt, andesite, and schist cropping out at the surface; the knoll may have an intrusive core. The Hg and Ag were derived from leaching by hydrothermal fluids of organic matter-rich sediments in basins adjacent to La Victoria knoll and, to a lesser extent, from continental basement rocks underlying the knoll and adjacent basins. Both rock types are notably enriched in Ag and Hg. Faults were the main fluid transport pathway, and hydrothermal circulation was driven by high heat flow associated with thinned crust. Other elements derived from the hydrothermal fluids include Tl, Cd, Cr, and Li. The main host for Hg and Ag is FeOOH, although MnO2 likely hosts some of the Ag. Minor sulfide and barite also may contain small amounts of these metals. Possible analogs in the geologic record for this deposit type are found in the Basin and Range province of the western United States and Mexico. The discovery highlights the fact that

  5. Marine organism concentrations, carbonate chemistry variables, and nutrient concentrations from Atlantis ecosystem model simulation output in the California Current from 2013-01-01 to 2053-12-31 to understand vulnerability of California current food webs and economics to ocean acidification (NCEI Accession 0131198)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This archival package contains the model output of a study to evaluate likely economic and ecological outcomes of ocean acidification in the California Current....

  6. Rainwater Harvesting and Social Networks: Visualising Interactions for Niche Governance, Resilience and Sustainability

    Directory of Open Access Journals (Sweden)

    Sarah Ward

    2016-11-01

    Full Text Available Visualising interactions across urban water systems to explore transition and change processes requires the development of methods and models at different scales. This paper contributes a model representing the network interactions of rainwater harvesting (RWH infrastructure innovators and other organisations in the UK RWH niche to identify how resilience and sustainability feature within niche governance in practice. The RWH network interaction model was constructed using a modified participatory social network analysis (SNA. The SNA was further analysed through the application of a two-part analytical framework based on niche management and the safe, resilient and sustainable (‘Safe and SuRe’ framework. Weak interactions between some RWH infrastructure innovators and other organisations highlighted reliance on a limited number of persuaders to influence the regime and landscape, which were underrepresented. Features from niche creation and management were exhibited by the RWH network interaction model, though some observed characteristics were not represented. Additional Safe and SuRe features were identified covering diverse innovation, responsivity, no protection, unconverged expectations, primary influencers, polycentric or adaptive governance and multiple learning-types. These features enable RWH infrastructure innovators and other organisations to reflect on improving resilience and sustainability, though further research in other sectors would be useful to verify and validate observation of the seven features.

  7. Alien invasive slider turtle in unpredicted habitat: a matter of niche shift or of predictors studied?

    Directory of Open Access Journals (Sweden)

    Dennis Rödder

    Full Text Available BACKGROUND: Species Distribution Models (SDMs aim on the characterization of a species' ecological niche and project it into geographic space. The result is a map of the species' potential distribution, which is, for instance, helpful to predict the capability of alien invasive species. With regard to alien invasive species, recently several authors observed a mismatch between potential distributions of native and invasive ranges derived from SDMs and, as an explanation, ecological niche shift during biological invasion has been suggested. We studied the physiologically well known Slider turtle from North America which today is widely distributed over the globe and address the issue of ecological niche shift versus choice of ecological predictors used for model building, i.e., by deriving SDMs using multiple sets of climatic predictor. PRINCIPAL FINDINGS: In one SDM, predictors were used aiming to mirror the physiological limits of the Slider turtle. It was compared to numerous other models based on various sets of ecological predictors or predictors aiming at comprehensiveness. The SDM focusing on the study species' physiological limits depicts the target species' worldwide potential distribution better than any of the other approaches. CONCLUSION: These results suggest that a natural history-driven understanding is crucial in developing statistical models of ecological niches (as SDMs while "comprehensive" or "standard" sets of ecological predictors may be of limited use.

  8. Thermal niche estimators and the capability of poor dispersal species to cope with climate change

    Science.gov (United States)

    Sánchez-Fernández, David; Rizzo, Valeria; Cieslak, Alexandra; Faille, Arnaud; Fresneda, Javier; Ribera, Ignacio

    2016-03-01

    For management strategies in the context of global warming, accurate predictions of species response are mandatory. However, to date most predictions are based on niche (bioclimatic) models that usually overlook biotic interactions, behavioral adjustments or adaptive evolution, and assume that species can disperse freely without constraints. The deep subterranean environment minimises these uncertainties, as it is simple, homogeneous and with constant environmental conditions. It is thus an ideal model system to study the effect of global change in species with poor dispersal capabilities. We assess the potential fate of a lineage of troglobitic beetles under global change predictions using different approaches to estimate their thermal niche: bioclimatic models, rates of thermal niche change estimated from a molecular phylogeny, and data from physiological studies. Using bioclimatic models, at most 60% of the species were predicted to have suitable conditions in 2080. Considering the rates of thermal niche change did not improve this prediction. However, physiological data suggest that subterranean species have a broad thermal tolerance, allowing them to stand temperatures never experienced through their evolutionary history. These results stress the need of experimental approaches to assess the capability of poor dispersal species to cope with temperatures outside those they currently experience.

  9. Legal and Policy Issues Regarding Niche Charter Schools: Race, Religion, Culture, and the Law

    Science.gov (United States)

    Eckes, Suzanne E.; Fox, Robert A.; Buchanan, Nina K.

    2011-01-01

    A growing number of ethnocentric or culturally oriented niche charter schools have opened around the country. These ethnic or culture-oriented models raise legal and policy concerns about church/state entanglement as well as concerns about diversity. Indeed, there has already been litigation focused on racial and ethnic aspects of charter schools…

  10. Fine-scale niche structure of Neotropical forests reflects a legacy of the Great American Biotic Interchange.

    Science.gov (United States)

    Sedio, Brian E; Paul, John R; Taylor, Charlotte M; Dick, Christopher W

    2013-01-01

    The tendency of species to retain their ancestral niches may link processes that determine community assembly with biogeographic histories that span geological time scales. Biogeographic history is likely to have had a particularly strong impact on Neotropical forests because of the influence of the Great American Biotic Interchange, which followed emergence of a land connection between North and South America ~3 Ma. Here we examine the community structure, ancestral niches and ancestral distributions of the related, hyperdiverse woody plant genera Psychotria and Palicourea (Rubiaceae) in Panama. We find that 49% of the variation in hydraulic traits, a strong determinant of community structure, is explained by species' origins in climatically distinct biogeographic regions. Niche evolution models for a regional sample of 152 species indicate that ancestral climatic niches are associated with species' habitat distributions, and hence local community structure and composition, even millions of years after dispersal into new geographic regions.

  11. Comparison of aerodynamically and model-derived roughness lengths (zo) over diverse surfaces, central Mojave Desert, California, USA

    Science.gov (United States)

    MacKinnon, D.J.; Clow, G.D.; Tigges, R.K.; Reynolds, R.L.; Chavez, P.S.

