Sample records for speciation modelling uncertainty
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Groenenberg, Jan E; Koopmans, Gerwin F; Comans, Rob N J
2010-02-15
Ion binding models such as the nonideal competitive adsorption-Donnan model (NICA-Donnan) and model VI successfully describe laboratory data of proton and metal binding to purified humic substances (HS). In this study model performance was tested in more complex natural systems. The speciation predicted with the NICA-Donnan model and the associated uncertainty were compared with independent measurements in soil solution extracts, including the free metal ion activity and fulvic (FA) and humic acid (HA) fractions of dissolved organic matter (DOM). Potentially important sources of uncertainty are the DOM composition and the variation in binding properties of HS. HS fractions of DOM in soil solution extracts varied between 14 and 63% and consisted mainly of FA. Moreover, binding parameters optimized for individual FA samples show substantial variation. Monte Carlo simulations show that uncertainties in predicted metal speciation, for metals with a high affinity for FA (Cu, Pb), are largely due to the natural variation in binding properties (i.e., the affinity) of FA. Predictions for metals with a lower affinity (Cd) are more prone to uncertainties in the fraction FA in DOM and the maximum site density (i.e., the capacity) of the FA. Based on these findings, suggestions are provided to reduce uncertainties in model predictions.
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Trace metal speciation in natural waters: Computational vs. analytical
Nordstrom, D. Kirk
1996-01-01
Improvements in the field sampling, preservation, and determination of trace metals in natural waters have made many analyses more reliable and less affected by contamination. The speciation of trace metals, however, remains controversial. Chemical model speciation calculations do not necessarily agree with voltammetric, ion exchange, potentiometric, or other analytical speciation techniques. When metal-organic complexes are important, model calculations are not usually helpful and on-site analytical separations are essential. Many analytical speciation techniques have serious interferences and only work well for a limited subset of water types and compositions. A combined approach to the evaluation of speciation could greatly reduce these uncertainties. The approach proposed would be to (1) compare and contrast different analytical techniques with each other and with computed speciation, (2) compare computed trace metal speciation with reliable measurements of solubility, potentiometry, and mean activity coefficients, and (3) compare different model calculations with each other for the same set of water analyses, especially where supplementary data on speciation already exist. A comparison and critique of analytical with chemical model speciation for a range of water samples would delineate the useful range and limitations of these different approaches to speciation. Both model calculations and analytical determinations have useful and different constraints on the range of possible speciation such that they can provide much better insight into speciation when used together. Major discrepancies in the thermodynamic databases of speciation models can be evaluated with the aid of analytical speciation, and when the thermodynamic models are highly consistent and reliable, the sources of error in the analytical speciation can be evaluated. Major thermodynamic discrepancies also can be evaluated by simulating solubility and activity coefficient data and testing various chemical models for their range of applicability. Until a comparative approach such as this is taken, trace metal speciation will remain highly uncertain and controversial.
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SOURCE APPORTIONMENT RESULTS, UNCERTAINTIES, AND MODELING TOOLS
Advanced multivariate receptor modeling tools are available from the U.S. Environmental Protection Agency (EPA) that use only speciated sample data to identify and quantify sources of air pollution. EPA has developed both EPA Unmix and EPA Positive Matrix Factorization (PMF) and ...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Park, J.Y.; Batchelor, B.
1999-03-01
Chemical equilibrium models are useful to evaluate stabilized/solidified waste. A general equilibrium model, SOLTEQ, a modified version of MINTEQA2 for S/S, was applied to predict the chemical speciations in the stabilized/solidified waste form. A method was developed to prepare SOLTEQ input data that can chemically represent various stabilized/solidified binders. Taylor`s empirical model was used to describe partitioning of alkali ions. As a result, SOLTEQ could represent chemical speciation in pure binder systems such as ordinary Portland cement and ordinary Portland cement + fly ash. Moreover, SOLTEQ could reasonably describe the effects on the chemical speciation due to variations in water-to-cement,more » fly ash contents, and hydration times of various binder systems. However, this application of SOLTEQ was not accurate in predicting concentrations of Ca, Si, and SO{sub 4} ions, due to uncertainties in the CSH solubility model and K{sub sp} values of cement hydrates at high pH values.« less
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Metal Ion Speciation and Dissolved Organic Matter Composition in Soil Solutions
NASA Astrophysics Data System (ADS)
Benedetti, M. F.; Ren, Z. L.; Bravin, M.; Tella, M.; Dai, J.
2014-12-01
Knowledge of the speciation of heavy metals and the role of dissolved organic matter (DOM) in soil solution is a key to understand metal mobility and ecotoxicity. In this study, soil column-Donnan membrane technique (SC-DMT) was used to measure metal speciation of Cd, Cu, Ni, Pb, and Zn in eighteen soil solutions, covering a wide range of metal sources and concentrations. DOM composition in these soil solutions was also determined. Our results show that in soil solution Pb and Cu are dominant in complex form, whereas Cd, Ni and Zn mainly exist as free ions; for the whole range of soil solutions, only 26.2% of DOM is reactive and consists mainly of fulvic acid (FA). The metal speciation measured by SC-DMT was compared to the predicted ones obtained via the NICA-Donnan model using the measured FA concentrations. The free ion concentrations predicted by speciation modelling were in good agreement with the measurements. Diffusive gradients in thin-films gels (DGT) were also performed to quantify the labile metal species in the fluxes from solid phase to solution in fourteen soils. The concentrations of metal species detected by DGT were compared with the free ion concentrations measured by DMT and the maximum concentrations calculated based on the predicted metal speciation in SC-DMT soil solutions. It is concluded that both inorganic species and a fraction of FA bound species account for the amount of labile metals measured by DGT, consistent with the dynamic features of this technique. The comparisons between measurements using analytical techniques and mechanistic model predictions provided mutual validation in their performance. Moreover, we show that to make accurate modelling of metal speciation in soil solutions, the knowledge of DOM composition is the crucial information, especially for Cu; like in previous studies the modelling of Pb speciation is not optimal and an updated of Pb generic binding parameters is required to reduce model prediction uncertainties.
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NASA Astrophysics Data System (ADS)
Li, M.; Zhang, Q.; Streets, D. G.; He, K. B.; Cheng, Y. F.; Emmons, L. K.; Huo, H.; Kang, S. C.; Lu, Z.; Shao, M.; Su, H.; Yu, X.; Zhang, Y.
2014-06-01
An accurate speciation mapping of non-methane volatile organic compounds (NMVOC) emissions has an important impact on the performance of chemical transport models (CTMs) in simulating ozone mixing ratios and secondary organic aerosols. Taking the INTEX-B Asian NMVOC emission inventory as the case, we developed an improved speciation framework to generate model-ready anthropogenic NMVOC emissions for various gas-phase chemical mechanisms commonly used in CTMs in this work, by using an explicit assignment approach and updated NMVOC profiles. NMVOC profiles were selected and aggregated from a wide range of new measurements and the SPECIATE database v.4.2. To reduce potential uncertainty from individual measurements, composite profiles were developed by grouping and averaging source profiles from the same category. The fractions of oxygenated volatile organic compounds (OVOC) were corrected during the compositing process for those profiles which used improper sampling and analyzing methods. Emissions of individual species were then lumped into species in different chemical mechanisms used in CTMs by applying mechanism-dependent species mapping tables, which overcomes the weakness of inaccurate mapping in previous studies. Emission estimates for individual NMVOC species differ between one and three orders of magnitude for some species when different sets of profiles are used, indicating that source profile is the most important source of uncertainties of individual species emissions. However, those differences are diminished in lumped species as a result of the lumping in the chemical mechanisms. Gridded emissions for eight chemical mechanisms at 30 min × 30 min resolution as well as the auxiliary data are available at http://mic.greenresource.cn/intex-b2006. The framework proposed in this work can be also used to develop speciated NMVOC emissions for other regions.
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NASA Astrophysics Data System (ADS)
Kalashnikova, O.; Xu, F.; Ge, C.; Wang, J.; Garay, M. J.; Diner, D. J.
2014-12-01
Exposure to ambient particulate matter (PM) has been consistently linked to cardiovascular and respiratory health effects. Although PM is currently monitored by a network of surface stations, these are too sparsely distributed to provide the level of spatial detail needed to link different aerosol species to given health effects, and expansion to denser coverage is impractical and cost prohibitive. We present a methodology for combining Chemical Transport Model (CTM) aerosol type information and multiangular spectropolarimetric data to establish the signature of specific aerosol types in top-of-atmosphere measurements, and relate it to speciated surface PM2.5 loadings. In particular, we employ the WRF-Chem model run at the University of Nebraska, and remote sensing data from the Airborne Multiangle SpectroPolarimetric Imager (AirMSPI) to explore the feasibility of this approach. We demonstrate that the CTM does well in predicting the types of aerosols present at a given location and time, however large uncertainties currently exist in CTM estimates of the concentration of the various aerosol species (e.g., black carbon, sulfate, dust, etc.) leading to large uncertainties to model-derived speciated PM 2.5. In order to constrain CTM aerosol surface concentrations we use AirMSPI UV-VIS-NIR observations of intensity, and blue, red, and NIR observations of the Q and U Stokes parameters. We select specific scenes observed by AirMSPI and use WRF-Chem to generate an initial distribution of aerosol composition. The relevant optical properties for each aerosol species are used to calculate aerosol light scattering information. This is then used in a vector (polarized) 1-D radiative transfer model to determine at-instrument Stokes parameters for the specific AirMSPI viewing geometries. As a first step, a match is sought between the CTM-predicted radiances and the AirMSPI observations. Then, the total aerosol optical depth and fractions of various aerosol species are modified via optimization to produce a better match to the observations, and converted to PM2.5 speciated loadings using CTM aerosol vertical profiles. Finally, the results are compared to available ground-based and in situ data to validate this approach.
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Chemical form specific exposure assessment for arsenic has long been identified as a source of uncertainty in estimating the risk associated with the aggregate exposure for a population. Some speciation based assessments document occurrence within an exposure route; however, the...
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A Bayesian framework to estimate diversification rates and their variation through time and space
2011-01-01
Background Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification. Results We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinidae) and Lupinus (Fabaceae). In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in diversification. Conclusions Our approach provides a flexible framework for the estimation of diversification parameters and hypothesis testing while simultaneously accounting for uncertainties in the divergence times and incomplete taxon sampling. PMID:22013891
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Park, Eun Sug; Symanski, Elaine; Han, Daikwon; Spiegelman, Clifford
2015-06-01
A major difficulty with assessing source-specific health effects is that source-specific exposures cannot be measured directly; rather, they need to be estimated by a source-apportionment method such as multivariate receptor modeling. The uncertainty in source apportionment (uncertainty in source-specific exposure estimates and model uncertainty due to the unknown number of sources and identifiability conditions) has been largely ignored in previous studies. Also, spatial dependence of multipollutant data collected from multiple monitoring sites has not yet been incorporated into multivariate receptor modeling. The objectives of this project are (1) to develop a multipollutant approach that incorporates both sources of uncertainty in source-apportionment into the assessment of source-specific health effects and (2) to develop enhanced multivariate receptor models that can account for spatial correlations in the multipollutant data collected from multiple sites. We employed a Bayesian hierarchical modeling framework consisting of multivariate receptor models, health-effects models, and a hierarchical model on latent source contributions. For the health model, we focused on the time-series design in this project. Each combination of number of sources and identifiability conditions (additional constraints on model parameters) defines a different model. We built a set of plausible models with extensive exploratory data analyses and with information from previous studies, and then computed posterior model probability to estimate model uncertainty. Parameter estimation and model uncertainty estimation were implemented simultaneously by Markov chain Monte Carlo (MCMC*) methods. We validated the methods using simulated data. We illustrated the methods using PM2.5 (particulate matter ≤ 2.5 μm in aerodynamic diameter) speciation data and mortality data from Phoenix, Arizona, and Houston, Texas. The Phoenix data included counts of cardiovascular deaths and daily PM2.5 speciation data from 1995-1997. The Houston data included respiratory mortality data and 24-hour PM2.5 speciation data sampled every six days from a region near the Houston Ship Channel in years 2002-2005. We also developed a Bayesian spatial multivariate receptor modeling approach that, while simultaneously dealing with the unknown number of sources and identifiability conditions, incorporated spatial correlations in the multipollutant data collected from multiple sites into the estimation of source profiles and contributions based on the discrete process convolution model for multivariate spatial processes. This new modeling approach was applied to 24-hour ambient air concentrations of 17 volatile organic compounds (VOCs) measured at nine monitoring sites in Harris County, Texas, during years 2000 to 2005. Simulation results indicated that our methods were accurate in identifying the true model and estimated parameters were close to the true values. The results from our methods agreed in general with previous studies on the source apportionment of the Phoenix data in terms of estimated source profiles and contributions. However, we had a greater number of statistically insignificant findings, which was likely a natural consequence of incorporating uncertainty in the estimated source contributions into the health-effects parameter estimation. For the Houston data, a model with five sources (that seemed to be Sulfate-Rich Secondary Aerosol, Motor Vehicles, Industrial Combustion, Soil/Crustal Matter, and Sea Salt) showed the highest posterior model probability among the candidate models considered when fitted simultaneously to the PM2.5 and mortality data. There was a statistically significant positive association between respiratory mortality and same-day PM2.5 concentrations attributed to one of the sources (probably industrial combustion). The Bayesian spatial multivariate receptor modeling approach applied to the VOC data led to a highest posterior model probability for a model with five sources (that seemed to be refinery, petrochemical production, gasoline evaporation, natural gas, and vehicular exhaust) among several candidate models, with the number of sources varying between three and seven and with different identifiability conditions. Our multipollutant approach assessing source-specific health effects is more advantageous than a single-pollutant approach in that it can estimate total health effects from multiple pollutants and can also identify emission sources that are responsible for adverse health effects. Our Bayesian approach can incorporate not only uncertainty in the estimated source contributions, but also model uncertainty that has not been addressed in previous studies on assessing source-specific health effects. The new Bayesian spatial multivariate receptor modeling approach enables predictions of source contributions at unmonitored sites, minimizing exposure misclassification and providing improved exposure estimates along with their uncertainty estimates, as well as accounting for uncertainty in the number of sources and identifiability conditions.
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2008-01-01
Background Marine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) "soft vicariance", where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs). Results Given the Marquesan data, we find strong evidence of simultaneous colonization across all seven cowrie gastropod endemics co-distributed in the Marquesas. In contrast, the lower sample sizes in the Hawaiian data lead to greater uncertainty associated with the Hawaiian estimates. Although, the hyper-parameter estimates point to soft vicariance in a subset of the 11 Hawaiian taxon-pairs, the hyper-prior and hyper-posterior are too similar to make a definitive conclusion. Both results are not inconsistent with what is known about the geologic history of the archipelagos. Simulations verify that our method can successfully distinguish these two histories across a wide range of conditions given sufficient sampling. Conclusion Although soft vicariance and colonization are likely to produce similar genetic patterns when a single taxon-pair is used, our hierarchical Bayesian model can potentially detect if either history is a dominant process across co-distributed taxon-pairs. As comparative phylogeographic datasets grow to include > 100 co-distributed taxon-pairs, the HABC approach will be well suited to dissect temporal patterns in community assembly and evolution, thereby providing a bridge linking comparative phylogeography with community ecology. PMID:19038027
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Particulate-phase mercury emissions from biomass burning ...
Mercury (Hg) emissions from biomass burning (BB) are an important source of atmospheric Hg and a major factor driving the interannual variation of Hg concentrations in the troposphere. The greatest fraction of Hg from BB is released in the form of elemental Hg (Hg0(g)). However, little is known about the fraction of Hg bound to particulate matter (HgP) released from BB, and the factors controlling this fraction are also uncertain. In light of the aims of the Minamata Convention to reduce intentional Hg use and emissions from anthropogenic activities, the relative importance of Hg emissions from BB will have an increasing impact on Hg deposition fluxes. Hg speciation is one of the most important factors determining the redistribution of Hg in the atmosphere and the geographical distribution of Hg deposition. Using the latest version of the Global Fire Emissions Database (GFEDv4.1s) and the global Hg chemistry transport model, ECHMERIT, the impact of Hg speciation in BB emissions, and the factors which influence speciation, on Hg deposition have been investigated for the year 2013. The role of other uncertainties related to physical and chemical atmospheric processes involving Hg and the influence of model parametrisations were also investigated, since their interactions with Hg speciation are complex. The comparison with atmospheric HgP concentrations observed at two remote sites, Amsterdam Island (AMD) and Manaus (MAN), in the Amazon showed a significant improve
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NASA Astrophysics Data System (ADS)
Li, M.; Zhang, Q.; Streets, D. G.; He, K. B.; Cheng, Y. F.; Emmons, L. K.; Huo, H.; Kang, S. C.; Lu, Z.; Shao, M.; Su, H.; Yu, X.; Zhang, Y.
2013-12-01
An accurate speciation mapping of non-methane volatile organic compounds (NMVOC) emissions has an important impact on the performance of chemical transport models (CTMs) in simulating ozone mixing ratios and secondary organic aerosols. In this work, we developed an improved speciation framework to generate model-ready anthropogenic Asian NMVOC emissions for various gas-phase chemical mechanisms commonly used in CTMs by using an explicit assignment approach and updated NMVOC profiles, based on the total NMVOC emissions in the INTEX-B Asian inventory for the year 2006. NMVOC profiles were selected and aggregated from a wide range of new measurements and the SPECIATE database. To reduce potential uncertainty from individual measurements, composite profiles were developed by grouping and averaging source profiles from the same category. The fractions of oxygenated volatile organic compounds (OVOC) were corrected during the compositing process for those profiles which used improper sampling and analyzing methods. Emissions of individual species were then lumped into species in different chemical mechanisms used in CTMs by applying mechanism-dependent species mapping tables, which overcomes the weakness of inaccurate mapping in previous studies. Gridded emissions for eight chemical mechanisms are developed at 30 min × 30 min resolution using various spatial proxies and are provided through the website: http://mic.greenresource.cn/intex-b2006. Emission estimates for individual NMVOC species differ between one and three orders of magnitude for some species when different sets of profiles are used, indicating that source profile is the most important source of uncertainties of individual species emissions. However, those differences are diminished in lumped species as a result of the lumping in the chemical mechanisms.
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Zhang, Xiaokai; Qin, Boqiang; Deng, Jianming; Wells, Mona
2017-10-01
As the world burden of environmental contamination increases, it is of the utmost importance to develop streamlined approaches to environmental risk assessment in order to prioritize mitigation measures. Whole-cell biosensors or bioreporters and speciation modeling have both become of increasing interest to determine the bioavailability of pollutants, as bioavailability is increasingly in use as an indicator of risk. Herein, we examine whether bioreporter results are able to reflect expectations based on chemical reactivity and speciation modeling, with the hope to extend the research into a wider framework of risk assessment. We study a specific test case concerning the bioavailability of lead (Pb) in aqueous environments containing Pb-complexing ligands. Ligands studied include ethylene diamine tetra-acetic acid (EDTA), meso-2,3 dimercaptosuccinic acid (DMSA), leucine, methionine, cysteine, glutathione, and humic acid (HA), and we also performed experiments using natural water samples from Lake Tai (Taihu), the third largest lake in China. We find that EDTA, DMSA, cysteine, glutathione, and HA amendment significantly reduced Pb bioavailability with increasing ligand concentration according to a log-sigmoid trend. Increasing dissolved organic carbon in Taihu water also had the same effect, whereas leucine and methionine had no notable effect on bioavailability at the concentrations tested. We find that bioreporter results are in accord with the reduction of aqueous Pb 2+ that we expect from the relative complexation affinities of the different ligands tested. For EDTA and HA, for which reasonably accurate ionization and complexation constants are known, speciation modeling is in agreement with bioreporter response to within the level of uncertainty recognised as reasonable by the United States Environmental Protection Agency for speciation-based risk assessment applications. These findings represent a first step toward using bioreporter technology to streamline the biological confirmation or validation of speciation modeling for use in environmental risk assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Chen, L-W Antony; Watson, John G; Chow, Judith C; DuBois, Dave W; Herschberger, Lisa
2011-11-01
Chemical mass balance (CMB) and trajectory receptor models were applied to speciated particulate matter with aerodynamic diameter ≤2.5 μm (PM 2.5 ) measurements from Speciation Trends Network (STN; part of the Chemical Speciation Network [CSN]) and Interagency Monitoring of Protected Visual Environments (IMPROVE) monitoring network across the state of Minnesota as part of the Minnesota PM 2.5 Source Apportionment Study (MPSAS). CMB equations were solved by the Unmix, positive matrix factorization (PMF), and effective variance (EV) methods, giving collective source contribution and uncertainty estimates. Geological source profiles developed from local dust materials were either incorporated into the EV-CMB model or used to verify factors derived from Unmix and PMF. Common sources include soil dust, calcium (Ca)-rich dust, diesel and gasoline vehicle exhausts, biomass burning, secondary sulfate, and secondary nitrate. Secondary sulfate and nitrate aerosols dominate PM 2.5 mass (50-69%). Mobile sources outweigh area sources at urban sites, and vice versa at rural sites due to traffic emissions. Gasoline and diesel contributions can be separated using data from the STN, despite significant uncertainties. Major differences between MPSAS and earlier studies on similar environments appear to be the type and magnitude of stationary sources, but these sources are generally minor (<7%) in this and other studies. Ensemble back-trajectory analysis shows that the lower Midwestern states are the predominant source region for secondary ammoniated sulfate in Minnesota. It also suggests substantial contributions of biomass burning and soil dust from out-of-state on occasions, although a quantitative separation of local and regional contributions was not achieved in the current study. Supplemental materials are available for this article. Go to the publisher's online edition of the Journal of the Air & Waste Management Association for a summary of input data, Unmix and PMF factor profiles, and additional maps. [Box: see text].
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Rumsey and Walker_AMT_2016_Figure 2.xlsx
Figure summarizes uncertainty (error) in hourly gradient flux measurements by individual analyte. Flux uncertainty is derived from estimates of uncertainty in chemical gradients and turbulent transfer velocity.This dataset is associated with the following publication:Rumsey, I. Application of an online ion chromatography-based instrument for gradient flux measurements of speciated nitrogen and sulfur. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 9(6): 2581-2592, (2016).
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This training provides general concepts on chemical speciation, the SPECIATE database and browser, and how to use the Speciation Tool to create model ready speciation inputs for a photochemical air quality model.
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McCann, Jamie; Stuessy, Tod F.; Villaseñor, Jose L.; Weiss-Schneeweiss, Hanna
2016-01-01
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction. PMID:27611687
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McCann, Jamie; Schneeweiss, Gerald M; Stuessy, Tod F; Villaseñor, Jose L; Weiss-Schneeweiss, Hanna
2016-01-01
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.
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Application of cause-and-effect analysis to potentiometric titration.
Kufelnicki, A; Lis, S; Meinrath, G
2005-08-01
A first attempt has been made to interpret physicochemical data from potentiometric titration analysis in accordance with the complete measurement-uncertainty budget approach (bottom-up) of ISO and Eurachem. A cause-and-effect diagram is established and discussed. Titration data for arsenazo III are used as a basis for this discussion. The commercial software Superquad is used and applied within a computer-intensive resampling framework. The cause-and-effect diagram is applied to evaluation of seven protonation constants of arsenazo III in the pH range 2-10.7. The data interpretation is based on empirical probability distributions and their analysis by second-order correct confidence estimates. The evaluated data are applied in the calculation of a speciation diagram including uncertainty estimates using the probabilistic speciation software Ljungskile.
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Impact of Measurement Uncertainties on Receptor Modeling of Speciated Atmospheric Mercury.
Cheng, I; Zhang, L; Xu, X
2016-02-09
Gaseous oxidized mercury (GOM) and particle-bound mercury (PBM) measurement uncertainties could potentially affect the analysis and modeling of atmospheric mercury. This study investigated the impact of GOM measurement uncertainties on Principal Components Analysis (PCA), Absolute Principal Component Scores (APCS), and Concentration-Weighted Trajectory (CWT) receptor modeling results. The atmospheric mercury data input into these receptor models were modified by combining GOM and PBM into a single reactive mercury (RM) parameter and excluding low GOM measurements to improve the data quality. PCA and APCS results derived from RM or excluding low GOM measurements were similar to those in previous studies, except for a non-unique component and an additional component extracted from the RM dataset. The percent variance explained by the major components from a previous study differed slightly compared to RM and excluding low GOM measurements. CWT results were more sensitive to the input of RM than GOM excluding low measurements. Larger discrepancies were found between RM and GOM source regions than those between RM and PBM. Depending on the season, CWT source regions of RM differed by 40-61% compared to GOM from a previous study. No improvement in correlations between CWT results and anthropogenic mercury emissions were found.
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Impact of Measurement Uncertainties on Receptor Modeling of Speciated Atmospheric Mercury
Cheng, I.; Zhang, L.; Xu, X.
2016-01-01
Gaseous oxidized mercury (GOM) and particle-bound mercury (PBM) measurement uncertainties could potentially affect the analysis and modeling of atmospheric mercury. This study investigated the impact of GOM measurement uncertainties on Principal Components Analysis (PCA), Absolute Principal Component Scores (APCS), and Concentration-Weighted Trajectory (CWT) receptor modeling results. The atmospheric mercury data input into these receptor models were modified by combining GOM and PBM into a single reactive mercury (RM) parameter and excluding low GOM measurements to improve the data quality. PCA and APCS results derived from RM or excluding low GOM measurements were similar to those in previous studies, except for a non-unique component and an additional component extracted from the RM dataset. The percent variance explained by the major components from a previous study differed slightly compared to RM and excluding low GOM measurements. CWT results were more sensitive to the input of RM than GOM excluding low measurements. Larger discrepancies were found between RM and GOM source regions than those between RM and PBM. Depending on the season, CWT source regions of RM differed by 40–61% compared to GOM from a previous study. No improvement in correlations between CWT results and anthropogenic mercury emissions were found. PMID:26857835
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This product provides training to air pollution inventory and modeling professionals to understand the US EPA's SPECIATE database base and Speciation Tool and their use to develop speciated emission inventories.
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Particulate matter speciation profiles for light-duty gasoline vehicles in the United States.
Sonntag, Darrell B; Baldauf, Richard W; Yanca, Catherine A; Fulper, Carl R
2014-05-01
Representative profiles for particulate matter particles less than or equal to 2.5 microm (PM2.5) are developed from the Kansas City Light-Duty Vehicle Emissions Study for use in the US. Environmental Protection Agency (EPA) vehicle emission model, the Motor Vehicle Emission Simulator (MOVES), and for inclusion in the EPA SPECIATE database for speciation profiles. The profiles are compatible with the inputs of current photochemical air quality models, including the Community Multiscale Air Quality Aerosol Module Version 6 (AE6). The composition of light-duty gasoline PM2.5 emissions differs significantly between cold start and hot stabilized running emissions, and between older and newer vehicles, reflecting both impacts of aging/deterioration and changes in vehicle technology. Fleet-average PM2.5 profiles are estimated for cold start and hot stabilized running emission processes. Fleet-average profiles are calculated to include emissions from deteriorated high-emitting vehicles that are expected to continue to contribute disproportionately to the fleet-wide PM2.5 emissions into the future. The profiles are calculated using a weighted average of the PM2.5 composition according to the contribution of PM2.5 emissions from each class of vehicles in the on-road gasoline fleet in the Kansas City Metropolitan Statistical Area. The paper introduces methods to exclude insignificant measurements, correct for organic carbon positive artifact, and control for contamination from the testing infrastructure in developing speciation profiles. The uncertainty of the PM2.5 species fraction in each profile is quantified using sampling survey analysis methods. The primary use of the profiles is to develop PM2.5 emissions inventories for the United States, but the profiles may also be used in source apportionment, atmospheric modeling, and exposure assessment, and as a basis for light-duty gasoline emission profiles for countries with limited data. PM2.5 speciation profiles were developed from a large sample of light-duty gasoline vehicles tested in the Kansas City area. Separate PM2.5 profiles represent cold start and hot stabilized running emission processes to distinguish important differences in chemical composition. Statistical analysis was used to construct profiles that represent PM2.5 emissions from the U.S. vehicle fleet based on vehicles tested from the 2005 calendar year Kansas City metropolitan area. The profiles have been incorporated into the EPA MOVES emissions model, as well as the EPA SPECIATE database, to improve emission inventories and provide the PM2.5 chemical characterization needed by CMAQv5.0 for atmospheric chemistry modeling.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Langton, C.; Meeussen, J.; Sloot, H.
2010-03-31
The objective of the work described in this report is to demonstrate the capabilities of the current version of LeachXS{trademark}/ORCHESTRA for simulating chemical behavior and constituent release processes in a range of applications that are relevant to the CBP. This report illustrates the use of LeachXS{trademark}/ORCHESTRA for the following applications: (1) Comparing model and experimental results for leaching tests for a range of cementitious materials including cement mortars, grout, stabilized waste, and concrete. The leaching test data includes liquid-solid partitioning as a function of pH and release rates based on laboratory column, monolith, and field testing. (2) Modeling chemical speciationmore » of constituents in cementitious materials, including liquid-solid partitioning and release rates. (3) Evaluating uncertainty in model predictions based on uncertainty in underlying composition, thermodynamic, and transport characteristics. (4) Generating predominance diagrams to evaluate predicted chemical changes as a result of material aging using the example of exposure to atmospheric conditions. (5) Modeling coupled geochemical speciation and diffusion in a three layer system consisting of a layer of Saltstone, a concrete barrier, and a layer of soil in contact with air. The simulations show developing concentration fronts over a time period of 1000 years. (6) Modeling sulfate attack and cracking due to ettringite formation. A detailed example for this case is provided in a separate article by the authors (Sarkar et al. 2010). Finally, based on the computed results, the sensitive input parameters for this type of modeling are identified and discussed. The chemical speciation behavior of substances is calculated for a batch system and also in combination with transport and within a three layer system. This includes release from a barrier to the surrounding soil as a function of time. As input for the simulations, the physical and chemical properties of the materials are used. The test cases used in this demonstration are taken from Reference Cases for Use in the Cementitious Barriers Partnership (Langton et al. 2009). Before it is possible to model the release of substances from stabilized waste or radioactive grout through a cement barrier into the engineered soil barrier or natural soil, the relevant characteristics of such materials must be known. Additional chemical characteristics are needed for mechanistic modeling to be undertaken, not just the physical properties relevant for modeling of transport. The minimum required properties for modeling are given in Section 5.0, 'Modeling the chemical speciation of a material'.« less
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NASA Astrophysics Data System (ADS)
Qiu, Xin; Cheng, Irene; Yang, Fuquan; Horb, Erin; Zhang, Leiming; Harner, Tom
2018-03-01
Two speciated and spatially resolved emissions databases for polycyclic aromatic compounds (PACs) in the Athabasca oil sands region (AOSR) were developed. The first database was derived from volatile organic compound (VOC) emissions data provided by the Cumulative Environmental Management Association (CEMA) and the second database was derived from additional data collected within the Joint Canada-Alberta Oil Sands Monitoring (JOSM) program. CALPUFF modelling results for atmospheric polycyclic aromatic hydrocarbons (PAHs), alkylated PAHs, and dibenzothiophenes (DBTs), obtained using each of the emissions databases, are presented and compared with measurements from a passive air monitoring network. The JOSM-derived emissions resulted in better model-measurement agreement in the total PAH concentrations and for most PAH species concentrations compared to results using CEMA-derived emissions. At local sites near oil sands mines, the percent error of the model compared to observations decreased from 30 % using the CEMA-derived emissions to 17 % using the JOSM-derived emissions. The improvement at local sites was likely attributed to the inclusion of updated tailings pond emissions estimated from JOSM activities. In either the CEMA-derived or JOSM-derived emissions scenario, the model underestimated PAH concentrations by a factor of 3 at remote locations. Potential reasons for the disagreement include forest fire emissions, re-emissions of previously deposited PAHs, and long-range transport not considered in the model. Alkylated PAH and DBT concentrations were also significantly underestimated. The CALPUFF model is expected to predict higher concentrations because of the limited chemistry and deposition modelling. Thus the model underestimation of PACs is likely due to gaps in the emissions database for these compounds and uncertainties in the methodology for estimating the emissions. Future work is required that focuses on improving the PAC emissions estimation and speciation methodologies and reducing the uncertainties in VOC emissions which are subsequently used in PAC emissions estimation.
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Balistrieri, L.S.; Blank, R.G.
2008-01-01
In order to evaluate thermodynamic speciation calculations inherent in biotic ligand models, the speciation of dissolved Cd, Cu, Pb, and Zn in aquatic systems influenced by historical mining activities is examined using equilibrium computer models and the diffusive gradients in thin films (DGT) technique. Several metal/organic-matter complexation models, including WHAM VI, NICA-Donnan, and Stockholm Humic model (SHM), are used in combination with inorganic speciation models to calculate the thermodynamic speciation of dissolved metals and concentrations of metal associated with biotic ligands (e.g., fish gills). Maximum dynamic metal concentrations, determined from total dissolved metal concentrations and thermodynamic speciation calculations, are compared with labile metal concentrations measured by DGT to assess which metal/organic-matter complexation model best describes metal speciation and, thereby, biotic ligand speciation, in the studied systems. Results indicate that the choice of model that defines metal/organic-matter interactions does not affect calculated concentrations of Cd and Zn associated with biotic ligands for geochemical conditions in the study area, whereas concentrations of Cu and Pb associated with biotic ligands depend on whether the speciation calculations use WHAM VI, NICA-Donnan, or SHM. Agreement between labile metal concentrations and dynamic metal concentrations occurs when WHAM VI is used to calculate Cu speciation and SHM is used to calculate Pb speciation. Additional work in systems that contain wide ranges in concentrations of multiple metals should incorporate analytical speciation methods, such as DGT, to constrain the speciation component of biotic ligand models. ?? 2008 Elsevier Ltd.
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Self-consistent approach for neutral community models with speciation
NASA Astrophysics Data System (ADS)
Haegeman, Bart; Etienne, Rampal S.
2010-03-01
Hubbell’s neutral model provides a rich theoretical framework to study ecological communities. By incorporating both ecological and evolutionary time scales, it allows us to investigate how communities are shaped by speciation processes. The speciation model in the basic neutral model is particularly simple, describing speciation as a point-mutation event in a birth of a single individual. The stationary species abundance distribution of the basic model, which can be solved exactly, fits empirical data of distributions of species’ abundances surprisingly well. More realistic speciation models have been proposed such as the random-fission model in which new species appear by splitting up existing species. However, no analytical solution is available for these models, impeding quantitative comparison with data. Here, we present a self-consistent approximation method for neutral community models with various speciation modes, including random fission. We derive explicit formulas for the stationary species abundance distribution, which agree very well with simulations. We expect that our approximation method will be useful to study other speciation processes in neutral community models as well.
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Given the complexity of the various, simultaneous (and competing) equilibrium reactions governing the speciation of ionic species in aquatic systems, EPA has developed and distributed the geochemical speciation model MINTEQA2 (Brown and Allison, 1987, Allison et al., 1991; Hydrog...
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NASA Astrophysics Data System (ADS)
Yan, Fang; Winijkul, Ekbordin; Bond, Tami C.; Streets, David G.
2014-04-01
Estimates of future emissions are necessary for understanding the future health of the atmosphere, designing national and international strategies for air quality control, and evaluating mitigation policies. Emission inventories are uncertain and future projections even more so, thus it is important to quantify the uncertainty inherent in emission projections. This paper is the second in a series that seeks to establish a more mechanistic understanding of future air pollutant emissions based on changes in technology. The first paper in this series (Yan et al., 2011) described a model that projects emissions based on dynamic changes of vehicle fleet, Speciated Pollutant Emission Wizard-Trend, or SPEW-Trend. In this paper, we explore the underlying uncertainties of global and regional exhaust PM emission projections from on-road vehicles in the coming decades using sensitivity analysis and Monte Carlo simulation. This work examines the emission sensitivities due to uncertainties in retirement rate, timing of emission standards, transition rate of high-emitting vehicles called “superemitters”, and emission factor degradation rate. It is concluded that global emissions are most sensitive to parameters in the retirement rate function. Monte Carlo simulations show that emission uncertainty caused by lack of knowledge about technology composition is comparable to the uncertainty demonstrated by alternative economic scenarios, especially during the period 2010-2030.
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Parkhurst, D.L.
1995-01-01
PHREEQC is a computer program written in the C pwgranuning language that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations, (2) reaction-path and advective-transport calculations involving specified irreversible reactions, mixing of solutions, mineral and gas equilibria surface-complex-ation reactions, and ion-exchange reactions, and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for composition differences between waters, within specified compositional uncertainties. PHREEQC is derived from the Fortran program PHREEQE, but it has been completely rewritten in C with the addition many new capabilities. New features include the capabilities to use redox couples to distribute redox elements among their valence states in speciation calculations; to model ion-exchange and surface-compiexation reactions; to model reactions with a fixed-pressure, multicomponent gas phase (that is, a gas bubble); to calculate the mass of water in the aqueous phase during reaction and transport calculations; to keep track of the moles of minerals present in the solid phases and determine antomaticaHy the thermodynamically stable phase assemblage; to simulate advective transport in combination with PHREEQC's reaction-modeling capability; and to make inverse modeling calculations that allow for uncertainties in the analytical data. The user interface is improved through the use of a simplified approach to redox reactions, which includes explicit mole-balance equations for hydrogen and oxygen; the use of a revised input that is modular and completely free format; and the use of mineral names and standard chemical symbolism rather than index numbers. The use of (2 eliminates nearly all limitations on army sizes, including numbers of elements, aqueous species, solutions, phases, and lengths of character strings. A new equation solver that optimizes a set of equalities subject to both equality and inequality constraints is used to determine the thermodynamically stable set of phases in equilibrium with a solution. A more complete Newton-Raphson formulation, master-species switching, and scaling of the algebraic equations reduce the number of failures of the nunmrical method in PHREEQC relative to PHREEQE. This report presents the equations that are the basis for chemical equilibrium and inverse-modeling calculations in PHREEQC, describes the input for the program, and presents twelve examples that demonstrate most of the program's capabilities.
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Non-pertechnetate Technetium Sensor Research and Development
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bryan, Samuel A.; Rapko, Brian M.; Branch, Shirmir D.
Several significant uncertainties remain regarding the understanding and modeling of the fate and speciation of technicium-99 ( 99Tc) in Hanford waste tanks, glass, and low-temperature waste forms. A significant (2% to 25%) fraction of the 99Tc in the water-soluble portion of the tank waste may be present as one or more non pertechnetate species that have not been identified and to date, cannot be effectively separated from the wastes. This task will provide a sensor specifically tuned to detect the Tc(I)-carbonyl species believed to constitute the main fraction of the non-pertechnetate form of technetium. By direct measurement of the non-pertechnetatemore » species, such a sensor will help reduce the uncertainties in the modeling of the fate and speciation of 99Tc in Hanford tanks and waste forms. This report summarizes work performed in FY2016 that was sponsored by the Department of Energy’s Office of Environmental Management and demonstrates the protocol for using fluorescent Tc(I)-tricarbonyl complex as a means to detect the non-pertechnetate species within tank waste solutions. The protocol was optimized with respect to ligand concentration, solvent choice, reaction temperature and time. This work culminated in the quantitation of Tc(I)-tricarbonyl within a waste simulant, using a standard addition method for measurement. This report also summarizes the synthesis and high-yield preparation of the low-valence technetium species, [Tc(CO) 3(H 2O) 3] +, which will be used as the technetium standard material for the demonstration of the non-pertechnetate species in actual wastes.« less
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Liu, Yayong; Xing, Jia; Wang, Shuxiao; Fu, Xiao; Zheng, Haotian
2018-08-01
Heavy metals are concerned for its adverse effect on human health and long term burden on biogeochemical cycling in the ecosystem. In this study, a provincial-level emission inventory of 13 kinds of heavy metals including V, Cr, Mn, Co, Ni, Cu, Zn, As, Cd, Sn, Sb, Ba and Pb from 10 anthropogenic sources was developed for China, based on the 2015 national emission inventory of primary particulate matters and source category-specific speciation profiles collected from 50 previous studies measured in China. Uncertainties associated with the speciation profiles were also evaluated. Our results suggested that total emissions of the 13 types of heavy metals in China are estimated at about 58000 ton for the year 2015. The iron production is the dominant source of heavy metal, contributing 42% of total emissions of heavy metals. The emissions of heavy metals vary significantly at regional scale, with largest amount of emissions concentrated in northern and eastern China. Particular, high emissions of Cr, Co, Ni, As and Sb (contributing 8%-18% of the national emissions) are found in Shandong where has large capacity of industrial production. Uncertainty analysis suggested that the implementation of province-specific source profiles in this study significantly reduced the emission uncertainties from (-89%, 289%) to (-99%, 91%), particularly for coal combustion. However, source profiles for industry sectors such as non-metallic mineral manufacturing are quite limited, resulting in a relative high uncertainty. The high-resolution emission inventories of heavy metals are essential not only for their distribution, deposition and transport studies, but for the design of policies to redress critical atmospheric environmental hazards at local and regional scales. Detailed investigation on source-specific profile in China are still needed to achieve more accurate estimations of heavy metals in the future. Copyright © 2018 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Menut, Laurent; Siour, Guillaume; Mailler, Sylvain; Couvidat, Florian; Bessagnet, Bertrand
2016-10-01
The aerosol speciation and size distribution is modeled during the summer 2013 and over a large area encompassing Africa, Mediterranean and western Europe. The modeled aerosol is compared to available measurements such as the AERONET aerosol optical depth (AOD) and aerosol size distribution (ASD) and the EMEP network for surface concentrations of particulate matter PM2.5, PM10 and inorganic species (nitrate, sulfate and ammonium). The main goal of this study is to quantify the model ability to realistically model the speciation and size distribution of the aerosol. Results first showed that the long-range transport pathways are well reproduced and mainly constituted by mineral dust: spatial correlation is ≈ 0.9 for AOD and Ångström exponent, when temporal correlations show that the day-to-day variability is more difficult to reproduce. Over Europe, PM2.5 and PM10 have a mean temporal correlation of ≈ 0.4 but the lowest spatial correlation ( ≈ 0.25 and 0.62, respectively), showing that the fine particles are not well localized or transported. Being short-lived species, the uncertainties on meteorology and emissions induce these lowest scores. However, time series of PM2.5 with the speciation show a good agreement between model and measurements and are useful for discriminating the aerosol composition. Using a classification from the south (Africa) to the north (northern Europe), it is shown that mineral dust relative mass contribution decreases from 50 to 10 % when nitrate increases from 0 to 20 % and all other species, sulfate, sea salt, ammonium, elemental carbon, primary organic matter, are constant. The secondary organic aerosol contribution is between 10 and 20 % with a maximum at the latitude of the Mediterranean Sea (Spanish stations). For inorganic species, it is shown that nitrate, sulfate and ammonium have a mean temporal correlation of 0.25, 0.37 and 0.17, respectively. The spatial correlation is better (0.25, 0.5 and 0.87), showing that the mean values may be biased but the spatial localization of sulfate and ammonium is well reproduced. The size distribution is compared to the AERONET product and it is shown that the model fairly reproduces the main values for the fine and coarse mode. In particular, for the fine mode, the model overestimates the aerosol mass in Africa and underestimates it in Europe.
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SPECIATE--EPA'S DATABASE OF SPECIATED EMISSION PROFILES
SPECIATE is EPA's repository of Total Organic Compound and Particulate Matter speciated profiles for a wide variety of sources. The profiles in this system are provided for air quality dispersion modeling and as a library for source-receptor and source apportionment type models. ...
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NASA Astrophysics Data System (ADS)
Rumsey, Ian C.; Walker, John T.
2016-06-01
The dry component of total nitrogen and sulfur atmospheric deposition remains uncertain. The lack of measurements of sufficient chemical speciation and temporal extent make it difficult to develop accurate mass budgets and sufficient process level detail is not available to improve current air-surface exchange models. Over the past decade, significant advances have been made in the development of continuous air sampling measurement techniques, resulting with instruments of sufficient sensitivity and temporal resolution to directly quantify air-surface exchange of nitrogen and sulfur compounds. However, their applicability is generally restricted to only one or a few of the compounds within the deposition budget. Here, the performance of the Monitor for AeRosols and GAses in ambient air (MARGA 2S), a commercially available online ion-chromatography-based analyzer is characterized for the first time as applied for air-surface exchange measurements of HNO3, NH3, NH4+, NO3-, SO2 and SO42-. Analytical accuracy and precision are assessed under field conditions. Chemical concentrations gradient precision are determined at the same sampling site. Flux uncertainty measured by the aerodynamic gradient method is determined for a representative 3-week period in fall 2012 over a grass field. Analytical precision and chemical concentration gradient precision were found to compare favorably in comparison to previous studies. During the 3-week period, percentages of hourly chemical concentration gradients greater than the corresponding chemical concentration gradient detection limit were 86, 42, 82, 73, 74 and 69 % for NH3, NH4+, HNO3, NO3-, SO2 and SO42-, respectively. As expected, percentages were lowest for aerosol species, owing to their relatively low deposition velocities and correspondingly smaller gradients relative to gas phase species. Relative hourly median flux uncertainties were 31, 121, 42, 43, 67 and 56 % for NH3, NH4+, HNO3, NO3-, SO2 and SO42-, respectively. Flux uncertainty is dominated by uncertainty in the chemical concentrations gradients during the day but uncertainty in the chemical concentration gradients and transfer velocity are of the same order at night. Results show the instrument is sufficiently precise for flux gradient applications.
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1992-01-01
the uncertainty. The above method can give an estimate of the precision of the * analysis. However, determining the accuracy can not be done as...speciation has been determined from analyzing model samples as well as comparison with other methods and combinations of other methods with this method . 3...laboratory. The output of the sensor is characterized over its working range and an appropriate response factor determined by linear regression of the
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Assessment of Important SPECIATE Profiles in EPA’s Emissions Modeling Platform and Current Data Gaps
The US Environmental Protection Agency (EPA)’s SPECIATE database contains speciation profiles for both particulate matter (PM) and volatile organic compounds (VOCs) that are key inputs for creating speciated emission inventories for air quality modeling. The objective of th...
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NASA Astrophysics Data System (ADS)
Zhao, S.; Mashayekhi, R.; Saeednooran, S.; Hakami, A.; Ménard, R.; Moran, M. D.; Zhang, J.
2016-12-01
We have developed a formal framework for documentation, quantification, and propagation of uncertainties in upstream emissions inventory data at various stages leading to the generation of model-ready gridded emissions through emissions processing software such as the EPA's SMOKE (Sparse Matrix Operator Kernel Emissions) system. To illustrate this framework we present a proof-of-concept case study of a bottom-up quantitative assessment of uncertainties in emissions from residential wood combustion (RWC) in the U.S. and Canada. Uncertainties associated with key inventory parameters are characterized based on existing information sources, including the American Housing Survey (AHS) from the U.S. Census Bureau, Timber Products Output (TPO) surveys from the U.S. Forest Service, TNS Canadian Facts surveys, and the AP-42 emission factor document from the U.S. EPA. The propagation of uncertainties is based on Monte Carlo simulation code external to SMOKE. Latin Hypercube Sampling (LHS) is implemented to generate a set of random realizations of each RWC inventory parameter, for which the uncertainties are assumed to be normally distributed. Random realizations are also obtained for each RWC temporal and chemical speciation profile and spatial surrogate field external to SMOKE using the LHS approach. SMOKE outputs for primary emissions (e.g., CO, VOC) using both RWC emission inventory realizations and perturbed temporal and chemical profiles and spatial surrogates show relative uncertainties of about 30-50% across the U.S. and about 70-100% across Canada. Positive skewness values (up to 2.7) and variable kurtosis values (up to 4.8) were also found. Spatial allocation contributes significantly to the overall uncertainty, particularly in Canada. By applying this framework we are able to produce random realizations of model-ready gridded emissions that along with available meteorological ensembles can be used to propagate uncertainties through chemical transport models. The approach described here provides an effective means for formal quantification of uncertainties in estimated emissions from various source sectors and for continuous documentation, assessment, and reduction of emission uncertainties.
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A complex speciation–richness relationship in a simple neutral model
Desjardins-Proulx, Philippe; Gravel, Dominique
2012-01-01
Speciation is the “elephant in the room” of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities. We focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. We use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations. PMID:22957181
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Peña, Carlos; Espeland, Marianne
2015-01-01
The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution. PMID:25830910
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Peña, Carlos; Espeland, Marianne
2015-01-01
The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution.
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NASA Astrophysics Data System (ADS)
von Schneidemesser, E.; Coates, J.; Denier van der Gon, H. A. C.; Visschedijk, A. J. H.; Butler, T. M.
2016-06-01
Non-methane volatile organic compounds (NMVOCs) are detrimental to human health owing to the toxicity of many of the NMVOC species, as well as their role in the formation of secondary air pollutants such as tropospheric ozone (O3) and secondary organic aerosol. The speciation and amount of NMVOCs emitted into the troposphere are represented in emission inventories (EIs) for input to chemical transport models that predict air pollutant levels. Much of the information in EIs pertaining to speciation of NMVOCs is likely outdated, but before taking on the task of providing an up-to-date and highly speciated EI, a better understanding of the sensitivity of models to the change in NMVOC input would be highly beneficial. According to the EIs, the solvent sector is the most important sector for NMVOC emissions. Here, the sensitivity of modelled tropospheric O3 to NMVOC emission inventory speciation was investigated by comparing the maximum potential difference in O3 produced using a variety of reported solvent sector EI speciations in an idealized study using a box model. The sensitivity was tested using three chemical mechanisms that describe O3 production chemistry, typically employed for different types of modelling scales - point (MCM v3.2), regional (RADM2), and global (MOZART-4). In the box model simulations, a maximum difference of 15 ppbv (ca. 22% of the mean O3 mixing ratio of 69 ppbv) between the different EI speciations of the solvent sector was calculated. In comparison, for the same EI speciation, but comparing the three different mechanisms, a maximum difference of 6.7 ppbv was observed. Relationships were found between the relative contribution of NMVOC compound classes (alkanes and oxygenated species) in the speciations to the amount of Ox produced in the box model. These results indicate that modelled tropospheric O3 is sensitive to the speciation of NMVOCs as specified by emission inventories, suggesting that detailed updates to the EI speciation information would be warranted. Furthermore, modelled tropospheric O3 was also sensitive to the choice of chemical mechanism and further evaluation of both of these sensitivities in more realistic chemical-transport models is needed.
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The US Environmental Protection Agency (EPA)’s SPECIATE database contains speciation profiles for both particulate matter (PM) and volatile organic compounds (VOCs) that are key inputs for creating speciated emission inventories for air quality modeling. The objective of th...
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The effect of calcium on aqueous uranium(VI) speciation and adsorption to ferrihydrite and quartz
Fox, P.M.; Davis, J.A.; Zachara, J.M.
2006-01-01
Recent studies of uranium(VI) geochemistry have focused on the potentially important role of the aqueous species, CaUO2 (CO3)32- and Ca2 UO2(CO3)30(aq), on inhibition of microbial reduction and uranium(VI) aqueous speciation in contaminated groundwater. However, to our knowledge, there have been no direct studies of the effects of these species on U(VI) adsorption by mineral phases. The sorption of U(VI) on quartz and ferrihydrite was investigated in NaNO3 solutions equilibrated with either ambient air (430 ppm CO2) or 2% CO2 in the presence of 0, 1.8, or 8.9 mM Ca2+. Under conditions where the Ca2UO2(CO3)30 (aq) species predominates U(VI) aqueous speciation, the presence of Ca in solution lowered U(VI) adsorption on quartz from 77% in the absence of Ca to 42% and 10% at Ca concentrations of 1.8 and 8.9 mM, respectively. U(VI) adsorption to ferrihydrite decreased from 83% in the absence of Ca to 57% in the presence of 1.8 mM Ca. Surface complexation model predictions that included the formation constant for aqueous Ca2UO2(CO3)30(aq) accurately simulated the effect of Ca2+ on U(VI) sorption onto quartz and ferrihydrite within the thermodynamic uncertainty of the stability constant value. This study confirms that Ca2+ can have a significant impact on the aqueous speciation of U(VI), and consequently, on the sorption and mobility of U(VI) in aquifers. ?? 2005 Elsevier Inc. All rights reserved.
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Frequency-dependent selection predicts patterns of radiations and biodiversity.
Melián, Carlos J; Alonso, David; Vázquez, Diego P; Regetz, James; Allesina, Stefano
2010-08-26
Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking pre-existing niches, whereas constant rates have been attributed to non-adaptive processes such as sexual selection and mutation. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the temporal trend in the speciation rate can also be explained by frequency-dependent selection. We construct a frequency-dependent and DNA sequence-based model of speciation. We compare our model to empirical diversity patterns observed for cichlid fish and Darwin's finches, two classic systems for which speciation rates and richness data exist. Negative frequency-dependent selection predicts well both the declining speciation rate found in cichlid fish and explains their species richness. For groups like the Darwin's finches, in which speciation rates are constant and diversity is lower, speciation rate is better explained by a model without frequency-dependent selection. Our analysis shows that differences in diversity may be driven by incipient species abundance with frequency-dependent selection. Our results demonstrate that genetic-distance-based speciation and frequency-dependent selection are sufficient to explain the high diversity observed in natural systems and, importantly, predict decay through time in speciation rate in the absence of pre-existing niches.
