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Sample records for california niche modeling

  1. Activity-specific ecological niche models for planning reintroductions of California condors (Gymnogyps californianus)

    Science.gov (United States)

    Jesse D’Elia; Susan M. Haig; Matthew Johnson; Richard Young; Bruce G. Marcot

    2015-01-01

    Ecological niche models can be a useful tool to identify candidate reintroduction sites for endangered species but have been infrequently used for this purpose. In this paper, we (1) develop activity-specific ecological niche models (nesting, roosting, and feeding) for the critically endangered California condor (Gymnogyps californianus) to aid in...

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

    Science.gov (United States)

    Holt, Ashley C; Salkeld, Daniel J; Fritz, Curtis L; Tucker, James R; Gong, Peng

    2009-01-01

    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. In addition, Maxent

  3. 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

  4. Phylogeography and Ecological Niche Modeling of the Desert Iguana (Dipsosaurus dorsalis, Baird & Girard 1852) in the Baja California Peninsula.

    Science.gov (United States)

    Valdivia-Carrillo, Tania; García-De León, Francisco J; Blázquez, Ma Carmen; Gutiérrez-Flores, Carina; González Zamorano, Patricia

    2017-09-01

    Understanding the factors that explain the patterns of genetic structure or phylogeographic breaks at an intraspecific level is key to inferring the mechanisms of population differentiation in its early stages. These topics have been well studied in the Baja California region, with vicariance and the dispersal ability of individuals being the prevailing hypothesis for phylogeographic breaks. In this study, we evaluated the phylogeographic patterns in the desert iguana (Dipsosaurus dorsalis), a species with a recent history in the region and spatial variation in life history traits. We analyzed a total of 307 individuals collected throughout 19 localities across the Baja California Peninsula with 15 microsatellite DNA markers. Our data reveal the existence of 3 geographically discrete genetic populations with moderate gene flow and an isolation-by-distance pattern presumably produced by the occurrence of a refugium in the Cape region during the Pleistocene Last Glacial Maximum. Bayesian methods and ecological niche modeling were used to assess the relationship between population genetic structure and present and past climatic preferences of the desert iguana. We found that the present climatic heterogeneity of the Baja California Peninsula has a marked influence on the population genetic structure of the species, suggesting that there are alternative explanations besides vicariance. The information obtained in this study provides data allowing a better understanding of how historical population processes in the Baja California Peninsula can be understood from an ecological perspective. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Ditch the niche - is the niche a useful concept in ecology or species distribution modelling?

    NARCIS (Netherlands)

    McInerny, Greg J.; Etienne, Rampal S.

    2012-01-01

    In this first of three papers we examine the use of niche concepts in ecology and especially in species distribution modelling (SDM). This paper deliberately focuses on the lack of clarity found in the term niche. Because its meanings are so diverse, the term niche tends to create confusion and

  6. Advances and links between ecological niche models and phylogeography

    OpenAIRE

    Sánchez-Fernández, David; Arribas, Paula; Abellán, Pedro

    2016-01-01

    Phylogeography and ecological niche modelling are two key approaches advancing biogeography. A special issue of Folia Zoologica (64: 2015) considers these advances in eight articles, including two reviews—on Next Generation Sequencing (NGS) and Ecological Niche Modelling (ENM)—and six research articles, plus two book reviews. The reviews on NGS and ENM stand out as the main interests of the issue. The six research articles provide different biogeographical case studies in which phylogeography...

  7. 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

  8. 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.

  9. Ecological Niche Modelling of Bank Voles in Western Europe

    Directory of Open Access Journals (Sweden)

    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.

  10. Genetically informed ecological niche models improve climate change predictions.

    Science.gov (United States)

    Ikeda, Dana H; Max, Tamara L; Allan, Gerard J; Lau, Matthew K; Shuster, Stephen M; Whitham, Thomas G

    2017-01-01

    We examined the hypothesis that ecological niche models (ENMs) more accurately predict species distributions when they incorporate information on population genetic structure, and concomitantly, local adaptation. Local adaptation is common in species that span a range of environmental gradients (e.g., soils and climate). Moreover, common garden studies have demonstrated a covariance between neutral markers and functional traits associated with a species' ability to adapt to environmental change. We therefore predicted that genetically distinct populations would respond differently to climate change, resulting in predicted distributions with little overlap. To test whether genetic information improves our ability to predict a species' niche space, we created genetically informed ecological niche models (gENMs) using Populus fremontii (Salicaceae), a widespread tree species in which prior common garden experiments demonstrate strong evidence for local adaptation. Four major findings emerged: (i) gENMs predicted population occurrences with up to 12-fold greater accuracy than models without genetic information; (ii) tests of niche similarity revealed that three ecotypes, identified on the basis of neutral genetic markers and locally adapted populations, are associated with differences in climate; (iii) our forecasts indicate that ongoing climate change will likely shift these ecotypes further apart in geographic space, resulting in greater niche divergence; (iv) ecotypes that currently exhibit the largest geographic distribution and niche breadth appear to be buffered the most from climate change. As diverse agents of selection shape genetic variability and structure within species, we argue that gENMs will lead to more accurate predictions of species distributions under climate change. © 2016 John Wiley & Sons Ltd.

  11. Using Ecological Niche Models and Niche Analyses to Understand Speciation Patterns: The Case of Sister Neotropical Orchid Bees

    Science.gov (United States)

    Silva, Daniel P.; Vilela, Bruno; De Marco, Paulo; Nemésio, André

    2014-01-01

    The role of past connections between the two major South American forested biomes on current species distribution has been recognized a long time ago. Climatic oscillations that further separated these biomes have promoted parapatric speciation, in which many species had their continuous distribution split, giving rise to different but related species (i.e., different potential distributions and realized niche features). The distribution of many sister species of orchid bees follow this pattern. Here, using ecological niche models and niche analyses, we (1) tested the role of ecological niche differentiation on the divergence between sister orchid-bees (genera Eulaema and Eufriesea) from the Amazon and Atlantic forests, and (2) highlighted interesting areas for new surveys. Amazonian species occupied different realized niches than their Atlantic sister species. Conversely, species of sympatric but distantly related Eulaema bees occupied similar realized niches. Amazonian species had a wide potential distribution in South America, whereas Atlantic Forest species were more limited to the eastern coast of the continent. Additionally, we identified several areas in need of future surveys. Our results show that the realized niche of Atlantic-Amazonian sister species of orchid bees, which have been previously treated as allopatric populations of three species, had limited niche overlap and similarity. These findings agree with their current taxonomy, which treats each of those populations as distinct valid species. PMID:25422941

  12. 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.

  13. Introducing MERGANSER: A Flexible Framework for Ecological Niche Modeling

    Science.gov (United States)

    Klawonn, M.; Dow, E. M.

    2015-12-01

    Ecological Niche Modeling (ENM) is a collection of techniques to find a "fundamental niche", the range of environmental conditions suitable for a species' survival in the absence of inter-species interactions, given a set of environmental parameters. Traditional approaches to ENM face a number of obstacles including limited data accessibility, data management problems, computational costs, interface usability, and model validation. The MERGANSER system, which stands for Modeling Ecological Residency Given A Normalized Set of Environmental Records, addresses these issues through powerful data persistence and flexible data access, coupled with a clear presentation of results and fine-tuned control over model parameters. MERGANSER leverages data measuring 72 weather related phenomena, land cover, soil type, population, species occurrence, general species information, and elevation, totaling over 1.5 TB of data. To the best of the authors' knowledge, MERGANSER uses higher-resolution spatial data sets than previously published models. Since MERGANSER stores data in an instance of Apache SOLR, layers generated in support of niche models are accessible to users via simplified Apache Lucene queries. This is made even simpler via an HTTP front end that generates Lucene queries automatically. Specifically, a user need only enter the name of a place and a species to run a model. Using this approach to synthesizing model layers, the MERGANSER system has successfully reproduced previously published niche model results with a simplified user experience. Input layers for the model are generated dynamically using OpenStreetMap and SOLR's spatial search functionality. Models are then run using either user-specified or automatically determined parameters after normalizing them into a common grid. Finally, results are visualized in the web interface, which allows for quick validation. Model results and all surrounding metadata are also accessible to the user for further study.

  14. The influence of social niche on cultural niche construction: modelling changes in belief about marriage form in Taiwan

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    Lipatov, Mikhail; Brown, Melissa J.; Feldman, Marcus W.

    2011-01-01

    With introduction of social niche effects into a model of cultural change, the frequency of a practice cannot predict the frequency of its underlying belief. The combination of a general model with empirical data from a specific case illustrates the importance of collaboration between modellers and field researchers, and identifies the type of quantitative data necessary for analysing case studies. Demographic data from colonial-period household registers in Taiwan document a shift in marriage form within 40 years, from a mixture of uxorilocal marriages and virilocal marriages to the latter's dominance. Ethnographic data indicate marriage-related beliefs, costs, ethnic effects and colonial policies as well as the importance of horizontal cultural transmission. We present a formal model for the effects of moral beliefs about marriage and a population economic index on the decline of uxorilocal marriage. We integrate empirical marriage rates and an estimated economic index to produce five projections of the historical frequencies of one belief. These projections demonstrate how economic development may affect a cultural niche. They also indicate the need for future research on the relationship between wealth and cultural variability, the motivational force of cultural versus social factors, and the process of cultural niche construction. PMID:21320903

  15. The influence of social niche on cultural niche construction: modelling changes in belief about marriage form in Taiwan.

    Science.gov (United States)

    Lipatov, Mikhail; Brown, Melissa J; Feldman, Marcus W

    2011-03-27

    With introduction of social niche effects into a model of cultural change, the frequency of a practice cannot predict the frequency of its underlying belief. The combination of a general model with empirical data from a specific case illustrates the importance of collaboration between modellers and field researchers, and identifies the type of quantitative data necessary for analysing case studies. Demographic data from colonial-period household registers in Taiwan document a shift in marriage form within 40 years, from a mixture of uxorilocal marriages and virilocal marriages to the latter's dominance. Ethnographic data indicate marriage-related beliefs, costs, ethnic effects and colonial policies as well as the importance of horizontal cultural transmission. We present a formal model for the effects of moral beliefs about marriage and a population economic index on the decline of uxorilocal marriage. We integrate empirical marriage rates and an estimated economic index to produce five projections of the historical frequencies of one belief. These projections demonstrate how economic development may affect a cultural niche. They also indicate the need for future research on the relationship between wealth and cultural variability, the motivational force of cultural versus social factors, and the process of cultural niche construction.

  16. Integrating coalescent and ecological niche modeling in comparative phylogeography.

    Science.gov (United States)

    Carstens, Bryan C; Richards, Corinne L

    2007-06-01

    Understanding the factors that contribute to the formation of population genetic structure is a central goal of phylogeographic research, but achieving this goal can be complicated by the stochastic variance inherent to genetic processes. Statistical approaches to testing phylogeographic hypotheses accommodate this stochasticity by evaluating competing models of putative historical population structure, often by simulating null distributions of the expected variance. The effectiveness of these tests depends on the biological realism of the models. Information from the fossil record can aid in reconstructing the historical distributions of some taxa. However, for the majority of taxa, which lack sufficient fossils, paleodistributional modeling can provide valuable spatial-geographic data concerning ancestral distributions. Paleodistributional models are generated by projecting ecological niche models, which predict the current distribution of each species, onto a model of past climatic conditions. Here, we generate paleodistributional models describing the suitable habitat during the last glacial maximum for lineages from the mesic forests of the Pacific Northwest of North America, and use these models to generate alternative phylogeographic hypotheses. Coalescent simulations are then used to test these hypotheses to improve our understanding of the historical events that promoted the formation of population genetic structure in this ecosystem. Results from Pacific Northwest mesic forest organisms demonstrate the utility of these combined approaches. Paleodistribution models and population genetic structure are congruent across three amphibian lineages, suggesting that they have responded in a concerted manner to environmental change. Two other species, a willow and a water vole, despite being currently codistributed and having similar population genetic structure, were predicted by the paleodistributional model to have had markedly different distributions during

  17. Environmental niche models for riverine desert fishes and their similarity according to phylogeny and functionality

    Science.gov (United States)

    Whitney, James E.; Whittier, Joanna B.; Paukert, Craig

    2017-01-01

    Environmental filtering and competitive exclusion are hypotheses frequently invoked in explaining species' environmental niches (i.e., geographic distributions). A key assumption in both hypotheses is that the functional niche (i.e., species traits) governs the environmental niche, but few studies have rigorously evaluated this assumption. Furthermore, phylogeny could be associated with these hypotheses if it is predictive of functional niche similarity via phylogenetic signal or convergent evolution, or of environmental niche similarity through phylogenetic attraction or repulsion. The objectives of this study were to investigate relationships between environmental niches, functional niches, and phylogenies of fishes of the Upper (UCRB) and Lower (LCRB) Colorado River Basins of southwestern North America. We predicted that functionally similar species would have similar environmental niches (i.e., environmental filtering) and that closely related species would be functionally similar (i.e., phylogenetic signal) and possess similar environmental niches (i.e., phylogenetic attraction). Environmental niches were quantified using environmental niche modeling, and functional similarity was determined using functional trait data. Nonnatives in the UCRB provided the only support for environmental filtering, which resulted from several warmwater nonnatives having dam number as a common predictor of their distributions, whereas several cool- and coldwater nonnatives shared mean annual air temperature as an important distributional predictor. Phylogenetic signal was supported for both natives and nonnatives in both basins. Lastly, phylogenetic attraction was only supported for native fishes in the LCRB and for nonnative fishes in the UCRB. Our results indicated that functional similarity was heavily influenced by evolutionary history, but that phylogenetic relationships and functional traits may not always predict the environmental distribution of species. However, the

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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

  20. To predict the niche, model colonization and extinction

    Science.gov (United States)

    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.

  1. To predict the niche, model colonization and extinction

    Science.gov (United States)

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

    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...

  2. Toward Improved Species Niche Modelling: Arnica montana in the Alps as a Case Study

    National Research Council Canada - National Science Library

    Gilberto Parolo; Graziano Rossi; Alessandro Ferrarini

    2008-01-01

    .... In this study, we used the recent Maxent algorithm for modelling the niche of Arnica montana within a Site of Community Importance in the Alps, with the ultimate aim of providing a rigorous evidence...

  3. 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

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Brice X Semmens

    Full Text Available 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.

  6. 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

  7. 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

  8. Adaptation, niche conservatism, and convergence: comparative studies of leaf evolution in the California chaparral.

    Science.gov (United States)

    Ackerly, David D

    2004-05-01

    Small leaves and low specific leaf area (SLA) have long been viewed as adaptations to Mediterranean-type climates in many species of evergreen woody plants. However, paleobotanical and floristic evidence suggests that in many cases these traits originated prior to the advent of the summer-drought climate regime. In this study, molecular phylogenies and ancestral state reconstructions were used to test the hypothesis of adaptive leaf evolution in 12 lineages of evergreen shrubs in the California chaparral. Across all lineages there was a small but significant shift toward lower SLA, but there were no trends in leaf size evolution. For individual lineages, adaptive changes were detected in only three cases for SLA and in one case for leaf size. Three of these cases of evolutionary change were observed in taxa derived from cool temperate ancestors (e.g., Heteromeles). In contrast, most lineages originating from subtropical ancestors exhibited relative stasis in leaf trait evolution (e.g., Ceanothus). The absence of change suggests that ancestors of chaparral taxa had already acquired appropriate traits that contributed to their success under Mediterranean-type climates. These results illustrate how biogeographic history may influence patterns of trait evolution and adaptation and highlight the contribution of ecological sorting processes to the assembly and functional ecology of regional biotas.

  9. Dissecting the stem cell niche with organoid models: an engineering-based approach.

    Science.gov (United States)

    Murrow, Lyndsay M; Weber, Robert J; Gartner, Zev J

    2017-03-15

    For many tissues, single resident stem cells grown in vitro under appropriate three-dimensional conditions can produce outgrowths known as organoids. These tissues recapitulate much of the cell composition and architecture of the in vivo organ from which they derive, including the formation of a stem cell niche. This has facilitated the systematic experimental manipulation and single-cell, high-throughput imaging of stem cells within their respective niches. Furthermore, emerging technologies now make it possible to engineer organoids from purified cellular and extracellular components to directly model and test stem cell-niche interactions. In this Review, we discuss how organoids have been used to identify and characterize stem cell-niche interactions and uncover new niche components, focusing on three adult-derived organoid systems. We also describe new approaches to reconstitute organoids from purified cellular components, and discuss how this technology can help to address fundamental questions about the adult stem cell niche. © 2017. Published by The Company of Biologists Ltd.

  10. Coastal California's Fog as a Unique Habitable Niche: Design for Autonomous Sampling and Preliminary Aerobiological Characterization

    Science.gov (United States)

    Gentry, Diana; Cynthia Ouandji; Arismendi, Dillon; Guarro, Marcello; Demachkie, Isabella; Crosbie, Ewan; Dadashazar, Hossein; MacDonald, Alex B.; Wang, Zhen; Sorooshian, Armin; hide

    2017-01-01

    Just as on the land or in the ocean, atmospheric regions may be more or less hospitable to life. The aerobiosphere, or collection of living things in Earth's atmosphere, is poorly understood due to the small number and ad hoc nature of samples studied. However, we know viable airborne microbes play important roles, such as providing cloud condensation nuclei. Knowing the distribution of such microorganisms and how their activity can alter water, carbon, and other geochemical cycles is key to developing criteria for planetary habitability, particularly for potential habitats with wet atmospheres but little stable surface water. Coastal California has regular, dense fog known to play a major transport role in the local ecosystem. In addition to the significant local (1 km) geographical variation in typical fog, previous studies have found that changes in height above surface of as little as a few meters can yield significant differences in typical concentrations, populations and residence times. No single current sampling platform (ground-based impactors, towers, balloons, aircraft) is capable of accessing all of these regions of interest.A novel passive fog and cloud water sampler, consisting of a lightweight passive impactor suspended from autonomous aerial vehicles (UAVs), is being developed to allow 4D point sampling within a single fog bank, allowing closer study of small-scale (100 m) system dynamics. Fog and cloud droplet water samples from low-altitude aircraft flights in nearby coastal waters were collected and assayed to estimate the required sample volumes, flight times, and sensitivity thresholds of the system under design.125 cloud water samples were collected from 16 flights of the Center for Interdisciplinary Remotely Piloted Aircraft Studies (CIRPAS) instrumented Twin Otter, equipped with a sampling tube collector, occurring between 18 July and 12 August 2016 below 1 km altitude off the central coast. The collector was flushed first with 70 ethanol

  11. Interpretation of Models of Fundamental Ecological Niches and Species’ Distributional Areas

    Directory of Open Access Journals (Sweden)

    Jorge Soberon

    2005-01-01

    Full Text Available Ecological niche modeling—that is, estimation of the dimensions of fundamental ecological niches of species—to predict their geographic distributions is increasingly being employed in systematics, ecology, conservation, public health, etc. This technique is often (of necessity based on data comprising records of presences only. In recent years, many modeling approaches have been devised to estimate these interrelated expressions of a species’ ecology, distributional biology, and evolutionary history—nevertheless, in many cases, a formal basis in ecological and evolutionary theory has been lacking. In this paper, we outline such a formal basis for the suite of techniques that can be termed ‘ecological niche modeling,’ analyze example situations that can be modeled using these techniques, and clarify the interpretation of results.

  12. Uses and Requirements of Ecological Niche Models and Related Distributional Models

    Directory of Open Access Journals (Sweden)

    A. Townsend Peterson

    2006-01-01

    Full Text Available Abstract.—Modeling approaches that relate known occurrences of species to landscape features to discover ecological properties and predict geographic occurrences have seen extensive recent application in ecology, systematics, and conservation. A key component in this process is estimation or characterization of species’ distributions in ecological space, which can then be useful in understanding their potential distributions in geographic space. Hence, this process is often termed ecological niche modeling or (less boldly species distribution modeling. Applications of this approach vary widely in their aims, products, and requirements; this variety is reviewed herein, examples are provided, and differences in data needs and possible interpretations are discussed.

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

    NARCIS (Netherlands)

    Cobben, M.M.P.; van Treuren, R.; Castañeda-Álvarez, N.P.; Khoury, C.K.; Kik, C.; van Hintum, 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

  14. Intestinal Stem Cell Niche Insights Gathered from Both In Vivo and Novel In Vitro Models

    Directory of Open Access Journals (Sweden)

    Nikolce Gjorevski

    2017-01-01

    Full Text Available Intestinal stem cells are located at the base of the crypts and are surrounded by a complex structure called niche. This environment is composed mainly of epithelial cells and stroma which provides signals that govern cell maintenance, proliferation, and differentiation. Understanding how the niche regulates stem cell fate by controlling developmental signaling pathways will help us to define how stem cells choose between self-renewal and differentiation and how they maintain their undifferentiated state. Tractable in vitro assay systems, which reflect the complexity of the in vivo situation but provide higher level of control, would likely be crucial in identifying new players and mechanisms controlling stem cell function. Knowledge of the intestinal stem cell niche gathered from both in vivo and novel in vitro models may help us improve therapies for tumorigenesis and intestinal damage and make autologous intestinal transplants a feasible clinical practice.

  15. A framework for using niche models to estimate impacts of climate change on species distributions.

    Science.gov (United States)

    Anderson, Robert P

    2013-09-01

    Predicting species geographic distributions in the future is an important yet exceptionally challenging endeavor. Overall, it requires a two-step process: (1) a niche model characterizing suitability, applied to projections of future conditions and linked to (2) a dispersal/demographic simulation estimating the species' future occupied distribution. Despite limitations, for the vast majority of species, correlative approaches are the most feasible avenue for building niche models. In addition to myriad technical issues regarding model building, researchers should follow critical principles for selecting predictor variables and occurrence data, demonstrating effective performance in prediction across space, and extrapolating into nonanalog conditions. Many of these principles relate directly to the niche space, dispersal/demographic noise, biotic noise, and human noise assumptions defined here. Issues requiring progress include modeling interactions between abiotic variables, integrating biotic variables, considering genetic heterogeneity, and quantifying uncertainty. Once built, the niche model identifying currently suitable conditions must be processed to approximate the areas that the species occupies. That estimate serves as a seed for the simulation of persistence, dispersal, and establishment in future suitable areas. The dispersal/demographic simulation also requires data regarding the species' dispersal ability and demography, scenarios for future land use, and the capability of considering multiple interacting species simultaneously. © 2013 New York Academy of Sciences.

  16. 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...

  17. Ecological niche modeling of rabies in the changing Arctic of Alaska.

    Science.gov (United States)

    Huettmann, Falk; Magnuson, Emily Elizabeth; Hueffer, Karsten

    2017-03-20

    Rabies is a disease of global significance including in the circumpolar Arctic. In Alaska enzootic rabies persist in northern and western coastal areas. Only sporadic cases have occurred in areas outside of the regions considered enzootic for the virus, such as the interior of the state and urbanized regions. Here we examine the distribution of diagnosed rabies cases in Alaska, explicit in space and time. We use a geographic information system (GIS), 20 environmental data layers and provide a quantitative non-parsimonious estimate of the predicted ecological niche, based on data mining, machine learning and open access data. We identify ecological correlates and possible drivers that determine the ecological niche of rabies virus in Alaska. More specifically, our models show that rabies cases are closely associated with human infrastructure, and reveal an ecological niche in remote northern wilderness areas. Furthermore a model utilizing climate modeling suggests a reduction of the current ecological niche for detection of rabies virus in Alaska, a state that is disproportionately affected by a changing climate. Our results may help to better inform public health decisions in the future and guide further studies on individual drivers of rabies distribution in the Arctic.

  18. Consequences of spatial autocorrelation for niche-based models

    DEFF Research Database (Denmark)

    Segurado, P.; Araújo, Miguel B.; Kunin, W. E.

    2006-01-01

    of the original variables. Univariate models of species' distributions using generalized linear models (GLM), generalized additive models (GAM) and classification tree analysis (CTA) were fitted for each variable permutation. Variation of accuracy measures with spatial autocorrelation of the original predictor......1.  Spatial autocorrelation is an important source of bias in most spatial analyses. We explored the bias introduced by spatial autocorrelation on the explanatory and predictive power of species' distribution models, and make recommendations for dealing with the problem. 2.  Analyses were based...... on the distribution of two species of freshwater turtle and two virtual species with simulated spatial structures within two equally sized areas located on the Iberian Peninsula. Sequential permutations of environmental variables were used to generate predictor variables that retained the spatial structure...

  19. Predicting Future Seed Sourcing of Platycladus orientalis (L. for Future Climates Using Climate Niche Models

    Directory of Open Access Journals (Sweden)

    Xian-Ge Hu

    2017-12-01

    Full Text Available Climate niche modeling has been widely used to assess the impact of climate change on forest trees at the species level. However, geographically divergent tree populations are expected to respond differently to climate change. Considering intraspecific local adaptation in modeling species responses to climate change will thus improve the credibility and usefulness of climate niche models, particularly for genetic resources management. In this study, we used five Platycladus orientalis (L. seed zones (Northwestern; Northern; Central; Southern; and Subtropical covering the entire species range in China. A climate niche model was developed and used to project the suitable climatic conditions for each of the five seed zones for current and various future climate scenarios (Representative Concentration Pathways: RCP2.6, RCP4.5, RCP6.0, and RCP8.5. Our results indicated that the Subtropical seed zone would show consistent reduction for all climate change scenarios. The remaining seed zones, however, would experience various degrees of expansion in suitable habitat relative to their current geographic distributions. Most of the seed zones would gain suitable habitats at their northern distribution margins and higher latitudes. Thus, we recommend adjusting the current forest management strategies to mitigate the negative impacts of climate change.

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

    Science.gov (United States)

    2007-07-01

    past landscapes and environments may lead to erroneous conclusions. For example, the Lepus arcticus ( Arctic Hare) phylogeographic prediction [52] is...Molecular Ecology 13: 3501–3514. 10. Fedorov V, Stenseth NC (2002) Multiple glacial refugia in the North American Arctic : inference from phylogeography...Meyer E, Soberón J, Sánchez-Cordero V, et al. (2005) Modeling distributional shifts of individual species and biomes . In: Lovejoy TE, Hannah L, eds

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

    Directory of Open Access Journals (Sweden)

    Gabriel Parra-Henao

    2016-01-01

    Full Text Available 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.

  2. 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.

  3. Temporal Definition of Haematopoietic Stem Cell Niches in a Large Animal Model of In Utero Stem Cell Transplantation

    Science.gov (United States)

    Jeanblanc, Christine; Goodrich, A. Daisy; Colletti, Evan; Mokhtari, Saloomeh; Porada, Christopher D.; Zanjani, Esmail D.; Almeida-Porada, Graça

    2014-01-01

    The fetal sheep model has served as a biologically relevant and translational model to study in utero haematopoietic stem cell transplantation (IUHSCT), yet little is known about the ontogeny of the bone marrow (BM) niches in this model. Because the BMmicroenvironment plays a critical role in the outcome of haematopoietic engraftment, we have established the correlation between the fetal-sheep and fetal-human BM niche ontogeny, so that studies addressing the role of niche development at the time of IUHSCT could be accurately performed. Immunofluorescence confocal microscopic analysis of sheep fetal bone from gestational days (gd) 25-68 showed that the BM microenvironment commences development with formation of the vascular niche between 25-36 gd in sheep; correlating with the events at 10-11 gestational weeks (gw) in humans. Subsequently, between 45-51 gd in sheep (~14 gw in humans), the osteoblastic/endosteal niche started developing, the presence of CD34+CD45+ cells were promptly detected, and their number increased with gestational age. IUHSCT, performed in sheep at 45 and 65 gd, showed significant haematopoietic engraftment only at the later time point, indicating that a fully functional BM microenvironment improved engraftment. These studies show that sheep niche ontogeny closely parallels human, validating this model for investigating niche influence/manipulation in IUHSCT engraftment. PMID:24673111

  4. Modeling the Ecological Niche of Bacillus anthracis to Map Anthrax Risk in Kyrgyzstan.

    Science.gov (United States)

    Blackburn, Jason K; Matakarimov, Saitbek; Kozhokeeva, Sabira; Tagaeva, Zhyldyz; Bell, Lindsay K; Kracalik, Ian T; Zhunushov, Asankadyr

    2017-03-01

    AbstractAnthrax, caused by the environmental bacterium Bacillus anthracis, is an important zoonosis nearly worldwide. In Central Asia, anthrax represents a major veterinary and public health concern. In the Republic of Kyrgyzstan, ongoing anthrax outbreaks have been reported in humans associated with handling infected livestock and contaminated animal by-products such as meat or hides. The current anthrax situation has prompted calls for improved insights into the epidemiology, ecology, and spatial distribution of the disease in Kyrgyzstan to better inform control and surveillance. Disease control for both humans and livestock relies on annual livestock vaccination ahead of outbreaks. Toward this, we used a historic database of livestock anthrax reported from 1932 to 2006 mapped at high resolution to develop an ecological niche model-based prediction of B. anthracis across Kyrgyzstan and identified spatial clusters of livestock anthrax using a cluster morphology statistic. We also defined the seasonality of outbreaks in livestock. Cattle were the most frequently reported across the time period, with the greatest number of cases in late summer months. Our niche models defined four areas as suitable to support pathogen persistence, the plateaus near Talas and Bishkek, the valleys of western Kyrgyzstan along the Fergana Valley, and the low-lying areas along the shore of Lake Isyk-Kul. These areas should be considered "at risk" for livestock anthrax and subsequent human cases. Areas defined by the niche models can be used to prioritize anthrax surveillance and inform efforts to target livestock vaccination campaigns.

  5. 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.

  6. Ecological Niche Modeling to Estimate the Distribution of Japanese Encephalitis Virus in Asia

    Science.gov (United States)

    Miller, Robin H.; Masuoka, Penny; Klein, Terry A.; Kim, Heung-Chul; Somer, Todd; Grieco, John

    2012-01-01

    Background Culex tritaeniorhynchus is the primary vector of Japanese encephalitis virus (JEV), a leading cause of encephalitis in Asia. JEV is transmitted in an enzootic cycle involving large wading birds as the reservoirs and swine as amplifying hosts. The development of a JEV vaccine reduced the number of JE cases in regions with comprehensive childhood vaccination programs, such as in Japan and the Republic of Korea. However, the lack of vaccine programs or insufficient coverage of populations in other endemic countries leaves many people susceptible to JEV. The aim of this study was to predict the distribution of Culex tritaeniorhynchus using ecological niche modeling. Methods/Principal Findings An ecological niche model was constructed using the Maxent program to map the areas with suitable environmental conditions for the Cx. tritaeniorhynchus vector. Program input consisted of environmental data (temperature, elevation, rainfall) and known locations of vector presence resulting from an extensive literature search and records from MosquitoMap. The statistically significant Maxent model of the estimated probability of Cx. tritaeniorhynchus presence showed that the mean temperatures of the wettest quarter had the greatest impact on the model. Further, the majority of human Japanese encephalitis (JE) cases were located in regions with higher estimated probability of Cx. tritaeniorhynchus presence. Conclusions/Significance Our ecological niche model of the estimated probability of Cx. tritaeniorhynchus presence provides a framework for better allocation of vector control resources, particularly in locations where JEV vaccinations are unavailable. Furthermore, this model provides estimates of vector probability that could improve vector surveillance programs and JE control efforts. PMID:22724030

  7. Modelling the multidimensional niche by linking functional traits to competitive performance.

    Science.gov (United States)

    Maynard, Daniel S; Leonard, Kenneth E; Drake, John M; Hall, David W; Crowther, Thomas W; Bradford, Mark A

    2015-07-22

    Linking competitive outcomes to environmental conditions is necessary for understanding species' distributions and responses to environmental change. Despite this importance, generalizable approaches for predicting competitive outcomes across abiotic gradients are lacking, driven largely by the highly complex and context-dependent nature of biotic interactions. Here, we present and empirically test a novel niche model that uses functional traits to model the niche space of organisms and predict competitive outcomes of co-occurring populations across multiple resource gradients. The model makes no assumptions about the underlying mode of competition and instead applies to those settings where relative competitive ability across environments correlates with a quantifiable performance metric. To test the model, a series of controlled microcosm experiments were conducted using genetically related strains of a widespread microbe. The model identified trait microevolution and performance differences among strains, with the predicted competitive ability of each organism mapped across a two-dimensional carbon and nitrogen resource space. Areas of coexistence and competitive dominance between strains were identified,and the predicted competitive outcomes were validated in approximately 95% of the pairings. By linking trait variation to competitive ability, our work demonstrates a generalizable approach for predicting and modelling competitive outcomes across changing environmental contexts.

  8. Microencapsulation of Neuroblastoma Cells and Mesenchymal Stromal Cells in Collagen Microspheres: A 3D Model for Cancer Cell Niche Study

    OpenAIRE

    Pan Yeung; Hoi Shun Sin; Shing Chan; Godfrey Chi Fung Chan; Barbara Pui Chan

    2015-01-01

    There is a growing trend for researchers to use in vitro 3D models in cancer studies, as they can better recapitulate the complex in vivo situation. And the fact that the progression and development of tumor are closely associated to its stromal microenvironment has been increasingly recognized. The establishment of such tumor supportive niche is vital in understanding tumor progress and metastasis. The mesenchymal origin of many cells residing in the cancer niche provides the rationale to in...

  9. 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

    2017-07-01

    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. © 2017 John Wiley & Sons Ltd.

  10. Conservatism of Ecological Niches in Evolutionary Time

    National Research Council Canada - National Science Library

    A. T. Peterson; J. Soberón; V. Sánchez-Cordero

    1999-01-01

    .... Reciprocal geographic predictions based on ecological niche models of sister taxon pairs of birds, mammals, and butterflies in southern Mexico indicate niche conservatism over several million years...

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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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.

  13. Modeling Gas Dynamics in California Sea Lions

    Science.gov (United States)

    2015-09-30

    observed blood PO2 levels during diving. A sensitivity analysis will be performed to assess the new and current parameter estimates and error of the model...1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Modeling Gas Dynamics in California Sea Lions Andreas...to update a current gas dynamics model with recently acquired data for respiratory compliance (P-V), and body compartment size estimates in

  14. 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 .

  15. 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.

  16. Modeling the ecologic niche of plague in sylvan and domestic animal hosts to delineate sources of human exposure in the western United States

    Directory of Open Access Journals (Sweden)

    Michael Walsh

    2015-12-01

    Full Text Available Plague has been established in the western United States (US since 1900 following the West Coast introduction of commensal rodents infected with Yersinia pestis via early industrial shipping. Over the last century, plague ecology has transitioned through cycles of widespread human transmission, urban domestic transmission among commensal rodents, and ultimately settled into the predominantly sylvan foci that remain today where it is maintained alternatively by enzootic and epizootic transmission. While zoonotic transmission to humans is much less common in modern times, significant plague risk remains in parts of the western US. Moreover, risk to some threatened species that are part of the epizootic cycle can be quite substantive. This investigation attempted to predict the risk of plague across the western US by modeling the ecologic niche of plague in sylvan and domestic animals identified between 2000 and 2015. A Maxent machine learning algorithm was used to predict this niche based on climate, altitude, land cover, and the presence of an important enzootic species, Peromyscus maniculatus. This model demonstrated good predictive ability (AUC = 86% and identified areas of high risk in central Colorado, north-central New Mexico, and southwestern and northeastern California. The presence of P. maniculatus, altitude, precipitation during the driest and wettest quarters, and distance to artificial surfaces, all contributed substantively to maximizing the gain function. These findings add to the known landscape epidemiology and infection ecology of plague in the western US and may suggest locations of particular risk to be targeted for wild and domestic animal intervention.

  17. Assessing environmental factors to the replacement of Neanderthals by modern humans in terms of eco-cultural niche modelling

    Science.gov (United States)

    Kondo, Yasuhisa; Sano, Katsuhiro; Kadowaki, Seiji; Naganuma, Masaki; Omori, Takayuki; Yoneda, Minoru; Nishiaki, Yoshihiro

    2014-05-01

    Eco-cultural niche modelling (ECNM) is an application of ecological niche modelling (ENM) to estimate the human niche in response to environmental settings. The niche probability is calculated for each spatial pixel, based on (1) the location of known archaeological sites as occurrence data and (2) environmental factors such palaeoclimate (temperature and precipitation), palaeovegetation (biome) and palaeotopography (elevation, slope and aspect). Some ENM software packages, including MaxEnt (maximum entropy model), output the percentage of contribution for each environmental factor, and therefore it is possible to identify and evaluate environmental constraints to the geographic expansion of human populations. Based on this thought, the authors applied ECNM to Palaeolithic stone tool industries in Europe and Siberia at 50-46 kya, the time period during which the first anatomically modern humans (AMHs) are presumed to have appeared in those regions, under the assumption that stone tool groups may reflect different human groups in terms of subsistence strategy. The preliminary results suggested that the population using Emiran and related industries (Bohunician and Bachokirian) were likely to construct their niches in the geographic zones where the long-term variability of the coldest month temperature was larger than in those occupied by the populations using the Late Mousterian, Szeletian and Châtelperronean stone tool industries.

  18. A Quiescent, Regeneration-Responsive Tissue Engineered Mesenchymal Stem Cell Bone Marrow Niche Model via Magnetic Levitation.

    Science.gov (United States)

    Lewis, Emily Elizabeth Louise; Wheadon, Helen; Lewis, Natasha; Yang, Jingli; Mullin, Margaret; Hursthouse, Andrew; Stirling, David; Dalby, Matthew John; Berry, Catherine Cecilia

    2016-09-27

    The bone marrow niche represents a specialized environment that regulates mesenchymal stem cell quiescence and self-renewal, yet fosters stem cell migration and differentiation upon demand. An in vitro model that embodies these features would open up the ability to perform detailed study of stem cell behavior. In this paper we present a simple bone marrow-like niche model, which comprises of nanomagnetically levitated stem cells cultured as multicellular spheroids within a type I collagen gel. The stem cells maintained are nestin positive and remain quiescent until regenerative demand is placed upon them. In response to coculture wounding, they migrate and appropriately differentiate upon engraftment. This tissue engineered regeneration-responsive bone marrow-like niche model will allow for greater understanding of stem cell response to injury and also facilitate as a testing platform for drug candidates in a multiwell plate format.

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

    Science.gov (United States)

    Xu, Min; Cao, Chunxiang; Li, Qun; Jia, Peng; Zhao, Jian

    2016-01-01

    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. PMID:27322296

  20. Hydrological-niche models predict water plant functional group distributions in diverse wetland types.

    Science.gov (United States)

    Deane, David C; Nicol, Jason M; Gehrig, Susan L; Harding, Claire; Aldridge, Kane T; Goodman, Abigail M; Brookes, Justin D

    2017-06-01

    Human use of water resources threatens environmental water supplies. If resource managers are to develop policies that avoid unacceptable ecological impacts, some means to predict ecosystem response to changes in water availability is necessary. This is difficult to achieve at spatial scales relevant for water resource management because of the high natural variability in ecosystem hydrology and ecology. Water plant functional groups classify species with similar hydrological niche preferences together, allowing a qualitative means to generalize community responses to changes in hydrology. We tested the potential for functional groups in making quantitative prediction of water plant functional group distributions across diverse wetland types over a large geographical extent. We sampled wetlands covering a broad range of hydrogeomorphic and salinity conditions in South Australia, collecting both hydrological and floristic data from 687 quadrats across 28 wetland hydrological gradients. We built hydrological-niche models for eight water plant functional groups using a range of candidate models combining different surface inundation metrics. We then tested the predictive performance of top-ranked individual and averaged models for each functional group. Cross validation showed that models achieved acceptable predictive performance, with correct classification rates in the range 0.68-0.95. Model predictions can be made at any spatial scale that hydrological data are available and could be implemented in a geographical information system. We show the response of water plant functional groups to inundation is consistent enough across diverse wetland types to quantify the probability of hydrological impacts over regional spatial scales. © 2017 by the Ecological Society of America.