    2004-01-01

    The vulnerability of dryland surfaces to wind erosion depends importantly on the absence or the presence and character of surface roughness elements, such as plants, clasts, and topographic irregularities that diminish wind speed near the surface. A model for the friction velocity ratio has been developed to account for wind sheltering by many different types of co-existing roughness elements. Such conditions typify a monitored area in the central Mojave Desert, California, that experiences frequent sand movement and dust emission. Two additional models are used to convert the friction velocity ratio to the surface roughness length (zo) for momentum. To calculate roughness lengths from these models, measurements were made at 11 sites within the monitored area to characterize the surface roughness element. Measurements included (1) the number of roughness species (e.g., plants, small-scale topography, clasts), and their associated heights and widths, (2) spacing among species, and (3) vegetation porosity (a measurement of the spatial distribution of woody elements of a plant). Documented or estimated values of drag coefficients for different species were included in the modeling. At these sites, wind-speed profiles were measured during periods of neutral atmospheric stability using three 9-m towers with three or four calibrated anemometers on each. Modeled roughness lengths show a close correspondence (correlation coefficient, 0.84-0.86) to the aerodynamically determined values at the field sites. The geometric properties of the roughness elements in the model are amenable to measurement at much higher temporal and spatial resolutions using remote-sensing techniques than can be accomplished through laborious ground-based methods. A remote-sensing approach to acquire values of the modeled roughness length is particularly important for the development of linked surface/atmosphere wind-erosion models sensitive to climate variability and land-use changes in areas such

  12. Bone Niches, Hematopoietic Stem Cells, and Vessel Formation

    Directory of Open Access Journals (Sweden)

    Roberto Tamma

    2017-01-01

    Full Text Available Bone marrow (BM is a source of hematopoietic stem cells (HSCs. HSCs are localized in both the endosteum, in the so-called endosteal niche, and close to thin-walled and fenestrated sinusoidal vessel in the center of BM, in the so-called vascular niche. HSCs give rise to all types of mature blood cells through a process finely controlled by numerous signals emerging from the bone marrow niches where HSCs reside. This review will focus on the description of the role of BM niches in the control of the fate of HSCs and will also highlight the role of the BM niches in the regulation of vasculogenesis and angiogenesis. Moreover, alterations of the signals in niche microenvironment are involved in many aspects of tumor progression and vascularization and further knowledge could provide the basis for the development of new therapeutic strategies.

  13. The Effects of Student Demographics and School Resources on California School Performance Gain: A Fixed Effects Panel Model

    Science.gov (United States)

    Wu, Mei-Jiun

    2013-01-01

    Background/Context: Recently emerged with the implementation of the California's Public Schools Accountability Act of 1999 and the NCLB Act of 2001 is an increase in the number of education production function studies estimating the relationship between educational inputs and APIs. While the majority of past research on California school…

  14. Niche Genetic Algorithm with Accurate Optimization Performance

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-hua; YAN De-kun

    2005-01-01

    Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolutionary direction dynamically during evolution. After evolution, the solutions's precision can be greatly improved by means of the local searching along the recorded direction. Simulation shows that this algorithm can not only keep population diversity but also find accurate solutions. Although using this method has to take more time compared with the standard GA, it is really worth applying to some cases that have to meet a demand for high solution precision.

  15. Chapter F. The Loma Prieta, California, Earthquake of October 17, 1989 - Tectonic Processes and Models

    Science.gov (United States)

    Simpson, Robert W.

    1994-01-01

    If there is a single theme that unifies the diverse papers in this chapter, it is the attempt to understand the role of the Loma Prieta earthquake in the context of the earthquake 'machine' in northern California: as the latest event in a long history of shocks in the San Francisco Bay region, as an incremental contributor to the regional deformation pattern, and as a possible harbinger of future large earthquakes. One of the surprises generated by the earthquake was the rather large amount of uplift that occurred as a result of the reverse component of slip on the southwest-dipping fault plane. Preearthquake conventional wisdom had been that large earthquakes in the region would probably be caused by horizontal, right-lateral, strike-slip motion on vertical fault planes. In retrospect, the high topography of the Santa Cruz Mountains and the elevated marine terraces along the coast should have provided some clues. With the observed ocean retreat and the obvious uplift of the coast near Santa Cruz that accompanied the earthquake, Mother Nature was finally caught in the act. Several investigators quickly saw the connection between the earthquake uplift and the long-term evolution of the Santa Cruz Mountains and realized that important insights were to be gained by attempting to quantify the process of crustal deformation in terms of Loma Prieta-type increments of northward transport and fault-normal shortening.

  16. Beyond climate: disturbance niche shifts in invasive species

    OpenAIRE

    González-Moreno, Pablo; Diez, Jeffrey M.; Richardson, David M.; Vilà, Montserrat

    2015-01-01

    Analysing how species niches shift between native and introduced ranges is a powerful tool for understanding the determinants of species distributions and for anticipating range expansions by invasive species. Most studies only consider the climatic niche, by correlating widely available presence-only data with regional climate. However, habitat characteristics and disturbance also shape species niches, thereby potentially confounding shifts attributed only to differences in climate. Here we ...

  17. Response in the water quality of the Salton Sea, California, to changes in phosphorus loading: An empirical modeling approach

    Science.gov (United States)

    Robertson, D.M.; Schladow, S.G.

    2008-01-01

    Salton Sea, California, like many other lakes, has become eutrophic because of excessive nutrient loading, primarily phosphorus (P). A Total Maximum Daily Load (TMDL) is being prepared for P to reduce the input of P to the Sea. In order to better understand how P-load reductions should affect the average annual water quality of this terminal saline lake, three different eutrophication programs (BATHTUB, WiLMS, and the Seepage Lake Model) were applied. After verifying that specific empirical models within these programs were applicable to this saline lake, each model was calibrated using water-quality and nutrient-loading data for 1999 and then used to simulate the effects of specific P-load reductions. Model simulations indicate that a 50% decrease in external P loading would decrease near-surface total phosphorus concentrations (TP) by 25-50%. Application of other empirical models demonstrated that this decrease in loading should decrease near-surface chlorophyll a concentrations (Chl a) by 17-63% and increase Secchi depths (SD) by 38-97%. The wide range in estimated responses in Chl a and SD were primarily caused by uncertainty in how non-algal turbidity would respond to P-load reductions. If only the models most applicable to the Salton Sea are considered, a 70-90% P-load reduction is required for the Sea to be classified as moderately eutrophic (trophic state index of 55). These models simulate steady-state conditions in the Sea; therefore, it is difficult to ascertain how long it would take for the simulated changes to occur after load reductions. ?? 2008 Springer Science+Business Media B.V.

  18. The Niche Hiker's Guide to Population Ecology : A logical reconstruction of organization ecology's niche theory

    NARCIS (Netherlands)

    Peli, G; Raftery, AE

    1997-01-01

    Logical formalization is a formal method for the analysis of theoretical arguments in the social sciences. Hannan and Freeman's organizational niche theory (1989) is rebuilt by means of First-Order Logic, and its predictions are derived as theorems. Translation into a formal language makes the theor

  19. Elements of a neural stem cell niche derived from embryonic stem cells.

    Science.gov (United States)

    Pierret, Chris; Spears, Kathleen; Morrison, Jason A; Maruniak, Joel A; Katz, Martin L; Kirk, Mark D

    2007-12-01

    Recent studies show that adult neural tissues can harbor stem cells within unique niches. In the mammalian central nervous system, neural stem cell (NSC) niches have been identified in the dentate gyrus and the subventricular zone (SVZ). Stem cells in the well-characterized SVZ exist in a microenvironment established by surrounding cells and tissue components, including transit-amplifying cells, neuroblasts, ependymal cells, blood vessels, and a basal lamina. Within this microenvironment, stem cell properties, including proliferation and differentiation, are maintained. Current NSC culture techniques often include the addition of molecular components found within the in vivo niche, such as mitogenic growth factors. Some protocols use bio-scaffolds to mimic the physical growth environment of living tissue. We describe a novel NSC culture system, derived from embryonic stem (ES) cells, that displays elements of an NSC niche in the absence of exogenously applied mitogens or complex physical scaffolding. Mouse ES cells were neuralized with retinoic acid and plated on an entactin-collagen-laminin-coated glass surface at high density (250,000 cells/cm(2)). Six to eight days after plating, complex multicellular structures consisting of heterogeneous cell types developed spontaneously. NSC and progenitor cell proliferation and differentiation continued within these structures. The identity of cellular and molecular components within the cultures was documented using RT-PCR, immunocytochemistry, and neurosphere-forming assays. We show that ES cells can be induced to form structures that exhibit key properties of a developing NSC niche. We believe this system can serve as a useful model for studies of neurogenesis and stem cell maintenance in the NSC niche as well as for applications in stem cell transplantation.

  20. Constitutive models for the Etchegoin Sands, Belridge Diatomite, and overburden formations at the Lost Hills oil field, California

    Energy Technology Data Exchange (ETDEWEB)

    FOSSUM,ARLO F.; FREDRICH,JOANNE T.