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NASA Astrophysics Data System (ADS)
D'Angiola, Ariela; Dawidowski, Laura; Gomez, Dario; Granier, Claire
2014-05-01
Since 2007, more than half of the world's population live in urban areas. Urban atmospheres are dominated by pollutants associated with vehicular emissions. Transport emissions are an important source of non-methane volatile organic compounds (NMVOCs) emissions, species of high interest because of their negative health effects and their contribution to the formation of secondary pollutants responsible for photochemical smog. NMVOCs emissions are generally not very well represented in emission inventories and their speciation presents a high level of uncertainty. In general, emissions from South American countries are still quite unknown for the international community, and usually present a high degree of uncertainty due to the lack of available data to compile emission inventories. Within the Inter-American Institute for Global Change Research (IAI, www.iai.int) projects, UMESAM (Urban Mobile Emissions in South American Megacities) and SAEMC (South American Emissions, Megacities and Climate, http://saemc.cmm.uchile.cl/), the effort was made to compute on-road transport emission inventories for South American megacities, namely Bogota, Buenos Aires, Lima, Sao Paulo and Santiago de Chile, considering megacities as urban agglomerations with more than 5 million inhabitants. The present work is a continuation of these projects, with the aim to extend the calculated NMVOCs emissions inventory into the individual species required by CTMs. The on-road mobile sector of the metropolitan area of Buenos Aires (MABA), Argentina, accounted for 70 Gg of NMVOCs emissions for 2006, without considering two-wheelers. Gasoline light-duty vehicles were responsible for 64% of NMVOCs emissions, followed by compressed natural gas (CNG) light-duty vehicles (22%), diesel heavy-duty vehicles (11%) and diesel light-duty vehicles (7%). NMVOCs emissions were speciated according to fuel and technology, employing the European COPERT (Ntziachristos & Samaras, 2000) VOCs speciation scheme for gasoline and diesel vehicles and the USEPA SPECIATE (Simon et al., 2010) profile for CNG vehicles. NMVOCs emissions were composed of 31% aromatic compounds, 29% linear alkanes, 20% olefins, 12% ramified alkanes, 7% aldehydes and negligible contributions from cycloalkanes, ketones, Polycyclic Aromatic Hydrocarbons (PAHs) and other NMVOCs. Aromatic compounds dominated gasoline light-duty vehicles' emissions (~45%), while linear alkanes those of CNG light-duty vehicles (~80%). Aldehydes' contributions increased for diesel light and heavy-duty vehicles. VOCs speciation schemes for transport emissions were collected from the literature from Europe, USA, Asia, Oceania and Latin America with the aim to account for the associated uncertainty by compound for each fuel and technology type. The resulting individual NMVOCs emissions were used to calculate the corresponding tropospheric ozone formation (Carter, 1994), as well as the human toxicity potential in terms of 1.4 dichlorobenzene. Olefins and aromatic compounds in terms of species, and gasoline in terms of fuels, were found to impose the highest risk in urban environments regarding air quality and human health.
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Tran, Lucy A P
2016-04-01
Biotic and abiotic factors often are treated as mutually exclusive drivers of diversification processes. In this framework, ecological specialists are expected to have higher speciation rates than generalists if abiotic factors are the primary controls on species diversity but lower rates if biotic interactions are more important. Speciation rate is therefore predicted to positively correlate with ecological specialization in the purely abiotic model but negatively correlate in the biotic model. In this study, I show that the positive relationship between ecological specialization and speciation expected from the purely abiotic model is recovered only when a species-specific trait, digestive strategy, is modeled in the terrestrial, herbivorous mammals (Mammalia). This result suggests a more nuanced model in which the response of specialized lineages to abiotic factors is dependent on a biological trait. I also demonstrate that the effect of digestive strategy on the ecological specialization-speciation rate relationship is not due to a difference in either the degree of ecological specialization or the speciation rate between foregut- and hindgut-fermenting mammals. Together, these findings suggest that a biological trait, alongside historical abiotic events, played an important role in shaping mammal speciation at long temporal and large geographic scales.
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New analytic results for speciation times in neutral models.
Gernhard, Tanja
2008-05-01
In this paper, we investigate the standard Yule model, and a recently studied model of speciation and extinction, the "critical branching process." We develop an analytic way-as opposed to the common simulation approach-for calculating the speciation times in a reconstructed phylogenetic tree. Simple expressions for the density and the moments of the speciation times are obtained. Methods for dating a speciation event become valuable, if for the reconstructed phylogenetic trees, no time scale is available. A missing time scale could be due to supertree methods, morphological data, or molecular data which violates the molecular clock. Our analytic approach is, in particular, useful for the model with extinction, since simulations of birth-death processes which are conditioned on obtaining n extant species today are quite delicate. Further, simulations are very time consuming for big n under both models.
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NASA Astrophysics Data System (ADS)
Stokes, M.; Perron, J. T.
2017-12-01
Freshwater systems host exceptionally species-rich communities whose spatial structure is dictated by the topology of the river networks they inhabit. Over geologic time, river networks are dynamic; drainage basins shrink and grow, and river capture establishes new connections between previously separated regions. It has been hypothesized that these changes in river network structure influence the evolution of life by exchanging and isolating species, perhaps boosting biodiversity in the process. However, no general model exists to predict the evolutionary consequences of landscape change. We couple a neutral community model of freshwater organisms to a landscape evolution model in which the river network undergoes drainage divide migration and repeated river capture. Neutral community models are macro-ecological models that include stochastic speciation and dispersal to produce realistic patterns of biodiversity. We explore the consequences of three modes of speciation - point mutation, time-protracted, and vicariant (geographic) speciation - by tracking patterns of diversity in time and comparing the final result to an equilibrium solution of the neutral model on the final landscape. Under point mutation, a simple model of stochastic and instantaneous speciation, the results are identical to the equilibrium solution and indicate the dominance of the species-area relationship in forming patterns of diversity. The number of species in a basin is proportional to its area, and regional species richness reaches its maximum when drainage area is evenly distributed among sub-basins. Time-protracted speciation is also modeled as a stochastic process, but in order to produce more realistic rates of diversification, speciation is not assumed to be instantaneous. Rather, each new species must persist for a certain amount of time before it is considered to be established. When vicariance (geographic speciation) is included, there is a transient signature of increased regional diversity after river capture. The results indicate that the mode of speciation and the rate of speciation relative to the rate of divide migration determine the evolutionary signature of river capture.
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A STUDY OF GAS-PHASE MERCURY SPECIATION USING DETAILED CHEMICAL KINETICS
Mercury (Hg) speciation in combustion-generated flue gas is modeled using a detailed chemical mechanism consisting of 60 reactions and 21 species. This speciation model accounts for chlorination and oxidation of key flue-gas components, including elemental mercury. Results indica...
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Chromosomes, conflict, and epigenetics: chromosomal speciation revisited.
Brown, Judith D; O'Neill, Rachel J
2010-01-01
Since Darwin first noted that the process of speciation was indeed the "mystery of mysteries," scientists have tried to develop testable models for the development of reproductive incompatibilities-the first step in the formation of a new species. Early theorists proposed that chromosome rearrangements were implicated in the process of reproductive isolation; however, the chromosomal speciation model has recently been questioned. In addition, recent data from hybrid model systems indicates that simple epistatic interactions, the Dobzhansky-Muller incompatibilities, are more complex. In fact, incompatibilities are quite broad, including interactions among heterochromatin, small RNAs, and distinct, epigenetically defined genomic regions such as the centromere. In this review, we will examine both classical and current models of chromosomal speciation and describe the "evolving" theory of genetic conflict, epigenetics, and chromosomal speciation.
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Ribas, Camila C.; Aleixo, Alexandre; Nogueira, Afonso C. R.; Miyaki, Cristina Y.; Cracraft, Joel
2012-01-01
Many hypotheses have been proposed to explain high species diversity in Amazonia, but few generalizations have emerged. In part, this has arisen from the scarcity of rigorous tests for mechanisms promoting speciation, and from major uncertainties about palaeogeographic events and their spatial and temporal associations with diversification. Here, we investigate the environmental history of Amazonia using a phylogenetic and biogeographic analysis of trumpeters (Aves: Psophia), which are represented by species in each of the vertebrate areas of endemism. Their relationships reveal an unforeseen ‘complete’ time-slice of Amazonian diversification over the past 3.0 Myr. We employ this temporally calibrated phylogeny to test competing palaeogeographic hypotheses. Our results are consistent with the establishment of the current Amazonian drainage system at approximately 3.0–2.0 Ma and predict the temporal pattern of major river formation over Plio-Pleistocene times. We propose a palaeobiogeographic model for the last 3.0 Myr of Amazonian history that has implications for understanding patterns of endemism, the temporal history of Amazonian diversification and mechanisms promoting speciation. The history of Psophia, in combination with new geological evidence, provides the strongest direct evidence supporting a role for river dynamics in Amazonian diversification, and the absence of such a role for glacial climate cycles and refugia. PMID:21795268
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A probabilistic approach to emissions from transportation sector in the coming decades
NASA Astrophysics Data System (ADS)
Yan, F.; Winijkul, E.; Bond, T. C.; Streets, D. G.
2010-12-01
Future emission estimates are necessary for understanding climate change, designing national and international strategies for air quality control and evaluating mitigation policies. Emission inventories are uncertain and future projections even more so. Most current emission projection models are deterministic; in other words, there is only single answer for each scenario. As a result, uncertainties have not been included in the estimation of climate forcing or other environmental effects, but it is important to quantify the uncertainty inherent in emission projections. We explore uncertainties of emission projections from transportation sector in the coming decades by sensitivity analysis and Monte Carlo simulations. These projections are based on a technology driven model: the Speciated Pollutants Emission Wizard (SPEW)-Trend, which responds to socioeconomic conditions in different economic and mitigation scenarios. The model contains detail about technology stock, including consumption growth rates, retirement rates, timing of emission standards, deterioration rates and transition rates from normal vehicles to vehicles with extremely high emission factors (termed “superemitters”). However, understanding of these parameters, as well as relationships with socioeconomic conditions, is uncertain. We project emissions from transportation sectors under four different IPCC scenarios (A1B, A2, B1, and B2). Due to the later implementation of advanced emission standards, Africa has the highest annual growth rate (1.2-3.1%) from 2010 to 2050. Superemitters begin producing more than 50% of global emissions around year 2020. We estimate uncertainties from the relationships between technological change and socioeconomic conditions and examine their impact on future emissions. Sensitivities to parameters governing retirement rates are highest, causing changes in global emissions from-26% to +55% on average from 2010 to 2050. We perform Monte Carlo simulations to examine how these uncertainties will affect total emissions if any input parameter that has inherent the uncertainties is substituted by a range of values-probability distribution and varies at the same time; the 95% confidence interval of global emission annual growth rate is -1.9% to +0.2% per year.
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SPECIATE 4.4: The Bridge Between Emissions Characterization and Modeling
SPECIATE is the U.S. Environmental Protection Agency’s (EPA) repository of volatile organic gas and particulate matter (PM) speciation profiles of air pollution sources. Some of the many uses of these source profiles include: (1) creating speciated emissions inventories for...
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Examination of Arsenic Speciation in Sulfidic Solutions Using X-ray Absorption Spectroscopy
The chemical speciation of arsenic in sulfidic waters is complicated by the existence of thioarsenic species. The purpose of this research was to use advanced spectroscopy techniques along with speciation modeling and chromatography to elucidate the chemical speciation of As in ...
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The shape and temporal dynamics of phylogenetic trees arising from geographic speciation.
Pigot, Alex L; Phillimore, Albert B; Owens, Ian P F; Orme, C David L
2010-12-01
Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.
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Technical Evaluation of Biogeochemical Transformation of Iodine at 200-UP-1, Hanford, WA
NASA Astrophysics Data System (ADS)
Lee, M. H.; Cordova, E.; Brooks, S.; Moser, E.; Wells, J.; Lee, B.
2015-12-01
From the 1940s through the early 1990s, liquid wastes from materials used and produced at the Hanford Site were disposed to the ground through cribs, ditches, ponds, and trenches. Primary groundwater and vadose zone contaminants include carbon tetrachloride, uranium, nitrate, chromium, 129I, 99Tc, and tritium. Iodine-129 is of environmental concern due to its long half-life, mobility, and hazardous potential to humans through bioaccumulation, and is one of the primary risk drivers for the Hanford site. The 200 West area of the Hanford Site contains two separate plumes covering 1,500 acres where 129I concentrations are ~3.5 pCi/L in Hanford groundwater. Speciation analysis shows that iodate comprises 70.6% of the iodine present, and organo-iodide and iodide comprise 25.8% and 3.6% respectively. While hydraulic containment is the currently selected remedy for 129I in the groundwater, there is currently no remedy selected for controlling migration of 129I from the vadose zone to the groundwater. Research is currently underway to develop a site conceptual model for understanding the biogeochemical drivers for iodine speciation and determine the processes that drive the fate and transport of 129I through the vadose zone and into groundwater. These data will provide the information to decrease the uncertainty related to the inventory, distribution, and transport properties which will lead to appropriate treatment strategies for the 129I plume(s). Understanding the mechanisms and contributors to iodine speciation is important in order to develop bioremediation strategies for contaminated areas. The effect that microbial communities and humic acid have on iodine speciation and sorption was explored using Ringold sediment from the 200 West Area exposed to varying levels of 129I contamination in conjunction with varying growth media constituents. Several isolates obtained from these batch studies have been shown to reduce over 80% of iodate present in growth media when nitrate was present. No iodate reduction was observed in the absence of nitrate. Additionally, several isolates have been identified that can oxidize iodide. Currently, analytical techniques are underway to quantify the effect of microbial interaction on iodine speciation along with characterization of these diverse microbial isolates.
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Bats (Chiroptera: Noctilionoidea) Challenge a Recent Origin of Extant Neotropical Diversity.
Rojas, Danny; Warsi, Omar M; Dávalos, Liliana M
2016-05-01
The mechanisms underlying the high extant biodiversity in the Neotropics have been controversial since the 19th century. Support for the influence of period-specific changes on diversification often rests on detecting more speciation events during a particular period. The timing of speciation events may reflect the influence of incomplete taxon sampling, protracted speciation, and null processes of lineage accumulation. Here we assess the influence of these factors on the timing of speciation with new multilocus data for New World noctilionoid bats (Chiroptera: Noctilionoidea). Biogeographic analyses revealed the importance of the Neotropics in noctilionoid diversification, and the critical role of dispersal. We detected no shift in speciation rate associated with the Quaternary or pre-Quaternary periods, and instead found an increase in speciation linked to the evolution of the subfamily Stenodermatinae (∼18 Ma). Simulations modeling constant speciation and extinction rates for the phylogeny systematically showed more speciation events in the Quaternary. Since recording more divergence events in the Quaternary can result from lineage accumulation, the age of extant sister species cannot be interpreted as supporting higher speciation rates during this period. Instead, analyzing the factors that influence speciation requires modeling lineage-specific traits and environmental, spatial, and ecological drivers of speciation. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Speciation genetics: current status and evolving approaches
Wolf, Jochen B. W.; Lindell, Johan; Backström, Niclas
2010-01-01
The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues. PMID:20439277
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Dutton, Steven J.; Vedal, Sverre; Piedrahita, Ricardo; Milford, Jana B.; Miller, Shelly L.; Hannigan, Michael P.
2012-01-01
Particulate matter less than 2.5 microns in diameter (PM2.5) has been linked with a wide range of adverse health effects. Determination of the sources of PM2.5 most responsible for these health effects could lead to improved understanding of the mechanisms of such effects and more targeted regulation. This has provided the impetus for the Denver Aerosol Sources and Health (DASH) study, a multi-year source apportionment and health effects study relying on detailed inorganic and organic PM2.5 speciation measurements. In this study, PM2.5 source apportionment is performed by coupling positive matrix factorization (PMF) with daily speciated PM2.5 measurements including inorganic ions, elemental carbon (EC) and organic carbon (OC), and organic molecular markers. A qualitative comparison is made between two models, PMF2 and ME2, commonly used for solving the PMF problem. Many previous studies have incorporated chemical mass balance (CMB) for organic molecular marker source apportionment on limited data sets, but the DASH data set is large enough to use multivariate factor analysis techniques such as PMF. Sensitivity of the PMF2 and ME2 models to the selection of speciated PM2.5 components and model input parameters was investigated in depth. A combination of diagnostics was used to select an optimum, 7-factor model using one complete year of daily data with pointwise measurement uncertainties. The factors included 1) a wintertime/methoxyphenol factor, 2) an EC/sterane factor, 3) a nitrate/polycyclic aromatic hydrocarbon (PAH) factor, 4) a summertime/selective aliphatic factor, 5) an n-alkane factor, 6) a middle oxygenated PAH/alkanoic acid factor and 7) an inorganic ion factor. These seven factors were qualitatively linked with known PM2.5 emission sources with varying degrees of confidence. Mass apportionment using the 7-factor model revealed the contribution of each factor to the mass of OC, EC, nitrate and sulfate. On an annual basis, the majority of OC and EC mass was associated with the summertime/selective aliphatic factor and the EC/sterane factor, respectively, while nitrate and sulfate mass were both dominated by the inorganic ion factor. This apportionment was found to vary substantially by season. Several of the factors identified in this study agree well with similar assessments conducted in St. Louis, MO and Pittsburgh, PA using PMF and organic molecular markers. PMID:22768005
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Yeung, Carol K.L.; Tsai, Pi-Wen; Chesser, R. Terry; Lin, Rong-Chien; Yao, Cheng-Te; Tian, Xiu-Hua; Li, Shou-Hsien
2011-01-01
Although founder effect speciation has been a popular theoretical model for the speciation of geographically isolated taxa, its empirical importance has remained difficult to evaluate due to the intractability of past demography, which in a founder effect speciation scenario would involve a speciational bottleneck in the emergent species and the complete cessation of gene flow following divergence. Using regression-weighted approximate Bayesian computation, we tested the validity of these two fundamental conditions of founder effect speciation in a pair of sister species with disjunct distributions: the royal spoonbill Platalea regia in Australasia and the black-faced spoonbill Pl. minor in eastern Asia. When compared with genetic polymorphism observed at 20 nuclear loci in the two species, simulations showed that the founder effect speciation model had an extremely low posterior probability (1.55 × 10-8) of producing the extant genetic pattern. In contrast, speciation models that allowed for postdivergence gene flow were much more probable (posterior probabilities were 0.37 and 0.50 for the bottleneck with gene flow and the gene flow models, respectively) and postdivergence gene flow persisted for a considerable period of time (more than 80% of the divergence history in both models) following initial divergence (median = 197,000 generations, 95% credible interval [CI]: 50,000-478,000, for the bottleneck with gene flow model; and 186,000 generations, 95% CI: 45,000-477,000, for the gene flow model). Furthermore, the estimated population size reduction in Pl. regia to 7,000 individuals (median, 95% CI: 487-12,000, according to the bottleneck with gene flow model) was unlikely to have been severe enough to be considered a bottleneck. Therefore, these results do not support founder effect speciation in Pl. regia but indicate instead that the divergence between Pl. regia and Pl. minor was probably driven by selection despite continuous gene flow. In this light, we discuss the potential importance of evolutionarily labile traits with significant fitness consequences, such as migratory behavior and habitat preference, in facilitating divergence of the spoonbills.
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Monte Carlo simulations of parapatric speciation
NASA Astrophysics Data System (ADS)
Schwämmle, V.; Sousa, A. O.; de Oliveira, S. M.
2006-06-01
Parapatric speciation is studied using an individual-based model with sexual reproduction. We combine the theory of mutation accumulation for biological ageing with an environmental selection pressure that varies according to the individuals geographical positions and phenotypic traits. Fluctuations and genetic diversity of large populations are crucial ingredients to model the features of evolutionary branching and are intrinsic properties of the model. Its implementation on a spatial lattice gives interesting insights into the population dynamics of speciation on a geographical landscape and the disruptive selection that leads to the divergence of phenotypes. Our results suggest that assortative mating is not an obligatory ingredient to obtain speciation in large populations at low gene flow.
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Visualizing speciation in artificial cichlid fish.
Clement, Ross
2006-01-01
The Cichlid Speciation Project (CSP) is an ALife simulation system for investigating open problems in the speciation of African cichlid fish. The CSP can be used to perform a wide range of experiments that show that speciation is a natural consequence of certain biological systems. A visualization system capable of extracting the history of speciation from low-level trace data and creating a phylogenetic tree has been implemented. Unlike previous approaches, this visualization system presents a concrete trace of speciation, rather than a summary of low-level information from which the viewer can make subjective decisions on how speciation progressed. The phylogenetic trees are a more objective visualization of speciation, and enable automated collection and summarization of the results of experiments. The visualization system is used to create a phylogenetic tree from an experiment that models sympatric speciation.
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Parkhurst, David L.; Appelo, C.A.J.
1999-01-01
PHREEQC version 2 is a computer program written in the C programming language that is designed to perform a wide variety of low-temperature aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations; (2) batch-reaction and one-dimensional (1D) transport calculations involving reversible reactions, which include aqueous, mineral, gas, solid-solution, surface-complexation, and ion-exchange equilibria, and irreversible reactions, which include specified mole transfers of reactants, kinetically controlled reactions, mixing of solutions, and temperature changes; and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for differences in composition between waters, within specified compositional uncertainty limits.New features in PHREEQC version 2 relative to version 1 include capabilities to simulate dispersion (or diffusion) and stagnant zones in 1D-transport calculations, to model kinetic reactions with user-defined rate expressions, to model the formation or dissolution of ideal, multicomponent or nonideal, binary solid solutions, to model fixed-volume gas phases in addition to fixed-pressure gas phases, to allow the number of surface or exchange sites to vary with the dissolution or precipitation of minerals or kinetic reactants, to include isotope mole balances in inverse modeling calculations, to automatically use multiple sets of convergence parameters, to print user-defined quantities to the primary output file and (or) to a file suitable for importation into a spreadsheet, and to define solution compositions in a format more compatible with spreadsheet programs. This report presents the equations that are the basis for chemical equilibrium, kinetic, transport, and inverse-modeling calculations in PHREEQC; describes the input for the program; and presents examples that demonstrate most of the program's capabilities.
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Rumsey and Walker_AMT_2016_Figure 1.xlsx
Figure summarizes diurnal profiles of uncertainty in the chemical gradient and transfer velocity measurements from which fluxes are calculated. This dataset is associated with the following publication:Rumsey, I. Application of an online ion chromatography-based instrument for gradient flux measurements of speciated nitrogen and sulfur. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 9(6): 2581-2592, (2016).
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Estimating the Rate of Occurrence of Renal Stones in Astronauts
NASA Technical Reports Server (NTRS)
Myers, J.; Goodenow, D.; Gokoglu, S.; Kassemi, M.
2016-01-01
Changes in urine chemistry, during and post flight, potentially increases the risk of renal stones in astronauts. Although much is known about the effects of space flight on urine chemistry, no inflight incidence of renal stones in US astronauts exists and the question "How much does this risk change with space flight?" remains difficult to accurately quantify. In this discussion, we tackle this question utilizing a combination of deterministic and probabilistic modeling that implements the physics behind free stone growth and agglomeration, speciation of urine chemistry and published observations of population renal stone incidences to estimate changes in the rate of renal stone presentation. The modeling process utilizes a Population Balance Equation based model developed in the companion IWS abstract by Kassemi et al. (2016) to evaluate the maximum growth and agglomeration potential from a specified set of urine chemistry values. Changes in renal stone occurrence rates are obtained from this model in a probabilistic simulation that interrogates the range of possible urine chemistries using Monte Carlo techniques. Subsequently, each randomly sampled urine chemistry undergoes speciation analysis using the well-established Joint Expert Speciation System (JESS) code to calculate critical values, such as ionic strength and relative supersaturation. The Kassemi model utilizes this information to predict the mean and maximum stone size. We close the assessment loop by using a transfer function that estimates the rate of stone formation from combining the relative supersaturation and both the mean and maximum free stone growth sizes. The transfer function is established by a simulation analysis which combines population stone formation rates and Poisson regression. Training this transfer function requires using the output of the aforementioned assessment steps with inputs from known non-stone-former and known stone-former urine chemistries. Established in a Monte Carlo system, the entire renal stone analysis model produces a probability distribution of the stone formation rate and an expected uncertainty in the estimate. The utility of this analysis will be demonstrated by showing the change in renal stone occurrence predicted by this method using urine chemistry distributions published in Whitson et al. 2009. A comparison to the model predictions to previous assessments of renal stone risk will be used to illustrate initial validation of the model.
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Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction.
Beaulieu, Jeremy M; O'Meara, Brian C
2016-07-01
The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Speciation in the Derrida-Higgs model with finite genomes and spatial populations
NASA Astrophysics Data System (ADS)
de Aguiar, Marcus A. M.
2017-02-01
The speciation model proposed by Derrida and Higgs demonstrated that a sexually reproducing population can split into different species in the absence of natural selection or any type of geographic isolation, provided that mating is assortative and the number of genes involved in the process is infinite. Here we revisit this model and simulate it for finite genomes, focusing on the question of how many genes it actually takes to trigger neutral sympatric speciation. We find that, for typical parameters used in the original model, it takes the order of 105 genes. We compare the results with a similar spatially explicit model where about 100 genes suffice for speciation. We show that when the number of genes is small the species that emerge are strongly segregated in space. For a larger number of genes, on the other hand, the spatial structure of the population is less important and the species distribution overlap considerably.
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Zhang, Ning; Brugger, Joël; Etschmann, Barbara; Ngothai, Yung; Zeng, Dewen
2015-01-01
Knowledge of the structure and speciation of aqueous Ni(II)-chloride complexes is important for understanding Ni behavior in hydrometallurgical extraction. The effect of concentration on the first-shell structure of Ni(II) in aqueous NiCl2 and NiCl2-MgCl2 solutions was investigated by Ni K edge X-ray absorption (XAS) and UV-Vis spectroscopy at ambient conditions. Both techniques show that no large structural change (e.g., transition from octahedral to tetrahedral-like configuration) occurs. Both methods confirm that the Ni(II) aqua ion (with six coordinated water molecules at R Ni-O = 2.07(2) Å) is the dominant species over the whole NiCl2 concentration range. However, XANES, EXAFS and UV-Vis data show subtle changes at high salinity (> 2 mol∙kg-1 NiCl2), which are consistent with the formation of small amounts of the NiCl+ complex (up to 0.44(23) Cl at a Ni-Cl distance of 2.35(2) Å in 5.05 mol∙kg-1 NiCl2) in the pure NiCl2 solutions. At high Cl:Ni ratio in the NiCl2-MgCl2-H2O solutions, small amounts of [NiCl2]0 are also present. We developed a speciation-based mixed-solvent electrolyte (MSE) model to describe activity-composition relationships in NiCl2-MgCl2-H2O solutions, and at the same time predict Ni(II) speciation that is consistent with our XAS and UV-Vis data and with existing literature data up to the solubility limit, resolving a long-standing uncertainty about the role of chloride complexing in this system. PMID:25885410
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Refining the conditions for sympatric ecological speciation.
Débarre, F
2012-12-01
Can speciation occur in a single population when different types of resources are available, in the absence of any geographical isolation, or any spatial or temporal variation in selection? The controversial topics of sympatric speciation and ecological speciation have already stimulated many theoretical studies, most of them agreeing on the fact that mechanisms generating disruptive selection, some level of assortment, and enough heterogeneity in the available resources, are critical for sympatric speciation to occur. Few studies, however, have combined the three factors and investigated their interactions. In this article, I analytically derive conditions for sympatric speciation in a general model where the distribution of resources can be uni- or bimodal, and where a parameter controls the range of resources that an individual can exploit. This approach bridges the gap between models of a unimodal continuum of resources and Levene-type models with discrete resources. I then test these conditions against simulation results from a recently published article (Thibert-Plante & Hendry, 2011, J. Evol. Biol. 24: 2186-2196) and confirm that sympatric ecological speciation is favoured when (i) selection is disruptive (i.e. individuals with an intermediate trait are at a local fitness minimum), (ii) resources are differentiated enough and (iii) mating is assortative. I also discuss the role of mating preference functions and the need (or lack thereof) for bimodality in resource distributions for diversification. © 2012 The Author. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.
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Meier, Joana I; Sousa, Vitor C; Marques, David A; Selz, Oliver M; Wagner, Catherine E; Excoffier, Laurent; Seehausen, Ole
2017-01-01
Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation. © 2016 John Wiley & Sons Ltd.
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Comparative tests of the role of dewlap size in Anolis lizard speciation
Harrison, Alexis; Mahler, D. Luke; Castañeda, María del Rosario; Glor, Richard E.; Herrel, Anthony; Stuart, Yoel E.; Losos, Jonathan B.
2016-01-01
Phenotypic traits may be linked to speciation in two distinct ways: character values may influence the rate of speciation or diversification in the trait may be associated with speciation events. Traits involved in signal transmission, such as the dewlap of Anolis lizards, are often involved in the speciation process. The dewlap is an important visual signal with roles in species recognition and sexual selection, and dewlaps vary among species in relative size as well as colour and pattern. We compile a dataset of relative dewlap size digitized from photographs of 184 anole species from across the genus' geographical range. We use phylogenetic comparative methods to test two hypotheses: that larger dewlaps are associated with higher speciation rates, and that relative dewlap area diversifies according to a speciational model of evolution. We find no evidence of trait-dependent speciation, indicating that larger signals do not enhance any role the dewlap has in promoting speciation. Instead, we find a signal of mixed speciational and gradual trait evolution, with a particularly strong signal of speciational change in the dewlaps of mainland lineages. This indicates that dewlap size diversifies in association with the speciation process, suggesting that divergent selection may play a role in the macroevolution of this signalling trait. PMID:28003450
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The reality and importance of founder speciation in evolution.
Templeton, Alan R
2008-05-01
A founder event occurs when a new population is established from a small number of individuals drawn from a large ancestral population. Mayr proposed that genetic drift in an isolated founder population could alter the selective forces in an epistatic system, an observation supported by recent studies. Carson argued that a period of relaxed selection could occur when a founder population is in an open ecological niche, allowing rapid population growth after the founder event. Selectable genetic variation can actually increase during this founder-flush phase due to recombination, enhanced survival of advantageous mutations, and the conversion of non-additive genetic variance into additive variance in an epistatic system, another empirically confirmed prediction. Templeton combined the theories of Mayr and Carson with population genetic models to predict the conditions under which founder events can contribute to speciation, and these predictions are strongly confirmed by the empirical literature. Much of the criticism of founder speciation is based upon equating founder speciation to an adaptive peak shift opposed by selection. However, Mayr, Carson and Templeton all modeled a positive interaction of selection and drift, and Templeton showed that founder speciation is incompatible with peak-shift conditions. Although rare, founder speciation can have a disproportionate importance in adaptive innovation and radiation, and examples are given to show that "rare" does not mean "unimportant" in evolution. Founder speciation also interacts with other speciation mechanisms such that a speciation event is not a one-dimensional process due to either selection alone or drift alone. (c) 2008 Wiley Periodicals, Inc.
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Matos-Maraví, Pável
2016-07-01
Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence. © 2016 The Author(s).
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Moran model as a dynamical process on networks and its implications for neutral speciation.
de Aguiar, Marcus A M; Bar-Yam, Yaneer
2011-09-01
In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.
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Moran model as a dynamical process on networks and its implications for neutral speciation
NASA Astrophysics Data System (ADS)
de Aguiar, Marcus A. M.; Bar-Yam, Yaneer
2011-03-01
In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.
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Mabilia, Rosanna; Cecinato, Angelo; Guerriero, Ettore; Possanzini, Massimiliano
2006-02-01
In this note we describe the speciated particle-phase PM2.5 polynuclear aromatic hydrocarbon (PAH) and gas-phase carbonyl emissions as collected from a heavy-duty diesel bus outfitted with an oxidation catalyst for exhaust after-treatment. The vehicle was run on a chassis dynamometer during a transient cycle test reproducing a typical city bus route (Azienda Tramviaria Municipalizzata cycle). The diluted tailpipe emissions were sampled for PAH using a 2.5 microm cut size cyclone glass fiber filter assembly, while carbonyls were absorbed onto dinitrophenyl hydrazine-coated silica cartridges. The former compounds were analysed by CGC-MS, the latter by HPLC-UV. Combining the two sets of speciation data resulting from 15 identical dynamometer tests provided a profile of both unregulated organic emissions. PAH emission rates decreased with the number of benzene fused rings. Fluoranthene and pyrene amounted to 90% of total PAHs quantified; six-ring PAHs accounted only for 0.5%. Similarly, formaldehyde and acetaldehyde accounted for approximately 80% of the total carbonyl emissions. Uncertainties of the method in the determination of individual emission factors were calculated. Statistical data processing revealed that all the measurements were quite unaffected by systematic errors and repeatability percentages did not exceed 50% for the majority of components of both groups.
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A Multivariate Dynamic Spatial Factor Model for Speciated Pollutants and Adverse Birth Outcomes
Kaufeld, Kimberly Ann; Fuentes, Montse; Reich, Brian J.; ...
2017-09-11
Evidence suggests that exposure to elevated concentrations of air pollution during pregnancy is associated with increased risks of birth defects and other adverse birth outcomes. While current regulations put limits on total PM2.5 concentrations, there are many speciated pollutants within this size class that likely have distinct effects on perinatal health. However, due to correlations between these speciated pollutants, it can be difficult to decipher their effects in a model for birth outcomes. To combat this difficulty, we develop a multivariate spatio-temporal Bayesian model for speciated particulate matter using dynamic spatial factors. These spatial factors can then be interpolated tomore » the pregnant women’s homes to be used to model birth defects. The birth defect model allows the impact of pollutants to vary across different weeks of the pregnancy in order to identify susceptible periods. Here, the proposed methodology is illustrated using pollutant monitoring data from the Environmental Protection Agency and birth records from the National Birth Defect Prevention Study.« less
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A Multivariate Dynamic Spatial Factor Model for Speciated Pollutants and Adverse Birth Outcomes
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kaufeld, Kimberly Ann; Fuentes, Montse; Reich, Brian J.
Evidence suggests that exposure to elevated concentrations of air pollution during pregnancy is associated with increased risks of birth defects and other adverse birth outcomes. While current regulations put limits on total PM2.5 concentrations, there are many speciated pollutants within this size class that likely have distinct effects on perinatal health. However, due to correlations between these speciated pollutants, it can be difficult to decipher their effects in a model for birth outcomes. To combat this difficulty, we develop a multivariate spatio-temporal Bayesian model for speciated particulate matter using dynamic spatial factors. These spatial factors can then be interpolated tomore » the pregnant women’s homes to be used to model birth defects. The birth defect model allows the impact of pollutants to vary across different weeks of the pregnancy in order to identify susceptible periods. Here, the proposed methodology is illustrated using pollutant monitoring data from the Environmental Protection Agency and birth records from the National Birth Defect Prevention Study.« less
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Diffusive mass transport in agglomerated glassy fallout from a near-surface nuclear test
NASA Astrophysics Data System (ADS)
Weisz, David G.; Jacobsen, Benjamin; Marks, Naomi E.; Knight, Kim B.; Isselhardt, Brett H.; Matzel, Jennifer E.
2018-02-01
Aerodynamically-shaped glassy fallout is formed when vapor phase constituents from the nuclear device are incorporated into molten carriers (i.e. fallout precursor materials derived from soil or other near-field environmental debris). The effects of speciation and diffusive transport of condensing constituents are not well defined in models of fallout formation. Previously we reported observations of diffuse micrometer scale layers enriched in Na, Fe, Ca, and 235U, and depleted in Al and Ti, at the interfaces of agglomerated fallout objects. Here, we derive the timescales of uranium mass transport in such fallout as it cools from 2500 K to 1500 K by applying a 1-dimensional planar diffusion model to the observed 235U/30Si variation at the interfaces. By modeling the thermal transport between the fireball and the carrier materials, the time of mass transport is calculated to be <0.6 s, <1 s, <2 s, and <3.5 s for fireball yields of 0.1 kt, 1 kt, 10 kt, and 100 kt respectively. Based on the calculated times of mass transport, a maximum temperature of deposition of uranium onto the carrier material of ∼2200 K is inferred (1σ uncertainty of ∼200 K). We also determine that the occurrence of micrometer scale layers of material enriched in relatively volatile Na-species as well as more refractory Ca-species provides evidence for an oxygen-rich fireball based on the vapor pressure of the two species under oxidizing conditions. These results represent the first application of diffusion-based modeling to derive material transport, thermal environments, and oxidation-speciation in near-surface nuclear detonation environments.
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Diffusive mass transport in agglomerated glassy fallout from a near-surface nuclear test
Weisz, David G.; Jacobsen, Benjamin; Marks, Naomi E.; ...
2017-12-15
Aerodynamically-shaped glassy fallout is formed when vapor phase constituents from the nuclear device are incorporated into molten carriers (i.e. fallout precursor materials derived from soil or other near-field environmental debris). The effects of speciation and diffusive transport of condensing constituents are not well defined in models of fallout formation. Previously we reported observations of diffuse micrometer scale layers enriched in Na, Fe, Ca, and 235U, and depleted in Al and Ti, at the interfaces of agglomerated fallout objects. Here in this paper, we derive the timescales of uranium mass transport in such fallout as it cools from 2500 K tomore » 1500 K by applying a 1-dimensional planar diffusion model to the observed 235U/ 30Si variation at the interfaces. By modeling the thermal transport between the fireball and the carrier materials, the time of mass transport is calculated to be <0.6 s, <1 s, <2 s, and <3.5 s for fireball yields of 0.1 kt, 1 kt, 10 kt, and 100 kt respectively. Based on the calculated times of mass transport, a maximum temperature of deposition of uranium onto the carrier material of ~2200 K is inferred (1σ uncertainty of ~200 K). We also determine that the occurrence of micrometer scale layers of material enriched in relatively volatile Na-species as well as more refractory Ca-species provides evidence for an oxygen-rich fireball based on the vapor pressure of the two species under oxidizing conditions. These results represent the first application of diffusion-based modeling to derive material transport, thermal environments, and oxidation-speciation in near-surface nuclear detonation environments.« less
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Diffusive mass transport in agglomerated glassy fallout from a near-surface nuclear test
DOE Office of Scientific and Technical Information (OSTI.GOV)
Weisz, David G.; Jacobsen, Benjamin; Marks, Naomi E.
Aerodynamically-shaped glassy fallout is formed when vapor phase constituents from the nuclear device are incorporated into molten carriers (i.e. fallout precursor materials derived from soil or other near-field environmental debris). The effects of speciation and diffusive transport of condensing constituents are not well defined in models of fallout formation. Previously we reported observations of diffuse micrometer scale layers enriched in Na, Fe, Ca, and 235U, and depleted in Al and Ti, at the interfaces of agglomerated fallout objects. Here in this paper, we derive the timescales of uranium mass transport in such fallout as it cools from 2500 K tomore » 1500 K by applying a 1-dimensional planar diffusion model to the observed 235U/ 30Si variation at the interfaces. By modeling the thermal transport between the fireball and the carrier materials, the time of mass transport is calculated to be <0.6 s, <1 s, <2 s, and <3.5 s for fireball yields of 0.1 kt, 1 kt, 10 kt, and 100 kt respectively. Based on the calculated times of mass transport, a maximum temperature of deposition of uranium onto the carrier material of ~2200 K is inferred (1σ uncertainty of ~200 K). We also determine that the occurrence of micrometer scale layers of material enriched in relatively volatile Na-species as well as more refractory Ca-species provides evidence for an oxygen-rich fireball based on the vapor pressure of the two species under oxidizing conditions. These results represent the first application of diffusion-based modeling to derive material transport, thermal environments, and oxidation-speciation in near-surface nuclear detonation environments.« less
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Updated methane, non-methane organic gas, and volatile organic compound calculations based on speciation data. Updated speciation and toxic emission rates for new model year 2010 and later heavy-duty diesel engines. Updated particulate matter emission rates for 2004 and later mod...
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Schneider, Arnaud R; Ponthieu, Marie; Cancès, Benjamin; Conreux, Alexandra; Morvan, Xavier; Gommeaux, Maxime; Marin, Béatrice; Benedetti, Marc F
2016-06-01
Trace element (TE) speciation modelling in soil solution is controlled by the assumptions made about the soil solution composition. To evaluate this influence, different assumptions using Visual MINTEQ were tested and compared to measurements of free TE concentrations. The soil column Donnan membrane technique (SC-DMT) was used to estimate the free TE (Cd, Cu, Ni, Pb and Zn) concentrations in six acidic soil solutions. A batch technique using DAX-8 resin was used to fractionate the dissolved organic matter (DOM) into four fractions: humic acids (HA), fulvic acids (FA), hydrophilic acids (Hy) and hydrophobic neutral organic matter (HON). To model TE speciation, particular attention was focused on the hydrous manganese oxides (HMO) and the Hy fraction, ligands not considered in most of the TE speciation modelling studies in soil solution. In this work, the model predictions of free ion activities agree with the experimental results. The knowledge of the FA fraction seems to be very useful, especially in the case of high DOM content, for more accurately representing experimental data. Finally, the role of the manganese oxides and of the Hy fraction on TE speciation was identified and, depending on the physicochemical conditions of the soil solution, should be considered in future studies. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Genetic change and rates of cladogenesis
DOE Office of Scientific and Technical Information (OSTI.GOV)
Avise, J.C.; Ayala, F.J.
1975-12-01
Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predictions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic distance between species is a function of time, mean genetic distances inmore » speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. The limited information presently available agrees better with the model predicting that genetic change is primarily a function of time, and is not correlated with rates of speciation. Further testing of the models is, however, required before firm conclusions can be drawn. (auth)« less
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Anagenesis, Cladogenesis, and Speciation on Islands.
Emerson, Brent C; Patiño, Jairo
2018-05-03
Anagenesis and cladogenesis are fundamental evolutionary concepts, but are increasingly being adopted as speciation models in the field of island biogeography. Here, we review the origin of the terms 'anagenetic' and 'cladogenetic' speciation, critique their utility, and finally suggest alternative terminology that better describes the geographical relationships of insular sister species. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Speciation has a spatial scale that depends on levels of gene flow.
Kisel, Yael; Barraclough, Timothy G
2010-03-01
Area is generally assumed to affect speciation rates, but work on the spatial context of speciation has focused mostly on patterns of range overlap between emerging species rather than on questions of geographical scale. A variety of geographical theories of speciation predict that the probability of speciation occurring within a given region should (1) increase with the size of the region and (2) increase as the spatial extent of intraspecific gene flow becomes smaller. Using a survey of speciation events on isolated oceanic islands for a broad range of taxa, we find evidence for both predictions. The probability of in situ speciation scales with island area in bats, carnivorous mammals, birds, flowering plants, lizards, butterflies and moths, and snails. Ferns are an exception to these findings, but they exhibit high frequencies of polyploid and hybrid speciation, which are expected to be scale independent. Furthermore, the minimum island size for speciation correlates across groups with the strength of intraspecific gene flow, as is estimated from a meta-analysis of published population genetic studies. These results indicate a general geographical model of speciation rates that are dependent on both area and gene flow. The spatial scale of population divergence is an important but neglected determinant of broad-scale diversity patterns.
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Chromosome speciation: Humans, Drosophila, and mosquitoes
Ayala, Francisco J.; Coluzzi, Mario
2005-01-01
Chromosome rearrangements (such as inversions, fusions, and fissions) may play significant roles in the speciation between parapatric (contiguous) or partly sympatric (geographically overlapping) populations. According to the “hybrid-dysfunction” model, speciation occurs because hybrids with heterozygous chromosome rearrangements produce dysfunctional gametes and thus have low reproductive fitness. Natural selection will, therefore, promote mutations that reduce the probability of intercrossing between populations carrying different rearrangements and thus promote their reproductive isolation. This model encounters a disabling difficulty: namely, how to account for the spread in a population of a chromosome rearrangement after it first arises as a mutation in a single individual. The “suppressed-recombination” model of speciation points out that chromosome rearrangements act as a genetic filter between populations. Mutations associated with the rearranged chromosomes cannot flow from one to another population, whereas genetic exchange will freely occur between colinear chromosomes. Mutations adaptive to local conditions will, therefore, accumulate differentially in the protected chromosome regions so that parapatric or partially sympatric populations will genetically differentiate, eventually evolving into different species. The speciation model of suppressed recombination has recently been tested by gene and DNA sequence comparisons between humans and chimpanzees, between Drosophila species, and between species related to Anopheles gambiae, the vector of malignant malaria in Africa. PMID:15851677
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In Vitro Model To Assess Arsenic Bioaccessibility and Speciation in Cooked Shrimp.
Chi, Haifeng; Zhang, Youchi; Williams, Paul N; Lin, Shanna; Hou, Yanwei; Cai, Chao
2018-05-09
Shrimp, a popular and readily consumed seafood, contains high concentrations of arsenic. However, few studies have focused on whether arsenic in the shrimp could be transformed during the cooking process and gastrointestinal digestion. In this study, a combined in vitro model [Unified Bioaccessibility Research Group of Europe (BARGE) Method-Simulator of Human Intestinal Microbial Ecosystem (UBM-SHIME)] was used to investigate arsenic bioaccessibility and its speciation in raw and cooked shrimps. The results showed that the cooking practices had little effect on the arsenic content and speciation. Bioaccessibility of arsenic in raw shrimp was at a high level, averaging 76.9 ± 4.28 and 86.7 ± 3.74% in gastric and small intestinal phases, respectively. Arsenic speciation was stable in all of the shrimp digestions, with nontoxic arsenobetaine (AsB) being the dominated speciation. The cooking practice significantly increased the bioaccessibility of arsenate ( p < 0.05) in shrimp digests, indicating the increase of the potential health risks.
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Cloutier-Hurteau, Benoît; Sauvé, Sébastien; Courchesne, François
2007-12-01
Metal speciation data calculated by modeling could give useful information regarding the fate of metals in the rhizospheric environment. However, no comparative study has evaluated the relative accuracy of speciation models in this microenvironment. Consequently, the present study evaluates the reliability of free Cu ion (Cu2+) activity modeled by WHAM 6 and MINEQL+ 4.5 for 18 bulk and 18 rhizospheric soil samples collected in two Canadian forested areas located near industrial facilities. The modeling of Cu speciation was performed on water extracts using pH, dissolved organic carbon (DOC), major ions, and total dissolved Al, Ca, Cu, Mg, and Zn concentrations as input data. Four scenarios representing the composition of dissolved organic substances using fulvic, humic, and acetic acids were derived from the literature and used in the modeling exercise. Different scenarios were used to contrast soil components (rhizosphere vs bulk) and soil pH levels (acidic vs neutral to alkaline). Reference Cu2+ activity values measured by an ion-selective electrode varied between 0.39 and 41 nM. The model MINEQL+ 4.5 provided good predictions of Cu2+ activities [root-mean-square residual (RMSR)= 0.37], while predictions from WHAM 6 were poor (RMSR = 1.74) because they overestimated Cu complexation with DOC. Modeling with WHAM 6 could be improved by adjusting the proportion of inert DOC and the composition of DOC (RMSR = 0.94), but it remained weaker than predictions with MINEQL+ 4.5. These results suggested that the discrepancies between speciation models were attributed to differences in the binding capacity of humic substances with Cu, where WHAM 6 appeared to be too aggressive. Therefore, we concluded that chemical interactions occurring between Cu and DOC were key factors for an accurate simulation of Cu speciation, especially in rhizospheric forest soils, where high variation of the DOC concentration and composition are observed.
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Quantitative traits and diversification.
FitzJohn, Richard G
2010-12-01
Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.
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Speciation of adsorbates on surface of solids by infrared spectroscopy and chemometrics.
Vilmin, Franck; Bazin, Philippe; Thibault-Starzyk, Frédéric; Travert, Arnaud
2015-09-03
Speciation, i.e. identification and quantification, of surface species on heterogeneous surfaces by infrared spectroscopy is important in many fields but remains a challenging task when facing strongly overlapped spectra of multiple adspecies. Here, we propose a new methodology, combining state of the art instrumental developments for quantitative infrared spectroscopy of adspecies and chemometrics tools, mainly a novel data processing algorithm, called SORB-MCR (SOft modeling by Recursive Based-Multivariate Curve Resolution) and multivariate calibration. After formal transposition of the general linear mixture model to adsorption spectral data, the main issues, i.e. validity of Beer-Lambert law and rank deficiency problems, are theoretically discussed. Then, the methodology is exposed through application to two case studies, each of them characterized by a specific type of rank deficiency: (i) speciation of physisorbed water species over a hydrated silica surface, and (ii) speciation (chemisorption and physisorption) of a silane probe molecule over a dehydrated silica surface. In both cases, we demonstrate the relevance of this approach which leads to a thorough surface speciation based on comprehensive and fully interpretable multivariate quantitative models. Limitations and drawbacks of the methodology are also underlined. Copyright © 2015 Elsevier B.V. All rights reserved.
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Dynamic coupled metal transport-speciation model: application to assess a zinc-contaminated lake.
Bhavsar, Satyendra P; Diamond, Miriam L; Gandhi, Nilima; Nilsen, Joel
2004-10-01
A coupled metal transport and speciation/complexation model (TRANSPEC) has been developed to estimate the speciation and fate of multiple interconverting species in surface aquatic systems. Dynamic-TRANSPEC loosely, sequentially couples the speciation/complexation and fate modules that, for the unsteady state formulation, run alternatively at every time step. The speciation module first estimates species abundance using, in this version, MINEQL+ considering time-dependent changes in water and pore-water chemistry. The fate module is based on the quantitative water air sediment interaction (QWASI) model and fugacity/aquivalence formulation, with the option of using a pseudo-steady state solution to account for past discharges. Similarly to the QWASI model for organic contaminants, TRANSPEC assumes the instantaneous equilibrium distribution of metal species among dissolved, colloidal, and particulate phases based on ambient chemistry parameters that can be collected through conventional field methods. The model is illustrated with its application to Ross Lake (Manitoba, Canada) that has elevated Zn concentrations due to discharges over 70 years from a mining operation. Using measurements from field studies, the model reproduces year-round variations in Zn water concentrations. A 10-year projection for current conditions suggests decreasing Zn remobilization and export from the lake. Decreasing Zn loadings increases sediment-to-water transport but decreases water concentrations, and vice versa. Species distribution is affected by pH such that a decrease in pH increases metal export from the lake and vice versa.
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NASA Astrophysics Data System (ADS)
Maggi, F.; Riley, W. J.
2009-12-01
The composition and location of 15N atoms on N2O isotopomers and isotopologues during isotope speciation has been used to characterize soil biological N cycling and N2O surface emissions. Although there exist few experimental observations, no attempt has been made to model N2O isotopomer speciation. The mathematical treatment of biological kinetic reactions in isotopic applications normally makes use of first-order and quasi steady-state complexation assumptions without taking into account changes in enzyme concentration, reaction stoichiometry, and isotopologue and isotopomer speciation. When multiatomic isotopically-labeled reactants are used in a multi-molecurar reaction, these assumptions may fail since they always lead to a constant fractionation factor and cannot describe speciation of isotopologues and isotopomers. We have developed a mathematical framework that is capable of describing isotopologue and isotopmer speciation and fractionation under the assumption of non-steady complexation during biological kinetic reactions that overcome the limitations mentioned above. This framework was applied to a case study of non-steady (variable and inverse) isotopic effects observed during N2O production and consumption in soils. Our mathematical treatment has led to generalized kinetic equations which replicate experimental observations with high accuracy and help interpret non-steady isotopic effects and isotopologue and isotopomer speciation. The kinetic equations introduced and applied here have general validity in describing isotopic effects in any biochemical reactions by considering: changing enzyme concentrations, mass and isotope conservation, and reaction stoichiometry. The equations also describe speciation of any isotopologue and isotopomer product from any isotopologue and isotopmer reactant.
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Why abundant tropical tree species are phylogenetically old.
Wang, Shaopeng; Chen, Anping; Fang, Jingyun; Pacala, Stephen W
2013-10-01
Neutral models of species diversity predict patterns of abundance for communities in which all individuals are ecologically equivalent. These models were originally developed for Panamanian trees and successfully reproduce observed distributions of abundance. Neutral models also make macroevolutionary predictions that have rarely been evaluated or tested. Here we show that neutral models predict a humped or flat relationship between species age and population size. In contrast, ages and abundances of tree species in the Panamanian Canal watershed are found to be positively correlated, which falsifies the models. Speciation rates vary among phylogenetic lineages and are partially heritable from mother to daughter species. Variable speciation rates in an otherwise neutral model lead to a demographic advantage for species with low speciation rate. This demographic advantage results in a positive correlation between species age and abundance, as found in the Panamanian tropical forest community.