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    U. L. Vaz

    Full Text Available Abstract 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, P<0.001, with a sharp increase in recent years, highlighting the widespread use of the ENMs. There was an increase in the diversity of journals that published papers about ENMs (r=0.97, P<0.001. The research was conducted in different countries, predominantly the United States of America (550 papers, and the most commonly used method was the Maximum Entropy method (312 papers. Regarding the taxonomic group, most research has been conducted on plants (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.

  3. Using worldwide edaphic data to model plant species niches: An assessment at a continental extent

    Science.gov (United States)

    Galvão, Franklin; Villalobos, Fabricio; De Marco Júnior, Paulo

    2017-01-01

    Ecological niche modeling (ENM) is a broadly used tool in different fields of plant ecology. Despite the importance of edaphic conditions in determining the niche of terrestrial plant species, edaphic data have rarely been included in ENMs of plant species perhaps because such data are not available for many regions. Recently, edaphic data has been made available at a global scale allowing its potential inclusion and evaluation on ENM performance for plant species. Here, we take advantage of such data and address the following main questions: What is the influence of distinct predictor variables (e.g. climatic vs edaphic) on different ENM algorithms? and what is the relationship between the performance of different predictors and geographic characteristics of species? We used 125 plant species distributed over the Neotropical region to explore the effect on ENMs of using edaphic data available from the SoilGrids database and its combination with climatic data from the CHELSA database. In addition, we related these different predictor variables to geographic characteristics of the target species and different ENM algorithms. The use of different predictors (climatic, edaphic, and both) significantly affected model performance and spatial complexity of the predictions. We showed that the use of global edaphic plus climatic variables generates ENMs with similar or better accuracy compared to those constructed only with climate variables. Moreover, the performance of models considering these different predictors, separately or jointly, was related to geographic properties of species records, such as number and distribution range. The large geographic extent, the variability of environments and the different species’ geographical characteristics considered here allowed us to demonstrate that global edaphic data adds useful information for plant ENMs. This is particularly valuable for studies of species that are distributed in regions where more detailed information on

  4. 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

    stochastic search variable selection incorporated in BEAST to identify historical dispersal patterns via ancestral state reconstruction. Ecological niche models (ENMs) were incorporated to reconstruct the potential geographic distribution of each species during the Last Glacial Maximum (LGM). Coalescent...... analyses suggest a North Island origin for E. lawsoni, with gene flow predominately north–south between adjacent regions. ENMs for E. lawsoni indicated glacial refugia in coastal regions of both main islands, consistent with phylogenetic patterns but at odds with the coalescent dates, which implicate much...... older topographic events. Dispersal matrices revealed patterns of gene flow consistent with projected refugia, suggesting long-term South Island survival with population vicariance around the Southern Alps. Phylogeographic relationships are more ambiguous for P. bakewelli, although long-term survival...

  5. 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.

  6. 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.

  7. 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.

  8. Pitch the niche - taking responsibility for the concepts we use in ecology and species distribution modelling

    NARCIS (Netherlands)

    McInerny, Greg J.; Etienne, Rampal S.

    2012-01-01

    In a discussion it is often easier to staunchly reject or offer resolute support for an idea. This third paper on the niche concept aims to develop a balanced argument by exploring general principles for determining an appropriate level for pitching the niche concept that will guide better use and

  9. Biologically informed ecological niche models for an example pelagic, highly mobile species

    Directory of Open Access Journals (Sweden)

    Ingenloff Kate

    2017-03-01

    Full Text Available Background: Although pelagic seabirds are broadly recognised as indicators of the health of marine systems, numerous gaps exist in knowledge of their at-sea distributions at the species level. These gaps have profound negative impacts on the robustness of marine conservation policies. Correlative modelling techniques have provided some information, but few studies have explored model development for non-breeding pelagic seabirds. Here, I present a first phase in developing robust niche models for highly mobile species as a baseline for further development. Methodology: Using observational data from a 12-year time period, 217 unique model parameterisations across three correlative modelling algorithms (boosted regression trees, Maxent and minimum volume ellipsoids were tested in a time-averaged approach for their ability to recreate the at-sea distribution of non-breeding Wandering Albatrosses (Diomedea exulans to provide a baseline for further development. Principle Findings/Results: Overall, minimum volume ellipsoids outperformed both boosted regression trees and Maxent. However, whilst the latter two algorithms generally overfit the data, minimum volume ellipsoids tended to underfit the data. Conclusions: The results of this exercise suggest a necessary evolution in how correlative modelling for highly mobile species such as pelagic seabirds should be approached. These insights are crucial for understanding seabird-environment interactions at macroscales, which can facilitate the ability to address population declines and inform effective marine conservation policy in the wake of rapid global change.

  10. 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.

  11. 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.

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

    Science.gov (United States)

    Yañez-Arenas, Carlos; Peterson, A Townsend; Mokondoko, Pierre; Rojas-Soto, Octavio; Martínez-Meyer, Enrique

    2014-01-01

    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).

  13. Evaluation of the impacts of climate change on disease vectors through ecological niche modelling.

    Science.gov (United States)

    Carvalho, B M; Rangel, E F; Vale, M M

    2017-08-01

    Vector-borne diseases are exceptionally sensitive to climate change. Predicting vector occurrence in specific regions is a challenge that disease control programs must meet in order to plan and execute control interventions and climate change adaptation measures. Recently, an increasing number of scientific articles have applied ecological niche modelling (ENM) to study medically important insects and ticks. With a myriad of available methods, it is challenging to interpret their results. Here we review the future projections of disease vectors produced by ENM, and assess their trends and limitations. Tropical regions are currently occupied by many vector species; but future projections indicate poleward expansions of suitable climates for their occurrence and, therefore, entomological surveillance must be continuously done in areas projected to become suitable. The most commonly applied methods were the maximum entropy algorithm, generalized linear models, the genetic algorithm for rule set prediction, and discriminant analysis. Lack of consideration of the full-known current distribution of the target species on models with future projections has led to questionable predictions. We conclude that there is no ideal 'gold standard' method to model vector distributions; researchers are encouraged to test different methods for the same data. Such practice is becoming common in the field of ENM, but still lags behind in studies of disease vectors.

  14. The significance of using satellite imagery data only in Ecological Niche Modelling of Iberian herps

    Directory of Open Access Journals (Sweden)

    Neftalí Sillero

    2012-12-01

    Full Text Available The environmental data used to calculate ecological niche models (ENM are obtained mainly from ground-based maps (e.g., climatic interpolated surfaces. These data are often not available for less developed areas, or may be at an inappropriate scale, and thus to obtain this information requires fieldwork. An alternative source of eco-geographical data comes from satellite imagery. Three sets of ENM were calculated exclusively with variables obtained (1 from optical and radar images only and (2 from climatic and altitude maps obtained by ground-based methods. These models were compared to evaluate whether satellite imagery can accurately generate ENM. These comparisons must be made in areas with well-known species distribution and with available satellite imagery and ground-based data. Thus, the study area was the south-western part of Salamanca (Spain, using amphibian and reptiles as species models. Models’ discrimination capacity was measured with ROC plots. Models’ covariation was measured with a Spatial Spearman correlation. Four modelling techniques were used (Bioclim, Mahalanobis distance, GARP and Maxent. The results of this comparison showed that there were no significant differences between models generated using remotely sensed imagery or ground-based data. However, the models built with satellite imagery data exhibited a larger diversity of values, probably related to the higher spatial resolution of the satellite imagery. Satellite imagery can produce accurate ENM, independently of the modelling technique or the dataset used. Therefore, biogeographical analysis of species distribution in remote areas can be accurately developed only with variables from satellite imagery.

  15. The Use of Ecological Niche Modeling to Infer Potential Risk Areas of Snakebite in the Mexican State of Veracruz

    OpenAIRE

    Carlos Yañez-Arenas; A. Townsend Peterson; Pierre Mokondoko; Octavio Rojas-Soto; Enrique Martínez-Meyer

    2014-01-01

    Background 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. Methodology/Principal Findings Ecological niche modeling (E...

  16. Tracking a Medically Important Spider: Climate Change, Ecological Niche Modeling, and the Brown Recluse (Loxosceles reclusa)

    Science.gov (United States)

    Saupe, Erin E.; Papes, Monica; Selden, Paul A.; Vetter, Richard S.

    2011-01-01

    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. PMID:21464985

  17. Geographic Distribution of Chagas Disease Vectors in Brazil Based on Ecological Niche Modeling

    Directory of Open Access Journals (Sweden)

    Rodrigo Gurgel-Gonçalves

    2012-01-01

    Full Text Available Although Brazil was declared free from Chagas disease transmission by the domestic vector Triatoma infestans, human acute cases are still being registered based on transmission by native triatomine species. For a better understanding of transmission risk, the geographic distribution of Brazilian triatomines was analyzed. Sixteen out of 62 Brazilian species that both occur in >20 municipalities and present synanthropic tendencies were modeled based on their ecological niches. Panstrongylus geniculatus and P. megistus showed broad ecological ranges, but most of the species sort out by the biome in which they are distributed: Rhodnius pictipes and R. robustus in the Amazon; R. neglectus, Triatoma sordida, and T. costalimai in the Cerrado; R. nasutus, P. lutzi, T. brasiliensis, T. pseudomaculata, T. melanocephala, and T. petrocchiae in the Caatinga; T. rubrovaria in the southern pampas; T. tibiamaculata and T. vitticeps in the Atlantic Forest. Although most occurrences were recorded in open areas (Cerrado and Caatinga, our results show that all environmental conditions in the country are favorable to one or more of the species analyzed, such that almost nowhere is Chagas transmission risk negligible.

  18. 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.

  19. 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.

  20. 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.

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

    Science.gov (United States)

    Saupe, Erin E; Papes, Monica; Selden, Paul A; Vetter, Richard S

    2011-03-25

    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.

  2. 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

  3. 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 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.

  4. 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

    2015-01-01

    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. PMID:25494960

  5. Ecological-niche modeling and prioritization of conservation-area networks for Mexican herpetofauna.

    Science.gov (United States)

    Urbina-Cardona, J Nicolás; Flores-Villela, Oscar

    2010-08-01

    One of the most important tools in conservation biology is information on the geographic distribution of species and the variables determining those patterns. We used maximum-entropy niche modeling to run distribution models for 222 amphibian and 371 reptile species (49% endemics and 27% threatened) for which we had 34,619 single geographic records. The planning region is in southeastern Mexico, is 20% of the country's area, includes 80% of the country's herpetofauna, and lacks an adequate protected-area system. We used probabilistic data to build distribution models of herpetofauna for use in prioritizing conservation areas for three target groups (all species and threatened and endemic species). The accuracy of species-distribution models was better for endemic and threatened species than it was for all species. Forty-seven percent of the region has been deforested and additional conservation areas with 13.7% to 88.6% more native vegetation (76% to 96% of the areas are outside the current protected-area system) are needed. There was overlap in 26 of the main selected areas in the conservation-area network prioritized to preserve the target groups, and for all three target groups the proportion of vegetation types needed for their conservation was constant: 30% pine and oak forests, 22% tropical evergreen forest, 17% low deciduous forest, and 8% montane cloud forests. The fact that different groups of species require the same proportion of habitat types suggests that the pine and oak forests support the highest proportion of endemic and threatened species and should therefore be given priority over other types of vegetation for inclusion in the protected areas of southeastern Mexico.

  6. Characterization of lung stem cell niches in a mouse model of bleomycin-induced fibrosis

    Science.gov (United States)

    2012-01-01

    Introduction In lung fibrosis, alveolar epithelium degenerates progressively. The goal of regenerative medicine is to aid repair and regeneration of the lost tissues in parenchyma and airways for which mobilization of tissue-resident endogenous or bone marrow-derived exogenous stem cells niches is a critical step. We used a lung injury model in mice to identify and characterize functional lung stem cells to clarify how stem cell niches counteract this degenerative process. Methods Short term assay (STA) - Bleomycin-induced lung inflammation and fibrosis were assessed in a model of idiopathic pulmonary fibrosis in wild-type (WT), gp91phox-/- (NOX-/-), and gp91phoxMMP-12 double knockout (DKO) mice on C57Bl/6 background and Hoechst 33322 dye effluxing side population (SP) cells characterized. Long term assay (LTA) - In a bleomycin induced lung fibrosis model in C57Bl6 mice, the number of mature cells were quantified over 7, 14, and 21 days in bone marrow (BM), peripheral blood (PB), lung parenchyma (LP) and brochoalveolar lavage (BAL) fluid by FACS. BrdU pulse chase experiment (10 weeks) was used to identify label retaining cells (LRC). BrdU+ and BrdU- cells were characterized by hematopoietic (CD45+), pluripotency (TTF1+, Oct3/4+, SSEA-3+, SSEA-4+, Sca1+, Lin-, CD34+, CD31+), and lung lineage-specific (SPC+, AQP-5+, CC-10+) markers. Clonogenic potential of LRCs were measured by CFU-c assays. Results STA- In lung, cellularity increased by 5-fold in WT and 6-fold in NOX-/- by d7. Lung epithelial markers were very low in expression in all SP flow sorted from lung of all three genotypes cultured ex vivo. (p bleomycin, the SP in NOX-/- lung increased by 3.6-fold over WT where it increased by 20-fold over controls. Type I and II alveolar epithelial cells progressively diminished in all three genotypes by d21 post-bleomycin. D7 post-bleomycin, CD45+ cells in BALf in NOX-/- was 1.7-fold > WT, 57% of which were Mf that decreased by 67% in WT and 83% in NOX-/- by d21.LTA

  7. 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....

  8. 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.

  9. Microencapsulation of Neuroblastoma Cells and Mesenchymal Stromal Cells in Collagen Microspheres: A 3D Model for Cancer Cell Niche Study.

    Directory of Open Access Journals (Sweden)

    Pan Yeung

    Full Text Available There is a growing trend for researchers to use in vitro 3D models in cancer studies, as they can better recapitulate the complex in vivo situation. And the fact that the progression and development of tumor are closely associated to its stromal microenvironment has been increasingly recognized. The establishment of such tumor supportive niche is vital in understanding tumor progress and metastasis. The mesenchymal origin of many cells residing in the cancer niche provides the rationale to include MSCs in mimicking the niche in neuroblastoma. Here we co-encapsulate and co-culture NBCs and MSCs in a 3D in vitro model and investigate the morphology, growth kinetics and matrix remodeling in the reconstituted stromal environment. Results showed that the incorporation of MSCs in the model lead to accelerated growth of cancer cells as well as recapitulation of at least partially the tumor microenvironment in vivo. The current study therefore demonstrates the feasibility for the collagen microsphere to act as a 3D in vitro cancer model for various topics in cancer studies.

  10. Microencapsulation of Neuroblastoma Cells and Mesenchymal Stromal Cells in Collagen Microspheres: A 3D Model for Cancer Cell Niche Study.

    Science.gov (United States)

    Yeung, Pan; Sin, Hoi Shun; Chan, Shing; Chan, Godfrey Chi Fung; Chan, Barbara Pui

    2015-01-01

    There is a growing trend for researchers to use in vitro 3D models in cancer studies, as they can better recapitulate the complex in vivo situation. And the fact that the progression and development of tumor are closely associated to its stromal microenvironment has been increasingly recognized. The establishment of such tumor supportive niche is vital in understanding tumor progress and metastasis. The mesenchymal origin of many cells residing in the cancer niche provides the rationale to include MSCs in mimicking the niche in neuroblastoma. Here we co-encapsulate and co-culture NBCs and MSCs in a 3D in vitro model and investigate the morphology, growth kinetics and matrix remodeling in the reconstituted stromal environment. Results showed that the incorporation of MSCs in the model lead to accelerated growth of cancer cells as well as recapitulation of at least partially the tumor microenvironment in vivo. The current study therefore demonstrates the feasibility for the collagen microsphere to act as a 3D in vitro cancer model for various topics in cancer studies.

  11. Ecological niche modeling of the rare bee Promelitta alboclypeata reveals possible cryptic differentiation across northern Africa and Arabia (Hymenoptera: Melittidae)

    OpenAIRE

    Hinojosa-Díaz, Ismael A.; Abdulaziz S. Alqarni; Lira-Noriega, Andrés; Engel, Michael S.

    2016-01-01

    International audience; AbstractThe scarcely collected bee Promelitta alboclypeata with known occurrence across northern Africa and the Arabian Peninsula is a typical example of the bee family Melittidae which encompasses a good number of species with sparse or disjunct distributions and particular flower preferences. Using records for 16 localities, we estimated ecological niche models for P. alboclypeata in Maxent on four sets of occurrences, to represent the disparity of the known records,...

  12. 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

    2011-02-01

    Full Text Available 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.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.In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species.

  13. 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.

  14. 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. © 2013 John Wiley & Sons Ltd.

  15. 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)...

  16. 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)...

  17. Port San Luis, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

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

  18. 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)...

  19. Eureka, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

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

  20. Arena Cove, California Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

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

  1. 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)...

  2. 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)...

  3. Targeting the Biophysical Properties of the Myeloma Initiating Cell Niches: A Pharmaceutical Synergism Analysis Using Multi-Scale Agent-Based Modeling: e85059

    National Research Council Canada - National Science Library

    Jing Su; Le Zhang; Wen Zhang; Dong Song Choi; Jianguo Wen; Beini Jiang; Chung-Che Chang; Xiaobo Zhou

    2014-01-01

    .... We first established a multi-scale agent-based model using the Markov Chain Monte Carlo approach to recapitulate the niche stiffness centric, pro-oncogenetic positive feedback loop between MICs...

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

    Science.gov (United States)

    Santos, Xavier; Felicísimo, Ángel M.

    2016-01-01

    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 parks. PMID

  5. Ecological niche modelling and differentiation between Rhodnius neglectus Lent, 1954 and Rhodnius nasutus Stål, 1859 (Hemiptera: Reduviidae: Triatominae) in Brazil

    OpenAIRE

    Batista,Taíza Almeida; Gurgel-Gonçalves,Rodrigo

    2009-01-01

    Ecological niche modelling was used to predict the potential geographical distribution of Rhodnius nasutus Stål and Rhodnius neglectus Lent, in Brazil and to investigate the niche divergence between these morphologically similar triatomine species. The distribution of R. neglectus covered mainly the cerrado of Central Brazil, but the prediction maps also revealed its occurrence in transitional areas within the caatinga, Pantanal and Amazon biomes. The potential distribution of R. nasutus cove...

  6. 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. © 2014 John Wiley & Sons Ltd.

  7. 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...

  8. Environmental (in)dependence of a hybrid zone: Insights from molecular markers and ecological niche modeling in a hybrid zone of Origanum (Lamiaceae) on the island of Crete.

    Science.gov (United States)

    Bariotakis, Michael; Koutroumpa, Konstantina; Karousou, Regina; Pirintsos, Stergios A

    2016-12-01

    The role of environment and the relative significance of endogenous versus exogenous selection in shaping hybrid zones have been crucial issues in the studies of hybridization. Recent advances in ecological niche modeling (ENM) offer new methodological tools, especially in combination with the genotyping of individuals in the hybrid zone. Here, we study the hybrid zone between the widely known spices Origanum onites and Origanum vulgare ssp. hirtum in Crete. We analyze the genetic structure of both parental taxa and their hybrid Origanum × intercendens using AFLP markers on 15 sympatric and 12 allopatric populations and employ ecological niche modeling and niche similarity tests to study their niche patterns. We complement these analyses with seed viability measurements. Our study revealed that the hybridizing taxa O. onites and O. vulgare ssp. hirtum and the resulting genotypic classes showed geographical and environmental niche similarities based on the predictions of ENMs and the subsequent similarity tests. The occurrence of the hybrid zone is not directly dependent on environmental factors which favor the fitness of the hybrid compared to the parental taxa, but rather on aspects such as historical factors and management practices, which may contribute to the localization and maintenance of the contact zone between parental species. Our results suggest that if a minimum required niche differentiation between genotypic classes is not achieved, environmental dependence might not have a prominent role on the outcome of the hybridization.

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

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    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.

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

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

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    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. © International & American Associations for Dental Research.

  12. Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of 'rear edge' populations.

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    Gugger, Paul F; González-Rodríguez, Antonio; Rodríguez-Correa, Hernando; Sugita, Shinya; Cavender-Bares, Jeannine

    2011-03-01

    • Poleward Pleistocene plant migration has been an important process structuring modern temperate and boreal plant communities, but the contribution of equatorward migration remains poorly understood. Paleobotanical evidence suggests Miocene or Pleistocene origin for temperate 'sky island' plant taxa in Mexico. These 'rear edge' populations situated in a biodiversity hotspot may be an important reserve of genetic diversity in changing climates. • We used mtDNA sequences, cpDNA sequences and chloroplast microsatellites to test hypotheses of Miocene vs Pleistocene colonization of temperate Douglas-fir in Mexico, explore geographic patterns of molecular variation in relation to Pleistocene climate history using ecological niche models, and assess the taxonomic and conservation implications. • We found strong evidence for Pleistocene divergence of Douglas-fir in Mexico (958 thousand yr before present (ka) with the 90% highest posterior density interval ranging from 1.6 million yr before present (Ma) to 491 ka), consistent with the southward Pleistocene migration hypothesis. Genetic diversity was high and strongly partitioned among populations. Spatial patterns of molecular variation and ecological niche models suggest a complex late Pleistocene history involving periods of isolation and expansion along mountain corridors. • These results highlight the importance of southward Pleistocene migration in establishing modern high-diversity plant communities and provide critical insights into proposals to conserve the unique biodiversity of Mexican Douglas-fir and associated taxa. © 2010 The Authors. New Phytologist © 2010 New Phytologist Trust.

  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

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    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.

  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.

    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.

  15. Effects of global changes on the climatic niche of the tick Ixodes ricinus inferred by species distribution modelling

    Science.gov (United States)

    2013-01-01

    Background Global climate change can seriously impact on the epidemiological dynamics of vector-borne diseases. In this study we investigated how future climatic changes could affect the climatic niche of Ixodes ricinus (Acari, Ixodida), among the most important vectors of pathogens of medical and veterinary concern in Europe. Methods Species Distribution Modelling (SDM) was used to reconstruct the climatic niche of I. ricinus, and to project it into the future conditions for 2050 and 2080, under two scenarios: a continuous human demographic growth and a severe increase of gas emissions (scenario A2), and a scenario that proposes lower human demographic growth than A2, and a more sustainable gas emissions (scenario B2). Models were reconstructed using the algorithm of “maximum entropy”, as implemented in the software Maxent 3.3.3e; 4,544 occurrence points and 15 bioclimatic variables were used. Results In both scenarios an increase of climatic niche of about two times greater than the current area was predicted as well as a higher climatic suitability under the scenario B2 than A2. Such an increase occurred both in a latitudinal and longitudinal way, including northern Eurasian regions (e.g. Sweden and Russia), that were previously unsuitable for the species. Conclusions Our models are congruent with the predictions of range expansion already observed in I. ricinus at a regional scale and provide a qualitative and quantitative assessment of the future climatically suitable areas for I. ricinus at a continental scale. Although the use of SDM at a higher resolution should be integrated by a more refined analysis of further abiotic and biotic data, the results presented here suggest that under future climatic scenarios most of the current distribution area of I. ricinus could remain suitable and significantly increase at a continental geographic scale. Therefore disease outbreaks of pathogens transmitted by this tick species could emerge in previous non

  16. Claims of potential expansion throughout the U.S. by invasive python species are contradicted by ecological niche models.

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    R Alexander Pyron

    Full Text Available BACKGROUND: Recent reports from the United States Geological Survey (USGS suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python are not known and the possible effects of global warming on the potential expansion of the species are also unclear. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that a predicted continental expansion is unlikely based on the ecology of the organism and the climate of the U.S. Our ecological niche models, which include variables representing climatic extremes as well as averages, indicate that the only suitable habitat in the U.S. for Burmese pythons presently occurs in southern Florida and in extreme southern Texas. Models based on the current distribution of the snake predict suitable habitat in essentially the only region in which the snakes are found in the U.S. Future climate models based on global warming forecasts actually indicate a significant contraction in suitable habitat for Burmese pythons in the U.S. as well as in their native range. CONCLUSIONS/SIGNIFICANCE: The Burmese python is strongly limited to the small area of suitable environmental conditions in the United States it currently inhabits due to the ecological niche preferences of the snake. The ability of the Burmese python to expand further into the U.S. is severely limited by ecological constraints. Global warming is predicted to significantly reduce the area of suitable habitat worldwide, underscoring the potential negative effects of climate change for many species.

  17. Claims of potential expansion throughout the U.S. by invasive python species are contradicted by ecological niche models.

    Science.gov (United States)

    Pyron, R Alexander; Burbrink, Frank T; Guiher, Timothy J

    2008-08-13

    Recent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python are not known and the possible effects of global warming on the potential expansion of the species are also unclear. Here we show that a predicted continental expansion is unlikely based on the ecology of the organism and the climate of the U.S. Our ecological niche models, which include variables representing climatic extremes as well as averages, indicate that the only suitable habitat in the U.S. for Burmese pythons presently occurs in southern Florida and in extreme southern Texas. Models based on the current distribution of the snake predict suitable habitat in essentially the only region in which the snakes are found in the U.S. Future climate models based on global warming forecasts actually indicate a significant contraction in suitable habitat for Burmese pythons in the U.S. as well as in their native range. The Burmese python is strongly limited to the small area of suitable environmental conditions in the United States it currently inhabits due to the ecological niche preferences of the snake. The ability of the Burmese python to expand further into the U.S. is severely limited by ecological constraints. Global warming is predicted to significantly reduce the area of suitable habitat worldwide, underscoring the potential negative effects of climate change for many species.

  18. Niche evolution and adaptive radiation: testing the order of trait divergence.

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    Ackerly, D D; Schwilk, D W; Webb, C O

    2006-07-01

    In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (alpha niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (beta niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This alpha niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (beta niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the beta niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of alpha niche traits might be a common feature of niche

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

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    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.

  20. Species Delimitation in the Continental Forms of the Genus Epicrates (Serpentes, Boidae) Integrating Phylogenetics and Environmental Niche Models

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    Rivera, Paula C.; Di Cola, Valeria; Martínez, Juan J.; Gardenal, Cristina N.; Chiaraviglio, Margarita

    2011-01-01

    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. PMID:21912634

  1. ECOLOGICAL NICHE MODELING AND WILDLIFE MANAGEMENT UNITS (UMAS: AN APPLICATION TO DEER IN CAMPECHE, MÉXICO

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    Tania Escalante

    2013-08-01

    Full Text Available The Units for the Conservation, Management and Sustainable Use of Wildlife (UMAs are instruments of conservation and management of specific species in Mexico. UMAs represent in southeastern Mexico an important way for deer management, but they have major problems related to the monitoring of species. In this paper, we propose a methodology based on the use of a ‘niche centroid approach’ for estimating ecological distances to the niche centroid in order to produce distribution maps containing information on the potential relative abundance of species to evaluate the capability of UMAs to maintain populations of deers. We modeled the abundance for Mazama temama, M. pandora and Odocoileus virginianus on the state of Campeche, Mexico. Our predictions of areas with most abundance of deer coincided with reports from literature. We identified the UMAs “Ik Balam” and “Ejido Carlos Cano Cruz” as areas with high proportion of suitable environment, while UMAs “Betito y Lupita”, “El Huanal”, “Puh”, “Refugio faunístico Jalotum”, “Ría Lagartos-Ría Celestun” and “Yocol Cab Balam” have not environmental conditions adequate to maintain deer populations. Although this is a preliminary study, it can be a starting point to establish institutional standards for the management of species.

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

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    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.

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

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    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

  4. Modeling electricity loads in California: a continuous-time approach

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    Weron, R.; Kozłowska, B.; Nowicka-Zagrajek, J.

    2001-10-01

    In this paper we address the issue of modeling electricity loads and prices with diffusion processes. More specifically, we study models which belong to the class of generalized Ornstein-Uhlenbeck processes. After comparing properties of simulated paths with those of deseasonalized data from the California power market and performing out-of-sample forecasts we conclude that, despite certain advantages, the analyzed continuous-time processes are not adequate models of electricity load and price dynamics.

  5. Modeling of the ecological niches of the anopheles spp in Ecuador by the use of geo-informatic tools.

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    Padilla, Oswaldo; Rosas, Pablo; Moreno, Wilson; Toulkeridis, Theofilos

    2017-06-01

    Ecuador in the northwestern edge of South America is struggling by vector-borne diseases with an endemic-epidemic behavior leading to an enormous public health problem. Malaria, which has a cyclicality in its dynamics, is closely related to climatic, ecological and socio-economic phenomena. The main objective of this research has been to compare three different prediction species models, the so-called Maxent, logistic regression and multi criteria evaluation with fuzzy logic, in order to determine the model which best describes the ecological niche of the Anopheles spp species, which transmits malaria within Ecuador. After performing a detailed data collection and data processing, we applied the mentioned models and validated them with a statistical analysis in order to discover that the Maxent model has been the model that best defines the distribution of Anopheles spp within the territory. The determined sites, which are of high strategic value and important for the increasing national development, will now be able to initiate preventive countermeasures based on this study. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Ecological Niche Modeling Identifies Fine-Scale Areas at High Risk of Dengue Fever in the Pearl River Delta, China

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    Qiaoxuan Li

    2017-06-01

    Full Text Available Dengue fever (DF is one of the most common and rapidly spreading mosquito-borne viral diseases in tropical and subtropical regions. In recent years, this imported disease has posed a serious threat to public health in China, especially in the Pearl River Delta (PRD. Although the severity of DF outbreaks in the PRD is generally associated with known risk factors, fine scale assessments of areas at high risk for DF outbreaks are limited. We built five ecological niche models to identify such areas including a variety of climatic, environmental, and socioeconomic variables, as well as, in some models, extracted principal components. All the models we tested accurately identified the risk of DF, the area under the receiver operating characteristic curve (AUC were greater than 0.8, but the model using all original variables was the most accurate (AUC = 0.906. Socioeconomic variables had a greater impact on this model (total contribution 55.27% than climatic and environmental variables (total contribution 44.93%. We found the highest risk of DF outbreaks on the border of Guangzhou and Foshan (in the central PRD, and in northern Zhongshan (in the southern PRD. Our fine-scale results may help health agencies to focus epidemic monitoring tightly on the areas at highest risk of DF outbreaks.

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

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    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

  8. Spatial distributions of niche-constructing populations

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    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.

  9. Niche modeling predictions of the potential distribution of Marmota himalayana, the host animal of plague in Yushu County of Qinghai

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    Liang Lu

    2016-02-01

    Full Text Available Abstract Background After the earthquake on 14, April 2010 at Yushu in China, a plague epidemic hosted by Himalayan marmot (Marmota himalayana became a major public health concern during the reconstruction period. A rapid assessment of the distribution of Himalayan marmot in the area was urgent. The aims of this study were to analyze the relationship between environmental factors and the distribution of burrow systems of the marmot and to predict the distribution of marmots. Methods Two types of marmot burrows (hibernation and temporary in Yushu County were investigated from June to September in 2011. The location of every burrow was recorded with a global positioning system receiver. An ecological niche model was used to determine the relationship between the burrow occurrence data and environmental variables, such as land surface temperature (LST in winter and summer, normalized difference vegetation index (NDVI in winter and summer, elevation, and soil type. The predictive accuracies of the models were assessed by the area under the curve of the receiving operator curve. Results The models for hibernation and temporary burrows both performed well. The contribution orders of the variables were LST in winter and soil type, NDVI in winter and elevation for the hibernation burrow model, and LST in summer, NDVI in summer, soil type and elevation in the temporary burrow model. There were non-linear relationships between the probability of burrow presence and LST, NDVI and elevation. LST of 14 and 23 °C, NDVI of 0.22 and 0.60, and 4100 m were inflection points. A substantially higher probability of burrow presence was observed in swamp soil and dark felty soil than in other soil types. The potential area for hibernation burrows was 5696 km2 (37.7 % of Yushu County, and the area for temporary burrows was 7711 km2 (51.0 % of Yushu County. Conclusions The results suggested that marmots preferred warm areas with relatively low altitudes and good

  10. Predicting the potential geographic distribution of cotton mealybug Phenacoccus solenopsis in India based on MAXENT ecological niche model.

    Science.gov (United States)

    Fand, Babasaheb B; Kumar, Mahesh; Kamble, Ankush L

    2014-09-01

    Mealybug, Phenacoccus solenopsis Tinsley has recently emerged as a serious insect pest of cotton in India. This study demonstrates the use of Maxent algorithm for modeling the potential geographic distribution of P. solenopsis in India with presence-only data. Predictions were made based on the analysis of the relationship between 111 occurrence records for P. solenopsis and the corresponding current and future climate data defined on the study area. The climate data from worldclim database for current (1950-2000) and future (SRES A2 emission scenario for 2050) conditions were used. DIVA-GIS, an open source software for conducting spatial analysis was used for mapping the predictions from Maxent. The algorithm provided reasonable estimates of the species range indicating better discrimination of suitable and unsuitable areas for its occurrence in India under both present and future climatic conditions. The fit for the model as measured by AUC was high, with value of 0.930 for the training data and 0.895 for the test data, indicating the high level of discriminatory power for the Maxent. A Jackknife test for variable importance indicated that mean temperature of coldest quarter with highest gain value was the most important environmental variable determining the potential geographic distribution of P. solenopsis. The approaches used for delineating the ecological niche and prediction of potential geographic distribution are described briefly. Possible applications and limitations of the present modeling approach in future research and as a decision making tool in integrated pest management are discussed.

  11. Using ecological niche models to predict the abundance and impact of invasive species: application to the common carp.

    Science.gov (United States)

    Kulhanek, Stefanie A; Leung, Brian; Ricciardi, Anthony

    2011-01-01

    In order to efficiently manage nonindigenous species (NIS), predictive tools are needed to prioritize locations where they are likely to become established and where their impacts will be most severe. While predicting the impact of a NIS has generally proved challenging, forecasting its abundance patterns across potential recipient locations should serve as a useful surrogate method of estimating the relative severity of the impacts to be expected. Yet such approaches have rarely been applied in invasion biology. We used long-term monitoring data for lakes within the state of Minnesota and artificial neural networks to model both the occurrence as well as the abundance of a widespread aquatic NIS, common carp (Cyprinus carpio). We then tested the ability of the resulting models to (1) interpolate to new sites within our main study region, (2) extrapolate to lakes in the neighboring state of South Dakota, and (3) assessed the relative contribution of each variable to model predictions. Our models correctly identified over 83% of sites where carp are either present or absent and explained 73% of the variation in carp abundance for validation lakes in Minnesota (i.e., lakes not used to build the model). When extrapolated to South Dakota, our models correctly classified carp occurrence in 79% of lakes and explained 32% of the variation in carp abundance. Variables related to climate and water quality were found to be the most important predictors of carp distribution. These results demonstrate that ecological niche-based modeling techniques can be used to forecast both the occurrence and abundance patterns of invasive species at a regional scale. Models also yielded sensible predictions when extrapolated to neighboring regions. Such predictions, when combined, should provide more useful estimates of the overall risk posed by NIS on potential recipient systems.

  12. Taxonomic utility of niche models in validating species concepts: A case study in Anthophora (Heliophila) (Hymenoptera: Apidae).

    Science.gov (United States)

    Orr, Michael C; Koch, Jonathan B; Griswold, Terry L; Pitts, James P

    2014-08-04

    Taxonomy has far-reaching effects throughout biology, and incorrect taxonomy can be detrimental in many ways. Polymorphic species complexes, many of which exist in the bee genus Anthophora Latreille, lend themselves to such difficulties. This study employs environmental niche mapping (ENM) and traditional morphological analyses to investigate the validity of the subjective synonymy of Anthophora (Heliophila) curta Provancher with the senior synonym A. squammulosa Dours. Eleven of fifty morphological characters consistently differentiate the two putative species, with an additional five characters sometimes separating them. Additionally, based on over 1000 georeferenced museum specimens, the geographic ranges of the two taxa do not overlap. The two entities also react differently to the bioclimatic variables based on correlation analysis. We further tested the two-species hypothesis by constructing ENMs with informative bioclimatic variables associated with locality records. Their modelled distributions overlapped less than 1%, suggesting discrete environmental boundaries. The variables which contributed most to each species' model also differed. These differences are explored in relation to their habitats. The combined morphological and biogeographic analysis indicates that A. curta and A. squammulosa are distinct species. Based on the accumulated evidence the synonymy is formally rejected and A. curta is recognized as a valid species. Five additional taxa (A. bispinosa Cockerell, A. franciscana Cockerell, A. usticauda Cockerell, A. u. cinerior Cockerell, A. zamoranella Cockerell) are newly synonymized with A. squammulosa and Anthophora curta var. melanops Cockerell is newly synonymized with A. curta. Implications outside of taxonomy are discussed. 

  13. A Statistical Graphical Model of the California Reservoir System

    Science.gov (United States)

    Taeb, A.; Reager, J. T.; Turmon, M.; Chandrasekaran, V.

    2017-11-01

    The recent California drought has highlighted the potential vulnerability of the state's water management infrastructure to multiyear dry intervals. Due to the high complexity of the network, dynamic storage changes in California reservoirs on a state-wide scale have previously been difficult to model using either traditional statistical or physical approaches. Indeed, although there is a significant line of research on exploring models for single (or a small number of) reservoirs, these approaches are not amenable to a system-wide modeling of the California reservoir network due to the spatial and hydrological heterogeneities of the system. In this work, we develop a state-wide statistical graphical model to characterize the dependencies among a collection of 55 major California reservoirs across the state; this model is defined with respect to a graph in which the nodes index reservoirs and the edges specify the relationships or dependencies between reservoirs. We obtain and validate this model in a data-driven manner based on reservoir volumes over the period 2003-2016. A key feature of our framework is a quantification of the effects of external phenomena that influence the entire reservoir network. We further characterize the degree to which physical factors (e.g., state-wide Palmer Drought Severity Index (PDSI), average temperature, snow pack) and economic factors (e.g., consumer price index, number of agricultural workers) explain these external influences. As a consequence of this analysis, we obtain a system-wide health diagnosis of the reservoir network as a function of PDSI.

  14. A comparison of empirical and modeled nitrogen critical loads for Mediterranean forests and shrublands in California

    Science.gov (United States)

    M.E. Fenn; H.-D. Nagel; I. Koseva; J. Aherne; S.E. Jovan; L.H. Geiser; A. Schlutow; T. Scheuschner; A. Bytnerowicz; B.S. Gimeno; F. Yuan; S.A. Watmough; E.B. Allen; R.F. Johnson; T. Meixner

    2014-01-01

    Nitrogen (N) deposition is impacting a number of ecosystem types in California. Critical loads (CLs) for N deposition determined for mixed conifer forests and chaparral/oak woodlands in the Sierra Nevada Mountains of California and the San Bernardino Mountains in southern California using empirical and various modelling approaches were compared. Models used included...