    2000-04-01

    This report documents the development of constitutive material models for the overburden formations, reservoir formations, and underlying strata at the Lost Hills oil field located about 45 miles northwest of Bakersfield in Kern County, California. Triaxial rock mechanics tests were performed on specimens prepared from cores recovered from the Lost Hills field, and included measurements of axial and radial stresses and strains under different load paths. The tested intervals comprise diatomaceous sands of the Etchegoin Formation and several diatomite types of the Belridge Diatomite Member of the Monterey Formation, including cycles both above and below the diagenetic phase boundary between opal-A and opal-CT. The laboratory data are used to drive constitutive parameters for the Extended Sandler-Rubin (ESR) cap model that is implemented in Sandia's structural mechanics finite element code JAS3D. Available data in the literature are also used to derive ESR shear failure parameters for overburden formations. The material models are being used in large-scale three-dimensional geomechanical simulations of the reservoir behavior during primary and secondary recovery.

  1. A New High Resolution Wave Modeling System for Renewable Energy Applications in California and the Mediterranean Sea

    Science.gov (United States)

    Galanis, G. N.; Kafatos, M.; Chu, P. C.; Hatzopoulos, N.; Emmanouil, G.; Kallos, G. B.

    2014-12-01

    The use of integrated high accuracy wave systems is of critical importance today for applications on renewable energy assessment and monitoring, especially over offshore areas where the availability of credible, quality controlled corresponding observations is limited. In this work a new wave modeling system developed by the Hellenic Naval Academy and the University of Athens, Greece, the Center of Excellence in Earth Systems Modeling & Observations of Schmid College of Science in Chapman University, USA and the Naval Ocean and Analysis Laboratory of the US-Naval Postgraduate School, is presented. The new wave system has been based on WAM (ECMWF parallel version) model and focuses on parameters that directly or not affect the estimation of wave power potential in offshore and near shore areas. The results obtained are utilized for monitoring the wave energy potential over the California and Eastern Mediterranean coastline. A detailed statistical analysis based on classical and non-conventional measures provides a solid framework for the quantification of the results. Extreme values-cases posing potential threats for renewable energy parks and platforms are particularly analyzed.

  2. Evolution of climatic niche specialization: a phylogenetic analysis in amphibians.

    Science.gov (United States)

    Bonetti, Maria Fernanda; Wiens, John J

    2014-11-22

    The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change.

  3. Reconsidering the specialist-generalist paradigm in niche breadth dynamics: resource gradient selection by Canada lynx and bobcat.

    Directory of Open Access Journals (Sweden)

    Michael J L Peers

    Full Text Available The long-standing view in ecology is that disparity in overall resource selection is the basis for identifying niche breadth patterns, with species having narrow selection being classified "specialists" and those with broader selection being "generalists". The standard model of niche breadth characterizes generalists and specialists as having comparable levels of overall total resource exploitation, with specialists exploiting resources at a higher level of performance over a narrower range of conditions. This view has gone largely unchallenged. An alternate model predicts total resource use being lower for the specialized species with both peaking at a comparable level of performance over a particular resource gradient. To reconcile the niche breadth paradigm we contrasted both models by developing range-wide species distribution models for Canada lynx, Lynx canadensis, and bobcat, Lynx rufus. Using a suite of environmental factors to define each species' niche, we determined that Canada lynx demonstrated higher total performance over a restricted set of variables, specifically those related to snow and altitude, while bobcat had higher total performance across most variables. Unlike predictions generated by the standard model, bobcat level of exploitation was not compromised by the trade-off with peak performance, and Canada lynx were not restricted to exploiting a narrower range of conditions. Instead, the emergent pattern was that specialist species have a higher total resource utilization and peak performance value within a smaller number of resources or environmental axes than generalists. Our results also indicate that relative differences in niche breadth are strongly dependent on the variable under consideration, implying that the appropriate model describing niche breadth dynamics between specialists and generalists may be more complex than either the traditional heuristic or our modified version. Our results demonstrate a need to re

  4. Users' guide to system dynamics model describing Coho salmon survival in Olema Creek, Point Reyes National Seashore, Marin County, California

    Science.gov (United States)

    Woodward, Andrea; Torregrosa, Alicia; Madej, Mary Ann; Reichmuth, Michael; Fong, Darren

    2014-01-01

    The system dynamics model described in this report is the result of a collaboration between U.S. Geological Survey (USGS) scientists and National Park Service (NPS) San Francisco Bay Area Network (SFAN) staff, whose goal was to develop a methodology to integrate inventory and monitoring data to better understand ecosystem dynamics and trends using salmon in Olema Creek, Marin County, California, as an example case. The SFAN began monitoring multiple life stages of coho salmon (Oncorhynchus kisutch) in Olema Creek during 2003 (Carlisle and others, 2013), building on previous monitoring of spawning fish and redds. They initiated water-quality and habitat monitoring, and had access to flow and weather data from other sources. This system dynamics model of the freshwater portion of the coho salmon life cycle in Olema Creek integrated 8 years of existing monitoring data, literature values, and expert opinion to investigate potential factors limiting survival and production, identify data gaps, and improve monitoring and restoration prescriptions. A system dynamics model is particularly effective when (1) data are insufficient in time series length and/or measured parameters for a statistical or mechanistic model, and (2) the model must be easily accessible by users who are not modelers. These characteristics helped us meet the following overarching goals for this model: Summarize and synthesize NPS monitoring data with data and information from other sources to describe factors and processes affecting freshwater survival of coho salmon in Olema Creek. Provide a model that can be easily manipulated to experiment with alternative values of model parameters and novel scenarios of environmental drivers. Although the model describes the ecological dynamics of Olema Creek, these dynamics are structurally similar to numerous other coastal streams along the California coast that also contain anadromous fish populations. The model developed for Olema can be used, at least as a

  5. Three-dimensional electrical resistivity model of the hydrothermal system in Long Valley Caldera, California, from magnetotellurics

    Science.gov (United States)

    Peacock, Jared R.; Mangan, Margaret T.; McPhee, Darcy K.; Wannamaker, Phil E.

    2016-01-01

    Though shallow flow of hydrothermal fluids in Long Valley Caldera, California, has been well studied, neither the hydrothermal source reservoir nor heat source has been well characterized. Here a grid of magnetotelluric data were collected around the Long Valley volcanic system and modeled in 3-D. The preferred electrical resistivity model suggests that the source reservoir is a narrow east-west elongated body 4 km below the west moat. The heat source could be a zone of 2–5% partial melt 8 km below Deer Mountain. Additionally, a collection of hypersaline fluids, not connected to the shallow hydrothermal system, is found 3 km below the medial graben, which could originate from a zone of 5–10% partial melt 8 km below the south moat. Below Mammoth Mountain is a 3 km thick isolated body containing fluids and gases originating from an 8 km deep zone of 5–10% basaltic partial melt.

  6. Phenotypic plasticity allows the Mediterranean parsley frog Pelodytes punctatus to exploit two temporal niches under continuous gene flow.

    Science.gov (United States)

    Jourdan-Pineau, Helene; David, Patrice; Crochet, Pierre-Andre

    2012-02-01

    Environmental changes, such as climate change, lead to the opening of new niches. In such situations, species that adapt to new niches can survive and/or expand their ranges. However, gene flow can hamper genetic adaptation to new environments. Alternatively, recent models have highlighted the importance of phenotypic plasticity in tracking environmental change. Here, we investigate whether phenotypic plasticity or genetic evolution (or both) allows an amphibian species to exploit two divergent climatic niches. In the Mediterranean region, the parsley frog Pelodytes punctatus breeds both in spring, as do most other species, and in autumn, a temporal niche not exploited by most other species, but which may become increasingly important with global warming. Conditions of development are dramatically different between the two seasons and deeply impact tadpole life-history traits. To determine whether these temporal niches are exploited by two genetically differentiated subpopulations, or whether the bimodal phenology arises in a panmictic population displaying plastic life-history traits, we use two complementary approaches. We measure both molecular genetic differentiation and quantitative-trait differentiation between spring and autumn cohorts, using microsatellites and common garden experiments, respectively. Seasonal cohorts were not genetically differentiated and differences in tadpole life history between cohorts were not maintained in laboratory conditions. We conclude that phenotypic plasticity, rather than genetic adaptation, allows Parsley frog to exploit two contrasting temporal niches.