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Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies.
Potter, Sally; Bragg, Jason G; Blom, Mozes P K; Deakin, Janine E; Kirkpatrick, Mark; Eldridge, Mark D B; Moritz, Craig
2017-01-01
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale . We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
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Lambert, Amaury; Stadler, Tanja
2013-12-01
Forward-in-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPPs), where trees grow "horizontally" by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPPs lead to extremely fast computation of tree likelihoods and simulation of reconstructed trees. Their topology always follows the uniform distribution on ranked tree shapes (URT). We characterize which forward-in-time models lead to URT reconstructed trees and among these, which lead to CPP reconstructed trees. We show that for any "asymmetric" diversification model in which speciation rates only depend on time and extinction rates only depend on time and on a non-heritable trait (e.g., age), the reconstructed tree is CPP, even if extant species are incompletely sampled. If rates additionally depend on the number of species, the reconstructed tree is (only) URT (but not CPP). We characterize the common distribution of speciation times in the CPP description, and discuss incomplete species sampling as well as three special model cases in detail: (1) the extinction rate does not depend on a trait; (2) rates do not depend on time; (3) mass extinctions may happen additionally at certain points in the past. Copyright © 2013 Elsevier Inc. All rights reserved.
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A test of the chromosomal theory of ecotypic speciation in Anopheles gambiae
Manoukis, Nicholas C.; Powell, Jeffrey R.; Touré, Mahamoudou B.; Sacko, Adama; Edillo, Frances E.; Coulibaly, Mamadou B.; Traoré, Sekou F.; Taylor, Charles E.; Besansky, Nora J.
2008-01-01
The role of chromosomal inversions in speciation has long been of interest to evolutionists. Recent quantitative modeling has stimulated reconsideration of previous conceptual models for chromosomal speciation. Anopheles gambiae, the most important vector of human malaria, carries abundant chromosomal inversion polymorphism nonrandomly associated with ecotypes that mate assortatively. Here, we consider the potential role of paracentric inversions in promoting speciation in A. gambiae via “ecotypification,” a term that refers to differentiation arising from local adaptation. In particular, we focus on the Bamako form, an ecotype characterized by low inversion polymorphism and fixation of an inversion, 2Rj, that is very rare or absent in all other forms of A. gambiae. The Bamako form has a restricted distribution by the upper Niger River and its tributaries that is associated with a distinctive type of larval habitat, laterite rock pools, hypothesized to be its optimal breeding site. We first present computer simulations to investigate whether the population dynamics of A. gambiae are consistent with chromosomal speciation by ecotypification. The models are parameterized using field observations on the various forms of A. gambiae that exist in Mali, West Africa. We then report on the distribution of larvae of this species collected from rock pools and more characteristic breeding sites nearby. Both the simulations and field observations support the thesis that speciation by ecotypification is occurring, or has occurred, prompting consideration of Bamako as an independent species. PMID:18287019
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Mechanisms of rapid sympatric speciation by sex reversal and sexual selection in cichlid fish.
Lande, R; Seehausen, O; van Alphen, J J
2001-01-01
Mechanisms of speciation in cichlid fish were investigated by analyzing population genetic models of sexual selection on sex-determining genes associated with color polymorphisms. The models are based on a combination of laboratory experiments and field observations on the ecology, male and female mating behavior, and inheritance of sex-determination and color polymorphisms. The models explain why sex-reversal genes that change males into females tend to be X-linked and associated with novel colors, using the hypothesis of restricted recombination on the sex chromosomes, as suggested by previous theory on the evolution of recombination. The models reveal multiple pathways for rapid sympatric speciation through the origin of novel color morphs with strong assortative mating that incorporate both sex-reversal and suppressor genes. Despite the lack of geographic isolation or ecological differentiation, the new species coexists with the ancestral species either temporarily or indefinitely. These results may help to explain different patterns and rates of speciation among groups of cichlids, in particular the explosive diversification of rock-dwelling haplochromine cichlids.
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Igea, Javier; Bogarín, Diego; Papadopulos, Alexander S T; Savolainen, Vincent
2015-02-01
Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy-based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.
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Florio, A M; Ingram, C M; Rakotondravony, H A; Louis, E E; Raxworthy, C J
2012-07-01
Species delimitation within recently evolved groups can be challenging because species may be difficult to distinguish morphologically. Following the General Lineage Concept, we apply a multiple evidence approach to assess species limits within the carpet chameleon Furcifer lateralis, which is endemic to Madagascar and exported in large numbers for the pet trade. Cryptic speciation within F. lateralis was considered likely because this species (1) has a vast distribution, (2) occupies exceptionally diverse habitats and (3) exhibits subtle regional differences in morphology. Phylogenetic trees reconstructed using nuclear and mitochondrial genes recovered three well-supported clades corresponding with geography. Morphological results based on canonical variates analysis show that these clades exhibit subtle differences in head casque morphology. Ecological niche modelling results found that these phylogenetic groups also occupy unique environmental space and exhibit patterns of regional endemism typical of other endemic reptiles. Combined, our findings provide diverse yet consistent evidence for the existence of three species. Consequently, we elevate the subspecies F. lateralis major to species rank and name a new species distributed in northern and western Madagascar. Initial ecological divergence, associated with speciation of F. lateralis in humid eastern habitat, fits the Ecographic Constraint model for species diversification in Madagascar. By contrast, the second speciation event provides some support for the Riverine Barrier model, with the Mangoky River possibly causing initial isolation between species. These findings thus support two contrasting models of speciation within closely related species and demonstrate the utility of applying a combined-evidence approach for detecting cryptic speciation. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.
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Xu, Shuqing; Schlüter, Philipp M
2015-01-01
Divergent selection by pollinators can bring about strong reproductive isolation via changes at few genes of large effect. This has recently been demonstrated in sexually deceptive orchids, where studies (1) quantified the strength of reproductive isolation in the field; (2) identified genes that appear to be causal for reproductive isolation; and (3) demonstrated selection by analysis of natural variation in gene sequence and expression. In a group of closely related Ophrys orchids, specific floral scent components, namely n-alkenes, are the key floral traits that control specific pollinator attraction by chemical mimicry of insect sex pheromones. The genetic basis of species-specific differences in alkene production mainly lies in two biosynthetic genes encoding stearoyl-acyl carrier protein desaturases (SAD) that are associated with floral scent variation and reproductive isolation between closely related species, and evolve under pollinator-mediated selection. However, the implications of this genetic architecture of key floral traits on the evolutionary processes of pollinator adaptation and speciation in this plant group remain unclear. Here, we expand on these recent findings to model scenarios of adaptive evolutionary change at SAD2 and SAD5, their effects on plant fitness (i.e., offspring number), and the dynamics of speciation. Our model suggests that the two-locus architecture of reproductive isolation allows for rapid sympatric speciation by pollinator shift; however, the likelihood of such pollinator-mediated speciation is asymmetric between the two orchid species O. sphegodes and O. exaltata due to different fitness effects of their predominant SAD2 and SAD5 alleles. Our study not only provides insight into pollinator adaptation and speciation mechanisms of sexually deceptive orchids but also demonstrates the power of applying a modeling approach to the study of pollinator-driven ecological speciation.
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Potential impact of climate change on air pollution-related human health effects.
Tagaris, Efthimios; Liao, Kuo-Jen; Delucia, Anthony J; Deck, Leland; Amar, Praveen; Russell, Armistead G
2009-07-01
The potential health impact of ambient ozone and PM2.5 concentrations modulated by climate change over the United States is investigated using combined atmospheric and health modeling. Regional air quality modeling for 2001 and 2050 was conducted using CMAQ Modeling System with meteorology from the GISS Global Climate Model, downscaled regionally using MM5,keeping boundary conditions of air pollutants, emission sources, population, activity levels, and pollution controls constant. BenMap was employed to estimate the air pollution health outcomes at the county, state, and national level for 2050 caused by the effect of meteorology on future ozone and PM2.5 concentrations. The changes in calculated annual mean PM2.5 concentrations show a relatively modest change with positive and negative responses (increasing PM2.5 levels across the northeastern U.S.) although average ozone levels slightly decrease across the northern sections of the U.S., and increase across the southern tier. Results suggest that climate change driven air quality-related health effects will be adversely affected in more then 2/3 of the continental U.S. Changes in health effects induced by PM2.5 dominate compared to those caused by ozone. PM2.5-induced premature mortality is about 15 times higher then that due to ozone. Nationally the analysis suggests approximately 4000 additional annual premature deaths due to climate change impacts on PM2.5 vs 300 due to climate change-induced ozone changes. However, the impacts vary spatially. Increased premature mortality due to elevated ozone concentrations will be offset by lower mortality from reductions in PM2.5 in 11 states. Uncertainties related to different emissions projections used to simulate future climate, and the uncertainties forecasting the meteorology, are large although there are potentially important unaddressed uncertainties (e.g., downscaling, speciation, interaction, exposure, and concentration-response function of the human health studies).
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Feder, Jeffrey L.; Nosil, Patrik; Flaxman, Samuel M.
2014-01-01
Many hypotheses have been put forth to explain the origin and spread of inversions, and their significance for speciation. Several recent genic models have proposed that inversions promote speciation with gene flow due to the adaptive significance of the genes contained within them and because of the effects inversions have on suppressing recombination. However, the consequences of inversions for the dynamics of genome wide divergence across the speciation continuum remain unclear, an issue we examine here. We review a framework for the genomics of speciation involving the congealing of the genome into alternate adaptive states representing species (“genome wide congealing”). We then place inversions in this context as examples of how genetic hitchhiking can potentially hasten genome wide congealing. Specifically, we use simulation models to (i) examine the conditions under which inversions may speed genome congealing and (ii) quantify predicted magnitudes of these effects. Effects of inversions on promoting speciation were most common and pronounced when inversions were initially fixed between populations before secondary contact and adaptation involved many genes with small fitness effects. Further work is required on the role of underdominance and epistasis between a few loci of major effect within inversions. The results highlight five important aspects of the roles of inversions in speciation: (i) the geographic context of the origins and spread of inversions, (ii) the conditions under which inversions can facilitate divergence, (iii) the magnitude of that facilitation, (iv) the extent to which the buildup of divergence is likely to be biased within vs. outside of inversions, and (v) the dynamics of the appearance and disappearance of exceptional divergence within inversions. We conclude by discussing the empirical challenges in showing that inversions play a central role in facilitating speciation with gene flow. PMID:25206365
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Stankowski, Sean
2013-05-01
Speciation is the process by which reproductive isolation evolves between populations. Two general models of speciation have been proposed: ecological speciation, where reproductive barriers evolve due to ecologically based divergent selection, and mutation-order speciation, where populations fix different mutations as they adapt to similar selection pressures. I evaluate these alternative models and determine the progress of speciation in a diverse group of land snails, genus Rhagada, inhabiting Rosemary Island. A recently derived keeled-flat morphotype occupies two isolated rocky hills, while globose-shelled snails inhabit the surrounding plains. The study of one hill reveals that they are separated by a narrow hybrid zone. As predicted by ecological speciation theory, there are local and landscape level associations between shell shape and habitat, and the morphological transition coincides with a narrow ecotone between the two distinct environments. Microsatellite DNA revealed a cline of hybrid index scores much wider than the morphological cline, further supporting the ecological maintenance of the morphotypes. The hybrid zone does not run through an area of low population density, as is expected for mutation-order hybrid zones, and there is a unimodal distribution of phenotypes at the centre, suggesting that there is little or no prezygotic isolation. Instead, these data suggest that the ecotypes are maintained by ecologically dependent postzygotic isolation (i.e. ecological selection against hybrids). Mitochondrial and Microsatellite DNA indicate that the keeled-flat form evolved recently, and without major historical disruptions to gene flow. The data also suggest that the two keeled-flat populations, inhabiting similar rocky hills, have evolved in parallel. These snails provide a complex example of ecological speciation in its early stages. © 2013 Blackwell Publishing Ltd.
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Speciation in birds: genes, geography, and sexual selection.
Edwards, Scott V; Kingan, Sarah B; Calkins, Jennifer D; Balakrishnan, Christopher N; Jennings, W Bryan; Swanson, Willie J; Sorenson, Michael D
2005-05-03
Molecular studies of speciation in birds over the last three decades have been dominated by a focus on the geography, ecology, and timing of speciation, a tradition traceable to Mayr's Systematics and the Origin of Species. However, in the recent years, interest in the behavioral and molecular mechanisms of speciation in birds has increased, building in part on the older traditions and observations from domesticated species. The result is that many of the same mechanisms proffered for model lineages such as Drosophila--mechanisms such as genetic incompatibilities, reinforcement, and sexual selection--are now being seriously entertained for birds, albeit with much lower resolution. The recent completion of a draft sequence of the chicken genome, and an abundance of single-nucleotide polymorphisms on the autosomes and sex chromosomes, will dramatically accelerate research on the molecular mechanisms of avian speciation over the next few years. The challenge for ornithologists is now to inform well studied examples of speciation in nature with increased molecular resolution-to clone speciation genes if they exist--and thereby evaluate the relative roles of extrinsic, intrinsic, deterministic, and stochastic causes for avian diversification.
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Sensitivity tests to define the source apportionment performance criteria in the DeltaSA tool
NASA Astrophysics Data System (ADS)
Pernigotti, Denise; Belis, Claudio A.
2017-04-01
Identification and quantification of the contribution of emission sources to a given area is a key task for the design of abatement strategies. Moreover, European member states are obliged to report this kind of information for zones where the pollution levels exceed the limit values. At present, little is known about the performance and uncertainty of the variety of methodologies used for source apportionment and the comparability between the results of studies using different approaches. The source apportionment Delta (SA Delta) is a tool developed by the EC-JRC to support the particulate matter source apportionment modellers in the identification of sources (for factor analysis studies) and/or in the measure of their performance. The source identification is performed by the tool measuring the proximity of any user chemical profile to preloaded repository data (SPECIATE and SPECIEUROPE). The model performances criteria are based on standard statistical indexes calculated by comparing participants' source contribute estimates and their time series with preloaded references data. Those preloaded data refer to previous European SA intercomparison exercises: the first with real world data (22 participants), the second with synthetic data (25 participants) and the last with real world data which was also extended to Chemical Transport Models (38 receptor models and 4 CTMs). The references used for the model performances are 'true' (predefined by JRC) for the synthetic while they are calculated as ensemble average of the participants' results in real world intercomparisons. The candidates used for each source ensemble reference calculation were selected among participants results based on a number of consistency checks plus the similarity between their chemical profiles to the repository measured data. The estimation of the ensemble reference uncertainty is crucial in order to evaluate the users' performances against it. For this reason a sensitivity analysis on different methods to estimate the ensemble references' uncertainties was performed re-analyzing the synthetic intercomparison dataset, the only one where 'true' reference and ensemble reference contributions were both present. The Delta SA is now available on-line and will be presented, with a critical discussion of the sensitivity analysis on the ensemble reference uncertainty. In particular the grade of among participants mutual agreement on the presence of a certain source should be taken into account. Moreover also the importance of the synthetic intercomparisons in order to catch receptor models common biases will be stressed.
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Kinetics of steel slag leaching: Batch tests and modeling
DOE Office of Scientific and Technical Information (OSTI.GOV)
De Windt, Laurent, E-mail: laurent.dewindt@mines-paristech.fr; Chaurand, Perrine; Rose, Jerome
2011-02-15
Reusing steel slag as an aggregate for road construction requires to characterize the leaching kinetics and metal releases. In this study, basic oxygen furnace (BOF) steel slag were subjected to batch leaching tests at liquid to solid ratios (L/S) of 10 and 100 over 30 days; the leachate chemistry being regularly sampled in time. A geochemical model of the steel slag is developed and validated from experimental data, particularly the evolution with leaching of mineralogical composition of the slag and trace element speciation. Kinetics is necessary for modeling the primary phase leaching, whereas a simple thermodynamic equilibrium approach can bemore » used for secondary phase precipitation. The proposed model simulates the kinetically-controlled dissolution (hydrolysis) of primary phases, the precipitation of secondary phases (C-S-H, hydroxide and spinel), the pH and redox conditions, and the progressive release of major elements as well as the metals Cr and V. Modeling indicates that the dilution effect of the L/S ratio is often coupled to solubility-controlled processes, which are sensitive to both the pH and the redox potential. A sensitivity analysis of kinetic uncertainties on the modeling of element releases is performed.« less
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Computer simulations of sympatric speciation in a simple food web
NASA Astrophysics Data System (ADS)
Luz-Burgoa, K.; Dell, Tony; de Oliveira, S. Moss
2005-07-01
Galapagos finches, have motivated much theoretical research aimed at understanding the processes associated with the formation of the species. Inspired by them, in this paper we investigate the process of sympatric speciation in a simple food web model. For that we modify the individual-based Penna model that has been widely used to study aging as well as other evolutionary processes. Initially, our web consists of a primary food source and a single herbivore species that feeds on this resource. Subsequently we introduce a predator that feeds on the herbivore. In both instances we manipulate directly a basal resource distribution and monitor the changes in the populations. Sympatric speciation is obtained for the top species in both cases, and our results suggest that the speciation velocity depends on how far up, in the food chain, the focus population is feeding. Simulations are done with three different sexual imprintinglike mechanisms, in order to discuss adaptation by natural selection.
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Sympatric speciation as a consequence of male pregnancy in seahorses
Jones, Adam G.; Moore, Glenn I.; Kvarnemo, Charlotta; Walker, DeEtte; Avise, John C.
2003-01-01
The phenomenon of male pregnancy in the family Syngnathidae (seahorses, pipefishes, and sea dragons) undeniably has sculpted the course of behavioral evolution in these fishes. Here we explore another potentially important but previously unrecognized consequence of male pregnancy: a predisposition for sympatric speciation. We present microsatellite data on genetic parentage that show that seahorses mate size-assortatively in nature. We then develop a quantitative genetic model based on these empirical findings to demonstrate that sympatric speciation indeed can occur under this mating regime in response to weak disruptive selection on body size. We also evaluate phylogenetic evidence bearing on sympatric speciation by asking whether tiny seahorse species are sister taxa to large sympatric relatives. Overall, our results indicate that sympatric speciation is a plausible mechanism for the diversification of seahorses, and that assortative mating (in this case as a result of male parental care) may warrant broader attention in the speciation process for some other taxonomic groups as well. PMID:12732712
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Minimal effects of latitude on present-day speciation rates in New World birds
Rabosky, Daniel L.; Title, Pascal O.; Huang, Huateng
2015-01-01
The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades. PMID:26019156
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2011-01-01
Background Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be selected for, he proposed that most events of speciation would occur through a process of separation and divergence, and this point of view is still shared by most evolutionary biologists today. Results I do, however, contend that, if so much speciation occurs, the most likely explanation is that there must be conditions where reproductive barriers can be directly selected for. In other words, situations where it is advantageous for individuals to reproduce preferentially within a small group and reduce their breeding with the rest of the ancestral population. This leads me to propose a model whereby new species arise not by populations splitting into separate branches, but by small inbreeding groups "budding" from an ancestral stock. This would be driven by several advantages of inbreeding, and mainly by advantageous recessive phenotypes, which could only be retained in the context of inbreeding. Reproductive barriers would thus not arise as secondary consequences of divergent evolution in populations isolated from one another, but under the direct selective pressure of ancestral stocks. Many documented cases of speciation in natural populations appear to fit the model proposed, with more speciation occurring in populations with high inbreeding coefficients, and many recessive characters identified as central to the phenomenon of speciation, with these recessive mutations expected to be surrounded by patterns of limited genomic diversity. Conclusions Whilst adaptive evolution would correspond to gains of function that would, most of the time, be dominant, this type of speciation by budding would thus be driven by mutations resulting in the advantageous loss of certain functions since recessive mutations very often correspond to the inactivation of a gene. A very important further advantage of inbreeding is that it reduces the accumulation of recessive mutations in genomes. A consequence of the model proposed is that the existence of species would correspond to a metastable equilibrium between inbreeding and outbreeding, with excessive inbreeding promoting speciation, and excessive outbreeding resulting in irreversible accumulation of recessive mutations that could ultimately only lead to extinction. Reviewer names Eugene V. Koonin, Patrick Nosil (nominated by Dr Jerzy Jurka), Pierre Pontarotti PMID:22152499
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Speciation of the trivalent f-elements Eu(III) and Cm(III) in digestive media.
Wilke, Claudia; Barkleit, Astrid; Stumpf, Thorsten; Ikeda-Ohno, Atsushi
2017-10-01
In case radioactive materials are released into the environment, their incorporation into our digestive system would be a significant concern. Trivalent f-elements, i.e., trivalent actinides and lanthanides, could potentially represent a serious health risk due to their chemo- and radiotoxicity, nevertheless the biochemical behavior of these elements are mostly unknown even to date. This study, therefore, focuses on the chemical speciation of trivalent f-elements in the human gastrointestinal tract. To simulate the digestive system artificial digestive juices (saliva, gastric juice, pancreatic juice and bile fluid) were prepared. The chemical speciation of lanthanides (as Eu(III)) and actinides (as Cm(III)) was determined experimentally by time-resolved laser-induced fluorescence spectroscopy (TRLFS) and the results were compared with thermodynamic modeling. The results indicate a dominant inorganic species with phosphate/carbonate in the mouth, while the aquo ion is predominantly formed with a minor contribution of the enzyme pepsin in the stomach. In the intestinal tract the most significant species are with the protein mucin. We demonstrated the first experimental results on the chemical speciation of trivalent f-elements in the digestive media by TRLFS. The results highlight a significant gap in chemical speciation between experiments and thermodynamic modeling due to the limited availability of thermodynamic stability constants particularly for organic species. Chemical speciation strongly influences the in vivo behavior of metal ions. Therefore, the results of this speciation study will help to enhance the assessment of health risks and to improve decorporation strategies after ingestion of these (radio-)toxic heavy metal ions. Copyright © 2017 Elsevier Inc. All rights reserved.
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A robust framework to predict mercury speciation in combustion flue gases.
Ticknor, Jonathan L; Hsu-Kim, Heileen; Deshusses, Marc A
2014-01-15
Mercury emissions from coal combustion have become a global concern as growing energy demands have increased the consumption of coal. The effective implementation of treatment technologies requires knowledge of mercury speciation in the flue gas, namely concentrations of elemental, oxidized and particulate mercury at the exit of the boiler. A model that can accurately predict mercury species in flue gas would be very useful in that context. Here, a Bayesian regularized artificial neural network (BRANN) that uses five coal properties and combustion temperature was developed to predict mercury speciation in flue gases before treatment technology implementation. The results of the model show that up to 97 percent of the variation in mercury species concentration is captured through the use of BRANNs. The BRANN model was used to conduct a parametric sensitivity which revealed that the coal chlorine content and coal calorific value were the most sensitive parameters, followed by the combustion temperature. The coal sulfur content was the least important parameter. The results demonstrate the applicability of BRANNs for predicting mercury concentration and speciation in combustion flue gas and provide a more efficient and effective technique when compared to other advanced non-mechanistic modeling strategies. Copyright © 2013 Elsevier B.V. All rights reserved.
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Phylogenetic evidence for cladogenetic polyploidization in land plants.
Zhan, Shing H; Drori, Michal; Goldberg, Emma E; Otto, Sarah P; Mayrose, Itay
2016-07-01
Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation". Whether polyploidization is associated with the formation of new species (cladogenesis) or simply occurs over time within a lineage (anagenesis), however, has never been assessed systematically. We tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera. © 2016 Botanical Society of America.
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Khatri, Bhavin S.; Goldstein, Richard A.
2015-01-01
Speciation is fundamental to understanding the huge diversity of life on Earth. Although still controversial, empirical evidence suggests that the rate of speciation is larger for smaller populations. Here, we explore a biophysical model of speciation by developing a simple coarse-grained theory of transcription factor-DNA binding and how their co-evolution in two geographically isolated lineages leads to incompatibilities. To develop a tractable analytical theory, we derive a Smoluchowski equation for the dynamics of binding energy evolution that accounts for the fact that natural selection acts on phenotypes, but variation arises from mutations in sequences; the Smoluchowski equation includes selection due to both gradients in fitness and gradients in sequence entropy, which is the logarithm of the number of sequences that correspond to a particular binding energy. This simple consideration predicts that smaller populations develop incompatibilities more quickly in the weak mutation regime; this trend arises as sequence entropy poises smaller populations closer to incompatible regions of phenotype space. These results suggest a generic coarse-grained approach to evolutionary stochastic dynamics, allowing realistic modelling at the phenotypic level. PMID:25936759
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Thermodynamic behavior of a phase transition in a model for sympatric speciation
NASA Astrophysics Data System (ADS)
Luz-Burgoa, K.; Moss de Oliveira, S.; Schwämmle, Veit; Sá Martins, J. S.
2006-08-01
We investigate the macroscopic effects of the ingredients that drive the origin of species through sympatric speciation. In our model, sympatric speciation is obtained as we tune up the strength of competition between individuals with different phenotypes. As a function of this control parameter, we can characterize, through the behavior of a macroscopic order parameter, a phase transition from a nonspeciation to a speciation state of the system. The behavior of the first derivative of the order parameter with respect to the control parameter is consistent with a phase transition and exhibits a sharp peak at the transition point. For different resources distribution, the transition point is shifted, an effect similar to pressure in a PVT system. The inverse of the parameter related to a sexual selection strength behaves like an external field in the system and, as thus, is also a control parameter. The macroscopic effects of the biological parameters used in our model are a reminiscent of the behavior of thermodynamic quantities in a phase transition of an equilibrium physical system.
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Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis
Feder, Jeffrey L.; Xie, Xianfa; Rull, Juan; Velez, Sebastian; Forbes, Andrew; Leung, Brian; Dambroski, Hattie; Filchak, Kenneth E.; Aluja, Martin
2005-01-01
The Rhagoletis pomonella sibling species complex is a model for sympatric speciation by means of host plant shifting. However, genetic variation aiding the sympatric radiation of the group in the United States may have geographic roots. Inversions on chromosomes 1-3 affecting diapause traits adapting flies to differences in host fruiting phenology appear to exist in the United States because of a series of secondary introgression events from Mexico. Here, we investigate whether these inverted regions of the genome may have subsequently evolved to become more recalcitrant to introgression relative to collinear regions, consistent with new models for chromosomal speciation. As predicted by the models, gene trees for six nuclear loci mapping to chromosomes other than 1-3 tended to have shallower node depths separating Mexican and U.S. haplotypes relative to an outgroup sequence than nine genes residing on chromosomes 1-3. We discuss the implications of secondary contact and differential introgression with respect to sympatric host race formation and speciation in Rhagoletis, reconciling some of the seemingly dichotomous views of Mayr, Dobzhansky, and Bush concerning modes of divergence. PMID:15851672
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Omanović, Dario; Pižeta, Ivanka; Vukosav, Petra; Kovács, Elza; Frančišković-Bilinski, Stanislav; Tamás, János
2015-04-01
The distribution and speciation of elements along a stream subjected to neutralised acid mine drainage (NAMD) effluent waters (Mátra Mountain, Hungary; Toka stream) were studied by a multi-methodological approach: dissolved and particulate fractions of elements were determined by HR-ICPMS, whereas speciation was carried out by DGT, supported by speciation modelling performed by Visual MINTEQ. Before the NAMD discharge, the Toka is considered as a pristine stream, with averages of dissolved concentrations of elements lower than world averages. A considerable increase of element concentrations caused by effluent water inflow is followed by a sharp or gradual concentration decrease. A large difference between total and dissolved concentrations was found for Fe, Al, Pb, Cu, Zn and As in effluent water and at the first downstream site, with high correlation factors between elements in particulate fraction, indicating their common behaviour, governed by the formation of ferri(hydr)oxides (co)precipitates. In-situ speciation by the DGT technique revealed that Zn, Cd, Ni, Co, Mn and U were predominantly present as a labile, potentially bioavailable fraction (>90%). The formation of strong complexes with dissolved organic matter (DOM) resulted in a relatively low DGT-labile concentration of Cu (42%), while low DGT-labile concentrations of Fe (5%) and Pb (12%) were presumably caused by their existence in colloidal (particulate) fraction which is not accessible to DGT. Except for Fe and Pb, a very good agreement between DGT-labile concentrations and those predicted by the applied speciation model was obtained, with an average correlation factor of 0.96. This study showed that the in-situ DGT technique in combination with model-predicted speciation and classical analysis of samples could provide a reasonable set of data for the assessment of the water quality status (WQS), as well as for the more general study of overall behaviour of the elements in natural waters subjected to high element loads. Copyright © 2014 Elsevier B.V. All rights reserved.
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Speciation: more likely through a genetic or through a learned habitat preference?
Beltman, J.B; Metz, J.A.J
2005-01-01
A problem in understanding sympatric speciation is establishing how reproductive isolation can arise when there is disruptive selection on an ecological trait. One of the solutions that has been proposed is that a habitat preference evolves, and that mates are chosen within the preferred habitat. We present a model where the habitat preference can evolve either by means of a genetic mechanism or by means of learning. Employing an adaptive-dynamical analysis, we show that evolution proceeds either to a single population of specialists with a genetic preference for their optimal habitat, or to a population of generalists without a habitat preference. The generalist population subsequently experiences disruptive selection. Learning promotes speciation because it increases the intensity of disruptive selection. An individual-based version of the model shows that, when loci are completely unlinked and learning confers little cost, the presence of disruptive selection most probably leads to speciation via the simultaneous evolution of a learned habitat preference. For high costs of learning, speciation is most likely to occur via the evolution of a genetic habitat preference. However, the latter only happens when the effect of mutations is large, or when there is linkage between genes coding for the different traits. PMID:16011920
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Crean, Daniel E; Livens, Francis R; Stennett, Martin C; Grolimund, Daniel; Borca, Camelia N; Hyatt, Neil C
2014-01-01
Use of depleted uranium (DU) munitions has resulted in contamination of the near-surface environment with penetrator residues. Uncertainty in the long-term environmental fate of particles produced by impact of DU penetrators with hard targets is a specific concern. In this study DU particles produced in this way and exposed to the surface terrestrial environment for longer than 30 years at a U.K. firing range were characterized using synchrotron X-ray chemical imaging. Two sites were sampled: a surface soil and a disposal area for DU-contaminated wood, and the U speciation was different between the two areas. Surface soil particles showed little extent of alteration, with U speciated as oxides U3O7 and U3O8. Uranium oxidation state and crystalline phase mapping revealed these oxides occur as separate particles, reflecting heterogeneous formation conditions. Particles recovered from the disposal area were substantially weathered, and U(VI) phosphate phases such as meta-ankoleite (K(UO2)(PO4) · 3H2O) were dominant. Chemical imaging revealed domains of contrasting U oxidation state linked to the presence of both U3O7 and meta-ankoleite, indicating growth of a particle alteration layer. This study demonstrates that substantial alteration of DU residues can occur, which directly influences the health and environmental hazards posed by this contamination.
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Cheng, Irene; Zhang, Leiming
2017-01-17
Gaseous oxidized mercury (GOM) measurement uncertainties undoubtedly impact the understanding of mercury biogeochemical cycling; however, there is a lack of consensus on the uncertainty magnitude. The numerical method presented in this study provides an alternative means of estimating the uncertainties of previous GOM measurements. Weekly GOM in ambient air was predicted from measured weekly mercury wet deposition using a scavenging ratio approach, and compared against field measurements of 2-4 hly GOM to estimate the measurement biases of the Tekran speciation instruments at 13 Atmospheric Mercury Network (AMNet) sites. Multiyear average GOM measurements were estimated to be biased low by more than a factor of 2 at six sites, between a factor of 1.5 and 1.8 at six other sites, and below a factor of 1.3 at one site. The differences between predicted and observed were significantly larger during summer than other seasons potentially because of higher ozone concentrations that may interfere with GOM sampling. The analysis data collected over six years at multiple sites suggests a systematic bias in GOM measurements, supporting the need for further investigation of measurement technologies and identifying the chemical composition of GOM.
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Ricklefs, Robert E; Bermingham, Eldredge
2004-08-01
Understanding patterns of diversity can be furthered by analysis of the dynamics of colonization, speciation, and extinction on islands using historical information provided by molecular phylogeography. The land birds of the Lesser Antilles are one of the most thoroughly described regional faunas in this context. In an analysis of colonization times, Ricklefs and Bermingham (2001) found that the cumulative distribution of lineages with respect to increasing time since colonization exhibits a striking change in slope at a genetic distance of about 2% mitochondrial DNA sequence divergence (about one million years). They further showed how this heterogeneity could be explained by either an abrupt increase in colonization rates or a mass extinction event. Cherry et al. (2002), referring to a model developed by Johnson et al. (2000), argued instead that the pattern resulted from a speciation threshold for reproductive isolation of island populations from their continental source populations. Prior to this threshold, genetic divergence is slowed by migration from the source, and species of varying age accumulate at a low genetic distance. After the threshold is reached, source and island populations diverge more rapidly, creating heterogeneity in the distribution of apparent ages of island taxa. We simulated of Johnson et al.'s speciation-threshold model, incorporating genetic divergence at rate k and fixation at rate M of genes that have migrated between the source and the island population. Fixation resets the divergence clock to zero. The speciation-threshold model fits the distribution of divergence times of Lesser Antillean birds well with biologically plausible parameter estimates. Application of the model to the Hawaiian avifauna, which does not exhibit marked heterogeneity of genetic divergence, and the West Indian herpetofauna, which does, required unreasonably high migration-fixation rates, several orders of magnitude greater than the colonization rate. However, the plausibility of the speciation-divergence model for Lesser Antillean birds emphasizes the importance of further investigation of historical biogeography on a regional scale for whole biotas, as well as the migration of genes between populations on long time scales and the achievement of reproductive isolation.
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Nozière, Barbara; Hanson, David R
2017-11-09
Organic peroxy radicals ("RO 2 ", with R organic) are key intermediates in most oxygen-rich systems, where organic compounds are oxidized (natural environment, flames, combustion engines, living organisms, etc). But, until recently, techniques able to monitor simultaneously and distinguish between RO 2 species ("speciated" detection) have been scarce, which has limited the understanding of complex systems containing these radicals. Mass spectrometry using proton transfer ionization has been shown previously to detect individual gas-phase RO 2 separately. In this work, we illustrate its ability to speciate and monitor several RO 2 simultaneously by investigating reactions involving CH 3 O 2 , CH 3 C(O)O 2 , c-C 6 H 11 O 2 , and (CH 3 ) 3 CO 2 . The detection sensitivity of each of these radicals was estimated by titration with NO to between 50 and 1000 Hz/ppb, with a factor from 3 to 5 of uncertainties, mostly due to the uncertainties in knowing the amounts of added NO. With this, the RO 2 concentration in the reactor was estimated between 1 × 10 10 and 1 × 10 12 molecules cm -3 . When adding a second radical species to the reactor, the kinetics of the cross-reaction could be studied directly from the decay of the first radical. The time-evolution of two and sometimes three different RO 2 was followed simultaneously, as the CH 3 O 2 produced in further reaction steps was also detected in some systems. The rate coefficients obtained are (in molecule -1 cm 3 s -1 ): k CH3O2+CH3C(O)O2 = 1.2 × 10 -11 , k CH3O2+t-butylO2 = 3.0 × 10 -15 , k c-hexylO2+CH3O2 = 1.2 × 10 -13 , k t-butylO2+CH3C(O)O2 = 3.7 × 10 -14 , and k c-hexylO2+t-butylO2 = 1.5 × 10 -15 . In spite of their good comparison with the literature and good reproducibility, large uncertainties (×5/5) are recommended on these results because of those in the detection sensitivities. This work is a first illustration of the potential applications of this technique for the investigation of organic radicals in laboratory and in more complex systems.
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Roccaro, Paolo; Chang, Hyun-shik; Vagliasindi, Federico G A; Korshin, Gregory V
2013-10-15
This study examined effects of bromide on yields and speciation of dihaloacetonitrile (DHAN) species that included dichloro-, bromochloro- and dibromoacetonitriles generated in chlorinated water. Experimental data obtained using two water sources, varying concentrations and characters of Natural Organic Matter (NOM), bromide concentrations, reaction times, chlorine doses, temperatures and pHs were interpreted using a semi-phenomenological model that assumed the presence of three kinetically distinct sites in NOM (denoted as sites S1, S2 and S3) and the occurrence of sequential incorporation of bromine and chlorine into them. One site was found to react very fast with the chlorine and bromine but its contribution in the DHAN generation was very low. The site with the highest contribution to the yield of DHAN (>70%) has the lowest reaction rates. The model introduced dimensionless coefficients (denoted as φ1(DHAN), φ2(DHAN) and φ3(DHAN)) applicable to the initial DHAN generation sites and their monochlorinated and monobrominated products, respectively. These parameters were used to quantify the kinetic preference to bromine incorporation over that of chlorine. Values of these coefficients optimized for DHAN formation were indicative of the strongly preferential incorporation of bromine into the engaged NOM sites. The same set of φ(i)(DHAN) coefficients could be used to model the speciation of DHAN released from their kinetically different precursors. The dimensionless speciation coefficients φ(i)(DHAN) were determined to be site specific and dependent on the NOM content and character as well as pH. The presented model of DHAN formation and speciation can help quantify in more detail the generation of DHAN and provide more insight necessary for further assessment of their potential health effects. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Fulvic acid-sulfide ion competition for mercury ion binding in the Florida everglades
Reddy, M.M.; Aiken, G.R.
2001-01-01
Negatively charged functional groups of fulvic acid compete with inorganic sulfide ion for mercury ion binding. This competition is evaluated here by using a discrete site-electrostatic model to calculate mercury solution speciation in the presence of fulvic acid. Model calculated species distributions are used to estimate a mercury-fulvic acid apparent binding constant to quantify fulvic acid and sulfide ion competition for dissolved inorganic mercury (Hg(II)) ion binding. Speciation calculations done with PHREEQC, modified to use the estimated mercury-fulvic acid apparent binding constant, suggest that mercury-fulvic acid and mercury-sulfide complex concentrations are equivalent for very low sulfide ion concentrations (about 10-11 M) in Everglades' surface water. Where measurable total sulfide concentration (about 10-7 M or greater) is present in Everglades' surface water, mercury-sulfide complexes should dominate dissolved inorganic mercury solution speciation. In the absence of sulfide ion (for example, in oxygenated Everglades' surface water), fulvic acid binding should dominate Everglades' dissolved inorganic mercury speciation.
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Edwards, Taylor; Tollis, Marc; Hsieh, PingHsun; Gutenkunst, Ryan N.; Liu, Zhen; Kusumi, Kenro; Culver, Melanie; Murphy, Robert W.
2016-01-01
Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA-seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best-fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Robinson, Troy A
2011-08-01
This dissertation explores lanthanide speciation in liquid solution systems related to separation schemes involving the acidic ligands: bis(2-ethylhexyl) phosphoric acid (HDEHP), lactate, and 8-hydroxyquinoline. Equilibrium speciation of neodymium (Nd 3+), sodium (Na+), HDEHP, water, and lactate in the TALSPEAK liquid-liquid extraction system was explored under varied Nd 3+ loading of HDEHP in the organic phase and through extraction from aqueous HCl and lactate media. System speciation was probed through vapor pressure osmometry, visible and Fourier Transform Infrared (FTIR) spectroscopy, 22Na and 13C labeled lactate radiotracer distribution measurements, Karl Fischer titrations, and equilibrium pH measurements. Distribution of Nd 3+, Na +,more » lactate, and equilibrium pH were modeled using the SXLSQI software to obtain logKNd and logKNa extraction constants under selected conditions. Results showed that high Nd 3+ loading of the HDEHP led to Nd 3+ speciation that departs from the ion exchange mechanism and includes formation of highly aggregated, polynuclear [NdLactate(DEHP) 2] x; (with x > 1). By substituting lanthanum (La 3+) for Nd 3+ in this system, NMR scoping experiments using 23Na, 31P nuclei and 13C labeled lactate were performed. Results indicated that this technique is sensitive to changes in system speciation, and that further experiments are warranted. In a homogeneous system representing the TALSPEAK aqueous phase, Lactate protonation behavior at various temperatures was characterized using a combination of potentiometric titration and modeling with the Hyperquad computer program. The temperature dependent deprotonation behavior of lactate showed little change with temperature at 2.0 M NaCl ionic strength. Cloud point extraction is a non-traditional separation technique that starts with a homogeneous phase that becomes heterogeneous by the micellization of surfactants through the increase of temperature. To better understand the behavior of europium (Eu 3+) and 8-hydroxyquinoline under cloud point extraction conditions, potentiometric and spectrophotometric titrations coupled with modeling with Hyperquad and SQUAD computer programs were performed to assess europium (Eu 3+) and 8-hydroxyquinoline speciation. Experiments in both water and a 1wt% Triton X-114/water mixed solvent were compared to understand the effect of Triton X-114 on the system speciation. Results indicated that increased solvation of 8-hydroxyquinoline by the mixed solvent lead to more stable complexes involving 8-hydroxyquinoline than in water, whereas competition between hydroxide and Triton X-114 for Eu 3+ led to lower stability hydrolysis complexes in the mixed solvent than in water. Lanthanide speciation is challenging due to the trivalent oxidation state that leads to multiple ligand complexes, including some mixed complexes. The complexity of the system demands well-designed and precise experiments that capture the nuances of the chemistry. This work increased the understanding of lanthanide speciation in the explored systems, but more work is required to produce a comprehensive understanding of the speciation involved.« less
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Sympatric speciation by sexual selection alone is unlikely.
Arnegard, Matthew E; Kondrashov, Alexey S
2004-02-01
According to Darwin, sympatric speciation is driven by disruptive, frequency-dependent natural selection caused by competition for diverse resources. Recently, several authors have argued that disruptive sexual selection can also cause sympatric speciation. Here, we use hypergeometric phenotypic and individual-based genotypic models to explore sympatric speciation by sexual selection under a broad range of conditions. If variabilities of preference and display traits are each caused by more than one or two polymorphic loci, sympatric speciation requires rather strong sexual selection when females exert preferences for extreme male phenotypes. Under this kind of mate choice, speciation can occur only if initial distributions of preference and display are close to symmetric. Otherwise, the population rapidly loses variability. Thus, unless allele replacements at very few loci are enough for reproductive isolation, female preferences for extreme male displays are unlikely to drive sympatric speciation. By contrast, similarity-based female preferences that do not cause sexual selection are less destabilizing to the maintenance of genetic variability and may result in sympatric speciation across a broader range of initial conditions. Certain groups of African cichlids have served as the exclusive motivation for the hypothesis of sympatric speciation by sexual selection. Mate choice in these fishes appears to be driven by female preferences for extreme male phenotypes rather than similarity-based preferences, and the evolution of premating reproductive isolation commonly involves at least several genes. Therefore, differences in female preferences and male display in cichlids and other species of sympatric origin are more likely to have evolved as isolating mechanisms under disruptive natural selection.
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The Origins of Tropical Rainforest Hyperdiversity.
Pennington, R Toby; Hughes, Mark; Moonlight, Peter W
2015-11-01
Traditional models for tropical species richness contrast rainforests as "museums" of old species or "cradles" of recent speciation. High plant species diversity in rainforests may be more likely to reflect high episodic evolutionary turnover of species--a scenario implicating high rates of both speciation and extinction through geological time.
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Rossetto, Maurizio; Allen, Chris B; Thurlby, Katie A G; Weston, Peter H; Milner, Melita L
2012-08-20
Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters corresponding to the four recognised species with the additional division of T. speciosissima into populations north and south of the Shoalhaven River valley. Unexpectedly, the northern disjunct population of T. oreades grouped with T. mongaensis and was identified as a hybrid swarm by the Bayesian assignment test implemented in NewHybrids. Present day and LGM environmental niche models differed dramatically, suggesting that distributions of all species had repeatedly expanded and contracted in response to Pleistocene climatic oscillations and confirming strongly marked historical distributional gaps among taxes. Genetic structure and bio-climatic modeling results are more consistent with a history of allopatric speciation followed by repeated episodes of secondary contact and localised hybridisation, rather than with parapatric speciation. This study on Telopea shows that the evidence for temporal exclusion of gene flow can be found even outside obvious geographical contexts, and that it is possible to make significant progress towards excluding parapatric speciation as a contributing evolutionary process.
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XAS Studies of Se Speciation in Selenite-Fed Rats
Weekley, Claire M.; Aitken, Jade B.; Witting, Paul K.; Harris, Hugh H.
2014-01-01
The biological activity of selenium is dependent on its chemical form. Therefore, knowledge of Se chemistry in vivo is required for efficacious use of selenium compounds in disease prevention and treatment. Using X-ray absorption spectroscopy, Se speciation in the kidney, liver, heart, spleen, testis and red blood cells of rats fed control (~0.3 ppm Se) or selenite-supplemented (1 ppm or 5 ppm Se) diets for 3 or 6 weeks, was investigated. X-ray absorption spectroscopy revealed the presence of Se–Se and Se–C species in the kidney and liver, and Se–S species in the kidney, but not the liver. X-ray absorption near edge structure (XANES) spectra showed that there was variation in speciation in the liver and kidneys, but Se speciation was much more uniform in the remaining organs. Using principal component analysis (PCA) to interpret the Se K-edge X-ray absorption spectra, we were able to directly compare the speciation of Se in two different models of selenite metabolism – human lung cancer cells and rat tissues. The effects of Se dose, tissue type and duration of diet on selenium speciation in rat tissues were investigated, and a relationship between the duration of the diet (3 weeks versus 6 weeks) and selenium speciation was observed. PMID:25363824
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A speciation solver for cement paste modeling and the semismooth Newton method
DOE Office of Scientific and Technical Information (OSTI.GOV)
Georget, Fabien, E-mail: fabieng@princeton.edu; Prévost, Jean H., E-mail: prevost@princeton.edu; Vanderbei, Robert J., E-mail: rvdb@princeton.edu
2015-02-15
The mineral assemblage of a cement paste may vary considerably with its environment. In addition, the water content of a cement paste is relatively low and the ionic strength of the interstitial solution is often high. These conditions are extreme conditions with respect to the common assumptions made in speciation problem. Furthermore the common trial and error algorithm to find the phase assemblage does not provide any guarantee of convergence. We propose a speciation solver based on a semismooth Newton method adapted to the thermodynamic modeling of cement paste. The strong theoretical properties associated with these methods offer practical advantages.more » Results of numerical experiments indicate that the algorithm is reliable, robust, and efficient.« less
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Deakin, Janine E; Kruger-Andrzejewska, Maya
2016-09-01
Chromosome rearrangements have been implicated in diseases, such as cancer, and speciation, but it remains unclear whether rearrangements are causal or merely a consequence of these processes. Two marsupial families with very different rates of karyotype evolution provide excellent models in which to study the role of chromosome rearrangements in a disease and evolutionary context. The speciose family Dasyuridae displays remarkable karyotypic conservation, with all species examined to date possessing nearly identical karyotypes. Despite the seemingly high degree of chromosome stability within this family, they appear prone to developing tumours, including transmissible devil facial tumours. In contrast, chromosome rearrangements have been frequent in the evolution of the species-rich family Macropodidae, which displays a high level of karyotypic diversity. In particular, the genus Petrogale (rock-wallabies) displays an extraordinary level of chromosome rearrangement among species. For six parapatric Petrogale species, it appears that speciation has essentially been caught in the act, providing an opportunity to determine whether chromosomal rearrangements are a cause or consequence of speciation in this system. This review highlights the reasons that these two marsupial families are excellent models for testing hypotheses for hotspots of chromosome rearrangement and deciphering the role of chromosome rearrangements in disease and speciation.
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NASA Technical Reports Server (NTRS)
Haines, Jennifer C.; Chen, Lung-Wen A.; Taubman, Brett F.; Doddridge, Bruce G.; Dickerson, Russell R.
2007-01-01
Reliable determination of the effects of air quality on public health and the environment requires accurate measurement of PM(sub 2.5) mass and the individual chemical components of fine aerosols. This study seeks to evaluate PM(sub 2.5) measurements that are part of a newly established national network by comparing them with a more conventional sampling system. Experiments were carried out during 2002 at a suburban site in Maryland, United States, where two samplers from the U.S. Environmental Protection Agency (USEPA) Speciation Trends Network: Met One Speciation Air Sampling System STNS and Thermo Scientific Reference Ambient Air Sampler STNR, two Desert Research Institute Sequential Filter Samplers DRIF, and a continuous TEOM monitor (Thermo Scientific Tapered Element Oscillating Microbalance) were sampling air in parallel. These monitors differ not only in sampling configuration but also in protocol-specific sample analysis procedures. Measurements of PM(sub 2.5) mass and major contributing species were well correlated among the different methods with r-values > 0.8. Despite the good correlations, daily concentrations of PM(sub 2.5) mass and major contributing species were significantly different at the 95% confidence level from 5 to 100% of the time. Larger values of PM(sub 2.5) mass and individual species were generally reported from STNR and STNS. The January STNR average PM(sub 2.5) mass (8.8 (micro)g/per cubic meter) was 1.5 (micro)g/per cubic meter larger than the DRIF average mass. The July STNS average PM(sub 2.5) mass (27.8 (micro)g/per cubic meter) was 3.8 (micro)g/per cubic meter larger than the DRIF average mass. These differences can only be partially accounted for by known random errors. Variations in flow control, face velocity, and sampling artifacts likely influence the measurement of PM(sub 2.5) speciation and mass closure. Simple statistical tests indicate that the current uncertainty estimates used in the STN network may underestimate the actual uncertainty.
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Gottscho, Andrew D; Marks, Sharyn B; Jennings, W Bryan
2014-01-01
The North American deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using isolation-with-migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The likelihood ratio test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia and define this species as a single evolutionarily significant unit for conservation purposes. PMID:25360285
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Role of demographic stochasticity in a speciation model with sexual reproduction
NASA Astrophysics Data System (ADS)
Lafuerza, Luis F.; McKane, Alan J.
2016-03-01
Recent theoretical studies have shown that demographic stochasticity can greatly increase the tendency of asexually reproducing phenotypically diverse organisms to spontaneously evolve into localized clusters, suggesting a simple mechanism for sympatric speciation. Here we study the role of demographic stochasticity in a model of competing organisms subject to assortative mating. We find that in models with sexual reproduction, noise can also lead to the formation of phenotypic clusters in parameter ranges where deterministic models would lead to a homogeneous distribution. In some cases, noise can have a sizable effect, rendering the deterministic modeling insufficient to understand the phenotypic distribution.
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Tromson, Clara; Bulle, Cécile; Deschênes, Louise
2017-03-01
In life cycle assessment (LCA), the potential terrestrial ecotoxicity effect of metals, calculated as the effect factor (EF), is usually extrapolated from aquatic ecotoxicological data using the equilibrium partitioning method (EqP) as it is more readily available than terrestrial data. However, when following the AMI recommendations (i.e. with at least enough species that represents three different phyla), there are not enough terrestrial data for which soil properties or metal speciation during ecotoxicological testing are specified to account for the influence of soil property variations on metal speciation when using this approach. Alternatively, the TBLM (Terrestrial Biotic Ligand Model) has been used to determine an EF that accounts for speciation, but is not available for metals; hence it cannot be consistently applied to metals in an LCA context. This paper proposes an approach to include metal speciation by regionalizing the EqP method for Cu, Ni and Zn with a geochemical speciation model (the Windermere Humic Aqueous Model 7.0), for 5213 soils selected from the Harmonized World Soil Database. Results obtained by this approach (EF EqP regionalized ) are compared to the EFs calculated with the conventional EqP method, to the EFs based on available terrestrial data and to the EFs calculated with the TBLM (EF TBLM regionalized ) when available. The spatial variability contribution of the EF to the overall spatial variability of the characterization factor (CF) has been analyzed. It was found that the EFs EqP regionalized show a significant spatial variability. The EFs calculated with the two non-regionalized methods (EqP and terrestrial data) fall within the range of the EFs EqP regionalized . The EFs TBLM regionalized cover a larger range of values than the EFs EqP regionalized but the two methods are not correlated. This paper highlights the importance of including speciation into the terrestrial EF and shows that using the regionalized EqP approach is not an acceptable proxy for terrestrial ecotoxicological data even if it can be applied to all metals. Copyright © 2016. Published by Elsevier B.V.
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Speciation of heavy metals in landfill leachate: a review.
Baun, Dorthe L; Christensen, Thomas H
2004-02-01
The literature was reviewed with respect to metal speciation methods in aquatic samples specifically emphasizing speciation of heavy metals in landfill leachate. Speciation here refers to physical fractionation (particulate, colloidal, dissolved), chemical fractionation (organic complexes, inorganic complexes, free metal ions), as well as computer-based thermodynamic models. Relatively few landfill leachate samples have been speciated in detail (less than 30) representing only a few landfills (less than 15). This suggests that our knowledge about metal species in landfill leachate still is indicative. In spite of the limited database and the different definitions of the dissolved fraction (< 0.45 microm or < 0.001 microm) the studies consistently show that colloids as well as organic and inorganic complexes are important for all heavy metals in landfill leachate. The free metal ion constitutes less than 30%, typically less than 10%, of the total metal concentration. This has significant implications for sampling, since no standardized procedures exist, and for assessing the content of metals in leachate in the context of its treatment, toxicity and migration in aquifers.