  15. 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.

  16. Spatial Heterogeneity of Habitat Suitability for Rift Valley Fever Occurrence in Tanzania: An Ecological Niche Modelling Approach.

    Directory of Open Access Journals (Sweden)

    Calvin Sindato

    2016-09-01

    Full Text Available Despite the long history of Rift Valley fever (RVF in Tanzania, extent of its suitable habitat in the country remains unclear. In this study we investigated potential effects of temperature, precipitation, elevation, soil type, livestock density, rainfall pattern, proximity to wild animals, protected areas and forest on the habitat suitability for RVF occurrence in Tanzania.Presence-only records of 193 RVF outbreak locations from 1930 to 2007 together with potential predictor variables were used to model and map the suitable habitats for RVF occurrence using ecological niche modelling. Ground-truthing of the model outputs was conducted by comparing the levels of RVF virus specific antibodies in cattle, sheep and goats sampled from locations in Tanzania that presented different predicted habitat suitability values.Habitat suitability values for RVF occurrence were higher in the northern and central-eastern regions of Tanzania than the rest of the regions in the country. Soil type and precipitation of the wettest quarter contributed equally to habitat suitability (32.4% each, followed by livestock density (25.9% and rainfall pattern (9.3%. Ground-truthing of model outputs revealed that the odds of an animal being seropositive for RVFV when sampled from areas predicted to be most suitable for RVF occurrence were twice the odds of an animal sampled from areas least suitable for RVF occurrence (95% CI: 1.43, 2.76, p < 0.001.The regions in the northern and central-eastern Tanzania were more suitable for RVF occurrence than the rest of the regions in the country. The modelled suitable habitat is characterised by impermeable soils, moderate precipitation in the wettest quarter, high livestock density and a bimodal rainfall pattern. The findings of this study should provide guidance for the design of appropriate RVF surveillance, prevention and control strategies which target areas with these characteristics.

  17. Spatial Heterogeneity of Habitat Suitability for Rift Valley Fever Occurrence in Tanzania: An Ecological Niche Modelling Approach.

    Science.gov (United States)

    Sindato, Calvin; Stevens, Kim B; Karimuribo, Esron D; Mboera, Leonard E G; Paweska, Janusz T; Pfeiffer, Dirk U

    2016-09-01

    Despite the long history of Rift Valley fever (RVF) in Tanzania, extent of its suitable habitat in the country remains unclear. In this study we investigated potential effects of temperature, precipitation, elevation, soil type, livestock density, rainfall pattern, proximity to wild animals, protected areas and forest on the habitat suitability for RVF occurrence in Tanzania. Presence-only records of 193 RVF outbreak locations from 1930 to 2007 together with potential predictor variables were used to model and map the suitable habitats for RVF occurrence using ecological niche modelling. Ground-truthing of the model outputs was conducted by comparing the levels of RVF virus specific antibodies in cattle, sheep and goats sampled from locations in Tanzania that presented different predicted habitat suitability values. Habitat suitability values for RVF occurrence were higher in the northern and central-eastern regions of Tanzania than the rest of the regions in the country. Soil type and precipitation of the wettest quarter contributed equally to habitat suitability (32.4% each), followed by livestock density (25.9%) and rainfall pattern (9.3%). Ground-truthing of model outputs revealed that the odds of an animal being seropositive for RVFV when sampled from areas predicted to be most suitable for RVF occurrence were twice the odds of an animal sampled from areas least suitable for RVF occurrence (95% CI: 1.43, 2.76, p Tanzania were more suitable for RVF occurrence than the rest of the regions in the country. The modelled suitable habitat is characterised by impermeable soils, moderate precipitation in the wettest quarter, high livestock density and a bimodal rainfall pattern. The findings of this study should provide guidance for the design of appropriate RVF surveillance, prevention and control strategies which target areas with these characteristics.

  18. The continuum model of selection in human tumors: general paradigm or niche product?

    Science.gov (United States)

    Leedham, Simon; Tomlinson, Ian

    2012-07-01

    Berger and colleagues recently proposed a continuum model of how somatic mutations cause tumors to grow, thus supplementing the established binary models, such as oncogene activation and "two hits" at tumor suppressor loci. In the basic continuum model, decreases or increases in gene function, short of full inactivation or activation, impact linearly on cancer development. An extension, called the fail-safe model, envisaged an optimum level of gene derangement for tumor growth, but proposed that the cell gained protection from tumorigenesis because additional mutations caused excessive derangement. Most of the evidence in support of the continuum model came from Pten mutant mice rather than humans. In this article, we assess the validity and applicability of the continuum and fail-safe models. We suggest that the latter is of limited use: In part, it restates the existing "just right" of optimum intermediate gene derangement in tumorigenesis, and in part it is inherently implausible that a cell should avoid becoming cancerous only when it is some way down the road to that state. In contrast, the basic continuum model is a very useful addition to the other genetic models of tumorigenesis, especially in certain scenarios. Fittingly for a quantitative model, we propose that the continuum model is most likely to apply where multiple, cancer-promoting mutations have relatively small, additive effects, either through the well-established case of additive germline predisposition alleles or in a largely hypothetical situation where cancers may have acquired several somatic "mini-driver" mutations, each with weaker effects than classical tumor suppressors or fully activated oncogenes. ©2012 AACR.

  19. 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...

  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. 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...

  3. 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...

  4. 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...

  5. 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...

  6. Inhibition of WNT signaling in the bone marrow niche prevents the development of MDS in the Apcdel/+ MDS mouse model.

    Science.gov (United States)

    Stoddart, Angela; Wang, Jianghong; Hu, Chunmei; Fernald, Anthony A; Davis, Elizabeth M; Cheng, Jason X; Le Beau, Michelle M

    2017-06-01

    There is accumulating evidence that functional alteration(s) of the bone marrow (BM) microenvironment contribute to the development of some myeloid disorders, such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). In addition to a cell-intrinsic role of WNT activation in leukemia stem cells, WNT activation in the BM niche is also thought to contribute to the pathogenesis of MDS and AML. We previously showed that the Apc-haploinsufficient mice (Apcdel/+ ) model MDS induced by an aberrant BM microenvironment. We sought to determine whether Apc, a multifunctional protein and key negative regulator of the canonical β-catenin (Ctnnb1)/WNT-signaling pathway, mediates this disease through modulating WNT signaling, and whether inhibition of WNT signaling prevents the development of MDS in Apcdel/+ mice. Here, we demonstrate that loss of 1 copy of Ctnnb1 is sufficient to prevent the development of MDS in Apcdel/+ mice and that altered canonical WNT signaling in the microenvironment is responsible for the disease. Furthermore, the US Food and Drug Administration (FDA)-approved drug pyrvinium delays and/or inhibits disease in Apcdel/+ mice, even when it is administered after the presentation of anemia. Other groups have observed increased nuclear CTNNB1 in stromal cells from a high frequency of MDS/AML patients, a finding that together with our results highlights a potential new strategy for treating some myeloid disorders. © 2017 by The American Society of Hematology.

  7. 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. 

  8. 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. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  9. Thermal niche for in situ seed germination by Mediterranean mountain streams: model prediction and validation for Rhamnus persicifolia seeds.

    Science.gov (United States)

    Porceddu, Marco; Mattana, Efisio; Pritchard, Hugh W; Bacchetta, Gianluigi

    2013-12-01

    Mediterranean mountain species face exacting ecological conditions of rainy, cold winters and arid, hot summers, which affect seed germination phenology. In this study, a soil heat sum model was used to predict field emergence of Rhamnus persicifolia, an endemic tree species living at the edge of mountain streams of central eastern Sardinia. Seeds were incubated in the light at a range of temperatures (10-25 and 25/10 °C) after different periods (up to 3 months) of cold stratification at 5 °C. Base temperatures (Tb), and thermal times for 50 % germination (θ50) were calculated. Seeds were also buried in the soil in two natural populations (Rio Correboi and Rio Olai), both underneath and outside the tree canopy, and exhumed at regular intervals. Soil temperatures were recorded using data loggers and soil heat sum (°Cd) was calculated on the basis of the estimated Tb and soil temperatures. Cold stratification released physiological dormancy (PD), increasing final germination and widening the range of germination temperatures, indicative of a Type 2 non-deep PD. Tb was reduced from 10·5 °C for non-stratified seeds to 2·7 °C for seeds cold stratified for 3 months. The best thermal time model was obtained by fitting probit germination against log °Cd. θ50 was 2·6 log °Cd for untreated seeds and 2·17-2·19 log °Cd for stratified seeds. When θ50 values were integrated with soil heat sum estimates, field emergence was predicted from March to April and confirmed through field observations. Tb and θ50 values facilitated model development of the thermal niche for in situ germination of R. persicifolia. These experimental approaches may be applied to model the natural regeneration patterns of other species growing on Mediterranean mountain waterways and of physiologically dormant species, with overwintering cold stratification requirement and spring germination.

  10. 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.

  11. Comparing mechanistic and empirical approaches to modeling the thermal niche of almond

    Science.gov (United States)

    Parker, Lauren E.; Abatzoglou, John T.

    2017-09-01

    Delineating locations that are thermally viable for cultivating high-value crops can help to guide land use planning, agronomics, and water management. Three modeling approaches were used to identify the potential distribution and key thermal constraints on on almond cultivation across the southwestern United States (US), including two empirical species distribution models (SDMs)—one using commonly used bioclimatic variables (traditional SDM) and the other using more physiologically relevant climate variables (nontraditional SDM)—and a mechanistic model (MM) developed using published thermal limitations from field studies. While models showed comparable results over the majority of the domain, including over existing croplands with high almond density, the MM suggested the greatest potential for the geographic expansion of almond cultivation, with frost susceptibility and insufficient heat accumulation being the primary thermal constraints in the southwestern US. The traditional SDM over-predicted almond suitability in locations shown by the MM to be limited by frost, whereas the nontraditional SDM showed greater agreement with the MM in these locations, indicating that incorporating physiologically relevant variables in SDMs can improve predictions. Finally, opportunities for geographic expansion of almond cultivation under current climatic conditions in the region may be limited, suggesting that increasing production may rely on agronomical advances and densifying current almond plantations in existing locations.

  12. 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.

  13. 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...

  14. 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...

  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. 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. © 2013 John Wiley & Sons Ltd.

  17. Assessing niche width of endothermic fish from genes to ecosystem

    Science.gov (United States)

    Madigan, Daniel J.; Carlisle, Aaron B.; Gardner, Luke D.; Jayasundara, Nishad; Micheli, Fiorenza; Schaefer, Kurt M.; Fuller, Daniel W.; Block, Barbara A.

    2015-01-01

    Endothermy in vertebrates has been postulated to confer physiological and ecological advantages. In endothermic fish, niche expansion into cooler waters is correlated with specific physiological traits and is hypothesized to lead to greater foraging success and increased fitness. Using the seasonal co-occurrence of three tuna species in the eastern Pacific Ocean as a model system, we used cardiac gene expression data (as a proxy for thermal tolerance to low temperatures), archival tag data, and diet analyses to examine the vertical niche expansion hypothesis for endothermy in situ. Yellowfin, albacore, and Pacific bluefin tuna (PBFT) in the California Current system used more surface, mesopelagic, and deep waters, respectively. Expression of cardiac genes for calcium cycling increased in PBFT and coincided with broader vertical and thermal niche utilization. However, the PBFT diet was less diverse and focused on energy-rich forage fishes but did not show the greatest energy gains. Ecosystem-based management strategies for tunas should thus consider species-specific differences in physiology and foraging specialization. PMID:26100889

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

    Science.gov (United States)

    Nekaris, K. Anne-Isola; Arnell, Andrew P.; Svensson, Magdalena S.

    2015-01-01

    Simple Summary Large “charismatic” animals (with widespread popular appeal) are often used as flagship species to raise awareness for conservation. Deforestation and forest fragmentation are among the main threats to biodiversity, and in many places such species are disappearing. In this paper we aim to find a suitable species among the less charismatic animal species left in the fragmented forests of South-western Sri Lanka. We selected ten candidates, using a questionnaire survey along with computer modelling of their distributions. The red slender loris and the fishing cat came out as finalists as they were both appealing to local people, and fulfilled selected ecological criteria. Abstract 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

  19. 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.

  20. Ecological niche of plant pathogens

    Directory of Open Access Journals (Sweden)

    Ecaterina Fodor

    2011-06-01

    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 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. 

  1. Toward a Periodic Table of Niches, or Exploring the Lizard Niche Hypervolume.

    Science.gov (United States)

    Pianka, Eric R; Vitt, Laurie J; Pelegrin, Nicolás; Fitzgerald, Daniel B; Winemiller, Kirk O

    2017-11-01

    Widespread niche convergence suggests that species can be organized according to functional trait combinations to create a framework analogous to a periodic table. We compiled ecological data for lizards to examine patterns of global and regional niche diversification, and we used multivariate statistical approaches to develop the beginnings for a periodic table of niches. Data (50+ variables) for five major niche dimensions (habitat, diet, life history, metabolism, defense) were compiled for 134 species of lizards representing 24 of the 38 extant families. Principal coordinates analyses were performed on niche dimensional data sets, and species scores for the first three axes were used as input for a principal components analysis to ordinate species in continuous niche space and for a regression tree analysis to separate species into discrete niche categories. Three-dimensional models facilitate exploration of species positions in relation to major gradients within the niche hypervolume. The first gradient loads on body size, foraging mode, and clutch size. The second was influenced by metabolism and terrestrial versus arboreal microhabitat. The third was influenced by activity time, life history, and diet. Natural dichotomies are activity time, foraging mode, parity mode, and habitat. Regression tree analysis identified 103 cases of extreme niche conservatism within clades and 100 convergences between clades. Extending this approach to other taxa should lead to a wider understanding of niche evolution.

  2. Competition influence in the segregation of the trophic niche of otariids: a case study using isotopic Bayesian mixing models in Galapagos pinnipeds.

    Science.gov (United States)

    Páez-Rosas, Diego; Rodríguez-Pérez, Mónica; Riofrío-Lazo, Marjorie

    2014-12-15

    The feeding success of predators is associated with the competition level for resources, and, thus, sympatric species are exposed to a potential trophic overlap. Isotopic Bayesian mixing models should provide a better understanding of the contribution of preys to the diet of predators and the feeding behavior of a species over time. The carbon and nitrogen isotopic signatures from pup hair samples of 93 Galapagos sea lions and 48 Galapagos fur seals collected between 2003 and 2009 in different regions (east and west) of the archipelago were analyzed. A PDZ Europa ANCA-GSL elemental analyzer interfaced with a PDZ Europa 20-20 continuous flow gas source mass spectrometer was employed. Bayesian models, SIAR and SIBER, were used to estimate the contribution of prey to the diet of predators, the niche breadth, and the trophic overlap level between the populations. Statistical differences in the isotopic values of both predators were observed over the time. The mixing model determined that Galapagos fur seals had a primarily teutophagous diet, whereas the Galapagos sea lions fed exclusively on fish in both regions of the archipelago. The SIBER analysis showed differences in the trophic niche between the two sea lion populations, with the western rookery of the Galapagos sea lion being the population with the largest trophic niche area. A trophic niche partitioning between Galapagos fur seals and Galapagos sea lions in the west of the archipelago is suggested by our results. At intraspecific level, the western population of the Galapagos sea lion (ZwW) showed higher trophic breadth than the eastern population, a strategy adopted by the ZwW to decrease the interspecific competition levels in the western region. Copyright © 2014 John Wiley & Sons, Ltd.

  3. 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.

  4. Numerical modeling of the seasonal circulation off the northern Baja California and southern California coasts

    Science.gov (United States)

    Mateos, E.; Marinone, S. G.; Pares-Sierra, A.

    2009-12-01

    The seasonal circulation off the northern Baja California and southern California was studied using the ROMS numerical model. The model was forced with the climatological output of the SODA (Simple Ocean Data Assimilation) roughly between 30 °N to 33.5 °N and 116.5 °W to 119.5 °W, heat fluxes from the COADS (The Comprehensive Ocean-Atmosphere Data Set) and daily winds of NARR (North American Regional Reanalysis). The winds are mainly southward and intense during spring time. The circulation is characterized by four main features: the Ensenada Frontal Current (EFC), and anticyclonic eddy (AE), a coastal surface current (CSC) and the undercurrent (UC). With the exception of the anticyclonic eddy, all structures are formed at the exterior of the model domain. The CSC is a coastal southward flow that reaches about 40 m of depth and is present during spring and summer. In spring the CSC it intensifies (25 cm s-1) close to the coast, due to local wind intensification, then it migrates offshore in summer, due to the generation of cyclonic eddies between the CSC and the coast. The UC is a persistent poleward flow with its nuclei at about 150 m depth. The UC emerges in summer at 15 m depth due to the CSC offshore migration, reaching speeds of 8 cm s-1. The EFC is a strong flow which approaches perpendicular to the coastline and splits into two branches: one northward and the second southwards. During the fall the EFC reaches maximum speeds (25 cm s-1) producing that part of the northward branch turns anticyclonically south of San Clemente Island, and forming the AE south of San Clemente Island, occupying (both EFC and AE) almost all the water column. However, they disappear at the surface layers during winter (due to the winds intensification) and summer (due to the CSC westward migration).

  5. The Multidimensional Stoichiometric Niche

    Directory of Open Access Journals (Sweden)

    Angélica L. González

    2017-09-01

    Full Text Available The niche concept is essential to understanding how biotic and abiotic factors regulate the abundance and distribution of living entities, and how these organisms utilize, affect and compete for resources in the environment. However, it has been challenging to determine the number and types of important niche dimensions. By contrast, there is strong mechanistic theory and empirical evidence showing that the elemental composition of living organisms shapes ecological systems, from organismal physiology to food web structure. We propose an approach based on a multidimensional elemental view of the ecological niche. Visualizing the stoichiometric composition of individuals in multivariate space permits quantification of niche dimensions within and across species. This approach expands on previous elemental characterizations of plant niches, and adapts metrics of niche volume, overlap and nestedness previously used to quantify isotopic niches. We demonstrate the applicability of the multidimensional stoichiometric niche using data on carbon, nitrogen, and phosphorus of terrestrial and freshwater communities composed by multiple trophic groups. First, we calculated the stoichiometric niche volumes occupied by terrestrial and freshwater food webs, by trophic groups, by individual species, and by individuals within species, which together give a measure of the extent of stoichiometric diversity within and across levels of organization. Then we evaluated complementarity between these stoichiometric niches, through metrics of overlap and nestedness. Our case study showed that vertebrates, invertebrates, and primary producers do not overlap in their stoichiometric niches, and that large areas of stoichiometric space are unoccupied by organisms. Within invertebrates, niche differences emerged between freshwater and terrestrial food webs, and between herbivores and non-herbivores (detritivores and predators. These niche differences were accompanied by

  6. 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...

  7. Historical biogeography and ecological niche modelling of the Asimina-Disepalum clade (Annonaceae): role of ecological differentiation in Neotropical-Asian disjunctions and diversification in Asia.

    Science.gov (United States)

    Li, Pui-Sze; Thomas, Daniel C; Saunders, Richard M K

    2017-08-14

    The Asimina-Disepalum clade (Annonaceae subfam. Annonoideae tribe Annoneae) includes a major Neotropical-Asian biogeographical disjunction. We evaluate whether this disjunction can be explained by the Eocene boreotropics hypothesis, which relies on the existence of extensive boreotropical forests during the Late Palaeocene-Early Eocene thermal maximum (52-50 Ma), followed by disruption of boreotropical vegetation during post-Eocene cooling. Molecular dating using an uncorrelated relaxed molecular clock (UCLD) model with two fossil calibrations, ancestral range estimation, and ecological niche modelling across evolutionary time were performed. Our focus was the geographical origin of Disepalum and general biogeographic patterns within this genus. Comparison of ecological tolerance among extant species and niche reconstructions at ancestral nodes within the clade enabled insights in likely migration routes of lineages, as well as evaluating the role of bioclimatic ecological differentiation in the diversification of Disepalum within Southeast Asia. The inferred vicariance event associated with the Asimina-Disepalum disjunction is estimated to have originated ca. 40 Mya [95% highest posterior density (HPD): 44.3-35.5 Mya]. The Disepalum crown lineage is estimated to have originated ca. 9 Mya (95% HPD: 10.6-7.6), either in western Malesia and continental Southeast Asia, or exclusively in western Malesia. Ecological niche modelling shows that seasonality of temperature and precipitation are major contributors determining the geographical range of species. Ancestral niche modelling furthermore indicates that the ancestor of the Asimina-Disepalum clade likely had bioclimatic preferences close to conditions found in current tropical and subtropical climates across Asia, whereas the ancestors of the Asimina and Disepalum crown groups are projected onto the more subtropical and tropical regions, respectively. The vicariance event associated with the Neotropical

  8. Trophic niche breadth and niche overlap in a guild of flower-visiting bees in a Brazilian dry forest

    OpenAIRE

    Aguiar, Cândida; Santos, Gilberto; Martins, Celso; Presley, Steven

    2013-01-01

    International audience; Trophic niche breadth and niche overlap of bees were studied in a region of Caatinga (a deciduous dry thorn scrub forest) in Brazil with the lowest mean annual rainfall of the country, highly seasonal environmental variation, and an unpredictable rainy season. A null model approach was used to determine if the observed niche overlap in the community differed from that expected by chance. In general, even bee species with wider trophic niches concentrated foraging effor...

  9. 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.

  10. 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

  11. Regional Air Toxics Modeling in California's San Francisco Bay Area

    Science.gov (United States)

    Martien, P. T.; Tanrikulu, S.; Tran, C.; Fairley, D.; Jia, Y.; Fanai, A.; Reid, S.; Yarwood, G.; Emery, C.

    2011-12-01

    Regional toxics modeling conducted for California's San Francisco Bay Area (SFBA) estimated potential cancer risk from diesel particulate matter (DPM) and four key reactive toxic gaseous pollutants (1,3-butadiene, benzene, formaldehyde, and acetaldehyde). Concentrations of other non-cancerous gaseous toxic air contaminants, including acrolein, were also generated. In this study, meteorological fields generated from July and December periods in 2000 and emissions from 2005 provided inputs to a three-dimensional air quality model at high spatial resolution (1x1 km^2 grid), from which a baseline set of annual risk values was estimated. Simulated risk maps show highest annual average DPM concentrations and cancer risks were located near and downwind of major freeways and near the Port of Oakland, a major container port in the area. Population weighted risks, using 2000 census data, were found to be highest in highly urbanized areas adjacent to significant DPM sources. For summer, the ratio of mean measured elemental carbon to mean modeled DPM was 0.78, conforming roughly to expectations. But for winter the ratio is 1.13, suggesting other sources of elemental carbon, such as wood smoke, are important. Simulated annual estimates for benzene and 1-3, butadiene compared well to measured annual estimates. Simulated acrolein and formaldehyde significantly under-predicted observed values. Simulations repeated using projected 2015 toxic emissions predicted that potential cancer risk dropped significantly in all areas throughout the SFBA. Emissions estimates for 2015 included the State of California's recently adopted on-road truck rule. Emission estimates of DPM are projected to drop about 70% between 2005 and 2015 in the SFBA, with a commensurate reduction in potential cancer risks. However, due to projected shifts in population during this period, with urban densification close to DPM sources outpacing emission reductions, there are some areas where population-weighted risks

  12. Cancer Immunoediting from Immunosurveillance to Tumor Escape in Microvillus-Formed Niche: A Study of Syngeneic Orthotopic Rat Bladder Cancer Model in Comparison with Human Bladder Cancer

    Directory of Open Access Journals (Sweden)

    Carl-Jørgen Arum

    2010-06-01

    Full Text Available Cancer cells can develop an attenuated immunogenicity and/or create an immunosuppressive microenvironment to prevent tumor eradication by host immune system, the so-called “cancer immunoediting” hypothesis. The aim of the present study was to find evidence for this hypothesis by using a rat orthotopic bladder cancer model. Fisher rats were inoculated with AY-27 cells (a Fisher rat bladder cancer cell line. Cultured cancer cells, rat and human bladder cancer tissues, and publicly available microarray data from human bladder cancer were analyzed by means of bioinformatics and morphology. Results showed that 12 of 24 differentially expressed pathways were concordant in connection to cell cycle and proliferation between rats and humans (both non-muscle-invasive and muscle-invasive tumors and that 11 of the 24 pathways, including major histocompatibility complex, were related to host immunosurveillance with activations of T cells and natural killer cells in rats. The altered pathways and morphogenesis of this rat model corresponded more closely with those of human muscle-invasive rather than non-muscle-invasive tumors. A unique ultrastructure displaying microvillus-formed niches was found in small areas within the tumor of both rats and humans. These niches were interconnected with desmosomes between cancer cells and without infiltration of lymphocytes. The expression of E-cadherin, selectins, PGP9.5, vascular endothelial growth factor, caspase-3, CD133, Oct-4, nestin, CD3, and CD45RA was lower in the tumor than in the adjacent normal epithelium. We suggest that the microvillus-formed niche that harbors a few implanted cancer cells might be the compartment that prevents the tumor eradication by the host immune system.

  13. California Rare Endemics and Climate Change

    Science.gov (United States)

    Espinoza, M.

    2010-12-01

    California is known for its wide variety of endemic flora, from its annuals such as the Eschscholzia californica (California poppy) to the perennials like the Arctostaphylos pallida (Alameda manzanita), which happens to be a rare species. Each species plays an important role in the biodiversity of California, yet there are species that are threatened, not only by human interaction and urbanization, but by climate change. Species that we seldom see are now on the verge of becoming eradicated; rare endemics similar to Arctostaphylos pallida are now facing a new challenge that may severely impair their survival. The climate has changed significantly over the twentieth century and it has affected the distribution of rare endemics in California, both geographically as well as within their climatic and edaphic niches. Lilaeopsis masonii is just one rare endemic, however it serves as a representative of the other 23 species that were studied. Using Maxent, a climate-modeling program, it was viable to construct two climate envelopes of the masonii species: the early century envelope (1930-1959) and the later century envelope (1990-2009). When these two climate envelopes were compared, it became clear that the later century climate envelope had contracted radically, reshaping the climate niche of all rare endemics in California due to an increase in temperature. It is possible to conclude that the future of rare endemics hangs in the balance, where one degree higher in temperature is enough to topple the scale.

  14. Do ecological niche model predictions reflect the adaptive landscape of species?: a test using Myristica malabarica Lam., an endemic tree in the Western Ghats, India.

    Science.gov (United States)

    Nagaraju, Shivaprakash K; Gudasalamani, Ravikanth; Barve, Narayani; Ghazoul, Jaboury; Narayanagowda, Ganeshaiah Kotiganahalli; Ramanan, Uma Shaanker

    2013-01-01

    Ecological niche models (ENM) have become a popular tool to define and predict the "ecological niche" of a species. An implicit assumption of the ENMs is that the predicted ecological niche of a species actually reflects the adaptive landscape of the species. Thus in sites predicted to be highly suitable, species would have maximum fitness compared to in sites predicted to be poorly suitable. As yet there are very few attempts to address this assumption. Here we evaluate this assumption. We used Bioclim (DIVA GIS version 7.3) and Maxent (version 3.3.2) to predict the habitat suitability of Myristica malabarica Lam., an economically important tree occurring in the Western Ghats, India. We located populations of the trees naturally occurring in different habitat suitability regimes (from highly suitable to poorly suitable) and evaluated them for their regeneration ability and genetic diversity. We also evaluated them for two plant functional traits, fluctuating asymmetry--an index of genetic homeostasis, and specific leaf weight--an index of primary productivity, often assumed to be good surrogates of fitness. We show a significant positive correlation between the predicted habitat quality and plant functional traits, regeneration index and genetic diversity of populations. Populations at sites predicted to be highly suitable had a higher regeneration and gene diversity compared to populations in sites predicted to be poor or unsuitable. Further, individuals in the highly suitable sites exhibited significantly less fluctuating asymmetry and significantly higher specific leaf weight compared to individuals in the poorly suitable habitats. These results for the first time provide an explicit test of the ENM with respect to the plant functional traits, regeneration ability and genetic diversity of populations along a habitat suitability gradient. We discuss the implication of these results for designing viable species conservation and restoration programs.

  15. California Wintertime Precipitation in Regional and Global Climate Models

    Energy Technology Data Exchange (ETDEWEB)

    Caldwell, P M

    2009-04-27

    In this paper, wintertime precipitation from a variety of observational datasets, regional climate models (RCMs), and general circulation models (GCMs) is averaged over the state of California (CA) and compared. Several averaging methodologies are considered and all are found to give similar values when model grid spacing is less than 3{sup o}. This suggests that CA is a reasonable size for regional intercomparisons using modern GCMs. Results show that reanalysis-forced RCMs tend to significantly overpredict CA precipitation. This appears to be due mainly to overprediction of extreme events; RCM precipitation frequency is generally underpredicted. Overprediction is also reflected in wintertime precipitation variability, which tends to be too high for RCMs on both daily and interannual scales. Wintertime precipitation in most (but not all) GCMs is underestimated. This is in contrast to previous studies based on global blended gauge/satellite observations which are shown here to underestimate precipitation relative to higher-resolution gauge-only datasets. Several GCMs provide reasonable daily precipitation distributions, a trait which doesn't seem tied to model resolution. GCM daily and interannual variability is generally underpredicted.

  16. Stochastic representation of fire behavior in a wildland fire protection planning model for California.

    Science.gov (United States)

    J. Keith Gilless; Jeremy S. Fried

    1998-01-01

    A fire behavior module was developed for the California Fire Economics Simulator version 2 (CFES2), a stochastic simulation model of initial attack on wildland fire used by the California Department of Forestry and Fire Protection. Fire rate of spread (ROS) and fire dispatch level (FDL) for simulated fires "occurring" on the same day are determined by making...

  17. Hydrologic model of the Modesto Region, California, 1960-2004

    Science.gov (United States)

    Phillips, Steven P.; Rewis, Diane L.; Traum, Jonathan A.

    2015-01-01

    Strategies for managing water supplies and groundwater quality in the Modesto region of the eastern San Joaquin Valley, California, are being formulated and evaluated by the Stanislaus and Tuolumne Rivers Groundwater Basin Association. Management issues and goals in the basin include an area in the lower part of the basin that requires drainage of the shallow water table to sustain agriculture, intra- and inter-basin migration of poor-quality groundwater, and efficient management of surface and groundwater supplies. To aid in the evaluation of water-management strategies, the U.S. Geological Survey and the Stanislaus and Tuolumne Rivers Groundwater Basin Association have developed a hydrologic model that simulates monthly groundwater and surface-water flow as governed by aquifer-system properties, annual and seasonal variations in climate, surface-water flow and availability, water use, and land use. The model was constructed by using the U.S. Geological Survey groundwater-modeling software MODFLOW-OWHM with the Farm Process.

  18. Statistical modeling of valley fever data in Kern County, California.

    Science.gov (United States)

    Talamantes, Jorge; Behseta, Sam; Zender, Charles S

    2007-03-01

    Coccidioidomycosis (valley fever) is a fungal infection found in the southwestern US, northern Mexico, and some places in Central and South America. The fungus that causes it (Coccidioides immitis) is normally soil-dwelling but, if disturbed, becomes air-borne and infects the host when its spores are inhaled. It is thus natural to surmise that weather conditions that foster the growth and dispersal of the fungus must have an effect on the number of cases in the endemic areas. We present here an attempt at the modeling of valley fever incidence in Kern County, California, by the implementation of a generalized auto regressive moving average (GARMA) model. We show that the number of valley fever cases can be predicted mainly by considering only the previous history of incidence rates in the county. The inclusion of weather-related time sequences improves the model only to a relatively minor extent. This suggests that fluctuations of incidence rates (about a seasonally varying background value) are related to biological and/or anthropogenic reasons, and not so much to weather anomalies.

  19. Unusual fungal niches.

    Science.gov (United States)

    Cantrell, S A; Dianese, J C; Fell, J; Gunde-Cimerman, N; Zalar, P

    2011-01-01

    Fungi are found in all aerobic ecosystems, colonizing a diversity of substrates and performing a wide diversity of functions, some of which are not well understood. Many spices of fungi are cosmopolitan and generalists or habitats. Unusual fungal niches are habitats where extreme conditions would be expected to prevent the development of a mycobiota. In this review we describe five unusual fungal habitats in which fungi occupy poorly understood niches: Antarctic dry valleys, high Arctic glaciers, salt flats and salterns, hypersaline microbial mats and plant trichomes. Yeasts, black yeast-like fungi, melanized filamentous species as well as representatives of Aspergillus and Penicillium seem to be dominant among the mycobiota adapted to cold and saline niches. Plant trichomes appear to be a taxa. The advent of new sequencing technologies is helping to elucidate the microbial diversity in many ecosystems, but more studies are needed to document the functional role of fungi in the microbial communities thriving in these unusual environments.

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

    Science.gov (United States)

    Improved quantification of diverse CH4 sources at the urban scale is needed to guide local greenhouse gas (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 land...

  1. Herbivores and edaphic factors constrain the realized niche of a native plant

    Science.gov (United States)

    J.A. Lau; A McCall; K Davies; J McKay; J Wright

    2008-01-01

    Biotic interactions, such as competition and herbivory, can limit plant species ranges to a subset of edaphically suitable habitats, termed the realized niche. Here we explored the role that herbivores play in restricting the niche of serpentine ecotypes of the native California annual Collinsia sparsiflora...

  2. Phylogeographic analysis and environmental niche modeling of the plain-bellied watersnake (Nerodia erythrogaster) reveals low levels of genetic and ecological differentiation.

    Science.gov (United States)

    Makowsky, Robert; Marshall, John C; McVay, John; Chippindale, Paul T; Rissler, Leslie J

    2010-06-01

    Species that exhibit geographically defined phenotypic variation traditionally have been divided into subspecies. Subspecies based on phenotypic features may not comprise monophyletic groups due to selection, gene flow, and/or convergent evolution. In many taxonomic groups the number of species once designated as widespread is dwindling rapidly, and many workers reject the concept of subspecies altogether. We tested whether currently recognized subspecies in the plain-bellied watersnake Nerodia erythrogaster are concordant with relationships based on mitochondrial markers, and whether it represents a single widespread species. The range of this taxon spans multiple potential biogeographic barriers (especially the Mississippi and Apalachicola Rivers) that correspond with lineage breaks in many species, including other snakes. We sequenced three mitochondrial genes (NADH-II, Cyt-b, Cox-I) from 156 geo-referenced specimens and developed ecological niche models using Maxent and spatially explicit climate data to examine historical and ecological factors affecting variation in N. erythrogaster across its range. Overall, we found little support for the recognized subspecies as either independent evolutionary lineages or geographically circumscribed units and conclude that although some genetic and niche differentiation has occurred, most populations assigned to N. erythrogaster appear to represent a single, widespread species. However, additional sampling and application of nuclear markers are necessary to clarify the status of the easternmost populations. 2010 Elsevier Inc. All rights reserved.

  3. 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

    Science.gov (United States)

    Kriticos, Darren J.; Morin, Louise; Leriche, Agathe; Anderson, Robert C.; Caley, Peter

    2013-01-01

    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. PMID:23704988

  4. 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.

  5. 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.

    Science.gov (United States)

    Kriticos, Darren J; Morin, Louise; Leriche, Agathe; Anderson, Robert C; Caley, Peter

    2013-01-01

    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.

  6. On the absence of the Green-tailed TrainbearerLesbia nuna(Trochilidae) from Venezuela: an analysis based on environmental niche modelling.

    Science.gov (United States)

    Ramoni Perazzi, Paolo; Schuchmann, Karl L; Ablan Bortone, Magdiel; Soto Werschitz, Alejandra

    2017-01-01

    Lesbia nuna , a hummingbird distributed in the tropical Andes, has been included in Venezuela's bird list on the basis of a specimen collected in 1873 at Sierra Nevada, Mérida and deposited in the Natural History Museum, London, with no further records for this country since then. This record, largely considered as valid by most authors, has been questioned by others, although without formal analyses. The potential habitat range of the Green-Tailed Trainbearer, Lesbia nuna gouldii (Trochilidae), in the northern Andes from Ecuador to Venezuela was modelled, using maximum entropy niche modelling, environmental covariates and records from locations across the Colombian Andes. The predicted suitable habitat range corresponded well to the known range of the subspecies L. n. gouldii in Colombia and clearly excluded Sierra Nevada. Therefore, these analyses suggest that this species should be removed from the Venezuelan bird list.

  7. Ecological Niche Modeling For Spatial-Temporal Quantification Of The Changing Dynamics Of Malaria Vector Distribution In Kenya Under Climate Change Forcing

    Directory of Open Access Journals (Sweden)

    Jacinta S. Kimuyu

    2017-06-01

    Full Text Available A new study in Kenya has spatially quantified the paradigm shift in the current and future malaria vectors ecology by use of BIOCLIM True or False model with IPCC HADCM3 projected future climate under A2a scenario. The study was designed to correlate the effect of climate change as an explanatory variable among other factors on malaria vectors distribution in Kenya. There has been reported malaria cases in new Counties that were never malaria endemic zones thus the study seeks to research on ecological changes that can be as a result of changing environmental factors to support malaria vectors to thrive in new areas. Predictive modeling was done to investigate the spatial-temporal vector distribution under different IPCC future climate projections. The period from 1950 2000 was treated as the current climate scenario to explain where malaria vectors are existing as per vector spatial presence data and the prediction of the ecological niches where the vectors would also be found to thrive. Ecological Niche Modeling demonstrated significant alteration in suitability of malaria vector habitats in Kenya from the current ecological zones by the years 2020 2050 and 2080. Most of the current malaria ecological niches were found to remain suitable while others turned out to be unsuitable after projection although new malaria hotspots were found to emerge. Prediction by the year 2050 demonstrated an alarming expansion of suitable malaria ecologies. By 2080 the predictions showed that the suitable ecologies will start to revert similar to the earlier suitability as in the current climate. Therefore climate change in Kenya will adversely affect the environment at an alarming rate by 2050 but beyond that there will be a level of stabilization where further change will trigger reversal to the past climate. This change in unsuitable to suitable malaria habitats can negatively affect the national effort to fight malaria under the ongoing towards zero campaign

  8. From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories

    Science.gov (United States)

    Smith, B. Eugene; Johnston, Mark K.; Lücking, Robert

    2016-01-01

    Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of

  9. From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories.

    Directory of Open Access Journals (Sweden)

    B Eugene Smith

    Full Text Available Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF, which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem

  10. LNG niche market development

    NARCIS (Netherlands)

    Beata Kviatek

    2011-01-01

    Project focusing on developing a public affairs advice for the corporate business case aiming at development of LNG niche market. The advice is based on research in five areas: (1) an overview of existent regulatory framework with regard to the use of LNG in a small scale market in the EU and

  11. Pre-metastatic niches

    DEFF Research Database (Denmark)

    Peinado, Héctor; Zhang, Haiying; Matei, Irina R.

    2017-01-01

    -secreted factors and tumour-shed extracellular vesicles that enable the 'soil' at distant metastatic sites to encourage the outgrowth of incoming cancer cells. In this Review, we summarize the main processes and new mechanisms involved in the formation of the pre-metastatic niche....