  7. Optimization of Rolling Force Distribution Based on Niche Genetic Algorithm in Continuous Hot Rolling Mills

    Institute of Scientific and Technical Information of China (English)

    LIU Zi-ping; LI Li-xin

    2013-01-01

    Based on the niche genetic algorithm, the intelligent and optimizing model for the rolling force distribution in hot strip mills was put forward. The research showed that the model had many advantages such as fast searching speed, high calculating pre-cision and suiting for on-line calculation. A good strip shape could be achieved by using the model and it is appropriate and practica-ble for rolling producing.

  8. Occupy the Financial Niche – Saturation and Crisis (discontinuous decisions

    Directory of Open Access Journals (Sweden)

    Ionut PURICA

    2014-09-01

    Full Text Available The model presented is proposing an approach that could verify the nonlinear behaviour during a crisis, such that to quantify and predict potential discontinuous behaviour. In this case, the crisis behaviour associated with financial funds reallocation among various credit instruments, described as memes with the sense of Dawkins, is shown to be of discontinuous nature stemming from a logistic penetration in the financial behaviour niche. Actually the logistic penetration is typical in creating cyclic behaviour of economic structures as shown by Marchetti and others from IIASA. A Fokker-Planck equation description results in a stationary solution having a bifurcation like solution with evolution trajectories on a ‘cusp’ type catastrophe that may describe discontinuous decision behaviour

  9. Integrated hydrologic model of Pajaro Valley, Santa Cruz and Monterey Counties, California

    Science.gov (United States)

    Hanson, Randall T.; Schmid, Wolfgang; Faunt, Claudia C.; Lear, Jonathan; Lockwood, Brian

    2014-01-01

    Increasing population, agricultural development (including shifts to more water-intensive crops), and climate variability are placing increasingly larger demands on available groundwater resources in the Pajaro Valley, one of the most productive agricultural regions in the world. This study provided a refined conceptual model, geohydrologic framework, and integrated hydrologic model of the Pajaro Valley. The goal of this study was to produce a model capable of being accurate at scales relevant to water management decisions that are being considered in the revision and updates to the Basin Management Plan (BMP). The Pajaro Valley Hydrologic Model (PVHM) was designed to reproduce the most important natural and human components of the hydrologic system and related climatic factors, permitting an accurate assessment of groundwater conditions and processes that can inform the new BMP and help to improve planning for long-term sustainability of water resources. Model development included a revision of the conceptual model of the flow system, reevaluation of the previous model transformed into MODFLOW, implementation of the new geohydrologic model and conceptual model, and calibration of the transient hydrologic model.

  10. In search of a temporal niche: Environmental factors

    NARCIS (Netherlands)

    Hut, Roelof A.; Kronfeld-Schor, Noga; van der Vinne, Vincent; De la Iglesia, Horacio

    2012-01-01

    Time as an ecological niche variable or "temporal niche" can be defined in the context of the most prominent environmental cycles, including the tidal cycle, the lunar day and month, the solar day, and the earth year. For the current review, we focus on the 24-h domain generated through the earth's

  11. Human embryonic stem cells create their own niche

    Institute of Scientific and Technical Information of China (English)

    Ying Jin

    2007-01-01

    @@ Experimental evidence demonstrates that the ability of stem cells to self-renew and to differentiate into different types of mature cells depends on both their intrinsic genetic programs and external control from their microenvironment or niche. The concept of stem cell niche was first proposed by Schofield in 1978 to describe a microenvironment that supports stem cells in a mammalian hematopoietic system [ 1 ].

  12. Using specialty advertising in a niche marketing plan.

    Science.gov (United States)

    Schwisow, C R

    1992-01-01

    While niche marketing is not a new strategy, an increasing number of competitors are pursuing the same niches, resulting in stiff competition within the health care industry, writes C. Ronald Schwisow. This means marketers need to be resourceful to maximize their communications efforts. One such approach is specialty advertising.

  13. Mechanical Modeling of Near-Fault Deformation Within the Dragon's Back Pressure Ridge, San Andreas Fault, Carrizo Plain, California

    Science.gov (United States)

    Hilley, G. E.; Arrowsmith, R.

    2011-12-01

    This contribution uses field observations and numerical modeling to understand how slip along the variably oriented fault surfaces in the upper few km of the San Andreas Fault (SAF) zone produces near-fault deformation observed within a 4.5-km-long Dragon's Back Pressure Ridge (DBPR) in the Carrizo Plain, central California. Geologic and geomorphic mapping of this feature indicates that the amplitude of monoclinal warping of Quaternary sediments increases from southeast to northwest along the southwestern third of the DBPR, and remains approximately constant throughout the remaining two thirds of the landform. When viewed with other structural observations and limited near-surface magnetotelluric imaging, these geologic observations are most compatible with a scenario in which shallow offset of the SAF to the northeast creates a structural knuckle that is anchored to the North American plate. Thus, deformation accrues as right-lateral strike-slip motion along the SAF moves this obstruction along the fault plane through the DBPR block. We have used the Gale numerical model to simulate deformation expected for geometries similar to those inferred within the vicinity of the DBPR. This is accomplished by relating stresses and strains in the upper crust according to a Drucker-Prager (plastic yielding) constitutive rule. Deformation in the model is driven by applying 35 mm/yr of right-lateral strike-slip motion to the model boundary; this displacement rate is likewise applied to the base of the model. The model geometry of the SAF at the beginning of the loading was fashioned to produce the discontinuity in the geometry of the fault plane that is inferred from field observations. The friction and cohesion of crust on each side of the fault were changed between models to determine the parameter values that preserve the structural discontinuity along the SAF as finite deformation accrued. The structural discontinuity over the ~4.5 km of model displacement is maintained in

  14. Isotopic niche variation in a higher trophic level ectotherm: highlighting the role of succulent plants in desert food webs.

    Directory of Open Access Journals (Sweden)

    Miguel Delibes

    Full Text Available Stable isotope analysis of animal tissues allows description of isotopic niches, whose axes in an n-dimensional space are the isotopic ratios, compared to a standard, of different isotope systems (e.g. δ(13C, δ(15N. Isotopic niches are informative about where an animal, population or species lives and about what it consumes. Here we describe inter- and intrapopulation isotopic niche (bidimensional δ(13C-δ(15N space of the Orange-throated whiptail (Aspidoscelis hyperythra, an arthropodivorous small lizard, in ten localities of Baja California Sur (Mexico. These localities range from extreme arid to subtropical conditions. Between 13 and 20 individuals were sampled at each locality and 1 cm of tail-tip was collected for isotope analysis. As expected, interpopulation niche width variation was much larger than intrapopulation one. Besides, isotopic variation was not related to age, sex or individual size of lizards. This suggests geographic variation of the isotopic niche was related to changes in the basal resources that fuel the trophic web at each locality. The position of Bayesian isotope ellipses in the δ-space indicated that whiptails in more arid localities were enriched in 13C, suggesting most of the carbon they ingested came from CAM succulent plants (cacti, agaves and in minor degree in C4 grasses. Contrarily, whiptails in subtropical areas were depleted in 13C, as they received more carbon from C3 scrubs and trees. Localities closer to sea-level tended to be enriched in 15N, but a clear influence of marine subsidies was detected only at individual level. The study contributes to identify the origin and pathways through which energy flows across the trophic webs of North American deserts.

  15. Exometabolite niche partitioning among sympatric soil bacteria

    Science.gov (United States)

    Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine; Hummel, Eric; Da Rocha, Ulisses Nunes; Chakraborty, Romy; Bowen, Benjamin P.; Karaoz, Ulas; Cadillo-Quiroz, Hinsby; Garcia-Pichel, Ferran; Northen, Trent R.

    2015-01-01

    Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13−26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity. PMID:26392107

  16. Biogeographic ranges do not support niche theory in radiating Canary Island plant clades

    DEFF Research Database (Denmark)

    Steinbauer, Manuel; Field, Richard; Fernández-Palacios, José María

    2016-01-01

    in allopatry. Main conclusions: The expectations from niche conservatism were frequently not met; instead our results suggest considerable climatic niche lability. All significant differences in climatic niche differentiation were opposite to the predictions from competitive displacement. These forces may...