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Parapatric speciation in three islands: dynamics of geographical configuration of allele sharing
Iwasa, Yoh
2017-01-01
We studied the time to speciation by geographical isolation for a species living on three islands connected by rare migration. We assumed that incompatibility was controlled by a number of quantitative loci and that individuals differing in loci by more than a threshold did not mix genetically with each other. For each locus, we defined the geographical configuration (GC), which specifies islands with common alleles, and traced the stochastic transitions between different GCs. From these results, we calculated the changes in genetic distances. As a single migration event provides an opportunity for transitions in multiple loci, the GCs of different loci are correlated, which can be evaluated by constructing the stochastic differential equations of the number of loci with different GCs. Our model showed that the low number of incompatibility loci facilitates parapatric speciation and that migrants arriving as a group shorten the waiting time to speciation compared with the same number of migrants arriving individually. We also discuss how speciation rate changes with geographical structure. PMID:28386439
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Development of a database for chemical mechanism assignments for volatile organic emissions.
Carter, William P L
2015-10-01
The development of a database for making model species assignments when preparing total organic gas (TOG) emissions input for atmospheric models is described. This database currently has assignments of model species for 12 different gas-phase chemical mechanisms for over 1700 chemical compounds and covers over 3000 chemical categories used in five different anthropogenic TOG profile databases or output by two different biogenic emissions models. This involved developing a unified chemical classification system, assigning compounds to mixtures, assigning model species for the mechanisms to the compounds, and making assignments for unknown, unassigned, and nonvolatile mass. The comprehensiveness of the assignments, the contributions of various types of speciation categories to current profile and total emissions data, inconsistencies with existing undocumented model species assignments, and remaining speciation issues and areas of needed work are also discussed. The use of the system to prepare input for SMOKE, the Speciation Tool, and for biogenic models is described in the supplementary materials. The database, associated programs and files, and a users manual are available online at http://www.cert.ucr.edu/~carter/emitdb . Assigning air quality model species to the hundreds of emitted chemicals is a necessary link between emissions data and modeling effects of emissions on air quality. This is not easy and makes it difficult to implement new and more chemically detailed mechanisms in models. If done incorrectly, it is similar to errors in emissions speciation or the chemical mechanism used. Nevertheless, making such assignments is often an afterthought in chemical mechanism development and emissions processing, and existing assignments are usually undocumented and have errors and inconsistencies. This work is designed to address some of these problems.
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Speciation and Neutral Molecular Evolution in One-Dimensional Closed Population
NASA Astrophysics Data System (ADS)
Semovski, Sergei V.; Bukin, Yuri S.; Sherbakov, Dmitry Yu.
Models are presented suitable for a description of speciation processes arising due to reproductive isolation depending on genetic distance. The main attention is paid to the model of a one-dimensional closed population, which describes the evolution of littoral benthic organisms. In order to correspond the modeling results to the results obtained in the course of experimental phylogenetic studies, all individual-based models described here involve neutrally evolving and maternally inherited DNA sequence. Sub-samples of the resulting sequences were used for a posteriori phylogenetic inferences which then were compared to the "true" evolutionary histories.
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Kao, Katy C.; Schwartz, Katja; Sherlock, Gavin
2010-01-01
The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts, which have small genomes and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair, comprising a mitochondrially targeted product of a nuclear gene and a mitochondrially encoded locus, has been found. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. We report here the first detailed genome-wide analysis of rare meiotic products from an otherwise sterile hybrid and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions, likely involving multiple loci having weak effects, may be responsible for their post-zygotic separation. The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that the accumulation of polymorphisms leads to gamete inviability due to the activities of anti-recombination mechanisms and/or incompatibilities between the species' transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation. PMID:20686707
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Uranium(IV) adsorption by natural organic matter in anoxic sediments
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bone, Sharon E.; Dynes, James J.; Cliff, John
Uranium is an important carbon-free fuel source and environmental contaminant that accumulates in the tetravalent state, U(IV), in anoxic sediments, such as ore deposits, marine basins, and contaminated aquifers. However, little is known about the speciation of U(IV) in low-temperature geochemical environments, inhibiting the development of a conceptual model of U behavior. Until recently, U(IV) was assumed to exist predominantly as the sparingly soluble mineral uraninite (UO 2+x) in anoxic sediments; however, studies now show that this is not often the case. Yet a model of U(IV) speciation in the absence of mineral formation under field-relevant conditions has not yetmore » been developed. Uranium(IV) speciation controls its reactivity, particularly its susceptibility to oxidative mobilization, impacting its distribution and toxicity. Here we show adsorption to organic carbon and organic carbon-coated clays dominate U(IV) speciation in an organic-rich natural substrate under field-relevant conditions. Whereas previous research assumed that U(IV) speciation is dictated by the mode of reduction (i.e., whether reduction is mediated by microbes or by inorganic reductants), our results demonstrate that mineral formation can be diminished in favor of adsorption, regardless of reduction pathway. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider U(IV) adsorption to organic matter within the sediment environment.« less
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Uranium(IV) adsorption by natural organic matter in anoxic sediments
Bone, Sharon E.; Dynes, James J.; Cliff, John; ...
2017-01-09
Uranium is an important carbon-free fuel source and environmental contaminant that accumulates in the tetravalent state, U(IV), in anoxic sediments, such as ore deposits, marine basins, and contaminated aquifers. However, little is known about the speciation of U(IV) in low-temperature geochemical environments, inhibiting the development of a conceptual model of U behavior. Until recently, U(IV) was assumed to exist predominantly as the sparingly soluble mineral uraninite (UO 2+x) in anoxic sediments; however, studies now show that this is not often the case. Yet a model of U(IV) speciation in the absence of mineral formation under field-relevant conditions has not yetmore » been developed. Uranium(IV) speciation controls its reactivity, particularly its susceptibility to oxidative mobilization, impacting its distribution and toxicity. Here we show adsorption to organic carbon and organic carbon-coated clays dominate U(IV) speciation in an organic-rich natural substrate under field-relevant conditions. Whereas previous research assumed that U(IV) speciation is dictated by the mode of reduction (i.e., whether reduction is mediated by microbes or by inorganic reductants), our results demonstrate that mineral formation can be diminished in favor of adsorption, regardless of reduction pathway. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider U(IV) adsorption to organic matter within the sediment environment.« less
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Pirie, M D; Oliver, E G H; Mugrabi de Kuppler, A; Gehrke, B; Le Maitre, N C; Kandziora, M; Bellstedt, D U
2016-09-17
The disproportionate species richness of the world's biodiversity hotspots could be explained by low extinction (the evolutionary "museum") and/or high speciation (the "hot-bed") models. We test these models using the largest of the species rich plant groups that characterise the botanically diverse Cape Floristic Region (CFR): the genus Erica L. We generate a novel phylogenetic hypothesis informed by nuclear and plastid DNA sequences of c. 60 % of the c. 800 Erica species (of which 690 are endemic to the CFR), and use this to estimate clade ages (using RELTIME; BEAST), net diversification rates (GEIGER), and shifts in rates of diversification in different areas (BAMM; MuSSE). The diversity of Erica species in the CFR is the result of a single radiation within the last c. 15 million years. Compared to ancestral lineages in the Palearctic, the rate of speciation accelerated across Africa and Madagascar, with a further burst of speciation within the CFR that also exceeds the net diversification rates of other Cape clades. Erica exemplifies the "hotbed" model of assemblage through recent speciation, implying that with the advent of the modern Cape a multitude of new niches opened and were successively occupied through local species diversification.
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Danley, Patrick D; Mullen, Sean P; Liu, Fenglong; Nene, Vishvanath; Quackenbush, John; Shaw, Kerry L
2007-01-01
Background As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but are extremely valuable models in other biological fields. Here we report the development of expressed sequence tags (EST's) in an orthopteroid insect, a model for the study of neurobiology, speciation, and evolution. Results We report the sequencing of 14,502 EST's from clones derived from a nerve cord cDNA library, and the subsequent construction of a Gene Index from these sequences, from the Hawaiian trigonidiine cricket Laupala kohalensis. The Gene Index contains 8607 unique sequences comprised of 2575 tentative consensus (TC) sequences and 6032 singletons. For each of the unique sequences, an attempt was made to assign a provisional annotation and to categorize its function using a Gene Ontology-based classification through a sequence-based comparison to known proteins. In addition, a set of unique 70 base pair oligomers that can be used for DNA microarrays was developed. All Gene Index information is posted at the DFCI Gene Indices web page Conclusion Orthopterans are models used to understand the neurophysiological basis of complex motor patterns such as flight and stridulation. The sequences presented in the cricket Gene Index will provide neurophysiologists with many genetic tools that have been largely absent in this field. The cricket Gene Index is one of only two gene indices to be developed in an evolutionary model system. Species within the genus Laupala have speciated recently, rapidly, and extensively. Therefore, the genes identified in the cricket Gene Index can be used to study the genomics of speciation. Furthermore, this gene index represents a significant EST resources for basal insects. As such, this resource is a valuable comparative tool for the understanding of invertebrate molecular evolution. The sequences presented here will provide much needed genomic resources for three distinct but overlapping fields of inquiry: neurobiology, speciation, and molecular evolution. PMID:17459168
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Biotic immigration events, speciation, and the accumulation of biodiversity in the fossil record
NASA Astrophysics Data System (ADS)
Stigall, Alycia L.; Bauer, Jennifer E.; Lam, Adriane R.; Wright, David F.
2017-01-01
Biotic Immigration Events (BIMEs) record the large-scale dispersal of taxa from one biogeographic area to another and have significantly impacted biodiversity throughout geologic time. BIMEs associated with biodiversity increases have been linked to ecologic and evolutionary processes including niche partitioning, species packing, and higher speciation rates. Yet substantial biodiversity decline has also been documented following BIMEs due to elevated extinction and/or reduced speciation rates. In this review, we develop a conceptual model for biodiversity accumulation that links BIMEs and geographic isolation with local (α) diversity, regional (β) diversity, and global (γ) diversity metrics. Within the model, BIME intervals are characterized by colonization of existing species within new geographic regions and a lack of successful speciation events. Thus, there is no change in γ-diversity, and α-diversity increases at the cost of β-diversity. An interval of regional isolation follows in which lineage splitting results in successful speciation events and diversity increases across all three metrics. Alternation of these two regimes can result in substantial biodiversity accumulation. We tested this conceptual model using a series of case studies from the paleontological record. We primarily focus on two intervals during the Middle through Late Ordovician Period (470-458 Ma): the globally pervasive BIMEs during the Great Ordovician Biodiversification Event (GOBE) and a regional BIME, the Richmondian Invasion. We further test the conceptual model by examining the Great Devonian Interchange, Neogene mollusk migrations and diversification, and the Great American Biotic Interchange. Paleontological data accord well with model predictions. Constraining the mechanisms of biodiversity accumulation provides context for conservation biology. Because α-, β-, and γ-diversity are semi-independent, different techniques should be considered for sustaining various diversity partitions. Maintaining natural migration routes and population sizes among isolated regions are vital to preserving both extant biodiversity and biogeographic pathways requisite for future diversity generation.
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Safran, Rebecca J; Scordato, Elizabeth S C; Symes, Laurel B; Rodríguez, Rafael L; Mendelson, Tamra C
2013-11-01
Speciation by divergent natural selection is well supported. However, the role of sexual selection in speciation is less well understood due to disagreement about whether sexual selection is a mechanism of evolution separate from natural selection, as well as confusion about various models and tests of sexual selection. Here, we outline how sexual selection and natural selection are different mechanisms of evolutionary change, and suggest that this distinction is critical when analyzing the role of sexual selection in speciation. Furthermore, we clarify models of sexual selection with respect to their interaction with ecology and natural selection. In doing so, we outline a research agenda for testing hypotheses about the relative significance of divergent sexual and natural selection in the evolution of reproductive isolation. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny
Obbard, Darren J.; Maclennan, John; Kim, Kang-Wook; Rambaut, Andrew; O’Grady, Patrick M.; Jiggins, Francis M.
2012-01-01
An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25–40 Ma) is closer to being compatible with independent fossil-derived dates (20–50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available. PMID:22683811
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Tracking niche variation over millennial timescales in sympatric killer whale lineages
Foote, Andrew D.; Newton, Jason; Ávila-Arcos, María C.; Kampmann, Marie-Louise; Samaniego, Jose A.; Post, Klaas; Rosing-Asvid, Aqqalu; Sinding, Mikkel-Holger S.; Gilbert, M. Thomas P.
2013-01-01
Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish. PMID:23945688
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Tracking niche variation over millennial timescales in sympatric killer whale lineages.
Foote, Andrew D; Newton, Jason; Ávila-Arcos, María C; Kampmann, Marie-Louise; Samaniego, Jose A; Post, Klaas; Rosing-Asvid, Aqqalu; Sinding, Mikkel-Holger S; Gilbert, M Thomas P
2013-10-07
Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish.
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Experiment to Characterize Aircraft Volatile Aerosol and Trace-Species Emissions (EXCAVATE)
NASA Technical Reports Server (NTRS)
Anderson, B. E.; Branham, H.-S.; Hudgins, C. H.; Plant, J. V.; Ballenthin, J. O.; Miller, T. M.; Viggiano, A. A.; Blake, D. R.; Boudries, H.; Canagaratna, M.
2005-01-01
The Experiment to Characterize Aircraft Volatile and Trace Species Emissions (EXCAVATE) was conducted at Langley Research Center (LaRC) in January 2002 and focused upon assaying the production of aerosols and aerosol precursors by a modern commercial aircraft, the Langley B757, during ground-based operation. Remaining uncertainty in the postcombustion fate of jet fuel sulfur contaminants, the need for data to test new theories of particle formation and growth within engine exhaust plumes, and the need for observations to develop air quality models for predicting pollution levels in airport terminal areas were the primary factors motivating the experiment. NASA's Atmospheric Effects of Aviation Project (AEAP) and the Ultra Effect Engine Technology (UEET) Program sponsored the experiment which had the specific objectives of determining ion densities; the fraction of fuel S converted from S(IV) to S(VI); the concentration and speciation of volatile aerosols and black carbon; and gas-phase concentrations of long-chain hydrocarbon and PAH species, all as functions of engine power, fuel composition, and plume age.
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The importance of ligand speciation in environmental research: a case study.
Sillanpää, M; Orama, M; Rämö, J; Oikari, A
2001-02-21
The speciations of EDTA and DTPA in process, waste and river waters are modelled and simulated, specifically to the mode of occurrence in the pulp and paper mill effluents and subsequently in receiving waters. Due to relatively short residence times in bleaching process and waste water treatment and slow exchange kinetics, it is expected that the thermodynamic equilibrium is not necessarily reached. Therefore, the initial speciation plays a key role. As such, the simulations have been extended to the process waters of the pulp and paper industry taking into account estimated average conditions. The results reveal that the main species are; Mn and Ca complexes of EDTA and DTPA in pulp mill process waters; Fe(III) and Mn complexes of EDTA and DTPA in waste waters; Fe(III) and Zn complexes of EDTA and DTPA in receiving waters. It is also shown how the increasing concentration of complexing agents effects the speciation. Alkaline earth metal chelation plays a significant role in the speciation of EDTA and DTPA when there is a noticeable molar excess of complexing agents compared with transition metals.
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Dang, Duc Huy; Evans, R Douglas
2018-03-01
High resolution electrospray ionization mass spectrometry (ESI-HRMS) was used to study the speciation of molybdate in interaction with halides (Cl, F, Br). Desolvation during electrospray ionization induced alteration of aqueous species but method optimization successfully suppressed artefact compounds. At low Mo concentrations, chloro(oxo)molybdate and fluoro(oxo)molybdate species were found and in natural samples, MoO 3 Cl was detected for the first time, to the best of our knowledge. Apparent equilibrium constants for Cl substitution on molybdate were calculated for a range of pH values from 4.5 to 8.5. A minor alteration in speciation during the gas phase (conversion of doubly charged MoO 4 2- to HMoO 4 - ) did not allow investigation of the molybdate acid-base properties; however this could be determined by speciation modeling. This study provides further evidence that ESI-HRMS is a fast and suitable tool to Deceasedassess the speciation of inorganic compounds such as Mo. Copyright © 2017 Elsevier B.V. All rights reserved.
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Mulder, Willem H; Crawford, Forrest W
2015-01-07
Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule process, in which new species are "born" from existing lineages at a constant rate. Recent work has illuminated some of the structural properties of Yule trees, but it remains mostly unknown how these properties affect sequence and trait patterns observed at the tips of the phylogenetic tree. Understanding the interplay between speciation and mutation under simple models of evolution is essential for deriving valid phylogenetic inference methods and gives insight into the optimal design of phylogenetic studies. In this work, we derive the probability distribution of interspecies covariance under Brownian motion and Ornstein-Uhlenbeck models of phenotypic change on a Yule tree. We compute the probability distribution of the number of mutations shared between two randomly chosen taxa in a Yule tree under discrete Markov mutation models. Our results suggest summary measures of phylogenetic information content, illuminate the correlation between site patterns in sequences or traits of related organisms, and provide heuristics for experimental design and reconstruction of phylogenetic trees. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Tait, Tara N; McGeer, James C; Smith, D Scott
2018-01-01
Speciation of copper in marine systems strongly influences the ability of copper to cause toxicity. Natural organic matter (NOM) contains many binding sites which provides a protective effect on copper toxicity. The purpose of this study was to characterize copper binding with NOM using fluorescence quenching techniques. Fluorescence quenching of NOM with copper was performed on nine sea water samples. The resulting stability constants and binding capacities were consistent with literature values of marine NOM, showing strong binding with [Formula: see text] values from 7.64 to 10.2 and binding capacities ranging from 15 to 3110 nmol mg [Formula: see text] Free copper concentrations estimated at total dissolved copper concentrations corresponding to previously published rotifer effect concentrations, in the same nine samples, were statistically the same as the range of free copper calculated for the effect concentration in NOM-free artificial seawater. These data confirms the applicability of fluorescence spectroscopy techniques for NOM and copper speciation characterization in sea water and demonstrates that such measured speciation is consistent with the chemical principles underlying the biotic ligand model approach for bioavailability-based metals risk assessment.
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Omnivory in birds is a macroevolutionary sink
Burin, Gustavo; Kissling, W. Daniel; Guimarães, Paulo R.; Şekercioğlu, Çağan H.; Quental, Tiago B.
2016-01-01
Diet is commonly assumed to affect the evolution of species, but few studies have directly tested its effect at macroevolutionary scales. Here we use Bayesian models of trait-dependent diversification and a comprehensive dietary database of all birds worldwide to assess speciation and extinction dynamics of avian dietary guilds (carnivores, frugivores, granivores, herbivores, insectivores, nectarivores, omnivores and piscivores). Our results suggest that omnivory is associated with higher extinction rates and lower speciation rates than other guilds, and that overall net diversification is negative. Trait-dependent models, dietary similarity and network analyses show that transitions into omnivory occur at higher rates than into any other guild. We suggest that omnivory acts as macroevolutionary sink, where its ephemeral nature is retrieved through transitions from other guilds rather than from omnivore speciation. We propose that these dynamics result from competition within and among dietary guilds, influenced by the deep-time availability and predictability of food resources. PMID:27052750
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lee, Ben H.; Mohr, Claudia; Lopez-Hilfiker, Felipe D.
Organic nitrates (ON = RONO2 + RO2NO2) are an important reservoir, if not sink, of atmospheric nitrogen oxides (NOx=NO+NO2). ON formed from isoprene oxidation alone are responsible for the export of 8 to 30% of anthropogenic NOx out of the U.S. continental boundary layer [Horowitz et al., 1998; Liang et al., 1998]. Regional NOx budgets and tropospheric ozone (O3) production, are therefore particularly sensitive to uncertainties in the yields and fates of ON [Beaver et al., 2012; Browne et al., 2013]. The yields implemented in modeling studies are determined from laboratory experiments in which only a few of the firstmore » generation gaseous ON or the total gas and particle-phase ON have been quantified [Perring et al., 2013 and references therein], while production of highly functionalized ON capable of strongly partitioning to the particle-phase have been inferred [Farmer et al., 2010; Ng et al., 2007; Nguyen et al., 2011; Perraud et al., 2012; Rollins et al., 2012], or directly measured [Ehn et al., 2014]. Addition of a nitrate (–ONO2) functional group to a hydrocarbon is estimated to lower the equilibrium saturation vapor pressure by 2.5 to 3 orders of magnitude [e.g. Capouet and Muller, 2006]. Thus, organic nitrate formation can potentially enhance particle-phase partitioning of hydrocarbons in regions with elevated levels of nitrogen oxides, contributing to secondary organic aerosol (SOA) formation [Ng et al., 2007]. There has, however, been no high time-resolved measurements of speciated ON in the particle-phase. We utilize a newly developed high-resolution time-of-flight chemical ionization mass spectrometer (HR-ToF-CIMS) using Iodide-adduct ionization [B H Lee et al., 2014a] with a filter inlet for gases and aerosols (FIGAERO) [Lopez-Hilfiker et al., 2014] that allows alternating in situ measurement of the molecular composition of gas and particle phases. We present observations of speciated ON in the particle-phase obtained during the 2013 Southern Oxidant and Aerosol Study (SOAS). We compare these speciated measurements to total unspeciated particulate organic nitrate measured by three independent methods, and analyze using a zero-dimensional box model the diel cycles of individual components to elucidate differential source and sink terms. Biogenic volatile organic compounds (VOCs), including isoprene, monoterpenes, and sesquiterpenes appear to dominate the ON sources during SOAS. We show that the molecular compositions that dominate the particle-phase are significantly more oxygenated than the most abundant gas-phase counterparts, consistent with volatility and solubility driven partitioning requirements. However, the detailed mechanisms by which most of these ON arise are not yet clear. These speciated measurements put a strong constraint on the extent to which ON directly contribute to SOA in regions with high biogenic hydrocarbon emissions, and illustrate that the fate of particulate ON can have significant implications for SOA and the reactive nitrogen budget.« less
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Lee, Ben H.; Mohr, Claudia; Lopez-Hilfiker, Felipe D.; ...
2016-01-25
Organic nitrates (ON = RONO2 + RO2NO2) are an important reservoir, if not sink, of atmospheric nitrogen oxides (NOx=NO+NO2). ON formed from isoprene oxidation alone are responsible for the export of 8 to 30% of anthropogenic NOx out of the U.S. continental boundary layer [Horowitz et al., 1998; Liang et al., 1998]. Regional NOx budgets and tropospheric ozone (O3) production, are therefore particularly sensitive to uncertainties in the yields and fates of ON [Beaver et al., 2012; Browne et al., 2013]. The yields implemented in modeling studies are determined from laboratory experiments in which only a few of the firstmore » generation gaseous ON or the total gas and particle-phase ON have been quantified [Perring et al., 2013 and references therein], while production of highly functionalized ON capable of strongly partitioning to the particle-phase have been inferred [Farmer et al., 2010; Ng et al., 2007; Nguyen et al., 2011; Perraud et al., 2012; Rollins et al., 2012], or directly measured [Ehn et al., 2014]. Addition of a nitrate (–ONO2) functional group to a hydrocarbon is estimated to lower the equilibrium saturation vapor pressure by 2.5 to 3 orders of magnitude [e.g. Capouet and Muller, 2006]. Thus, organic nitrate formation can potentially enhance particle-phase partitioning of hydrocarbons in regions with elevated levels of nitrogen oxides, contributing to secondary organic aerosol (SOA) formation [Ng et al., 2007]. There has, however, been no high time-resolved measurements of speciated ON in the particle-phase. We utilize a newly developed high-resolution time-of-flight chemical ionization mass spectrometer (HR-ToF-CIMS) using Iodide-adduct ionization [B H Lee et al., 2014a] with a filter inlet for gases and aerosols (FIGAERO) [Lopez-Hilfiker et al., 2014] that allows alternating in situ measurement of the molecular composition of gas and particle phases. We present observations of speciated ON in the particle-phase obtained during the 2013 Southern Oxidant and Aerosol Study (SOAS). We compare these speciated measurements to total unspeciated particulate organic nitrate measured by three independent methods, and analyze using a zero-dimensional box model the diel cycles of individual components to elucidate differential source and sink terms. Biogenic volatile organic compounds (VOCs), including isoprene, monoterpenes, and sesquiterpenes appear to dominate the ON sources during SOAS. We show that the molecular compositions that dominate the particle-phase are significantly more oxygenated than the most abundant gas-phase counterparts, consistent with volatility and solubility driven partitioning requirements. However, the detailed mechanisms by which most of these ON arise are not yet clear. These speciated measurements put a strong constraint on the extent to which ON directly contribute to SOA in regions with high biogenic hydrocarbon emissions, and illustrate that the fate of particulate ON can have significant implications for SOA and the reactive nitrogen budget.« less
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The fossilized birth–death process for coherent calibration of divergence-time estimates
Heath, Tracy A.; Huelsenbeck, John P.; Stadler, Tanja
2014-01-01
Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data—most commonly, fossil age estimates—are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the “fossilized birth–death” (FBD) process—a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene. PMID:25009181
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Model for macroevolutionary dynamics.
Maruvka, Yosef E; Shnerb, Nadav M; Kessler, David A; Ricklefs, Robert E
2013-07-02
The highly skewed distribution of species among genera, although challenging to macroevolutionists, provides an opportunity to understand the dynamics of diversification, including species formation, extinction, and morphological evolution. Early models were based on either the work by Yule [Yule GU (1925) Philos Trans R Soc Lond B Biol Sci 213:21-87], which neglects extinction, or a simple birth-death (speciation-extinction) process. Here, we extend the more recent development of a generic, neutral speciation-extinction (of species)-origination (of genera; SEO) model for macroevolutionary dynamics of taxon diversification. Simulations show that deviations from the homogeneity assumptions in the model can be detected in species-per-genus distributions. The SEO model fits observed species-per-genus distributions well for class-to-kingdom-sized taxonomic groups. The model's predictions for the appearance times (the time of the first existing species) of the taxonomic groups also approximately match estimates based on molecular inference and fossil records. Unlike estimates based on analyses of phylogenetic reconstruction, fitted extinction rates for large clades are close to speciation rates, consistent with high rates of species turnover and the relatively slow change in diversity observed in the fossil record. Finally, the SEO model generally supports the consistency of generic boundaries based on morphological differences between species and provides a comparator for rates of lineage splitting and morphological evolution.
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Bonnet-Lebrun, Anne-Sophie; Manica, Andrea; Eriksson, Anders; Rodrigues, Ana S L
2017-05-01
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities-that is with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities-from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in preequilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under preequilibrium conditions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.
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Hybrid Speciation in a Marine Mammal: The Clymene Dolphin (Stenella clymene)
Amaral, Ana R.; Lovewell, Gretchen; Coelho, Maria M.; Amato, George; Rosenbaum, Howard C.
2014-01-01
Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow. PMID:24421898
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Hybrid speciation in a marine mammal: the clymene dolphin (Stenella clymene).
Amaral, Ana R; Lovewell, Gretchen; Coelho, Maria M; Amato, George; Rosenbaum, Howard C
2014-01-01
Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow.
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X exceptionalism in Caenorhabditis speciation.
Cutter, Asher D
2017-11-13
Speciation genetics research in diverse organisms shows the X-chromosome to be exceptional in how it contributes to "rules" of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial interfertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X-chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large-X effect hypothesis. Studies to date implicate improper chromatin regulation of the X-chromosome by small RNA pathways as integral to hybrid male dysfunction. Sexual transitions in reproductive mode to self-fertilizing hermaphroditism inject distinctive molecular evolutionary features into the speciation process for some species. Caenorhabditis also provides unique opportunities for analysis in a system with XO sex determination that lacks a Y-chromosome, sex chromosome-dependent sperm competition differences and mechanisms of gametic isolation, exceptional accessibility to the development process and rapid experimental evolution. As genetic analysis of reproductive isolation matures with investigation of multiple pairs of Caenorhabditis species and new species discovery, nematodes will provide a powerful complement to more established study organisms for deciphering the genetic basis of and rules to speciation. © 2017 John Wiley & Sons Ltd.
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SPECIATE 4.3: Addendum to SPECIATE 4.2--Speciation database development documentation
SPECIATE is the U.S. Environmental Protection Agency's (EPA) repository of volatile organic gas and particulate matter (PM) speciation profiles of air pollution sources. Among the many uses of speciation data, these source profiles are used to: (1) create speciated emissions inve...
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SPECIATE 4.0: SPECIATION DATABASE DEVELOPMENT DOCUMENTATION--FINAL REPORT
SPECIATE is the U.S. EPA's repository of total organic compounds (TOC) and particulate matter (PM) speciation profiles of air pollution sources. This report documents how EPA developed the SPECIATE 4.0 database that replaces the prior version, SPECIATE 3.2. SPECIATE 4.0 includes ...
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Aerosol Measurements in the Mid-Atlantic: Trends and Uncertainty
NASA Astrophysics Data System (ADS)
Hains, J. C.; Chen, L. A.; Taubman, B. F.; Dickerson, R. R.
2006-05-01
Elevated levels of PM2.5 are associated with cardiovascular and respiratory problems and even increased mortality rates. In 2002 we ran two commonly used PM2.5 speciation samplers (an IMPROVE sampler and an EPA sampler) in parallel at Fort Meade, Maryland (a suburban site located in the Baltimore- Washington urban corridor). The filters were analyzed at different labs. This experiment allowed us to calculate the 'real world' uncertainties associated with these instruments. The EPA method retrieved a January average PM2.5 mass of 9.3 μg/m3 with a standard deviation of 2.8 μg/m3, while the IMPROVE method retrieved an average mass of 7.3 μg/m3 with a standard deviation of 2.1 μg/m3. The EPA method retrieved a July average PM2.5 mass of 26.4 μg/m3 with a standard deviation of 14.6 μg/m3, while the IMPROVE method retrieved an average mass of 23.3 μg/m3 with a standard deviation of 13.0 μg/m3. We calculated a 5% uncertainty associated with the EPA and IMPROVE methods that accounts for uncertainties in flow control strategies and laboratory analysis. The RMS difference between the two methods in January was 2.1 μg/m3, which is about 25% of the monthly average mass and greater than the uncertainty we calculated. In July the RMS difference between the two methods was 5.2 μg/m3, about 20% of the monthly average mass, and greater than the uncertainty we calculated. The EPA methods retrieve consistently higher concentrations of PM2.5 than the IMPROVE methods on a daily basis in January and July. This suggests a systematic bias possibly resulting from contamination of either of the sampling methods. We reconstructed the mass and found that both samplers have good correlation between reconstructed and gravimetric mass, though the IMPROVE method has slightly better correlation than the EPA method. In January, organic carbon is the largest contributor to PM2.5 mass, and in July both sulfate and organic matter contribute substantially to PM2.5. Source apportionment models suggest that regional and local power plants are the major sources of sulfate, while mobile and vegetative burning factors are the major sources of organic carbon.
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Sachet, Jean-Marie; Roques, Alain; Després, Laurence
2006-12-01
Phytophagous insects provide useful models for the study of ecological speciation. Much attention has been paid to host shifts, whereas situations where closely related lineages of insects use the same plant during different time periods have been relatively neglected in previous studies of insect diversification. Flies of the genus Strobilomyia are major pests of conifers in Eurasia and North America. They are specialized feeders in cones and seeds of Abies (fir), Larix (larch) ,and Picea (spruce). This close association is accompanied by a large number of sympatric Strobilomyia species coexisting within each tree genus. We constructed a molecular phylogeny with a 1320 base-pair fragment of mitochondrial DNA that demonstrated contrasting patterns of speciation in larch cone flies, as opposed to spruce and fir cone flies; this despite their comparable geographic distributions and similar resource quality of the host. Species diversity is the highest on larch, and speciation is primarily driven by within-host phenological shifts, followed by allopatric speciation during geographical expansion. By contrast, fewer species exploit spruce and fir, and within-host phenological shifts did not occur. This study illustrates within-host adaptive radiation through phenological shifts, a neglected mode of sympatric speciation.
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Speciation and Oxidative Stability of Alkaline Soluble, Non-Pertechnetate Technetium
DOE Office of Scientific and Technical Information (OSTI.GOV)
Levitskaia, Tatiana G.; Rapko, Brian M.; Anderson, Amity
2014-09-30
The long half-life, complex chemical behavior in tank waste, limited incorporation in mid- to high-temperature immobilization processes, and high mobility in subsurface environments make technetium (Tc) one of the most difficult contaminants to dispose of and/or remediate. Technetium exists predominantly in the liquid tank waste phase as the relatively mobile form of pertechnetate, TcO 4 -. However, based on experimentation to date a significant fraction of the soluble Tc cannot be effectively separated from the wastes and may be present as a non- pertechnetate species. The presence of a non-pertechnetate species significantly complicates disposition of low-activity waste (LAW), and themore » development of methods to either convert them to pertechnetate or to separate directly is needed. The challenge is the uncertainty regarding the chemical form of the alkaline-soluble low-valent non-pertechnetate species in the liquid tank waste. This report summarizes work done in fiscal year (FY) 2014 exploring the chemistry of a low-valence technetium(I) species, [(CO) 3Tc(H 2O) 3] +, a compound of interest due to its implication in the speciation of alkaline-soluble technetium in several Hanford tank waste supernatants.« less
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Iron Speciation and Mixing in Single Aerosol Particles from the Asian Continental Outflow
DOE Office of Scientific and Technical Information (OSTI.GOV)
Moffet, Ryan C.; Furutani, Hiroshi; Rodel, Tobias
2012-04-04
Bioavailable iron from atmospheric aerosol is an essential nutrient that can control oceanic productivity, thereby impacting the global carbon budget and climate. Particles collected on Okinawa Island during an atmospheric pollution transport event from China were analyzed using complementary single particle techniques to determine the iron source and speciation. Comparing the spatial distribution of iron within ambient particles and standard Asian mineral dust, it was determined that field-collected atmospheric Fe-containing particles have numerous sources, including anthropogenic sources such as coal combustion. Fe-containing particles were found to be internally mixed with secondary species such as sulfate, soot, and organic carbon. Themore » mass weighted average Fe(II) fraction (defined as Fe(II)/[Fe(II)+Fe(III)]) was determined to be 0.33 {+-} 0.08. Within the experimental uncertainty, this value lies close to the range of 0.26-0.30 determined for representative Asian mineral dust. Previous studies have indicated that the solubility of iron from combustion is much higher than that from mineral dust. Therefore, chemical and/or physical differences other than oxidation state may help explain the higher solubility of iron in atmospheric particles.« less
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NASA Astrophysics Data System (ADS)
Brown, M. Alex; Paulenova, Alena; Tkac, Peter
2010-03-01
The stability constant of the Pu(IV)-acetohydroxamic acid complex Pu(AHA)3+ at 1 M ionic strength (pH = 0) has been investigated by method of solvent extraction. Di(2-ethylhexyl) phosphoric acid (HDEHP) was used to extract Pu(IV) from perchloric and nitric acid media at various AHA concentrations. Distribution ratios over a range of ligand concentrations were used in conjunction with graphical methods to obtain logβ1 = 14.3 ± 0.03 in perchloric acid. The stability constant determined from solutions in nitric acid was excluded because of the uncertainty in plutonium speciation.
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A methodology for ecosystem-scale modeling of selenium
Presser, T.S.; Luoma, S.N.
2010-01-01
The main route of exposure for selenium (Se) is dietary, yet regulations lack biologically based protocols for evaluations of risk. We propose here an ecosystem-scale model that conceptualizes and quantifies the variables that determinehow Se is processed from water through diet to predators. This approach uses biogeochemical and physiological factors from laboratory and field studies and considers loading, speciation, transformation to particulate material, bioavailability, bioaccumulation in invertebrates, and trophic transfer to predators. Validation of the model is through data sets from 29 historic and recent field case studies of Se-exposed sites. The model links Se concentrations across media (water, particulate, tissue of different food web species). It can be used to forecast toxicity under different management or regulatory proposals or as a methodology for translating a fish-tissue (or other predator tissue) Se concentration guideline to a dissolved Se concentration. The model illustrates some critical aspects of implementing a tissue criterion: 1) the choice of fish species determines the food web through which Se should be modeled, 2) the choice of food web is critical because the particulate material to prey kinetics of bioaccumulation differs widely among invertebrates, 3) the characterization of the type and phase of particulate material is important to quantifying Se exposure to prey through the base of the food web, and 4) the metric describing partitioning between particulate material and dissolved Se concentrations allows determination of a site-specific dissolved Se concentration that would be responsible for that fish body burden in the specific environment. The linked approach illustrates that environmentally safe dissolved Se concentrations will differ among ecosystems depending on the ecological pathways and biogeochemical conditions in that system. Uncertainties and model sensitivities can be directly illustrated by varying exposure scenarios based on site-specific knowledge. The model can also be used to facilitate site-specific regulation and to present generic comparisons to illustrate limitations imposed by ecosystem setting and inhabitants. Used optimally, the model provides a tool for framing a site-specific ecological problem or occurrence of Se exposure, quantify exposure within that ecosystem, and narrow uncertainties abouthowto protect it by understanding the specifics of the underlying system ecology, biogeochemistry, and hydrology.?? 2010 SETAC.
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A methodology for ecosystem-scale modeling of selenium.
Presser, Theresa S; Luoma, Samuel N
2010-10-01
The main route of exposure for selenium (Se) is dietary, yet regulations lack biologically based protocols for evaluations of risk. We propose here an ecosystem-scale model that conceptualizes and quantifies the variables that determine how Se is processed from water through diet to predators. This approach uses biogeochemical and physiological factors from laboratory and field studies and considers loading, speciation, transformation to particulate material, bioavailability, bioaccumulation in invertebrates, and trophic transfer to predators. Validation of the model is through data sets from 29 historic and recent field case studies of Se-exposed sites. The model links Se concentrations across media (water, particulate, tissue of different food web species). It can be used to forecast toxicity under different management or regulatory proposals or as a methodology for translating a fish-tissue (or other predator tissue) Se concentration guideline to a dissolved Se concentration. The model illustrates some critical aspects of implementing a tissue criterion: 1) the choice of fish species determines the food web through which Se should be modeled, 2) the choice of food web is critical because the particulate material to prey kinetics of bioaccumulation differs widely among invertebrates, 3) the characterization of the type and phase of particulate material is important to quantifying Se exposure to prey through the base of the food web, and 4) the metric describing partitioning between particulate material and dissolved Se concentrations allows determination of a site-specific dissolved Se concentration that would be responsible for that fish body burden in the specific environment. The linked approach illustrates that environmentally safe dissolved Se concentrations will differ among ecosystems depending on the ecological pathways and biogeochemical conditions in that system. Uncertainties and model sensitivities can be directly illustrated by varying exposure scenarios based on site-specific knowledge. The model can also be used to facilitate site-specific regulation and to present generic comparisons to illustrate limitations imposed by ecosystem setting and inhabitants. Used optimally, the model provides a tool for framing a site-specific ecological problem or occurrence of Se exposure, quantify exposure within that ecosystem, and narrow uncertainties about how to protect it by understanding the specifics of the underlying system ecology, biogeochemistry, and hydrology. © 2010 SETAC.
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Andújar, Carmelo; Pérez-González, Sergio; Arribas, Paula; Zaballos, Juan P; Vogler, Alfried P; Ribera, Ignacio
2017-11-01
Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species' habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below-ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement inside the soil. We studied a species-rich endogean ground beetle lineage, Typhlocharina, including three genera and more than 60 species, as a model for the evolutionary biology of dispersal and speciation in the deep soil. A time-calibrated molecular phylogeny generated from >400 individuals was used to delimit candidate species, to study the accumulation of lineages through space and time by species-area-age relationships and to determine the geographical structure of the diversification using the relationship between phylogenetic and geographic distances across the phylogeny. Our results indicated a small spatial scale of speciation in Typhlocharina and low dispersal capacity combined with sporadic long distance, presumably passive dispersal events that fuelled the speciation process. Analysis of lineage growth within Typhlocharina revealed a richness plateau correlated with the range of distribution of lineages, suggesting a long-term species richness equilibrium mediated by density dependence through limits of habitat availability. The interplay of area- and age-dependent processes ruling the lineage diversification in Typhlocharina may serve as a general model for the evolution of high species diversity in endogean mesofauna. © 2017 John Wiley & Sons Ltd.
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Vďačný, Peter; Rajter, Ľubomír; Shazib, Shahed Uddin Ahmed; Jang, Seok Won; Shin, Mann Kyoon
2017-08-30
Ciliates are a suitable microbial model to investigate trait-dependent diversification because of their comparatively complex morphology and high diversity. We examined the impact of seven intrinsic traits on speciation, extinction, and net-diversification of rhynchostomatians, a group of comparatively large, predatory ciliates with proboscis carrying a dorsal brush (sensoric structure) and toxicysts (organelles used to kill the prey). Bayesian estimates under the binary-state speciation and extinction model indicate that two types of extrusomes and two-rowed dorsal brush raise diversification through decreasing extinction. On the other hand, the higher number of contractile vacuoles and their dorsal location likely increase diversification via elevating speciation rate. Particular nuclear characteristics, however, do not significantly differ in their diversification rates and hence lineages with various macronuclear patterns and number of micronuclei have similar probabilities to generate new species. Likelihood-based quantitative state diversification analyses suggest that rhynchostomatians conform to Cope's rule in that their diversity linearly grows with increasing body length and relative length of the proboscis. Comparison with other litostomatean ciliates indicates that rhynchostomatians are not among the cladogenically most successful lineages and their survival over several hundred million years could be associated with their comparatively large and complex bodies that reduce the risk of extinction.
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Drozdzak, Jagoda; Leermakers, Martine; Gao, Yue; Elskens, Marc; Phrommavanh, Vannapha; Descostes, Michael
2016-03-24
The performance of the Diffusive Gradients in Thin films (DGT) technique with Chelex(®)-100, Metsorb™ and Diphonix(®) as binding phases was evaluated in the vicinity of the former uranium mining sites of Chardon and L'Ecarpière (Loire-Atlantique department in western France). This is the first time that the DGT technique with three different binding agents was employed for the aqueous U determination in the context of uranium mining environments. The fractionation and speciation of uranium were investigated using a multi-methodological approach using filtration (0.45 μm, 0.2 μm), ultrafiltration (500 kDa, 100 kDa and 10 kDa) coupled to geochemical speciation modelling (PhreeQC) and the DGT technique. The ultrafiltration data showed that at each sampling point uranium was present mostly in the 10 kDa truly dissolved fraction and the geochemical modelling speciation calculations indicated that U speciation was markedly predominated by CaUO2(CO3)3(2-). In natural waters, no significant difference was observed in terms of U uptake between Chelex(®)-100 and Metsorb™, while similar or inferior U uptake was observed on Diphonix(®) resin. In turn, at mining influenced sampling spots, the U accumulation on DGT-Diphonix(®) was higher than on DGT-Chelex(®)-100 and DGT-Metsorb™, probably because their performance was disturbed by the extreme composition of the mining waters. The use of Diphonix(®) resin leads to a significant advance in the application and development of the DGT technique for determination of U in mining influenced environments. This investigation demonstrated that such multi-technique approach provides a better picture of U speciation and enables to assess more accurately the potentially bioavailable U pool. Copyright © 2016 Elsevier B.V. All rights reserved.
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Wesener, Thomas; Raupach, Michael J.; Decker, Peter
2011-01-01
To elucidate the speciation mechanisms prevalent within hotspots of biodiversity, and the evolutionary processes behind the rise of their species-rich and endemic biota, we investigated the phylogeny of the giant fire-millipede genus Aphistogoniulus Silvestri, 1897, a Malagasy endemic. This study is the first comprehensive (molecular and morphological) phylogenetic study focusing on millipede (class Diplopoda) speciation on Madagascar. The morphological analysis is based on 35 morphological characters and incorporates ten described as well as two newly described species (A. rubrodorsalis n. sp. and A. jeekeli n. sp.) of Aphistogoniulus. The molecular analysis is based on both mitochondrial (COI and 16S), and nuclear genes (complete 18S rDNA), together comprised of 3031 base pairs, which were successfully sequenced for 31 individual specimens and eight species of Aphistogoniulus. In addition to the null-model (speciation by distance), two diversification models, mountain refugia and ecotone shift, were discovered to play a role in the speciation of soil arthropods on Madagascar. Mountain refugia were important in the speciation of the A. cowani clade, with three species occurring in the Andringitra and Ranomafana Mountains in the southeast (A. cowani), the Ambohijanahary and Ambohitantely Mountains in the mid-west (A. sanguineus), and the Marojejy Mountain in the northeast (A. rubrodorsalis n. sp.). An ecotone shift from the eastern rainforest to the unique subarid spiny forest of Mahavelo was discovered in the A. vampyrus - A. aridus species-pair. In the monophyletic A. diabolicus clade, evidence for divergent evolution of sexual morphology was detected: species with greatly enlarged gonopods are sister-taxa to species with normal sized gonopods. Among the large-bodied Spirobolida genera of Madagascar, Colossobolus and Sanguinobolus were found to be close sister-genera to Aphistogoniulus. Forest destruction has caused forest corridors between populations to disappear, which might limit the possible resolution of biogeographic analyses on Madagascar. PMID:22162998
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Fujita, Eric M; Zielinska, Barbara; Campbell, David E; Arnott, W Patrick; Sagebiel, John C; Mazzoleni, Lynn; Chow, Judith C; Gabele, Peter A; Crews, William; Snow, Richard; Clark, Nigel N; Wayne, W Scott; Lawson, Douglas R
2007-06-01
The U.S. Department of Energy Gasoline/Diesel PM Split Study examined the sources of uncertainties in using an organic compound-based chemical mass balance receptor model to quantify the contributions of spark-ignition (SI) and compression-ignition (CI) engine exhaust to ambient fine particulate matter (PM2.5). This paper presents the chemical composition profiles of SI and CI engine exhaust from the vehicle-testing portion of the study. Chemical analysis of source samples consisted of gravimetric mass, elements, ions, organic carbon (OC), and elemental carbon (EC) by the Interagency Monitoring of Protected Visual Environments (IMPROVE) and Speciation Trends Network (STN) thermal/optical methods, polycyclic aromatic hydrocarbons (PAHs), hopanes, steranes, alkanes, and polar organic compounds. More than half of the mass of carbonaceous particles emitted by heavy-duty diesel trucks was EC (IMPROVE) and emissions from SI vehicles contained predominantly OC. Although total carbon (TC) by the IMPROVE and STN protocols agreed well for all of the samples, the STN/IMPROVE ratios for EC from SI exhaust decreased with decreasing sample loading. SI vehicles, whether low or high emitters, emitted greater amounts of high-molecular-weight particulate PAHs (benzo[ghi]perylene, indeno[1,2,3-cd]pyrene, and coronene) than did CI vehicles. Diesel emissions contained higher abundances of two- to four-ring semivolatile PAHs. Diacids were emitted by CI vehicles but are also prevalent in secondary organic aerosols, so they cannot be considered unique tracers. Hopanes and steranes were present in lubricating oil with similar composition for both gasoline and diesel vehicles and were negligible in gasoline or diesel fuels. CI vehicles emitted greater total amounts of hopanes and steranes on a mass per mile basis, but abundances were comparable to SI exhaust normalized to TC emissions within measurement uncertainty. The combustion-produced high-molecular-weight PAHs were found in used gasoline motor oil but not in fresh oil and are negligible in used diesel engine oil. The contributions of lubrication oils to abundances of these PAHs in the exhaust were large in some cases and were variable with the age and consumption rate of the oil. These factors contributed to the observed variations in their abundances to total carbon or PM2.5 among the SI composition profiles.
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SPECIATE 4.2: speciation Database Development Documentation
SPECIATE is the U.S. Environmental Protection Agency's (EPA) repository of volatile organic gas and particulate matter (PM) speciation profiles of air pollution sources. Among the many uses of speciation data, these source profiles are used to: (1) create speciated emissions inve...
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The evolution of sensory divergence in the context of limited gene flow in the bumblebee bat
Puechmaille, Sébastien J.; Gouilh, Meriadeg Ar; Piyapan, Piyathip; Yokubol, Medhi; Mie, Khin Mie; Bates, Paul J.; Satasook, Chutamas; Nwe, Tin; Bu, Si Si Hla; Mackie, Iain J.; Petit, Eric J.; Teeling, Emma C.
2011-01-01
The sensory drive theory of speciation predicts that populations of the same species inhabiting different environments can differ in sensory traits, and that this sensory difference can ultimately drive speciation. However, even in the best-known examples of sensory ecology driven speciation, it is uncertain whether the variation in sensory traits is the cause or the consequence of a reduction in levels of gene flow. Here we show strong genetic differentiation, no gene flow and large echolocation differences between the allopatric Myanmar and Thai populations of the world's smallest mammal, Craseonycteris thonglongyai, and suggest that geographic isolation most likely preceded sensory divergence. Within the geographically continuous Thai population, we show that geographic distance has a primary role in limiting gene flow rather than echolocation divergence. In line with sensory-driven speciation models, we suggest that in C. thonglongyai, limited gene flow creates the suitable conditions that favour the evolution of sensory divergence via local adaptation. PMID:22146392
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Ruiz-Sanchez, Eduardo; Specht, Chelsea D.
2014-01-01
The hypothesis of ecological speciation states that as populations diverge in different niches, reproductive isolation evolves as a by-product of adaptation to these different environments. In this context, we used Nolina parviflora as a model to test if this species evolved via ecological speciation and to explore current and historical gene flow among its populations. Nolina parviflora is a montane species endemic to Mexico with its geographical distribution restricted largely to the Trans-Mexican Volcanic Belt. This mountain range is one of the most complex geological regions in Mexico, having undergone volcanism from the mid-Miocene to the present. Ecologically, the Trans-Mexican Volcanic Belt possesses different types of vegetation, including tropical dry forest; oak, pine, pine-oak, and pine-juniper forests; and xerophytic scrub - all of which maintain populations of N. parviflora. Using species distribution models, climatic analyses, spatial connectivity and morphological comparisons, we found significant differences in climatic and morphological variables between populations of N. parviflora in two distinct Trans-Mexican Volcanic Belt regions (east vs. west). This could mean that the geographically isolated populations diverged from one another via niche divergence, indicating ecological speciation. Spatial connectivity analysis revealed no connectivity between these regions under the present or last glacial maximum climate models, indicating a lack of gene flow between the populations of the two regions. The results imply that these populations may encompass more than a single species. PMID:24905911
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Ruiz-Sanchez, Eduardo; Specht, Chelsea D
2014-01-01
The hypothesis of ecological speciation states that as populations diverge in different niches, reproductive isolation evolves as a by-product of adaptation to these different environments. In this context, we used Nolina parviflora as a model to test if this species evolved via ecological speciation and to explore current and historical gene flow among its populations. Nolina parviflora is a montane species endemic to Mexico with its geographical distribution restricted largely to the Trans-Mexican Volcanic Belt. This mountain range is one of the most complex geological regions in Mexico, having undergone volcanism from the mid-Miocene to the present. Ecologically, the Trans-Mexican Volcanic Belt possesses different types of vegetation, including tropical dry forest; oak, pine, pine-oak, and pine-juniper forests; and xerophytic scrub--all of which maintain populations of N. parviflora. Using species distribution models, climatic analyses, spatial connectivity and morphological comparisons, we found significant differences in climatic and morphological variables between populations of N. parviflora in two distinct Trans-Mexican Volcanic Belt regions (east vs. west). This could mean that the geographically isolated populations diverged from one another via niche divergence, indicating ecological speciation. Spatial connectivity analysis revealed no connectivity between these regions under the present or last glacial maximum climate models, indicating a lack of gene flow between the populations of the two regions. The results imply that these populations may encompass more than a single species.
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Matzke, Nicholas J
2014-11-01
Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC + J, which adds founder-event speciation, the importance of which is governed by a new free parameter, [Formula: see text]. The identifiability of DEC and DEC + J is tested on data sets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC + J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes + J. DEC and DEC + J are compared on 13 empirical data sets drawn from studies of island clades. Likelihood-ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC + J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC + J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.
Roux, Camille; Fraïsse, Christelle; Romiguier, Jonathan; Anciaux, Yoann; Galtier, Nicolas; Bierne, Nicolas
2016-12-01
Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids-the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.