  12. 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...

  13. 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...

  14. 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...

  15. Modeling Studies of Wind and Thermohaline Forcing on the California Current System

    National Research Council Canada - National Science Library

    Vance, Phillip

    1997-01-01

    A high-resolution, multi-level, primitive equation model is initialized with climatological data to study the combined effects of wind and thermohaline forcing on the ocean circulation of the California Current System (CCS...

  16. 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 pHgeochemical habitat of any high-level microbial taxon and the first application of a C-SVM to microbial ecology.

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

    Directory of Open Access Journals (Sweden)

    Pawel Wasowicz

    2016-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    Wasowicz, Pawel; 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.

  19. 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.

  20. Stress field models from Maxwell stress functions: southern California

    Science.gov (United States)

    Bird, Peter

    2017-08-01

    shallow stress maxima and discontinuous horizontal compression at the Moho, which the new model can only approximate. The new model also lacks the spatial resolution to portray the localized stress states that may occur near the central surfaces of weak faults; instead, the model portrays the regional or background stress field which provides boundary conditions for weak faults. Peak shear stresses in one registered model and one alternate model are 120 and 150 MPa, respectively, while peak vertically integrated shear stresses are 2.9 × 1012 and 4.1 × 1012 N m-1. Channeling of deviatoric stress along the strong Great Valley and the western slope of the Peninsular Ranges is evident. In the neotectonics of southern California, it appears that deviatoric stress and long-term strain rate have a negative correlation, because regions of low heat flow are strong and act as stress guides, while undergoing very little internal deformation. In contrast, active faults lie preferentially in areas with higher heat flow, and their low strength keeps deviatoric stresses locally modest.

  1. 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

  2. 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...

  3. Establishment of a green fluorescent protein tracing murine model focused on the functions of host components in necrosis repair and the niche of subcutaneously implanted glioma.

    Science.gov (United States)

    Lu, Zhao-Hui; Lv, Ke; Zhang, Jin-Shi; Dai, Chun-Gang; Liu, Bin; Ma, Xiao-Yu; He, Lin-Ming; Jia, Jing-Yun; Chen, Yan-Ming; Dai, Xing-Liang; Wang, Ai-Dong; Dong, Jun; Zhang, Quan-Bin; Lan, Qing; Huang, Qiang

    2014-02-01

    Due to progress in the research of glioma stem cells and the glioma niche, development of an animal model that facilitates the elucidation of the roles of the host tissue and cells is necessary. The aim of the present study was to develop a subcutaneous xenograft green fluorescent protein nude mouse model and use this model to analyze the roles of host cells in tumor necrosis repair. Tumors derived from the human glioma stem/progenitor cell line SU3 were subcutaneously implanted in green fluorescent protein nude mice. The implanted tumors were then passed from animal to animal for 10 generations. Finally, subcutaneous xenografts were assayed with traditional pathology, immunopathological techniques and fluorescence photography. For each generation, the tumorigenicity rate was 100%. Subcutaneous xenografts were rich in blood vessels, and necrotic and hemorrhagic foci, which highly expressed hypoxia-inducible factor-1α, tumor necrosis factor, Ki-67, CD68 and CD11b. In the interstitial tissue, particularly in old hemorrhagic foci, there were numerous cells expressing green fluorescent protein, CD68 and CD11b. Green fluorescent protein nude mouse subcutaneous xenografts not only consistently maintained the high invasiveness and tumorigenicity of glioma stem/progenitor cells, but also consisted of a high concentration of tumor blood vessels and necrotic and hemorrhagic foci. Subcutaneous xenografts also expressed high levels of tumor microenvironment-related proteins and host-derived tumor interstitial molecules. The model has significant potential for further research on tumor tissue remodeling and the tumor microenvironment.

  4. 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.

  5. Modeling and Prediction of Wildfire Hazard in Southern California, Integration of Models with Imaging Spectrometry

    Science.gov (United States)

    Roberts, Dar A.; Church, Richard; Ustin, Susan L.; Brass, James A. (Technical Monitor)

    2001-01-01

    Large urban wildfires throughout southern California have caused billions of dollars of damage and significant loss of life over the last few decades. Rapid urban growth along the wildland interface, high fuel loads and a potential increase in the frequency of large fires due to climatic change suggest that the problem will worsen in the future. Improved fire spread prediction and reduced uncertainty in assessing fire hazard would be significant, both economically and socially. Current problems in the modeling of fire spread include the role of plant community differences, spatial heterogeneity in fuels and spatio-temporal changes in fuels. In this research, we evaluated the potential of Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and Airborne Synthetic Aperture Radar (AIRSAR) data for providing improved maps of wildfire fuel properties. Analysis concentrated in two areas of Southern California, the Santa Monica Mountains and Santa Barbara Front Range. Wildfire fuel information can be divided into four basic categories: fuel type, fuel load (live green and woody biomass), fuel moisture and fuel condition (live vs senesced fuels). To map fuel type, AVIRIS data were used to map vegetation species using Multiple Endmember Spectral Mixture Analysis (MESMA) and Binary Decision Trees. Green live biomass and canopy moisture were mapped using AVIRIS through analysis of the 980 nm liquid water absorption feature and compared to alternate measures of moisture and field measurements. Woody biomass was mapped using L and P band cross polarimetric data acquired in 1998 and 1999. Fuel condition was mapped using spectral mixture analysis to map green vegetation (green leaves), nonphotosynthetic vegetation (NPV; stems, wood and litter), shade and soil. Summaries describing the potential of hyperspectral and SAR data for fuel mapping are provided by Roberts et al. and Dennison et al. To utilize remotely sensed data to assess fire hazard, fuel-type maps were translated

  6. Fully Integrated Atmospheric, Surface, and Subsurface Model of the California Basin

    Science.gov (United States)

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

    2016-12-01

    The recent drought in the Western United States has crippled agriculture in California's Central Valley. Farmers, facing reduced surface water flow, have turned to groundwater as their primary solution to the water crisis. However, the unsustainable pumping rates seen throughout California have drastically decreased the surface and subsurface water levels. For this reason, we developed a coupled subsurface, surface, and atmospheric model for the entire California Basin that captures the feedbacks between the three domains at an extremely high spatial and temporal resolution. Our coupled model framework integrates HydroGeoSphere (HGS), a fully implicit three-dimensional control-volume finite element surface and variably saturated subsurface model with evapotranspiration process, to Weather Research and Forecasting (WRF), a three-dimensional mesoscale nonhydrostatic atmospheric model. HGS replaces the land surface component within WRF, and provides WRF with the actual evapotranspiration (AET) and soil saturation. In return, WRF provides HGS with the potential evapotranspiration (PET) and precipitation fluxes. The flexible coupling technique allows HGS and WRF to have unique meshing and projection characteristics and links the domains based on their geographic coordinates (i.e., latitude and longitude). The California Basin model successfully simulated similar drawdown rates to the Gravity Recovery and Climate Experiment (GRACE) and replicated the Klamath and Sacramento River hydrographs. Furthermore, our simulation results reproduced field measured precipitation and evapotranspiration. Currently, our coupled California Basin model is the most complete water resource simulator because we combine the surface, subsurface, and atmosphere into a single domain.

  7. 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.

  8. 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.

  9. Carving out Their Own Niche

    Science.gov (United States)

    Lum, Lydia

    2007-01-01

    Asian-American performers were few and far between when Dr. Oliver Wang was growing up in the 1970s and '80s. Looking back, Dr. Wang, an assistant professor in sociology at California State University-Long Beach, says the lack of artists may have been the result of a lack of role models, since Asian immigrants did not begin to arrive in the United…

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

    Science.gov (United States)

    A previously created Geographic Information Systems model designed to identify regions of West Nile virus (WNV) transmission risk is tested and calibrated in Santa Clara County, California. American Crows that died from WNV infection in 2005 provide the spatial and temporal ground truth. Model param...

  11. California Geriatric Education Center Logic Model: An Evaluation and Communication Tool

    Science.gov (United States)

    Price, Rachel M.; Alkema, Gretchen E.; Frank, Janet C.

    2009-01-01

    A logic model is a communications tool that graphically represents a program's resources, activities, priority target audiences for change, and the anticipated outcomes. This article describes the logic model development process undertaken by the California Geriatric Education Center in spring 2008. The CGEC is one of 48 Geriatric Education…

  12. Ecological niche modelling of Hemipteran insects in Cameroon; the paradox of a vector-borne transmission for Mycobacterium ulcerans, the causative agent of Buruli ulcer.

    Science.gov (United States)

    Carolan, Kevin; Ebong, Solange Meyin A; Garchitorena, Andres; Landier, Jordi; Sanhueza, Daniel; Texier, Gaëtan; Marsollier, Laurent; Gall, Philipe Le; Guégan, Jean-François; Lo Seen, Danny

    2014-10-25

    The mode of transmission of the emerging neglected disease Buruli ulcer is unknown. Several potential transmission pathways have been proposed, such as amoebae, or transmission through food webs. Several lines of evidence have suggested that biting aquatic insects, Naucoridae and Belostomatidae, may act as vectors, however this proposal remains controversial. Herein, based on sampling in Cameroon, we construct an ecological niche model of these insects to describe their spatial distribution. We predict their distribution across West Africa, describe important environmental drivers of their abundance, and examine the correlation between their abundance and Buruli ulcer prevalence in the context of the Bradford-Hill guidelines. We find a significant positive correlation between the abundance of the insects and the prevalence of Buruli ulcer. This correlation changes in space and time, it is significant in one Camerounese study region in (Akonolinga) and not other (Bankim). We discuss notable environmental differences between these regions. We interpret the presence of, and change in, this correlation as evidence (though not proof) that these insects may be locally important in the environmental persistence, or transmission, of Mycobacterium. ulcerans. This is consistent with the idea of M. ulcerans as a pathogen transmitted by multiple modes of infection, the importance of any one pathway changing from region to region, depending on the local environmental conditions.

  13. 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. PMID:24244301

  14. Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber, Tetrastigma hemsleyanum (Vitaceae): insights into Plio-Pleistocene range dynamics of evergreen forest in subtropical China.

    Science.gov (United States)

    Wang, Yi-Han; Jiang, Wei-Mei; Comes, Hans Peter; Hu, Feng Sheng; Qiu, Ying-Xiong; Fu, Cheng-Xin

    2015-04-01

    Warm-temperate evergreen (WTE) forest represents the typical vegetation type of subtropical China, but how its component species responded to past environmental change remains largely unknown. Here, we reconstruct the evolutionary history of Tetrastigma hemsleyanum, an herbaceous climber restricted to the WTE forest. Twenty populations were genotyped using chloroplast DNA sequences and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and ecological niche modeling (ENM) of the species distributions during the Last Glacial Maximum (LGM) and at present. Lineages in Southwest vs Central-South-East China diverged through climate/tectonic-induced vicariance of an ancestral southern range during the early Pliocene. Long-term stability in the Southwest contrasts with latitudinal range shifts in the Central-South-East region during the early-to-mid-Pleistocene. Genetic and ENM data strongly suggest refugial persistence in situ at the LGM. Pre-Quaternary environmental changes appear to have had a persistent influence on the population genetic structure of this subtropical WTE forest species. Our findings suggest relative demographic stability of this biome in China over the last glacial-interglacial cycle, in contrast with palaeobiome reconstructions showing that this forest biome retreated to areas of today's tropical South China during the LGM. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  15. Coexistence of the niche and neutral perspectives in community ecology.

    Science.gov (United States)

    Leibold, Mathew A; McPeek, Mark A

    2006-06-01

    The neutral theory for community structure and biodiversity is dependent on the assumption that species are equivalent to each other in all important ecological respects. We explore what this concept of equivalence means in ecological communities, how such species may arise evolutionarily, and how the possibility of ecological equivalents relates to previous ideas about niche differentiation. We also show that the co-occurrence of ecologically similar or equivalent species is not incompatible with niche theory as has been supposed, because niche relations can sometimes favor coexistence of similar species. We argue that both evolutionary and ecological processes operate to promote the introduction and to sustain the persistence of ecologically similar and in many cases nearly equivalent species embedded in highly structured food webs. Future work should focus on synthesizing niche and neutral perspectives rather than dichotomously debating whether neutral or niche models provide better explanations for community structure and biodiversity.

  16. Ecological Niche Modeling for Filoviruses: A Risk Map for Ebola and Marburg Virus Disease Outbreaks in Uganda.

    Science.gov (United States)

    Nyakarahuka, Luke; Ayebare, Samuel; Mosomtai, Gladys; Kankya, Clovice; Lutwama, Julius; Mwiine, Frank Norbert; Skjerve, Eystein

    2017-09-05

    Uganda has reported eight outbreaks caused by filoviruses between 2000 to 2016, more than any other country in the world. We used species distribution modeling to predict where filovirus outbreaks are likely to occur in Uganda to help in epidemic preparedness and surveillance. The MaxEnt software, a machine learning modeling approach that uses presence-only data was used to establish filovirus - environmental relationships. Presence-only data for filovirus outbreaks were collected from the field and online sources. Environmental covariates from Africlim that have been downscaled to a nominal resolution of 1km x 1km were used. The final model gave the relative probability of the presence of filoviruses in the study area obtained from an average of 100 bootstrap runs. Model evaluation was carried out using Receiver Operating Characteristic (ROC) plots. Maps were created using ArcGIS 10.3 mapping software. We showed that bats as potential reservoirs of filoviruses are distributed all over Uganda. Potential outbreak areas for Ebola and Marburg virus disease were predicted in West, Southwest and Central parts of Uganda, which corresponds to bat distribution and previous filovirus outbreaks areas. Additionally, the models predicted the Eastern Uganda region and other areas that have not reported outbreaks before to be potential outbreak hotspots. Rainfall variables were the most important in influencing model prediction compared to temperature variables. Despite the limitations in the prediction model due to lack of adequate sample records for outbreaks, especially for the Marburg cases, the models provided risk maps to the Uganda surveillance system on filovirus outbreaks. The risk maps will aid in identifying areas to focus the filovirus surveillance for early detection and responses hence curtailing a pandemic. The results from this study also confirm previous findings that suggest that filoviruses are mainly limited by the amount of rainfall received in an area.

  17. Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada.

    Science.gov (United States)

    Starrett, James; Hayashi, Cheryl Y; Derkarabetian, Shahan; Hedin, Marshal

    2018-01-01

    The relative roles of ecological niche conservatism versus niche divergence in promoting montane speciation remains an important topic in biogeography. Here, our aim was to test whether lineage diversification in a species complex of trapdoor spiders corresponds with riverine barriers or with an ecological gradient associated with elevational tiering. Aliatypus janus was sampled from throughout its range, with emphasis on populations in the southern Sierra Nevada Mountains of California. We collected multi-locus genetic data to generate a species tree for A. janus and its close relatives. Coalescent based hypothesis tests were conducted to determine if genetic breaks within A. janus conform to riverine barriers. Ecological niche models (ENM) under current and Last Glacial Maximum (LGM) conditions were generated and hypothesis tests of niche conservatism and divergence were performed. Coalescent analyses reveal deeply divergent genetic lineages within A. janus, likely corresponding to cryptic species. Two primary lineages meet along an elevational gradient on the western slopes of the southern Sierra Nevada Mountains. ENMs under both current and LGM conditions indicate that these groups occupy largely non-overlapping niches. ENM hypothesis testing rejected niche identity between the two groups, and supported a sharp ecological gradient occurring where the groups meet. However, the niche similarity test indicated that the two groups may not inhabit different background niches. The Sierra Nevada Mountains provide a natural laboratory for simultaneously testing ecological niche divergence and conservatism and their role in speciation across a diverse range of taxa. Aliatypus janus represents a species complex with cryptic lineages that may have diverged due to parapatric speciation along an ecological gradient, or been maintained by the evolution of ecological niche differences following allopatric speciation. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Elevation Shift in Abies Mill. (Pinaceae) of Subtropical and Temperate China and Vietnam-Corroborative Evidence from Cytoplasmic DNA and Ecological Niche Modeling.

    Science.gov (United States)

    Shao, Yi-Zhen; Zhang, Xian-Chun; Phan, Loc Ke; Xiang, Qiao-Ping

    2017-01-01

    The "elevational shift" scenario has been proposed as a model to explain the response of cold-adapted organisms to Quaternary climatic fluctuations in Europe and North America. However, the elevational shift model has not been well-explored in eastern Asia, which is more topographically complex than the other Northern Hemisphere biogeographic regions. Here, we evaluated the role of elevational shift in the closely related firs, or Abies Mill., of subtropical and temperate China. These firs are typical alpine trees with sensitivity to climate change. We tested the elevational shift hypothesis in firs of China using phylogeographic methods and ecological niche models. Our phylogeographic analyses comprised mitochondrial and chloroplast polymorphisms surveyed across 479 individuals from 43 populations representing 11 species. M1 of the 11 mitotypes and C1 of the 25 chlorotypes were inferred as the ancestral haplotype, and they had the widest distribution. The results of our phylogeographic survey revealed multiple centers of genetic diversity in distinct geographic regions and no latitudinal trend. Moreover, our results showed range expansions for seven taxa during the last glacial (64.9-18.2 or 32.5-9.1 kya), and this was consistent with the Quaternary fossil record of Abies in China. Taken together, our findings support a historical biogeographic pattern in firs of glacial expansions, probably through corridors at lower elevation, and interglacial fragmentations, through isolation at higher elevation peaks. Therefore, Abies in China probably undergoes elevational shift in response to climate change. Facing the forecasting global warming, the risk of several critically endangered firs was further enhanced as these species would have little escape space in situ to higher altitudes. According to our ENMs, we proposed an ex situ conservation strategy in the southern Hengduan Mountains region of south western China.

  19. Target article with commentaries: developmental niche construction.

    Science.gov (United States)

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

    2013-03-01

    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 discussion between researchers interested in niche construction and those interested in human cognitive development by highlighting some of the related processes. We discuss the transmission of culturally relevant information, how the human mind is a symbol-generating and artefact-devising system, and how these processes are bi-directional, with infants and children both being directed, and directing, their own development. We reflect on these in the light of four approaches: natural pedagogy, activity theory, distributed cognition and situated learning. Throughout, we highlight pertinent examples in non-humans that parallel or further explicate the processes discussed. Finally we offer three future directions; two involving the use of new techniques in the realms of neuroscience and modelling, and the third suggesting exploration of changes in the effects of niche construction across the lifespan. © 2012 Blackwell Publishing Ltd.

  20. 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......, evolutionary biology and CEMs for a better understanding of niche dynamics across space and time....

  1. Re?establishing the pecking order: Niche models reliably predict suitable habitats for the reintroduction of red?billed oxpeckers

    OpenAIRE

    Kalle, Riddhika; Combrink, Leigh; Ramesh, Tharmalingam; Downs, Colleen T.

    2017-01-01

    Abstract Distributions of avian mutualists are affected by changes in biotic interactions and environmental conditions driven directly/indirectly by human actions. The range contraction of red?billed oxpeckers (Buphagus erythrorhynchus) in South Africa is partly a result of the widespread use of acaracides (i.e., mainly cattle dips), toxic to both ticks and oxpeckers. We predicted the habitat suitability of red?billed oxpeckers in South Africa using ensemble models to assist the ongoing reint...

  2. Ecological niche modeling and distribution of Ornithodoros hermsi associated with tick-borne relapsing fever in western North America.

    Science.gov (United States)

    Sage, Kylie M; Johnson, Tammi L; Teglas, Michael B; Nieto, Nathan C; Schwan, Tom G

    2017-10-01

    Tick-borne relapsing fever in western North America is a zoonosis caused by the spirochete bacterium, Borrelia hermsii, which is transmitted by the bite of infected Ornithodoros hermsi ticks. The pathogen is maintained in natural cycles involving small rodent hosts such as chipmunks and tree squirrels, as well as the tick vector. In order for these ticks to establish sustained and viable populations, a narrow set of environmental parameters must exist, primarily moderate temperatures and moderate to high amounts of precipitation. Maximum Entropy Species Distribution Modeling (Maxent) was used to predict the species distribution of O. hermsi and B. hermsii through time and space based on current climatic trends and future projected climate changes. From this modeling process, we found that the projected current distributions of both the tick and spirochete align with known endemic foci for the disease. Further, global climate models predict a shift in the distribution of suitable habitat for the tick vector to higher elevations. Our predictions are useful for targeting surveillance efforts in areas of high risk in western North America, increasing the efficiency and accuracy of public health investigations and vector control efforts.

  3. Ecological niche modeling and distribution of Ornithodoros hermsi associated with tick-borne relapsing fever in western North America.

    Directory of Open Access Journals (Sweden)

    Kylie M Sage

    2017-10-01

    Full Text Available Tick-borne relapsing fever in western North America is a zoonosis caused by the spirochete bacterium, Borrelia hermsii, which is transmitted by the bite of infected Ornithodoros hermsi ticks. The pathogen is maintained in natural cycles involving small rodent hosts such as chipmunks and tree squirrels, as well as the tick vector. In order for these ticks to establish sustained and viable populations, a narrow set of environmental parameters must exist, primarily moderate temperatures and moderate to high amounts of precipitation. Maximum Entropy Species Distribution Modeling (Maxent was used to predict the species distribution of O. hermsi and B. hermsii through time and space based on current climatic trends and future projected climate changes. From this modeling process, we found that the projected current distributions of both the tick and spirochete align with known endemic foci for the disease. Further, global climate models predict a shift in the distribution of suitable habitat for the tick vector to higher elevations. Our predictions are useful for targeting surveillance efforts in areas of high risk in western North America, increasing the efficiency and accuracy of public health investigations and vector control efforts.

  4. Ecological niche modeling and land cover risk areas for rift valley fever vector, culex tritaeniorhynchus giles in Jazan, Saudi Arabia.

    Directory of Open Access Journals (Sweden)

    Mohamed F Sallam

    Full Text Available BACKGROUND: The mosquito, Culex tritaeniorhynchus Giles is a prevalent and confirmed Rift Valley Fever virus (RVFV vector. This vector, in association with Aedimorphus arabiensis (Patton, was responsible for causing the outbreak of 2000 in Jazan Province, Saudi Arabia. METHODOLOGY/PRINCIPAL FINDINGS: Larval occurrence records and a total of 19 bioclimatic and three topographic layers imported from Worldclim Database were used to predict the larval suitable breeding habitats for this vector in Jazan Province using ArcGIS ver.10 and MaxEnt modeling program. Also, a supervised land cover classification from SPOT5 imagery was developed to assess the land cover distribution within the suitable predicted habitats. Eleven bioclimatic and slope attributes were found to be the significant predictors for this larval suitable breeding habitat. Precipitation and temperature were strong predictors of mosquito distribution. Among six land cover classes, the linear regression model (LM indicated wet muddy substrate is significantly associated with high-very high suitable predicted habitats (R(2 = 73.7%, P<0.05. Also, LM indicated that total dissolved salts (TDS was a significant contributor (R(2 = 23.9%, P<0.01 in determining mosquito larval abundance. CONCLUSION/SIGNIFICANCE: This model is a first step in understanding the spatial distribution of Cx. tritaeniorhynchus and consequently the risk of RVFV in Saudi Arabia and to assist in planning effective mosquito surveillance and control programs by public health personnel and researchers.

  5. The importance of niches for the maintenance of species diversity.

    Science.gov (United States)

    Levine, Jonathan M; HilleRisLambers, Janneke

    2009-09-10

    Ecological communities characteristically contain a wide diversity of species with important functional, economic and aesthetic value. Ecologists have long questioned how this diversity is maintained. Classic theory shows that stable coexistence requires competitors to differ in their niches; this has motivated numerous investigations of ecological differences presumed to maintain diversity. That niche differences are key to coexistence, however, has recently been challenged by the neutral theory of biodiversity, which explains coexistence with the equivalence of competitors. The ensuing controversy has motivated calls for a better understanding of the collective importance of niche differences for the diversity observed in ecological communities. Here we integrate theory and experimentation to show that niche differences collectively stabilize the dynamics of experimental communities of serpentine annual plants. We used field-parameterized population models to develop a null expectation for community dynamics without the stabilizing effects of niche differences. The population growth rates predicted by this null model varied by several orders of magnitude between species, which is sufficient for rapid competitive exclusion. Moreover, after two generations of community change in the field, Shannon diversity was over 50 per cent greater in communities stabilized by niche differences relative to those exhibiting dynamics predicted by the null model. Finally, in an experiment manipulating species' relative abundances, population growth rates increased when species became rare--the demographic signature of niche differences. Our work thus provides strong evidence that species differences have a critical role in stabilizing species diversity.

  6. Ecological niche modeling and land cover risk areas for rift valley fever vector, culex tritaeniorhynchus giles in Jazan, Saudi Arabia.

    Science.gov (United States)

    Sallam, Mohamed F; Al Ahmed, Azzam M; Abdel-Dayem, Mahmoud S; Abdullah, Mohamed A R

    2013-01-01

    The mosquito, Culex tritaeniorhynchus Giles is a prevalent and confirmed Rift Valley Fever virus (RVFV) vector. This vector, in association with Aedimorphus arabiensis (Patton), was responsible for causing the outbreak of 2000 in Jazan Province, Saudi Arabia. Larval occurrence records and a total of 19 bioclimatic and three topographic layers imported from Worldclim Database were used to predict the larval suitable breeding habitats for this vector in Jazan Province using ArcGIS ver.10 and MaxEnt modeling program. Also, a supervised land cover classification from SPOT5 imagery was developed to assess the land cover distribution within the suitable predicted habitats. Eleven bioclimatic and slope attributes were found to be the significant predictors for this larval suitable breeding habitat. Precipitation and temperature were strong predictors of mosquito distribution. Among six land cover classes, the linear regression model (LM) indicated wet muddy substrate is significantly associated with high-very high suitable predicted habitats (R(2) = 73.7%, Pplanning effective mosquito surveillance and control programs by public health personnel and researchers.

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

    OpenAIRE

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

    2011-01-01

    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 earth...

  8. A seamless, high-resolution digital elevation model (DEM) of the north-central California coast

    Science.gov (United States)

    Foxgrover, Amy C.; Barnard, Patrick L.

    2012-01-01

    A seamless, 2-meter resolution digital elevation model (DEM) of the north-central California coast has been created from the most recent high-resolution bathymetric and topographic datasets available. The DEM extends approximately 150 kilometers along the California coastline, from Half Moon Bay north to Bodega Head. Coverage extends inland to an elevation of +20 meters and offshore to at least the 3 nautical mile limit of state waters. This report describes the procedures of DEM construction, details the input data sources, and provides the DEM for download in both ESRI Arc ASCII and GeoTIFF file formats with accompanying metadata.

  9. A GSSHA Model of the Perris Basin of the San Jacinto River Watershed, Riverside County, California

    Science.gov (United States)

    2007-06-01

    ERDC/CHL CHETN-III-76 June 2007 A GSSHA Model of the Perris Basin of the San Jacinto River Watershed, Riverside County, California by Moira T...POINTS OF CONTACT: For additional information, contact Moira Fong, U.S. Army Engineer Research and Development Center, Information Technology Laboratory

  10. Development and Pilot Application of the California Urban and Biodiversity Analysis (CURBA) Model

    OpenAIRE

    Landis, John D.; Monzon, Juan Pablo; Reilly, Michael; Cogan, Chris

    1998-01-01

    The California Urban and Biodiversity Analysis (CURBA) model was developed as a tool to help urban planners to evaluate the possible effects of alternative urban growth patterns and policies on biodiversity and natural habitat quality. CURBA can help direct urban growth while promoting environmental and ecological quality.

  11. Growth models for ponderosa pine: I. Yield of unthinned plantations in northern California.

    Science.gov (United States)

    William W. Oliver; Robert F. Powers

    1978-01-01

    Yields for high-survival, unthinned ponderosa pine (Pinus ponderosa Laws.) plantations in northern California are estimated. Stems of 367 trees in 12 plantations were analyzed to produce a growth model simulating stand yields. Diameter, basal area, and net cubic volume yields by Site Indices50 40 through 120 are tabulated for...

  12. Predicting the distribution and ecological niche of unexploited snow crab (Chionoecetes opilio) populations in Alaskan waters: a first open-access ensemble model.

    Science.gov (United States)

    Hardy, Sarah M; Lindgren, Michael; Konakanchi, Hanumantharao; Huettmann, Falk

    2011-10-01

    Populations of the snow crab (Chionoecetes opilio) are widely distributed on high-latitude continental shelves of the North Pacific and North Atlantic, and represent a valuable resource in both the United States and Canada. In US waters, snow crabs are found throughout the Arctic and sub-Arctic seas surrounding Alaska, north of the Aleutian Islands, yet commercial harvest currently focuses on the more southerly population in the Bering Sea. Population dynamics are well-monitored in exploited areas, but few data exist for populations further north where climate trends in the Arctic appear to be affecting species' distributions and community structure on multiple trophic levels. Moreover, increased shipping traffic, as well as fisheries and petroleum resource development, may add additional pressures in northern portions of the range as seasonal ice cover continues to decline. In the face of these pressures, we examined the ecological niche and population distribution of snow crabs in Alaskan waters using a GIS-based spatial modeling approach. We present the first quantitative open-access model predictions of snow-crab distribution, abundance, and biomass in the Chukchi and Beaufort Seas. Multi-variate analysis of environmental drivers of species' distribution and community structure commonly rely on multiple linear regression methods. The spatial modeling approach employed here improves upon linear regression methods in allowing for exploration of nonlinear relationships and interactions between variables. Three machine-learning algorithms were used to evaluate relationships between snow-crab distribution and environmental parameters, including TreeNet, Random Forests, and MARS. An ensemble model was then generated by combining output from these three models to generate consensus predictions for presence-absence, abundance, and biomass of snow crabs. Each algorithm identified a suite of variables most important in predicting snow-crab distribution, including

  13. 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.

  14. Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (hypericaceae).

    Science.gov (United States)

    Meseguer, Andrea S; Lobo, Jorge M; Ree, Richard; Beerling, David J; Sanmartín, Isabel

    2015-03-01

    In disciplines such as macroevolution that are not amenable to experimentation, scientists usually rely on current observations to test hypotheses about historical events, assuming that "the present is the key to the past." Biogeographers, for example, used this assumption to reconstruct ancestral ranges from the distribution of extant species. Yet, under scenarios of high extinction rates, the biodiversity we observe today might not be representative of the historical diversity and this could result in incorrect biogeographic reconstructions. Here, we introduce a new approach to incorporate into biogeographic inference the temporal, spatial, and environmental information provided by the fossil record, as a direct evidence of the extinct biodiversity fraction. First, inferences of ancestral ranges for those nodes in the phylogeny calibrated with the fossil record are constrained to include the geographic distribution of the fossil. Second, we use fossil distribution and past climate data to reconstruct the climatic preferences and potential distribution of ancestral lineages over time, and use this information to build a biogeographic model that takes into account "ecological connectivity" through time. To show the power of this approach, we reconstruct the biogeographic history of the large angiosperm genus Hypericum, which has a fossil record extending back to the Early Cenozoic. Unlike previous reconstructions based on extant species distributions, our results reveal that Hypericum stem lineages were already distributed in the Holarctic before diversification of its crown-group, and that the geographic distribution of the genus has been relatively stable throughout the climatic oscillations of the Cenozoic. Geographical movement was mediated by the existence of climatic corridors, like Beringia, whereas the equatorial tropical belt acted as a climatic barrier, preventing Hypericum lineages to reach the southern temperate regions. Our study shows that an

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

    Science.gov (United States)

    Dai, Chuanyin; Zhao, Na; Wang, Wenjuan; Lin, Congtian; Gao, Bin; Yang, Xiaojun; Zhang, Zhengwang; Lei, Fumin

    2011-01-01

    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.

  16. Profound Climatic Effects on Two East Asian Black-Throated Tits (Ave: Aegithalidae), Revealed by Ecological Niche Models and Phylogeographic Analysis

    Science.gov (United States)

    Wang, Wenjuan; Lin, Congtian; Gao, Bin; Yang, Xiaojun; Zhang, Zhengwang; Lei, Fumin

    2011-01-01

    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. PMID:22195047

  17. Aryl Hydrocarbon Receptor Deficiency in an Exon 3 Deletion Mouse Model Promotes Hematopoietic Stem Cell Proliferation and Impacts Endosteal Niche Cells

    Directory of Open Access Journals (Sweden)

    Zeenath Unnisa

    2016-01-01

    Full Text Available The aryl hydrocarbon receptor (AHR is a ligand-activated transcription factor belonging to the Per-Arnt-Sim (PAS family of proteins. The AHR is involved in hematopoietic stem cell (HSC functions including self-renewal, proliferation, quiescence, and differentiation. We hypothesize that AHR impacts HSC functions by influencing genes that have roles in HSC maintenance and function and that this may occur through regulation of bone marrow (BM niche cells. We examined BM and niche cells harvested from 8-week-old AHR null-allele (KO mice in which exon 3 was deleted in the Ahr gene and compared these data to cells from B6 control mice; young and old (10 months animals were also compared. We report changes in HSCs and peripheral blood cells in mice lacking AHR. Serial transplantation assays revealed a significant increase in long term HSCs. There was a significant increase in mesenchymal stem cells constituting the endosteal BM niche. Gene expression analyses of HSCs revealed an increase in expression of genes involved in proliferation and maintenance of quiescence. Our studies infer that loss of AHR results in increased proliferation and self-renewal of long term HSCs, in part, by influencing the microenvironment in the niche regulating the balance between quiescence and proliferation in HSCs.

  18. Niche entrepreneurs in urban systems integration : On the role of individuals in niche formation

    NARCIS (Netherlands)

    Pesch, U.; Vernay, A.L.; van Bueren, E.M.; Pandis Iveroth, S

    2017-01-01

    In many sustainable urban innovation projects, the efforts, endurance and enthusiasm of individuals at key positions are considered a crucial factor for success. This article studies the role of individual agency in sociotechnical niches by using Kingdon’s agenda-setting model. Although strategic

  19. Modeling when, where, and how to manage a forest epidemic, motivated by sudden oak death in California

    Science.gov (United States)

    Nik J. Cunniffe; Richard C. Cobb; Ross K. Meentemeyer; David M. Rizzo; Christopher A. Gilligan

    2016-01-01

    Sudden oak death, caused by Phytophthora ramorum, has killed millions of oak and tanoak in California since its first detection in 1995. Despite some localized small-scale management, there has been no large-scale attempt to slow the spread of the pathogen in California. Here we use a stochastic spatially-explicit model parameterized using data on...

  20. Improved Coefficient Calculator for the California Energy Commission 6 Parameter Photovoltaic Module Model

    Energy Technology Data Exchange (ETDEWEB)

    Dobos, A. P.

    2012-05-01

    This paper describes an improved algorithm for calculating the six parameters required by the California Energy Commission (CEC) photovoltaic (PV) Calculator module model. Rebate applications in California require results from the CEC PV model, and thus depend on an up-to-date database of module characteristics. Currently, adding new modules to the database requires calculating operational coefficients using a general purpose equation solver - a cumbersome process for the 300+ modules added on average every month. The combination of empirical regressions and heuristic methods presented herein achieve automated convergence for 99.87% of the 5487 modules in the CEC database and greatly enhance the accuracy and efficiency by which new modules can be characterized and approved for use. The added robustness also permits general purpose use of the CEC/6 parameter module model by modelers and system analysts when standard module specifications are known, even if the module does not exist in a preprocessed database.

  1. Cellular population dynamics control the robustness of the stem cell niche

    Directory of Open Access Journals (Sweden)

    Adam L. MacLean

    2015-11-01

    Full Text Available Within populations of cells, fate decisions are controlled by an indeterminate combination of cell-intrinsic and cell-extrinsic factors. In the case of stem cells, the stem cell niche is believed to maintain ‘stemness’ through communication and interactions between the stem cells and one or more other cell-types that contribute to the niche conditions. To investigate the robustness of cell fate decisions in the stem cell hierarchy and the role that the niche plays, we introduce simple mathematical models of stem and progenitor cells, their progeny and their interplay in the niche. These models capture the fundamental processes of proliferation and differentiation and allow us to consider alternative possibilities regarding how niche-mediated signalling feedback regulates the niche dynamics. Generalised stability analysis of these stem cell niche systems enables us to describe the stability properties of each model. We find that although the number of feasible states depends on the model, their probabilities of stability in general do not: stem cell–niche models are stable across a wide range of parameters. We demonstrate that niche-mediated feedback increases the number of stable steady states, and show how distinct cell states have distinct branching characteristics. The ecological feedback and interactions mediated by the stem cell niche thus lend (surprisingly high levels of robustness to the stem and progenitor cell population dynamics. Furthermore, cell–cell interactions are sufficient for populations of stem cells and their progeny to achieve stability and maintain homeostasis. We show that the robustness of the niche – and hence of the stem cell pool in the niche – depends only weakly, if at all, on the complexity of the niche make-up: simple as well as complicated niche systems are capable of supporting robust and stable stem cell dynamics.

  2. Niche divergence and lineage diversification among closely related Sistrurus rattlesnakes.

    Science.gov (United States)

    Wooten, J A; Gibbs, H L

    2012-02-01

    Comparing niche divergence among closely related taxa can yield important insights into the ecological distinctiveness of genetically similar forms, and identify the processes that are responsible for diversification in such organisms. Here, we apply newly developed techniques for analysing niche divergence to assess how ecologically distinct a group of closely related rattlesnakes (Sistrurus sp.) are and to explore the role that niche divergence may have played in their diversification. We find that all taxa even the most recently evolved subspecies (approximately 100,000 years old) are now ecologically distinct, implying a role for ecology in the diversification process. Statistical analysis based on comparisons with null models show that niche divergence between forms is more common than niche conservation. Finally, there is nonlinear relationship between phylogenetic and niche divergence in this group whereby niche divergence develops more rapidly between recently diverged subspecies than more distantly related forms. Overall, our results argue that ecology may play an important role in the diversification process in these snakes. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  3. Ecological niche of plant pathogens

    OpenAIRE

    Ecaterina Fodor

    2011-01-01

    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 ni...

  4. Modeling the yield potential of dryland canola under current and future climates in California

    Science.gov (United States)

    George, N.; Kaffka, S.; Beeck, C.; Bucaram, S.; Zhang, J.

    2012-12-01

    Models predict that the climate of California will become hotter, drier and more variable under future climate change scenarios. This will lead to both increased irrigation demand and reduced irrigation water availability. In addition, it is predicted that most common Californian crops will suffer a concomitant decline in productivity. To remain productive and economically viable, future agricultural systems will need to have greater water use efficiency, tolerance of high temperatures, and tolerance of more erratic temperature and rainfall patterns. Canola (Brassica napus) is the third most important oilseed globally, supporting large and well-established agricultural industries in Canada, Europe and Australia. It is an agronomically useful and economically valuable crop, with multiple end markets, that can be grown in California as a dryland winter rotation with little to no irrigation demand. This gives canola great potential as a new crop for Californian farmers both now and as the climate changes. Given practical and financial limitations it is not always possible to immediately or widely evaluate a crop in a new region. Crop production models are therefore valuable tools for assessing the potential of new crops, better targeting further field research, and refining research questions. APSIM is a modular modeling framework developed by the Agricultural Production Systems Research Unit in Australia, it combines biophysical and management modules to simulate cropping systems. This study was undertaken to examine the yield potential of Australian canola varieties having different water requirements and maturity classes in California using APSIM. The objective of the work was to identify the agricultural regions of California most ideally suited to the production of Australian cultivars of canola and to simulate the production of canola in these regions to estimate yield-potential. This will establish whether the introduction and in-field evaluation of better

  5. 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.