  17. Impact of global climate change on ozone, particulate matter, and secondary organic aerosol concentrations in California: A model perturbation analysis

    Science.gov (United States)

    Horne, Jeremy R.; Dabdub, Donald

    2017-03-01

    Air quality simulations are performed to determine the impact of changes in future climate and emissions on regional air quality in the South Coast Air Basin (SoCAB) of California. The perturbation parameters considered in this study include (1) temperature, (2) absolute humidity, (3) biogenic VOC emissions due to temperature changes, and (4) boundary conditions. All parameters are first perturbed individually. In addition, the impact of simultaneously perturbing more than one parameter is analyzed. Air quality is simulated with meteorology representative of a summertime ozone pollution episode using both a baseline 2005 emissions inventory and a future emissions projection for the year 2023. Different locations within the modeling domain exhibit varying degrees of sensitivity to the perturbations considered. Afternoon domain wide average ozone concentrations are projected to increase by 13-18% as a result of changes in future climate and emissions. Afternoon increases at individual locations range from 10 to 36%. The change in afternoon particulate matter (PM) levels is a strong function of location in the basin, ranging from -7.1% to +4.7% when using 2005 emissions and -8.6% to +1.7% when using 2023 emissions. Afternoon secondary organic aerosol (SOA) concentrations for the entire domain are projected to decrease by over 15%, and the change in SOA levels is not a strong function of the emissions inventory utilized. Temperature increases play the dominant role in determining the overall impact on ozone, PM, and SOA concentrations in both the individual and combined perturbation scenarios.

  18. Water Hyacinth Identification Using CART Modeling With Hyperspectral Data in the Sacramento-San Joaquin River Delta of California

    Science.gov (United States)

    Khanna, S.; Hestir, E. L.; Santos, M. J.; Greenberg, J. A.; Ustin, S. L.

    2007-12-01

    Water hyacinth (Eichhornia crassipes) is an invasive aquatic weed that is causing severe economic and ecological impacts in the Sacramento-San Joaquin River Delta (California, USA). Monitoring its distribution using remote sensing is the crucial first step in modeling its predicted spread and implementing control and eradication efforts. However, accurately mapping this species is confounded by its several phenological forms, namely a healthy vegetative canopy, flowering canopy with dense conspicuous terminal flowers above the foliage, and floating dead and senescent forms. The full range of these phenologies may be simultaneously present at any time, given the heterogeneity of environmental and ecological conditions in the Delta. There is greater spectral variation within water hyacinth than between any of the co-occurring species (pennywort and water primrose), so classification approaches must take these different phenological stages into consideration. We present an approach to differentiating water hyacinth from co-occurring species based on knowledge of relevant variation in leaf chlorophyll, floral pigments, foliage water content, and variation in leaf structure using a classification and regression tree (CART) applied to airborne hyperspectral remote sensing imagery.

  19. Tropospheric Ozone Source Attribution in Southern California during Summer 2014 Based on Lidar Measurements and Model Simulations

    Science.gov (United States)

    Granados Munoz, Maria Jose; Johnson, Matthew S.; Leblanc, Thierry

    2016-01-01

    In the past decades, significant efforts have been made to increase tropospheric ozone long-term monitoring. A large number of ground-based, airborne and space-borne instruments are currently providing valuable data to contribute to better understand tropospheric ozone budget and variability. Nonetheless, most of these instruments provide in-situ surface and column-integrated data, whereas vertically resolved measurements are still scarce. Besides ozonesondes and aircraft, lidar measurements have proven to be valuable tropospheric ozone profilers. Using the measurements from the tropospheric ozone differential absorption lidar (DIAL) located at the JPL Table Mountain Facility, California, and the GEOS-Chem and GEOS-5 model outputs, the impact of the North American monsoon on tropospheric ozone during summer 2014 is investigated. The influence of the Monsoon lightning-induced NOx will be evaluated against other sources (e.g. local anthropogenic emissions and the stratosphere) using also complementary data such as backward-trajectories analysis, coincident water vapor lidar measurements, and surface ozone in-situ measurements.

  20. Introducing the Clean-Tech Adoption Model: A California Case Study

    NARCIS (Netherlands)

    Bijlveld, P.C. (Paul); Riezebos, P. (Peter); Wierstra, E. (Erik)

    2012-01-01

    Abstract. The Clean-Tech Adoption Model (C-TAM) explains the adoption process of clean technology. Based on the Unified Theory of Acceptance and Usage of Technology (UTAUT) combined with qualitative research and empirical data gathering, the model predicts adoption based on the perceived quality, ef

  1. Monitoring and modeling conditions for regional shallow landslide initiation in the San Francisco Bay area, California

    Science.gov (United States)

    Collins, B. D.; Stock, J. D.; Godt, J. W.

    2012-12-01

    Intense winter storms in the San Francisco Bay area (SFBA) of California often trigger widespread landsliding, including debris flows that originate as shallow (initiation thresholds are available for the SFBA, antecedent soil moisture conditions also play a major role in determining the likelihood for landslide generation from a given storm. Previous research has demonstrated that antecedent triggering conditions can be obtained using pre-storm precipitation thresholds (e.g., 250-400 mm of seasonal pre-storm rainfall). However, these types of thresholds do not account for the often cyclic pattern of wetting and drying that can occur early in the winter storm season (i.e. October - December), and which may skew the applicability of precipitation-only based thresholds. To account for these cyclic and constantly evolving soil moisture conditions, we have pursued methods to measure soil moisture directly and integrate these measurements into predictive analyses. During the past three years, the USGS installed a series of four subsurface hydrology monitoring stations in shallow landslide-prone locations of the SFBA to establish a soil-moisture-based antecedent threshold. In addition to soil moisture sensors, the monitoring stations are each equipped with piezometers to record positive pore water pressure that is likely required for shallow landslide initiation and a rain gauge to compare storm intensities with existing precipitation-based thresholds. Each monitoring station is located on a natural, grassy hillslope typically composed of silty sands, underlain by sandstone, sloping at approximately 30°, and with a depth to bedrock of approximately 1 meter - conditions typical of debris flow generation in the SFBA. Our observations reveal that various locations respond differently to seasonal precipitation, with some areas (e.g., Marin County) remaining at higher levels of saturation for longer periods of time during the winter compared to other areas (e.g., the East

  2. Modeling a thick unsaturated zone at San Gorgonio Pass, California: lessons learned after five years of artificial recharge

    Science.gov (United States)

    Flint, Alan L.; Ellett, Kevin M.; Christensen, Allen H.; Martin, Peter

    2012-01-01

    The information flow among the tasks of framework assessment, numerical modeling, model forecasting and hind casting, and system-performance monitoring is illustrated. Results provide an understanding of artificial recharge in high-altitude desert settings where large vertical distances may separate application ponds from their target aquifers. Approximately 3.8 million cubic meters of surface water was applied to spreading ponds from 2003–2007 to artificially recharge the underlying aquifer through a 200-meter thick unsaturated zone in the San Gorgonio Pass area in southern California. A study was conducted between 1997 and 2003, and a numerical model was developed to help determine the suitability of the site for artificial recharge. Ongoing monitoring results indicated that the existing model needed to be modified and recalibrated to more accurately predict artificial recharge at the site. The objective of this work was to recalibrate the model by using observation of the application rates, the rise and fall of the water level above a perching layer, and the approximate arrival time to the water table during the 5-yr monitoring period following initiation of long-term artificial recharge. Continuous monitoring of soil-matric potential, temperature, and water levels beneath the site indicated that artificial recharge reached the underlying water table between 3.75 and 4.5 yr after the initial application of the recharge water. The model was modified to allow the simulation to more adequately match the perching layer dynamics and the time of arrival at the water table. The instrumentation also showed that the lag time between changes in application of water at the surface and the response at the perching layer decreased from about 4 mo to less than 1 mo due to the wet-up of the unsaturated zone and the increase in relative permeability. The results of this study demonstrate the importance of iteratively monitoring and modeling the unsaturated zone in layered

  3. Assessing Drought Impacts on Water Storage using GRACE Satellites and Regional Groundwater Modeling in the Central Valley of California

    Science.gov (United States)

    Scanlon, B. R.; Zhang, Z.; Save, H.; Faunt, C. C.; Dettinger, M. D.