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Sensitivity model study of regional mercury dispersion in the atmosphere
NASA Astrophysics Data System (ADS)
Gencarelli, Christian N.; Bieser, Johannes; Carbone, Francesco; De Simone, Francesco; Hedgecock, Ian M.; Matthias, Volker; Travnikov, Oleg; Yang, Xin; Pirrone, Nicola
2017-01-01
Atmospheric deposition is the most important pathway by which Hg reaches marine ecosystems, where it can be methylated and enter the base of food chain. The deposition, transport and chemical interactions of atmospheric Hg have been simulated over Europe for the year 2013 in the framework of the Global Mercury Observation System (GMOS) project, performing 14 different model sensitivity tests using two high-resolution three-dimensional chemical transport models (CTMs), varying the anthropogenic emission datasets, atmospheric Br input fields, Hg oxidation schemes and modelling domain boundary condition input. Sensitivity simulation results were compared with observations from 28 monitoring sites in Europe to assess model performance and particularly to analyse the influence of anthropogenic emission speciation and the Hg0(g) atmospheric oxidation mechanism. The contribution of anthropogenic Hg emissions, their speciation and vertical distribution are crucial to the simulated concentration and deposition fields, as is also the choice of Hg0(g) oxidation pathway. The areas most sensitive to changes in Hg emission speciation and the emission vertical distribution are those near major sources, but also the Aegean and the Black seas, the English Channel, the Skagerrak Strait and the northern German coast. Considerable influence was found also evident over the Mediterranean, the North Sea and Baltic Sea and some influence is seen over continental Europe, while this difference is least over the north-western part of the modelling domain, which includes the Norwegian Sea and Iceland. The Br oxidation pathway produces more HgII(g) in the lower model levels, but overall wet deposition is lower in comparison to the simulations which employ an O3 / OH oxidation mechanism. The necessity to perform continuous measurements of speciated Hg and to investigate the local impacts of Hg emissions and deposition, as well as interactions dependent on land use and vegetation, forests, peat bogs, etc., is highlighted in this study.
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NASA Astrophysics Data System (ADS)
Shaw, Patrick
The Dust REgional Atmospheric Model (DREAM) predicts concentrations of mineral dust aerosols in time and space, but validation is challenging with current in situ particulate matter (PM) concentration measurements. Measured levels of ambient PM often contain anthropogenic components as well as windblown mineral dust. In this study, two approaches to model validation were performed with data from preexisting air quality monitoring networks: using hourly concentrations of total PM with aerodynamic diameter less than 2.5 μm (PM 2.5); and using a daily averaged speciation-derived soil component. Validation analyses were performed for point locations within the cities of El Paso (TX), Austin (TX), Phoenix (AZ), Salt Lake City (UT) and Bakersfield (CA) for most of 2006. Hourly modeled PM 2.5 did not validate at all with hourly observations among the sites (combined R < 0.00, N = 24,302 hourly values). Aerosol chemical speciation data distinguished between mineral (soil) dust from anthropogenic ambient PM. As expected, statistically significant improvements in correlation among all stations (combined R = 0.16, N = 343 daily values) were found when the soil component alone was used to validate DREAM. The validation biases that result from anthropogenic aerosols were also reduced using the soil component. This is seen in the reduction of the root mean square error between hourly in situ versus hourly modeled (RMSE hourly = 18.6 μg m -3) and 24-h in situ speciation values versus daily averaged observed (RMSE soil = 12.0 μg m -3). However, the lack of a total reduction in RMSE indicates there is still room for improvement in the model. While the soil component is the theoretical proxy of choice for a dust transport model, the current sparse and infrequent sampling is not ideal for routine hourly air quality forecast validation.
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Advances in Time Estimation Methods for Molecular Data.
Kumar, Sudhir; Hedges, S Blair
2016-04-01
Molecular dating has become central to placing a temporal dimension on the tree of life. Methods for estimating divergence times have been developed for over 50 years, beginning with the proposal of molecular clock in 1962. We categorize the chronological development of these methods into four generations based on the timing of their origin. In the first generation approaches (1960s-1980s), a strict molecular clock was assumed to date divergences. In the second generation approaches (1990s), the equality of evolutionary rates between species was first tested and then a strict molecular clock applied to estimate divergence times. The third generation approaches (since ∼2000) account for differences in evolutionary rates across the tree by using a statistical model, obviating the need to assume a clock or to test the equality of evolutionary rates among species. Bayesian methods in the third generation require a specific or uniform prior on the speciation-process and enable the inclusion of uncertainty in clock calibrations. The fourth generation approaches (since 2012) allow rates to vary from branch to branch, but do not need prior selection of a statistical model to describe the rate variation or the specification of speciation model. With high accuracy, comparable to Bayesian approaches, and speeds that are orders of magnitude faster, fourth generation methods are able to produce reliable timetrees of thousands of species using genome scale data. We found that early time estimates from second generation studies are similar to those of third and fourth generation studies, indicating that methodological advances have not fundamentally altered the timetree of life, but rather have facilitated time estimation by enabling the inclusion of more species. Nonetheless, we feel an urgent need for testing the accuracy and precision of third and fourth generation methods, including their robustness to misspecification of priors in the analysis of large phylogenies and data sets. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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NASA Astrophysics Data System (ADS)
Chorover, J.; Kong, S.; Root, R. A.; Thomas, A.
2015-12-01
Bioaccessibility of contaminant metals in geomedia is often measured on the basis of kinetic release to solution during in vitro reaction with biofluid simulants. We postulate that development of a predictive-mechanistic understanding of bioaccessibility requires knowledge of metal(loid) molecular speciation upon sample introduction, as well as its change over the course of the in vitro reaction. Our results - including data from batch, column, mesocosm and field studies pertaining to arsenic, lead, and zinc contaminated materials - indicate the strong influence of organic matter and associated biological activity on metal(loid) speciation in mine tailings and related model systems. Furthermore, presence/absence of organic matter during bioassays affects the kinetics of metal(loid) release into biofluid simulants through multiple mechanisms.
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Speciation of Mg in biogenic calcium carbonates
NASA Astrophysics Data System (ADS)
Farges, F.; Meibom, A.; Flank, A.-M.; Lagarde, P.; Janousch, M.; Stolarski, J.
2009-11-01
A selection of marine biominerals, mostly aragonitic coral skeletons were probed at the Mg K-edge by XANES spectroscopy coupled to μXRF methods and compared to an extensive set of relevant model compounds (silicates, carbonates, oxides and organic). Extensive methodologies are required to better describe the speciation of Mg in those minerals. A combination of ab-initio XANES calculations for defective clusters around Mg in aragonite together with wavelets analyzes of the XANES region are required to robustly interpret the spectra. When using those methodologies, the speciation of Mg ranges from a magnesite-type environment in some scleractinian corals to an organic-type environment. In all environments, the Mg-domains probed appear to be less than 1 nm in size.
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NASA Astrophysics Data System (ADS)
Hauffe, Torsten; Albrecht, Christian; Wilke, Thomas
2016-05-01
The Balkan Lake Ohrid is the oldest and most diverse freshwater lacustrine system in Europe. However, it remains unclear whether species community composition, as well as the diversification of its endemic taxa, is mainly driven by dispersal limitation, environmental filtering, or species interaction. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics, as provided by the unifying framework of the "metacommunity speciation model".The current study used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process-based metacommunity analyses. Specifically, the study aimed (1) to identifying the relative importance of the three community assembly processes and (2) to test whether the importance of these individual processes changes gradually with lake depth or discontinuously with eco-zone shifts.Based on automated eco-zone detection and process-specific simulation steps, we demonstrated that dispersal limitation had the strongest influence on gastropod community composition. However, it was not the exclusive assembly process, but acted together with the other two processes - environmental filtering and species interaction. The relative importance of the community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter.This suggests that environmental characteristics have a pronounced effect on shaping gastropod communities via assembly processes. Moreover, the study corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community composition) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental filtering and biotic interaction also suggests a small but significant influence of ecological speciation. These findings contribute to the main goal of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) deep drilling initiative - inferring the drivers of biotic evolution - and might provide an integrative perspective on biological and limnological dynamics in ancient Lake Ohrid.
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Quantifying variation in speciation and extinction rates with clade data.
Paradis, Emmanuel; Tedesco, Pablo A; Hugueny, Bernard
2013-12-01
High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.
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Defense Coastal/Estuarine Research Program (DCERP) Baseline Monitoring Plan
2007-09-19
climatological stress (e.g., temperature, drought) and shorter-term air pollutant stress (oxidants and metals ). Heavy metals of fine PM have been...speciation of the fine and coarse PM fractions will allow distinction between different PM sources such as wind blown soil dust, including dust...emitting 12% of the total PM2.5 mass (U.S. EPA, 2004b). Source apportionment modeling of PM2.5 mass concentrations from 24 Speciation Defense Coastal
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Mimicry on the QT(L): genetics of speciation in Mimulus.
Bleiweiss, R
2001-08-01
Ecological studies suggest that hummingbird-pollinated plants in North America mimic each other to increase visitation by birds. Published quantitative trait locus (QTL) data for two Mimulus species indicate that floral traits associated with hummingbird versus bee pollination results from a few loci with major effects on morphology, as predicted by classical models for the evolution of mimicry. Thus, the architecture of genetic divergence associated with speciation may depend on the ecological context.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Nitsche, H.; Gatti, R.C.; Standifer, E.M.
1993-07-01
Solubility and speciation data are important in understanding aqueous radionuclide transport through the geosphere. They define the source term for transport retardation processes such as sorption and colloid formation. Solubility and speciation data are useful in verifying the validity of geochemical codes that are part of predictive transport models. Results are presented from solubility and speciation experiments of {sup 237}NpO{sub 2}{sup +}, {sup 239}Pu{sup 4+}, {sup 241}Am{sup 3+}/Nd{sup 3+}, and {sup 243}Am{sup 3+} in J-13 groundwater (from the Yucca Mountain region, Nevada, which is being investigated as a potential high-level nuclear waste disposal site) at three different temperatures (25{degree}, 60{degree},more » and 90{degree}C) and pH values (5.9, 7.0, and 8.5). The solubility-controlling steady-state solids were identified and the speciation and/or oxidation states present in the supernatant solutions were determined. The neptunium solubility decreased with increasing temperature and pH. Plutonium concentrations decreased with increasing temperature and showed no trend with pH. The americium solutions showed no clear solubility trend with increasing temperature and increasing pH.« less
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Hudspith, M; Reichelt-Brushett, Amanda; Harrison, Peter L
2017-03-01
Significant amounts of trace metals have been released into both nearshore and deep sea environments in recent years, resulting in increased concentrations that can be toxic to marine organisms. Trace metals can negatively affect external fertilization processes in marine broadcast spawners and may cause a reduction in fertilization success at elevated concentrations. Due to its sensitivity and ecological importance, fertilization success has been widely used as a toxicity endpoint in ecotoxicological testing, which is an important method of evaluating the toxicity of contaminants for management planning. Ecotoxicological data regarding fertilization success are available across the major marine phyla, but there remain uncertainties that impair our ability to confidently interpret and analyse these data. At present, the cellular and biochemical events underlying trace metal toxicity in external fertilization are not known. Metal behavior and speciation play an important role in bioavailability and toxicity but are often overlooked, and disparities in experimental designs between studies limit the degree to which results can be synthesised and compared to those of other relevant species. We reviewed all available literature covering cellular toxicity mechanisms, metal toxicities and speciation, and differences in methodologies between studies. We conclude that the concept of metal toxicity should be approached in a more holistic manner that involves elucidating toxicity mechanisms, improving the understanding of metal behavior and speciation on bioavailability and toxicity, and standardizing the fertilization assay methods among different groups of organisms. We identify opportunities to improve the fertilization assay that will allow robust critical and comparative analysis between species and their sensitivities to trace metals during external fertilization, and enable data to be more readily extrapolated to field conditions. Copyright © 2017 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Bulgin, Claire E.; Palmer, Paul I.; Merchant, Christopher J.; Siddans, Richard; Gonzi, Siegfried; Poulsen, Caroline A.; Thomas, Gareth E.; Sayer, Andrew M.; Carboni, Elisa; Grainger, Roy G.; Highwood, Eleanor J.; Ryder, Claire L.
2011-03-01
We test the response of the Oxford-RAL Aerosol and Cloud (ORAC) retrieval algorithm for Meteosat Second Generation Spinning Enhanced Visible and InfraRed Imager (MSG SEVIRI) to changes in the aerosol properties used in the dust aerosol model, using data from the Dust Outflow and Deposition to the Ocean (DODO) flight campaign in August 2006. We find that using the observed DODO free tropospheric aerosol size distribution and refractive index increases simulated top of the atmosphere radiance at 0.55 μm assuming a fixed aerosol optical depth of 0.5 by 10-15%, reaching a maximum difference at low solar zenith angles. We test the sensitivity of the retrieval to the vertical distribution of the aerosol and find that this is unimportant in determining simulated radiance at 0.55 μm. We also test the ability of the ORAC retrieval when used to produce the GlobAerosol data set to correctly identify continental aerosol outflow from the African continent, and we find that it poorly constrains aerosol speciation. We develop spatially and temporally resolved prior distributions of aerosols to inform the retrieval which incorporates five aerosol models: desert dust, maritime, biomass burning, urban, and continental. We use a Saharan Dust Index and the GEOS-Chem chemistry transport model to describe dust and biomass burning aerosol outflow and compare AOD using our speciation against the GlobAerosol retrieval during January and July 2006. We find AOD discrepancies of 0.2-1 over regions of intense biomass burning outflow, where AOD from our aerosol speciation and GlobAerosol speciation can differ by as much as 50-70%.
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Jones, Adele M; Xue, Youjia; Kinsela, Andrew S; Wilcken, Klaus M; Collins, Richard N
2016-03-15
Donnan dialysis has been applied to forty filtered drainage waters collected from five coastal lowland acid sulfate soil (CLASS) catchments across north-eastern NSW, Australia. Despite having average pH values<3.9, 78 and 58% of Al and total Fe, respectively, were present as neutral or negatively-charged species. Complementary isotope dilution experiments with (55)Fe and (26)Al demonstrated that only soluble (i.e. no colloidal) species were present. Trivalent rare earth elements (REEs) were also mainly present (>70%) as negatively-charged complexes. In contrast, the speciation of the divalent trace metals Co, Mn, Ni and Zn was dominated by positively-charged complexes and was strongly correlated with the alkaline earth metals Ca and Mg. Thermodynamic equilibrium speciation calculations indicated that natural organic matter (NOM) complexes dominated Fe(III) speciation in agreement with that obtained by Donnan dialysis. In the case of Fe(II), however, the free cation was predicted to dominate under thermodynamic equilibrium, whilst our results indicated that Fe(II) was mainly present as neutral or negatively-charged complexes (most likely with sulfate). For all other divalent metals thermodynamic equilibrium speciation calculations agreed well with the Donnan dialysis results. The proportion of Al and REEs predicted to be negatively-charged was also grossly underestimated, relative to the experimental results, highlighting possible inaccuracies in the stability constants developed for these trivalent Me(SO4)2(-) and/or Me-NOM complexes and difficulties in modeling complex environmental samples. These results will help improve metal mobility and toxicity models developed for CLASS-affected environments, and also demonstrate that Australian CLASS environments can discharge REEs at concentrations an order of magnitude greater than previously reported. Copyright © 2015 Elsevier B.V. All rights reserved.
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Pan, Yang; Zhang, Xiangru
2013-02-05
Bromide is naturally present in source waters worldwide. Chlorination of drinking water can generate a variety of chlorinated and brominated disinfection byproducts (DBPs). Although substantial efforts have been made to examine the effect of bromide concentration on the formation and speciation of halogenated DBPs, almost all previous studies have focused on trihalomethanes and haloacetic acids. Given that about 50% of total organic halogen formed in chlorination remains unknown, it is still unclear how bromide concentration affects the formation and speciation of the new/unknown halogenated DBPs. In this study, chlorinated drinking water samples with different bromide concentrations were prepared, and a novel approach-precursor ion scan using ultra performance liquid chromatography/electrospray ionization-triple quadrupole mass spectrometry-was adopted for the detection and identification of polar halogenated DBPs in these water samples. With this approach, 11 new putative aromatic halogenated DBPs were identified, and they were classified into four groups: dihalo-4-hydroxybenzaldehydes, dihalo-4-hydroxybenzoic acids, dihalo-salicylic acids, and trihalo-phenols. A mechanism for the formation of the four groups of new aromatic halogenated DBPs was proposed. It was found that increasing the bromide concentration shifted the entire polar halogenated DBPs as well as the four groups of new DBPs from being less brominated to being more brominated; these new aromatic halogenated DBPs might be important intermediate DBPs formed in drinking water chlorination. Moreover, the speciation of the four groups of new DBPs was modeled: the speciation patterns of the four groups of new DBPs well matched those determined from the model equations, and the reactivity differences between HOBr and HOCl in reactions forming the four groups of new DBPs were larger than those in reactions forming trihalomethanes and haloacetic acids.
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Sierra, Jordi; Roig, Neus; Giménez Papiol, Gemma; Pérez-Gallego, Elena; Schuhmacher, Marta
2017-12-15
The aim of this work is to predict the bioavailability of the Potentially Toxic Elements (PTEs) Cd, Pb, Hg, Ni, Cu, Zn, As, Cr and Se in 6 sites within the Ebro River basin. In situ Diffusive gradient in thin-films (DGTs) and classical sampling have been used and compared. The potentially bioavailable fractions of each PTE was estimated by modelling their chemical speciation using three programs (WHAM 7.0, Visual MINTEQ 3.1 and Bio-met), following the suggestions published in recent European regulations. Results of the equilibrium-based models WHAM 7.0 and Visual MINTEQ 3.1 indicate that As, Cd, Ni, Se and Zn, predominate as free metals ions or forming inorganic soluble complexes. Copper, Pb and Hg bioavailability is conditioned by their affinity to dissolved humic substances. According to Visual MINTEQ 3.1, Cr is subjected to redox reactions, being Cr (VI) present (at low concentrations) in the studied rivers. According to Bio-met model, the bioavailability of Cu and Zn is highly influenced by soluble organic matter and water hardness, respectively. For most PTEs, the bioavailability estimated by deploying DGTs in river waters tends to be slightly lower than the estimation obtained with speciation models, since in real conditions more environmental factors take place comparing to the finite number of parameters considered in models. Copyright © 2017 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Renggli, C. J.; King, P. L.; Henley, R. W.; Norman, M. D.
2017-06-01
The transport of metals in volcanic gases on the Moon differs greatly from their transport on the Earth because metal speciation depends largely on gas composition, temperature, pressure and oxidation state. We present a new thermochemical model for the major and trace element composition of lunar volcanic gas during pyroclastic eruptions of picritic magmas calculated at 200-1500 °C and over 10-9-103 bar. Using published volatile component concentrations in picritic lunar glasses, we have calculated the speciation of major elements (H, O, C, Cl, S and F) in the coexisting volcanic gas as the eruption proceeds. The most abundant gases are CO, H2, H2S, COS and S2, with a transition from predominantly triatomic gases to diatomic gases with increasing temperatures and decreasing pressures. Hydrogen occurs as H2, H2S, H2S2, HCl, and HF, with H2 making up 0.5-0.8 mol fractions of the total H. Water (H2O) concentrations are at trace levels, which implies that H-species other than H2O need to be considered in lunar melts and estimates of the bulk lunar composition. The Cl and S contents of the gas control metal chloride gas species, and sulfide gas and precipitated solid species. We calculate the speciation of trace metals (Zn, Ga, Cu, Pb, Ni, Fe) in the gas phase, and also the pressure and temperature conditions at which solids form from the gas. During initial stages of the eruption, elemental gases are the dominant metal species. As the gas loses heat, chloride and sulfide species become more abundant. Our chemical speciation model is applied to a lunar pyroclastic eruption model with isentropic gas decompression. The relative abundances of the deposited metal-bearing solids with distance from the vent are predicted for slow cooling rates (<5 °C/s). Close to a volcanic vent we predict native metals are deposited, whereas metal sulfides dominate with increasing distance from the vent. Finally, the lunar gas speciation model is compared with the speciation of a H2O-, CO2- and Cl-rich volcanic gas from Erta Ale volcano (Ethiopia) as an analogy for more oxidized planetary eruptions. In the terrestrial Cl-rich gas the metals are predominantly transported as chlorides, as opposed to metallic vapors and sulfides in the lunar gas. Due to the presence of Cl-species, metal transport is more efficient in the volcanic gas from Erta Ale compared to the Moon.
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NASA Astrophysics Data System (ADS)
Tumiati, S.; Tiraboschi, C.; Recchia, S.; Poli, S.
2014-12-01
The quantitative assessment of species in COH fluids is crucial in modelling mantle processes. For instance, H2O/CO2 ratio in the fluid phase influences the location of the solidus and of carbonation/decarbonation reactions in peridotitic systems . In the scientific literature, the speciation of COH fluids has been generally assumed on the basis of thermodynamic calculations using equations of state of simple H2O-non-polar gas systems (e.g., H2O-CO2-CH4). Only few authors dealt with the experimental determination of high-pressure COH fluid species at different conditions, using diverse experimental and analytical approaches (e.g., piston cylinder+capsule-piercing+gas-chromatography/mass-spectrometry; cold-seal+silica glass capsules+Raman). We performed experiments on COH fluids using a capsule-piercing device coupled with a quadrupole mass spectrometry. This type of analyzer ensures superior performances in terms of selectivity of molecules to be detected, high acquisition rates and extended linear response range. Experiments were carried out in a rocking piston cylinder apparatus at pressure of 1 GPa and temperatures from 800 to 900°C. Carbon-saturated fluids were generated through the addition of oxalic acid dihydrate and graphite. Single/double capsules and different packing materials (BN and MgO) were used to evaluate the divergence from the thermodynamic speciation model. Moreover, to assess the effect of solutes on COH fluid speciation we also performed a set of experiments adding synthetic forsterite to the charge. To determine the speciation we assembled a capsule-piercing device that allows to puncture the capsule in a gas-tight vessel at 80°C. The extraction Teflon vessel is composed of a base part, where the capsule is allocated on a steel support, and a top part where a steel drill is mounted. To release the quenched fluids from the capsule, the base part of vessel is hand-tighten to the top part, allowing the steel pointer to pierce the capsule. The evolved gases are then convoyed to a quadrupole mass spectrometer through a heated line to avoid the condensation of water. Our results suggest that fluid speciation can diverge considerably compared to the thermodynamic model depending on the experimental strategies adopted and on the presence of solutes in complex COH systems.
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Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
Kordi, Misagh; Bansal, Mukul S
2017-06-01
Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation seeks to reconcile gene trees with species trees by postulating speciation, duplication, transfer, and loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. In practice, however, gene trees are often non-binary due to uncertainty in the gene tree topologies, and DTL reconciliation with non-binary gene trees is known to be NP-hard. In this paper, we present the first exact algorithms for DTL reconciliation with non-binary gene trees. Specifically, we (i) show that the DTL reconciliation problem for non-binary gene trees is fixed-parameter tractable in the maximum degree of the gene tree, (ii) present an exponential-time, but in-practice efficient, algorithm to track and enumerate all optimal binary resolutions of a non-binary input gene tree, and (iii) apply our algorithms to a large empirical data set of over 4700 gene trees from 100 species to study the impact of gene tree uncertainty on DTL-reconciliation and to demonstrate the applicability and utility of our algorithms. The new techniques and algorithms introduced in this paper will help biologists avoid incorrect evolutionary inferences caused by gene tree uncertainty.
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NASA Astrophysics Data System (ADS)
Muntean, Marilena; Janssens-Maenhout, Greet; Song, Shaojie; Giang, Amanda; Selin, Noelle E.; Zhong, Hui; Zhao, Yu; Olivier, Jos G. J.; Guizzardi, Diego; Crippa, Monica; Schaaf, Edwin; Dentener, Frank
2018-07-01
Speciated mercury gridded emissions inventories together with chemical transport models and concentration measurements are essential when investigating both the effectiveness of mitigation measures and the mercury cycle in the environment. Since different mercury species have contrasting behaviour in the atmosphere, their proportion in anthropogenic emissions could determine the spatial impacts. In this study, the time series from 1970 to 2012 of the EDGARv4.tox2 global mercury emissions inventory are described; the total global mercury emission in 2010 is 1772 tonnes. Global grid-maps with geospatial distribution of mercury emissions at a 0.1° × 0.1° resolution are provided for each year. Compared to the previous tox1 version, tox2 provides updates for more recent years and improved emissions in particular for agricultural waste burning, power generation and artisanal and small-scale gold mining (ASGM) sectors. We have also developed three retrospective emissions scenarios based on different hypotheses related to the proportion of mercury species in the total mercury emissions for each activity sector; improvements in emissions speciation are seen when using information primarily from field measurements. We evaluated them using the GEOS-Chem 3-D mercury model in order to explore the influence of speciation shifts, to reactive mercury forms in particular, on regional wet deposition patterns. The reference scenario S1 (EDGARv4.tox2_S1) uses speciation factors from the Arctic Monitoring and Assessment Programme (AMAP); scenario S2 ("EPA_power") uses factors from EPA's Information Collection Request (ICR); and scenario S3 ("Asia_filedM") factors from recent scientific publications. In the reference scenario, the sum of reactive mercury emissions (Hg-P and Hg2+) accounted for 25.3% of the total global emissions; the regions/countries that have shares of reactive mercury emissions higher than 6% in total global reactive mercury are China+ (30.9%), India+ (12.5%) and the United States (9.9%). In 2010, the variations of reactive mercury emissions amongst the different scenarios are in the range of -19.3 t/yr (China+) to 4.4 t/yr (OECD_Europe). However, at the sector level, the variation could be different, e.g., for the iron and steel industry in China reaches 15.4 t/yr. Model evaluation at the global level shows a variation of approximately ±10% in wet deposition for the three emissions scenarios. An evaluation of the impact of mercury speciation within nested grid sensitivity simulations is performed for the United States and modelled wet deposition fluxes are compared with measurements. These studies show that using the S2 and S3 emissions of reactive mercury, can improve wet deposition estimates near sources.
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NASA Astrophysics Data System (ADS)
Stindl, Reinhard
2014-03-01
Charles Darwin knew that the fossil record is not overwhelmingly supportive of genetic and phenotypic gradualism; therefore, he developed the core of his theory on the basis of breeding experiments. Here, I present evidence for the existence of a cell biological mechanism that strongly points to the almost forgotten European concept of saltatory evolution of nonadaptive characters, which is in perfect agreement with the gaps in the fossil record. The standard model of chromosomal evolution has always been handicapped by a paradox, namely, how speciation can occur by spontaneous chromosomal rearrangements that are known to decrease the fertility of heterozygotes in a population. However, the hallmark of almost all closely related species is a differing chromosome complement and therefore chromosomal rearrangements seem to be crucial for speciation. Telomeres, the caps of eukaryotic chromosomes, erode in somatic tissues during life, but have been thought to remain stable in the germline of a species. Recently, a large human study spanning three healthy generations clearly found a cumulative telomere effect, which is indicative of transgenerational telomere erosion in the human species. The telomeric sync model of speciation presented here is based on telomere erosion between generations, which leads to identical fusions of chromosomes and triggers a transposon-mediated genomic repatterning in the germline of many individuals of a species. The phenotypic outcome of the telomere-triggered transposon activity is the saltatory appearance of nonadaptive characters simultaneously in many individuals. Transgenerational telomere erosion is therefore the material basis of aging at the species level.
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Pandey, Mayank; Pandey, Ashutosh Kumar; Mishra, Ashutosh; Tripathi, B D
2015-09-01
Present study deals with the river Ganga water quality and its impact on metal speciation in its sediments. Concentration of physico-chemical parameters was highest in summer season followed by winter and lowest in rainy season. Metal speciation study in river sediments revealed that exchangeable, reducible and oxidizable fractions were dominant in all the studied metals (Cr, Ni, Cu, Zn, Cd, Pb) except Mn and Fe. High pollution load index (1.64-3.89) recommends urgent need of mitigation measures. Self-organizing Map-Artificial Neural Network (SOM-ANN) was applied to the data set for the prediction of major point sources of pollution in the river Ganga. Copyright © 2015 Elsevier Ltd. All rights reserved.
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A forecast for extinction debt in the presence of speciation.
Sgardeli, Vasiliki; Iwasa, Yoh; Varvoglis, Harry; Halley, John M
2017-02-21
Predicting biodiversity relaxation following a disturbance is of great importance to conservation biology. Recently-developed models of stochastic community assembly allow us to predict the evolution of communities on the basis of mechanistic processes at the level of individuals. The neutral model of biodiversity, in particular, has provided closed-form solutions for the relaxation of biodiversity in isolated communities (no immigration or speciation). Here, we extend these results by deriving a relaxation curve for a neutral community in which new species are introduced through the mechanism of random fission speciation (RFS). The solution provides simple closed-form expressions for the equilibrium species richness, the relaxation time and the species-individual curve, which are good approximation to the more complicated formulas existing for the same model. The derivation of the relaxation curve is based on the assumption of a broken-stick species-abundance distribution (SAD) as an initial community configuration; yet for commonly observed SADs, the maximum deviation from the curve does not exceed 10%. Importantly, the solution confirms theoretical results and observations showing that the relaxation time increases with community size and thus habitat area. Such simple and analytically tractable models can help crystallize our ideas on the leading factors affecting biodiversity loss. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Hua, Xia
2016-07-27
Being invoked as one of the candidate mechanisms for the latitudinal patterns in biodiversity, Janzen's hypothesis states that the limited seasonal temperature variation in the tropics generates greater temperature stratification across elevations, which makes tropical species adapted to narrower ranges of temperatures and have lower effective dispersal across elevations than species in temperate regions. Numerous empirical studies have documented latitudinal patterns in species elevational ranges and thermal niche breadths that are consistent with the hypothesis, but the theoretical underpinnings remain unclear. This study presents the first mathematical model to examine the evolutionary processes that could back up Janzen's hypothesis and assess the effectiveness of limited seasonal temperature variation to promote speciation along elevation in the tropics. Results suggest that trade-offs in thermal tolerances provide a mechanism for Janzen's hypothesis. Limited seasonal temperature variation promotes gradient speciation not due to the reduction in gene flow that is associated with narrow thermal niche, but due to the pleiotropic effects of more stable divergent selection of thermal tolerance on the evolution of reproductive incompatibility. The proposed modelling approach also provides a potential way to test a speciation model against genetic data. © 2016 The Author(s).
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Signatures of microevolutionary processes in phylogenetic patterns.
Costa, Carolina L N; Lemos-Costa, Paula; Marquitti, Flavia M D; Fernandes, Lucas D; Ramos, Marlon F; Schneider, David M; Martins, Ayana B; Aguiar, Marcus A M
2018-06-23
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.
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den Tex, Robert-Jan; Thorington, Richard; Maldonado, Jesus E; Leonard, Jennifer A
2010-05-01
Tropical rainforests are well known for their extraordinarily high levels of biodiversity. The origin of this species richness is still debated. For instance, the museum hypothesis states that over evolutionary time more and more species will accumulate with relatively few extinctions. In contrast, the Pleistocene diversification model argues that during the last 2 million years, climatic factors (glaciations) caused environmental changes that drove isolation and vicariant speciation events. In this study, we construct a molecular phylogeny of the Sundaland (Malay Peninsula, Sumata, Borneo, Palawan) and Greater Mindanao (Mindanao, Samar, Leyte) tree squirrels (genus Sundasciurus). Our results show that most speciation events in this forest dependent taxon occurred before the Pleistocene and that even the timing of intra-specific splits among populations from different landmasses are relatively old. Additionally, we found unexpectedly high divergence within and between highland populations of S. tenuis on Sumatra and the Malay Peninsula, highlighting the importance of Pliocene events in both speciation and within species divergences in this region. Copyright 2010 Elsevier Inc. All rights reserved.
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The relationship between mantle pH and the deep nitrogen cycle
NASA Astrophysics Data System (ADS)
Mikhail, Sami; Barry, Peter H.; Sverjensky, Dimitri A.
2017-07-01
Nitrogen is distributed throughout all terrestrial geological reservoirs (i.e., the crust, mantle, and core), which are in a constant state of disequilibrium due to metabolic factors at Earth's surface, chemical weathering, diffusion, and deep N fluxes imposed by plate tectonics. However, the behavior of nitrogen during subduction is the subject of ongoing debate. There is a general consensus that during the crystallization of minerals from melts, monatomic nitrogen behaves like argon (highly incompatible) and ammonium behaves like potassium and rubidium (which are relatively less incompatible). Therefore, the behavior of nitrogen is fundamentally underpinned by its chemical speciation. In aqueous fluids, the controlling factor which determines if nitrogen is molecular (N2) or ammonic (inclusive of both NH4+ and NH30) is oxygen fugacity, whereas pH designates if ammonic nitrogen is NH4+ or NH30. Therefore, to address the speciation of nitrogen at high pressures and temperatures, one must also consider pH at the respective pressure-temperature conditions. To accomplish this goal we have used the Deep Earth Water Model (DEW) to calculate the activities of aqueous nitrogen from 1-5 GPa and 600-1000 °C in equilibrium with a model eclogite-facies mineral assemblage of jadeite + kyanite + quartz/coesite (metasediment), jadeite + pyrope + talc + quartz/coesite (metamorphosed mafic rocks), and carbonaceous eclogite (metamorphosed mafic rocks + elemental carbon). We then compare these data with previously published data for the speciation of aqueous nitrogen across these respective P-T conditions in equilibrium with a model peridotite mineral assemblage (Mikhail and Sverjensky, 2014). In addition, we have carried out full aqueous speciation and solubility calculations for the more complex fluids in equilibrium with jadeite + pyrope + kyanite + diamond, and for fluids in equilibrium with forsterite + enstatite + pyrope + diamond. Our results show that the pH of the fluid is controlled by mineralogy for a given pressure and temperature, and that pH can vary by several units in the pressure-temperature range of 1-5 GPa and 600-1000 °C. Our data show that increasing temperature stabilizes molecular nitrogen and increasing pressure stabilizes ammonic nitrogen. Our model also predicts a stark difference for the dominance of ammonic vs. molecular and ammonium vs. ammonia for aqueous nitrogen in equilibrium with eclogite-facies and peridotite mineralogies, and as a function of the total dissolved nitrogen in the aqueous fluid where lower N concentrations favor aqueous ammonic nitrogen stabilization and higher N concentrations favor aqueous N2. Overall, we present thermodynamic evidence for nitrogen to be reconsidered as an extremely dynamic (chameleon) element whose speciation and therefore behavior is determined by a combination of temperature, pressure, oxygen fugacity, chemical activity, and pH. We show that altering the mineralogy in equilibrium with the fluid can lead to a pH shift of up to 4 units at 5 GPa and 1000 °C. Therefore, we conclude that pH imparts a strong control on nitrogen speciation, and thus N flux, and should be considered a significant factor in high temperature geochemical modeling in the future. Finally, our modelling demonstrates that pH plays an important role in controlling speciation, and thus mass transport, of Eh-pH sensitive elements at temperatures up to at least 1000 °C.
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2009-01-01
Background The full power of modern genetics has been applied to the study of speciation in only a small handful of genetic model species - all of which speciated allopatrically. Here we report the first large expressed sequence tag (EST) study of a candidate for ecological sympatric speciation, the apple maggot Rhagoletis pomonella, using massively parallel pyrosequencing on the Roche 454-FLX platform. To maximize transcript diversity we created and sequenced separate libraries from larvae, pupae, adult heads, and headless adult bodies. Results We obtained 239,531 sequences which assembled into 24,373 contigs. A total of 6810 unique protein coding genes were identified among the contigs and long singletons, corresponding to 48% of all known Drosophila melanogaster protein-coding genes. Their distribution across GO classes suggests that we have obtained a representative sample of the transcriptome. Among these sequences are many candidates for potential R. pomonella "speciation genes" (or "barrier genes") such as those controlling chemosensory and life-history timing processes. Furthermore, we identified important marker loci including more than 40,000 single nucleotide polymorphisms (SNPs) and over 100 microsatellites. An initial search for SNPs at which the apple and hawthorn host races differ suggested at least 75 loci warranting further work. We also determined that developmental expression differences remained even after normalization; transcripts expected to show different expression levels between larvae and pupae in D. melanogaster also did so in R. pomonella. Preliminary comparative analysis of transcript presences and absences revealed evidence of gene loss in Drosophila and gain in the higher dipteran clade Schizophora. Conclusions These data provide a much needed resource for exploring mechanisms of divergence in this important model for sympatric ecological speciation. Our description of ESTs from a substantial portion of the R. pomonella transcriptome will facilitate future functional studies of candidate genes for olfaction and diapause-related life history timing, and will enable large scale expression studies. Similarly, the identification of new SNP and microsatellite markers will facilitate future population and quantitative genetic studies of divergence between the apple and hawthorn-infesting host races. PMID:20035631
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EPA’s SPECIATE 4.4 Database:Development and Uses
SPECIATE is the U.S. Environmental Protection Agency's (EPA)repository of volatile organic gas and particulate matter (PM) speciation profiles for air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, VOC, total...
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EPA’s SPECIATE 4.4 Database: Development and Uses
SPECIATE is the U.S. Environmental Protection Agency's (EPA)repository of volatile organic gas and particulate matter (PM) speciation profiles for air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, VOC, total...
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Gandhi, N.; Bhavsar, S.P.; Diamond, M.L.; Kuwabara, J.S.; Marvin-DiPasquale, M.; Krabbenhoft, D.P.
2007-01-01
A mathematically linked mercury transport, speciation, kinetic, and simple biotic uptake (BIOTRANSPEC) model has been developed. An extension of the metal transport and speciation (TRANSPEC) model, BIOTRANSPEC estimates the fate and biotic uptake of inorganic (Hg(II)), elemental (Hg(0)) and organic (MeHg) forms of mercury and their species in the dissolved, colloidal (e.g., dissolved organic matter [DOM]), and particulate phases of surface aquatic systems. A pseudo-steady state version of the model was used to describe mercury dynamics in Lahontan Reservoir (near Carson City, NV, USA), where internal loading of the historically deposited mercury is remobilized, thereby maintaining elevated water concentrations. The Carson River is the main source of total mercury (THg), of which more than 90% is tightly bound in a gold-silver-mercury amalgam, to the system through loadings in the spring, with negligible input from the atmospheric deposition. The speciation results suggest that aqueous species are dominated by Hg-DOM, Hg(OH)2, and HgClOH. Sediment-to-water diffusion of MeHg and Hg-DOM accounts for approximately 10% of total loadings to the water column. The water column acts as a net sink for MeHg by reducing its levels through two competitive processes: Uptake by fish, and net MeHg demethylation. Although reservoir sediments produce significant amounts of MeHg (4 g/d), its transport from sediment to water is limited (1.6 g/d), possibly because of its adsorption on metal oxides of iron and manganese at the sediment-water interface. Fish accumulate approximately 45% of the total MeHg mass in the water column, and 9% of total MeHg uptake by fish leaves the system because of fishing. Results from this new model reiterate the previous conclusion that more than 90% of THg input is retained in sediment, which perpetuates elevated water concentrations. ?? 2007 SETAC.
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Mercury speciation comparison. BrooksApplied Laboratories and Eurofins Frontier Global Sciences
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bannochie, C. J.; Wilmarth, W. R.
2016-12-16
The Savannah River National Laboratory (SRNL) was tasked with preparing and shipping samples for Hg speciation by Eurofins Frontier Global Sciences (FGS), Inc. in Bothell, WA on behalf of the Savannah River Remediation (SRR) Mercury Program Team. These samples were analyzed for seven species including: total mercury, dissolved mercury, inorganic mercury ((Hg(I) and Hg(II)), elemental mercury, methylmercury, ethylmercury, and dimethylmercury, with an eighth species, particulate mercury, calculated from the difference between total and dissolved mercury after subtracting the elemental mercury. The species fraction of total mercury measured has ranged broadly from a low of 32% to a high of 146%,more » though the vast majority of samples have been <100%. This can be expected since one is summing multiple values that each have at least a ± 20% measurement uncertainty. Two liquid waste tanks particularly important to understanding the distribution of mercury species in the Savannah River Site (SRS) Tank Farm were selected for a round robin analysis by Eurofins FGS and BrooksApplied Laboratories (BAL). The analyses conducted by BAL on the Tank 22 and 38 samples and their agreement with those obtained from Eurofins FGS for total mercury, dissolved mercury, methylmercury, ethylmercury, and dimethylmercury provide a strong degree of confidence in these species measurements« less
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Ferreira, Milena; Garcia, Caroline; Matoso, Daniele A.; de Jesus, Isac S.; Cioffi, Marcelo de B.; Bertollo, Luiz A. C.; Zuanon, Jansen; Feldberg, Eliana
2017-01-01
Bunocephalus is the most species-rich Aspredinidae genus, corresponding to a monophyletic clade with 13 valid species. However, many species have their classification put in question. Here, we analyzed individuals from four Amazonian populations of Bunocephalus coracoideus by cytogenetic and molecular procedures. The geographic distribution, genetic distances and karyotype data indicate that each population represents an Evolutionary Significant Unit (ESU). Cytogenetic markers showed distinct 2n and karyotype formulas, as well as different numbers and locations of the rDNA sites among ESUs. One of such populations (ESU-D) highlighted an extensive polymorphic condition, with several cytotypes probably due to chromosomal rearrangements and meiotic non-disjunctions. This resulted in several aneuploid karyotypes, which was also supported by the mapping of telomeric sequences. Phylograms based on Maximum Likelihood (ML) and Neighbor Joining (NJ) analyses grouped each ESU on particular highly supported clades, with the estimation of evolutionary divergence indicating values being higher than 3.8–12.3% among them. Our study reveals a huge degree of chromosomal and genetic diversity in B. coracoideus and highly points to the existence of four ESUs in allopatric and sympatric speciation processes. In fact, the high divergences found among the ESUs allowed us to delimitate lineages with taxonomic uncertainties in this nominal species. PMID:28983316
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Ferreira, Milena; Garcia, Caroline; Matoso, Daniele A; de Jesus, Isac S; Cioffi, Marcelo de B; Bertollo, Luiz A C; Zuanon, Jansen; Feldberg, Eliana
2017-01-01
Bunocephalus is the most species-rich Aspredinidae genus, corresponding to a monophyletic clade with 13 valid species. However, many species have their classification put in question. Here, we analyzed individuals from four Amazonian populations of Bunocephalus coracoideus by cytogenetic and molecular procedures. The geographic distribution, genetic distances and karyotype data indicate that each population represents an Evolutionary Significant Unit (ESU). Cytogenetic markers showed distinct 2n and karyotype formulas, as well as different numbers and locations of the rDNA sites among ESUs. One of such populations (ESU-D) highlighted an extensive polymorphic condition, with several cytotypes probably due to chromosomal rearrangements and meiotic non-disjunctions. This resulted in several aneuploid karyotypes, which was also supported by the mapping of telomeric sequences. Phylograms based on Maximum Likelihood (ML) and Neighbor Joining (NJ) analyses grouped each ESU on particular highly supported clades, with the estimation of evolutionary divergence indicating values being higher than 3.8-12.3% among them. Our study reveals a huge degree of chromosomal and genetic diversity in B. coracoideus and highly points to the existence of four ESUs in allopatric and sympatric speciation processes. In fact, the high divergences found among the ESUs allowed us to delimitate lineages with taxonomic uncertainties in this nominal species.
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Using X-ray absorption to probe sulfur oxidation states in complex molecules
NASA Astrophysics Data System (ADS)
Vairavamurthy, A.
1998-10-01
X-ray absorption near-edge structure (XANES) spectroscopy offers an important non-destructive tool for determining oxidation states and for characterizing chemical speciation. The technique was used to experimentally verify the oxidation states of sulfur in different types of complex molecules because there are irregularities and uncertainties in assigning the values traditionally. The usual practice of determining oxidation states involves using a set of conventional rules. The oxidation state is an important control in the chemical speciation of sulfur, ranging from -2 to +6 in its different compounds. Experimental oxidation-state values for various types of sulfur compounds, using their XANES peak-energy positions, were assigned from a scale in which elemental sulfur and sulfate are designated as 0 and +6, respectively. Because these XANES-based values differed considerably from conventionally determined oxidation states for most sulfur compounds, a new term 'oxidation index' was coined to describe them. The experimental values were closer to those conventional values obtained by assigning shared electrons to the more electronegative atoms than to those based on other customary rules for assigning them. Because the oxidation index is distinct and characteristic for each different type of sulfur functionality, it becomes an important parameter for characterizing sulfur species, and for experimentally verifying uncertain oxidation states.
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NASA Astrophysics Data System (ADS)
Ullrich, Maria K.; Pope, James G.; Seward, Terry M.; Wilson, Nathaniel; Planer-Friedrich, Britta
2013-07-01
Champagne Pool, a sulfidic hot spring in New Zealand, exhibits distinct diurnal variations in antimony (Sb) and arsenic (As) concentrations, with daytime high and night-time low concentrations. To identify the underlying mobilization mechanisms, five sites along the drainage channel of Champagne Pool were sampled every 2 h during a 24 h period. Temporal variations in elemental concentrations and Sb, As, and sulfur (S) speciation were monitored in the discharging fluid. Total trace element concentrations in filtered and unfiltered samples were analyzed using ICP-MS, and Sb, As and S species were determined by IC-ICP-MS. Sulfur speciation in the drainage channel was dominated by thiosulfate and sulfide at night, while sulfate dominated during the day. The distinct diurnal changes suggest that the transformations are caused by phototrophic sulfur-oxidizing bacteria. These bacteria metabolize thiosulfate and sulfide in daylight to form sulfate and, as suggested by modeling with PhreeqC, elemental sulfur. Sulfide consumption during the day results in undersaturation of antimony sulfides, which triggers the additional release of dissolved Sb. For As, diurnal cycles were much more pronounced in speciation than in total concentrations, with di- and trithioarsenate forming at night due to excess sulfide, and monothioarsenate forming from arsenite and elemental sulfur during the day. Sulfur speciation was thus found to control Sb and As in terms of both solubility and speciation.
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The genetic signature of recent speciation in manta rays (Manta alfredi and M. birostris).
Kashiwagi, Tom; Marshall, Andrea D; Bennett, Michael B; Ovenden, Jennifer R
2012-07-01
Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondrial CO1 (574 bp) and ND5 genes (1188 bp). The assay with CO1 sequences, widely used in DNA barcoding, failed to distinguish the two species. The two species were clearly distinguishable, however, with no shared RAG1 or ND5 haplotypes. The species were reciprocally monophyletic for RAG1, but paraphyletic for ND5 sequences. Qualitative evidence and statistical inferences using the 'Isolation-with-Migration models' indicated that these results were better explained with post-divergence gene flow in the recent past rather than incomplete lineage sorting with zero gene flow since speciation. An estimate of divergence time was less than 0.5 Ma with an upper confidence limit of within 1 Ma. Recent speciation of highly mobile species in the marine environment is of great interest, as it suggests that speciation may have occurred in the absence of long-term physical barriers to gene flow. We propose that the ecologically driven forces such as habitat choice played a significant role in speciation in manta rays. Copyright © 2012 Elsevier Inc. All rights reserved.
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Zhao, Fang-Jie; Rooney, Corinne P; Zhang, Hao; McGrath, Steve P
2006-03-01
The toxicity effect concentrations (10% effective concentration [EC10] and 50% effective concentration [EC50]) of total added Cu derived from barley root elongation and tomato growth assays varied widely among 18 European soils. We investigated whether this variation could be explained by the solubility or speciation of Cu in soil solutions or the diffusive gradients in thin-films (DGT) measurement. Solubility and Cu speciation varied greatly among the soils tested. However, the EC10 and EC50 of soil solution Cu or free Cu2+ activity varied even more widely than those based on the total added Cu, indicating that solubility or soil solution speciation alone could not explain intersoil variation in Cu toxicity. Estimated EC10 and EC50 of free Cu2+ activity correlated closely and negatively with soil pH, indicating a protective effect of H+, which is consistent with the biotic ligand model concept. The DGT measurement was found to narrow the intersoil variation in EC50 considerably and to be a better predictor of plant Cu concentrations than either soil solution Cu or free Cu2+ activity. We conclude that plant bioavailability of Cu in soil depends on Cu speciation, interactions with protective ions (particularly H+), and the resupply from the solid phase, and we conclude that the DGT measurement provides a useful indicator of Cu bioavailability in soil.
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US EPA's SPECIATE 4.4 Database: Development and Uses
SPECIATE is the U.S. Environmental Protection Agency’s (EPA) repository of volatile organic gas and particulate matter (PM) speciation profiles of air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, volatile o...
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EPA’s SPECIATE 4.4 Database: Bridging Data Sources and Data Users
SPECIATE is the U.S. Environmental Protection Agency's (EPA)repository of volatile organic gas and particulate matter (PM) speciation profiles for air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, VOC, total...
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Clustering and Phase Transitions on a Neutral Landscape
NASA Astrophysics Data System (ADS)
Scott, Adam; King, Dawn; Maric, Nevena; Bahar, Sonya
2012-02-01
The problem of speciation and species aggregation on a neutral landscape, subject to random mutational fluctuations rather than selective drive, has been a focus of research since the seminal work of Kimura on genetic drift. These ideas have received increased attention due to the more recent development of a neutral ecological theory by Hubbell. De Aguiar et al. recently demonstrated, in a computational model, that speciation can occur under neutral conditions; this study bears some comparison with more mathematical studies of clustering on neutral landscapes in the context of branching and annihilating random walks. Here, we show that clustering can occur on a neutral landscape where the dimensions specify the simulated organisms' phenotypes. Unlike the De Aguiar et al. model, we simulate sympatric speciation: the organisms cluster phenotypically, but are not spatially separated. Moreover, we find that clustering occurs not only in the case of assortative mating, but also in the case of asexual fission. Clustering is not observed in a control case where organisms can mate randomly. We find that the population size and the number of clusters undergo phase-transition-like behavior as the maximum mutation size is varied.
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Invasive species and biodiversity crises: testing the link in the late devonian.
Stigall, Alycia L
2010-12-29
During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the modern biodiversity crisis.
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Bi, S P; An, S Q; Yang, M; Chen, T
2001-05-01
This paper reports an investigation of the dynamics of aluminum (Al) speciation in the forest-well waters from study site 110 of the Rhode River watershed, a representative sub-unit of Chesapeake Bay. Seasonal changes of Al speciation are evaluated by a modified MINEQL computer model using chemical equilibrium calculation. It was found that Al-F and Al-Org complexes were the dominate forms, whereas toxic forms of Al3+ and Al-OH were not significant. This indicates that Al toxicity is not very serious in the Rhode River area due to the high concentrations of fluoride and organic materials, even though sometimes pH is very low (approximately 4). Increased H+ or some other associated factors may be responsible for the decline in fish and amphibian population on the watershed.
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Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min
2014-10-01
Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus. © 2014 John Wiley & Sons Ltd.
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The evolution of conditional dispersal and reproductive isolation along environmental gradients
Payne, Joshua L.; Mazzucco, Rupert; Dieckmann, Ulf
2011-01-01
Dispersal modulates gene flow throughout a population’s spatial range. Gene flow affects adaptation at local spatial scales, and consequently impacts the evolution of reproductive isolation. A recent theoretical investigation has demonstrated that local adaptation along an environmental gradient, facilitated by the evolution of limited dispersal, can lead to parapatric speciation even in the absence of assortative mating. This and other studies assumed unconditional dispersal, so individuals start dispersing without regard to local environmental conditions. However, many species disperse conditionally; their propensity to disperse is contingent upon environmental cues, such as the degree of local crowding or the availability of suitable mates. Here, we use an individual-based model in continuous space to investigate by numerical simulation the relationship between the evolution of threshold-based conditional dispersal and parapatric speciation driven by frequency-dependent competition along environmental gradients. We find that, as with unconditional dispersal, parapatric speciation occurs under a broad range of conditions when reproduction is asexual, and under a more restricted range of conditions when reproduction is sexual. In both the asexual and sexual cases, the evolution of conditional dispersal is strongly influenced by the slope of the environmental gradient: shallow environmental gradients result in low dispersal thresholds and high dispersal distances, while steep environmental gradients result in high dispersal thresholds and low dispersal distances. The latter, however, remain higher than under unconditional dispersal, thus undermining isolation by distance, and hindering speciation in sexual populations. Consequently, the speciation of sexual populations under conditional dispersal is triggered by a steeper gradient than under unconditional dispersal. Enhancing the disruptiveness of frequency-dependent selection, more box-shaped competition kernels dramatically lower the speciation-enabling slope of the environmental gradient. PMID:21194533
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The evolution of conditional dispersal and reproductive isolation along environmental gradients.