    2017-01-01

    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.

  6. 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

  7. An open source hydroeconomic model for California's water supply system: PyVIN

    Science.gov (United States)

    Dogan, M. S.; White, E.; Herman, J. D.; Hart, Q.; Merz, J.; Medellin-Azuara, J.; Lund, J. R.

    2016-12-01

    Models help operators and decision makers explore and compare different management and policy alternatives, better allocate scarce resources, and predict the future behavior of existing or proposed water systems. Hydroeconomic models are useful tools to increase benefits or decrease costs of managing water. Bringing hydrology and economics together, these models provide a framework for different disciplines that share similar objectives. This work proposes a new model to evaluate operation and adaptation strategies under existing and future hydrologic conditions for California's interconnected water system. This model combines the network structure of CALVIN, a statewide optimization model for California's water infrastructure, along with an open source solver written in the Python programming language. With the flexibilities of the model, reservoir operations, including water supply and hydropower, groundwater pumping, and the Delta water operations and requirements can now be better represented. Given time series of hydrologic inputs to the model, typical outputs include urban, agricultural and wildlife refuge water deliveries and shortage costs, conjunctive use of surface and groundwater systems, and insights into policy and management decisions, such as capacity expansion and groundwater management policies. Water market operations also represented in the model, allocating water from lower-valued users to higher-valued users. PyVIN serves as a cross-platform, extensible model to evaluate systemwide water operations. PyVIN separates data from the model structure, enabling model to be easily applied to other parts of the world where water is a scarce resource.

  8. Management of California Oak Woodlands: Uncertainties and Modeling

    Science.gov (United States)

    Jay E. Noel; Richard P. Thompson

    1995-01-01

    A mathematical policy model of oak woodlands is presented. The model illustrates the policy uncertainties that exist in the management of oak woodlands. These uncertainties include: (1) selection of a policy criterion function, (2) woodland dynamics, (3) initial and final state of the woodland stock. The paper provides a review of each of the uncertainty issues. The...

  9. Stem cell dynamics in the hair follicle niche

    Science.gov (United States)

    Rompolas, Panteleimon; Greco, Valentina

    2014-01-01

    Hair follicles are skin appendages of the mammalian skin that have the ability to periodically and stereotypically regenerate in order to continuously produce new hair over our lifetime. The ability of the hair follicle to regenerate is due to the presence of stem cells that along with other cell populations and non-cellular components, including molecular signals and extracellular material, make up a niche microenvironment. Mounting evidence suggests that the niche is critical for regulating stem cell behavior and thus the process of regeneration. Here we review the literature concerning past and current studies that have utilized mouse genetic models, combined with other approaches to dissect the molecular and cellular composition of the hair follicle niche. We also discuss our current understanding of how stem cells operate within the niche during the process of tissue regeneration and the factors that regulate their behavior. PMID:24361866

  10. 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...

  11. 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...

  12. Dislocation model for aseismic crustal deformation at Hollister, California

    Science.gov (United States)

    Matsuura, Mitsuhiro; Jackson, David D.; Cheng, Abe

    1986-01-01

    A model of crustal deformation during the interseismic phase is developed and applied (using the improved Bayesian inversion algorithm described by Jackson and Matsu'ura, 1985) to trilateration data for the USGS Hollister (CA) network. In the model, rigid blocks in motion relative to each other experience friction only in a brittle upper zone, while their ductile lower zones slide freely; the Hollister model comprises five blocks and nine rectangular fault patches. The data and results are presented in tables, graphs, and maps and characterized in detail. The model predicts steady block motion on time scales between 10 yr and 1 Myr, with net motion across the San Andreas/Calaveras fault system 38 + or - 3 mm/yr and brittle/ductile transition depths ranging from 0.4 to 11 km. Two San Andreas segments with higher probabilities of moderate-to-large earthquakes are identified.

  13. Analysis of Eddy Resolving Model of the California Current System

    National Research Council Canada - National Science Library

    Cipriano, Nicholas

    1998-01-01

    A high-resolution, multi-level, primitive equation ocean model is used to investigate the combined role of seasonal wind forcing, thermohaline gradients, and coastline irregularities on the formation...

  14. 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...

  15. Metagenomics and the niche concept.

    Science.gov (United States)

    Marco, Diana

    2008-08-01

    The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.

  16. 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

  17. Mammalian niche conservation through deep time.

    Science.gov (United States)

    DeSantis, Larisa R G; Beavins Tracy, Rachel A; Koontz, Cassandra S; Roseberry, John C; Velasco, Matthew C

    2012-01-01

    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 terminal Pleistocene

  18. 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,...

  19. MODFLOW2000_FMP1_1 model used to simulate the groundwater flow of the Central Valley Aquifer, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A three-dimensional groundwater flow model (MODFLOW200-FMP1_1) of the Central Valley in California was developed to aid water managers in understanding how water...

  20. Chemical transport model simulations of organic aerosol in southern California: model evaluation and gasoline and diesel source contributions

    Science.gov (United States)

    Jathar, Shantanu H.; Woody, Matthew; Pye, Havala O. T.; Baker, Kirk R.; Robinson, Allen L.

    2017-03-01

    Gasoline- and diesel-fueled engines are ubiquitous sources of air pollution in urban environments. They emit both primary particulate matter and precursor gases that react to form secondary particulate matter in the atmosphere. In this work, we updated the organic aerosol module and organic emissions inventory of a three-dimensional chemical transport model, the Community Multiscale Air Quality Model (CMAQ), using recent, experimentally derived inputs and parameterizations for mobile sources. The updated model included a revised volatile organic compound (VOC) speciation for mobile sources and secondary organic aerosol (SOA) formation from unspeciated intermediate volatility organic compounds (IVOCs). The updated model was used to simulate air quality in southern California during May and June 2010, when the California Research at the Nexus of Air Quality and Climate Change (CalNex) study was conducted. Compared to the Traditional version of CMAQ, which is commonly used for regulatory applications, the updated model did not significantly alter the predicted organic aerosol (OA) mass concentrations but did substantially improve predictions of OA sources and composition (e.g., POA-SOA split), as well as ambient IVOC concentrations. The updated model, despite substantial differences in emissions and chemistry, performed similar to a recently released research version of CMAQ (Woody et al., 2016) that did not include the updated VOC and IVOC emissions and SOA data. Mobile sources were predicted to contribute 30-40 % of the OA in southern California (half of which was SOA), making mobile sources the single largest source contributor to OA in southern California. The remainder of the OA was attributed to non-mobile anthropogenic sources (e.g., cooking, biomass burning) with biogenic sources contributing to less than 5 % to the total OA. Gasoline sources were predicted to contribute about 13 times more OA than diesel sources; this difference was driven by differences in

  1. 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.

  2. Viscoelastic coupling model of the San Andreas fault along the big bend, southern California

    Science.gov (United States)

    Savage, J.C.; Lisowski, M.

    1997-01-01

    The big bend segment of the San Andreas fault is the 300-km-long segment in southern California that strikes about N65??W, roughly 25?? counterclockwise from the local tangent to the small circle about the Pacific-North America pole of rotation. The broad distribution of deformation of trilateration networks along this segment implies a locking depth of at least 25 km as interpreted by the conventional model of strain accumulation (continuous slip on the fault below the locking depth at the rate of relative plate motion), whereas the observed seismicity and laboratory data on fault strength suggest that the locking depth should be no greater than 10 to 15 km. The discrepancy is explained by the viscoelastic coupling model which accounts for the viscoelastic response of the lower crust. Thus the broad distribution of deformation observed across the big bend segment can be largely associated with the San Andreas fault itself, not subsidiary faults distributed throughout the region. The Working Group on California Earthquake Probabilities [1995] in using geodetic data to estimate the seismic risk in southern California has assumed that strain accumulated off the San Andreas fault is released by earthquakes located off the San Andreas fault. Thus they count the San Andreas contribution to total seismic moment accumulation more than once, leading to an overestimate of the seismicity for magnitude 6 and greater earthquakes in their Type C zones.

  3. Dissipation of the Herbicide Benzobicyclon Hydrolysate in a Model California Rice Field Soil.

    Science.gov (United States)

    Williams, Katryn L; Gladfelder, Joshua J; Quigley, Lindsay L; Ball, David B; Tjeerdema, Ronald S

    2017-10-25

    The herbicide benzobicyclon (BZB; 3-(2-chloro-4-(methylsulfonyl)benzoyl)-2-phenylthiobicyclo[3.2.1]oct-2-en-4-one) has recently been approved for use on California rice fields by the United States Environmental Protection Agency (U.S. EPA). Hydrolysis of BZB rapidly forms the active compound, benzobicyclon hydrolysate (BH), whose fate is currently not well understood. A model California rice soil was used to determine BH soil dissipation. The pKa and aqueous solubility were also determined, as experimental values are not currently available. Sorption data indicate BH does not bind tightly, or irreversibly, with this soil. Flooding resulted in decreased BH loss, indicating anaerobic microbes are less likely to transform BH compared to aerobic microorganisms. Temperature increased dissipation, while autoclaving decreased BH loss. Overall, dissipation was slow regardless of treatment. Further investigation is needed to elucidate the exact routes of loss in soil, though BH is expected to dissipate slowly in flooded rice field soil.

  4. How does pollen versus seed dispersal affect niche evolution?

    Science.gov (United States)

    Aguilée, Robin; Shaw, Frank H; Rousset, François; Shaw, Ruth G; Ronce, Ophélie

    2013-03-01

    In heterogeneous landscapes, the genetic and demographic consequences of dispersal influence the evolution of niche width. Unless pollen is limiting, pollen dispersal does not contribute directly to population growth. However, by disrupting local adaptation, it indirectly affects population dynamics. We compare the effect of pollen versus seed dispersal on the evolution of niche width in heterogeneous habitats, explicitly considering the feedback between maladaptation and demography. We consider two scenarios: the secondary contact of two subpopulations, in distinct, formerly isolated habitats, and the colonization of an empty habitat with dispersal between the new and ancestral habitat. With an analytical model, we identify critical levels of genetic variance leading to niche contraction (secondary contact scenario), or expansion (new habitat scenario). We confront these predictions with simulations where the genetic variance freely evolves. Niche contraction occurs when habitats are very different. It is faster as total gene flow increases or as pollen predominates in overall gene flow. Niche expansion occurs when habitat heterogeneity is not too high. Seed dispersal accelerates it, whereas pollen dispersal tends to retard it. In both scenarios very high seed dispersal leads to extinction. Overall, our results predict a wider niche for species dispersing seeds more than pollen. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  5. Disjunct populations of European vascular plant species keep the same climatic niches

    DEFF Research Database (Denmark)

    Wasof, Safaa; Lenoir, Jonathan; Aarrestad, Per Arild

    2015-01-01

    Aim: Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been...... disjunct populations and 358 species having either a contiguous or a patchy distribution with distant populations. First, we used species distribution modelling to test for a region effect on each species' climatic niche. Second, we quantified niche overlap and shifts in niche width (i.e. ecological...... between populations that are separated between the Alps and Fennoscandia and have probably been so for 10,000-15,000 years. Therefore, the basic assumption of species distribution models that a species' climatic niche is constant in space and time - at least on time scales 104 years or less - seems...

  6. 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

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

    Science.gov (United States)

    Barney, Jacob N; DiTomaso, Joseph M

    2011-03-09

    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 the climate

  8. 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

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

    Directory of Open Access Journals (Sweden)

    Anna J Studwell

    Full Text Available 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

  10. 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

  11. Crowdfunding niches? : exploring the potential of crowdfunding for financing renewable energy niches in the Netherlands

    OpenAIRE

    Vasileiadou, E Eleftheria; Huijben, JCCM Boukje; Raven, RPJM Rob

    2014-01-01

    TThere is a huge gap between demand and supply of finance for energy transitions, and the financial and economic crisis have had a negative impact in the already meagre funds for transforming the energy system towards renewable resources. In this paper we explore whether crowdfunding can provide an adequate business model for the creation, nurturing and upscaling of renewable energy niches. We empirically investigate crowdfunding initiatives and platforms linked to renewable electricity proje...

  12. 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

  13. 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

  14. Similar but not equivalent: ecological niche comparison across closely-related Mexican white pines

    OpenAIRE

    Aguirre-Gutiérrez, J.; Serna-Chavez, H.M.; Villalobos-Arambula, A.R.; Pérez de la Rosa, J.A.; Raes, N.

    2015-01-01

    Aim In the face of global environmental change, identifying the factors that shape the ecological niches of species and understanding the mechanisms behind them can help to draft effective conservation plans. The differences in the ecological factors that shape species distributions may then help to highlight differences between closely related taxa. We investigate the applicability of ecological niche modelling and the comparison of species distributions in ecological niche space to detect a...

  15. 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.

  16. Competition theory, evolution, and the concept of an ecological niche.

    Science.gov (United States)

    Alley, T R

    1982-01-01

    This article examines some of the main tenets of competition theory in light of the theory of evolution and the concept of an ecological niche. The principle of competitive exclusion and the related assumption that communities exist at competitive equilibrium - fundamental parts of many competition theories and models - may be violated if non-equilibrium conditions exist in natural communities or are incorporated into competition models. Furthermore, these two basic tenets of competition theory are not compatible with the theory of evolution. Variation in ecologically significant environmental factors and non-equilibrium in population numbers should occur in most natural communities, and such changes have important effects on community relations, niche overlap, and the evolution of ecosystems. Ecologists should view competition as a process occurring within a complex dynamic system, and should be wary of theoretical positions built upon simple laboratory experiments or simplistic mathematical models. In considering the relationship between niche overlap and competition, niche overlap should not be taken as a sufficient condition for competition; many factors may prevent or diminish competition between population with similar resource utilization patterns. The typically opposing forces of intraspecific and interspecific competition need to be simultaneously considered, for it is the balance between them that in large part determines niche boundaries.

  17. Fault slip rates from three-dimensional models of the Los Angeles metropolitan area, California

    Science.gov (United States)

    Cooke, Michele L.; Marshall, Scott T.

    2006-11-01

    We present results from the first mechanical model of active tectonics in the Los Angeles region to use non-planar, geologically representative fault surfaces compiled by the Southern California Earthquake Center Community Fault Model. The fault slip rates from our three-dimensional model match well the available geologic slip rates. Discrepancies in reverse slip along the Upper Elysian Park fault and strike-slip along the Raymond fault may reflect imprecise knowledge of local fault geometry. Discrepancy in the average dip slip rate along the Palos Verdes fault reveals variations in dip slip along that surface; model predictions at the location of the geological investigation have good match to geologic data. The validated model is used to estimate dip and strike slip rates for 26 active faults in the Los Angeles metropolitan region, many of which are otherwise unconstrained by geologic evidence.

  18. Validating high-resolution California coastal flood modeling with Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR)

    Science.gov (United States)

    O'Neill, A.

    2015-12-01

    The Coastal Storm Modeling System (CoSMoS) is a numerical modeling scheme used to predict coastal flooding due to sea level rise and storms influenced by climate change, currently in use in central California and in development for Southern California (Pt. Conception to the Mexican border). Using a framework of circulation, wave, analytical, and Bayesian models at different geographic scales, high-resolution results are translated as relevant hazards projections at the local scale that include flooding, wave heights, coastal erosion, shoreline change, and cliff failures. Ready access to accurate, high-resolution coastal flooding data is critical for further validation and refinement of CoSMoS and improved coastal hazard projections. High-resolution Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) provides an exceptional data source as appropriately-timed flights during extreme tides or storms provide a geographically-extensive method for determining areas of inundation and flooding extent along expanses of complex and varying coastline. Landward flood extents are numerically identified via edge-detection in imagery from single flights, and can also be ascertained via change detection using additional flights and imagery collected during average wave/tide conditions. The extracted flooding positions are compared against CoSMoS results for similar tide, water level, and storm-intensity conditions, allowing for robust testing and validation of CoSMoS and providing essential feedback for supporting regional and local model improvement.

  19. 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.

  20. Estimation and application of a growth and yield model for uneven-aged mixed conifer stands in California.

    Science.gov (United States)

    Jingjing Liang; J. Buongiorno; R.A. Monserud

    2005-01-01

    A growth model for uneven-aged mixed-conifer stands in California was developed with data from 205 permanent plots. The model predicts the number of softwood and hardwood trees in nineteen diameter classes, based on equations for diameter growth rates, mortality arid recruitment. The model gave unbiased predictions of the expected number of trees by diameter class and...

  1. A mouse model of acrodermatitis enteropathica: loss of intestine zinc transporter ZIP4 (Slc39a4 disrupts the stem cell niche and intestine integrity.

    Directory of Open Access Journals (Sweden)

    Jim Geiser

    Full Text Available Mutations in the human Zip4 gene cause acrodermatitis enteropathica, a rare, pseudo-dominant, lethal genetic disorder. We created a tamoxifen-inducible, enterocyte-specific knockout of this gene in mice which mimics this human disorder. We found that the enterocyte Zip4 gene in mice is essential throughout life, and loss-of-function of this gene rapidly leads to wasting and death unless mice are nursed or provided excess dietary zinc. An initial effect of the knockout was the reprogramming of Paneth cells, which contribute to the intestinal stem cell niche in the crypts. Labile zinc in Paneth cells was lost, followed by diminished Sox9 (sex determining region Y-box 9 and lysozyme expression, and accumulation of mucin, which is normally found in goblet cells. This was accompanied by dysplasia of the intestinal crypts and significantly diminished small intestine cell division, and attenuated mTOR1 activity in villus enterocytes, indicative of increased catabolic metabolism, and diminished protein synthesis. This was followed by disorganization of the absorptive epithelium. Elemental analyses of small intestine, liver, and pancreas from Zip4-intestine knockout mice revealed that total zinc was dramatically and rapidly decreased in these organs whereas iron, manganese, and copper slowly accumulated to high levels in the liver as the disease progressed. These studies strongly suggest that wasting and lethality in acrodermatitis enteropathica patients reflects the loss-of-function of the intestine zinc transporter ZIP4, which leads to abnormal Paneth cell gene expression, disruption of the intestinal stem cell niche, and diminished function of the intestinal mucosa. These changes, in turn, cause a switch from anabolic to catabolic metabolism and altered homeostasis of several essential metals, which, if untreated by excess dietary zinc, leads to dramatic weight loss and death.

  2. Analyzing carbon dioxide and methane emissions in California using airborne measurements and model simulations

    Science.gov (United States)

    Johnson, M. S.; Yates, E. L.; Iraci, L. T.; Jeong, S.; Fischer, M. L.

    2013-12-01

    Greenhouse gas (GHG) concentrations have increased over the past decades and are linked to global temperature increases and climate change. These changes in climate have been suggested to have varying effects, and uncertain consequences, on agriculture, water supply, weather, sea-level rise, the economy, and energy. To counteract the trend of increasing atmospheric concentrations of GHGs, the state of California has passed the California Global Warming Act of 2006 (AB-32). This requires that by the year 2020, GHG (e.g., carbon dioxide (CO2) and methane (CH4)) emissions will be reduced to 1990 levels. To quantify GHG fluxes, emission inventories are routinely compiled for the State of California (e.g., CH4 emissions from the California Greenhouse Gas Emissions Measurement (CALGEM) Project). The major sources of CO2 and CH4 in the state of California are: transportation, electricity production, oil and gas extraction, cement plants, agriculture, landfills/waste, livestock, and wetlands. However, uncertainties remain in these emission inventories because many factors contributing to these processes are poorly quantified. To alleviate these uncertainties, a synergistic approach of applying air-borne measurements and chemical transport modeling (CTM) efforts to provide a method of quantifying local and regional GHG emissions will be performed during this study. Additionally, in order to further understand the temporal and spatial distributions of GHG fluxes in California and the impact these species have on regional climate, CTM simulations of daily variations and seasonality of total column CO2 and CH4 will be analyzed. To assess the magnitude and spatial variation of GHG emissions and to identify local 'hot spots', airborne measurements of CH4 and CO2 were made by the Alpha Jet Atmospheric eXperiment (AJAX) over the San Francisco Bay Area (SFBA) and San Joaquin Valley (SJV) in January and February 2013 during the Discover-AQ-CA study. High mixing ratios of GHGs were

  3. Including irrigation in niche modelling of the invasive wasp Vespula germanica (Fabricius) improves model fit to predict potential for further spread.

    Science.gov (United States)

    de Villiers, Marelize; Kriticos, Darren J; Veldtman, Ruan

    2017-01-01

    The European wasp, Vespula germanica (Fabricius) (Hymenoptera: Vespidae), is of Palaearctic origin, being native to Europe, northern Africa and Asia, and introduced into North America, Chile, Argentina, Iceland, Ascension Island, South Africa, Australia and New Zealand. Due to its polyphagous nature and scavenging behaviour, V. germanica threatens agriculture and silviculture, and negatively affects biodiversity, while its aggressive nature and venomous sting pose a health risk to humans. In areas with warmer winters and longer summers, queens and workers can survive the winter months, leading to the build-up of large nests during the following season; thereby increasing the risk posed by this species. To prevent or prepare for such unwanted impacts it is important to know where the wasp may be able to establish, either through natural spread or through introduction as a result of human transport. Distribution data from Argentina and Australia, and seasonal phenology data from Argentina were used to determine the potential distribution of V. germanica using CLIMEX modelling. In contrast to previous models, the influence of irrigation on its distribution was also investigated. Under a natural rainfall scenario, the model showed similarities to previous models. When irrigation is applied, dry stress is alleviated, leading to larger areas modelled climatically suitable compared with previous models, which provided a better fit with the actual distribution of the species. The main areas at risk of invasion by V. germanica include western USA, Mexico, small areas in Central America and in the north-western region of South America, eastern Brazil, western Russia, north-western China, Japan, the Mediterranean coastal regions of North Africa, and parts of southern and eastern Africa.

  4. Including irrigation in niche modelling of the invasive wasp Vespula germanica (Fabricius improves model fit to predict potential for further spread.

    Directory of Open Access Journals (Sweden)

    Marelize de Villiers

    Full Text Available The European wasp, Vespula germanica (Fabricius (Hymenoptera: Vespidae, is of Palaearctic origin, being native to Europe, northern Africa and Asia, and introduced into North America, Chile, Argentina, Iceland, Ascension Island, South Africa, Australia and New Zealand. Due to its polyphagous nature and scavenging behaviour, V. germanica threatens agriculture and silviculture, and negatively affects biodiversity, while its aggressive nature and venomous sting pose a health risk to humans. In areas with warmer winters and longer summers, queens and workers can survive the winter months, leading to the build-up of large nests during the following season; thereby increasing the risk posed by this species. To prevent or prepare for such unwanted impacts it is important to know where the wasp may be able to establish, either through natural spread or through introduction as a result of human transport. Distribution data from Argentina and Australia, and seasonal phenology data from Argentina were used to determine the potential distribution of V. germanica using CLIMEX modelling. In contrast to previous models, the influence of irrigation on its distribution was also investigated. Under a natural rainfall scenario, the model showed similarities to previous models. When irrigation is applied, dry stress is alleviated, leading to larger areas modelled climatically suitable compared with previous models, which provided a better fit with the actual distribution of the species. The main areas at risk of invasion by V. germanica include western USA, Mexico, small areas in Central America and in the north-western region of South America, eastern Brazil, western Russia, north-western China, Japan, the Mediterranean coastal regions of North Africa, and parts of southern and eastern Africa.

  5. Niche-specific cognitive strategies

    DEFF Research Database (Denmark)

    Hulgard, K.; Ratcliffe, J. M.

    2014-01-01

    Related species with different diets are predicted to rely on different cognitive strategies: those best suited for locating available and appropriate foods. Here we tested two predictions of the niche-specific cognitive strategies hypothesis in bats, which suggests that predatory species should......, these would interfere with their subsequent learning of a spatial memory task. We trained free-flying Myotis nattereri to approach palatable and unpalatable insect prey suspended below polystyrene objects. Experimentally naive bats learned to associate different objects with palatable and unpalatable prey...... the niche-specific cognitive strategies hypothesis and suggest that for gleaning and clutter-resistant aerial hawking bats, learning to associate shape with food interferes with subsequent spatial memory learning....

  6. Fine-scale WRF-CMAQ Modeling for the 2013 DISCOVER-AQ Campaign in California

    Science.gov (United States)

    Gilliam, R. C.; Pleim, J. E.; Appel, W.

    2014-12-01

    Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality (DISCOVER-AQ) is an ongoing four year NASA campaign to improve remote sensing in order to better resolve the distribution of pollutants in the lower atmosphere for public health reasons. These observational campaigns are a prime opportunity to evaluate and improve weather and air quality models, in particular the finer scales, since the collected observations are not only unique (boundary layer profiles, planetary boundary layer height and LIDAR), but of high spatial density. For the first campaign in the Washington DC-Baltimore region, a number of meteorological model improvements were crucial for quality results at the finer grid scales. The main techniques tested in the DISCOVER-AQ Washington DC-Baltimore experiment were iterative indirect soil nudging, a simple urban parameterization based on highly resolved impervious surface data, and the use of a high resolution 1 km sea surface temperature dataset. A fourth technique, first tested in a separate cold season application in the US Rocky Mountains, was the assimilation of high resolution 1 km SNOw Data Assimilation System (SNODAS) data for better snow cover representation in retrospective modeling. These methods will be leveraged using a nested 12-4-2 km WRF-CMAQ modeling platform for the 2013 DISCOVER-AQ California campaign where the 2 km domain covers the entire San Joaquin Valley (SJV), coastal areas and all of Los Angeles. The purpose is to demonstrate methods to derive high quality meteorology for retrospective air quality modeling over geographically complex areas of the Western US where current coarser resolution modeling may not be sufficient. Accurate air quality modeling is particularly important for California, which has some of the most polluted areas in the US, within the SJV. Furthermore, this work may inform modeling in other areas of the Intermountain West that are experiencing air

  7. Beyond the continuum: a multi-dimensional phase space for neutral-niche community assembly.

    Science.gov (United States)

    Latombe, Guillaume; Hui, Cang; McGeoch, Melodie A

    2015-12-22

    Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multi-dimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral-niche community dynamics. The neutral-niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology. © 2015 The Author(s).

  8. How is the rate of climatic-niche evolution related to climatic-niche breadth?

    Science.gov (United States)

    Fisher-Reid, M Caitlin; Kozak, Kenneth H; Wiens, John J

    2012-12-01

    The rate of climatic-niche evolution is important to many research areas in ecology, evolution, and conservation biology, including responses of species to global climate change, spread of invasive species, speciation, biogeography, and patterns of species richness. Previous studies have implied that clades with higher rates of climatic-niche evolution among species should have species with narrower niche breadths, but there is also evidence suggesting the opposite pattern. However, the relationships between rate and breadth have not been explicitly analyzed. Here, we examine the relationships between the rate of climatic-niche evolution and climatic-niche breadth using phylogenetic and climatic data for 250 species in the salamander family Plethodontidae, a group showing considerable variation in both rates of climatic-niche evolution and climatic-niche breadths. Contrary to some expectations, we find no general relationship between climatic-niche breadth and the rate of climatic-niche evolution. Climatic-niche breadths for some ecologically important climatic variables considered separately (temperature seasonality and annual precipitation) do show significant relationships with the rate of climatic-niche evolution, but rates are faster in clades in which species have broader (not narrower) niche breadths. In summary, our results show that narrower niche breadths are not necessarily associated with faster rates of niche evolution. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  9. A Crustal Velocity Model for South Mexicali Valley, Baja California, México.

    Science.gov (United States)

    Ramirez, E.; Vidal-Villegas, A.; Stock, J. M.; Gonzalez-Fernandez, A.

    2016-12-01

    The northern Baja California region consists of two subregions of different geological features: the Peninsular Ranges of Baja California, of granitic composition, and the Mexicali Valley region, characterized by a series of sedimentary basins: the Laguna Salada and the Mexicali Valley. Due to the lack of an appropriate crust model for South Mexicali Valley, a refraction study was conducted. We installed 16 three-component short period stations (2 Hz) and one broadband station (100 s - 50 Hz). The stations, spaced 6 km along a refraction profile, recorded a blast performed in the southwest Arizona near the border with Sonora, Mexico. Records gathered were used to estimate a crust velocity structure model for South Mexicali Valley. The beginning of the profile is at San Luis Rio Colorado (SLRC), Sonora and its ending is at the middle of Sierra Juarez, Baja California. As a "reverse shot", for a 47 km section between SLRC and El Mayor Mountain, we used an aftershock M 3.4 of the 2010 M 7.2 El Mayor - Cucapah earthquake. Record sections show seismograms with impulsive P arrivals for nearby stations. The arrival Pn wave is observed at three stations located in Laguna Salada and Sierra Juarez. From the first arrivals of refractions and reflections of the P wave we performed direct modeling of travel times and relative amplitudes (normalized synthetic seismograms). Method based on asymptotic ray theory programed in the RAYINVR software (Zelt and Smith, 1992). We propose an average-three-layer velocity structure model: 2.9, 5.6 and 6.9 km/s, with thicknesses of 1.2, 4.4 and 9.6 km, respectively. Velocities of our model for the region under study are about 1 km/s higher than the model proposed by McMechan and Mooney (1984) for the Imperial Valley. The preliminary interpretation using the "reverse shot" indicates a crust of 15 km depth beneath the Mexicali Valley and 19 km under the El Mayor Mountain and Laguna Salada basin. On the eastern side of the El Mayor Mountain we

  10. Developing ecological site and state-and-transition models for grazed riparian pastures at Tejon Ranch, California

    Science.gov (United States)

    Felix P. Ratcliff; James Bartolome; Michele Hammond; Sheri Spiegal; Michael White

    2015-01-01

    Ecological site descriptions and associated state-and-transition models are useful tools for understanding the variable effects of management and environment on range resources. Models for woody riparian sites have yet to be fully developed. At Tejon Ranch, in the southern San Joaquin Valley of California, we are using ecological site theory to investigate the role of...

  11. Diversity, dilemmas, and monopolies of niche construction.

    Science.gov (United States)

    Krakauer, David C; Page, Karen M; Erwin, Douglas H

    2009-01-01

    The behavior of organisms can contribute to the transformation of their environments. When organismal impacts on the environment feed back to influence organismal density, viability, fertility, or persistence, the environment can be construed as an extension of the organism. This process of fitness-enhancing environmental transformation has been called niche construction. We focus on the relationship of niche construction with species or strain diversity and on the variability of investment in niche construction versus reproduction. We demonstrate a fundamental dilemma of niche construction, whereby the construction of a shared resource leads to a tragedy of the commons, with competition tending to eliminate niche construction strategies. The ability to monopolize a niche, either through spatial proximity or through preferential exploitation, can stabilize niche construction and promote ecological coexistence among polymorphic constructors. We consider both sympatric and allopatric origins of niche construction. Under a variety of different construction mechanisms, variability in the investment in niche construction versus reproduction suggests reproductive altruism but is fully consistent with selfish behavior. We discuss the implications of niche-construction theory on the evolution of life cycles and development, behavioral plasticity, the division of labor, and long-term macroevolutionary trends.

  12. Niche tracking and rapid establishment of distributional equilibrium in the house sparrow show potential responsiveness of species to climate change.

    Directory of Open Access Journals (Sweden)

    William B Monahan

    changes to the realized environmental space. Such insights may be used to conceptualize mechanistic climatic niche models in birds and other taxa.

  13. 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.

  14. Using Google Earth to Explore Strain Rate Models of Southern California

    Science.gov (United States)

    Richard, G. A.; Bell, E. A.; Holt, W. E.

    2007-12-01

    A series of strain rate models for the Transverse Ranges of southern California were developed based on Quaternary fault slip data and geodetic data from high precision GPS stations in southern California. Pacific-North America velocity boundary conditions are applied for all models. Topography changes are calculated using the model dilatation rates, which predict crustal thickness changes under the assumption of Airy isostasy and a specified rate of crustal volume loss through erosion. The models were designed to produce graphical and numerical output representing the configuration of the region from 3 million years ago to 3 million years into the future at intervals of 50 thousand years. Using a North American reference frame, graphical output for the topography and faults and numerical output for locations of faults and points on the crust marked by the locations on cities were used to create data in KML format that can be used in Google Earth to represent time intervals of 50 thousand years. As markers familiar to students, the cities provide a geographic context that can be used to quantify crustal movement, using the Google Earth ruler tool. By comparing distances that markers for selected cities have moved in various parts of the region, students discover that the greatest amount of crustal deformation has occurred in the vicinity of the boundary between the North American and Pacific plates. Students can also identify areas of compression or extension by finding pairs of city markers that have converged or diverged, respectively, over time. The Google Earth layers also reveal that faults that are not parallel to the plate boundary have tended to rotate clockwise due to the right lateral motion along the plate boundary zone. KML TimeSpan markup was added to two versions of the model, enabling the layers to be displayed in an automatic sequenced loop for a movie effect. The data is also available as QuickTime (.mov) and Graphics Interchange Format (.gif

  15. Modeling nitrate at domestic and public-supply well depths in the Central Valley, California

    Science.gov (United States)

    Nolan, Bernard T.; Gronberg, JoAnn M.; Faunt, Claudia C.; Eberts, Sandra M.; Belitz, Ken

    2014-01-01

    Aquifer vulnerability models were developed to map groundwater nitrate concentration at domestic and public-supply well depths in the Central Valley, California. We compared three modeling methods for ability to predict nitrate concentration >4 mg/L: logistic regression (LR), random forest classification (RFC), and random forest regression (RFR). All three models indicated processes of nitrogen fertilizer input at the land surface, transmission through coarse-textured, well-drained soils, and transport in the aquifer to the well screen. The total percent correct predictions were similar among the three models (69–82%), but RFR had greater sensitivity (84% for shallow wells and 51% for deep wells). The results suggest that RFR can better identify areas with high nitrate concentration but that LR and RFC may better describe bulk conditions in the aquifer. A unique aspect of the modeling approach was inclusion of outputs from previous, physically based hydrologic and textural models as predictor variables, which were important to the models. Vertical water fluxes in the aquifer and percent coarse material above the well screen were ranked moderately high-to-high in the RFR models, and the average vertical water flux during the irrigation season was highly significant (p < 0.0001) in logistic regression.

  16. 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.

  17. 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.

  18. Prospective and retrospective evaluation of five-year earthquake forecast models for California

    Science.gov (United States)

    Strader, Anne; Schneider, Max; Schorlemmer, Danijel

    2017-10-01

    The Collaboratory for the Study of Earthquake Predictability was developed to prospectively test earthquake forecasts through reproducible and transparent experiments within a controlled environment. From January 2006 to December 2010, the Regional Earthquake Likelihood Models (RELM) Working Group developed and evaluated thirteen time-invariant prospective earthquake mainshock forecasts. The number, spatial and magnitude components of the forecasts were compared to the observed seismicity distribution using a set of likelihood-based consistency tests. In this RELM experiment update, we assess the long-term forecasting potential of the RELM forecasts. Additionally, we evaluate RELM forecast performance against the Uniform California Earthquake Rupture Forecast (UCERF2) and the National Seismic Hazard Mapping Project (NSHMP) forecasts, which are used for seismic hazard analysis for California. To test each forecast's long-term stability, we also evaluate each forecast from January 2006 to December 2015, which contains both five-year testing periods, and the 40-year period from January 1967 to December 2006. Multiple RELM forecasts, which passed the N-test during the retrospective (January 2006 to December 2010) period, overestimate the number of events from January 2011 to December 2015, although their forecasted spatial distributions are consistent with observed earthquakes. Both the UCERF2 and NSHMP forecasts pass all consistency tests for the two five-year periods; however, they tend to underestimate the number of observed earthquakes over the 40-year testing period. The smoothed seismicity model Helmstetter-et-al.Mainshock outperforms both United States Geological Survey (USGS) models during the second five-year experiment, and contains higher forecasted seismicity rates than the USGS models at multiple observed earthquake locations.

  19. 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…

  20. Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula.

    Science.gov (United States)

    Alexander Pyron, R; Burbrink, Frank T

    2009-08-01

    Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographical barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographical barriers are possible: (i) niche conservatism at a physical barrier; (ii) niche divergence at a physical barrier; and (iii) niche divergence in the absence of a physical barrier. We test for the presence of these patterns in a transcontinentally distributed snake species, the common kingsnake (Lampropeltis getula), to determine the relative frequency of niche conservatism or divergence in a single species complex inhabiting multiple distinct ecoregions. We infer the phylogeographic structure of the kingsnake using a range-wide data set sampled for the mitochondrial gene cytochrome b. We use coalescent simulation methods to test for the presence of structured lineage formation vs. fragmentation of a widespread ancestor. Finally, we use statistical techniques for creating and evaluating ecological niche models to test for conservatism of ecological niche preferences. Significant geographical structure is present in the kingsnake, for which coalescent tests indicate structured population division. Surprisingly, we find evidence for all three patterns of conservatism and divergence. This suggests that ecological niche preferences may be labile on recent phylogenetic timescales, and that lineage formation in widespread species can result from an interaction between inertial tendencies of niche conservatism and natural selection on populations in ecologically divergent habitats.

  1. A nowcast model for tides and tidal currents in San Francisco Bay, California

    Science.gov (United States)

    Cheng, Ralph T.; Smith, Richard E.

    1998-01-01

    National Oceanographic and Atmospheric Administration (NOAA) installed Physical Oceanographic Real-Time System (PORTS) in San Francisco Bay, California to provide observations of tides, tidal currents, and meteorological conditions. PORTS data are used for optimizing vessel operations, increasing margin of safety for navigation, and guiding hazardous material spill prevention and response. Because tides and tidal currents in San Francisco Bay are extremely complex, limited real-time observations are insufficient to provide spatial resolution for variations of tides and tidal currents. To fill the information gaps, a highresolution, robust, semi-implicit, finite-difference nowcast numerical model has been implemented for San Francisco Bay. The model grid and water depths are defined on coordinates based on Mercator projection so the model outputs can be directly superimposed on navigation charts. A data assimilation algorithm has been established to derive the boundary conditions for model simulations. The nowcast model is executed every hour continuously for tides and tidal currents starting from 24 hours before the present time (now) covering a total of 48 hours simulation. Forty-eight hours of nowcast model results are available to the public at all times through the World Wide Web (WWW). Users can view and download the nowcast model results for tides and tidal current distributions in San Francisco Bay for their specific applications and for further analysis.