    2015-12-01

    Increasing concerns about drought impacts on water resources in California underscores the need to better understand effects of drought on water storage and coping strategies. Here we use a new GRACE mascons solution with high spatial resolution (1 degree) developed at the Univ. of Texas Center for Space Research (CSR) and output from the most recent regional groundwater model developed by the U.S. Geological Survey to evaluate changes in water storage in response to recent droughts. We also extend the analysis of drought impacts on water storage back to the 1980s using modeling and monitoring data. The drought has been intensifying since 2012 with almost 50% of the state and 100% of the Central Valley under exceptional drought in 2015. Total water storage from GRACE data declined sharply during the current drought, similar to the rate of depletion during the previous drought in 2007 - 2009. However, only 45% average recovery between the two droughts results in a much greater cumulative impact of both droughts. The CSR GRACE Mascons data offer unprecedented spatial resolution with no leakage to the oceans and no requirement for signal restoration. Snow and reservoir storage declines contribute to the total water storage depletion estimated by GRACE with the residuals attributed to groundwater storage. Rates of groundwater storage depletion are consistent with the results of regional groundwater modeling in the Central Valley. Traditional approaches to coping with these climate extremes has focused on surface water reservoir storage; however, increasing conjunctive use of surface water and groundwater and storing excess water from wet periods in depleted aquifers is increasing in the Central Valley.

  4. Thermal modeling of the Clear Lake magmatic system, California: Implications for conventional and hot dry rock geothermal development

    Energy Technology Data Exchange (ETDEWEB)

    Stimac, J.; Goff, F.; Wohletz, K.

    1997-06-01

    The combination of recent volcanism, high heat flow ({ge} HFU or 167 mW/m{sup 2}), and high conductive geothermal gradient (up to 120{degree} C/km) makes the Clear Lake region of northern California one of the best prospects for hot dry rock (HDR) geothermal development in the US. The lack of permeability in exploration wells and lack of evidence for widespread geothermal reservoirs north of the Collayomi fault zone are not reassuring indications for conventional geothermal development. This report summarizes results of thermal modeling of the Clear Lake magmatic system, and discusses implications for HDR site selection in the region. The thermal models incorporate a wide range of constraints including the distribution and nature of volcanism in time and space, water and gas geochemistry, well data, and geophysical surveys. The nature of upper crustal magma bodies at Clear Lake is inferred from studying sequences of related silicic lavas, which tell a story of multistage mixing of silicic and mafic magma in clusters of small upper crustal chambers. Thermobarometry on metamorphic xenoliths yield temperature and pressure estimates of {approximately}780--900 C and 4--6 kb respectively, indicating that at least a portion of the deep magma system resided at depths from 14 to 21 km (9 to 12 mi). The results of thermal modeling support previous assessments of the high HDR potential of the area, and suggest the possibility that granitic bodies similar to The Geysers felsite may underlie much of the Clear Lake region at depths as little as 3--6 km. This is significant because future HDR reservoirs could potentially be sited in relatively shallow granitoid plutons rather than in structurally complex Franciscan basement rocks.

  5. Top-down estimate of methane emissions in California using a mesoscale inverse modeling technique: The South Coast Air Basin

    Science.gov (United States)

    Cui, Yu Yan; Brioude, Jerome; McKeen, Stuart A.; Angevine, Wayne M.; Kim, Si-Wan; Frost, Gregory J.; Ahmadov, Ravan; Peischl, Jeff; Bousserez, Nicolas; Liu, Zhen; Ryerson, Thomas B.; Wofsy, Steve C.; Santoni, Gregory W.; Kort, Eric A.; Fischer, Marc L.; Trainer, Michael

    2015-07-01

    Methane (CH4) is the primary component of natural gas and has a larger global warming potential than CO2. Recent top-down studies based on observations showed CH4 emissions in California's South Coast Air Basin (SoCAB) were greater than those expected from population-apportioned bottom-up state inventories. In this study, we quantify CH4 emissions with an advanced mesoscale inverse modeling system at a resolution of 8 km × 8 km, using aircraft measurements in the SoCAB during the 2010 Nexus of Air Quality and Climate Change campaign to constrain the inversion. To simulate atmospheric transport, we use the FLEXible PARTicle-Weather Research and Forecasting (FLEXPART-WRF) Lagrangian particle dispersion model driven by three configurations of the Weather Research and Forecasting (WRF) mesoscale model. We determine surface fluxes of CH4 using a Bayesian least squares method in a four-dimensional inversion. Simulated CH4 concentrations with the posterior emission inventory achieve much better correlations with the measurements (R2 = 0.7) than using the prior inventory (U.S. Environmental Protection Agency's National Emission Inventory 2005, R2 = 0.5). The emission estimates for CH4 in the posterior, 46.3 ± 9.2 Mg CH4/h, are consistent with published observation-based estimates. Changes in the spatial distribution of CH4 emissions in the SoCAB between the prior and posterior inventories are discussed. Missing or underestimated emissions from dairies, the oil/gas system, and landfills in the SoCAB seem to explain the differences between the prior and posterior inventories. We estimate that dairies contributed 5.9 ± 1.7 Mg CH4/h and the two sectors of oil and gas industries (production and downstream) and landfills together contributed 39.6 ± 8.1 Mg CH4/h in the SoCAB.

  6. Integrated geomorphic and geodynamic modeling of a potential blind thrust in the San Francisco Bay area, California

    Science.gov (United States)

    Johnson, Courtney B.; Furlong, Kevin P.; Kirby, Eric

    2009-06-01

    Geometries and slip budgets of the faults in the San Francisco Bay area imply previously unrecognized fault linkages, including examples of blind thrust structures that appear to connect segments of strike-slip faults and accommodate along-strike variations in slip rate along these structures. Displacement along linking faults may be associated with the development of topography and also may serve as earthquake sources. In Marin County, California, systematic spatial patterns in landscape topography and geomorphic indices suggest that the region north of Mt. Tamalpais is experiencing differential rock uplift. We suggest that a blind thrust underlies the elevated area, creating the observed topography and possibly resolving a slip discrepancy between the Hayward and San Andreas Fault in this region. We have developed and implemented an integrative approach that combines observations from tectonic deformation and geomorphic properties to identify a potential blind thrust beneath Marin County. Elastic displacement modeling has been tested for compatibility with the blind thrust hypothesis and to assess the sensitivity of observables to fault geometry and orientation; from this, a set of plausible blind thrust structures are defined. We use a range of empirical relationships between channel steepness index and erosion rate to estimate spatial variations in erosion rate along Bolinas Ridge. By coupling these erosion estimates with elastic displacement fault modeling, we can use the resulting topographic envelopes to constrain the rate and duration of deformation. These constraints, along with spatial bounds on the possible fault models, are used to calculate potential seismic moment and moment magnitude. With an assumed recurrence interval of ~ 100 years, such blind thrusts can produce a Mw ~ 6.3 earthquake, while a longer recurrence time (~ 1000 years) results in a maximum Mw ~ 7.0 earthquake. Although such events are not likely to be catastrophic, they are large

  7. Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives.

    Science.gov (United States)

    Matthews, Thomas J; Whittaker, Robert J

    2014-06-01

    Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.