Payne, Joshua L; Mazzucco, Rupert; Dieckmann, Ulf
2011-03-21
Dispersal modulates gene flow throughout a population's spatial range. Gene flow affects adaptation at local spatial scales, and consequently impacts the evolution of reproductive isolation. A recent theoretical investigation has demonstrated that local adaptation along an environmental gradient, facilitated by the evolution of limited dispersal, can lead to parapatric speciation even in the absence of assortative mating. This and other studies assumed unconditional dispersal, so individuals start dispersing without regard to local environmental conditions. However, many species disperse conditionally; their propensity to disperse is contingent upon environmental cues, such as the degree of local crowding or the availability of suitable mates. Here, we use an individual-based model in continuous space to investigate by numerical simulation the relationship between the evolution of threshold-based conditional dispersal and parapatric speciation driven by frequency-dependent competition along environmental gradients. We find that, as with unconditional dispersal, parapatric speciation occurs under a broad range of conditions when reproduction is asexual, and under a more restricted range of conditions when reproduction is sexual. In both the asexual and sexual cases, the evolution of conditional dispersal is strongly influenced by the slope of the environmental gradient: shallow environmental gradients result in low dispersal thresholds and high dispersal distances, while steep environmental gradients result in high dispersal thresholds and low dispersal distances. The latter, however, remain higher than under unconditional dispersal, thus undermining isolation by distance, and hindering speciation in sexual populations. Consequently, the speciation of sexual populations under conditional dispersal is triggered by a steeper gradient than under unconditional dispersal. Enhancing the disruptiveness of frequency-dependent selection, more box-shaped competition kernels dramatically lower the speciation-enabling slope of the environmental gradient. Copyright © 2010 Elsevier Ltd. All rights reserved.
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Gottscho, Andrew D.; Wood, Dustin A.; Vandergast, Amy; Lemos Espinal, Julio A.; Gatesy, John; Reeder, Tod
2017-01-01
Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of theUma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence and single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM >1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata x cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.
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Trade-offs drive resource specialization and the gradual establishment of ecotypes
2014-01-01
Background Speciation is driven by many different factors. Among those are trade-offs between different ways an organism utilizes resources, and these trade-offs can constrain the manner in which selection can optimize traits. Limited migration among allopatric populations and species interactions can also drive speciation, but here we ask if trade-offs alone are sufficient to drive speciation in the absence of other factors. Results We present a model to study the effects of trade-offs on specialization and adaptive radiation in asexual organisms based solely on competition for limiting resources, where trade-offs are stronger the greater an organism’s ability to utilize resources. In this model resources are perfectly substitutable, and fitness is derived from the consumption of these resources. The model contains no spatial parameters, and is therefore strictly sympatric. We quantify the degree of specialization by the number of ecotypes evolved and the niche breadth of the population, and observe that these are sensitive to resource influx and trade-offs. Resource influx has a strong effect on the degree of specialization, with a clear transition between minimal diversification at high influx and multiple species evolving at low resource influx. At low resource influx the degree of specialization further depends on the strength of the trade-offs, with more ecotypes evolving the stronger trade-offs are. The specialized organisms persist through negative frequency-dependent selection. In addition, by analyzing one of the evolutionary radiations in greater detail we demonstrate that a single mutation alone is not enough to establish a new ecotype, even though phylogenetic reconstruction identifies that mutation as the branching point. Instead, it takes a series of additional mutations to ensure the stable coexistence of the new ecotype in the background of the existing ones. Conclusions Trade-offs are sufficient to drive the evolution of specialization in sympatric asexual populations. Without trade-offs to restrain traits, generalists evolve and diversity decreases. The observation that several mutations are required to complete speciation, even when a single mutation creates the new species, highlights the gradual nature of speciation and the importance of phyletic evolution. PMID:24885598
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Pardo, Tania; Bes, Cleménce; Bernal, Maria Pilar; Clemente, Rafael
2016-11-01
Tailings are considered one of the most relevant sources of contamination associated with mining activities. Phytostabilization of mine spoils may need the application of the adequate combination of amendments to facilitate plant establishment and reduce their environmental impact. Two pot experiments were set up to assess the capability of 2 inorganic materials (calcium carbonate and a red mud derivate, ViroBind TM ), alone or in combination with organic amendments, for the stabilization of highly acidic trace element-contaminated mine tailings using Atriplex halimus. The effects of the treatments on tailings and porewater physico-chemical properties and trace-element accumulation by the plants, as well as the processes governing trace elements speciation and solubility in soil solution and their bioavailability were modeled. The application of the amendments increased tailings pH and decreased (>99%) trace elements solubility in porewater, but also changed the speciation of soluble Cd, Cu, and Pb. All the treatments made A. halimus growth in the tailings possible; organic amendments increased plant biomass and nutritional status, and reduced trace-element accumulation in the plants. Tailings amendments modified trace-element speciation in porewater (favoring the formation of chlorides and/or organo-metallic forms) and their solubility and plant uptake, which were found to be mainly governed by tailing/porewater pH, electrical conductivity, and organic carbon content, as well as soluble/available trace-element concentrations. Environ Toxicol Chem 2016;35:2874-2884. © 2016 SETAC. © 2016 SETAC.
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Theoretical size distribution of fossil taxa: analysis of a null model
Reed, William J; Hughes, Barry D
2007-01-01
Background This article deals with the theoretical size distribution (of number of sub-taxa) of a fossil taxon arising from a simple null model of macroevolution. Model New species arise through speciations occurring independently and at random at a fixed probability rate, while extinctions either occur independently and at random (background extinctions) or cataclysmically. In addition new genera are assumed to arise through speciations of a very radical nature, again assumed to occur independently and at random at a fixed probability rate. Conclusion The size distributions of the pioneering genus (following a cataclysm) and of derived genera are determined. Also the distribution of the number of genera is considered along with a comparison of the probability of a monospecific genus with that of a monogeneric family. PMID:17376249
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Toward a theory of topopatric speciation: The role of genetic assortative mating
NASA Astrophysics Data System (ADS)
Schneider, David M.; do Carmo, Eduardo; Martins, Ayana B.; de Aguiar, Marcus A. M.
2014-09-01
We discuss a minimalist model of assortative mating for sexually reproducing haploid individuals with two biallelic loci. Assortativeness is introduced in the model by preventing mating between individuals whose alleles differ at both loci. Using methods of dynamical systems and population genetics we provide a full description of the evolution of the system for the case of very large populations. We derive the equations governing the evolution of haplotype frequencies and study the equilibrium solutions, stability, and speed of convergence to equilibrium. We find a constant of motion which allows us to introduce a geometrical construction that makes it straightforward to predict the fate of initial conditions. Finally, we discuss the consequences of this class of assortative mating models, including their possible extensions and implications for sympatric and topopatric speciation.
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Arsenic Speciation in Groundwater: Role of Thioanions
The behavior of arsenic in groundwater environments is fundamentally linked to its speciation. Understanding arsenic speciation is important because chemical speciation impacts reactivity, bioavailability, toxicity, and transport and fate processes. In aerobic environments arsen...
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Uranium(VI) adsorption to ferrihydrite: Application of a surface complexation model
Waite, T.D.; Davis, J.A.; Payne, T.E.; Waychunas, G.A.; Xu, N.
1994-01-01
A study of U(VI) adsorption by ferrihydrite was conducted over a wide range of U(VI) concentrations, pH, and at two partial pressures of carbon dioxide. A two-site (strong- and weak-affinity sites, FesOH and FewOH, respectively) surface complexation model was able to describe the experimental data well over a wide range of conditions, with only one species formed with each site type: an inner-sphere, mononuclear, bidentate complex of the type (FeO2)UO2. The existence of such a surface species was supported by results of uranium EXAFS spectroscopy performed on two samples with U(VI) adsorption density in the upper range observed in this study (10 and 18% occupancy of total surface sites). Adsorption data in the alkaline pH range suggested the existence of a second surface species, modeled as a ternary surface complex with UO2CO30 binding to a bidentate surface site. Previous surface complexation models for U(VI) adsorption have proposed surface species that are identical to the predominant aqueous species, e.g., multinuclear hydrolysis complexes or several U(VI)-carbonate complexes. The results demonstrate that the speciation of adsorbed U(VI) may be constrained by the coordination environment at the surface, giving rise to surface speciation for U(VI) that is significantly less complex than aqueous speciation.
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Beryllium chemical speciation in elemental human biological fluids.
Sutton, Mark; Burastero, Stephen R
2003-09-01
The understanding of beryllium chemistry in human body fluids is important for understanding the prevention and treatment of chronic beryllium disease. Thermodynamic modeling has traditionally been used to study environmental contaminant migration and rarely in the examination of metal (particularly beryllium) toxicology. In this work, a chemical thermodynamic speciation code (MINTEQA2) has been used to model and understand the chemistry of beryllium in simulated human biological fluids such as intracellular, interstitial, and plasma fluids, a number of airway surface fluids for patients with lung conditions, saliva, sweat, urine, bile, gastric juice, and pancreatic fluid. The results show that predicted beryllium solubility and speciation vary markedly between each simulated biological fluid. Formation of beryllium hydroxide and/or phosphate was observed in most of the modeled fluids, and results support the postulation that beryllium absorption in the gastrointestinal tract may be limited by the formation of beryllium phosphate solids. It is also postulated that beryllium is potentially 13% less soluble in the airway surface fluid of a patient with asthma when compared to a "normal" case. The results of this work, supported by experimental validation, can aid in the understanding of beryllium toxicology. Our results can potentially be applied to assessing the feasibility of biological monitoring or chelation treatment of beryllium body burden.
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Siebers, Nina; Kruse, Jens; Eckhardt, Kai-Uwe; Hu, Yongfeng; Leinweber, Peter
2012-07-01
Cadmium (Cd) has a high toxicity and resolving its speciation in soil is challenging but essential for estimating the environmental risk. In this study partial least-square (PLS) regression was tested for its capability to deconvolute Cd L(3)-edge X-ray absorption near-edge structure (XANES) spectra of multi-compound mixtures. For this, a library of Cd reference compound spectra and a spectrum of a soil sample were acquired. A good coefficient of determination (R(2)) of Cd compounds in mixtures was obtained for the PLS model using binary and ternary mixtures of various Cd reference compounds proving the validity of this approach. In order to describe complex systems like soil, multi-compound mixtures of a variety of Cd compounds must be included in the PLS model. The obtained PLS regression model was then applied to a highly Cd-contaminated soil revealing Cd(3)(PO(4))(2) (36.1%), Cd(NO(3))(2)·4H(2)O (24.5%), Cd(OH)(2) (21.7%), CdCO(3) (17.1%) and CdCl(2) (0.4%). These preliminary results proved that PLS regression is a promising approach for a direct determination of Cd speciation in the solid phase of a soil sample.
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Modeling the binding of fulvic acid by goethite: the speciation of adsorbed FA molecules
NASA Astrophysics Data System (ADS)
Filius, Jeroen D.; Meeussen, Johannes C. L.; Lumsdon, David G.; Hiemstra, Tjisse; van Riemsdijk, Willem H.
2003-04-01
Under natural conditions, the adsorption of ions at the solid-water interface may be strongly influenced by the adsorption of organic matter. In this paper, we describe the adsorption of fulvic acid (FA) by metal(hydr)oxide surfaces with a heterogeneous surface complexation model, the ligand and charge distribution (LCD) model. The model is a self-consistent combination of the nonideal competitive adsorption (NICA) equation and the CD-MUSIC model. The LCD model can describe simultaneously the concentration, pH, and salt dependency of the adsorption with a minimum of only three adjustable parameters. Furthermore, the model predicts the coadsorption of protons accurately for an extended range of conditions. Surface speciation calculations show that almost all hydroxyl groups of the adsorbed FA molecules are involved in outer sphere complexation reactions. The carboxylic groups of the adsorbed FA molecule form inner and outer sphere complexes. Furthermore, part of the carboxylate groups remain noncoordinated and deprotonated.
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Hardy, Nate B.; Otto, Sarah P.
2014-01-01
Evolutionary biologists have often assumed that ecological generalism comes at the expense of less intense exploitation of specific resources and that this trade-off will promote the evolution of ecologically specialized daughter species. Using a phylogenetic comparative approach with butterflies as a model system, we test hypotheses that incorporate changes in niche breadth and location into explanations of the taxonomic diversification of insect herbivores. Specifically, we compare the oscillation hypothesis, where speciation is driven by host-plant generalists giving rise to specialist daughter species, to the musical chairs hypothesis, where speciation is driven by host-plant switching, without changes in niche breadth. Contrary to the predictions of the oscillation hypothesis, we recover a negative relationship between host-plant breadth and diversification rate and find that changes in host breadth are seldom coupled to speciation events. By contrast, we present evidence for a positive relationship between rates of host switching and butterfly diversification, consonant with the musical chairs hypothesis. These results suggest that the costs of trophic generalism in plant-feeding insects may have been overvalued and that transitions from generalists to ecological specialists may not be an important driver of speciation in general. PMID:25274368
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Evolution, biogeography, and systematics of Puriana: evolution and speciation in Ostracoda, III.
Cronin, T. M.
1987-01-01
Three types of geographic isolation - land barriers, deep water barriers, and climatic barriers - resulted in three distinct evolutionary responses in Neogene and Quaternary species of the epineritic ostracode genus Puriana. Through systematic, paleobiogeographic, and morphologic study of several hundred fossil and Recent populations from the eastern Pacific, western Atlantic, Gulf of Mexico, and the Caribbean, the phylogeny of the genus and the geography of speciation events were determined. Isolation of large populations by the Isthumus of Panama during the Pliocene did not lead to lineage splitting in species known to have existed before the Isthmus formed. Conversely, the establishment of small isolated populations on Caribbean islands by passive dispersal mechanisms frequently led to the evolution of new species or subspecies. Climatic changes along the southeastern United States during the Pliocene also catalyzed possible parapatric speciation as populations that immigrated to the northeastern periphery of the genus' range split to form new species. The results provide evidence that evolutionary models describing the influence of abiotic events on patterns of evolution and speciation can be tested using properly selected tectonic and climatic events and fossil groups amenable to species-level analysis. Two new species, P. bajaensis and P. paikensis, are described. -Author
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NASA Astrophysics Data System (ADS)
Meng, X.; Liu, Y.; Diner, D. J.; Garay, M. J.
2016-12-01
Ambient fine particle (PM2.5) has been positively associated with increased mortality and morbidity worldwide. Recent studies highlight the characteristics and differential toxicity of PM2.5 chemical components, which are important for identifying sources, developing targeted particulate matter (PM) control strategies, and protecting public health. Modelling with satellite retrieved data has been proved as the most cost-effective way to estimate ground PM2.5 levels; however, limited studies have predict PM2.5 chemical components with this method. In this study, the experimental MISR 4.4 km aerosol retrievals were used to predict ground-level particle sulfate, nitrite, organic carbon and element carbon concentrations in 16 counties of southern California. The PM2.5 chemical components concentrations were obtained from the National Chemical Speciation Network (CSN) and the Interagency Monitoring of Protected Visual Environments (IMPROVE) network. A generalized additive model (GAM) was developed based on 16-years data (2000-2015) by combining the MISR aerosol retrievals, meteorological variables and geographical indicators together. Model performance was assessed by model fitted R2 and root-mean-square error (RMSE) and 10-fold cross validation. Spatial patterns of sulfate, nitrate, OC and EC concentrations were also examined with 2-D prediction surfaces. This is the first attempt to develop high-resolution spatial models to predict PM2.5 chemical component concentrations with MISR retrieved aerosol properties, which will provide valuable population exposure estimates for future studies on the characteristics and differential toxicity of PM2.5 speciation.
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Nested-grid simulation of mercury over North America
NASA Astrophysics Data System (ADS)
Zhang, Y.; Jaeglé, L.; van Donkelaar, A.; Martin, R. V.; Holmes, C. D.; Amos, H. M.; Wang, Q.; Talbot, R.; Artz, R.; Brooks, S.; Luke, W.; Holsen, T. M.; Felton, D.; Miller, E. K.; Perry, K. D.; Schmeltz, D.; Steffen, A.; Tordon, R.; Weiss-Penzias, P.; Zsolway, R.
2012-01-01
We have developed a new high-resolution (1/2° latitude by 2/3° longitude) nested-grid mercury (Hg) simulation over North America employing the GEOS-Chem global chemical transport model. Emissions, chemistry, deposition, and meteorology are self-consistent between the global and nested domains. Compared to the global model (4° latitude by 5° longitude), the nested model shows improved skill at capturing the high spatial and temporal variability of Hg wet deposition over North America observed by the Mercury Deposition Network (MDN) in 2008-2009. The nested simulation resolves features such as land/ocean contrast and higher deposition due to orographic precipitation, and predicts more efficient convective rain scavenging of Hg over the southeast United States. However, the nested model overestimates Hg wet deposition over the Ohio River Valley region (ORV) by 27%. We modify anthropogenic emission speciation profiles in the US EPA National Emission Inventory (NEI) to account for the rapid in-plume reduction of reactive to elemental Hg (IPR simulation). This leads to a decrease in the model bias to +3% over the ORV region. Over the contiguous US, the correlation coefficient (r) between MDN observations and our IPR simulation increases from 0.63 to 0.78. The IPR nested simulation generally reproduces the seasonal cycle in surface concentrations of speciated Hg from the Atmospheric Mercury Network (AMNet) and Canadian Atmospheric Mercury Network (CAMNet). In the IPR simulation, annual mean reactive gaseous and particulate-bound Hg are within 80% and 10% of observations, respectively. In contrast, the simulation with unmodified anthropogenic Hg speciation profiles overestimates these observations by factors of 2 to 4. The nested model shows improved skill at capturing the horizontal variability of Hg observed over California during the ARCTAS aircraft campaign. We find that North American anthropogenic emissions account for 10-22% of Hg wet deposition flux over the US, depending on the anthropogenic emissions speciation profile assumed. The percent contribution can be as high as 60% near large point emission sources in ORV. The contribution for the dry deposition is 13-20%.
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Wang, Ning; Liang, Bin; Wang, Jichao; Yeh, Chia-Fen; Liu, Yang; Liu, Yanlin; Liang, Wei; Yao, Cheng-Te; Li, Shou-Hsien
2016-09-01
Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process. Copyright © 2016 Elsevier Inc. All rights reserved.
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MINTEQA2 is a equilibrium speciation model that can be used to calculate the equilibrium composition of dilute aqueous solutions in the laboratory or in natural aqueous systems. The model is useful for calculating the equilibrium mass distribution among dissolved species, adsorb...
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Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Groussin, Mathieu; Mazel, Florent; Sanders, Jon G.; Smillie, Chris S.; Lavergne, Sébastien; Thuiller, Wilfried; Alm, Eric J.
2017-01-01
Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution. PMID:28230052
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Convergent and divergent evolution in carnivorous pitcher plant traps.
Thorogood, Chris J; Bauer, Ulrike; Hiscock, Simon J
2018-02-01
Contents Summary 1035 I. Introduction 1035 II. Evolution of the pitcher 1036 III. Convergent evolution 1036 IV. Divergent evolution 1038 V. Adaptive radiation and speciation 1040 VI. Conclusions and perspectives 1040 Acknowledgements 1040 References 1040 SUMMARY: The pitcher trap is a striking example of convergent evolution across unrelated carnivorous plant lineages. Convergent traits that have evolved across pitcher plant lineages are essential for trap function, suggesting that key selective pressures are in action. Recent studies have also revealed patterns of divergent evolution in functional pitcher morphology within genera. Adaptations to differences in local prey assemblages may drive such divergence and, ultimately, speciation. Here, we review recent research on convergent and divergent evolution in pitcher plant traps, with a focus on the genus Nepenthes, which we propose as a new model for research into adaptive radiation and speciation. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.
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Energy gradients and the geographic distribution of local ant diversity.
Kaspari, Michael; Ward, Philip S; Yuan, May
2004-08-01
Geographical diversity gradients, even among local communities, can ultimately arise from geographical differences in speciation and extinction rates. We evaluated three models--energy-speciation, energy-abundance, and area--that predict how geographic trends in net diversification rates generate trends in diversity. We sampled 96 litter ant communities from four provinces: Australia, Madagascar, North America, and South America. The energy-speciation hypothesis best predicted ant species richness by accurately predicting the slope of the temperature diversity curve, and accounting for most of the variation in diversity. The communities showed a strong latitudinal gradient in species richness as well as inter-province differences in diversity. The former vanished in the temperature-diversity residuals, suggesting that the latitudinal gradient arises primarily from higher diversification rates in the tropics. However, inter-province differences in diversity persisted in those residuals--South American communities remained more diverse than those in North America and Australia even after the effects of temperature were removed.
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Vink, J P M; Meeussen, J C L
2007-08-01
The chemical speciation model BIOCHEM was extended with ecotoxicological transfer functions for uptake of metals (As, Cd, Cu, Ni, Pb, and Zn) by plants and soil invertebrates. It was coupled to the object-oriented framework ORCHESTRA to achieve a flexible and dynamic decision support system (DSS) to analyse natural or anthropogenic changes that occur in river systems. The DSS uses the chemical characteristics of soils and sediments as input, and calculates speciation and subsequent uptake by biota at various scenarios. Biotic transfer functions were field-validated, and actual hydrological conditions were derived from long-term monitoring data. The DSS was tested for several scenarios that occur in the Meuse catchment areas, such as flooding and sedimentation of riverine sediments on flood plains. Risks are expressed in terms of changes in chemical mobility, and uptake by flood plain key species (flora and fauna).
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Optimisation of the storage of natural freshwaters before organotin speciation.
Bancon-Montigny, C; Lespes, G; Potin-Gautier, M
2001-01-01
The speciation of organotin compounds is essential due to the species-dependent toxicity, especially in natural waters. Precautions have to be taken during sampling and storage of waters in order to prevent degradations and losses. Experimental design methodology has been used to study the conditions of stability of organotins after water sampling in rivers. The modelling of results allows the determination of optimal conditions of preservation. After acidification at pH = 4 with nitric acid, the storage in polyethylene containers at 4 degrees C in the dark is suitable to preserve the most degradable trisubstituted (butyl- and phenyl-) species over 1 month. These conditions of sampling and storage are applied to two different freshwaters. The rate of species decomposition appears to be only dependent on the water nature, whatever the organotin concentrations in the sample. Speciation could be so preserved between 1 and 3 months.
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Borrok, D.; Turner, B.F.; Fein, J.B.
2005-01-01
Adsorption onto bacterial cell walls can significantly affect the speciation and mobility of aqueous metal cations in many geologic settings. However, a unified thermodynamic framework for describing bacterial adsorption reactions does not exist. This problem originates from the numerous approaches that have been chosen for modeling bacterial surface protonation reactions. In this study, we compile all currently available potentiometric titration datasets for individual bacterial species, bacterial consortia, and bacterial cell wall components. Using a consistent, four discrete site, non-electrostatic surface complexation model, we determine total functional group site densities for all suitable datasets, and present an averaged set of 'universal' thermodynamic proton binding and site density parameters for modeling bacterial adsorption reactions in geologic systems. Modeling results demonstrate that the total concentrations of proton-active functional group sites for the 36 bacterial species and consortia tested are remarkably similar, averaging 3.2 ?? 1.0 (1??) ?? 10-4 moles/wet gram. Examination of the uncertainties involved in the development of proton-binding modeling parameters suggests that ignoring factors such as bacterial species, ionic strength, temperature, and growth conditions introduces relatively small error compared to the unavoidable uncertainty associated with the determination of cell abundances in realistic geologic systems. Hence, we propose that reasonable estimates of the extent of bacterial cell wall deprotonation can be made using averaged thermodynamic modeling parameters from all of the experiments that are considered in this study, regardless of bacterial species used, ionic strength, temperature, or growth condition of the experiment. The average site densities for the four discrete sites are 1.1 ?? 0.7 ?? 10-4, 9.1 ?? 3.8 ?? 10-5, 5.3 ?? 2.1 ?? 10-5, and 6.6 ?? 3.0 ?? 10-5 moles/wet gram bacteria for the sites with pKa values of 3.1, 4.7, 6.6, and 9.0, respectively. It is our hope that this thermodynamic framework for modeling bacteria-proton binding reactions will also provide the basis for the development of an internally consistent set of bacteria-metal binding constants. 'Universal' constants for bacteria-metal binding reactions can then be used in conjunction with equilibrium constants for other important metal adsorption and complexation reactions to calculate the overall distribution of metals in realistic geologic systems.
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EPAs SPECIATE 4.4 Database: Development and Uses
SPECIATE is the U.S. Environmental Protection Agency’s (EPA) repository of source category-specific particulate matter (PM), volatile organic gas, and other gas speciation profiles of air pollutant emissions. Abt Associates, Inc. developed SPECIATE 4.4 through a collaborat...
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SPECIATE Version 4.4 Database Development Documentation
SPECIATE is the U.S. Environmental Protection Agency’s (EPA) repository of volatile organic gas and particulate matter (PM) speciation profiles of air pollution sources. Some of the many uses of these source profiles include: (1) creating speciated emissions inventories for regi...
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SPECIATE - EPA'S DATABASE OF SPECIATED EMISSION PROFILES
SPECIATE is the U.S. Environmental Protection Agency's (EPA) repository of total organic compound (TOC) and particulate matter (PM) speciation profiles for emissions from air pollution sources. The data base has recently been updated and an associated report has recently been re...
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The importance of trace element speciation in biomedical science.
Templeton, Douglas M
2003-04-01
According to IUPAC terminology, trace element speciation reflects differences in chemical composition at multiple levels from nuclear and electronic structure to macromolecular complexation. In the medical sciences, all levels of composition are important in various circumstances, and each can affect the bioavailability, distribution, physiological function, toxicity, diagnostic utility, and therapeutic potential of an element. Here we discuss, with specific examples, three biological principles in the intimate relation between speciation and biological behavior: i) the kinetics of interconversion of species determines distribution within the organism, ii) speciation governs transport across various biological barriers, and iii) speciation can limit potentially undesirable interactions between physiologically essential elements. We will also describe differences in the speciation of iron in states of iron overload, to illustrate how speciation analysis can provide insight into cellular processes in human disease.
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Theoretical size distribution of fossil taxa: analysis of a null model.
Reed, William J; Hughes, Barry D
2007-03-22
This article deals with the theoretical size distribution (of number of sub-taxa) of a fossil taxon arising from a simple null model of macroevolution. New species arise through speciations occurring independently and at random at a fixed probability rate, while extinctions either occur independently and at random (background extinctions) or cataclysmically. In addition new genera are assumed to arise through speciations of a very radical nature, again assumed to occur independently and at random at a fixed probability rate. The size distributions of the pioneering genus (following a cataclysm) and of derived genera are determined. Also the distribution of the number of genera is considered along with a comparison of the probability of a monospecific genus with that of a monogeneric family.
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Web-phreeq: a WWW instructional tool for modeling the distribution of chemical species in water
NASA Astrophysics Data System (ADS)
Saini-Eidukat, Bernhardt; Yahin, Andrew
1999-05-01
A WWW-based tool, WEB-PHREEQ, was developed for classroom teaching and for routine calculation of low temperature aqueous speciation. Accessible with any computer that has an internet-connected forms-capable WWW-browser, WEB-PHREEQ provides user interface and other support for modeling, creates a properly formatted input file, passes it to the public domain program PHREEQC and returns the output to the WWW browser. Users can calculate the equilibrium speciation of a solution over a range of temperatures or can react solid minerals or gases with a particular water and examine the resulting chemistry. WEB-PHREEQ is one of a number of interactive distributed-computing programs available on the WWW that are of interest to geoscientists.
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NASA Astrophysics Data System (ADS)
Xing, J.; Mathur, R.; Pleim, J.; Hogrefe, C.; Gan, C.-M.; Wong, D. C.; Wei, C.; Gilliam, R.; Pouliot, G.
2015-03-01
Trends in air quality across the Northern Hemisphere over a 21-year period (1990-2010) were simulated using the Community Multiscale Air Quality (CMAQ) multiscale chemical transport model driven by meteorology from Weather Research and Forecasting (WRF) simulations and internally consistent historical emission inventories obtained from EDGAR. Thorough comparison with several ground observation networks mostly over Europe and North America was conducted to evaluate the model performance as well as the ability of CMAQ to reproduce the observed trends in air quality over the past 2 decades in three regions: eastern China, the continental United States and Europe. The model successfully reproduced the observed decreasing trends in SO2, NO2, 8 h O3 maxima, SO42- and elemental carbon (EC) in the US and Europe. However, the model fails to reproduce the decreasing trends in NO3- in the US, potentially pointing to uncertainties of NH3 emissions. The model failed to capture the 6-year trends of SO2 and NO2 in CN-API (China - Air Pollution Index) from 2005 to 2010, but reproduced the observed pattern of O3 trends shown in three World Data Centre for Greenhouse Gases (WDCGG) sites over eastern Asia. Due to the coarse spatial resolution employed in these calculations, predicted SO2 and NO2 concentrations are underestimated relative to all urban networks, i.e., US-AQS (US - Air Quality System; normalized mean bias (NMB) = -38% and -48%), EU-AIRBASE (European Air quality data Base; NMB = -18 and -54%) and CN-API (NMB = -36 and -68%). Conversely, at the rural network EU-EMEP (European Monitoring and Evaluation Programme), SO2 is overestimated (NMB from 4 to 150%) while NO2 is simulated well (NMB within ±15%) in all seasons. Correlations between simulated and observed O3 wintertime daily 8 h maxima (DM8) are poor compared to other seasons for all networks. Better correlation between simulated and observed SO42- was found compared to that for SO2. Underestimation of summer SO42- in the US may be associated with the uncertainty in precipitation and associated wet scavenging representation in the model. The model exhibits worse performance for NO3- predictions, particularly in summer, due to high uncertainties in the gas/particle partitioning of NO3- as well as seasonal variations of NH3 emissions. There are high correlations (R > 0.5) between observed and simulated EC, although the model underestimates the EC concentration by 65% due to the coarse grid resolution as well as uncertainties in the PM speciation profile associated with EC emissions. The almost linear response seen in the trajectory of modeled O3 changes in eastern China over the past 2 decades suggests that control strategies that focus on combined control of NOx and volatile organic compound (VOC) emissions with a ratio of 0.46 may provide the most effective means for O3 reductions for the region devoid of nonlinear response potentially associated with NOx or VOC limitation resulting from alternate strategies. The response of O3 is more sensitive to changes in NOx emissions in the eastern US because the relative abundance of biogenic VOC emissions tends to reduce the effectiveness of VOC controls. Increasing NH3 levels offset the relative effectiveness of NOx controls in reducing the relative fraction of aerosol NO3- formed from declining NOx emissions in the eastern US, while the control effectiveness was assured by the simultaneous control of NH3 emission in Europe.
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NASA Astrophysics Data System (ADS)
Meng, Xia; Garay, Michael J.; Diner, David J.; Kalashnikova, Olga V.; Xu, Jin; Liu, Yang
2018-05-01
Research efforts to better characterize the differential toxicity of PM2.5 (particles with aerodynamic diameters less than or equal to 2.5 μm) speciation are often hindered by the sparse or non-existent coverage of ground monitors. The Multi-angle Imaging SpectroRadiometer (MISR) aboard NASA's Terra satellite is one of few satellite aerosol sensors providing information of aerosol shape, size and extinction globally for a long and continuous period that can be used to estimate PM2.5 speciation concentrations since year 2000. Currently, MISR only provides a 17.6 km product for its entire mission with global coverage every 9 days, a bit too coarse for air pollution health effects research and to capture local spatial variability of PM2.5 speciation. In this study, generalized additive models (GAMs) were developed using MISR prototype 4.4 km-resolution aerosol data with meteorological variables and geographical indicators, to predict ground-level concentrations of PM2.5 sulfate, nitrate, organic carbon (OC) and elemental carbon (EC) in Southern California between 2001 and 2015 at the daily level. The GAMs are able to explain 66%, 62%, 55% and 58% of the daily variability in PM2.5 sulfate, nitrate, OC and EC concentrations during the whole study period, respectively. Predicted concentrations capture large regional patterns as well as fine gradients of the four PM2.5 species in urban areas of Los Angeles and other counties, as well as in the Central Valley. This study is the first attempt to use MISR prototype 4.4 km-resolution AOD (aerosol optical depth) components data to predict PM2.5 sulfate, nitrate, OC and EC concentrations at the sub-regional scale. In spite of its low temporal sampling frequency, our analysis suggests that the MISR 4.4 km fractional AODs provide a promising way to capture the spatial hotspots and long-term temporal trends of PM2.5 speciation, understand the effectiveness of air quality controls, and allow our estimated PM2.5 speciation data to be linked with common spatial units such as census tract or zip code in epidemiological studies. This modeling strategy needs to be validated in other regions when more MISR 4.4 km data becoming available in the future.
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Holman, Eric W
2017-11-01
It is known that phylogenetic trees are more imbalanced than expected from a birth-death model with constant rates of speciation and extinction, and also that imbalance can be better fit by allowing the rate of speciation to decrease as the age of the parent species increases. If imbalance is measured in more detail, at nodes within trees as a function of the number of species descended from the nodes, age-dependent models predict levels of imbalance comparable to real trees for small numbers of descendent species, but predicted imbalance approaches an asymptote not found in real trees as the number of descendent species becomes large. Age-dependence must therefore be complemented by another process such as inheritance of different rates along different lineages, which is known to predict insufficient imbalance at nodes with few descendent species, but can predict increasing imbalance with increasing numbers of descendent species. [Crump-Mode-Jagers process; diversification; macroevolution; taxon sampling; tree of life.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Jiang, Ping; Liu, Guangliang; Cui, Wenbin; Cai, Yong
2018-06-01
The geochemical model PHREEQC, abbreviated from PH (pH), RE (redox), EQ (equilibrium), and C (program written in C), was employed on the datasets generated by the USEPA Everglades Regional Environmental Monitoring and Assessment Program (R-EMAP) to determine the speciation distribution of inorganic mercury (iHg) in Everglades water and to explore the implications of iHg speciation on mercury cycling. The results suggest that sulfide and DOM were the key factors that regulate inorganic Hg speciation in the Everglades. When sulfide was present at measurable concentrations (>0.02 mg/L), Hg-S complexes dominated iHg species, occurring in the forms of HgS 2 2- , HgHS 2 - , and Hg(HS) 2 that were affected by a variety of environmental factors. When sulfide was assumed nonexistent, Hg-DOM complexes occurred as the predominant Hg species, accounting for almost 100% of iHg species. However, when sulfide was presumably present at a very low, environmentally relevant concentration (3.2 × 10 -7 mg/L), both Hg-DOM and Hg-S complexes were present as the major iHg species. These Hg-S species and Hg-DOM complex could be related to methylmercury (MeHg) in environmental matrices such floc, periphyton, and soil, and the correlations are dependent upon different circumstances (e.g., sulfide concentrations). The implications of the distribution of iHg species on MeHg production and fate in the Everglades were discussed. Copyright © 2018 Elsevier B.V. All rights reserved.
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DeChaine, Eric G; Wendling, Barry M; Forester, Brenna R
2014-01-01
Many arctic-alpine plant genera have undergone speciation during the Quaternary. The bases for these radiations have been ascribed to geographic isolation, abiotic and biotic differences between populations, and/or hybridization and polyploidization. The Cordilleran Campanula L. (Campanulaceae Juss.), a monophyletic clade of mostly endemic arctic-alpine taxa from western North America, experienced a recent and rapid radiation. We set out to unravel the factors that likely influenced speciation in this group. To do so, we integrated environmental, genetic, and morphological datasets, tested biogeographic hypotheses, and analyzed the potential consequences of the various factors on the evolutionary history of the clade. We created paleodistribution models to identify potential Pleistocene refugia for the clade and estimated niche space for individual taxa using geographic and climatic data. Using 11 nuclear loci, we reconstructed a species tree and tested biogeographic hypotheses derived from the paleodistribution models. Finally, we tested 28 morphological characters, including floral, vegetative, and seed characteristics, for their capacity to differentiate taxa. Our results show that the combined effect of Quaternary climatic variation, isolation among differing environments in the mountains in western North America, and biotic factors influencing floral morphology contributed to speciation in this group during the mid-Pleistocene. Furthermore, our biogeographic analyses uncovered asynchronous consequences of interglacial and glacial periods for the timing of refugial isolation within the southern and northwestern mountains, respectively. These findings have broad implications for understanding the processes promoting speciation in arctic-alpine plants and the rise of numerous endemic taxa across the region. PMID:25505522
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GEOCHEMICAL MODELING OF ARSENIC SPECIATION AND MOBILIZATION: IMPLICATIONS FOR BIOREMEDIATION
Geochemical modeling techniques were used to examine the biogeochemical linkages between Fe, S, and As in shallow alluvial aquifers. We modeled: 1) the adsorption and desorption of As on the surface of hydrous ferric oxides (HFO’s) in stream beds under aerobic conditions; 2) red...
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Extraordinarily rapid speciation in a marine fish
Momigliano, Paolo; Jokinen, Henri; Fraimout, Antoine; Florin, Ann-Britt; Norkko, Alf; Merilä, Juha
2017-01-01
Divergent selection may initiate ecological speciation extremely rapidly. How often and at what pace ecological speciation proceeds to yield strong reproductive isolation is more uncertain. Here, we document a case of extraordinarily rapid speciation associated with ecological selection in the postglacial Baltic Sea. European flounders (Platichthys flesus) in the Baltic exhibit two contrasting reproductive behaviors: pelagic and demersal spawning. Demersal spawning enables flounders to thrive in the low salinity of the Northern Baltic, where eggs cannot achieve neutral buoyancy. We show that demersal and pelagic flounders are a species pair arising from a recent event of speciation. Despite having a parapatric distribution with extensive overlap, the two species are reciprocally monophyletic and show strongly bimodal genotypic clustering and no evidence of contemporary migration, suggesting strong reproductive isolation. Divergence across the genome is weak but shows strong signatures of selection, a pattern suggestive of a recent ecological speciation event. We propose that spawning behavior in Baltic flounders is the trait under ecologically based selection causing reproductive isolation, directly implicating a process of ecological speciation. We evaluated different possible evolutionary scenarios under the approximate Bayesian computation framework and estimate that the speciation process started in allopatry ∼2,400 generations ago, following the colonization of the Baltic by the demersal lineage. This is faster than most known cases of ecological speciation and represents the most rapid event of speciation ever reported for any marine vertebrate. PMID:28533412
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Condamine, Fabien L; Rolland, Jonathan; Höhna, Sebastian; Sperling, Felix A H; Sanmartín, Isabel
2018-02-09
In macroevolution, the Red Queen (RQ) model posits that biodiversity dynamics depend mainly on species-intrinsic biotic factors such as interactions among species or life-history traits, while the Court Jester (CJ) model states that extrinsic environmental abiotic factors have a stronger role. Until recently, a lack of relevant methodological approaches has prevented the unraveling of contributions from these two types of factors to the evolutionary history of a lineage. Here we take advantage of the rapid development of new macroevolution models that tie diversification rates to changes in paleoenvironmental (extrinsic) and/or biotic (intrinsic) factors. We inferred a robust and fully-sampled species-level phylogeny, as well as divergence times and ancestral geographic ranges, and related these to the radiation of Apollo butterflies (Parnassiinae) using both extant (molecular) and extinct (fossil/morphological) evidence. We tested whether their diversification dynamics are better explained by a RQ or CJ hypothesis, by assessing whether speciation and extinction were mediated by diversity-dependence (niche filling) and clade-dependent host-plant association (RQ) or by large-scale continuous changes in extrinsic factors such as climate or geology (CJ). For the RQ hypothesis, we found significant differences in speciation rates associated with different host-plants but detected no sign of diversity-dependence. For CJ, the role of Himalayan-Tibetan building was substantial for biogeography but not a driver of high speciation, while positive dependence between warm climate and speciation/extinction was supported by continuously varying maximum-likelihood models. We find that rather than a single factor, the joint effect of multiple factors (biogeography, species traits, environmental drivers, and mass extinction) is responsible for current diversity patterns, and that the same factor might act differently across clades, emphasizing the notion of opportunity. This study confirms the importance of the confluence of several factors rather than single explanations in modeling diversification within lineages. © The Author(s) 2018. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Nitrogen speciation and trends, and prediction of denitrification extent, in shallow US groundwater
Hinkle, Stephen R.; Tesoriero, Anthony J.
2014-01-01
Uncertainties surrounding nitrogen cycling complicate assessments of the environmental effects of nitrogen use and our understanding of the global carbon–nitrogen cycle. In this paper, we synthesize data from 877 ambient-monitoring wells across the US to frame broad patterns of nitrogen speciation and trends. At these sites, groundwater frequently contains substantial co-occurring NO3− and XSN2 (N2 from denitrification), reflecting active/ongoing denitrification and/or a mixture of undenitrified and denitrified groundwater. NO3− and NH4+ essentially do not co-occur, indicating that the dominant source of NH4+ at these sites likely is not dissimilatory reduction of NO3− to NH4+. Positive correlations of NH4+ with apparent age, CH4, dissolved organic carbon, and indicators of reduced conditions are consistent with NH4+ mobilization from degradation of aquifer organic matter and contraindicate an anthropogenic source of NH4+ for most sites. Glacial aquifers and eastern sand and gravel aquifers generally have lower proportions of NO3− and greater proportions of XSN2 than do fractured rock and karst aquifers and western sand and gravel aquifers. NO3− dominates in the youngest groundwater, but XSN2 increases as residence time increases. Temporal patterns of nitrogen speciation and concentration reflect (1) changing NO3− loads over time, (2) groundwater residence-time controls on NH4+ mobilization from solid phases, and (3) groundwater residence-time controls on denitrification. A simple classification tree using readily available variables (a national coverage of soil water depth, generalized geology) or variables reasonably estimated in many aquifers (residence time) identifies categorical denitrification extent (<10%, 10–50%, and >50%) with 79% accuracy in an independent testing set, demonstrating a predictive application based on the interconnected effects of redox, geology, and residence time.
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The Development of Molybdenum Speciation as a Paleoredox Tool
NASA Astrophysics Data System (ADS)
Rodley, J.; Peacock, C.; Mosselmans, J. F. W.; Poulton, S.
2017-12-01
The redox state of the oceans has changed throughout geological time and an understanding of these changes is essential to elucidate links between ocean chemistry, climate and life. Due to its abundance in seawater and redox-sensitive nature, molybdenum has enormous potential as a paleoredox proxy. Although a significant amount of research has been done on molybdenum in ancient and modern sediments in terms of its concentrations and isotopic ratios there remains a limited understanding of the drawdown mechanisms of molybdenum under different redox conditions restricting its use in identifying a range of redox states. In order to address these uncertainties, we have developed a novel sequential extraction technique to examine molybdenum concentrations in six sediment fractions from modern samples that represent oxic, nitrogenous, ferruginous and euxinic environments. In addition we use µ-XRF and µ-XANES synchrotron spectroscopy to examine the molybdenum speciation within these fractions and environments. To interpret our µ-XANES data we have developed an extensive library of molybdenum XANES standards that represent molybdenum sequestration by the sediment fractions identified from the sequential extraction. To further verify our synchrotron results we developed a series of µ-XANES micro-column experiments to examine preferential uptake pathways of molybdenum to different sediment phases under a euxinic water column. The initial data from both the sequential extraction and µ-XANES methods indicate that molybdenum is not limited to a single burial pathway in any of the redox environments. We find that each of the redox environments can be characterised by a limited set of molybdenum phase associations, with molybdenum adsorption to pyrite likely the dominant burial pathway. These findings agree with existing research for molybdenum speciation in euxinic environments suggesting that both pyrite and sulphidised organic matter act as important molybdenum sinks. Our new research shows that pyrite is also an important sink for molybdenum in other redox environments.
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NASA Astrophysics Data System (ADS)
Ye, Y.; Völker, C.; Wolf-Gladrow, D. A.
2009-10-01
A one-dimensional model of Fe speciation and biogeochemistry, coupled with the General Ocean Turbulence Model (GOTM) and a NPZD-type ecosystem model, is applied for the Tropical Eastern North Atlantic Time-Series Observatory (TENATSO) site. Among diverse processes affecting Fe speciation, this study is focusing on investigating the role of dust particles in removing dissolved iron (DFe) by a more complex description of particle aggregation and sinking, and explaining the abundance of organic Fe-binding ligands by modelling their origin and fate. The vertical distribution of different particle classes in the model shows high sensitivity to changing aggregation rates. Using the aggregation rates from the sensitivity study in this work, modelled particle fluxes are close to observations, with dust particles dominating near the surface and aggregates deeper in the water column. POC export at 1000 m is a little higher than regional sediment trap measurements, suggesting further improvement of modelling particle aggregation, sinking or remineralisation. Modelled strong ligands have a high abundance near the surface and decline rapidly below the deep chlorophyll maximum, showing qualitative similarity to observations. Without production of strong ligands, phytoplankton concentration falls to 0 within the first 2 years in the model integration, caused by strong Fe-limitation. A nudging of total weak ligands towards a constant value is required for reproducing the observed nutrient-like profiles, assuming a decay time of 7 years for weak ligands. This indicates that weak ligands have a longer decay time and therefore cannot be modelled adequately in a one-dimensional model. The modelled DFe profile is strongly influenced by particle concentration and vertical distribution, because the most important removal of DFe in deeper waters is colloid formation and aggregation. Redissolution of particulate iron is required to reproduce an observed DFe profile at TENATSO site. Assuming colloidal iron is mainly composed of inorganic colloids, the modelled colloidal to soluble iron ratio is lower that observations, indicating the importance of organic colloids.
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Trait-based diversification shifts reflect differential extinction among fossil taxa.
Wagner, Peter J; Estabrook, George F
2014-11-18
Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.
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NASA Astrophysics Data System (ADS)
Sarkar, M.; Venkataraman, C.; Guttikunda, S.; Sadavarte, P.
2016-06-01
Non-methane volatile organic compounds (NMVOCs) are important precursors to reactions producing tropospheric ozone and secondary organic aerosols. The present work uses a detailed technology-linked NMVOC emission database for India, along with a standard mapping method to measured NMVOC profiles, to develop speciated NMVOC emissions, which are aggregated into multiple chemical mechanisms used in chemical transport models. The fully speciated NMVOC emissions inventory with 423 constituent species, was regrouped into model-ready reactivity classes of the RADM2, SAPRC99 and CB-IV chemical mechanisms, and spatially distributed at 25 × 25 km2 resolution, using source-specific spatial proxies. Emissions were considered from four major sectors, i.e. industry, transport, agriculture and residential and from non-combustion activities (use of solvents and paints). It was found that residential cooking with biomass fuels, followed by agricultural residue burning in fields and on-road transport, were largest contributors to the highest reactivity group of NMVOC emissions from India. The emissions were evaluated using WRF-CAMx simulations, using the SAPRC99 photochemical mechanism, over India for contrasting months of April, July and October 2010. Modelled columnar abundance of NO2, CO and O3 agreed well with satellite observations both in magnitude and spatial distribution, in the three contrasting months. Evaluation of monthly and spatial differences between model predictions and observations indicates the need for further refinement of the spatial distribution of NOX emissions, spatio-temporal distribution of agricultural residue burning emissions.
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-11-19
... results of speciation data analyses, air quality modeling studies, chemical tracer studies, emission... Demonstration 1. Pollutants Addressed 2. Emission Inventory Requirements 3. Modeling 4. Reasonably Available... modeling (40 CFR 51.1007) that is performed in accordance with EPA modeling guidance (EPA-454/B-07-002...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Nitsche, H.; Roberts, K.; Prussin, T.
1994-04-01
Solubility and speciation are important in understanding aqueous radionuclide transport through the geosphere. They define the source term for transport retardation processes such as sorption and colloid formation. Solubility and speciation data are useful in verifying the validity of geochemical codes that are a part of predictive transport models. Results are presented from solubility and speciation experiments of {sup 237}NpO{sub 2}{sup +}, {sup 239}Pu{sup 4+}, and {sup 241}Am{sup 3+}/Nd{sup 3+} in a modified UE-25p No. 1 groundwater (from the Yucca Mountain region, Nevada, which is being investigated as a potential high-level nuclear waste disposal site) at two different temperatures (25{degree}more » and 60{degree}C) and three pH values (6.0, 7.0, 8.5). The solubility-controlling steady-state solids were identified and the speciation and/or oxidation states present in the supernatant solutions were determined. The neptunium solubility decreased with increasing temperature and pH. Plutonium concentrations significantly decreased with increasing temperature at pH 6 and 7. The concentration at pH 8.5 hardly decreased at all with increasing temperature. At both temperatures the concentrations were highest at pH 8.5, lowest at pH 7, and in between at pH 6. For the americium/neodymium solutions, the solubility decreased significantly with increasing temperature and increased somewhat with increasing pH.« less
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Kong, Hanghui; Condamine, Fabien L; Harris, A J; Chen, Junlin; Pan, Bo; Möller, Michael; Hoang, Van Sam; Kang, Ming
2017-11-01
Karst ecosystems in southern China are species-rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to assess the origin and cause of species diversification due to palaeoenvironmental changes and edaphic specialization in Primulina. We found that speciation was positively associated with changes in past temperatures and East Asian monsoons through the evolutionary history of Primulina. Climatic change around the mid-Miocene triggered an early burst followed by a slowdown of diversification rate towards the present with the climate cooling. We detected different speciation rates among edaphic types, and transitions among soil types were infrequently and did not impact the overall speciation rate. Our findings suggest that both global temperature changes and East Asian monsoons have played crucial roles in floristic diversification within the karst ecosystems in southern China, such that speciation was higher when climate was warmer and wetter. This is the first study to directly demonstrate that past monsoon activity is positively correlated with speciation rate in East Asia. This case study could motivate further investigations to assess the impacts of past environmental changes on the origin and diversification of biodiversity in global karst ecosystems, most of which are under threat. © 2017 John Wiley & Sons Ltd.
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pH-dependent biotransformation of ionizable organic micropollutants in activated sludge.
Gulde, Rebekka; Helbling, Damian E; Scheidegger, Andreas; Fenner, Kathrin
2014-12-02
Removal of micropollutants (MPs) during activated sludge treatment can mainly be attributed to biotransformation and sorption to sludge flocs, whereby the latter process is known to be of minor importance for polar organic micropollutants. In this work, we investigated the influence of pH on the biotransformation of MPs with cationic-neutral speciation in an activated sludge microbial community. We performed batch biotransformation, sorption control, and abiotic control experiments for 15 MPs with cationic-neutral speciation, one control MP with neutral-anionic speciation, and two neutral MPs at pHs 6, 7, and 8. Biotransformation rate constants corrected for sorption and abiotic processes were estimated from measured concentration time series with Bayesian inference. We found that biotransformation is pH-dependent and correlates qualitatively with the neutral fraction of the ionizable MPs. However, a simple speciation model based on the assumption that only the neutral species is efficiently taken up and biotransformed by the cells tends to overpredict the effect of speciation. Therefore, additional mechanisms such as uptake of the ionic species and other more complex attenutation mechanisms are discussed. Finally, we observed that the sorption coefficients derived from our control experiments were small and showed no notable pH-dependence. From this we conclude that pH-dependent removal of polar, ionizable organic MPs in activated sludge systems is less likely an effect of pH-dependent sorption but rather of pH-dependent biotransformation. The latter has the potential to cause marked differences in the removal of polar, ionizable MPs at different operational pHs during activated sludge treatment.
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Detecting local diversity-dependence in diversification.
Xu, Liang; Etienne, Rampal S
2018-04-06
Whether there are ecological limits to species diversification is a hotly debated topic. Molecular phylogenies show slowdowns in lineage accumulation, suggesting that speciation rates decline with increasing diversity. A maximum-likelihood (ML) method to detect diversity-dependent (DD) diversification from phylogenetic branching times exists, but it assumes that diversity-dependence is a global phenomenon and therefore ignores that the underlying species interactions are mostly local, and not all species in the phylogeny co-occur locally. Here, we explore whether this ML method based on the nonspatial diversity-dependence model can detect local diversity-dependence, by applying it to phylogenies, simulated with a spatial stochastic model of local DD speciation, extinction, and dispersal between two local communities. We find that type I errors (falsely detecting diversity-dependence) are low, and the power to detect diversity-dependence is high when dispersal rates are not too low. Interestingly, when dispersal is high the power to detect diversity-dependence is even higher than in the nonspatial model. Moreover, estimates of intrinsic speciation rate, extinction rate, and ecological limit strongly depend on dispersal rate. We conclude that the nonspatial DD approach can be used to detect diversity-dependence in clades of species that live in not too disconnected areas, but parameter estimates must be interpreted cautiously. © 2018 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.
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Lohse, Konrad; Clarke, Magnus; Ritchie, Michael G.; Etges, William J.
2015-01-01
Models of speciation‐with‐gene‐flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here, we present an analysis of whole genome data from a pair of cactophilic fruit flies, Drosophila mojavensis and D. arizonae, which are reproductively isolated in the wild and differ by several large inversions on three chromosomes. We found an increase in divergence at rearranged compared to colinear chromosomes. Using the density of divergent sites in short sequence blocks we fit a series of explicit models of species divergence in which gene flow is restricted to an initial period after divergence and may differ between colinear and rearranged parts of the genome. These analyses show that D. mojavensis and D. arizonae have experienced postdivergence gene flow that ceased around 270 KY ago and was significantly reduced in chromosomes with fixed inversions. Moreover, we show that these inversions most likely originated around the time of species divergence which is compatible with theoretical models that posit a role of inversions in speciation with gene flow. PMID:25824653
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Determination of an organic-acid analog of DOC for use in copper toxicity studies on salmonids
DOE Office of Scientific and Technical Information (OSTI.GOV)
MacRae, R.K.; Meyer, J.S.; Hansen, J.A.