  2. Habitat-Based Density Models for Three Cetacean Species off Southern California Illustrate Pronounced Seasonal Differences

    Directory of Open Access Journals (Sweden)

    Elizabeth A. Becker

    2017-05-01

    Full Text Available Managing marine species effectively requires spatially and temporally explicit knowledge of their density and distribution. Habitat-based density models, a type of species distribution model (SDM that uses habitat covariates to estimate species density and distribution patterns, are increasingly used for marine management and conservation because they provide a tool for assessing potential impacts (e.g., from fishery bycatch, ship strikes, anthropogenic sound over a variety of spatial and temporal scales. The abundance and distribution of many pelagic species exhibit substantial seasonal variability, highlighting the importance of predicting density specific to the season of interest. This is particularly true in dynamic regions like the California Current, where significant seasonal shifts in cetacean distribution have been documented at coarse scales. Finer scale (10 km habitat-based density models were previously developed for many cetacean species occurring in this region, but most models were limited to summer/fall. The objectives of our study were two-fold: (1 develop spatially-explicit density estimates for winter/spring to support management applications, and (2 compare model-predicted density and distribution patterns to previously developed summer/fall model results in the context of species ecology. We used a well-established Generalized Additive Modeling framework to develop cetacean SDMs based on 20 California Cooperative Oceanic Fisheries Investigations (CalCOFI shipboard surveys conducted during winter and spring between 2005 and 2015. Models were fit for short-beaked common dolphin (Delphinus delphis delphis, Dall's porpoise (Phocoenoides dalli, and humpback whale (Megaptera novaeangliae. Model performance was evaluated based on a variety of established metrics, including the percentage of explained deviance, ratios of observed to predicted density, and visual inspection of predicted and observed distributions. Final models were

  3. Application of Bayesian methods to habitat selection modeling of the northern spotted owl in California: new statistical methods for wildlife research

    Science.gov (United States)

    Howard B. Stauffer; Cynthia J. Zabel; Jeffrey R. Dunk

    2005-01-01

    We compared a set of competing logistic regression habitat selection models for Northern Spotted Owls (Strix occidentalis caurina) in California. The habitat selection models were estimated, compared, evaluated, and tested using multiple sample datasets collected on federal forestlands in northern California. We used Bayesian methods in interpreting...

  4. 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

  5. A Predictive Model for Readmissions Among Medicare Patients in a California Hospital.

    Science.gov (United States)

    Duncan, Ian; Huynh, Nhan

    2017-11-17

    Predictive models for hospital readmission rates are in high demand because of the Centers for Medicare & Medicaid Services (CMS) Hospital Readmission Reduction Program (HRRP). The LACE index is one of the most popular predictive tools among hospitals in the United States. The LACE index is a simple tool with 4 parameters: Length of stay, Acuity of admission, Comorbidity, and Emergency visits in the previous 6 months. The authors applied logistic regression to develop a predictive model for a medium-sized not-for-profit community hospital in California using patient-level data with more specific patient information (including 13 explanatory variables). Specifically, the logistic regression is applied to 2 populations: a general population including all patients and the specific group of patients targeted by the CMS penalty (characterized as ages 65 or older with select conditions). The 2 resulting logistic regression models have a higher sensitivity rate compared to the sensitivity of the LACE index. The C statistic values of the model applied to both populations demonstrate moderate levels of predictive power. The authors also build an economic model to demonstrate the potential financial impact of the use of the model for targeting high-risk patients in a sample hospital and demonstrate that, on balance, whether the hospital gains or loses from reducing readmissions depends on its margin and the extent of its readmission penalties.

  6. 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. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  7. Microhabitat and Climatic Niche Change Explain Patterns of Diversification among Frog Families.

    Science.gov (United States)

    Moen, Daniel S; Wiens, John J

    2017-07-01

    A major goal of ecology and evolutionary biology is to explain patterns of species richness among clades. Differences in rates of net diversification (speciation minus extinction over time) may often explain these patterns, but the factors that drive variation in diversification rates remain uncertain. Three important candidates are climatic niche position (e.g., whether clades are primarily temperate or tropical), rates of climatic niche change among species within clades, and microhabitat (e.g., aquatic, terrestrial, arboreal). The first two factors have been tested separately in several studies, but the relative importance of all three is largely unknown. Here we explore the correlates of diversification among families of frogs, which collectively represent ∼88% of amphibian species. We assemble and analyze data on phylogeny, climate, and microhabitat for thousands of species. We find that the best-fitting phylogenetic multiple regression model includes all three types of variables: microhabitat, rates of climatic niche change, and climatic niche position. This model explains 67% of the variation in diversification rates among frog families, with arboreal microhabitat explaining ∼31%, niche rates ∼25%, and climatic niche position ∼11%. Surprisingly, we show that microhabitat can have a much stronger influence on diversification than climatic niche position or rates of climatic niche change.

  8. 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

  9. Reactive Transport of Nitrate in Northern California Groundwater basins: An Integrated Characterization and Modeling Approach

    Science.gov (United States)

    Esser, B. K.; Moran, J. E.; Hudson, G. B.; Carle, S. F.; McNab, W.; Tompson, A. F.; Moore, K.; Beller, H.; Kane, S.; Eaton, G.

    2003-12-01

    More than 1/3 of active public drinking water supply wells in California produce water with nitrate-N levels indicative of anthropogenic inputs (> 4 mg/L). Understanding how the distribution of nitrate in California groundwater basins will evolve is vital to water supply and infrastructure planning. To address this need, we are studying the basin-scale reactive transport of nitrate in the Livermore and Llagas basins of Northern California. Both basins have increasingly urban populations heavily reliant on groundwater. A distinct nitrate "plume" exists in the Livermore Basin (Alameda County) whereas pervasive nitrate contamination exists in shallow groundwaters of the Llagas Basin (Santa Clara County). The sources and timing of nitrate contamination in these basins are not definitively known; septic systems, irrigated agriculture and livestock operations exist or have existed in both areas. The role of denitrification in controlling nitrate distribution is also unknown; dissolved oxygen levels are sufficiently low in portions of each basin as to indicate the potential for denitrification. We have collected water from 60 wells, and are determining both groundwater age (by the 3H/3He method) and the extent of denitrification (by the excess N2 method). Excess nitrogen is being determined by both membrane-inlet and noble gas mass spectrometry, using Ar and Ne content to account for atmospheric N2. We are also analyzing for stable istotopes of nitrate and water, nitrate co-contaminants, and general water quality parameters. Preliminary analysis of archival water district data from both basins suggests positive correlations of nitrate with Ca+2, Mg+2 and bicarbonate and negative correlation with pH. In the Llagas Basin, a negative correlation also exists between nitrate and temperature. Flow path-oriented reactive transport modeling is being explored as a tool to aid in the identification of both the sources of nitrate and evidence for denitrification in both basins

  10. Hydrodynamic properties of San Quintin Bay, Baja California: Merging models and observations.

    Science.gov (United States)

    Melaku Canu, Donata; Aveytua-Alcázar, Leslie; Camacho-Ibar, Victor F; Querin, Stefano; Solidoro, Cosimo

    2016-07-15

    We investigated the physical dynamics of San Quintin Bay, a coastal lagoon located on the Pacific coast of northern Baja California, Mexico. We implemented, validated and used a finite element 2-D hydrodynamic model to characterize the spatial and temporal variability of the hydrodynamic of the bay in response to variability in the tidal regime and in meteorological forcing patterns. Our analysis of general circulation, residual currents, residence times, and tidal propagation delays allowed us to characterize spatial variability in the hydrodynamic basin features. The eulerian water residence time is -on average and under reference conditions- approximately 7days, although this can change significantly by region and season and under different tidal and meteorological conditions. Ocean upwelling events that bring colder waters into the bay mouth affect hydrodynamic properties in all areas of the lagoon and may affect ecological dynamics. A return to pre-upwelling conditions would take approximately 10days. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Modeling climate and fuel reduction impacts on mixed-conifer forest carbon stocks in the Sierra Nevada, California

    Science.gov (United States)

    Matthew D. Hurteau; Timothy A. Robards; Donald Stevens; David Saah; Malcolm North; George W. Koch

    2014-01-01

    Quantifying the impacts of changing climatic conditions on forest growth is integral to estimating future forest carbon balance. We used a growth-and-yield model, modified for climate sensitivity, to quantify the effects of altered climate on mixed-conifer forest growth in the Lake Tahoe Basin, California. Estimates of forest growth and live tree carbon stocks were...

  12. Stitch the niche - a practical philosophy and visual schematic for the niche concept

    NARCIS (Netherlands)

    McInerny, Greg J.; Etienne, Rampal S.

    2012-01-01

    By over-focusing on precise definitions, ecology has produced a confused idea of the niche concept. This, our second paper, develops a practical philosophy for the niche that approaches the concept at the correct level of abstraction. We deconstruct the niche into effect and response components and

  13. 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.

  14. 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...

  15. Shifting Niches for Community Structure Detection

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...... 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...... 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....

  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. 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

  18. 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.

  19. 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

  20. 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.

  1. Linking life-history traits, ecology, and niche breadth evolution in North American eriogonoids (Polygonaceae).

    Science.gov (United States)

    Kostikova, Anna; Litsios, Glenn; Salamin, Nicolas; Pearman, Peter B

    2013-12-01

    Macroevolutionary and microevolutionary studies provide complementary explanations of the processes shaping the evolution of niche breadth. Macroevolutionary approaches scrutinize factors such as the temporal and spatial environmental heterogeneities that drive differentiation among species. Microevolutionary studies, in contrast, focus on the processes that affect intraspecific variability. We combine these perspectives by using macroevolutionary models in a comparative study of intraspecific variability. We address potential differences in rates of evolution of niche breadth and position in annual and perennial plants of the Eriogonoideae subfamily of the Polygonaceae. We anticipated higher rates of evolution in annuals than in perennials owing to differences in generation time that are paralleled by rates of molecular evolution. Instead, we found that perennial eriogonoid species present greater environmental tolerance (wider climate niche) than annual species. Niche breadth of perennial species has evolved two to four times faster than in annuals, while niche optimum has diversified more rapidly among annual species than among perennials. Niche breadth and average elevation of species are correlated. Moreover, niche breadth increases more rapidly with mean species elevation in perennials than in annuals. Our results suggest that both environmental gradients and life-history strategy influence rates and patterns of niche breadth evolution.

  2. 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.

  3. Modeling the periodic stratification and gravitational circulation in San Francisco Bay, California

    Science.gov (United States)

    Cheng, Ralph T.; Casulli, Vincenzo

    1996-01-01

    A high resolution, three-dimensional (3-D) hydrodynamic numerical model is applied to San Francisco Bay, California to simulate the periodic tidal stratification caused by tidal straining and stirring and their long-term effects on gravitational circulation. The numerical model is formulated using fixed levels in the vertical and uniform computational mesh on horizontal planes. The governing conservation equations, the 3-D shallow water equations, are solved by a semi-implicit finite-difference scheme. Numerical simulations for estuarine flows in San Francisco Bay have been performed to reproduce the hydrodynamic properties of tides, tidal and residual currents, and salt transport. All simulations were carried out to cover at least 30 days, so that the spring-neap variance in the model results could be analyzed. High grid resolution used in the model permits the use of a simple turbulence closure scheme which has been shown to be sufficient to reproduce the tidal cyclic stratification and well-mixed conditions in the water column. Low-pass filtered 3-D time-series reveals the classic estuarine gravitational circulation with a surface layer flowing down-estuary and an up-estuary flow near the bottom. The intensity of the gravitational circulation depends upon the amount of freshwater inflow, the degree of stratification, and spring-neap tidal variations.

  4. Bed composition generation for morphodynamic modeling: Case study of San Pablo Bay in California, USA

    Science.gov (United States)

    van der Wegen, M.; Dastgheib, A.; Jaffe, B.E.; Roelvink, D.

    2011-01-01

    Applications of process-based morphodynamic models are often constrained by limited availability of data on bed composition, which may have a considerable impact on the modeled morphodynamic development. One may even distinguish a period of "morphodynamic spin-up" in which the model generates the bed level according to some ill-defined initial bed composition rather than describing the realistic behavior of the system. The present paper proposes a methodology to generate bed composition of multiple sand and/or mud fractions that can act as the initial condition for the process-based numerical model Delft3D. The bed composition generation (BCG) run does not include bed level changes, but does permit the redistribution of multiple sediment fractions over the modeled domain. The model applies the concept of an active layer that may differ in sediment composition above an underlayer with fixed composition. In the case of a BCG run, the bed level is kept constant, whereas the bed composition can change. The approach is applied to San Pablo Bay in California, USA. Model results show that the BCG run reallocates sand and mud fractions over the model domain. Initially, a major sediment reallocation takes place, but development rates decrease in the longer term. Runs that take the outcome of a BCG run as a starting point lead to more gradual morphodynamic development. Sensitivity analysis shows the impact of variations in the morphological factor, the active layer thickness, and wind waves. An important but difficult to characterize criterion for a successful application of a BCG run is that it should not lead to a bed composition that fixes the bed so that it dominates the "natural" morphodynamic development of the system. Future research will focus on a decadal morphodynamic hindcast and comparison with measured bathymetries in San Pablo Bay so that the proposed methodology can be tested and optimized. ?? 2010 The Author(s).

  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. Generalists, specialists and opportunists: niche metrics of ...

    African Journals Online (AJOL)

    There are distinct differences in the way in which Poicephalus parrots utilise food resources within their distributional range. Our study evaluated the niche metrics of all Poicephalus parrots studied thus far for evidence of linkages between body mass, distributional range and niche breadth. We calibrated the degree of ...

  7. 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…

  8. Terrain-based Predictive Modeling of a Functional Riparian Corridor in a Coastal Northern California Watershed

    Science.gov (United States)

    Robinson, T.; Davis, J. D.

    2016-12-01

    Riparian corridors and their associated geomorphic landforms (e.g., channels, floodplains, and terraces) and vegetation communities (e.g., forests and wetlands) have been significantly degraded in California, prompting an expansion of efforts to delineate riparian corridors and identify priorities for conservation via deed restrictions and easements. Current techniques to delineate riparian corridors for these purposes include fixed-width buffers based on stream centerlines and digitization of woody vegetation from aerial photos. Although efficient, these delineation methods do not accurately capture the extent of ecologically functional riparian corridors and result in riparian habitat being excluded from conservation efforts while non-riparian is included. From a physical perspective, ecologically functional riparian corridors have widths that vary with topography and ample space for dynamic fluvial geomorphic processes that create and maintain river morphology and vegetation and sustain ecological interactions that extend from the stream channel laterally into upland ecosystems and up- and downstream ecosystems in longitudinal directions. New terrain-based spatial analysis techniques and high-resolution digital terrain data show promise in delineating ecologically functional riparian corridors. In this study, we compare the efficacy of three terrain-based predictors of riparian corridors that have emerged in the literature—elevation above channel, flow accumulation, and distance from channel. The results of each terrain predictor are compared with field-based indicators of the riparian corridor of an alluvial reach of Mark West Creek in Sonoma County, California (a mediterranean climate). Indicators include soil type, fluvial geomorphic landforms, and vegetation. A one-meter digital terrain model from LiDAR (Light Detection and Ranging) supplied by a NASA ROSES grant is used as the base terrain data for spatial analysis. We discuss in detail the use of

  9. The niche party concept and its measurement.

    Science.gov (United States)

    Meyer, Thomas M; Miller, Bernhard

    2015-03-01

    The concept of the niche party has become increasingly popular in analyses of party competition. Yet, existing approaches vary in their definitions and their measurement approaches. We propose using a minimal definition that allows us to compare political parties in terms of their 'nicheness'. We argue that the conceptual core of the niche party concept is based on issue emphasis and that a niche party emphasizes policy areas neglected by its rivals. Based on this definition, we propose a continuous measure that allows for more fine-grained measurement of a party's 'nicheness' than the dominant, dichotomous approaches and thereby limits the risk of measurement error. Drawing on data collected by the Comparative Manifesto Project, we show that (1) our measure has high face validity and (2) exposes differences among parties that are not captured by alternative, static or dichotomous measures.

  10. Is There Any Evidence for Rapid, Genetically-Based, Climatic Niche Expansion in the Invasive Common Ragweed?

    Directory of Open Access Journals (Sweden)

    Laure Gallien

    Full Text Available Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a likely genetically-based climatic niche expansion of an annual plant invader, the common ragweed (Ambrosia artemisiifolia L., a highly allergenic invasive species causing substantial public health issues. To do so, we looked for recent evolutionary change at the upward migration front of its adventive range in the French Alps. Based on species climatic niche models estimated at both global and regional scales we stratified our sampling design to adequately capture the species niche, and localized populations suspected of niche expansion. Using a combination of species niche modeling, landscape genetics models and common garden measurements, we then related the species genetic structure and its phenotypic architecture across the climatic niche. Our results strongly suggest that the common ragweed is rapidly adapting to local climatic conditions at its invasion front and that it currently expands its niche toward colder and formerly unsuitable climates in the French Alps (i.e. in sites where niche models would not predict its occurrence. Such results, showing that species climatic niches can evolve on very short time scales, have important implications for predictive models of biological invasions that do not account for evolutionary processes.

  11. Is There Any Evidence for Rapid, Genetically-Based, Climatic Niche Expansion in the Invasive Common Ragweed?

    Science.gov (United States)

    Gallien, Laure; Thuiller, Wilfried; Fort, Noémie; Boleda, Marti; Alberto, Florian J; Rioux, Delphine; Lainé, Juliette; Lavergne, Sébastien

    2016-01-01

    Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a likely genetically-based climatic niche expansion of an annual plant invader, the common ragweed (Ambrosia artemisiifolia L.), a highly allergenic invasive species causing substantial public health issues. To do so, we looked for recent evolutionary change at the upward migration front of its adventive range in the French Alps. Based on species climatic niche models estimated at both global and regional scales we stratified our sampling design to adequately capture the species niche, and localized populations suspected of niche expansion. Using a combination of species niche modeling, landscape genetics models and common garden measurements, we then related the species genetic structure and its phenotypic architecture across the climatic niche. Our results strongly suggest that the common ragweed is rapidly adapting to local climatic conditions at its invasion front and that it currently expands its niche toward colder and formerly unsuitable climates in the French Alps (i.e. in sites where niche models would not predict its occurrence). Such results, showing that species climatic niches can evolve on very short time scales, have important implications for predictive models of biological invasions that do not account for evolutionary processes.

  12. Risks of ocean acidification in the California Current food web and fisheries: ecosystem model projections.

    Science.gov (United States)

    Marshall, Kristin N; Kaplan, Isaac C; Hodgson, Emma E; Hermann, Albert; Busch, D Shallin; McElhany, Paul; Essington, Timothy E; Harvey, Chris J; Fulton, Elizabeth A

    2017-04-01

    The benefits and ecosystem services that humans derive from the oceans are threatened by numerous global change stressors, one of which is ocean acidification. Here, we describe the effects of ocean acidification on an upwelling system that already experiences inherently low pH conditions, the California Current. We used an end-to-end ecosystem model (Atlantis), forced by downscaled global climate models and informed by a meta-analysis of the pH sensitivities of local taxa, to investigate the direct and indirect effects of future pH on biomass and fisheries revenues. Our model projects a 0.2-unit drop in pH during the summer upwelling season from 2013 to 2063, which results in wide-ranging magnitudes of effects across guilds and functional groups. The most dramatic direct effects of future pH may be expected on epibenthic invertebrates (crabs, shrimps, benthic grazers, benthic detritivores, bivalves), and strong indirect effects expected on some demersal fish, sharks, and epibenthic invertebrates (Dungeness crab) because they consume species known to be sensitive to changing pH. The model's pelagic community, including marine mammals and seabirds, was much less influenced by future pH. Some functional groups were less affected to changing pH in the model than might be expected from experimental studies in the empirical literature due to high population productivity (e.g., copepods, pteropods). Model results suggest strong effects of reduced pH on nearshore state-managed invertebrate fisheries, but modest effects on the groundfish fishery because individual groundfish species exhibited diverse responses to changing pH. Our results provide a set of projections that generally support and build upon previous findings and set the stage for hypotheses to guide future modeling and experimental analysis on the effects of OA on marine ecosystems and fisheries. © 2017 John Wiley & Sons Ltd.

  13. Feeding niches of four large herbivores in the Hluhluwe Game ...

    African Journals Online (AJOL)

    ... communities; connochaetes taurinus taurinus; discriminant function analysis; equus burchelli burchelli; feeding; grass; grasses; habitat; herbivores; hluhluwe game reserve; kwazulu-natal; large herbivores; latent roots; natal; niche; niche overlap; niche separation; south africa; syncerus caffer caffer; white rhinoceros; ...

  14. The clumping transition in niche competition: a robust critical phenomenon

    Science.gov (United States)

    Fort, H.; Scheffer, M.; van Nes, E.

    2010-05-01

    We show analytically and numerically that the appearance of lumps and gaps in the distribution of n competing species along a niche axis is a robust phenomenon whenever the finiteness of the niche space is taken into account. In this case, depending on whether the niche width of the species σ is above or below a threshold σc, which for large n coincides with 2/n, there are two different regimes. For σ > σc the lumpy pattern emerges directly from the dominant eigenvector of the competition matrix because its corresponding eigenvalue becomes negative. For σ <= σc the lumpy pattern disappears. Furthermore, this clumping transition exhibits critical slowing down as σ is approached from above. We also find that the number of lumps of the species distribution versus σ displays a stair-step structure. The positions of these steps are distributed according to a power law. It is thus straightforward to predict the number of groups that can be packed along a niche axis and this value is consistent with field measurements for a wide range of the model parameters.

  15. 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.

  16. 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.

  17. 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.

  18. Social intelligence, human intelligence and niche construction.

    Science.gov (United States)

    Sterelny, Kim

    2007-04-29

    This paper is about the evolution of hominin intelligence. I agree with defenders of the social intelligence hypothesis in thinking that externalist models of hominin intelligence are not plausible: such models cannot explain the unique cognition and cooperation explosion in our lineage, for changes in the external environment (e.g. increasing environmental unpredictability) affect many lineages. Both the social intelligence hypothesis and the social intelligence-ecological complexity hybrid I outline here are niche construction models. Hominin evolution is hominin response to selective environments that earlier hominins have made. In contrast to social intelligence models, I argue that hominins have both created and responded to a unique foraging mode; a mode that is both social in itself and which has further effects on hominin social environments. In contrast to some social intelligence models, on this view, hominin encounters with their ecological environments continue to have profound selective effects. However, though the ecological environment selects, it does not select on its own. Accidents and their consequences, differential success and failure, result from the combination of the ecological environment an agent faces and the social features that enhance some opportunities and suppress others and that exacerbate some dangers and lessen others. Individuals do not face the ecological filters on their environment alone, but with others, and with the technology, information and misinformation that their social world provides.

  19. 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

  20. Niche-habitat mechanisms and biotic interactions explain the coexistence and abundance of congeneric sandgrouse species.

    Science.gov (United States)

    Benítez-López, Ana; Viñuela, Javier; Suárez, Francisco; Hervás, Israel; García, Jesús T

    2014-09-01

    Ascertaining which niche processes allow coexistence between closely related species is of special interest in ecology. We quantified variations in the environmental niches and densities of two congeneric species, the pin-tailed and the black-bellied sandgrouse (Pterocles alchata and Pterocles orientalis) in allopatry and sympatry under similar abiotic, habitat and dispersal contexts to understand their coexistence. Using principal component analysis, we defined environmental gradients (niche dimensions) including abiotic, habitat and anthropogenic variables, and calculated niche breadth, position and overlap of both species in sympatry and allopatry. Additionally, sandgrouse density was modelled as a function of the niche dimensions and the density of the other species. We found evidence that each species occupies distinct environmental niches in sympatry and in allopatry. The black-bellied sandgrouse exploits a broader range of environmental conditions (wider niche breadth) while the pin-tailed sandgrouse reaches high densities where conditions seem to match its optimum. In sympatry, both species shift their niches to intermediate positions, indicating the importance of abiotic factors in setting coexistence areas. Environmental conditions determine regional densities of pin-tailed sandgrouse whereas biotic interactions explain the density of the black-bellied sandgrouse in areas with abiotic conditions similarly conducive for both species. Highly suitable areas for the pin-tailed sandgrouse fall beyond the upper thermal limit of the black-bellied sandgrouse, leading to niche segregation and low densities for the latter. Finally, local niche shift and expansion plus possible heterospecific aggregation allow the pin-tailed sandgrouse to thrive in a priori less favourable environments. This work provides insight into how different mechanisms allow species coexistence and how species densities vary in sympatry compared to allopatry as a result of environmental

  1. American trees shift their niches when invading Western Europe: evaluating invasion risks in a changing climate.

    Science.gov (United States)

    Camenen, Etienne; Porté, Annabel J; Benito Garzón, Marta

    2016-10-01

    Four North American trees are becoming invasive species in Western Europe: Acer negundo, Prunus serotina, Quercus rubra, and Robinia pseudoacacia. However, their present and future potential risks of invasion have not been yet evaluated. Here, we assess niche shifts between the native and invasive ranges and the potential invasion risk of these four trees in Western Europe. We estimated niche conservatism in a multidimensional climate space using niche overlap Schoener's D, niche equivalence, and niche similarity tests. Niche unfilling and expansion were also estimated in analogous and nonanalogous climates. The capacity for predicting the opposite range between the native and invasive areas (transferability) was estimated by calibrating species distribution models (SDMs) on each range separately. Invasion risk was estimated using SDMs calibrated on both ranges and projected for 2050 climatic conditions. Our results showed that native and invasive niches were not equivalent with low niche overlap for all species. However, significant similarity was found between the invasive and native ranges of Q. rubra and R. pseudoacacia. Niche expansion was lower than 15% for all species, whereas unfilling ranged from 7 to 56% when it was measured using the entire climatic space and between 5 and 38% when it was measured using analogous climate only. Transferability was low for all species. SDMs calibrated over both ranges projected high habitat suitability in Western Europe under current and future climates. Thus, the North American and Western European ranges are not interchangeable irrespective of the studied species, suggesting that other environmental and/or biological characteristics are shaping their invasive niches. The current climatic risk of invasion is especially high for R. pseudoacacia and A. negundo. In the future, the highest risks of invasion for all species are located in Central and Northern Europe, whereas the risk is likely to decrease in the

  2. The thermal niche of Neotropical nectar-feeding bats: Its evolution and application to predict responses to global warming.

    Science.gov (United States)

    Ortega-García, Stephanie; Guevara, Lázaro; Arroyo-Cabrales, Joaquín; Lindig-Cisneros, Roberto; Martínez-Meyer, Enrique; Vega, Ernesto; Schondube, Jorge E

    2017-09-01

    The thermal niche of a species is one of the main determinants of its ecology and biogeography. In this study, we determined the thermal niche of 23 species of Neotropical nectar-feeding bats of the subfamily Glossophaginae (Chiroptera, Phyllostomidae). We calculated their thermal niches using temperature data obtained from collection records, by generating a distribution curve of the maximum and minimum temperatures per locality, and using the inflection points of the temperature distributions to estimate the species optimal (STZ) and suboptimal (SRZ) zones of the thermal niche. Additionally, by mapping the values of the STZ and SRZ on a phylogeny of the group, we generated a hypothesis of the evolution of the thermal niches of this clade of nectar-feeding bats. Finally, we used the characteristics of their thermal niches to predict the responses of these organisms to climate change. We found a large variation in the width and limits of the thermal niches of nectar-feeding bats. Additionally, while the upper limits of the thermal niches varied little among species, their lower limits differ wildly. The ancestral reconstruction of the thermal niche indicated that this group of Neotropical bats evolved under cooler temperatures. The two clades inside the Glossophaginae differ in the evolution of their thermal niches, with most members of the clade Choeronycterines evolving "colder" thermal niches, while the majority of the species in the clade Glossophagines evolving "warmer" thermal niches. By comparing thermal niches with climate change models, we found that all species could be affected by an increase of 1°C in temperature at the end of this century. This suggests that even nocturnal species could suffer important physiological costs from global warming. Our study highlights the value of scientific collections to obtain ecologically significant physiological data for a large number of species.

  3. 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.

  4. Thermal modeling of flow in the San Diego Aqueduct, California, and its relation to evaporation

    Science.gov (United States)

    Jobson, Harvey E.

    1980-01-01

    The thermal balance of the 26-kilometer long concrete-lined San Diego Aqueduct, a canal in southern California, was studied to determine the coefficients in a Dalton type evaporation formula. Meteorologic and hydraulic variables, as well as water temperature, were monitored continuously for a 1-year period. A thermal model was calibrated by use of data obtained during a 28-day period to determine the coefficients which best described the thermal balance of the canal. The coefficients applicable to the San Diego Aqueduct are similar to those commonly obtained from lake evaporation studies except that a greater evaporation at low windspeeds is indicated. The model was verified by use of data obtained during 113 days which did not include the calibration data. These data verified that the derived wind function realistically represents the canal evaporation. An annual evaporation of 2.08 meters was computed which is about 91 percent of the amount of water evaporated annually from nearby class A evaporation pans. (Kosco-USGS)

  5. 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.

  6. Dynamic Rupture Models of Earthquakes on the Bartlett Springs Fault, Northern California

    Science.gov (United States)

    Lozos, J.; Harris, R.; Murray, J. R.; Lienkaemper, J. J.; Abrahamson, N. A.

    2014-12-01

    The Bartlett Springs Fault is a major right-lateral component of the San Andreas fault system in northern California. Fault slip-rate models inferred from GPS data [Murray et al., 2013] and alignment array data [McFarland et al., 2009] both indicate that the Bartlett Springs fault experiences aseismic creep. We use the three-dimensional finite element computer code of Barall [2009] to conduct models of dynamic spontaneous rupture on this fault, both to determine characteristics of potential earthquakes, and to gauge the ability of rupture to propagate in the creeping regions. Within the framework of slip-weakening friction, we represent locked portions of the fault as regions of positive stress drop, and creeping regions as having zero or negative stress drop. Using the fault geometry and creep distribution from studies by Murray et al., we examine simulations that implement either homogeneous initial stresses or a regional stress field, along with several different parameterizations of the contrast in frictional properties between locked and creeping zones. We compare the earthquake source characteristics for the same fault geometry with and without the known creeping sections. These comparisons can be used to estimate the impacts of the creeping sections on ground motion predictions.

  7. A statistical learning framework for groundwater nitrate models of the Central Valley, California, USA

    Science.gov (United States)

    Nolan, Bernard T.; Fienen, Michael N.; Lorenz, David L.

    2015-12-01

    We used a statistical learning framework to evaluate the ability of three machine-learning methods to predict nitrate concentration in shallow groundwater of the Central Valley, California: boosted regression trees (BRT), artificial neural networks (ANN), and Bayesian networks (BN). Machine learning methods can learn complex patterns in the data but because of overfitting may not generalize well to new data. The statistical learning framework involves cross-validation (CV) training and testing data and a separate hold-out data set for model evaluation, with the goal of optimizing predictive performance by controlling for model overfit. The order of prediction performance according to both CV testing R2 and that for the hold-out data set was BRT > BN > ANN. For each method we identified two models based on CV testing results: that with maximum testing R2 and a version with R2 within one standard error of the maximum (the 1SE model). The former yielded CV training R2 values of 0.94-1.0. Cross-validation testing R2 values indicate predictive performance, and these were 0.22-0.39 for the maximum R2 models and 0.19-0.36 for the 1SE models. Evaluation with hold-out data suggested that the 1SE BRT and ANN models predicted better for an independent data set compared with the maximum R2 versions, which is relevant to extrapolation by mapping. Scatterplots of predicted vs. observed hold-out data obtained for final models helped identify prediction bias, which was fairly pronounced for ANN and BN. Lastly, the models were compared with multiple linear regression (MLR) and a previous random forest regression (RFR) model. Whereas BRT results were comparable to RFR, MLR had low hold-out R2 (0.07) and explained less than half the variation in the training data. Spatial patterns of predictions by the final, 1SE BRT model agreed reasonably well with previously observed patterns of nitrate occurrence in groundwater of the Central Valley.

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

    DEFF Research Database (Denmark)

    Vrijenhoek, Robert C.; Parker, Dave

    2009-01-01

    Clonally reproducing all-female lineages of plants and animals are often more frequent at higher latitudes and altitudes, on islands, and in disturbed habitats. Attempts to explain this pattern, known as geographical parthenogenesis, generally treat the parthenogens as fugitive species that occupy...... 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......, they are complex syllogisms that share common assumptions regarding the likely origins of clonal diversity and the strength of interclonal selection in shaping the ecological breadth of asexual populations. Both models find support in ecological and phylogeographic studies of a wide range of organisms...

  9. THE NICHE CONSTRUCTION PERSPECTIVE: A CRITICAL APPRAISAL*

    Science.gov (United States)

    Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

    2014-01-01

    Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). PMID:24325256

  10. 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

  11. Correspondence of biological condition models of California streams at statewide and regional scales

    Science.gov (United States)

    May, Jason T.; Brown, Larry R.; Rehn, Andrew C.; Waite, Ian R.; Ode, Peter R; Mazor, Raphael D; Schiff, Kenneth C

    2015-01-01

    taxonomic completeness is imperative for sound management. Our results suggest that invertebrate taxonomic completeness is affected by human disturbance at the statewide and regional levels, with some differences among regions in the importance of natural gradients and types of human disturbance. The construction and application of models similar to the ones presented here could be useful in the planning and prioritization of actions for protection and conservation of biodiversity in California streams.

  12. Modeling of Geodetic Crustal Motion Velocities in Southern California: Undergraduate Research

    Science.gov (United States)

    McGill, S. F.; Barley, M. E.; Hams, J. E.; Hobart, K.; Ramirez, J.; Fryxell, J. E.; Lyzenga, G. A.; McGill, J. D.

    2003-12-01

    With funding from the National Science Foundation's Opportunities for Enhancing Diversity in the Geosciences, we have undertaken a project with two primary goals: (1) to introduce undergraduate students and K-14 educators to research in geology/geophysics, and (2) to use GPS to monitor deformation across the boundary between the Pacific and North American plates in southern California, and to model the slip on specific faults that could be responsible for that deformation. Starting in July 2002, we collected campaign-style GPS data twice a year from 13 sites along a line across the San Andreas and San Jacinto faults from Norco through San Bernardino to Lucerne Valley. We are also modeling data from the SCEC Crustal Deformation Velocity Map 2.0 [http://www.scecdc.scec.org/group_e/release.v2/]. Our initial approach has been to use a one-dimensional model of dislocations in an elastic half-space. We are studying the portion of the plate boundary from San Bernardino southward to the U.S.-Mexico border. We have divided this region into seven transects that are perpendicular to the plate boundary. We used a spreadsheet macro to systematically model a range of slip rates and locking depths for each fault. Out of hundreds or thousands of possible combinations for each transect, we sorted the models according to their goodness of fit, using the sum of the squares of the residuals as a criterion. We are also beginning to use the program Simplex (G. Lyzenga. J. Parker) to model the velocity data from all transects simultaneously. This will allow us to take into account the complex fault geometry of the region. Our preliminary results from the one-dimensional modeling suggest that the best-fitting slip rate of the San Andreas fault is 26 mm/yr for the section from Indio to Durmid. However, slip rates in the range of 20-30 mm/yr also fit the geodetic data relatively well. Slip rates of 15 or 35 mm/yr do not fit well. For the San Jacinto fault, the best-fitting slip rate is 13

  13. 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...

  14. 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...

  15. Dynamic Ambient Noise Model Comparison with Point Sur, California, In Situ data

    National Research Council Canada - National Science Library

    Leigh, Charlotte V; Eller, Anthony I

    2006-01-01

    ... 1.0 against both in situ ambient noise (AN) measurements collected in 1998 offshore Point Sur, California, and against predicted AN spectrum levels computed with the Ambient Noise Directionality Estimation System (ANDES...

  16. Prognostic Factors for Niche Development in the Uterine Caesarean Section Scar.

    Science.gov (United States)

    Voet, Lucy Lucet F van der; Vaate, A Marjolein J Bij de; Heymans, Martijn W; Brölmann, Hans A M; Veersema, Sebastiaan; Huirne, Judith A F

    2017-06-01

    In a prospective study on 134 women after their first cesarean section prognostic factors for developing an uterine niche (scar defect) measured with sonohysterography were evaluated. With multivariable logistic regression anlaysis the following prognostic factors were identified; enlarged cervical dilatation and induction of labour. Contractions before labour reduced the risk for niche development. The predictive value of the model made with this prognostic factors was low. The development of a niche is a multifactorial proces and more studies are needed. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    Liu, Jinxun; Vogelmann, James E.; Zhu, Zhiliang; Key, Carl H.; Sleeter, Benjamin M.; Price, D.T.; Chen, Jing M.; Cochrane, Mark A.; Eidenshink, Jeffery C.; Howard, Stephen M.; Bliss, Norman B.; Jiang, Hong

    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 77.1 Tg C yr−1 (1 teragram = 1012 g), mainly due to CO2 fertilization, since the climate hardly changed during this period. Similarly, heterotrophic respiration increased by 5%, from 69.4 to 73.1 Tg C yr−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 3.0 Tg C yr−1 (total of 149 Tg C). As with NEP, the net biome production (NBP) was also highly variable but averaged −0.55 Tg C yr−1 (total of –27.3 Tg C) because NBP in the 1980s was very low (–5.34 Tg C yr−1). During the study period, a total of 126 Tg carbon were removed by logging and land use change, and 50 Tg carbon were directly removed by wildland fires. For carbon pools, the estimated total living upper canopy (tree) biomass decreased from 928 to 834 Tg C, and the understory (including shrub and grass) biomass increased from 59 to 63 Tg C. Soil carbon and dead biomass carbon increased from 1136 to 1197 Tg C.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

  18. Performance and Economic Modeling of Horizontally Drilled Ground-Source Heat Pumps in Select California Climates

    Science.gov (United States)

    Wiryadinata, Steven

    Service life modeling was performed to gage the viability of unitary 3.5 kWt, ground-source terminal heat pumps (GTHP) employing horizontal directionally drilled geothermal heat exchangers (GHX) over air-source terminal heat pumps (PTHP) in hotels and motels and residential apartment building sectors in California's coastal and inland climates. Results suggest the GTHP can reduce hourly peak demand for the utility by 7%-25% compared to PTHP, depending on the climate and building type. The annual energy savings, which range from -1% to 5%, are highly dependent on the GTHP pump energy use relative to the energy savings attributed to the difference in ground and air temperatures (DeltaT). In mild climates with small ?T, the pump energy use may overcome any advantage to utilizing a GHX. The majority of total levelized cost savings - ranging from 0.18/ft2 to 0.3/ft 2 - are due to reduced maintenance and lifetime capital cost normally associated with geothermal heat pump systems. Without these reductions (not validated for the GTHP system studied), the GTHP technology does not appear to offer significant advantages over PTHP in the climate zones studied here. The GTHP levelized cost was most sensitive to variations in installed cost and in some cases, energy use (influenced by climate zone choice), which together highlights the importance of climate selection for installation, and the need for larger market penetration of ground-source systems in order to bring down installed costs as the technology matures.

  19. 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.

  20. Monitoring biodiversity using ecosystem assessment surveys and regional ocean models within the California Current

    Science.gov (United States)

    Schroeder, I. D.; Santora, J. A.; Field, J. C.; Hazen, E. L.; Bograd, S. J.