  8. Diet and trophic niche of Lithobates catesbeianus (Amphibia: Anura

    Directory of Open Access Journals (Sweden)

    Peterson T. Leivas

    2012-10-01

    Full Text Available Lithobates catesbeianus (Shaw, 1802 is an invasive anuran introduced in Brazil that is associated with the displacement and the decline of populations of native species worldwide. There is evidence that biological invasions are facilitated by certain attributes of the invading species, for instance niche breath, and that invasive species have a broader ecological niche with respect to native ones. We designed a study to ascertain the temporal, ontogenetic, and sex differences in the niche dynamics of the American bullfrog. We sampled monthly from June 2008 to May 2009 in the state of Paraná, southern Brazil. For each individual, we gathered biometric and stomach content data. We then estimated the niche breath of the juveniles and adults, and compared it between the sexes. A total of 104 females and 77 males were sampled. Lithobates catesbeianus has a generalist diet, preying upon invertebrates and vertebrates. Even though the diet of the studied population varied seasonally, it did not differ between the sexes nor did it respond to biometric variables. Niche breadth was more restricted in the winter than in the autumn. The trophic niche of juveniles and adults did not overlap much when compared with the trophic niche overlap between males and females. Adult males and females had a considerable niche overlap, but females had a broader trophic niche than males in the winter and in the spring. These niche characteristics point to an opportunistic predation strategy that may have facilitated the process of invasion and establishment of this species in the study area.

  9. Spatial niche facilitates clonal reproduction in seed plants under temporal disturbance.

    Science.gov (United States)

    Fukui, Shin; Araki, Kiwako S

    2014-01-01

    The evolutionary origins and advantages of clonal reproduction relative to sexual reproduction have been discussed for several taxonomic groups. In particular, organisms with a sessile lifestyle are often exposed to spatial and temporal environmental fluctuations. Thus, clonal propagation may be advantageous in such fluctuating environments, for sessile species that can reproduce both sexually and clonally. Here we introduce the concept of niche to a lattice space that changes spatially and temporally, by incorporating the compatibility between the characteristics of a sessile clonal plant with its habitat into a spatially explicit individual-based model. We evaluate the impact of spatially and temporally heterogeneous environments on the evolution of reproductive strategies: the optimal balance between seed and clonal reproduction of a clonal plant. The spatial niche case with local habitats led to avoidance of specialization in reproductive strategy, whereas stable environments or intensive environmental change tended to result in specialization in either clonal or seed reproduction under neutral conditions. Furthermore, an increase in spatial niches made clonal reproduction advantageous, as a consequence of competition among several genets under disturbed conditions, because a ramet reached a favorable habitat through a rare long-distance dispersal event via seed production. Thus, the existence of spatial niches could explain the advantages of clonal propagation.

  10. Regulatory T Cells Occupy an Isolated Niche in the Intestine that Is Antigen Independent

    Directory of Open Access Journals (Sweden)

    Lisa L. Korn

    2014-12-01

    Full Text Available Regulatory T cells (Tregs are CD4+ T cells that maintain immune homeostasis and prevent autoimmunity. Like all CD4+ T cells, Tregs require antigen-specific signals via T cell receptor-major histocompatibility complex class II (TCR-MHCII interactions for their development. However, the requirement for MHCII in Treg homeostasis in tissues such as intestinal lamina propria (LP is unknown. We examined LP Treg homeostasis in a transgenic mouse model that lacks peripheral TCR-MHCII interactions and generation of extrathymic Tregs (iTregs. Thymically generated Tregs entered the LP of weanlings and proliferated independently of MHCII to fill the compartment. The adult LP was a closed niche; new thymic Tregs were excluded, and Tregs in parabiotic pairs were LP resident. The isolated LP niche was interleukin-2 (IL-2 independent but dependent on commensal bacteria. Thus, an LP Treg niche can be filled, isolated, and maintained independently of antigen signals and iTregs. This niche may represent a tissue-specific mechanism for maintaining immune tolerance.

  11. Niche Limits of Symbiotic Gut Microbiota Constrain the Salinity Tolerance of Brine Shrimp.

    Science.gov (United States)

    Nougué, Odrade; Gallet, Romain; Chevin, Luis-Miguel; Lenormand, Thomas

    2015-09-01

    Symbiosis generally causes an expansion of the niche of each partner along the axis for which a service is mutually provided. However, for other axes, the niche can be restricted to the intersection of each partner's niche and can thus be constrained rather than expanded by mutualism. We explore this phenomenon using Artemia as a model system. This crustacean is able to survive at very high salinities but not at low salinities, although its hemolymph's salinity is close to freshwater. We hypothesized that this low-salinity paradox results from poor performance of its associated microbiota at low salinity. We showed that, in sterile conditions, Artemia had low survival at all salinities when algae were the only source of carbon. In contrast, survival was high at all salinities when fed with yeast. We also demonstrated that bacteria isolated from Artemia's gut reached higher densities at high salinities than at low salinities, including when grown on algae. Taken together, our results show that Artemia can survive at low salinities, but their gut microbiota, which are required for algae digestion, have reduced fitness. Widespread facultative symbiosis may thus be an important determinant of niche limits along axes not specific to the mutualistic interaction.

  12. Life-cycle switching and coexistence of species with no niche differentiation.

    Directory of Open Access Journals (Sweden)

    Javier Montero-Pau

    Full Text Available The increasing evidence of coexistence of cryptic species with no recognized niche differentiation has called attention to mechanisms reducing competition that are not based on niche-differentiation. Only sex-based mechanisms have been shown to create the negative feedback needed for stable coexistence of competitors with completely overlapping niches. Here we show that density-dependent sexual and diapause investment can mediate coexistence of facultative sexual species having identical niches. We modelled the dynamics of two competing cyclical parthenogens with species-specific density-dependent sexual and diapause investment and either equal or different competitive abilities. We show that investment in sexual reproduction creates an opportunity for other species to invade and become established. This may happen even if the invading species is an inferior competitor. Our results suggests a previously unnoticed mechanism for species coexistence and can be extended to other facultative sexual species and species investing in diapause where similar density-dependent life-history switches could act to promote coexistence.

  13. Habitat suitability and conservation of the giant gartersnake (Thamnophis gigas) in the Sacramento Valley of California

    Science.gov (United States)

    Halstead, Brian J.; Wylie, Glenn D.; Casazza, Michael L.

    2010-01-01

    Resource managers often have little information regarding the habitat requirements and distribution of rare species. Factor analysis-based habitat suitability models describe the ecological niche of a species and identify locations where these conditions occur on the landscape using existing occurrence data.We used factor analyses to assess the suitability of habitats for Thamnophis gigas (Giant Gartersnake), a rare, threatened species endemic to the Central Valley of California, USA, and to map the locations of habitat suitable for T. gigas in the Sacramento Valley. Factor analyses indicated that the niche of T. gigas is composed of sites near rice agriculture with low stream densities. Sites with high canal densities and near wetlands also appeared suitable, but results for these variables were sensitive to potential sampling bias. In the Sacramento Valley, suitable habitats occur primarily in the central portion of the valley floor. Based upon the results of the factor analyses, recovery planning for T. gigas will require an on-the-ground assessment of the current distribution and abundance of T. gigas, maintaining the few remaining natural wetlands and the practice of rice agriculture in the Sacramento Valley, and studying the effects of agricultural practices and land use changes on populations of T. gigas.

  14. Tracking of climatic niche boundaries under recent climate change.

    Science.gov (United States)

    La Sorte, Frank A; Jetz, Walter

    2012-07-01

    1. Global climate has changed significantly during the past 30 years and especially in northern temperate regions which have experienced poleward shifts in temperature regimes. While there is evidence that some species have responded by moving their distributions to higher latitudes, the efficiency of this response in tracking species' climatic niche boundaries over time has yet to be addressed. 2. Here, we provide a continental assessment of the temporal structure of species responses to recent spatial shifts in climatic conditions. We examined geographic associations with minimum winter temperature for 59 species of winter avifauna at 476 Christmas Bird Count circles in North America from 1975 to 2009 under three sampling schemes that account for spatial and temporal sampling effects. 3. Minimum winter temperature associated with species occurrences showed an overall increase with a weakening trend after 1998. Species displayed highly variable responses that, on average and across sampling schemes, contained a strong lag effect that weakened in strength over time. In general, the conservation of minimum winter temperature was relevant when all species were considered together but only after an initial lag period (c. 35 years) was overcome. The delayed niche tracking observed at the combined species level was likely supported by the post1998 lull in the warming trend. 4. There are limited geographic and ecological explanations for the observed variability, suggesting that the efficiency of species' responses under climate change is likely to be highly idiosyncratic and difficult to predict. This outcome is likely to be even more pronounced and time lags more persistent for less vagile taxa, particularly during the periods of consistent or accelerating warming. Current modelling efforts and conservation strategies need to better appreciate the variation, strength and duration of lag effects and their association with climatic variability. Conservation

  15. A 3-Dimensional Model of Water-Bearing Sequences in the Dominguez Gap Region, Long Beach, California

    Science.gov (United States)

    Ponti, Daniel J.; Ehman, Kenneth D.; Edwards, Brian D.; Tinsley, John C.; Hildenbrand, Thomas; Hillhouse, John W.; Hanson, Randall T.; McDougall, Kristen; Powell, Charles L.; Wan, Elmira; Land, Michael; Mahan, Shannon; Sarna-Wojcicki, Andrei M.