1995-12-31
Concentrations of dissolved copper in streams draining mine sites often exceed concentrations shown to cause acute and chronic mortality in salmonids. However, toxicity and impaired behaviors may be modified by dissolved organic carbon (DOC) and other inorganic components present in the site water. The effects of DOC on copper speciation, and thus bioavailability and toxicity, were determined by titrating stream waters with copper, using a cupric ion-specific electrode to detect free copper concentrations. Effects of various competing cations (e.g., Ca{sup +2}, Co{sup +2}) on copper-DOC binding were also evaluated. Titration results were evaluated using Scatchard and non-linear regression analyses tomore » quantify the strength and capacity of copper-DOC binding. Inorganic speciation was determined using the geochemical model MINEQL{sup +}. Results of these titrations indicated the presence of two or three distinct copper binding components in site water DOC. Three commercially available organic acids where then chosen to mimic the binding characteristics of natural DOC. This DOC-analog was used successfully in fish toxicity studies to evaluate the influence of DOC on copper bioavailability. Geochemical models were developed to predict copper speciation in both laboratory test waters and site waters, for any typical combination of water chemistry parameters (pH, alkalinity, [DOC], etc.). A combined interpretation of fish toxicity and modeling results indicate that some DOC-bound copper was bioavailable.« less
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The development of a site-specific water-quality standard for copper
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sinclair, R.M.
This dissertation proposes to determine, for one toxic chemical, copper, if the Federal water quality standard and the state interpretation of that standard are appropriate for the Duck River, some 50 miles south of Nashville, Tennessee. This involved conducting toxicity tests in Duck River water, and the use of the computer metal speciation program MINTEQA1 to predict instream impact. The speciation model chosen for the determination of chemical equilibria in this study was MINTEQA1. To test the validity of the MINTEQA1 speciation model, water chemistry from the Duck River was entered into the model. At the typical site pH ofmore » 7.8, 55.7% of the copper is bound as Cu(OH){sub 2}, 29.8% is bound as copper humate, and 12.7% is found as CuCO{sub 3}. Of extreme importance to the toxicity of copper in the site water is the complete absence of the most toxic species, ionic copper. The test species were the brook silversides minnow (Labidesthes sicculus), mosquitofish (Gambusia affinis), caddisfly larvae (Cheumatopsyche sp.), fathead minnow (Pimephales promelas), geniculate river snail (Lithasia geniculata), sunfish (Lepomis sp.), and the amphipod (Hyalella azeca). The test concentrations were confirmed by atomic absorption spectroscopy on selected concentrations. The caddisfly larvae was the single most tolerant species observed during this study, while the amphipod and snail were the two most sensitive species tested.« less
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Quantifying the sensitivity of aerosol optical depths retrieved from MSG SEVIRI to a priori data
NASA Astrophysics Data System (ADS)
Bulgin, C. E.; Palmer, P. I.; Merchant, C. J.; Siddans, R.; Poulsen, C.; Grainger, R. G.; Thomas, G.; Carboni, E.; McConnell, C.; Highwood, E.
2009-12-01
Radiative forcing contributions from aerosol direct and indirect effects remain one of the most uncertain components of the climate system. Satellite observations of aerosol optical properties offer important constraints on atmospheric aerosols but their sensitivity to prior assumptions must be better characterized before they are used effectively to reduce uncertainty in aerosol radiative forcing. We assess the sensitivity of the Oxford-RAL Aerosol and Cloud (ORAC) optimal estimation retrieval of aerosol optical depth (AOD) from the Spinning Enhanced Visible and InfraRed Imager (SEVIRI) to a priori aerosol data. SEVIRI is a geostationary satellite instrument centred over Africa and the neighbouring Atlantic Ocean, routinely sampling desert dust and biomass burning outflow from Africa. We quantify the uncertainty in SEVIRI AOD retrievals in the presence of desert dust by comparing retrievals that use prior information from the Optical Properties of Aerosol and Cloud (OPAC) database, with those that use measured aerosol properties during the Dust Outflow and Deposition to the Ocean (DODO) aircraft campaign (August, 2006). We also assess the sensitivity of retrieved AODs to changes in solar zenith angle, and the vertical profile of aerosol effective radius and extinction coefficient input into the retrieval forward model. Currently the ORAC retrieval scheme retrieves AODs for five aerosol types (desert dust, biomass burning, maritime, urban and continental) and chooses the most appropriate AOD based on the cost functions. We generate an improved prior aerosol speciation database for SEVIRI based on a statistical analysis of a Saharan Dust Index (SDI) determined using variances of different brightness temperatures, and organic and black carbon tracers from the GEOS-Chem chemistry transport model. This database is described as a function of season and time of day. We quantify the difference in AODs between those chosen based on prior information from the SDI and GEOS-Chem and those chosen based on the smallest cost function.
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Adding to the Mercury Speciation Toolbox
NASA Astrophysics Data System (ADS)
Fitts, J. P.; Northrup, P. A.; Chidambaram, D.; Kalb, P. D.
2007-12-01
Mercury was used to separate lithium-6 isotope for weapons production at the Y-12 Plant in Oak Ridge, TN in the 1950s and 1960s. A large portion of the waste Hg entered the environment and continues to move throughout the sub-surface and surface waters in the area. Environmental management of Hg contamination within this complex hydrologic system, where Hg speciation and the mobile fraction have been found to vary widely, will require ongoing characterization and predictive modeling of Hg speciation. State-of-the-art spectroscopic tools that can directly probe Hg speciation in preserved aqueous and sediment samples with greater sensitivity, however, are required to determine rates and mechanisms of biogeochemical reactions. We will present the first results demonstrating the use of x-ray absorption spectroscopy (XAS) at the Hg M5 edge (2295 eV) to fingerprint Hg species. Heavy-metal M5 absorption edges can have very sharp features due to local electron transitions, and therefore, we are developing this edge as a tool for quantitative measurement of Hg species. In addition, sulfur speciation using the sulfur K absorption edge, which is at a similar energy (2472 eV), can be measured in the same scan as the Hg M5 edge. Potentially important organic and inorganic sulfur species (sulfide, disulfide, elemental sulfur, sulfite and sulfate) are readily differentiated, and thereby, provides an independent method for monitoring the redox state of the system along with changes in S-Hg bonding. We will also present x-ray microprobe 2-D concentration maps of Hg and other elements at the grain and pore scales to identify its microscopic distribution and chemical associations. When used in combination with established sequential extraction and direct spectroscopic methods, the addition of XAS at the Hg M5 edge should provide a significant advancement in the determination of Hg speciation in complex biogeochemical environments.
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Chemical Mass Balance (CMB) Model
The EPA-CMB Version 8.2 uses source profiles and speciated ambient data to quantify source contributions. Contributions are quantified from chemically distinct source-types rather than from individual emitters.
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Wogan, Guinevere O.U.; Richmond, Jonathan Q.
2015-01-01
Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate-based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by-product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size-divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype–environment associations that further support the case for ecological speciation in these lizards.
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Teng, Huajing; Zhang, Yaohua; Shi, Chengmin; Mao, Fengbiao; Cai, Wanshi; Lu, Liang; Zhao, Fangqing; Sun, Zhongsheng; Zhang, Jianxu
2017-01-01
Abstract Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation. PMID:28482038
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NASA Astrophysics Data System (ADS)
Bray, Timothy C.; Bocak, Ladislav
2016-09-01
We demonstrate the controversial origin of a biological species within an area of a few kilometres in the absence of physical barriers. We employed nuclear rRNA/mitochondrial and genome-wide SNP approaches to infer relationships of four species of net-winged beetles characterised by female neoteny. Three species are distributed at low elevations and a single population colonised a 40 km2 highland plateau and established distinct biological species despite incomplete genetic isolation. The speciation process is extreme in the highly localised spatial scale, due to the low dispersal power of neotenics, and provides clear support for a microallopatric model based on ecological conditions. In contrast with neutral evolution in a homogenous environment, as demonstrated by the genetic divergence and morphological similarity of two widely distributed low-mountain species, the environmental characteristics of the high-mountain plateau led to the origin of a species adapted to the local mimetic pattern and characterised by morphologically distinct genitalia. We conclude that the low dispersal propensity promotes neutral genetic differentiation in the first stage, but environmental characteristics play an important role the final phase of the speciation process. The unexpected speciation at such an extreme geographic scale points to the in situ origin and uniqueness of the mountain fauna.
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The evolution of recombination rates in finite populations during ecological speciation.
Reeve, James; Ortiz-Barrientos, Daniel; Engelstädter, Jan
2016-10-26
Recombination can impede ecological speciation with gene flow by mixing locally adapted genotypes with maladapted migrant genotypes from a divergent population. In such a scenario, suppression of recombination can be selectively favoured. However, in finite populations evolving under the influence of random genetic drift, recombination can also facilitate adaptation by reducing Hill-Robertson interference between loci under selection. In this case, increased recombination rates can be favoured. Although these two major effects on recombination have been studied individually, their joint effect on ecological speciation with gene flow remains unexplored. Using a mathematical model, we investigated the evolution of recombination rates in two finite populations that exchange migrants while adapting to contrasting environments. Our results indicate a two-step dynamic where increased recombination is first favoured (in response to the Hill-Robertson effect), and then disfavoured, as the cost of recombining locally with maladapted migrant genotypes increases over time (the maladaptive gene flow effect). In larger populations, a stronger initial benefit for recombination was observed, whereas high migration rates intensify the long-term cost of recombination. These dynamics may have important implications for our understanding of the conditions that facilitate incipient speciation with gene flow and the evolution of recombination in finite populations. © 2016 The Author(s).
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Divergence with gene flow across a speciation continuum of Heliconius butterflies.
Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A
2015-09-24
A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.
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2014-01-01
Background The role of tectonic uplift in stimulating speciation in South Africa’s only alpine zone, the Drakensberg, has not been explicitly examined. Tectonic processes may influence speciation both through the creation of novel habitats and by physically isolating plant populations. We use the Afrotemperate endemic daisy genus Macowania to explore the timing and mode (geographic versus adaptive) of speciation in this region. Between sister species pairs we expect high morphological divergence where speciation has happened in sympatry (adaptive) while with geographic (vicariant) speciation we may expect to find less morphological divergence and a greater degree of allopatry. A dated molecular phylogenetic hypothesis for Macowania elucidates species’ relationships and is used to address the potential impact of uplift on diversification. Morphological divergence of a small sample of reproductive and vegetative characters, used as a proxy for adaptive divergence, is measured against species’ range distributions to estimate mode of speciation across two subclades in the genus. Results The Macowania crown age is consistent with the hypothesis of post-uplift diversification, and we find evidence for both vicariant and adaptive speciation between the two subclades within Macowania. Both subclades exhibit strong signals of range allopatry, suggesting that geographic isolation was important in speciation. One subclade, associated with dry, rocky environments at high altitudes, shows very little morphological and ecological differentiation but high range allopatry. The other subclade occupies a greater variety of habitats and exhibits far greater morphological differentiation, but contains species with overlapping distribution ranges. Conclusions Species in Macowania are likely to have diversified in response to tectonic uplift, and we invoke uplift and uplift-mediated erosion as the main drivers of speciation. The greater relative morphological divergence in sympatric species of Macowania indicates that speciation in the non-sympatric taxa may not have required obvious adaptive differences, implying that simple geographic isolation was the driving force for speciation (‘neutral speciation’). PMID:24524661
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Rosser, Neil; Kozak, Krzysztof M; Phillimore, Albert B; Mallet, James
2015-06-30
Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry. Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32%-95% of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved. Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on "strict and " "relaxed" biological species concepts (BSC), as well as on a surrogate for the widely-used "diagnostic" version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two groups. To establish whether heliconiines are exceptional will require biogeographic comparative studies for a wider range of animal taxa including many more invertebrates.
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The role of Quaternary environmental change in plant macroevolution: the exception or the rule?
Willis, Katherine J; Niklas, Karl J
2004-01-01
The Quaternary has been described as an important time for genetic diversification and speciation. This is based on the premise that Quaternary climatic conditions fostered the isolation of populations and, in some instances, allopatric speciation. However, the 'Quaternary Ice-Age speciation model' rests on two key assumptions: (i) that biotic responses to climate change during the Quaternary were significantly different from those of other periods in Earth's history; and (ii) that the mechanisms of isolation during the Quaternary were sufficient in time and space for genetic diversification to foster speciation. These assumptions are addressed by examining the plant fossil record for the Quaternary (in detail) and for the past 410 Myr, which encompasses previous intervals of icehouse Earth. Our examination of the Quaternary record indicates that floristic responses to climate changes during the past 1.8 Myr were complex and that a distinction has to be made between those plants that were able to withstand the extremes of glacial conditions and those that could not. Generation times are also important as are different growth forms (e.g. herbaceous annuals and arborescent perennials), resulting in different responses in terms of genetic divergence rates during isolation. Because of these variations in the duration of isolation of populations and genomic diversification rates, no canonical statement about the predominant floristic response to climatic changes during the Quaternary (i.e. elevated rates of speciation or extinction, or stasis) is currently possible. This is especially true because of a sampling bias in terms of the fossil record of tree species over that of species with non-arborescent growth forms. Nevertheless, based on the available information, it appears that the dominant response of arborescent species during the Quaternary was extinction rather than speciation or stasis. By contrast, our examination of the fossil record of vascular plants for the past 410 Myr indicates that speciation rates often increased during long intervals of icehouse Earth (spanning up to 50 Myr). Therefore, longer periods of icehouse Earth than those occurring during the Quaternary may have isolated plant populations for sufficiently long periods of time to foster genomic diversification and allopatric speciation. Our results highlight the need for more detailed study of the fossil record in terms of finer temporal and spatial resolution than is currently available to examine the significance of intervals of icehouse Earth. It is equally clear that additional and detailed molecular studies of extant populations of Quaternary species are required in order to determine the extent to which these 'relic' species have genomically diversified across their current populations. PMID:15101573
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NetpathXL - An Excel Interface to the Program NETPATH
Parkhurst, David L.; Charlton, Scott R.
2008-01-01
NetpathXL is a revised version of NETPATH that runs under Windows? operating systems. NETPATH is a computer program that uses inverse geochemical modeling techniques to calculate net geochemical reactions that can account for changes in water composition between initial and final evolutionary waters in hydrologic systems. The inverse models also can account for the isotopic composition of waters and can be used to estimate radiocarbon ages of dissolved carbon in ground water. NETPATH relies on an auxiliary, database program, DB, to enter the chemical analyses and to perform speciation calculations that define total concentrations of elements, charge balance, and redox state of aqueous solutions that are then used in inverse modeling. Instead of DB, NetpathXL relies on Microsoft Excel? to enter the chemical analyses. The speciation calculation formerly included in DB is implemented within the program NetpathXL. A program DBXL can be used to translate files from the old DB format (.lon files) to NetpathXL spreadsheets, or to create new NetpathXL spreadsheets. Once users have a NetpathXL spreadsheet with the proper format, new spreadsheets can be generated by copying or saving NetpathXL spreadsheets. In addition, DBXL can convert NetpathXL spreadsheets to PHREEQC input files. New capabilities in PHREEQC (version 2.15) allow solution compositions to be written to a .lon file, and inverse models developed in PHREEQC to be written as NetpathXL .pat and model files. NetpathXL can open NetpathXL spreadsheets, NETPATH-format path files (.pat files), and NetpathXL-format path files (.pat files). Once the speciation calculations have been performed on a spreadsheet file or a .pat file has been opened, the NetpathXL calculation engine is identical to the original NETPATH. Development of models and viewing results in NetpathXL rely on keyboard entry as in NETPATH.
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NASA Astrophysics Data System (ADS)
Chandrasekhar, Anoop; Sander, Sylvia; Milnes, Angie; Boyd, Philip
2015-04-01
Iron plays a significant role in the ocean productivity as a micro nutrient that facilitates the growth of marine phytoplankton and microbes. The bioavailability of iron in the ocean depends on it speciation. Iron is bio available in its dissolved form and about 99.9% of dissolved iron in seawater is organically complexed with natural ligands. The competitive ligand equilibration - adsorptive cathodic stripping voltammetry (CLE-AdCSV) is the widely used technique to examine Fe speciation. The method has its own limitations. The analytical window employed in this technique has a distinct impact on Fe speciation results (Buck, Moffett et al. 2012). Recently, (Pizeta, Sander et al. in preparation) have shown that the accuracy of complexometric titrations improve if multiple analytical windows (MAW) are solved as a united dataset. Several programs are now available that enable this approach with the KMS (Kineteql.xls , Hudson 2014), which is based on an Excel application based on speciation calculation (Hudson, Rue et al. 2003, Sander, Hunter et al. 2011), being one of them. In the present work, the unified MAW data analysis method is applied to determine iron speciation by CLE-AdCSV with salicyl aldoxime (SA) (Abualhaija and van den Berg 2014) in real seawater samples from the Spring bloom FeCycle III voyage, which took place in an anticyclonic eddy in subtropical waters east of New Zealand in spring 2012. Two different analytical windows (5 and 15µM SA) were applied to samples from depth profiles taken during this cruise. The data obtained was analysed using the program KMS (Kineteql.xls). Most samples only returned one Fe-binding ligands class. Higher ligand concentrations were observed in the upper water column and the stability constants were above 22 (e.g. 22.25 ± 0.21 for station 63). Our results will be discussed in the context of microbial community distribution as well as other biogeochemical parameters. Abualhaija, M. M. and C. M. G. van den Berg (2014). "Chemical speciation of iron in seawater using catalytic cathodic stripping voltammetry with ligand competition against salicylaldoxime." Marine Chemistry 164(0): 60-74. Buck, K. N., J. Moffett, K. A. Barbeau, R. M. Bundy, Y. Kondo and J. Wu (2012). "The organic complexation of iron and copper: an intercomparison of competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV) techniques " Limnology and Oceanography: Methods 10: 496-515. Hudson, R. J. M., E. L. Rue and K. W. Bruland (2003). "Modeling Complexometric Titrations of Natural Water Samples." Environ. Sci. Tech. 37: 1553-1562. Pizeta, I., S. G. Sander, O. Baars, K. Buck, R. Bundy, G. Carrasco, P. Croot, C. Garnier, L. Gerringa, M. Gledhill, K. Hirose, D. R. Hudson, Y. Kondo-Jacquot, L. Laglera, D. Omanovic, M. Rijkenberg, B. Twining and M. Wells (in preparation). "Intercomparison of estimating metal binding ligand parameters from simulated titration data using different fitting approaches." for Limnology and Oceanography: Methods. Sander, S. G., K. A. Hunter, H. Harms and M. Wells (2011). "Numerical approach to speciation and estimation of parameters used in modeling trace metal bioavailability." Environmental Science and Technology 45(15): 6388-6395.
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NASA Astrophysics Data System (ADS)
Hauffe, T.; Albrecht, C.; Wilke, T.
2015-09-01
The Balkan Lake Ohrid is the oldest and most speciose freshwater lacustrine system in Europe. However, it remains unclear whether the diversification of its endemic taxa is mainly driven by neutral processes, environmental factors, or species interactions. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics. Such a unifying framework - the metacommunity speciation model - considers how community assembly affects diversification and vice versa by assessing the relative contribution of the three main community assembly processes, dispersal limitation, environmental filtering, and species interaction. The current study therefore used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process based metacommunity analyses. Specifically, the study aimed at (i) identifying the relative importance of the three community assembly processes and (ii) to test whether the importance of these individual processes changes gradually with lake depth or whether they are distinctively related to eco-zones. Based on specific simulation steps for each of the three processes, it could be demonstrated that dispersal limitation had the strongest influence on gastropod community structures in Lake Ohrid. However, it was not the exclusive assembly process but acted together with the other two processes - environmental filtering, and species interaction. In fact, the relative importance of the three community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter. The study thus corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community structure) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental filtering and biotic interaction also suggests a small but significant influence of ecological speciation. These findings contribute to the main goal of the SCOPSCO initiative - inferring the drivers of biotic evolution - and might provide an integrative perspective on biological and limnological dynamics in ancient Lake Ohrid.
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Effects of aqueous uranyl speciation on the kinetics of microbial uranium reduction
Belli, Keaton M.; DiChristina, Thomas J.; Van Cappellen, Philippe; ...
2015-02-16
The ability to predict the success of the microbial reduction of soluble U(VI) to highly insoluble U(IV) as an in situ bioremediation strategy is complicated by the wide range of geochemical conditions at contaminated sites and the strong influence of aqueous uranyl speciation on the bioavailability and toxicity of U(VI) to metal-reducing bacteria. In order to determine the effects of aqueous uranyl speciation on uranium bioreduction kinetics, incubations and viability assays with Shewanella putrefaciens strain 200 were conducted over a range of pH and dissolved inorganic carbon (DIC), Ca 2+, and Mg 2+ concentrations. A speciation-dependent kinetic model was developedmore » to reproduce the observed time series of total dissolved uranium concentration over the range of geochemical conditions tested. The kinetic model yielded the highest rate constant for the reduction of uranyl non-carbonate species (i.e., the ‘free’ hydrated uranyl ion, uranyl hydroxides, and other minor uranyl complexes), indicating that they represent the most readily reducible fraction of U(VI) despite being the least abundant uranyl species in solution. In the presence of DIC, Ca 2+, and Mg 2+ is suppressed during the formation of more bioavailable uranyl non-carbonate species and resulted in slower bioreduction rates. At high concentrations of bioavailable U(VI), however, uranium toxicity to S. putrefaciens inhibited bioreduction, and viability assays confirmed that the concentration of non-carbonate uranyl species best predicts the degree of toxicity. The effect of uranium toxicity was accounted for by incorporating the free ion activity model of metal toxicity into the bioreduction rate law. These results demonstrate that, in the absence of competing terminal electron acceptors, uranium bioreduction kinetics can be predicted over a wide range of geochemical conditions based on the bioavailability and toxicity imparted on U(VI) by solution composition. Finally, these findings also imply that the concentration of uranyl non-carbonate species, despite being extremely low, is a determining factor controlling uranium bioreduction at contaminated sites.« less
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Miscibility and Speciation in the Water/carbon Dioxide System
NASA Astrophysics Data System (ADS)
Abramson, E.; Bollengier, O.; Brown, J. M.
2017-12-01
We have been exploring fluid-fluid solubilities and speciation in mixed systems of CO2-H2O. Fluid-fluid immiscibility extends to the highest pressures and temperatures yet explored (7 GPa, 700K). In this region, commonly used COH fluid models agree neither with the data nor among themselves. The range of immiscibility is extended by addition of NaCl, but miscibility limits determined in preliminary experiments are not as expected from extrapolation of lower pressure (<0.2 GPa) results. For majority-water systems (XCO2<0.5) an abrupt increase of solubility with pressure is linked to an observed change in speciation as CO2(aq) reacts with water. The identity of the newly formed species is, as of the writing of this abstract, unknown, but presumed to be either H2CO3 or HCO3-. A reasonable match between the observed equilibria and an application of HKF theory suggests that the new species is, indeed, HCO3-, but with a Raman frequency shifted from that found in the dilute aqueous solution. Application of HKF theory to the CO2(f)-CO2(aq) equilibrium suffers from an incompatibility of the usual formulation of the theory with known molar volumes of CO2(f) at higher pressures. On the basis of these studies we conclude that models of CO2-H2O fluids must take into account major changes in speciation, and that simple equations-of-state, of a few fitted parameters, will not afford an adequate description of such fluids. "First principles" models, tested against real data, seem more likely to yield the desired results. This statement extends as well to the calculation of the dielectric constants of these mixed fluids, the basis of ionic solution chemistry. Further, semi-empirical formulations of solution thermodynamics, which function well at pressures of kbars, ought to be re-worked for use over larger pressure ranges.
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Lathouri, Maria; Korre, Anna
2015-12-15
Although significant progress has been made in understanding how environmental factors modify the speciation, bioavailability and toxicity of metals such as copper in aquatic environments, the current methods used to establish water quality standards do not necessarily consider the different geological and geochemical characteristics of a given site and the factors that affect copper fate, bioavailability potential and toxicity. In addition, the temporal variation in the concentration and bioavailable metal fraction is also important in freshwater systems. The work presented in this paper illustrates the temporal and seasonal variability of a range of water quality parameters, and Cu speciation, bioavailability and toxicity at four freshwaters sites in the UK. Rivers Coquet, Cree, Lower Clyde and Eden (Kent) were selected to cover a broad range of different geochemical environments and site characteristics. The monitoring data used covered a period of around six years at almost monthly intervals. Chemical equilibrium modelling was used to study temporal variations in Cu speciation and was combined with acute toxicity modelling to assess Cu bioavailability for two aquatic species, Daphnia magna and Daphnia pulex. The estimated copper bioavailability, toxicity levels and the corresponding ecosystem risks were analysed in relation to key water quality parameters (alkalinity, pH and DOC). Although copper concentrations did not vary much during the sampling period or between the seasons at the different sites; copper bioavailability varied markedly. In addition, through the chronic-Cu BLM-based on the voluntary risk assessment approach, the potential environmental risk in terms of the chronic toxicity was assessed. A much higher likelihood of toxicity effects was found during the cold period at all sites. It is suggested that besides the metal (copper) concentration in the surface water environment, the variability and seasonality of other important water quality parameters should be considered in setting appropriately protective environmental quality standards for metals. Copyright © 2015 Elsevier B.V. All rights reserved.
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Evolutionary Roots and Diversification of the Genus Aeromonas.
Sanglas, Ariadna; Albarral, Vicenta; Farfán, Maribel; Lorén, J G; Fusté, M C
2017-01-01
Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa. The investigation of evolutionary patterns in prokaryotes constitutes a challenge due to a very scarce fossil record, limited morphological differentiation and frequently complex taxonomic relationships, which make even species recognition difficult. Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available. More recently, several methods based on molecular sequence data have been developed to estimate speciation and extinction rates from phylogenies reconstructed from contemporary taxa. In this work, we determined the divergence time and temporal diversification of the genus Aeromonas by applying these methods widely used with eukaryotic taxa. Our analysis involved 150 Aeromonas strains using the concatenated sequences of two housekeeping genes (approximately 2,000 bp). Dating and diversification model analyses were performed using two different approaches: obtaining the consensus sequence from the concatenated sequences corresponding to all the strains belonging to the same species, or generating the species tree from multiple alignments of each gene. We used BEAST to perform a Bayesian analysis to estimate both the phylogeny and the divergence times. A global molecular clock cannot be assumed for any gene. From the chronograms obtained, we carried out a diversification analysis using several approaches. The results suggest that the genus Aeromonas began to diverge approximately 250 millions of years (Ma) ago. All methods used to determine Aeromonas diversification gave similar results, suggesting that the speciation process in this bacterial genus followed a rate-constant (Yule) diversification model, although there is a small probability that a slight deceleration occurred in recent times. We also determined the constant of diversification (λ) values, which in all cases were very similar, about 0.01 species/Ma, a value clearly lower than those described for different eukaryotes.
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Evolutionary Roots and Diversification of the Genus Aeromonas
Sanglas, Ariadna; Albarral, Vicenta; Farfán, Maribel; Lorén, J. G.; Fusté, M. C.
2017-01-01
Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa. The investigation of evolutionary patterns in prokaryotes constitutes a challenge due to a very scarce fossil record, limited morphological differentiation and frequently complex taxonomic relationships, which make even species recognition difficult. Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available. More recently, several methods based on molecular sequence data have been developed to estimate speciation and extinction rates from phylogenies reconstructed from contemporary taxa. In this work, we determined the divergence time and temporal diversification of the genus Aeromonas by applying these methods widely used with eukaryotic taxa. Our analysis involved 150 Aeromonas strains using the concatenated sequences of two housekeeping genes (approximately 2,000 bp). Dating and diversification model analyses were performed using two different approaches: obtaining the consensus sequence from the concatenated sequences corresponding to all the strains belonging to the same species, or generating the species tree from multiple alignments of each gene. We used BEAST to perform a Bayesian analysis to estimate both the phylogeny and the divergence times. A global molecular clock cannot be assumed for any gene. From the chronograms obtained, we carried out a diversification analysis using several approaches. The results suggest that the genus Aeromonas began to diverge approximately 250 millions of years (Ma) ago. All methods used to determine Aeromonas diversification gave similar results, suggesting that the speciation process in this bacterial genus followed a rate-constant (Yule) diversification model, although there is a small probability that a slight deceleration occurred in recent times. We also determined the constant of diversification (λ) values, which in all cases were very similar, about 0.01 species/Ma, a value clearly lower than those described for different eukaryotes. PMID:28228750
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Liquid-vapor phase relations in the Si-O system: A calorically constrained van der Waals-type model
NASA Astrophysics Data System (ADS)
Connolly, James A. D.
2016-09-01
This work explores the use of several van der Waals (vW)-type equations of state (EoS) for predicting vaporous phase relations and speciation in the Si-O system, with emphasis on the azeotropic boiling curve of SiO2-rich liquid. Comparison with the observed Rb and Hg boiling curves demonstrates that prediction accuracy is improved if the a-parameter of the EoS, which characterizes vW forces, is constrained by ambient pressure heat capacities. All EoS considered accurately reproduce metal boiling curve trajectories, but absent knowledge of the true critical compressibility factor, critical temperatures remain uncertain by ~500 K. The EoS plausibly represent the termination of the azeotropic boiling curve of silica-rich liquid by a critical point across which the dominant Si oxidation state changes abruptly from the tetravalent state characteristic of the liquid to the divalent state characteristic of the vapor. The azeotropic composition diverges from silica toward metal-rich compositions with increasing temperature. Consequently, silica boiling is divariant and atmospheric loss after a giant impact would enrich residual silicate liquids in reduced silicon. Two major sources of uncertainty in the boiling curve prediction are the heat capacity of silica liquid, which may decay during depolymerization from the near-Dulong-Petit limit heat capacity of the ionic liquid to value characteristic of the molecular liquid, and the unknown liquid affinity of silicon monoxide. Extremal scenarios for these uncertainties yield critical temperatures and compositions of 5200-6200 K and Si1.1O2-Si1.4O2. The lowest critical temperatures are marginally consistent with shock experiments and are therefore considered more probable.
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A model-averaging method for assessing groundwater conceptual model uncertainty.
Ye, Ming; Pohlmann, Karl F; Chapman, Jenny B; Pohll, Greg M; Reeves, Donald M
2010-01-01
This study evaluates alternative groundwater models with different recharge and geologic components at the northern Yucca Flat area of the Death Valley Regional Flow System (DVRFS), USA. Recharge over the DVRFS has been estimated using five methods, and five geological interpretations are available at the northern Yucca Flat area. Combining the recharge and geological components together with additional modeling components that represent other hydrogeological conditions yields a total of 25 groundwater flow models. As all the models are plausible given available data and information, evaluating model uncertainty becomes inevitable. On the other hand, hydraulic parameters (e.g., hydraulic conductivity) are uncertain in each model, giving rise to parametric uncertainty. Propagation of the uncertainty in the models and model parameters through groundwater modeling causes predictive uncertainty in model predictions (e.g., hydraulic head and flow). Parametric uncertainty within each model is assessed using Monte Carlo simulation, and model uncertainty is evaluated using the model averaging method. Two model-averaging techniques (on the basis of information criteria and GLUE) are discussed. This study shows that contribution of model uncertainty to predictive uncertainty is significantly larger than that of parametric uncertainty. For the recharge and geological components, uncertainty in the geological interpretations has more significant effect on model predictions than uncertainty in the recharge estimates. In addition, weighted residuals vary more for the different geological models than for different recharge models. Most of the calibrated observations are not important for discriminating between the alternative models, because their weighted residuals vary only slightly from one model to another.
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A Bayesian Framework of Uncertainties Integration in 3D Geological Model
NASA Astrophysics Data System (ADS)
Liang, D.; Liu, X.
2017-12-01
3D geological model can describe complicated geological phenomena in an intuitive way while its application may be limited by uncertain factors. Great progress has been made over the years, lots of studies decompose the uncertainties of geological model to analyze separately, while ignored the comprehensive impacts of multi-source uncertainties. Great progress has been made over the years, while lots of studies ignored the comprehensive impacts of multi-source uncertainties when analyzed them item by item from each source. To evaluate the synthetical uncertainty, we choose probability distribution to quantify uncertainty, and propose a bayesian framework of uncertainties integration. With this framework, we integrated data errors, spatial randomness, and cognitive information into posterior distribution to evaluate synthetical uncertainty of geological model. Uncertainties propagate and cumulate in modeling process, the gradual integration of multi-source uncertainty is a kind of simulation of the uncertainty propagation. Bayesian inference accomplishes uncertainty updating in modeling process. Maximum entropy principle makes a good effect on estimating prior probability distribution, which ensures the prior probability distribution subjecting to constraints supplied by the given information with minimum prejudice. In the end, we obtained a posterior distribution to evaluate synthetical uncertainty of geological model. This posterior distribution represents the synthetical impact of all the uncertain factors on the spatial structure of geological model. The framework provides a solution to evaluate synthetical impact on geological model of multi-source uncertainties and a thought to study uncertainty propagation mechanism in geological modeling.
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Ikeda-Ohno, Atsushi; Harrison, Jennifer J; Thiruvoth, Sangeeth; Wilsher, Kerry; Wong, Henri K Y; Johansen, Mathew P; Waite, T David; Payne, Timothy E
2014-09-02
During the 1960s, radioactive waste containing small amounts of plutonium (Pu) and americium (Am) was disposed in shallow trenches at the Little Forest Burial Ground (LFBG), located near the southern suburbs of Sydney, Australia. Because of periodic saturation and overflowing of the former disposal trenches, Pu and Am have been transferred from the buried wastes into the surrounding surface soils. The presence of readily detected amounts of Pu and Am in the trench waters provides a unique opportunity to study their aqueous speciation under environmentally relevant conditions. This study aims to comprehensively investigate the chemical speciation of Pu and Am in the trench water by combining fluoride coprecipitation, solvent extraction, particle size fractionation, and thermochemical modeling. The predominant oxidation states of dissolved Pu and Am species were found to be Pu(IV) and Am(III), and large proportions of both actinides (Pu, 97.7%; Am, 86.8%) were associated with mobile colloids in the submicron size range. On the basis of this information, possible management options are assessed.
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Zhang, L.; Blanchard, P.; Gay, D.A.; Prestbo, E.M.; Risch, M.R.; Johnson, D.; Narayan, J.; Zsolway, R.; Holsen, T.M.; Miller, E.K.; Castro, M.S.; Graydon, J.A.; St. Louis, V.L.; Dalziel, J.
2012-01-01
Dry deposition of speciated mercury, i.e., gaseous oxidized mercury (GOM), particulate-bound mercury (PBM), and gaseous elemental mercury (GEM), was estimated for the year 2008–2009 at 19 monitoring locations in eastern and central North America. Dry deposition estimates were obtained by combining monitored two- to four-hourly speciated ambient concentrations with modeled hourly dry deposition velocities (Vd) calculated using forecasted meteorology. Annual dry deposition of GOM+PBM was estimated to be in the range of 0.4 to 8.1 μg m−2 at these locations with GOM deposition being mostly five to ten times higher than PBM deposition, due to their different modeled Vd values. Net annual GEM dry deposition was estimated to be in the range of 5 to 26 μg m−2 at 18 sites and 33 μg m−2 at one site. The estimated dry deposition agrees very well with limited surrogate-surface dry deposition measurements of GOM and PBM, and also agrees with litterfall mercury measurements conducted at multiple locations in eastern and central North America. This study suggests that GEM contributes much more than GOM+PBM to the total dry deposition at the majority of the sites considered here; the only exception is at locations close to significant point sources where GEM and GOM+PBM contribute equally to the total dry deposition. The relative magnitude of the speciated dry deposition and their good comparisons with litterfall deposition suggest that mercury in litterfall originates primarily from GEM, which is consistent with the limited number of previous field studies. The study also supports previous analyses suggesting that total dry deposition of mercury is equal to, if not more important than, wet deposition of mercury on a regional scale in eastern North America.
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Alderman, Phillip D.; Stanfill, Bryan
2016-10-06
Recent international efforts have brought renewed emphasis on the comparison of different agricultural systems models. Thus far, analysis of model-ensemble simulated results has not clearly differentiated between ensemble prediction uncertainties due to model structural differences per se and those due to parameter value uncertainties. Additionally, despite increasing use of Bayesian parameter estimation approaches with field-scale crop models, inadequate attention has been given to the full posterior distributions for estimated parameters. The objectives of this study were to quantify the impact of parameter value uncertainty on prediction uncertainty for modeling spring wheat phenology using Bayesian analysis and to assess the relativemore » contributions of model-structure-driven and parameter-value-driven uncertainty to overall prediction uncertainty. This study used a random walk Metropolis algorithm to estimate parameters for 30 spring wheat genotypes using nine phenology models based on multi-location trial data for days to heading and days to maturity. Across all cases, parameter-driven uncertainty accounted for between 19 and 52% of predictive uncertainty, while model-structure-driven uncertainty accounted for between 12 and 64%. Here, this study demonstrated the importance of quantifying both model-structure- and parameter-value-driven uncertainty when assessing overall prediction uncertainty in modeling spring wheat phenology. More generally, Bayesian parameter estimation provided a useful framework for quantifying and analyzing sources of prediction uncertainty.« less
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Nattier, Romain; Grandcolas, Philippe; Elias, Marianne; Desutter-Grandcolas, Laure; Jourdan, Hervé; Couloux, Arnaud; Robillard, Tony
2012-01-01
Islands are bounded areas where high endemism is explained either by allopatric speciation through the fragmentation of the limited amount of space available, or by sympatric speciation and accumulation of daughter species. Most empirical evidence point out the dominant action of allopatric speciation. We evaluate this general view by looking at a case study where sympatric speciation is suspected. We analyse the mode, tempo and geography of speciation in Agnotecous, a cricket genus endemic to New Caledonia showing a generalized pattern of sympatry between species making sympatric speciation plausible. We obtained five mitochondrial and five nuclear markers (6.8 kb) from 37 taxa corresponding to 17 of the 21 known extant species of Agnotecous, and including several localities per species, and we conducted phylogenetic and dating analyses. Our results suggest that the diversification of Agnotecous occurred mostly through allopatric speciation in the last 10 Myr. Highly microendemic species are the most recent ones (<2 Myr) and current sympatry is due to secondary range expansion after allopatric speciation. Species distribution should then be viewed as a highly dynamic process and extreme microendemism only as a temporary situation. We discuss these results considering the influence of climatic changes combined with intricate soil diversity and mountain topography. A complex interplay between these factors could have permitted repeated speciation events and range expansion.
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Weekley, Claire M.; Aitken, Jade B.; Finney, Lydia; Vogt, Stefan; Witting, Paul K.; Harris, Hugh H.
2013-01-01
Determining the speciation of selenium in vivo is crucial to understanding the biological activity of this essential element, which is a popular dietary supplement due to its anti-cancer properties. Hyphenated techniques that combine separation and detection methods are traditionally and effectively used in selenium speciation analysis, but require extensive sample preparation that may affect speciation. Synchrotron-based X-ray absorption and fluorescence techniques offer an alternative approach to selenium speciation analysis that requires minimal sample preparation. We present a brief summary of some key HPLC-ICP-MS and ESI-MS/MS studies of the speciation of selenium in cells and rat tissues. We review the results of a top-down approach to selenium speciation in human lung cancer cells that aims to link the speciation and distribution of selenium to its biological activity using a combination of X-ray absorption spectroscopy (XAS) and X-ray fluorescence microscopy (XFM). The results of this approach highlight the distinct fates of selenomethionine, methylselenocysteine and selenite in terms of their speciation and distribution within cells: organic selenium metabolites were widely distributed throughout the cells, whereas inorganic selenium metabolites were compartmentalized and associated with copper. New data from the XFM mapping of electrophoretically-separated cell lysates show the distribution of selenium in the proteins of selenomethionine-treated cells. Future applications of this top-down approach are discussed. PMID:23698165
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NASA Astrophysics Data System (ADS)
Salzburger, Walter; Meyer, Axel
With more than 3,000 species, the fish family Cichlidae is one of the most species-rich families of vertebrates. Cichlids occur in southern and central America, Africa, Madagascar, and India. The hotspot of their biodiversity is East Africa, where they form adaptive radiations composed of hundreds of endemic species in several lakes of various sizes and ages. The unparalleled species richness of East African cichlids has been something of a conundrum for evolutionary biologists and ecologists, since it has been in doubt whether these hundreds of species arose by allopatric speciation or whether it is necessary to invoke somewhat less traditional models of speciation, such as micro-allopatric, peripatric, or even sympatric speciation or evolution through sexual selection mediated by female choice. Ernst Mayr's analyses of these evolutionary uniquely diverse species assemblages have contributed to a more direct approach to this problem and have led to a deeper understanding of the patterns and processes that caused the formation of these huge groups of species. We review here recent molecular data on population differentiation and phylogenetics, which have helped to unravel, to some extent, the patterns and processes that led to the formation and ecological maintenance of cichlid species flocks. It is becoming apparent that sexually selected traits do play an important role in speciation in micro-allopatric or even sympatric settings. Species richness seems to be roughly correlated with the surface area, but not the age, of the lakes. We observe that the oldest lineages of a species flock of cichlids are often less species-rich and live in the open water or deepwater habitats. While the species flocks of the Lake Malawai and the Lake Victoria areas were shown to be monophyletic, the cichlid assemblage of Lake Tanganyika seems to consist of several independent species flocks. Cichlids emerge as an evolutionary model system in which many fundamental questions in evolution and ecology can be tested successfully, yet for other fish species flocks the relative importance of alternative mechanisms of speciation is likely to differ from that in cichlid fish.
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Model structures amplify uncertainty in predicted soil carbon responses to climate change.
Shi, Zheng; Crowell, Sean; Luo, Yiqi; Moore, Berrien
2018-06-04
Large model uncertainty in projected future soil carbon (C) dynamics has been well documented. However, our understanding of the sources of this uncertainty is limited. Here we quantify the uncertainties arising from model parameters, structures and their interactions, and how those uncertainties propagate through different models to projections of future soil carbon stocks. Both the vertically resolved model and the microbial explicit model project much greater uncertainties to climate change than the conventional soil C model, with both positive and negative C-climate feedbacks, whereas the conventional model consistently predicts positive soil C-climate feedback. Our findings suggest that diverse model structures are necessary to increase confidence in soil C projection. However, the larger uncertainty in the complex models also suggests that we need to strike a balance between model complexity and the need to include diverse model structures in order to forecast soil C dynamics with high confidence and low uncertainty.
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Wang, Peng; Ying, Qi; Zhang, Hongliang; Hu, Jianlin; Lin, Yingchao; Mao, Hongjun
2018-06-01
A Community Multiscale Air Quality (CMAQ) model with source-oriented lumped SAPRC-11 (S11L) photochemical mechanism and secondary organic aerosol (SOA) module was applied to determine the contributions of anthropogenic and biogenic sources to SOA concentrations in China. A one-year simulation of 2013 using the Multi-resolution Emission Inventory for China (MEIC) shows that summer SOA are generally higher (10-15 μg m -3 ) due to large contributions of biogenic (country average 60%) and industrial sources (17%). In winter, SOA formation was mostly due to anthropogenic emissions from industries (40%) and residential sources (38%). Emissions from other countries in southeast China account for approximately 14% of the SOA in both summer and winter, and 46% in spring due to elevated open biomass burning in southeast Asia. The Regional Emission inventory in ASia v2.1 (REAS2) was applied in this study for January and August 2013. Two sets of simulations with the REAS2 inventory were conducted using two different methods to speciate total non-methane carbon into model species. One approach uses total non-methane hydrocarbon (NMHC) emissions and representative speciation profiles from the SPECIATE database. The other approach retains the REAS2 speciated species that can be directly mapped to S11L model species and uses source specific splitting factors to map other REAS2 lumped NMHC species. Biogenic emissions are still the most significant contributor in summer based on these two sets of simulations. However, contributions from the transportation sector to SOA in January are predicted to be much more important based on the two REAS2 emission inventories (∼30-40% vs. ∼5% by MEIC), and contributions from residential sources according to REAS2 was much lower (∼21-24% vs. ∼42%). These discrepancies in source contributions to SOA need to be further investigated as the country seeks for optimal emission control strategies to fight severe air pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Model parameter uncertainty analysis for an annual field-scale P loss model
NASA Astrophysics Data System (ADS)
Bolster, Carl H.; Vadas, Peter A.; Boykin, Debbie
2016-08-01
Phosphorous (P) fate and transport models are important tools for developing and evaluating conservation practices aimed at reducing P losses from agricultural fields. Because all models are simplifications of complex systems, there will exist an inherent amount of uncertainty associated with their predictions. It is therefore important that efforts be directed at identifying, quantifying, and communicating the different sources of model uncertainties. In this study, we conducted an uncertainty analysis with the Annual P Loss Estimator (APLE) model. Our analysis included calculating parameter uncertainties and confidence and prediction intervals for five internal regression equations in APLE. We also estimated uncertainties of the model input variables based on values reported in the literature. We then predicted P loss for a suite of fields under different management and climatic conditions while accounting for uncertainties in the model parameters and inputs and compared the relative contributions of these two sources of uncertainty to the overall uncertainty associated with predictions of P loss. Both the overall magnitude of the prediction uncertainties and the relative contributions of the two sources of uncertainty varied depending on management practices and field characteristics. This was due to differences in the number of model input variables and the uncertainties in the regression equations associated with each P loss pathway. Inspection of the uncertainties in the five regression equations brought attention to a previously unrecognized limitation with the equation used to partition surface-applied fertilizer P between leaching and runoff losses. As a result, an alternate equation was identified that provided similar predictions with much less uncertainty. Our results demonstrate how a thorough uncertainty and model residual analysis can be used to identify limitations with a model. Such insight can then be used to guide future data collection and model development and evaluation efforts.
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Scanza, R. A.; Mahowald, N.; Ghan, S.; ...
2014-07-02
The mineralogy of desert dust is important due to its effect on radiation, clouds and biogeochemical cycling of trace nutrients. This study presents the simulation of dust radiative forcing as a function of both mineral composition and size at the global scale using mineral soil maps for estimating emissions. Externally mixed mineral aerosols in the bulk aerosol module in the Community Atmosphere Model version 4 (CAM4) and internally mixed mineral aerosols in the modal aerosol module in the Community Atmosphere Model version 5.1 (CAM5) embedded in the Community Earth System Model version 1.0.5 (CESM) are speciated into common mineral componentsmore » in place of total dust. The simulations with mineralogy are compared to available observations of mineral atmospheric distribution and deposition along with observations of clear-sky radiative forcing efficiency. Based on these simulations, we estimate the all-sky direct radiative forcing at the top of the atmosphere as +0.05 W m −2 for both CAM4 and CAM5 simulations with mineralogy and compare this both with simulations of dust in release versions of CAM4 and CAM5 (+0.08 and +0.17 W m −2) and of dust with optimized optical properties, wet scavenging and particle size distribution in CAM4 and CAM5, −0.05 and −0.17 W m −2, respectively. The ability to correctly include the mineralogy of dust in climate models is hindered by its spatial and temporal variability as well as insufficient global in-situ observations, incomplete and uncertain source mineralogies and the uncertainties associated with data retrieved from remote sensing methods.« less
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Scanza, Rachel; Mahowald, N.; Ghan, Steven J.; ...
2015-01-01
The mineralogy of desert dust is important due to its effect on radiation, clouds and biogeochemical cycling of trace nutrients. This study presents the simulation of dust radiative forcing as a function of both mineral composition and size at the global scale, using mineral soil maps for estimating emissions. Externally mixed mineral aerosols in the bulk aerosol module in the Community Atmosphere Model version 4 (CAM4) and internally mixed mineral aerosols in the modal aerosol module in the Community Atmosphere Model version 5.1 (CAM5) embedded in the Community Earth System Model version 1.0.5 (CESM) are speciated into common mineral componentsmore » in place of total dust. The simulations with mineralogy are compared to available observations of mineral atmospheric distribution and deposition along with observations of clear-sky radiative forcing efficiency. Based on these simulations, we estimate the all-sky direct radiative forcing at the top of the atmosphere as + 0.05 Wm⁻² for both CAM4 and CAM5 simulations with mineralogy. We compare this to the radiative forcing from simulations of dust in release versions of CAM4 and CAM5 (+0.08 and +0.17 Wm⁻²) and of dust with optimized optical properties, wet scavenging and particle size distribution in CAM4 and CAM5, -0.05 and -0.17 Wm⁻², respectively. The ability to correctly include the mineralogy of dust in climate models is hindered by its spatial and temporal variability as well as insufficient global in situ observations, incomplete and uncertain source mineralogies and the uncertainties associated with data retrieved from remote sensing methods.« less
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Can preference for oviposition sites initiate reproductive isolation in Callosobruchus maculatus?
Rova, Emma; Björklund, Mats
2011-01-31
Theory has identified a variety of evolutionary processes that may lead to speciation. Our study includes selection experiments using different host plants and test key predictions concerning models of speciation based on host plant choice, such as the evolution of host use (preference and performance) and assortative mating. This study shows that after only ten generations of selection on different resources/hosts in allopatry, strains of the seed beetle Callosobruchus maculatus develop new resource preferences and show resource-dependent assortative mating when given the possibility to choose mates and resources during secondary contact. The resulting reduced gene flow between the different strains remained for two generations after contact before being overrun by disassortative mating. We show that reduced gene flow can evolve in a population due to a link between host preference and assortative mating, although this result was not found in all lines. However, consistent with models of speciation, assortative mating alone is not sufficient to maintain reproductive isolation when individuals disperse freely between hosts. We conclude that the evolution of reproductive isolation in this system cannot proceed without selection against hybrids. Other possible factors facilitating the evolution of isolation would be longer periods of allopatry, the build up of local adaptation or reduced migration upon secondary contact.
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Uranium(IV) adsorption by natural organic matter in anoxic sediments
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bone, Sharon E.; Dynes, James J.; Cliff, John
2017-01-09
Uranium is an important fuel source and a global environmental contaminant. It accumulates in the tetravalent state, U(IV), in anoxic sediments, including ore deposits, marine basins, and contaminated aquifers. However, very little is known about the speciation of U(IV) in low temperature geochemical environments, inhibiting the development of a conceptual model of U behavior. Until recently, U(IV) was assumed to exist predominantly as the sparingly soluble mineral uraninite (UO 2) in anoxic sediments; yet studies now show that UO 2 is not often dominant in these environments. However, a model of U(IV) speciation under environmentally relevant conditions has not yetmore » been developed. Here we show that complexes of U(IV) adsorb on organic carbon and organic carbon-coated clays in an organic-rich natural substrate under field-relevant conditions. Whereas previous research assumed that the U(IV) product depended on the reduction pathway, our results demonstrate that UO 2 formation can be inhibited simply by decreasing the U:solid ratio. Thus, it is the number and type of surface ligands that controls U(IV) speciation subsequent to U(VI) reduction. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider retention of U(IV) ions within the local sediment environment.« less
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Folens, K; Van Hulle, S; Vanhaecke, F; Du Laing, G
2016-01-01
Palladium is used in several industrial applications and, given its high intrinsic value, intense efforts are made to recover the element. In this hydrometallurgic perspective, ion-exchange (IEX) technologies are principal means. Yet, without incorporating the chemical and physical properties of the Pd present in real, plant-specific conditions, the recovery cannot reach its technical nor economic optimum. This study characterized a relevant Pd-containing waste stream of a mirror manufacturer to provide input for a speciation model, predicting the Pd speciation as a function of pH and chloride concentration. Besides the administered neutral PdCl2 form, both positively and negatively charged [PdCln](2-n) species occur depending on the chloride concentration in solution. Purolite C100 and Relite 2AS IEX resins were selected and applied in combination with other treatment steps to optimize the Pd recovery. A combination of the cation and anion exchange resins was found successful to quantitatively recover Pd. Given the fact that Pd was also primarily associated with particles, laboratory-scale experiments focused on physical removal of the Pd-containing flow were conducted, which showed that particle-bound Pd can already be removed by physical pre-treatment prior to IEX, while the ionic fraction remains fully susceptible to the IEX mechanism.
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Trait-based diversification shifts reflect differential extinction among fossil taxa
Wagner, Peter J.; Estabrook, George F.
2014-01-01
Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models. PMID:25331898
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Methylmercury is a known neurotoxin with deleterious health effects on humans and wildlife. Atmospheric deposition is the largest source of mercury loading to most terrestrial and aquatic ecosystems. Regional scale air quality models are needed to quantify mercury deposition resu...