    2016-02-01

    The National Marine Fisheries Service has conducted an annual midwater trawl survey for juvenile rockfish and other pelagic micronekton every May and June from 1983 to the present. Although both the spatial and temporal coverage have varied over time, a "core" region has been sampled continuously for the region that extends from Monterey Bay to just north of San Francisco Bay, California. Stations are located from nearshore waters to the offshore environment, but generally within 60 km from land. The mid-water trawl targets a diverse micronekton community spanning a range of juvenile stages of fishes, adult forage fishes and various invertebrates. Here we use the historical catch data to investigate biodiversity across space and time, specifically through developing indices of richness, diversity and evenness. The interannual variability of these indices is coherent over three unique ecological regions located along the shelf, Monterey Bay submarine canyon, and offshore habitats. Spatiotemporal changes in diversity reflect different taxa such as juvenile groundfish, rockfish and forage fish, and influx of oceanic species to nearshore habitat during anomalous years. Finally, data from CTD casts and from a data-assimilative ROMS model links changes in biodiversity with changing environmental conditions. The results of this project will be used to help inform researchers in the creation of a Marine Biodiversity Observation Network (MBON) in the Monterey Bay National Marine Sanctuary.

  1. 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

  2. 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

  3. A combined modeling and measurement technique for estimating windblown dust emissions at Owens (dry) Lake, California

    Science.gov (United States)

    Gillette, Dale; Ono, Duane; Richmond, Kenneth

    2004-03-01

    The problem of dust emissions from playa sources is an important one both in terms of human health and in terms of global dust issues, distribution of loess, and mineral cycling. A refined method of modeling atmospheric dust concentrations due to wind erosion was developed using real-time saltation flux measurements and ambient dust monitoring data at Owens Lake, California. This modeling method may have practical applications for modeling the atmospheric effects of wind erosion in other areas. Windblown dust from the Owens Lake bed often causes violations of federal air quality standards for particulate matter (PM10) that are the highest levels measured in the United States. The goal of this study was to locate dust source areas on the exposed lake bed, estimate their PM10 emissions, and use air pollution modeling techniques to determine which areas caused or contributed to air quality violations. Previous research indicates that the vertical flux of PM10 (Fa) is generally proportional to the total horizontal saltation flux (q) for a given soil texture and surface condition. For this study, hourly PM10 emissions were estimated using Fa = K' × m15, where m15 is the measured sand flux at 15 cm above the surface, and K' was derived empirically by comparing air quality model predictions to monitored PM10 concentrations. Hourly sand flux was measured at 135 sites (1 km spacing) on the lake bed, and PM10 was monitored at six off-lake sites for a 30 month period. K' was found to change spatially and temporally over the sampling period. These changes appeared to be linked to different soil textures and to seasonal surface changes. K' values compared favorably with other Fa/q values measured at Owens Lake using portable wind tunnel and micrometeorological methods. Hourly trends for the model-predicted PM10 concentrations agreed well with monitored PM10 concentrations. Dust production was estimated at 7.2 × 104 t of PM10 for a 12 month period. A single storm accounted for

  4. Human niche construction in interdisciplinary focus.

    Science.gov (United States)

    Kendal, Jeremy; Tehrani, Jamshid J; Odling-Smee, John

    2011-03-27

    Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene-culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue.

  5. Human niche construction in interdisciplinary focus

    Science.gov (United States)

    Kendal, Jeremy; Tehrani, Jamshid J.; Odling-Smee, John

    2011-01-01

    Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene–culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue. PMID:21320894

  6. 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...

  7. 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...

  8. Artificial niche substrates for embryonic and induced pluripotent stem cell cultures.

    Science.gov (United States)

    Joddar, Binata; Ito, Yoshihiro

    2013-10-20

    Stem cells possess the ability to self-renew and differentiate into other cell types. In vivo, stem cells reside in their own anatomic niches in a defined physiological environment, from which they are released to differentiate into a required cell type when deemed appropriate. While a resident within the niche, the stem cell receives signals that in turn maintain the cell in a pluripotent state. In addition, the niche also provides nourishment to the cell. Physically, the niche also serves to anchor the cell via various ECM components and cell-adhesion molecules. Therefore, in vitro models that replicate the in vivo niche will lead to a better understanding of stem cell fate and turnover. In turn, this will help inform attempts to culture stem cells in vitro on artificial niche-like substrates. In this review, we have highlighted recent studies describing artificial niche-like substrates used to culture embryonic and induced pluripotent stem cells in vitro. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  9. Altruists Proliferate Even at a Selective Disadvantage within Their Own Niche

    Science.gov (United States)

    Wilder, Bryan; Stanley, Kenneth O.

    2015-01-01

    The evolutionary origin of altruism is a long-standing puzzle. Numerous explanations have been proposed, most prominently based on inclusive fitness or group selection. One possibility that has not yet been considered is that new niches will be created disproportionately often when altruism appears, perhaps by chance, causing altruists to be over-represented in such new niches. This effect is a novel variant of group selection in which altruistic groups benefit by discovering unoccupied niches instead of by competing for the limited resources within a single niche. Both an analytical population genetics model and computational simulations support that altruism systematically arises due to this side effect of increased carrying capacity even when it is strongly selected against within any given niche. In fact, even when selection is very strongly negative and altruism does not develop in most populations, it can still be expected to be observed in a consistent fraction of species. The ecological structure provided by niches thereby may be sufficient for altruists to proliferate even if they are always at a disadvantage within each niche considered individually. PMID:26030734

  10. Dynamics of niche width and resource partitioning.

    OpenAIRE

    Dobrev, S.; Kim, T-Y; Hannan, M.T.

    2001-01-01

    This article examines the effects of crowding in a market center on rates of change in organizational niche width and on organizational mortality. It proposes that, although firms with wide niches benefit from risk spreading and economies of scale, they are simultaneously exposed to intense competition. An analysis of organizational dynamics in automobile manufacturing firms in France, Germany, and Great Britain shows that competitive pressure not only increases the hazard of disbanding but a...

  11. Ecological niche modeling for visceral leishmaniasis in the state of Bahia, Brazil, using genetic algorithm for rule-set prediction and growing degree day-water budget analysis

    Directory of Open Access Journals (Sweden)

    Prixia Nieto

    2006-11-01

    Full Text Available Two predictive models were developed within a geographic information system using Genetic Algorithm Rule-Set Prediction (GARP and the growing degree day (GDD-water budget (WB concept to predict the distribution and potential risk of visceral leishmaniasis (VL in the State of Bahia, Brazil. The objective was to define the environmental suitability of the disease as well as to obtain a deeper understanding of the eco-epidemiology of VL by associating environmental and climatic variables with disease prevalence. Both the GARP model and the GDDWB model, using different analysis approaches and with the same human prevalence database, predicted similar distribution and abundance patterns for the Lutzomyia longipalpis-Leishmania chagasi system in Bahia. High and moderate prevalence sites for VL were significantly related to areas of high and moderate risk prediction by: (i the area predicted by the GARP model, depending on the number of pixels that overlapped among eleven annual model years, and (ii the number of potential generations per year that could be completed by the Lu. longipalpis-L. chagasi system by GDD-WB analysis. When applied to the ecological zones of Bahia, both the GARP and the GDD-WB prediction models suggest that the highest VL risk is in the interior region of the state, characterized by a semi-arid and hot climate known as Caatinga, while the risk in the Bahia interior forest and the Cerrado ecological regions is lower. The Bahia coastal forest was predicted to be a low-risk area due to the unsuitable conditions for the vector and VL transmission.

  12. Isotopic niches support the resource breadth hypothesis.

    Science.gov (United States)

    Rader, Jonathan A; Newsome, Seth D; Sabat, Pablo; Chesser, R Terry; Dillon, Michael E; Martínez Del Rio, Carlos

    2017-03-01

    Because a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges. We investigated isotopic niche width in a small radiation of South American birds in the genus Cinclodes. We analysed feathers of 12 species of Cinclodes to test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology. We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology. Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

  13. Isotopic niches support the resource breadth hypothesis

    Science.gov (United States)

    Rader, Jonathan A.; Newsome, Seth D.; Sabat, Pablo; Chesser, R. Terry; Dillon, Michael E.; Martinez del Rio, Carlos

    2017-01-01

    Because a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges.We investigated isotopic niche width in a small radiation of South American birds in the genus Cinclodes. We analysed feathers of 12 species of Cinclodes to test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology.We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology.Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies.

  14. Sustainability of Human Ecological Niche Construction

    Directory of Open Access Journals (Sweden)

    Forest Isbell

    2014-03-01

    Full Text Available Humans influence and depend on natural systems worldwide, creating complex societal-ecological feedbacks that make it difficult to assess the long-term sustainability of contemporary human activities. We use ecological niche theory to consider the short-term (transient and long-term (equilibrium effects of improvements in health, agriculture, or efficiency on the abundances of humans, our plant and animal resources, and our natural enemies. We also consider special cases of our model where humans shift to a completely vegetarian diet, or completely eradicate natural enemies. We find that although combinations of health, agriculture, and efficiency improvements tend to support more people and plant resources, they also result in more natural enemies and fewer animal resources. Considering each of these improvements separately reveals that they lead to different, and sometimes opposing, long-term effects. For example, health improvements can reduce pathogen abundances and make it difficult to sustain livestock production, whereas agricultural improvements tend to counterbalance these effects. Our exploratory analysis of a deliberately simple model elucidates trade-offs and feedbacks that could arise from the cascading effects of human activities.

  15. Invasive plants have broader physiological niches.

    Science.gov (United States)

    Higgins, Steven I; Richardson, David M

    2014-07-22

    Invasive species cost the global economy billions of dollars each year, but ecologists have struggled to predict the risk of an introduced species naturalizing and invading. Although carefully designed experiments are needed to fully elucidate what makes some species invasive, much can be learned from unintentional experiments involving the introduction of species beyond their native ranges. Here, we assess invasion risk by linking a physiologically based species distribution model with data on the invasive success of 749 Australian acacia and eucalypt tree species that have, over more than a century, been introduced around the world. The model correctly predicts 92% of occurrences observed outside of Australia from an independent dataset. We found that invasiveness is positively associated with the projection of physiological niche volume in geographic space, thereby illustrating that species tolerant of a broader range of environmental conditions are more likely to be invasive. Species achieve this broader tolerance in different ways, meaning that the traits that define invasive success are context-specific. Hence, our study reconciles studies that have failed to identify the traits that define invasive success with the urgent and pragmatic need to predict invasive success.

  16. Modeling species’ realized climatic niche space and predicting their response to global warming for several western forest species with small geographic distributions

    Science.gov (United States)

    Marcus V. Warwell; Gerald E. Rehfeldt; Nicholas L. Crookston

    2010-01-01

    The Random Forests multiple regression tree was used to develop an empirically based bioclimatic model of the presence-absence of species occupying small geographic distributions in western North America. The species assessed were subalpine larch (Larix lyallii), smooth Arizona cypress (Cupressus arizonica ssp. glabra...

  17. 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

  18. Species radiation by niche shifts in New Zealand's rockcresses (Pachycladon, Brassicaceae).

    Science.gov (United States)

    Joly, Simon; Heenan, Peter B; Lockhart, Peter J

    2014-03-01

    Adaptive radiations such as the Darwin finches in the Galapagos or the cichlid fishes from the Eastern African Great Lakes have been a constant source of inspiration for biologists and a stimulus for evolutionary thinking. A central concept behind adaptive radiation is that of evolution by niche shifts, or ecological speciation. Evidence for adaptive radiations generally requires a strong correlation between phenotypic traits and the environment. But adaptive traits are often cryptic, hence making this phenotype-environment approach difficult to implement. Here we propose a procedure for detecting adaptive radiation that focuses on species' ecological niche comparisons. It evaluates whether past ecological disparity in a group fits better a neutral Brownian motion model of ecological divergence or a niche shift model. We have evaluated this approach on New Zealand rockcresses (Pachycladon) that recently radiated in the New Zealand Alps. We show that the pattern of ecological divergence rejects the neutral model and is consistent with that of a niche shift model. Our approach to detect adaptive radiation has the advantage over alternative approaches that it focuses on ecological niches, a key concept behind adaptive radiation. It also provides a way to evaluate the importance of ecological speciation in adaptive radiations and will have general application in evolutionary studies. In the case of Pachycladon, the high estimated diversification rate, the distinctive ecological niches of species, and the evidence for ecological speciation suggest a remarkable example of adaptive radiation.

  19. When does it pay to invest in a patch? The evolution of intentional niche construction.

    Science.gov (United States)

    Mohlenhoff, Kathryn A; Codding, Brian F

    2017-09-01

    Humans modify their environments in ways that significantly transform the earth's ecosystems. Recent research suggests that such niche-constructing behaviors are not passive human responses to environmental variation, but instead should be seen as active and intentional management of the environment. Although such research is useful in highlighting the interactive dynamics between humans and their natural world, the niche-construction framework, as currently applied, fails to explain why people would decide to modify their environments in the first place. To help resolve this problem, we use a model of technological intensification to analyze the cost-benefit trade-offs associated with niche construction as a form of patch investment. We use this model to assess the costs and benefits of three paradigmatic cases of intentional niche construction in Western North America: the application of fire in acorn groves, the manufacture of fishing weirs, and the adoption of maize agriculture. Intensification models predict that investing in patch modification (niche construction) only provides a net benefit when the amount of resources needed crosses a critical threshold that makes the initial investment worthwhile. From this, it follows that low-cost investments, such as burning in oak groves, should be quite common, while more costly investments, such as maize agriculture, should be less common and depend on the alternatives available in the local environment. We examine how patterns of mobility, risk management, territoriality, and private property also co-evolve with the costs and benefits of niche construction. This approach illustrates that explaining niche-constructing behavior requires understanding the economic trade-offs involved in patch investment. Integrating concepts from niche construction and technological intensification models within a behavioral ecological framework provides insights into the coevolution and active feedback between adaptive behaviors and

  20. Old health risks in new places? An ecological niche model for I. ricinus tick distribution in Europe under a changing climate.

    Science.gov (United States)

    Boeckmann, Melanie; Joyner, T Andrew

    2014-11-01

    Climate change will likely have impacts on disease vector distribution. Posing a significant health threat in the 21st century, risk of tick-borne diseases may increase with higher annual mean temperatures and changes in precipitation. We modeled the current and future potential distribution of the Ixodes ricinus tick species in Europe. The Genetic Algorithm for Rule-set Prediction (GARP) was utilized to predict potential distributions of I. ricinus based on current (1990-2010 averages) and future (2040-2060 averages) environmental variables. A ten model best subset was created out of a possible 200 models based on omission and commission criteria. Our results show that under the A2 climate change scenario the potential habitat range for the I. ricinus tick in Europe will expand into higher elevations and latitudes (e.g., Scandinavia, the Baltics, and Belarus), while contracting in other areas (e.g., Alps, Pyrenees, interior Italy, and northwestern Poland). Overall, a potential habitat expansion of 3.8% in all of Europe is possible. Our results may be used to inform climate change adaptation efforts in Europe. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. 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. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  2. Incorporating Anthropogenic Influences into Fire Probability Models: Effects of Human Activity and Climate Change on Fire Activity in California.

    Directory of Open Access Journals (Sweden)

    Michael L Mann

    Full Text Available The costly interactions between humans and wildfires throughout California demonstrate the need to understand the relationships between them, 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, with previously published estimates of increases ranging from nine to fifty-three percent by the end of the century. Our goal is to assess the role of climate and anthropogenic influences on the state's fire regimes from 1975 to 2050. We develop an empirical model that integrates estimates of biophysical indicators relevant to plant communities and anthropogenic influences at each forecast time step. Historically, we find that anthropogenic influences account for up to fifty percent of explanatory power in the model. We also find that the total area burned is likely to increase, with burned area expected to increase by 2.2 and 5.0 percent by 2050 under climatic bookends (PCM and GFDL climate models, respectively. Our two climate models show considerable agreement, but due to potential shifts in rainfall patterns, substantial uncertainty remains for the semiarid inland deserts and coastal areas of the south. Given the strength of human-related variables in some regions, however, it is clear that comprehensive projections of future fire activity should include both anthropogenic and biophysical influences. Previous findings of substantially increased numbers of fires and burned area for California may be tied to omitted variable bias from the exclusion of human influences. The omission of anthropogenic variables in our model would overstate the importance of climatic ones by at least 24%. As such, the failure to include anthropogenic effects in many models likely overstates the response of wildfire to climatic change.

  3. Incorporating Anthropogenic Influences into Fire Probability Models: Effects of Human Activity and Climate Change on Fire Activity in California.

    Science.gov (United States)

    Mann, Michael L; Batllori, Enric; Moritz, Max A; Waller, Eric K; Berck, Peter; Flint, Alan L; Flint, Lorraine E; Dolfi, Emmalee

    2016-01-01

    The costly interactions between humans and wildfires throughout California demonstrate the need to understand the relationships between them, 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, with previously published estimates of increases ranging from nine to fifty-three percent by the end of the century. Our goal is to assess the role of climate and anthropogenic influences on the state's fire regimes from 1975 to 2050. We develop an empirical model that integrates estimates of biophysical indicators relevant to plant communities and anthropogenic influences at each forecast time step. Historically, we find that anthropogenic influences account for up to fifty percent of explanatory power in the model. We also find that the total area burned is likely to increase, with burned area expected to increase by 2.2 and 5.0 percent by 2050 under climatic bookends (PCM and GFDL climate models, respectively). Our two climate models show considerable agreement, but due to potential shifts in rainfall patterns, substantial uncertainty remains for the semiarid inland deserts and coastal areas of the south. Given the strength of human-related variables in some regions, however, it is clear that comprehensive projections of future fire activity should include both anthropogenic and biophysical influences. Previous findings of substantially increased numbers of fires and burned area for California may be tied to omitted variable bias from the exclusion of human influences. The omission of anthropogenic variables in our model would overstate the importance of climatic ones by at least 24%. As such, the failure to include anthropogenic effects in many models likely overstates the response of wildfire to climatic change.

  4. Modeling ecological niches and predicting geographic distributions: a test of six presence-only methods Modelado de nichos ecológicos y predicción de distribuciones geográficas: comparación de seis métodos

    OpenAIRE

    Ortega-Huerta, Miguel A.; A. Townsend Peterson

    2008-01-01

    Modeling ecological niches of species as a means to predict geographic distributions is a growing field that has been applied to numerous challenges of importance in ecology, systematics, and human well-being. The increasing availability and variety of such predictive algorithms requires testing their performance. In this study, we compare 6 such algorithms (Maxent, BioMapper, DOMAIN, FloraMap, the genetic algorithm GARP, and weights of evidence) as regards their ability to predict the geogra...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Building a Community Thermal Model for Southern California Using Heat Flow, Geologic, Seismologic and Petrologic Constraints I: Thermophysical Parameters

    Science.gov (United States)

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

    2016-12-01

    We are building a community thermal model (CTM) for Southern California that will provide temperatures and their uncertainties throughout the lithosphere. The CTM is an essential ingredient for a community rheologic model to simulate lithospheric deformation and constrain earthquake cycle movements in southern California. Lithospheric geotherms parametric in surface heat flow include: (1) models of conductive heat transfer in the lithosphere, (2) lithology of the crust and lithospheric mantle, and (3) thermophysical properties (thermal conductivity, k, and radiogenic heat production, A) to be assigned in the lithologic model. Inexact knowledge of the lithology of the crust can lead to large temperature uncertainties. Lab measurements show that thermal conductivity can vary from 1 to 6 W m-1 K-1 in near-surface rocks depending primarily on quartz vs clay content, but varies only from 2 to 3 W m-1 K-1 for mafic rocks of the lower crust and ultramafic rocks of the upper mantle. Likewise, heat production is highly variable at the surface but decreases progressively by three orders of magnitude between likely upper crustal felsic rocks, the more mafic rocks of the lower crust, and ultramafic mantle rocks. In southern California the lithologic model is constrained by mapped surface geology and subsurface structure is guided by seismic investigations. Where direct sampling of the crust and upper mantle is not possible we apply empirical fits between seismic velocity and thermophysical parameters. As a test case we apply our thermophysical parameter assignment along the LARSE 1 seismic transect. Even along this relatively well studied transect the model uncertainties are large, forcing us to seek bounds on deeper lithospheric temperatures. As shown in our companion poster (Thatcher et al., this meeting) seismic estimates of lithosphere-asthenosphere boundary depth and temperature inferred from petrologic bounds on asthenospheric melting provide useful additional

  10. Why developmental niche construction is not selective niche construction: and why it matters.

    Science.gov (United States)

    Stotz, Karola

    2017-10-06

    In the last decade, niche construction has been heralded as the neglected process in evolution. But niche construction is just one way in which the organism's interaction with and construction of the environment can have potential evolutionary significance. The constructed environment does not just select for, it also produces new variation. Nearly 3 decades ago, and in parallel with Odling-Smee's article 'Niche-constructing phenotypes', West and King introduced the 'ontogenetic niche' to give the phenomena of exogenetic inheritance a formal name. Since then, a range of fields in the life sciences and medicine has amassed evidence that parents influence their offspring by means other than DNA (parental effects), and proposed mechanisms for how heritable variation can be environmentally induced and developmentally regulated. The concept of 'developmental niche construction' (DNC) elucidates how a diverse range of mechanisms contributes to the transgenerational transfer of developmental resources. My most central of claims is that whereas the selective niche of niche construction theory is primarily used to explain the active role of the organism in its selective environment, DNC is meant to indicate the active role of the organism in its developmental environment. The paper highlights the differences between the construction of the selective and the developmental niche, and explores the overall significance of DNC for evolutionary theory.

  11. Leukemic cells create bone marrow niches that disrupt the behavior of normal hematopoietic progenitor cells.

    Science.gov (United States)

    Colmone, Angela; Amorim, Maria; Pontier, Andrea L; Wang, Sheng; Jablonski, Elizabeth; Sipkins, Dorothy A

    2008-12-19

    The host tissue microenvironment influences malignant cell proliferation and metastasis, but little is known about how tumor-induced changes in the microenvironment affect benign cellular ecosystems. Applying dynamic in vivo imaging to a mouse model, we show that leukemic cell growth disrupts normal hematopoietic progenitor cell (HPC) bone marrow niches and creates abnormal microenvironments that sequester transplanted human CD34+ (HPC-enriched) cells. CD34+ cells in leukemic mice declined in number over time and failed to mobilize into the peripheral circulation in response to cytokine stimulation. Neutralization of stem cell factor (SCF) secreted by leukemic cells inhibited CD34+ cell migration into malignant niches, normalized CD34+ cell numbers, and restored CD34+ cell mobilization in leukemic mice. These data suggest that the tumor microenvironment causes HPC dysfunction by usurping normal HPC niches and that therapeutic inhibition of HPC interaction with tumor niches may help maintain normal progenitor cell function in the setting of malignancy.

  12. Stochastic dynamics for two biological species and ecological niches

    Science.gov (United States)

    Ruziska, Flávia M.; Arashiro, Everaldo; Tomé, Tânia

    2018-01-01

    We consider an ecological system in which two species interact with two niches. To this end we introduce a stochastic model with four states. Our analysis is founded in three approaches: Monte Carlo simulations of the model on a square lattice, mean-field approximation, and birth and death master equation. From this last approach we obtain a description in terms of Langevin equations which show in an explicit way the role of noise in population biology. We focus mainly on the description of time oscillations of the species population and the alternating dominance between them. The model treated here may provide insights on these properties.

  13. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau.

    Science.gov (United States)

    Wang, Bin; Xie, Feng; Li, Jiannan; Wang, Gang; Li, Cheng; Jiang, Jianping

    2017-01-01

    The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

  14. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau

    Directory of Open Access Journals (Sweden)

    Bin Wang

    2017-09-01

    Full Text Available The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

  15. The niche, biogeography and species interactions

    Science.gov (United States)

    Wiens, John J.

    2011-01-01

    In this paper, I review the relevance of the niche to biogeography, and what biogeography may tell us about the niche. The niche is defined as the combination of abiotic and biotic conditions where a species can persist. I argue that most biogeographic patterns are created by niche differences over space, and that even ‘geographic barriers’ must have an ecological basis. However, we know little about specific ecological factors underlying most biogeographic patterns. Some evidence supports the importance of abiotic factors, whereas few examples exist of large-scale patterns created by biotic interactions. I also show how incorporating biogeography may offer new perspectives on resource-related niches and species interactions. Several examples demonstrate that even after a major evolutionary radiation within a region, the region can still be invaded by ecologically similar species from another clade, countering the long-standing idea that communities and regions are generally ‘saturated’ with species. I also describe the somewhat paradoxical situation where competition seems to limit trait evolution in a group, but does not prevent co-occurrence of species with similar values for that trait (called here the ‘competition–divergence–co-occurrence conundrum’). In general, the interface of biogeography and ecology could be a major area for research in both fields. PMID:21768150

  16. The Hematopoietic Niche in Myeloproliferative Neoplasms

    Directory of Open Access Journals (Sweden)

    Annette H. Schmitt-Graeff

    2015-01-01

    Full Text Available Specialized microanatomical areas of the bone marrow provide the signals that are mandatory for the maintenance and regulation of hematopoietic stem cells (HSCs and progenitor cells. A complex microenvironment adjacent to the marrow vasculature (vascular niche and close to the endosteum (endosteal niche harbors multiple cell types including mesenchymal stromal cells and their derivatives such as CAR cells expressing high levels of chemokines C-X-C motif ligand 12 and early osteoblastic lineage cells, endothelial cells, and megakaryocytes. The characterization of the cellular and molecular networks operating in the HSC niche has opened new perspectives for the understanding of the bidirectional cross-talk between HSCs and stromal cell populations in normal and malignant conditions. A structural and functional remodeling of the niche may contribute to the development of myeloproliferative neoplasms (MPN. Malignant HSCs may alter the function and survival of MSCs that do not belong to the neoplastic clone. For example, a regression of nestin+ MSCs by apoptosis has been attributed to neuroglial damage in MPN. Nonneoplastic MSCs in turn can promote aggressiveness and drug resistance of malignant cells. In the future, strategies to counteract the pathological interaction between the niche and neoplastic HSCs may offer additional treatment strategies for MPN patients.

  17. Niche Konselor di Indonesia dalam Pendidikan Formal

    Directory of Open Access Journals (Sweden)

    Galang Surya Gumilang

    2017-08-01

    Full Text Available Abstract: This article describes and discusses (1 understanding of "niche", (2 niche counselor in Indonesia, (3 niche counselor on formal education, (4 niche counselor "to come" in Indonesia. Constraints to realize the role of school counselors, among others, principals and subject teachers who do not understand the function of guidance and counseling. Many school counselors who are not graduates of Guidance and Counseling but are merely odd or functional. Many and almost average in school School counselors do not have adequate facilities to work ideally, so the counselor's performance is less than optimal. School counselors are not considered important by students and educational components in schools. To overcome these obstacles required the participation of both governments, ABKIN, own counselor, and community environment, especially the school environment. From the counselor and the institution that shelter it needs to show good performance and from other components need to give trust and opportunity to the counselor to show its performance.Keywords: Niche, Counselor, Formal Education

  18. 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.

  19. Habitat modeling and movements of the Yosemite toad (Anaxyrus (=Bufo) canorus) in the Sierra Nevada, California

    Science.gov (United States)

    C.T. Liang

    2010-01-01

    The Yosemite toad (Anaxyrus (=Bufo) canorus) is a high-elevation species endemic to the Sierra Nevada mountain range in California and is part of the world-wide amphibian declines phenomenon. The toad is thought to have disappeared from over 50% of its historic range even in seemingly undisturbed areas, and...

  20. Average niche breadths of species in lake macrophyte communities respond to ecological gradients variably in four regions on two continents.

    Science.gov (United States)

    Alahuhta, Janne; Virtala, Antti; Hjort, Jan; Ecke, Frauke; Johnson, Lucinda B; Sass, Laura; Heino, Jani

    2017-05-01

    Different species' niche breadths in relation to ecological gradients are infrequently examined within the same study and, moreover, species niche breadths have rarely been averaged to account for variation in entire ecological communities. We investigated how average environmental niche breadths (climate, water quality and climate-water quality niches) in aquatic macrophyte communities are related to ecological gradients (latitude, longitude, altitude, species richness and lake area) among four distinct regions (Finland, Sweden and US states of Minnesota and Wisconsin) on two continents. We found that correlations between the three different measures of average niche breadths and ecological gradients varied considerably among the study regions, with average climate and average water quality niche breadth models often showing opposite trends. However, consistent patterns were also found, such as widening of average climate niche breadths and narrowing of average water quality niche breadths of aquatic macrophytes along increasing latitudinal and altitudinal gradients. This result suggests that macrophyte species are generalists in relation to temperature variations at higher latitudes and altitudes, whereas species in southern, lowland lakes are more specialised. In contrast, aquatic macrophytes growing in more southern nutrient-rich lakes were generalists in relation to water quality, while specialist species are adapted to low-productivity conditions and are found in highland lakes. Our results emphasise that species niche breadths should not be studied using only coarse-scale data of species distributions and corresponding environmental conditions, but that investigations on different kinds of niche breadths (e.g., climate vs. local niches) also require finer resolution data at broad spatial extents.

  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......Scholarly communities are dependent on and often measured by their ability to attract and develop doctoral students. Recent literature suggests that most scholarly communities entail ecological niches in which the doctoral students learn the codes and practices of research. In this article, we...

  2. Advection and starvation cause krill (Euphausia pacifica) decreases in 2005 Northern California coastal populations: Implications from a model study

    Science.gov (United States)

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

    2011-02-01

    A decrease in krill abundance during 2005 in regions of the California Current has been hypothesized to have had immediate (seabird) and long-term (salmon) negative impacts on upper trophic level predators. We use a suite of coupled models to examine the population biology and spatial and temporal distribution of the krill species Euphausia pacifica during the winter/spring of 2001, a “normal” year, and 2005, an “anomalous” year, to determine if this hypothesis is supported mechanistically. Ocean conditions were simulated using the Regional Ocean Modeling System (ROMS), which forced an individual-based model parameterized to simulate the population biology of E. pacifica. Poleward transport during winter 2005 advected particles north of Cape Mendocino, away from seabirds and salmon feeding in the Gulf of the Farallons region. Few of the particles that were advected north in 2005 returned to their region of release throughout the model run time (200 days). Moreover, the “condition” of those particles remaining within the domain was poor in 2005, with greater mortality from starvation and a decreased mean particle weight. Our results indicate that both physical processes (anomalous northern advection) and biological processes (greater starvation and less weight per individual) contributed to reduced krill availability to predators in the northern California region during 2005, and that the productivity and survival of seabirds and salmonids is dependent on krill during critical life history stages.

  3. 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

  4. Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range.

    Science.gov (United States)

    López-Alvarez, Diana; Manzaneda, Antonio J; Rey, Pedro J; Giraldo, Patricia; Benavente, Elena; Allainguillaume, Joël; Mur, Luis; Caicedo, Ana L; Hazen, Samuel P; Breiman, Adina; Ezrati, Smadar; Catalán, Pilar

    2015-07-01

    • We conducted environmental niche modeling (ENM) of the Brachypodium distachyon s.l. complex, a model group of two diploid annual grasses (B. distachyon, B. stacei) and their derived allotetraploid (B. hybridum), native to the circum-Mediterranean region. We (1) investigated the ENMs of the three species in their native range based on present and past climate data; (2) identified potential overlapping niches of the diploids and their hybrid across four Quaternary windows; (3) tested whether speciation was associated with niche divergence/conservatism in the complex species; and (4) tested for the potential of the polyploid outperforming the diploids in the native range.• Geo-referenced data, altitude, and 19 climatic variables were used to construct the ENMs. We used paleoclimate niche models to trace the potential existence of ancestral gene flow among the hybridizing species of the complex.• Brachypodium distachyon grows in higher, cooler, and wetter places, B. stacei in lower, warmer, and drier places, and B. hybridum in places with intermediate climatic features. Brachypodium hybridum had the largest niche overlap with its parent niches, but a similar distribution range and niche breadth.• Each species had a unique environmental niche though there were multiple niche overlapping areas for the diploids across time, suggesting the potential existence of several hybrid zones during the Pleistocene and the Holocene. No evidence of niche divergence was found, suggesting that species diversification was not driven by ecological speciation but by evolutionary history, though it could be associated to distinct environmental adaptations. © 2015 Botanical Society of America, Inc.

  5. 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

  6. A comparison among observations and earthquake simulator results for the allcal2 California fault model

    Science.gov (United States)

    Tullis, Terry. E.; Richards-Dinger, Keith B.; Barall, Michael; Dieterich, James H.; Field, Edward H.; Heien, Eric M.; Kellogg, Louise; Pollitz, Fred F.; Rundle, John B.; Sachs, Michael K.; Turcotte, Donald L.; Ward, Steven N.; Yikilmaz, M. Burak

    2012-01-01

    In order to understand earthquake hazards we would ideally have a statistical description of earthquakes for tens of thousands of years. Unfortunately the ∼100‐year instrumental, several 100‐year historical, and few 1000‐year paleoseismological records are woefully inadequate to provide a statistically significant record. Physics‐based earthquake simulators can generate arbitrarily long histories of earthquakes; thus they can provide a statistically meaningful history of simulated earthquakes. The question is, how realistic are these simulated histories? This purpose of this paper is to begin to answer that question. We compare the results between different simulators and with information that is known from the limited instrumental, historic, and paleoseismological data.As expected, the results from all the simulators show that the observational record is too short to properly represent the system behavior; therefore, although tests of the simulators against the limited observations are necessary, they are not a sufficient test of the simulators’ realism. The simulators appear to pass this necessary test. In addition, the physics‐based simulators show similar behavior even though there are large differences in the methodology. This suggests that they represent realistic behavior. Different assumptions concerning the constitutive properties of the faults do result in enhanced capabilities of some simulators. However, it appears that the similar behavior of the different simulators may result from the fault‐system geometry, slip rates, and assumed strength drops, along with the shared physics of stress transfer.This paper describes the results of running four earthquake simulators that are described elsewhere in this issue of Seismological Research Letters. The simulators ALLCAL (Ward, 2012), VIRTCAL (Sachs et al., 2012), RSQSim (Richards‐Dinger and Dieterich, 2012), and ViscoSim (Pollitz, 2012) were run on our most recent all‐California fault

  7. Niche models tell half the story

    DEFF Research Database (Denmark)

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

    2012-01-01

    the relative influence of climate change and a range of fire regimes on the viability of a long-lived plant population. Specifically, we investigate whether range shift due to climate change is a greater threat to an obligate seeding fire-prone shrub than altered fire frequency and how these two threatening...

  8. Human bone perivascular niche-on-a-chip for studying metastatic colonization.

    Science.gov (United States)

    Marturano-Kruik, Alessandro; Nava, Michele Maria; Yeager, Keith; Chramiec, Alan; Hao, Luke; Robinson, Samuel; Guo, Edward; Raimondi, Manuela Teresa; Vunjak-Novakovic, Gordana

    2018-02-06

    Eight out of 10 breast cancer patients die within 5 years after the primary tumor has spread to the bones. Tumor cells disseminated from the breast roam the vasculature, colonizing perivascular niches around blood capillaries. Slow flows support the niche maintenance by driving the oxygen, nutrients, and signaling factors from the blood into the interstitial tissue, while extracellular matrix, endothelial cells, and mesenchymal stem cells regulate metastatic homing. Here, we show the feasibility of developing a perfused bone perivascular niche-on-a-chip to investigate the progression and drug resistance of breast cancer cells colonizing the bone. The model is a functional human triculture with stable vascular networks within a 3D native bone matrix cultured on a microfluidic chip. Providing the niche-on-a-chip with controlled flow velocities, shear stresses, and oxygen gradients, we established a long-lasting, self-assembled vascular network without supplementation of angiogenic factors. We further show that human bone marrow-derived mesenchymal stem cells, which have undergone phenotypical transition toward perivascular cell lineages, support the formation of capillary-like structures lining the vascular lumen. Finally, breast cancer cells exposed to interstitial flow within the bone perivascular niche-on-a-chip persist in a slow-proliferative state associated with increased drug resistance. We propose that the bone perivascular niche-on-a-chip with interstitial flow promotes the formation of stable vasculature and mediates cancer cell colonization.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Development of a laboratory niche Web site.

    Science.gov (United States)

    Dimenstein, Izak B; Dimenstein, Simon I

    2013-10-01

    This technical note presents the development of a methodological laboratory niche Web site. The "Grossing Technology in Surgical Pathology" (www.grossing-technology.com) Web site is used as an example. Although common steps in creation of most Web sites are followed, there are particular requirements for structuring the template's menu on methodological laboratory Web sites. The "nested doll principle," in which one object is placed inside another, most adequately describes the methodological approach to laboratory Web site design. Fragmentation in presenting the Web site's material highlights the discrete parts of the laboratory procedure. An optimally minimal triad of components can be recommended for the creation of a laboratory niche Web site: a main set of media, a blog, and an ancillary component (host, contact, and links). The inclusion of a blog makes the Web site a dynamic forum for professional communication. By forming links and portals, cloud computing opens opportunities for connecting a niche Web site with other Web sites and professional organizations. As an additional source of information exchange, methodological laboratory niche Web sites are destined to parallel both traditional and new forms, such as books, journals, seminars, webinars, and internal educational materials. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Niche construction and the evolution of leadership

    NARCIS (Netherlands)

    Spisak, B.R.; O'Brien, M.; Nicholson, N.; van Vugt, M.

    2015-01-01

    We use the concept of niche construction - the process whereby individuals, through their activities, interactions, and choices, modify their own and each other's environments - as an example of how biological evolution and cultural evolution interacted to form an integrative foundation of modern

  16. Adhesion in the stem cell niche: biological roles and regulation

    Science.gov (United States)

    Chen, Shuyi; Lewallen, Michelle; Xie, Ting

    2013-01-01

    Stem cell self-renewal is tightly controlled by the concerted action of stem cell-intrinsic factors and signals within the niche. Niche signals often function within a short range, allowing cells in the niche to self-renew while their daughters outside the niche differentiate. Thus, in order for stem cells to continuously self-renew, they are often anchored in the niche via adhesion molecules. In addition to niche anchoring, however, recent studies have revealed other important roles for adhesion molecules in the regulation of stem cell function, and it is clear that stem cell-niche adhesion is crucial for stem cell self-renewal and is dynamically regulated. Here, we highlight recent progress in understanding adhesion between stem cells and their niche and how this adhesion is regulated. PMID:23250203

  17. 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.

  18. Developing Cultural Awareness. Grade 1 Model Lesson for Standard 5. California History-Social Science Course Models.

    Science.gov (United States)

    Sing, Sandi; Stewart, Linda; Roth, Patsy; Porter, Priscilla

    The students in California's classrooms live in a world of diversity. They eat unique foods, wear different types of clothes, live in different types of homes, and speak and hear many languages. This unit focuses on cultures, customs, ceremonies, traditions, foods, clothing, and shelter. These basic universal necessities of life--food, clothing,…

  19. Estimates of fault-slip rates in southern California by using non-block viscoelastic sheet models

    Science.gov (United States)

    Chuang, R. Y.; Johnson, K. M.