    2007-01-01

    A 3-dimensional computer model of the Quaternary sequence stratigraphy in the Dominguez gap region of Long Beach, California has been developed to provide a robust chronostratigraphic framework for hydrologic and tectonic studies. The model consists of 13 layers within a 16.5 by 16.1 km (10.25 by 10 mile) square area and extends downward to an altitude of -900 meters (-2952.76 feet). Ten sequences of late Pliocene to Holocene age are identified and correlated within the model. Primary data to build the model comes from five reference core holes, extensive high-resolution seismic data obtained in San Pedro Bay, and logs from several hundred water and oil wells drilled in the region. The model is best constrained in the vicinity of the Dominguez gap seawater intrusion barrier where a dense network of subsurface data exist. The resultant stratigraphic framework and geologic structure differs significantly from what has been proposed in earlier studies. An important new discovery from this approach is the recognition of ongoing tectonic deformation throughout nearly all of Quaternary time that has impacted the geometry and character of the sequences. Anticlinal folding along a NW-SE trend, probably associated with Quaternary reactivation of the Wilmington anticline, has uplifted and thinned deposits along the fold crest, which intersects the Dominguez gap seawater barrier near Pacific Coast Highway. A W-NW trending fault system that approximately parallels the fold crest has also been identified. This fault progressively displaces all but the youngest sequences down to the north and serves as the southern termination of the classic Silverado aquifer. Uplift and erosion of fining-upward paralic sequences along the crest of the young fold has removed or thinned many of the fine-grained beds that serve to protect the underlying Silverado aquifer from seawater contaminated shallow groundwater. As a result of this process, the potential exists for vertical migration of

  16. GIS SUPPORTED HEDONIC MODEL FOR ASSESSING PROPERTY VALUE IN WEST OAKLAND, CALIFORNIA

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A hedonic linear regression model is constructed in this paper to estimate property value. In our model, the property value (sales price) is a function of several selected variables such as the property characteristics, social neighborhoods, level of neighborhood environmental contaminations, level of neighborhood crimes, and locational accessibility to jobs or services. Definitions and calculation of these variables are approached by using Geographic Information System tools. For improving estimation, gravity model is employed to measure both levels of neighborhood toxic sites and crimes; and a time-based method is used to measure the locational accessibility rather than simple straight-line distance measurement. This study discovers that the relationship between house value and its nearby highway is nonlinear. The methodology could help policy makers assess the external effects ora property. Our model also could be used potentially to identify the current and historic trends of development caused by neighborhood or environments change in the study area.

  17. Quantifying Slopes with Digital Elevation Models of the Verdugo Hills, California: Effects of Resolution

    Science.gov (United States)

    Fielding, E. J.; Burbank, D. W.; Duncan, C. C.

    1996-01-01

    Quantification of surface slope angles is valuable in a wide variety of earth sciences. Slopes measured from digital elevation models (DEMs) or other topographic data sets depend strongly on the length scale or window size used in the slope calculations.

  18. A 30 meter Digital Elevation Model (DEM) of the San Gorgonio Pass area, Riverside County, California.

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Digital Elevation Models (DEMs) are digital records of terrain elevations at regularly spaced intervals. The interval between elevations of 7.5 minute DEMs is...

  19. Development And Application Of A Hydrothermal Model For The Salton Sea Geothermal Field, California

    Energy Technology Data Exchange (ETDEWEB)

    Kasameyer, P.; Younker, L.; Hanson, J.

    1984-01-01

    A simple lateral flow model adequately explains many of the features associated with the Salton Sea Geothermal Field. Earthquake swarms, a magnetic anomaly, and aspects of the gravity anomaly are all indirect evidence for the igneous activity which is the ultimate source of heat for the system. Heat is transferred from this area of intrusion by lateral spreading of hot water in a reservoir beneath an impermeable cap rock. A two dimensional analytic model encompassing this transport mechanism matches general features of the thermal anomaly and has been used to estimate the age of the presently observed thermal system. The age is calculated by minimizing the variance between the observed surface heat-flow data and the model. Estimates of the system age for this model range from 3,000 to 20,000 years.

  20. An update of the Death Valley regional groundwater flow system transient model, Nevada and California

    Science.gov (United States)

    Belcher, Wayne R.; Sweetkind, Donald S.; Faunt, Claudia C.; Pavelko, Michael T.; Hill, Mary C.

    2017-01-19

    Since the original publication of the Death Valley regional groundwater flow system (DVRFS) numerical model in 2004, more information on the regional groundwater flow system in the form of new data and interpretations has been compiled. Cooperators such as the Bureau of Land Management, National Park Service, U.S. Fish and Wildlife Service, the Department of Energy, and Nye County, Nevada, recognized a need to update the existing regional numerical model to maintain its viability as a groundwater management tool for regional stakeholders. The existing DVRFS numerical flow model was converted to MODFLOW-2005, updated with the latest available data, and recalibrated. Five main data sets were revised: (1) recharge from precipitation varying in time and space, (2) pumping data, (3) water-level observations, (4) an updated regional potentiometric map, and (5) a revision to the digital hydrogeologic framework model.The resulting DVRFS version 2.0 (v. 2.0) numerical flow model simulates groundwater flow conditions for the Death Valley region from 1913 to 2003 to correspond to the time frame for the most recently published (2008) water-use data. The DVRFS v 2.0 model was calibrated by using the Tikhonov regularization functionality in the parameter estimation and predictive uncertainty software PEST. In order to assess the accuracy of the numerical flow model in simulating regional flow, the fit of simulated to target values (consisting of hydraulic heads and flows, including evapotranspiration and spring discharge, flow across the model boundary, and interbasin flow; the regional water budget; values of parameter estimates; and sensitivities) was evaluated. This evaluation showed that DVRFS v. 2.0 simulates conditions similar to DVRFS v. 1.0. Comparisons of the target values with simulated values also indicate that they match reasonably well and in some cases (boundary flows and discharge) significantly better than in DVRFS v. 1.0.

  1. Model of the heat source of the Cerro Prieto magma-hydrothermal system, Baja California, Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Elders, W.A.; Bird, D.K.; Williams, A.E.; Schiffman, P.; Cox, B.

    1982-08-10

    Earlier studies at Cerro Prieto by UCR have led to the development of a qualitative model for field flow in the geothermal system before it was drilled and perturbed by production. Current efforts are directed towards numerical modelling of heat and mass transfer in the system in this undisturbed state. A two-dimensional model assumes that the heat sources were a single basalt/gabbro intrusion which provided heat to the system as it cooled. After compiling various information on the physical properties of the reservoir, the enthalpy contained in two 1cm thick section across the reservoir orthogonal to each other was calculated. Next various shapes, sizes and depths for the intrusion as initial conditions and boundary conditions for the calculation of heat transfer were considered. A family of numerical models which so far gives the best matches to the conditions observed in the field today have in common a funnel-shaped intrusion with a top 4km wide emplaced at a depth of 5km some 30,000 to 50,000 years ago, providing heat to the geothermal system. Numerical modelling is still in progress. Although none of the models so far computed may be a perfect match for the thermal history of the reservoir, they all indicate that the intrusive heat source is young, close and large.