    2013-12-01

    Fault slip rate estimates from geodetic data are becoming increasingly important for earthquake hazard studies. In order to estimate fault slip rates, GPS-constrained kinematic models such as elastic block models are widely used. However, kinematic block models are inherently non-unique and provide limited insight into the mechanics of deformation. In addition, assumed discrete tectonic blocks may not exist everywhere as not every region of the western US displays mature, through-going geologic structures that naturally divide the crust into tectonic blocks. For example, the eastern California shear zone and regions of the Basin and Range Province are best described as broad zones of interacting, discontinuous fault strands. We build a mechanical model of present-day surface motions in which deformation is a response to plate boundary forces, gravitational loading, and rheological properties of the lithosphere. To model long-term fault-slip rates in the southwestern US, we populate an elastico-visco thin sheet (plane stress) with thin viscous shear zones (faults) and impose far-field plate motions and gravitational loading to compute the long-term fault slip rates and crustal motions. The mechanical model inherently allows slips along through-going and discontinuous faults and the viscosity of the lithospheric sheet relaxes unreasonable stress build-up. The fault zone viscosity provides resistance and directly relates stress to slip rates. We incorporate static stress on the fault due to regional gravitational potential energy derived from Flesch et al. (2007). We calculate long-term fault-slip rates in southern California and incorporate backslip as interseismic deformation due to locking of faults to compare the total present-day deformation field (long-term plus intersesismic) with the GPS-derived velocity field.

  20. Multi-model comparison on the effects of climate change on tree species in the eastern U.S.: results from an enhanced niche model and process-based ecosystem and landscape models

    Science.gov (United States)

    Louis R. Iverson; Frank R. Thompson; Stephen Matthews; Matthew Peters; Anantha Prasad; William D. Dijak; Jacob Fraser; Wen J. Wang; Brice Hanberry; Hong He; Maria Janowiak; Patricia Butler; Leslie Brandt; Chris Swanston

    2016-01-01

    Context. Species distribution models (SDM) establish statistical relationships between the current distribution of species and key attributes whereas process-based models simulate ecosystem and tree species dynamics based on representations of physical and biological processes. TreeAtlas, which uses DISTRIB SDM, and Linkages and LANDIS PRO, process...

  1. 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.

  2. 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. © 2015 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

  3. Modeling of Trans-boundary Transport of Air Pollutants in the California-Mexico Border Region during Cal-Mex 2010

    Science.gov (United States)

    Bei, N.; Zavala, M. A.; Lei, W.; Li, G.; Molina, L. T.

    2010-12-01

    The US and Mexico share a common air basin along the ~200 km border between California and Baja California. The economical activities in this region are heavily influenced by the international trade and commerce between Mexico and the US that mainly occurs through the borders of the sister cities of San Diego-Tijuana and Calexico-Mexicali. The diversity and differences in the characteristics of emissions sources of air pollutants in the California-Mexico border region make this an important area for the study of the chemistry and trans-boundary transport of air pollutants. During May-June of 2010, the Cal-Mex 2010 field campaign included a series of measurements aimed at characterizing the emissions from major sources in the California-Mexico border region and assessing the possible impacts of these emissions on local and regional air quality. In this work we will present the results of the use of the Comprehensive Air quality model with extensions (CAMx) in a modeling domain that includes the sister cities of San Diego-Tijuana and Calexico-Mexicali for studying events of trans-boundary transport of air pollutants during Cal-Mex 2010. The measurements obtained during the Cal-Mex 2010 field campaign are used in the evaluation of the model performance and in the design of air quality improvement policies in the California-Mexico border region.

  4. Basalt models for the Mars penetrator mission: Geology of the Amboy Lava Field, California

    Science.gov (United States)

    Greeley, R.; Bunch, T. E.

    1976-01-01

    Amboy lava field (San Bernardino County, California) is a Holocene basalt flow selected as a test site for potential Mars Penetrators. A discussion is presented of (1) the general relations of basalt flow features and textures to styles of eruptions on earth, (2) the types of basalt flows likely to be encountered on Mars and the rationale for selection of the Amboy lava field as a test site, (3) the general geology of the Amboy lava field, and (4) detailed descriptions of the target sites at Amboy lava field.

  5. Molecular signatures of the primitive prostate stem cell niche reveal novel mesenchymal-epithelial signaling pathways.

    Directory of Open Access Journals (Sweden)

    Roy Blum

    2010-09-01

    Full Text Available 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.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.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 be common to mammalian niches in general. This study provides a

  6. Molecular signatures of the primitive prostate stem cell niche reveal novel mesenchymal-epithelial signaling pathways.

    Science.gov (United States)

    Blum, Roy; Gupta, Rashmi; Burger, Patricia E; Ontiveros, Christopher S; Salm, Sarah N; Xiong, Xiaozhong; Kamb, Alexander; Wesche, Holger; Marshall, Lisa; Cutler, Gene; Wang, Xiangyun; Zavadil, Jiri; Moscatelli, David; Wilson, E Lynette

    2010-09-30

    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. 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. 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 be common to mammalian niches in general. This study provides a comprehensive source

  7. 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...

  8. Two-dimensional, high-resolution modeling of urban dam-break flooding: A case study of Baldwin Hills, California

    Science.gov (United States)

    Gallegos, Humberto A.; Schubert, Jochen E.; Sanders, Brett F.

    2009-08-01

    Modeling of dam-break flooding in an urban residential area in southern California is presented. Modeling is performed using BreZo, an unstructured grid, Godunov-type, finite volume model that solves the shallow-water equations. The model uses terrain data from a 1.5 m Light Detection and Ranging (LiDAR) Digital Terrain Model (DTM) and contour data depicting the reservoir and breach geometry. A spatially distributed Manning coefficient based on a landcover classification derived from digital orthophotos and vector data (e.g., parcel outlines) is also used, and the interception of flow by storm drains is modeled with sink terms in the 2D continuity equation. The model is validated with flood extent and stream flow measurements, and a sensitivity analysis is completed to identify the necessary level of data and model complexity for accuracy purposes. Results show street depressions in the land surface should be resolved by the computational mesh for flood extent and stream flow accuracy. A ca. 5 m resolution mesh that spans streets by approximately 3 cells achieves a good balance between accuracy and computational effort. Results also show that heterogeneous resistance is important for stream flow accuracy, and the interception of overland flow by storm sewers is important for flood extent accuracy. The sensitivity of predictions to several additional factors such as the reservoir level, breach geometry and DTM source (LiDAR, National Elevation Data, Shuttle Radar Topography Mission Data) is also reported.

  9. Modeling the oxidative capacity of the atmosphere of the south coast air basin of California. 2. HOx radical production.

    Science.gov (United States)

    Griffin, Robert J

    2004-02-01

    The production of HOx radicals in the South Coast Air Basin of California is investigated during the smog episode of September 9, 1993 using the California Institute of Technology (CIT) air-quality model. Sources of HOx(hydroxyl, hydroperoxy, and organic peroxy radicals) incorporated into the associated gas-phase chemical mechanism include the combination of excited-state singlet oxygen (formed from ozone (O3) photolysis (hv)) with water, the photolysis of nitrous acid, hydrogen peroxide (H2O2), and carbonyl compounds (formaldehyde (HCHO) or higher aldehydes and ketones), the consumption of aldehydes and alkenes (ALK) by the nitrate radical, and the consumption of alkenes by O3 and the oxygen atom (O). At a given time or location for surface cells and vertical averages, each route of HOx formation may be the greatest contributor to overall formation except HCHO-hv, H2O2-hv, and ALK-O, the latter two of which are insignificant pathways in general. The contribution of the ALK-O3 pathway is dependent on the stoichiometric yield of OH, but this pathway, at least for the studied smog episode, may not be as generally significant as previous research suggests. Future emissions scenarios yield lower total HOx production rates and a shift in the relative importance of individual pathways.

  10. Modeling the oxidative capacity of the atmosphere of the south coast air basin of California. 1. Ozone formation metrics.

    Science.gov (United States)

    Griffin, Robert J; Revelle, Meghan K; Dabdub, Donald

    2004-02-01

    Metrics associated with ozone (O3) formation are investigated using the California Institute of Technology (CIT) three-dimensional air-quality model. Variables investigated include the O3 production rate (P(O3)), O3 production efficiency (OPE), and total reactivity (the sum of the reactivity of carbon monoxide (CO) and all organic gases that react with the hydroxyl radical). Calculations are spatially and temporally resolved; surface-level and vertically averaged results are shown for September 9, 1993 for three Southern California locations: Central Los Angeles, Azusa, and Riverside. Predictions indicate increasing surface-level O3 concentrations with distance downwind, in line with observations. Surface-level and vertically averaged P(O3) values peak during midday and are highest downwind; surface P(O3) values are greater than vertically averaged values. Surface OPEs generally are highest downwind and peak during midday in downwind locations. In contrast, peaks occur in early morning and late afternoon in the vertically averaged case. Vertically averaged OPEs tend to be greater than those for the surface. Total reactivities are highest in upwind surface locations and peak during rush hours; vertically averaged reactivities are smaller and tend to be more uniform temporally and spatially. Total reactivity has large contributions from CO, alkanes, alkenes, aldehydes, unsubstituted monoaromatics, and secondary organics. Calculations using estimated emissions for 2010 result in decreases in P(O3) values and reactivities but increases in OPEs.

  11. Modeling cold curing of Pierce's disease in Vitis vinifera 'Pinot Noir' and 'Cabernet Sauvignon' grapevines in California.

    Science.gov (United States)

    Lieth, J H; Meyer, M M; Yeo, K-H; Kirkpatrick, B C

    2011-12-01

    Pierce's disease (PD) of Vitis vinifera grapevines is caused by the bacterium Xylella fastidiosa, a pathogen with a wide plant host range. Exposure of X. fastidiosa-infected plant tissue to cold temperatures has been shown to be effective at eliminating the pathogen from some plant hosts such as grapevines. This "cold curing" phenomenon suggests itself as a potential method for disease management and perhaps control. We investigated cold therapy of PD-affected 'Pinot Noir' and 'Cabernet Sauvignon' grapevine. In the fall, inoculated plants and controls of each cultivar were transported to each of four field sites in California (Foresthill, McLaughlin, Hopland, and Davis) that differed in the magnitude of cold winter temperatures. A model for progression of the elimination of plant disease in relation to temperature was conceptualized to be a temperature-duration effect, where temperatures below a particular threshold kill X. fastidiosa with increasing efficacy as the temperature decreases to some value Pinot Noir and T(0) = 6°C, N(100) = 302 h, N(10) = 170 h, and K(x) = 0.41 for Cabernet Sauvignon. With the parameter estimates optimized by model calibration, the simulation model was effective at predicting cold curing in four locations during the experiment, although there were some differences between Hopland for Pinot Noir and Davis for Cabernet Sauvignon. Using historical temperature data, the model accurately predicted the known severity of PD in other grape-growing regions of California, suggesting that it may have utility in assessing the relative risk of developing PD in proposed new vineyard sites.

  12. 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.

  13. Development and use of a mathematical model of the San Bernardino Valley ground-water basin, California

    Science.gov (United States)

    Hardt, William F.; Hutchinson, C.B.

    1980-01-01

    Part of the San Bernardino urbanized area in California overlies formerly swampy lands with a history of flowing wells. This area , upgradient from and adjacent to the San Jacinto fault, contains a zone in an alluvial ground-water basin that is under artesian pressure. Since 1945, withdrawals have exceeded recharge and caused head declines of more than 100 feet. Artificial recharge of imported water in the upgradient areas may cause ground-water levels to rise, which could cause abandoned but unplugged wells to resume flowing. If so, structures could be damaged. A two-layer Galerkin finite-element digital model was used for predicting the rate and extent of the rise in water levels from 1975 to 2000. Six hydrologic conditions were modeled for the basin. Artificial recharge of one-half entitlement and full entitlement from the California Aqueduct were each coupled with low, average, and high natural recharge to the basin. According to model predictions, the greatest water level rises will be along the San Bernardino front. This area encompasses the artificial recharge sites and also has a thick section of unsaturated sediments for storing ground water. The formerly swampy lands between Warm Creek and the Santa Ana River adjacent to the San Jacinto fault have little additional storage capacity, and water levels could rise to the land surface as early as 1983 under maximum recharge conditions and 1970-74 average pumping conditions. If pumping rates are reduced in the Warm Creek area, water levels may rise to land surface prior to the dates predicted by the model, regardless of the artificial-recharge program. (USGS)

  14. 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.

  15. [Concept and connotation development of niche and its ecological orientation].

    Science.gov (United States)

    Peng, Wen-jun; Wang, Xiao-ming

    2016-01-01

    Proceeding from the niche concept; the article commented the main points of each concept's connotation basing on a systematic review of development on niche concepts, and divided the process into four phases including germination, standardization, quantification and perfection, with two main academic schools. Questions and challenges during niche's development and advancement were presented to extract the characteristics and components of niche concept. On these bases, we explored the orientation of niche concept in ecology, and suggested to position it as a macro concept and detail it in specific applications. Further research points and application perspectives were stated in the end.

  16. Kinematic Models of Southern California Deformation calibrated to GPS Velocities and a Strain Energy Minimization Criterion: How do they Differ?

    Science.gov (United States)

    Hearn, E. H.

    2015-12-01

    Fault slip rates inferred from GPS-calibrated kinematic models may be influenced by seismic-cycle and other transient effects, whereas models that minimize strain energy ("TSEM models") represent average deformation rates over geological timescales. To explore differences in southern California fault slip rates inferred from these two approaches, I have developed kinematic, finite-element models incorporating the UCERF3 block model-bounding fault geometry and slip rates from the UCERF3 report (Field et al., 2014). A fault segment (the "Ventura-Oak Ridge segment") was added to represent shortening accommodated collectively by the San Cayetano, Ventura, Oak Ridge, Red Mountain and other faults in the Transverse Ranges. Fault slip rates are randomly sampled from ranges given in the UCERF3 report, assuming a "boxcar" distribution, and models are scored by their misfit to GPS site velocities or to their total strain energy, for cases with locked and unlocked faults. Both Monte Carlo and Independence Sampler MCMC methods are used to identify the best models of each category. All four suites of models prefer low slip rates (i.e. less than about 5 mm/yr) on the Ventura-Oak Ridge fault system. For TSEM models, low rates ( 13 and > 3 mm/yr, respectively), and a somewhat low rate for the Mojave segment of the SAF (25-34 mm/yr). Because blind thrust faults of the Los Angeles Basin are not represented in the model, the inferred Ventura-Oak Ridge slip rate should be high, but the opposite is observed. GPS-calibrated models decisively prefer a lower slip rate along the Mojave segment of the SAF than TSEM models, consistent with viscoelastic velocity perturbations late in the SSAF seismic cycle. The low San Gorgonio SAF slip rates inferred from TSEM models are consistent with strain transfer from the SAF Coachella segment to the ECSZ, bypassing the San Gorgonio SAF segment (e.g., Wallace, 1984).

  17. 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.

  18. Cigarette Smoke Alters the Hematopoietic Stem Cell Niche

    Directory of Open Access Journals (Sweden)

    Robert W. Siggins

    2014-02-01

    Full Text Available Effects of tobacco smoke on hematologic derangements have received little attention. This study employed a mouse model of cigarette smoke exposure to explore the effects on bone marrow niche function. While lung cancer is the most widely studied consequence of tobacco smoke exposure, other malignancies, including leukemia, are associated with tobacco smoke exposure. Animals received cigarette smoke exposure for 6 h/day, 5 days/week for 9 months. Results reveal that the hematopoietic stem and progenitor cell (HSPC pool size is reduced by cigarette smoke exposure. We next examined the effect of cigarette smoke exposure on one supporting cell type of the niche, the mesenchymal stromal cells (MSCs. Smoke exposure decreased the number of MSCs. Transplantation of naïve HSPCs into irradiated mice with cigarette smoke exposure yielded fewer numbers of engrafted HSPCs. This result suggests that smoke-exposed mice possess dysfunctional niches, resulting in abnormal hematopoiesis. Co-culture experiments using MSCs isolated from control or cigarette smoke-exposed mice with naïve HSPCs in vitro showed that MSCs from cigarette smoke-exposed mice generated marked expansion of naïve HSPCs. These data show that cigarette smoke exposure decreases in vivo MSC and HSC number and also increases pro-proliferative gene expression by cigarette smoke-exposed MSCs, which may stimulate HSPC expansion. These results of this investigation are clinically relevant to both bone marrow donors with a history of smoking and bone marrow transplant (BMT recipients with a history of smoking.

  19. UNTANGLING THE FUNGAL NICHE: A TRAIT-BASED APPROACH

    Directory of Open Access Journals (Sweden)

    Thomas W Crowther

    2014-10-01

    Full Text Available Fungi are prominent components of most terrestrial ecosystems, both in terms of biomass and ecosystem functioning, but the hyper-diverse nature of most communities has obscured the search for unifying principles governing community organization. In particular, unlike plants and animals, observational studies provide little evidence for the existence of niche processes in structuring fungal communities at broad spatial scales. This limits our capacity to predict how communities, and their functioning, vary across landscapes. We outline how a shift in focus, from taxonomy towards functional traits, might prove to be valuable in the search for general patterns in fungal ecology. We build on theoretical advances in plant and animal ecology to provide an empirical framework for a trait-based approach in fungal community ecology. Drawing upon specific characteristics of the fungal system, we highlight the significance of drought stress and combat in structuring free-living fungal communities. We propose a conceptual model to formalize how trade-offs between stress-tolerance and combative dominance are likely to organize communities across environmental gradients. Given that the survival of a fungus in a given environment is contingent on its ability to tolerate antagonistic competitors, measuring variation in combat trait expression along environmental gradients provides a means of elucidating realized, from fundamental niche spaces. We conclude that, using a trait-based understanding of how niche processes structure fungal communities across time and space, we can ultimately link communities with ecosystem functioning. Our trait-based framework highlights fundamental uncertainties that require testing in the fungal system, given their potential to uncover general mechanisms in fungal ecology.

  20. [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.

  1. 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.

  2. 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

  3. A Combination of Divergence and Conservatism in the Niche Evolution of the Moorish Gecko, Tarentola mauritanica (Gekkota: Phyllodactylidae.

    Directory of Open Access Journals (Sweden)

    Catarina Rato

    Full Text Available The quantification of realized niche overlap and the integration of species distribution models (SDMs with calibrated phylogenies to study niche evolution are becoming not only powerful tools to understand speciation events, but can also be used as proxies regarding the delimitation of cryptic species. We applied these techniques in order to unravel how the fundamental niche evolved during cladogenesis within the Tarentola mauritanica species-complex. Our results suggest that diversification within this complex, during the Miocene and Pleistocene, is associated with both niche divergence and niche conservatism, with a pattern that varies depending on whether the variables involved are related to the mean or seasonality of temperature and humidity. Moreover, climatic variables related to humidity and temperature seasonality were involved in the niche shift and genetic diversification of the European/North African clade during the Pleistocene and in its maintenance in a fundamental niche distinct from that of the remaining members of the group. This study further highlights the need for a taxonomic revision of the T. mauritanica species-complex.

  4. 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.

  5. "Ghost transients" in the southern California GPS velocity field: An investigation using finite-fault earthquake cycle models

    Science.gov (United States)

    Hearn, E. H.; Pollitz, F. F.; Thatcher, W. R.; Onishi, C. T.

    2011-12-01

    Elastic block models are generally used to infer slip rates on fault segments in tectonically complex areas, such as southern California (e.g. McCaffrey, 2005; Meade et al., 2005). These models implicitly assume steady-state deformation. However, owing to viscoelastic effects of past large earthquakes, deformation rates and patterns around major faults are expected to vary with time. Where viscoelasticity has been incorporated into block models, differences in inferred slip rates have resulted (Johnson et al., 2007). Here, we investigate the extent to which viscoelastic velocity perturbations (or "ghost transients") from individual earthquakes can affect elastic block model-based inferences of fault slip rates from GPS velocity fields. We focus on the southern California GPS velocity field, exploring the effects of known, large earthquakes for end-member rheological structures. For selected faults, an idealized earthquake history is constructed, consisting of a sequence of periodic, identical repeating slip events. For each earthquake, we first calculate average velocities and time-dependent perturbations relative to this average at all GPS sites in the neighborhood of an earthquake. (We deal with perturbations because to recover the velocities, we would have to compute and sum cycle-average velocities and perturbations for all fault segments in the region.) Next, we invert two GPS velocity fields for slip rates using a block modeling approach: one field that has been corrected for the perturbation, and one which has not, and we compare the resulting slip rates. For now, the viscoelastic models are simple (layers with linear rheologies), and locking depth is fixed in the block models. We find that if asthenosphere viscosities are low enough (3 x 10**18 Pa-s) the current GPS velocity field is significantly perturbed by the 1857 M 7.9 San Andreas Fault (SAF) earthquake sequence; that is, current strain rates around the SAF are lower than their average values

  6. Species versus guild level differentiation revealed across the annual cycle by isotopic niche examination.

    Science.gov (United States)

    Bodey, Thomas W; Ward, Eric J; Phillips, Richard A; McGill, Rona A R; Bearhop, Stuart

    2014-03-01

    Interspecific competitive interactions typically result in niche differentiation to alleviate competition through mechanisms including character displacement. However, competition is not the sole constraint on resource partitioning, and its effects are mediated by factors including the environmental context in which species coexist. Colonial seabirds provide an excellent opportunity to investigate the importance of competition in shaping realized niche widths because their life histories lead to variation in intra- and interspecific competition across the annual cycle. Dense breeding aggregations result in intense competition for prey in surrounding waters, whereas non-breeding dispersal to larger geographical areas produces lower densities of competitors. Bayesian hierarchical models of the isotopic niche, closely aligned to the trophic niche, reveal the degree of segregation between species and functional groups during both time periods. Surprisingly, species explained far more of the variance in the isotopic niche during the non-breeding than the breeding period. Our results underline the key role of non-breeding dynamics in alleviating competition and promoting distinctions between species through the facilitation of resource partitioning. Such situations may be common in a diverse range of communities sustained by ephemeral but abundant food items. This highlights how consideration of the hierarchical grouping of competitive interactions alongside consideration of abiotic constraints across the complete annual cycle allows a full understanding of the role of competition in driving patterns of character displacement. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

  7. 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…

  8. Simulation and thermal imaging of the 2006 Esperanza Wildfire in southern California: application of a coupled weather-wildland fire model

    Science.gov (United States)

    Janice L. Coen; Philip J Riggan

    2014-01-01

    The 2006 Esperanza Fire in Riverside County, California, was simulated with the Coupled Atmosphere-Wildland Fire Environment (CAWFE) model to examine how dynamic interactions of the atmosphere with large-scale fire spread and energy release may affect observed patterns of fire behavior as mapped using the FireMapper thermal imaging radiometer. CAWFE simulated the...

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

    Science.gov (United States)

    Hegermiller, Christie; Erikson, Li; Barnard, Patrick

    2016-01-01

    As part of the Coastal Storm Modeling System (CoSMoS), time series of hindcast, historical, and 21st-century nearshore wave parameters (wave height, period, and direction) were simulated for the southern California coast from Point Conception to the Mexican border. The hindcast (1980-2010) time series represents reanalysis-forced offshore waves propagated to the nearshore, whereas the historical (1976-2005) and 21st-century (2012-2100) time series represent global climate model-forced offshore waves propagated to the nearshore. Changes in deep-water wave conditions directly regulate the energy driving coastal processes. However, a number of physical processes, for example, refraction on continental shelves and/or diffraction by islands, transform deep-water waves as they propagate to the coast, which complicates large-scale modeling efforts. In this work, a hindcast of nearshore waves was simulated by forcing a numerical wave model with hindcasted intermediate-water waves and reanalysis winds. A lookup table was created by relating corresponding offshore winds and waves with nearshore wave conditions. Using the lookup table, historical and 21st-century nearshore wave time series were generated for global climate model-forced offshore winds and waves.

  10. Dietary niche expansion of a kelp forest predator recovering from intense commercial exploitation.

    Science.gov (United States)

    Hamilton, Scott L; Newsome, Seth D; Caselle, Jennifer E

    2014-01-01

    Marine ecosystems are increasingly at risk from overexploitation and fisheries collapse. As managers implement recovery plans, shifts in species interactions may occur broadly with potential consequences for ecosystem structure and function. In kelp forests off San Nicolas Island, California, USA, we describe striking changes in size structure and life history traits (e.g., size at maturation and sex change) of a heavily fished, ecologically important predator, the California sheephead (Semicossyphus pulcher). These changes occurred in two phases: (1) after intense commercial fishery exploitation in the late 1990s and (2) following recovery in the late 2000s, nearly a decade after management intervention. Using gut contents and stable-isotope values of sheephead and their prey, we found evidence for a dietary niche expansion upon recovery of population size structure to include increased consumption of sea urchins and other mobile invertebrate grazers by larger sized fish. By examining historical diet data and a time series of benthic community composition, we conclude that changes in dietary niche breadth are more likely due to the recovery of size structure from fishing than major shifts in prey availability. Size-dependent predator-prey interactions may have ecosystem consequences and management measures that preserve or restore size structure, and therefore historical trophic roles of key predators, could be vital for maintaining kelp forest ecosystem health.

  11. 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.

  12. Incremental by Design? On the Role of Incumbents in Technology Niches

    DEFF Research Database (Denmark)

    Hain, Daniel S.; Jurowetzki, Roman

    activities on emerging technologies shielded from the selection pressure on open markets. The engagement of large incumbent actors in the development of emerging technologies, and especially joint research projects together with young SME's, is generally positively perceived, since their high resource...... endowment and experience enables them to stem large research projects and bring them all the way to the market. However, the involvement of incumbents might alter niche dynamics, making technology outcomes more incremental and adapted to the current unsustainable sociotechnical regime. The incumbents...... will enable them to inherit central and dominant positions and thus shape the niche's further development by their will. Deploying a stochastic-actor-based model, we analyze if network dynamics of public funded R&DD in technological niches favor incumbent actors in a way that they are able to occupy central...

  13. 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.

  14. 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. © 2015 The Fisheries Society of the British Isles.

  15. Lizard assemblage from a sand dune habitat from southeastern Brazil: a niche overlap analysis.

    Science.gov (United States)

    Winck, Gisele R; Hatano, Fabio; Vrcibradic, Davor; VAN Sluys, Monique; Rocha, Carlos F D

    2016-01-01

    Communities are structured by interactions of historical and ecological factors, which influence the use of different resources in time and space. We acquired data on time of activity, microhabitat use and diet of a lizard assemblage from a sand dune habitat in a coastal area, southeastern Brazil (Restinga de Jurubatiba). We analyzed the data of niche overlap among species in these three axes (temporal, spatial and trophic) using null models. We found a significant overlap within the trophic niche, whereas the overlap for the other axes did not differ from the expected. Based on this result, we discuss the factors acting on the structure of the local lizard community.

  16. 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.

    2011-01-01

    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. PMID:21320900

  17. 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 UG; 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

    2014-01-01

    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. DOI: http://dx.doi.org/10.7554/eLife.04395.001 PMID:25201877

  18. 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

  19. Mercury speciation in terrestrial biota from coastal and inland food webs in California: A provisional model

    Science.gov (United States)

    Weiss-Penzias, P. S.; Wilmers, C.; Houghtaling, P.; Torregrosa, A.; Bank, M. S.

    2016-12-01

    Previous research has suggested that coastal ocean emissions of volatile methylated inorganic mercury (Hg) compounds are the source of elevated concentrations of toxic monomethylmercury (MMHg) in summertime marine fog on the coast of California relative to MMHg concentrations found in rain. Here we evaluate a priori predictions that speciated Hg (total Hg and MMHg) concentrations would be higher in the terrestrial biota from the coastal versus inland environments in California, which may reflect an additional Hg burden from fog deposition. Total Hg concentrations were determined in the following biota from the coastal Santa Cruz Mountains (SCM) and the inland Sierra Nevada foothills (SNF): puma (Puma concolor) whisker and fur, deer (Odocoileus hemionus) fur, and specimens from eight plant species that are consumed by deer. In addition, MMHg concentrations were determined in the eight plant species. Average total Hg concentrations were significantly higher in the SCM puma whisker (1.04 ug/g, N = 77) compared with SNF puma whisker (0.15 ug/g, N = 12). Average total Hg concentrations were also significantly higher in SCM deer fur (0.035 ug/g, N = 35) compared with SNF deer fur (0.010 ug/g, N = 4). Average total Hg concentrations were not significantly higher in all plant species from SCM (0.029 ug/g) compared with SNF (0.021 ug/g). Similarly average MMHg concentrations were not significantly higher in all plant species from SCM (0.95 ng/g, N = 15) compared with SNF (0.66 ng/g, N = 12). However, the difference in average MMHg concentration among oak leaves between SCM (1.39 ng/g, N = 8) and SNF (0.62 ng/g, N = 5) was significant (p < 0.10). Within the SCM, the spatial distribution of MMHg concentrations in oak leaves was significantly correlated (r2 = 0.70) with fog and low cloud cover (FLCC) frequency as determined by ten years of summertime GOES satellite images. Work is ongoing to measure the Hg isotope ratios in biota from the coastal and inland areas to evaluate

  20. Improving assessments of tropospheric ozone injury to Mediterranean montane conifer forests in California (USA) and Catalonia (Spain) with GIS models related to plant water relations

    Science.gov (United States)

    Kefauver, Shawn C.; Peñuelas, Josep; Ustin, Susan L.

    2012-12-01

    The impacts of tropospheric ozone on conifer health in the Sierra Nevada of California, USA, and the Pyrenees of Catalonia, Spain, were measured using field assessments and GIS variables of landscape gradients related to plant water relations, stomatal conductance and hence to ozone uptake. Measurements related to ozone injury included visible chlorotic mottling, needle retention, needle length, and crown depth, which together compose the Ozone Injury Index (OII). The OII values observed in Catalonia were similar to those in California, but OII alone correlated poorly to ambient ozone in all sites. Combining ambient ozone with GIS variables related to landscape variability of plant hydrological status, derived from stepwise regressions, produced models with R2 = 0.35, p = 0.016 in Catalonia, R2 = 0.36, p < 0.001 in Yosemite and R2 = 0.33, p = 0.007 in Sequoia/Kings Canyon National Parks in California. Individual OII components in Catalonia were modeled with improved success compared to the original full OII, in particular visible chlorotic mottling (R2 = 0.60, p < 0.001). The results show that ozone is negatively impacting forest health in California and Catalonia and also that modeling ozone injury improves by including GIS variables related to plant water relations.

  1. Modeling when, where, and how to manage a forest epidemic, motivated by sudden oak death in California.

    Science.gov (United States)

    Cunniffe, Nik J; Cobb, Richard C; Meentemeyer, Ross K; Rizzo, David M; Gilligan, Christopher A

    2016-05-17

    Sudden oak death, caused by Phytophthora ramorum, has killed millions of oak and tanoak in California since its first detection in 1995. Despite some localized small-scale management, there has been no large-scale attempt to slow the spread of the pathogen in California. Here we use a stochastic spatially explicit model parameterized using data on the spread of P. ramorum to investigate whether and how the epidemic can be controlled. We find that slowing the spread of P. ramorum is now not possible, and has been impossible for a number of years. However, despite extensive cryptic (i.e., presymptomatic) infection and frequent long-range transmission, effective exclusion of the pathogen from large parts of the state could, in principle, have been possible were it to have been started by 2002. This is the approximate date by which sufficient knowledge of P. ramorum epidemiology had accumulated for large-scale management to be realistic. The necessary expenditure would have been very large, but could have been greatly reduced by optimizing the radius within which infected sites are treated and careful selection of sites to treat. In particular, we find that a dynamic strategy treating sites on the epidemic wave front leads to optimal performance. We also find that "front loading" the budget, that is, treating very heavily at the start of the management program, would greatly improve control. Our work introduces a framework for quantifying the likelihood of success and risks of failure of management that can be applied to invading pests and pathogens threatening forests worldwide.

  2. Citizen-science, Geoethics and Human Niche

    Science.gov (United States)

    Bohle, Martin

    2017-04-01

    The anthropogenic biogeosphere or 'human niche' is the intersection of the biogeosphere and the sphere of human activities of social, economic, cultural and political nature. The application case for geoethics, namely "appropriate behaviours and practices, wherever human activities interact with the Earth system" [1], is about niche building. Geoethics is about the conduct of people and geoscientists, respectively their ordinary lifestyles and professional activities. Geoscience professionals notice the diverse economic, social and cultural living conditions of people, and the application cases of geosciences mirror the diversity of the global social sphere. Subsequently it is argued: A) when considering the ethical dimensions of global niche building then geosciences should feature 'citizen geoscience'; and B) when considering the functioning of a knowledge-based society under conditions of anthropogenic global change then 'citizen geoscience' facilitates applying that knowledge base. (A) Regarding 'niche building': The design of production systems and consumption patterns embeds geoscience know-how and relates it to the everyday life. Any citizen's activities purposefully interconnect to the biogeosphere for well-being, care-taking, and reproduction, although habitually without involving a geoscientist in professional capacity. In that implicit manner the everyday behaviours and practices of people influence Earth system dynamic. This renders their inherent geoscience know-how a public good as it makes their ignorance a public risk. A comfortable human niche for billions of people requires a global biogeosphere that is disrupted little by citizens' activities and exposes them to hazards that can be tamed. Quite the reverse, anthropogenic global change will disturb living conditions for many citizen. Much geoscience know-how will have to be deployed to tame disturbances in a socially sustainable manner. Sustainability in turn needs involvement of citizens in

  3. 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.

  4. Impacts of CO2 taxes when there are niche markets and learning-by-doing

    NARCIS (Netherlands)

    Gerlagh, R.; van der Zwaan, B.C.C.; Hofkes, M.W.; Klaassen, G.

    2004-01-01

    In this paper, we analyse the impact of carbon taxes on emission levels, when niche markets exist for new carbon-free technologies, and when these technologies experience "learning-by-doing" effects. For this purpose, a general equilibrium model has been developed, DEMETER, that specifies two energy

  5. 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

    2016-03-17

    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.

  6. A sampling theory for dispersal-limited, niche-structured communities

    NARCIS (Netherlands)

    A.E. Noble; N.M. Temme (Nico); W.F. Fagan; T.H. Keitt

    2011-01-01

    textabstractWe introduce the first analytical model of a dispersal-limited, niche-structured community to yield Hubbell's neutral theory in the limit of functional equivalence among all species. Dynamics of the multivariate species abundance distribution (SAD) for an asymmetric local community are

  7. 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…

  8. RECONSTRUCTING THE ORIGINS OF HIGH-ALPINE NICHES AND CUSHION LIFE FORM IN THE GENUS ANDROSACE S.L. (PRIMULACEAE)

    Science.gov (United States)

    Boucher, Florian C.; Thuiller, Wilfried; Roquet, Cristina; Douzet, Rolland; Aubert, Serge; Alvarez, Nadir; Lavergne, Sébastien

    2014-01-01

    Relatively, few species have been able to colonize extremely cold alpine environments. We investigate the role played by the cushion life form in the evolution of climatic niches in the plant genus Androsace s.l., which spreads across the mountain ranges of the Northern Hemisphere. Using robust methods that account for phylogenetic uncertainty, intraspecific variability of climatic requirements and different life-history evolution scenarios, we show that climatic niches of Androsace s.l. exhibit low phylogenetic signal and that they evolved relatively recently and punctually. Models of niche evolution fitted onto phylogenies show that the cushion life form has been a key innovation providing the opportunity to occupy extremely cold environments, thus contributing to rapid climatic niche diversification in the genus Androsace s.l. We then propose a plausible scenario for the adaptation of plants to alpine habitats. PMID:22486702

  9. Dynamic modeling of organophosphate pesticide load in surface water in the northern San Joaquin Valley watershed of California

    Energy Technology Data Exchange (ETDEWEB)

    Luo Yuzhou [Department of Land, Air and Water Resources, University of California, Davis, CA 95616 (United States); Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou, 325000 (China); Zhang Xuyang [Department of Land, Air and Water Resources, University of California, Davis, CA 95616 (United States); Liu Xingmei [Department of Land, Air and Water Resources, University of California, Davis, CA 95616 (United States); Institute of Soil, Water and Environmental Science, Zhejiang University, Hangzhou 310029 (China); Ficklin, Darren [Department of Land, Air and Water Resources, University of California, Davis, CA 95616 (United States); Zhang Minghua [Department of Land, Air and Water Resources, University of California, Davis, CA 95616 (United States); Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou, 325000 (China)], E-mail: mhzhang@ucdavis.edu

    2008-12-15

    The hydrology, sediment, and pesticide transport components of the Soil and Water Assessment Tool (SWAT) were evaluated on the northern San Joaquin Valley watershed of California. The Nash-Sutcliffe coefficients for monthly stream flow and sediment load ranged from 0.49 to 0.99 over the watershed during the study period of 1992-2005. The calibrated SWAT model was applied to simulate fate and transport processes of two organophosphate pesticides of diazinon and chlorpyrifos at watershed scale. The model generated satisfactory predictions of dissolved pesticide loads relative to the monitoring data. The model also showed great success in capturing spatial patterns of dissolved diazinon and chlorpyrifos loads according to the soil properties and landscape morphology over the large agricultural watershed. This study indicated that curve number was the major factor influencing the hydrology while pesticide fate and transport were mainly affected by surface runoff and pesticide application and in the study area. - Major factors governing the instream loads of organophosphate pesticides are magnitude and timing of surface runoff and pesticide application.

  10. High-resolution model for estimating the economic and policy implications of agricultural soil salinization in California

    Science.gov (United States)

    Welle, Paul D.; Mauter, Meagan S.

    2017-09-01

    This work introduces a generalizable approach for estimating the field-scale agricultural yield losses due to soil salinization. When integrated with regional data on crop yields and prices, this model provides high-resolution estimates for revenue losses over large agricultural regions. These methods account for the uncertainty inherent in model inputs derived from satellites, experimental field data, and interpreted model results. We apply this method to estimate the effect of soil salinity on agricultural outputs in California, performing the analysis with both high-resolution (i.e. field scale) and low-resolution (i.e. county-scale) data sources to highlight the importance of spatial resolution in agricultural analysis. We estimate that soil salinity reduced agricultural revenues by 3.7 billion (1.7-7.0 billion) in 2014, amounting to 8.0 million tons of lost production relative to soil salinities below the crop-specific thresholds. When using low-resolution data sources, we find that the costs of salinization are underestimated by a factor of three. These results highlight the need for high-resolution data in agro-environmental assessment as well as the challenges associated with their integration.

  11. A new seamless, high-resolution digital elevation model of the San Francisco Bay-Delta Estuary, California

    Science.gov (United States)

    Fregoso, Theresa; Wang, Rueen-Fang; Ateljevich, Eli; Jaffe, Bruce E.

    2017-06-14

    Climate change, sea-level rise, and human development have contributed to the changing geomorphology of the San Francisco Bay - Delta (Bay-Delta) Estuary system. The need to predict scenarios of change led to the development of a new seamless, high-resolution digital elevation model (DEM) of the Bay – Delta that can be used by modelers attempting to understand potential future changes to the estuary system. This report details the three phases of the creation of this DEM. The first phase took a bathymetric-only DEM created in 2005 by the U.S. Geological Survey (USGS), refined it with additional data, and identified areas that would benefit from new surveys. The second phase began a USGS collaboration with the California Department of Water Resources (DWR) that updated a 2012 DWR seamless bathymetric/topographic DEM of the Bay-Delta with input from the USGS and modifications to fit the specific needs of USGS modelers. The third phase took the work from phase 2 and expanded the coverage area in the north to include the Yolo Bypass up to the Fremont Weir, the Sacramento River up to Knights Landing, and the American River up to the Nimbus Dam, and added back in the elevations for interior islands. The constant evolution of the Bay-Delta will require continuous updates to the DEM of the Delta, and there still are areas with older data that would benefit from modern surveys. As a result, DWR plans to continue updating the DEM.

  12. Marine organism