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NASA Astrophysics Data System (ADS)
Tang, Xiong; Zhang, Xiaoshan; Ci, Zhijia; Guo, Jia; Wang, Jiaqi
2016-05-01
In the winter and summer of 2013-2014, we used a sampling system, which consists of annular denuder, back-up filter and thermal desorption set-up, to measure the speciation of major inorganic salts in aerosols and the associated trace gases in Beijing. This sampling system can separate volatile ammonium salts (NH4NO3 and NH4Cl) from non-volatile ammonium salts ((NH4)2SO4), as well as the non-volatile nitrate and chloride. The measurement data was used as input of a thermodynamic equilibrium model (ISORROPIA II) to investigate the gas-aerosol equilibrium characteristics. Results show that (NH4)2SO4, NH4NO3 and NH4Cl were the major inorganic salts in aerosols and mainly existed in the fine particles. The sulfate, nitrate and chloride associated with crustal ions were also important in Beijing where mineral dust concentrations were high. About 19% of sulfate in winter and 11% of sulfate in summer were associated with crustal ions and originated from heterogeneous reactions or direct emissions. The non-volatile nitrate contributed about 33% and 15% of nitrate in winter and summer, respectively. Theoretical thermodynamic equilibrium calculations for NH4NO3 and NH4Cl suggest that the gaseous precursors were sufficient to form stable volatile ammonium salts in winter, whereas the internal mixing with sulfate and crustal species were important for the formation of volatile ammonium salts in summer. The results of the thermodynamic equilibrium model reasonably agreed with the measurements of aerosols and gases, but large discrepancy existed in predicting the speciation of inorganic ammonium salts. This indicates that the assumption on crustal species in the model was important for obtaining better understanding on gas-aerosol partitioning and improving the model prediction.
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Cadena, Carlos Daniel; Zapata, Felipe; Jiménez, Iván
2018-03-01
Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: 1) reliance on graphical analyses that convey little information on phenotype frequencies; 2) exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and 3) use of measures of central tendency to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models (NMMs) and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwin's ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of "Sisyphean" evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. We discuss how NMMs offer new perspectives in the kind of inferences available to systematists, with significant repercussions on ideas about the phenotypic structure of biodiversity.
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2012-01-01
The theory of speciation is dominated by adaptationist thinking, with less attention to mechanisms that do not affect species adaptation. Degeneracy – the imperfect specificity of interactions between diverse elements of biological systems and their environments – is key to the adaptability of populations. A mathematical model was explored in which population and resource were distributed one-dimensionally according to trait value. Resource consumption was degenerate – neither strictly location-specific nor location-independent. As a result, the competition for resources among the elements of the population was non-local. Two modeling approaches, a modified differential-integral Verhulstian equation and a cellular automata model, showed similar results: narrower degeneracy led to divergent dynamics with suppression of intermediate forms, whereas broader degeneracy led to suppression of diversifying forms, resulting in population stasis with increasing phenotypic homogeneity. Such behaviors did not increase overall adaptation because they continued after the model populations achieved maximal resource consumption rates, suggesting that degeneracy-driven distributed competition for resources rather than selective pressure toward more efficient resource exploitation was the driving force. The solutions were stable in the presence of limited environmental stochastic variability or heritable phenotypic variability. A conclusion was made that both dynamic diversification and static homogeneity of populations may be outcomes of the same process – distributed competition for resource not affecting the overall adaptation – with the difference between them defined by the spread of trait degeneracy in a given environment. Thus, biological degeneracy is a driving force of both speciation and stasis in biology, which, by themselves, are not necessarily adaptive in nature. PMID:23268831
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Reusable launch vehicle model uncertainties impact analysis
NASA Astrophysics Data System (ADS)
Chen, Jiaye; Mu, Rongjun; Zhang, Xin; Deng, Yanpeng
2018-03-01
Reusable launch vehicle(RLV) has the typical characteristics of complex aerodynamic shape and propulsion system coupling, and the flight environment is highly complicated and intensely changeable. So its model has large uncertainty, which makes the nominal system quite different from the real system. Therefore, studying the influences caused by the uncertainties on the stability of the control system is of great significance for the controller design. In order to improve the performance of RLV, this paper proposes the approach of analyzing the influence of the model uncertainties. According to the typical RLV, the coupling dynamic and kinematics models are built. Then different factors that cause uncertainties during building the model are analyzed and summed up. After that, the model uncertainties are expressed according to the additive uncertainty model. Choosing the uncertainties matrix's maximum singular values as the boundary model, and selecting the uncertainties matrix's norm to show t how much the uncertainty factors influence is on the stability of the control system . The simulation results illustrate that the inertial factors have the largest influence on the stability of the system, and it is necessary and important to take the model uncertainties into consideration before the designing the controller of this kind of aircraft( like RLV, etc).
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Modeling Low-temperature Geochemical Processes
NASA Astrophysics Data System (ADS)
Nordstrom, D. K.
2003-12-01
Geochemical modeling has become a popular and useful tool for a wide number of applications from research on the fundamental processes of water-rock interactions to regulatory requirements and decisions regarding permits for industrial and hazardous wastes. In low-temperature environments, generally thought of as those in the temperature range of 0-100 °C and close to atmospheric pressure (1 atm=1.01325 bar=101,325 Pa), complex hydrobiogeochemical reactions participate in an array of interconnected processes that affect us, and that, in turn, we affect. Understanding these complex processes often requires tools that are sufficiently sophisticated to portray multicomponent, multiphase chemical reactions yet transparent enough to reveal the main driving forces. Geochemical models are such tools. The major processes that they are required to model include mineral dissolution and precipitation; aqueous inorganic speciation and complexation; solute adsorption and desorption; ion exchange; oxidation-reduction; or redox; transformations; gas uptake or production; organic matter speciation and complexation; evaporation; dilution; water mixing; reaction during fluid flow; reaction involving biotic interactions; and photoreaction. These processes occur in rain, snow, fog, dry atmosphere, soils, bedrock weathering, streams, rivers, lakes, groundwaters, estuaries, brines, and diagenetic environments. Geochemical modeling attempts to understand the redistribution of elements and compounds, through anthropogenic and natural means, for a large range of scale from nanometer to global. "Aqueous geochemistry" and "environmental geochemistry" are often used interchangeably with "low-temperature geochemistry" to emphasize hydrologic or environmental objectives.Recognition of the strategy or philosophy behind the use of geochemical modeling is not often discussed or explicitly described. Plummer (1984, 1992) and Parkhurst and Plummer (1993) compare and contrast two approaches for modeling groundwater chemistry: (i) "forward modeling," which predicts water compositions from hypothesized reactions and user assumptions and (ii) "inverse modeling," which uses water, mineral, and isotopic compositions to constrain hypothesized reactions. These approaches simply reflect the amount of information one has to work with. With minimal information on a site, a modeler is forced to rely on forward modeling. Optimal information would include detailed mineralogy on drill cores or well cuttings combined with detailed water analyses at varying depths and sufficient spatial distribution to follow geochemical reactions and mixing of waters along defined flow paths. With optimal information, a modeler will depend on inverse modeling.This chapter outlines the main concepts and key developments in the field of geochemical modeling for low-temperature environments and illustrates their use with examples. It proceeds with a short discussion of what modeling is, continues with concepts and definitions commonly used, and follows with a short history of geochemical models, a discussion of databases, the codes that embody models, and recent examples of how these codes have been used in water-rock interactions. An important new stage of development seems to have been reached in this field with questions of reliability and validity of models. Future work will be obligated to document ranges of certainty and sources of uncertainty, sensitivity of models and codes to parameter errors and assumptions, propagation of errors, and delineation of the range of applicability.
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Huijbregts, Mark A J; Gilijamse, Wim; Ragas, Ad M J; Reijnders, Lucas
2003-06-01
The evaluation of uncertainty is relatively new in environmental life-cycle assessment (LCA). It provides useful information to assess the reliability of LCA-based decisions and to guide future research toward reducing uncertainty. Most uncertainty studies in LCA quantify only one type of uncertainty, i.e., uncertainty due to input data (parameter uncertainty). However, LCA outcomes can also be uncertain due to normative choices (scenario uncertainty) and the mathematical models involved (model uncertainty). The present paper outlines a new methodology that quantifies parameter, scenario, and model uncertainty simultaneously in environmental life-cycle assessment. The procedure is illustrated in a case study that compares two insulation options for a Dutch one-family dwelling. Parameter uncertainty was quantified by means of Monte Carlo simulation. Scenario and model uncertainty were quantified by resampling different decision scenarios and model formulations, respectively. Although scenario and model uncertainty were not quantified comprehensively, the results indicate that both types of uncertainty influence the case study outcomes. This stresses the importance of quantifying parameter, scenario, and model uncertainty simultaneously. The two insulation options studied were found to have significantly different impact scores for global warming, stratospheric ozone depletion, and eutrophication. The thickest insulation option has the lowest impact on global warming and eutrophication, and the highest impact on stratospheric ozone depletion.
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Rix, Michael G; Edwards, Danielle L; Byrne, Margaret; Harvey, Mark S; Joseph, Leo; Roberts, J Dale
2015-08-01
The south-western land division of Western Australia (SWWA), bordering the temperate Southern and Indian Oceans, is the only global biodiversity hotspot recognised in Australia. Renowned for its extraordinary diversity of endemic plants, and for some of the largest and most botanically significant temperate heathlands and woodlands on Earth, SWWA has long fascinated biogeographers. Its flat, highly weathered topography and the apparent absence of major geographic factors usually implicated in biotic diversification have challenged attempts to explain patterns of biogeography and mechanisms of speciation in the region. Botanical studies have always been central to understanding the biodiversity values of SWWA, although surprisingly few quantitative botanical analyses have allowed for an understanding of historical biogeographic processes in both space and time. Faunistic studies, by contrast, have played little or no role in defining hotspot concepts, despite several decades of accumulating quantitative research on the phylogeny and phylogeography of multiple lineages. In this review we critically analyse datasets with explicit supporting phylogenetic data and estimates of the time since divergence for all available elements of the terrestrial fauna, and compare these datasets to those available for plants. In situ speciation has played more of a role in shaping the south-western Australian fauna than has long been supposed, and has occurred in numerous endemic lineages of freshwater fish, frogs, reptiles, snails and less-vagile arthropods. By contrast, relatively low levels of endemism are found in birds, mammals and highly dispersive insects, and in situ speciation has played a negligible role in generating local endemism in birds and mammals. Quantitative studies provide evidence for at least four mechanisms driving patterns of endemism in south-western Australian animals, including: (i) relictualism of ancient Gondwanan or Pangaean taxa in the High Rainfall Province; (ii) vicariant isolation of lineages west of the Nullarbor divide; (iii) in situ speciation; and (iv) recent population subdivision. From dated quantitative studies we derive four testable models of historical biogeography for animal taxa in SWWA, each explicit in providing a spatial, temporal and topological perspective on patterns of speciation or divergence. For each model we also propose candidate lineages that may be worthy of further study, given what we know of their taxonomy, distributions or relationships. These models formalise four of the strongest patterns seen in many animal taxa from SWWA, although other models are clearly required to explain particular, idiosyncratic patterns. Generating numerous new datasets for suites of co-occurring lineages in SWWA will help refine our understanding of the historical biogeography of the region, highlight gaps in our knowledge, and allow us to derive general postulates from quantitative (rather than qualitative) results. For animals, this process has now begun in earnest, as has the process of taxonomically documenting many of the more diverse invertebrate lineages. The latter remains central to any attempt to appreciate holistically biogeographic patterns and processes in SWWA, and molecular phylogenetic studies should - where possible - also lead to tangible taxonomic outcomes. © 2014 The Authors. Biological Reviews © 2014 Cambridge Philosophical Society.
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Speciations and Extinctions in a Self-Organizing Critical Model of Tree-Like Evolution
NASA Astrophysics Data System (ADS)
Kramer, M.; Vandewalle, N.; Ausloos, M.
1996-04-01
We study analytically a simple model of a self-organized critical evolution. The model considers both extinction and speciation events leading to the growth of phylogenetic-like trees. Through a mean-field like theory, we study the evolution of the local configurations for the tree leaves. The fitness threshold, below which life activity takes place through avalanches of all sizes is calculated. The transition between speciating (evolving) and dead trees is obtained and is in agreement with numerical simulations. Moreover, this theoretical work suggests that the structure of the tree is strongly dependent on the extinction strength. Nous étudions analytiquement un modèle simple d'évolution auto-organisée critique. Le modèle considère des extinctions et des spéciations conduisant à une croissance d'arbre phylogénétiques. Nous étudions ici par une théorie de champ moyen l'évolution des configurations des extrémités de l'arbre. Le seuil critique de “fitness” en-dessous duquel des explosions d'activité biologique de toutes tailles se produisent est calculé. La transition entre arbres croissants et arbres éteints est également obtenue en accord avec les simulations. En outre, ce travail théorique suggère que la structure des arbres générés dépend fortement du paramètre d'extinctions.
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Phylogenetics and biogeography of the two-wing flyingfish (Exocoetidae: Exocoetus).
Lewallen, Eric A; Bohonak, Andrew J; Bonin, Carolina A; van Wijnen, Andre J; Pitman, Robert L; Lovejoy, Nathan R
2017-03-01
Two-wing flyingfish ( Exocoetus spp .) are widely distributed, epipelagic, mid-trophic organisms that feed on zooplankton and are preyed upon by numerous predators (e.g., tunas, dolphinfish, tropical seabirds), yet an understanding of their speciation and systematics is lacking. As a model of epipelagic fish speciation and to investigate mechanisms that increase biodiversity, we studied the phylogeny and biogeography of Exocoetus , a highly abundant holoepipelagic fish taxon of the tropical open ocean. Morphological and molecular data were used to evaluate the phylogenetic relationships, species boundaries, and biogeographic patterns of the five putative Exocoetus species. We show that the most widespread species ( E. volitans ) is sister to all other species, and we find no evidence for cryptic species in this taxon. Sister relationship between E. monocirrhus (Indo-Pacific) and E. obtusirostris (Atlantic) indicates the Isthmus of Panama and/or Benguela Barrier may have played a role in their divergence via allopatric speciation. The sister species E. peruvianus and E. gibbosus are found in different regions of the Pacific Ocean; however, our molecular results do not show a clear distinction between these species, indicating recent divergence or ongoing gene flow. Overall, our phylogeny reveals that the most spatially restricted species are more recently derived, suggesting that allopatric barriers may drive speciation, but subsequent dispersal and range expansion may affect the distributions of species.
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Blakemore, James D.; Hull, Jonathan F.
2012-01-01
The speciation behavior of a water-soluble manganese(III) tetrasulfonated phthalocyanine complex was investigated with UV-visible and electron paramagnetic resonance (EPR) spectroscopies, as well as cyclic voltammetry. Parallel-mode EPR (in dimethylformamide:pyridine solvent mix) reveals a six-line hyperfine signal, centered at a g-value of 8.8, for the manganese(III) monomer, characteristic of the d4 S=2 system. The color of an aqueous solution containing the complex is dependent upon the pH of the solution; the phthalocyanine complex can exist as a water-bound monomer, a hydroxide-bound monomer, or an oxo-bridged dimer. Addition of coordinating bases such as borate or pyridine changes the speciation behavior by coordinating the manganese center. From the UV-visible spectra, complete speciation diagrams are plotted by global analysis of the pH-dependent UV-visible spectra, and a complete set of pKa values is obtained by fitting the data to a standard pKa model. Electrochemical studies reveal a pH-independent quasi-reversible oxidation event for the monomeric species, which likely involves oxidation of the organic ligand to the radical cation species. Adsorption of the phthalocyanine complex on the carbon working electrode was sometimes observed. The pKa values and electrochemistry data are discussed in the context of the development of mononuclear water-oxidation catalysts. PMID:22585306
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Teng, Huajing; Zhang, Yaohua; Shi, Chengmin; Mao, Fengbiao; Cai, Wanshi; Lu, Liang; Zhao, Fangqing; Sun, Zhongsheng; Zhang, Jianxu
2017-09-01
Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Shock tube and chemical kinetic modeling study of the oxidation of 2,5-dimethylfuran.
Sirjean, Baptiste; Fournet, René; Glaude, Pierre-Alexandre; Battin-Leclerc, Frédérique; Wang, Weijing; Oehlschlaeger, Matthew A
2013-02-21
A detailed kinetic model describing the oxidation of 2,5-dimethylfuran (DMF), a potential second-generation biofuel, is proposed. The kinetic model is based upon quantum chemical calculations for the initial DMF consumption reactions and important reactions of intermediates. The model is validated by comparison to new DMF shock tube ignition delay time measurements (over the temperature range 1300-1831 K and at nominal pressures of 1 and 4 bar) and the DMF pyrolysis speciation measurements of Lifshitz et al. [ J. Phys. Chem. A 1998 , 102 ( 52 ), 10655 - 10670 ]. Globally, modeling predictions are in good agreement with the considered experimental targets. In particular, ignition delay times are predicted well by the new model, with model-experiment deviations of at most a factor of 2, and DMF pyrolysis conversion is predicted well, to within experimental scatter of the Lifshitz et al. data. Additionally, comparisons of measured and model predicted pyrolysis speciation provides validation of theoretically calculated channels for the oxidation of DMF. Sensitivity and reaction flux analyses highlight important reactions as well as the primary reaction pathways responsible for the decomposition of DMF and formation and destruction of key intermediate and product species.
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NASA Astrophysics Data System (ADS)
Ye, M.; Chen, Z.; Shi, L.; Zhu, Y.; Yang, J.
2017-12-01
Nitrogen reactive transport modeling is subject to uncertainty in model parameters, structures, and scenarios. While global sensitivity analysis is a vital tool for identifying the parameters important to nitrogen reactive transport, conventional global sensitivity analysis only considers parametric uncertainty. This may result in inaccurate selection of important parameters, because parameter importance may vary under different models and modeling scenarios. By using a recently developed variance-based global sensitivity analysis method, this paper identifies important parameters with simultaneous consideration of parametric uncertainty, model uncertainty, and scenario uncertainty. In a numerical example of nitrogen reactive transport modeling, a combination of three scenarios of soil temperature and two scenarios of soil moisture leads to a total of six scenarios. Four alternative models are used to evaluate reduction functions used for calculating actual rates of nitrification and denitrification. The model uncertainty is tangled with scenario uncertainty, as the reduction functions depend on soil temperature and moisture content. The results of sensitivity analysis show that parameter importance varies substantially between different models and modeling scenarios, which may lead to inaccurate selection of important parameters if model and scenario uncertainties are not considered. This problem is avoided by using the new method of sensitivity analysis in the context of model averaging and scenario averaging. The new method of sensitivity analysis can be applied to other problems of contaminant transport modeling when model uncertainty and/or scenario uncertainty are present.
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Uncertainty Modeling for Structural Control Analysis and Synthesis
NASA Technical Reports Server (NTRS)
Campbell, Mark E.; Crawley, Edward F.
1996-01-01
The development of an accurate model of uncertainties for the control of structures that undergo a change in operational environment, based solely on modeling and experimentation in the original environment is studied. The application used throughout this work is the development of an on-orbit uncertainty model based on ground modeling and experimentation. A ground based uncertainty model consisting of mean errors and bounds on critical structural parameters is developed. The uncertainty model is created using multiple data sets to observe all relevant uncertainties in the system. The Discrete Extended Kalman Filter is used as an identification/parameter estimation method for each data set, in addition to providing a covariance matrix which aids in the development of the uncertainty model. Once ground based modal uncertainties have been developed, they are localized to specific degrees of freedom in the form of mass and stiffness uncertainties. Two techniques are presented: a matrix method which develops the mass and stiffness uncertainties in a mathematical manner; and a sensitivity method which assumes a form for the mass and stiffness uncertainties in macroelements and scaling factors. This form allows the derivation of mass and stiffness uncertainties in a more physical manner. The mass and stiffness uncertainties of the ground based system are then mapped onto the on-orbit system, and projected to create an analogous on-orbit uncertainty model in the form of mean errors and bounds on critical parameters. The Middeck Active Control Experiment is introduced as experimental verification for the localization and projection methods developed. In addition, closed loop results from on-orbit operations of the experiment verify the use of the uncertainty model for control analysis and synthesis in space.
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New global fire emission estimates and evaluation of volatile organic compounds
C. Wiedinmyer; L. K. Emmons; S. K. Akagi; R. J. Yokelson; J. J. Orlando; J. A. Al-Saadi; A. J. Soja
2010-01-01
A daily, high-resolution, global fire emissions model has been built to estimate emissions from open burning for air quality modeling applications: The Fire INventory from NCAR (FINN version 1). The model framework uses daily fire detections from the MODIS instruments and updated emission factors, specifically for speciated non-methane organic compounds (NMOC). Global...
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Framework for Uncertainty Assessment - Hanford Site-Wide Groundwater Flow and Transport Modeling
NASA Astrophysics Data System (ADS)
Bergeron, M. P.; Cole, C. R.; Murray, C. J.; Thorne, P. D.; Wurstner, S. K.
2002-05-01
Pacific Northwest National Laboratory is in the process of development and implementation of an uncertainty estimation methodology for use in future site assessments that addresses parameter uncertainty as well as uncertainties related to the groundwater conceptual model. The long-term goals of the effort are development and implementation of an uncertainty estimation methodology for use in future assessments and analyses being made with the Hanford site-wide groundwater model. The basic approach in the framework developed for uncertainty assessment consists of: 1) Alternate conceptual model (ACM) identification to identify and document the major features and assumptions of each conceptual model. The process must also include a periodic review of the existing and proposed new conceptual models as data or understanding become available. 2) ACM development of each identified conceptual model through inverse modeling with historical site data. 3) ACM evaluation to identify which of conceptual models are plausible and should be included in any subsequent uncertainty assessments. 4) ACM uncertainty assessments will only be carried out for those ACMs determined to be plausible through comparison with historical observations and model structure identification measures. The parameter uncertainty assessment process generally involves: a) Model Complexity Optimization - to identify the important or relevant parameters for the uncertainty analysis; b) Characterization of Parameter Uncertainty - to develop the pdfs for the important uncertain parameters including identification of any correlations among parameters; c) Propagation of Uncertainty - to propagate parameter uncertainties (e.g., by first order second moment methods if applicable or by a Monte Carlo approach) through the model to determine the uncertainty in the model predictions of interest. 5)Estimation of combined ACM and scenario uncertainty by a double sum with each component of the inner sum (an individual CCDF) representing parameter uncertainty associated with a particular scenario and ACM and the outer sum enumerating the various plausible ACM and scenario combinations in order to represent the combined estimate of uncertainty (a family of CCDFs). A final important part of the framework includes identification, enumeration, and documentation of all the assumptions, which include those made during conceptual model development, required by the mathematical model, required by the numerical model, made during the spatial and temporal descretization process, needed to assign the statistical model and associated parameters that describe the uncertainty in the relevant input parameters, and finally those assumptions required by the propagation method. Pacific Northwest National Laboratory is operated for the U.S. Department of Energy under Contract DE-AC06-76RL01830.
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Rates of speciation in the fossil record
NASA Technical Reports Server (NTRS)
Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)
1998-01-01
Data from palaeontology and biodiversity suggest that the global biota should produce an average of three new species per year. However, the fossil record shows large variation around this mean. Rates of origination have declined through the Phanerozoic. This appears to have been largely a function of sorting among higher taxa (especially classes), which exhibit characteristic rates of speciation (and extinction) that differ among them by nearly an order of magnitude. Secular decline of origination rates is hardly constant, however; many positive deviations reflect accelerated speciation during rebounds from mass extinctions. There has also been general decline in rates of speciation within major taxa through their histories, although rates have tended to remain higher among members in tropical regions. Finally, pulses of speciation appear sometimes to be associated with climate change, although moderate oscillations of climate do not necessarily promote speciation despite forcing changes in species' geographical ranges.
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Speciation driven by hybridization and chromosomal plasticity in a wild yeast.
Leducq, Jean-Baptiste; Nielly-Thibault, Lou; Charron, Guillaume; Eberlein, Chris; Verta, Jukka-Pekka; Samani, Pedram; Sylvester, Kayla; Hittinger, Chris Todd; Bell, Graham; Landry, Christian R
2016-01-11
Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfil all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the interpretation that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here, we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.
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Quantifying model uncertainty in seasonal Arctic sea-ice forecasts
NASA Astrophysics Data System (ADS)
Blanchard-Wrigglesworth, Edward; Barthélemy, Antoine; Chevallier, Matthieu; Cullather, Richard; Fučkar, Neven; Massonnet, François; Posey, Pamela; Wang, Wanqiu; Zhang, Jinlun; Ardilouze, Constantin; Bitz, Cecilia; Vernieres, Guillaume; Wallcraft, Alan; Wang, Muyin
2017-04-01
Dynamical model forecasts in the Sea Ice Outlook (SIO) of September Arctic sea-ice extent over the last decade have shown lower skill than that found in both idealized model experiments and hindcasts of previous decades. Additionally, it is unclear how different model physics, initial conditions or post-processing techniques contribute to SIO forecast uncertainty. In this work, we have produced a seasonal forecast of 2015 Arctic summer sea ice using SIO dynamical models initialized with identical sea-ice thickness in the central Arctic. Our goals are to calculate the relative contribution of model uncertainty and irreducible error growth to forecast uncertainty and assess the importance of post-processing, and to contrast pan-Arctic forecast uncertainty with regional forecast uncertainty. We find that prior to forecast post-processing, model uncertainty is the main contributor to forecast uncertainty, whereas after forecast post-processing forecast uncertainty is reduced overall, model uncertainty is reduced by an order of magnitude, and irreducible error growth becomes the main contributor to forecast uncertainty. While all models generally agree in their post-processed forecasts of September sea-ice volume and extent, this is not the case for sea-ice concentration. Additionally, forecast uncertainty of sea-ice thickness grows at a much higher rate along Arctic coastlines relative to the central Arctic ocean. Potential ways of offering spatial forecast information based on the timescale over which the forecast signal beats the noise are also explored.
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A structured analysis of uncertainty surrounding modeled impacts of groundwater-extraction rules
NASA Astrophysics Data System (ADS)
Guillaume, Joseph H. A.; Qureshi, M. Ejaz; Jakeman, Anthony J.
2012-08-01
Integrating economic and groundwater models for groundwater-management can help improve understanding of trade-offs involved between conflicting socioeconomic and biophysical objectives. However, there is significant uncertainty in most strategic decision-making situations, including in the models constructed to represent them. If not addressed, this uncertainty may be used to challenge the legitimacy of the models and decisions made using them. In this context, a preliminary uncertainty analysis was conducted of a dynamic coupled economic-groundwater model aimed at assessing groundwater extraction rules. The analysis demonstrates how a variety of uncertainties in such a model can be addressed. A number of methods are used including propagation of scenarios and bounds on parameters, multiple models, block bootstrap time-series sampling and robust linear regression for model calibration. These methods are described within the context of a theoretical uncertainty management framework, using a set of fundamental uncertainty management tasks and an uncertainty typology.
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Hydrocarbon emissions characterization in the Colorado Front Range: A pilot study
NASA Astrophysics Data System (ADS)
Pétron, Gabrielle; Frost, Gregory; Miller, Benjamin R.; Hirsch, Adam I.; Montzka, Stephen A.; Karion, Anna; Trainer, Michael; Sweeney, Colm; Andrews, Arlyn E.; Miller, Lloyd; Kofler, Jonathan; Bar-Ilan, Amnon; Dlugokencky, Ed J.; Patrick, Laura; Moore, Charles T., Jr.; Ryerson, Thomas B.; Siso, Carolina; Kolodzey, William; Lang, Patricia M.; Conway, Thomas; Novelli, Paul; Masarie, Kenneth; Hall, Bradley; Guenther, Douglas; Kitzis, Duane; Miller, John; Welsh, David; Wolfe, Dan; Neff, William; Tans, Pieter
2012-02-01
The multispecies analysis of daily air samples collected at the NOAA Boulder Atmospheric Observatory (BAO) in Weld County in northeastern Colorado since 2007 shows highly correlated alkane enhancements caused by a regionally distributed mix of sources in the Denver-Julesburg Basin. To further characterize the emissions of methane and non-methane hydrocarbons (propane, n-butane, i-pentane, n-pentane and benzene) around BAO, a pilot study involving automobile-based surveys was carried out during the summer of 2008. A mix of venting emissions (leaks) of raw natural gas and flashing emissions from condensate storage tanks can explain the alkane ratios we observe in air masses impacted by oil and gas operations in northeastern Colorado. Using the WRAP Phase III inventory of total volatile organic compound (VOC) emissions from oil and gas exploration, production and processing, together with flashing and venting emission speciation profiles provided by State agencies or the oil and gas industry, we derive a range of bottom-up speciated emissions for Weld County in 2008. We use the observed ambient molar ratios and flashing and venting emissions data to calculate top-down scenarios for the amount of natural gas leaked to the atmosphere and the associated methane and non-methane emissions. Our analysis suggests that the emissions of the species we measured are most likely underestimated in current inventories and that the uncertainties attached to these estimates can be as high as a factor of two.
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NASA Astrophysics Data System (ADS)
Morgan, G. B., VI; Chou, I.-Ming; Pasteris, J. D.
1992-01-01
Fluid speciations and their related reaction pathways were studied in C-O-H-system fluids produced by the thermal dissociation of oxalic acid dihydrate (OAD: H 2C 2O 4 · 2H 2O) sealed in silica glass capsules. Experiments were conducted in the temperature range 230-750°C, with bulk fluid densities in the range 0.01-0.53 g/cm 3. Pressure was controlled by temperature and density in the isochoric systems. The quenched products of dissociation experiments were an aqueous liquid and one (supercritical fluid) or, rarely, two (vapor plus liquid) carbonic phase (s). In-situ Raman microanalyses were performed on the quenched carbonic phases at room temperature, at which fluid pressures ranged from about 50 to 340 bars. Bulk fluid speciations were reconstructed from the Raman analyses via mass balance constraints, and appear to monitor the true fluid speciations at run conditions. In experiments from the lowtemperature range (230-350°C), fluid speciations record the dissociation of OAD according to the reaction OAD = CO2 + CO + 3 H2O. A process of the form CO + H2O = CO2 + H2 is driven to the right with increasing temperature. The hydrogen gas produced tends to escape from the sample systems via diffusion into/through the silica glass capsules, shifting bulk compositions toward equimolar binary H 2O-CO 2 mixtures. The speciations of fluids in experiments with minimal hydrogen loss show poor agreement with speciations calculated for equilibrium fluids by the corresponding-states model of SAXENA and FEI (1988). Such disagreement suggests that the formations of CH 4 and graphite are metastably inhibited in the current experiments, which correlates with their absence or trivial abundances in experimental products. Moreover, calculations in which the stabilities of methane and graphite are suppressed suggest that such metastable equilibrium is approached only in experiments at temperatures greater than about 600-650°C. These results have applications to fluid processes in geological environments, in addition to considerations of using oxalate compounds as volatile sources in experimental studies. It is possible that disequilibrium or metastable fluids may be entrapped as inclusions; re-speciation (toward metastable or stable equilibrium) during P-T evolution of a given terrain would place the fluid inclusion on a new isochore that would not project through the original conditions of entrapment. Moreover, the disequilibrium to metastable nature of dissociation reactions, coupled with the diffusional mobility of hydrogen gas observed in the current experiments, suggests that the predominance of binary H 2O-CO 2 fluid mixtures in natural inclusions from medium- to high-grade metamorphic terrains may be more than a coincidence of similar initial bulk compositions.
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Morgan, G.B.; Chou, I.-Ming; Pasteris, J.D.
1992-01-01
Fluid speciations and their related reaction pathways were studied in C-O-H-system fluids produced by the thermal dissociation of oxalic acid dihydrate (OAD: H2C2O4 ?? 2H2O) sealed in silica glass capsules. Experiments were conducted in the temperature range 230-750??C, with bulk fluid densities in the range 0.01-0.53 g/cm3. Pressure was controlled by temperature and density in the isochoric systems. The quenched products of dissociation experiments were an aqueous liquid and one (supercritical fluid) or, rarely, two (vapor plus liquid) carbonic phase (s). In-situ Raman microanalyses were performed on the quenched carbonic phases at room temperature, at which fluid pressures ranged from about 50 to 340 bars. Bulk fluid speciations were reconstructed from the Raman analyses via mass balance constraints, and appear to monitor the true fluid speciations at run conditions. In experiments from the lowtemperature range (230-350??C), fluid speciations record the dissociation of OAD according to the reaction OAD = CO2 + CO + 3H2O. A process of the form CO + H2O = CO2 + H2 is driven to the right with increasing temperature. The hydrogen gas produced tends to escape from the sample systems via diffusion into/through the silica glass capsules, shifting bulk compositions toward equimolar binary H2O-CO2 mixtures. The speciations of fluids in experiments with minimal hydrogen loss show poor agreement with speciations calculated for equilibrium fluids by the corresponding-states model of Saxena and Fei (1988). Such disagreement suggests that the formations of CH4 and graphite are metastably inhibited in the current experiments, which correlates with their absence or trivial abundances in experimental products. Moreover, calculations in which the stabilities of methane and graphite are suppressed suggest that such metastable equilibrium is approached only in experiments at temperatures greater than about 600-650??C. These results have applications to fluid processes in geological environments, in addition to considerations of using oxalate compounds as volatile sources in experimental studies. It is possible that disequilibrium or metastable fluids may be entrapped as inclusions; re-speciation (toward metastable or stable equilibrium) during P-T evolution of a given terrain would place the fluid inclusion on a new isochore that would not project through the original conditions of entrapment. Moreover, the disequilibrium to metastable nature of dissociation reactions, coupled with the diffusional mobility of hydrogen gas observed in the current experiments, suggests that the predominance of binary H2O-CO2 fluid mixtures in natural inclusions from medium- to high-grade metamorphic terrains may be more than a coincidence of similar initial bulk compositions. ?? 1992.
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NASA Astrophysics Data System (ADS)
Migliavacca, M.; Sonnentag, O.; Keenan, T. F.; Cescatti, A.; O'Keefe, J.; Richardson, A. D.
2012-01-01
Phenology, the timing of recurring life cycle events, controls numerous land surface feedbacks to the climate systems through the regulation of exchanges of carbon, water and energy between the biosphere and atmosphere. Land surface models, however, are known to have systematic errors in the simulation of spring phenology, which potentially could propagate to uncertainty in modeled responses to future climate change. Here, we analyzed the Harvard Forest phenology record to investigate and characterize the sources of uncertainty in phenological forecasts and the subsequent impacts on model forecasts of carbon and water cycling in the future. Using a model-data fusion approach, we combined information from 20 yr of phenological observations of 11 North American woody species with 12 phenological models of different complexity to predict leaf bud-burst. The evaluation of different phenological models indicated support for spring warming models with photoperiod limitations and, though to a lesser extent, to chilling models based on the alternating model structure. We assessed three different sources of uncertainty in phenological forecasts: parameter uncertainty, model uncertainty, and driver uncertainty. The latter was characterized running the models to 2099 using 2 different IPCC climate scenarios (A1fi vs. B1, i.e. high CO2 emissions vs. low CO2 emissions scenario). Parameter uncertainty was the smallest (average 95% CI: 2.4 day century-1 for scenario B1 and 4.5 day century-1 for A1fi), whereas driver uncertainty was the largest (up to 8.4 day century-1 in the simulated trends). The uncertainty related to model structure is also large and the predicted bud-burst trends as well as the shape of the smoothed projections varied somewhat among models (±7.7 day century-1 for A1fi, ±3.6 day century-1 for B1). The forecast sensitivity of bud-burst to temperature (i.e. days bud-burst advanced per degree of warming) varied between 2.2 day °C-1 and 5.2 day °C-1 depending on model structure. We quantified the impact of uncertainties in bud-burst forecasts on simulated carbon and water fluxes using a process-based terrestrial biosphere model. Uncertainty in phenology model structure led to uncertainty in the description of the seasonality of processes, which accumulated to uncertainty in annual model estimates of gross primary productivity (GPP) and evapotranspiration (ET) of 9.6% and 2.9% respectively. A sensitivity analysis shows that a variation of ±10 days in bud-burst dates led to a variation of ±5.0% for annual GPP and about ±2.0% for ET. For phenology models, differences among future climate scenarios represent the largest source of uncertainty, followed by uncertainties related to model structure, and finally, uncertainties related to model parameterization. The uncertainties we have quantified will affect the description of the seasonality of processes and in particular the simulation of carbon uptake by forest ecosystems, with a larger impact of uncertainties related to phenology model structure, followed by uncertainties related to phenological model parameterization.
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Determination of Uncertainties for the New SSME Model
NASA Technical Reports Server (NTRS)
Coleman, Hugh W.; Hawk, Clark W.
1996-01-01
This report discusses the uncertainty analysis performed in support of a new test analysis and performance prediction model for the Space Shuttle Main Engine. The new model utilizes uncertainty estimates for experimental data and for the analytical model to obtain the most plausible operating condition for the engine system. This report discusses the development of the data sets and uncertainty estimates to be used in the development of the new model. It also presents the application of uncertainty analysis to analytical models and the uncertainty analysis for the conservation of mass and energy balance relations is presented. A new methodology for the assessment of the uncertainty associated with linear regressions is presented.
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NASA Astrophysics Data System (ADS)
Langer, P.; Sepahvand, K.; Guist, C.; Bär, J.; Peplow, A.; Marburg, S.
2018-03-01
The simulation model which examines the dynamic behavior of real structures needs to address the impact of uncertainty in both geometry and material parameters. This article investigates three-dimensional finite element models for structural dynamics problems with respect to both model and parameter uncertainties. The parameter uncertainties are determined via laboratory measurements on several beam-like samples. The parameters are then considered as random variables to the finite element model for exploring the uncertainty effects on the quality of the model outputs, i.e. natural frequencies. The accuracy of the output predictions from the model is compared with the experimental results. To this end, the non-contact experimental modal analysis is conducted to identify the natural frequency of the samples. The results show a good agreement compared with experimental data. Furthermore, it is demonstrated that geometrical uncertainties have more influence on the natural frequencies compared to material parameters and material uncertainties are about two times higher than geometrical uncertainties. This gives valuable insights for improving the finite element model due to various parameter ranges required in a modeling process involving uncertainty.
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Speciation in Drosophila: from phenotypes to molecules.
Orr, H Allen; Masly, J P; Phadnis, Nitin
2007-01-01
Study of the genetics of speciation--and especially of the genetics of intrinsic postzygotic isolation-has enjoyed remarkable progress over the last 2 decades. Indeed progress has been so rapid that one might be tempted to ask if the genetics of postzygotic isolation is now wrapped up. Here we argue that the genetics of speciation is far from complete. In particular, we review 2 topics where recent work has revealed major surprises: 1) the role of meiotic drive in hybrid sterility and 2) the role of gene transposition in speciation. These surprises, and others like them, suggest that evolutionary biologists may understand less about the genetic basis of speciation than seemed likely a few years ago.
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Evaluating Predictive Uncertainty of Hyporheic Exchange Modelling
NASA Astrophysics Data System (ADS)
Chow, R.; Bennett, J.; Dugge, J.; Wöhling, T.; Nowak, W.
2017-12-01
Hyporheic exchange is the interaction of water between rivers and groundwater, and is difficult to predict. One of the largest contributions to predictive uncertainty for hyporheic fluxes have been attributed to the representation of heterogeneous subsurface properties. This research aims to evaluate which aspect of the subsurface representation - the spatial distribution of hydrofacies or the model for local-scale (within-facies) heterogeneity - most influences the predictive uncertainty. Also, we seek to identify data types that help reduce this uncertainty best. For this investigation, we conduct a modelling study of the Steinlach River meander, in Southwest Germany. The Steinlach River meander is an experimental site established in 2010 to monitor hyporheic exchange at the meander scale. We use HydroGeoSphere, a fully integrated surface water-groundwater model, to model hyporheic exchange and to assess the predictive uncertainty of hyporheic exchange transit times (HETT). A highly parameterized complex model is built and treated as `virtual reality', which is in turn modelled with simpler subsurface parameterization schemes (Figure). Then, we conduct Monte-Carlo simulations with these models to estimate the predictive uncertainty. Results indicate that: Uncertainty in HETT is relatively small for early times and increases with transit times. Uncertainty from local-scale heterogeneity is negligible compared to uncertainty in the hydrofacies distribution. Introducing more data to a poor model structure may reduce predictive variance, but does not reduce predictive bias. Hydraulic head observations alone cannot constrain the uncertainty of HETT, however an estimate of hyporheic exchange flux proves to be more effective at reducing this uncertainty. Figure: Approach for evaluating predictive model uncertainty. A conceptual model is first developed from the field investigations. A complex model (`virtual reality') is then developed based on that conceptual model. This complex model then serves as the basis to compare simpler model structures. Through this approach, predictive uncertainty can be quantified relative to a known reference solution.
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Trends in PM2.5 emissions, concentrations and apportionments in Detroit and Chicago
NASA Astrophysics Data System (ADS)
Milando, Chad; Huang, Lei; Batterman, Stuart
2016-03-01
PM2.5 concentrations throughout much of the U.S. have decreased over the last 15 years, but emissions and concentration trends can vary by location and source type. Such trends should be understood to inform air quality management and policies. This work examines trends in emissions, concentrations and source apportionments in two large Midwest U.S. cities, Detroit, Michigan, and Chicago, Illinois. Annual and seasonal trends were investigated using National Emission Inventory (NEI) data for 2002 to 2011, speciated ambient PM2.5 data from 2001 to 2014, apportionments from positive matrix factorization (PMF) receptor modeling, and quantile regression. Over the study period, county-wide data suggest emissions from point sources decreased (Detroit) or held constant (Chicago), while emissions from on-road mobile sources were constant (Detroit) or increased (Chicago), however changes in methodology limit the interpretation of inventory trends. Ambient concentration data also suggest source and apportionment trends, e.g., annual median concentrations of PM2.5 in the two cities declined by 3.2-3.6%/yr (faster than national trends), and sulfate concentrations (due to coal-fired facilities and other point source emissions) declined even faster; in contrast, organic and elemental carbon (tracers of gasoline and diesel vehicle exhaust) declined more slowly or held constant. The PMF models identified nine sources in Detroit and eight in Chicago, the most important being secondary sulfate, secondary nitrate and vehicle emissions. A minor crustal dust source, metals sources, and a biomass source also were present in both cities. These apportionments showed that the median relative contributions from secondary sulfate sources decreased by 4.2-5.5% per year in Detroit and Chicago, while contributions from metals sources, biomass sources, and vehicles increased from 1.3 to 9.2% per year. This first application of quantile regression to trend analyses of speciated PM2.5 data reveals that source contributions to PM2.5 varied as PM2.5 concentrations decreased, and that the fraction of PM2.5 due to emissions from vehicles and other local emissions has increased. Each data source has uncertainties, but emissions, monitoring and PMF data provide complementary information that can help to discern trends and identify contributing sources. Study results emphasize the need to target specific sources in policies and regulations aimed at decreasing PM2.5 concentrations in urban areas.
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Oxygen Oases Before and After the GOE: Insights From Metals and Models
NASA Astrophysics Data System (ADS)
Olson, S. L.; Reinhard, C. T.; Planavsky, N. J.; Lyons, T. W.; Roy, M.; Anbar, A. D.
2014-12-01
The evolution of oxygenic photosynthesis fundamentally changed the structure of the marine biosphere and the chemistry of Earth's ocean-atmosphere system. Atmospheric oxygenation, however, was decoupled from the onset of biological O2 production—possibly lagging by as much as half a billion years—and O2 remained low for two billion years following initial O2 accumulation. Although uncertainties remain regarding the fate of biogenic O2 during the Precambrian, it is becoming clear that the consequences of oxygenesis were both spatially and temporally variable. Several lines of evidence support the existence of aerobic ecosystems associated with O2 oases within an otherwise anoxic Archean ocean; however—with notable exceptions—atmospheric O2 remained low enough to severely curtail oxidative weathering processes on long-term average throughout the Archean. During the subsequent Great Oxidation Event (GOE) in the early Paleoproterozoic, atmospheric O2 irreversibly increased above the sensitivity thresholds of several well-established proxies, but the level at which O2 eventually stabilized remains unclear. Consequently, the dynamics of O2 cycling are poorly characterized both before and after the GOE. Nevertheless, recent analytical and numerical results suggest exceptionally low O2 levels that may have favored Archean-style O2 oases in the mid-Proterozoic. We used Fe speciation and trace metal records from Precambrian shales, including data from two new cores that target the 2.7 Ga Roy Hill Shale, to investigate pre- and post- GOE redox heterogeneity in Earth's surface environments. Fe speciation supports the reconstruction of local marine redox conditions, and, in this context, trace metals can allow glimpses of redox conditions beyond the local environment, which may have throttled the supply of key redox-sensitive trace metals to the ocean. Then, using O2 constraints derived from these inorganic proxies, we use an Earth System model to explore C, O, and nutrient cycling in the late Archean and into the mid-Proterozoic. Although our results allow profound perturbation to several biogeochemical cycles and the climate system as a result of the GOE, we find that the GOE may have had only minor significance for the long-term average O2 content of typical surface seawater in the Proterozoic.
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NASA Astrophysics Data System (ADS)
Kumar, V.; Nayagum, D.; Thornton, S.; Banwart, S.; Schuhmacher2, M.; Lerner, D.
2006-12-01
Characterization of uncertainty associated with groundwater quality models is often of critical importance, as for example in cases where environmental models are employed in risk assessment. Insufficient data, inherent variability and estimation errors of environmental model parameters introduce uncertainty into model predictions. However, uncertainty analysis using conventional methods such as standard Monte Carlo sampling (MCS) may not be efficient, or even suitable, for complex, computationally demanding models and involving different nature of parametric variability and uncertainty. General MCS or variant of MCS such as Latin Hypercube Sampling (LHS) assumes variability and uncertainty as a single random entity and the generated samples are treated as crisp assuming vagueness as randomness. Also when the models are used as purely predictive tools, uncertainty and variability lead to the need for assessment of the plausible range of model outputs. An improved systematic variability and uncertainty analysis can provide insight into the level of confidence in model estimates, and can aid in assessing how various possible model estimates should be weighed. The present study aims to introduce, Fuzzy Latin Hypercube Sampling (FLHS), a hybrid approach of incorporating cognitive and noncognitive uncertainties. The noncognitive uncertainty such as physical randomness, statistical uncertainty due to limited information, etc can be described by its own probability density function (PDF); whereas the cognitive uncertainty such estimation error etc can be described by the membership function for its fuzziness and confidence interval by ?-cuts. An important property of this theory is its ability to merge inexact generated data of LHS approach to increase the quality of information. The FLHS technique ensures that the entire range of each variable is sampled with proper incorporation of uncertainty and variability. A fuzzified statistical summary of the model results will produce indices of sensitivity and uncertainty that relate the effects of heterogeneity and uncertainty of input variables to model predictions. The feasibility of the method is validated to assess uncertainty propagation of parameter values for estimation of the contamination level of a drinking water supply well due to transport of dissolved phenolics from a contaminated site in the UK.
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Lorén, J. Gaspar; Farfán, Maribel; Fusté, M. Carmen
2014-01-01
Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process. PMID:24586399
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Modeling uncertainty: quicksand for water temperature modeling
Bartholow, John M.
2003-01-01
Uncertainty has been a hot topic relative to science generally, and modeling specifically. Modeling uncertainty comes in various forms: measured data, limited model domain, model parameter estimation, model structure, sensitivity to inputs, modelers themselves, and users of the results. This paper will address important components of uncertainty in modeling water temperatures, and discuss several areas that need attention as the modeling community grapples with how to incorporate uncertainty into modeling without getting stuck in the quicksand that prevents constructive contributions to policy making. The material, and in particular the reference, are meant to supplement the presentation given at this conference.
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Assessing Uncertainty in Risk Assessment Models (BOSC CSS meeting)
In vitro assays are increasingly being used in risk assessments Uncertainty in assays leads to uncertainty in models used for risk assessments. This poster assesses uncertainty in the ER and AR models.
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NASA Astrophysics Data System (ADS)
Blanchard-Wrigglesworth, E.; Barthélemy, A.; Chevallier, M.; Cullather, R.; Fučkar, N.; Massonnet, F.; Posey, P.; Wang, W.; Zhang, J.; Ardilouze, C.; Bitz, C. M.; Vernieres, G.; Wallcraft, A.; Wang, M.
2017-08-01
Dynamical model forecasts in the Sea Ice Outlook (SIO) of September Arctic sea-ice extent over the last decade have shown lower skill than that found in both idealized model experiments and hindcasts of previous decades. Additionally, it is unclear how different model physics, initial conditions or forecast post-processing (bias correction) techniques contribute to SIO forecast uncertainty. In this work, we have produced a seasonal forecast of 2015 Arctic summer sea ice using SIO dynamical models initialized with identical sea-ice thickness in the central Arctic. Our goals are to calculate the relative contribution of model uncertainty and irreducible error growth to forecast uncertainty and assess the importance of post-processing, and to contrast pan-Arctic forecast uncertainty with regional forecast uncertainty. We find that prior to forecast post-processing, model uncertainty is the main contributor to forecast uncertainty, whereas after forecast post-processing forecast uncertainty is reduced overall, model uncertainty is reduced by an order of magnitude, and irreducible error growth becomes the main contributor to forecast uncertainty. While all models generally agree in their post-processed forecasts of September sea-ice volume and extent, this is not the case for sea-ice concentration. Additionally, forecast uncertainty of sea-ice thickness grows at a much higher rate along Arctic coastlines relative to the central Arctic ocean. Potential ways of offering spatial forecast information based on the timescale over which the forecast signal beats the noise are also explored.
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Irreducible Uncertainty in Terrestrial Carbon Projections
NASA Astrophysics Data System (ADS)
Lovenduski, N. S.; Bonan, G. B.
2016-12-01
We quantify and isolate the sources of uncertainty in projections of carbon accumulation by the ocean and terrestrial biosphere over 2006-2100 using output from Earth System Models participating in the 5th Coupled Model Intercomparison Project. We consider three independent sources of uncertainty in our analysis of variance: (1) internal variability, driven by random, internal variations in the climate system, (2) emission scenario, driven by uncertainty in future radiative forcing, and (3) model structure, wherein different models produce different projections given the same emission scenario. Whereas uncertainty in projections of ocean carbon accumulation by 2100 is 100 Pg C and driven primarily by emission scenario, uncertainty in projections of terrestrial carbon accumulation by 2100 is 50% larger than that of the ocean, and driven primarily by model structure. This structural uncertainty is correlated with emission scenario: the variance associated with model structure is an order of magnitude larger under a business-as-usual scenario (RCP8.5) than a mitigation scenario (RCP2.6). In an effort to reduce this structural uncertainty, we apply various model weighting schemes to our analysis of variance in terrestrial carbon accumulation projections. The largest reductions in uncertainty are achieved when giving all the weight to a single model; here the uncertainty is of a similar magnitude to the ocean projections. Such an analysis suggests that this structural uncertainty is irreducible given current terrestrial model development efforts.
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Uncertainty of climate change impact on groundwater reserves - Application to a chalk aquifer
NASA Astrophysics Data System (ADS)
Goderniaux, Pascal; Brouyère, Serge; Wildemeersch, Samuel; Therrien, René; Dassargues, Alain
2015-09-01
Recent studies have evaluated the impact of climate change on groundwater resources for different geographical and climatic contexts. However, most studies have either not estimated the uncertainty around projected impacts or have limited the analysis to the uncertainty related to climate models. In this study, the uncertainties around impact projections from several sources (climate models, natural variability of the weather, hydrological model calibration) are calculated and compared for the Geer catchment (465 km2) in Belgium. We use a surface-subsurface integrated model implemented using the finite element code HydroGeoSphere, coupled with climate change scenarios (2010-2085) and the UCODE_2005 inverse model, to assess the uncertainty related to the calibration of the hydrological model. This integrated model provides a more realistic representation of the water exchanges between surface and subsurface domains and constrains more the calibration with the use of both surface and subsurface observed data. Sensitivity and uncertainty analyses were performed on predictions. The linear uncertainty analysis is approximate for this nonlinear system, but it provides some measure of uncertainty for computationally demanding models. Results show that, for the Geer catchment, the most important uncertainty is related to calibration of the hydrological model. The total uncertainty associated with the prediction of groundwater levels remains large. By the end of the century, however, the uncertainty becomes smaller than the predicted decline in groundwater levels.
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How humans drive speciation as well as extinction
Maron, M.
2016-01-01
A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity. PMID:27358365
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How humans drive speciation as well as extinction.
Bull, J W; Maron, M
2016-06-29
A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation-and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon 'no net loss' conservation literature-considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity. © 2016 The Author(s).
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Q-Speciation and Network Structure Evolution in Invert Calcium Silicate Glasses.
Kaseman, Derrick C; Retsinas, A; Kalampounias, A G; Papatheodorou, G N; Sen, S
2015-07-02
Binary silicate glasses in the system CaO-SiO2 are synthesized over an extended composition range (42 mol % ≤ CaO ≤ 61 mol %), using container-less aerodynamic levitation techniques and CO2-laser heating. The compositional evolution of Q speciation in these glasses is quantified using (29)Si and (17)O magic angle spinning nuclear magnetic resonance spectroscopy. The results indicate progressive depolymerization of the silicate network upon addition of CaO and significant deviation of the Q speciation from the binary model. The equilibrium constants for the various Q species disproportionation reactions for these glasses are found to be similar to (much smaller than) those characteristic of Li (Mg)-silicate glasses, consistent with the corresponding trends in the field strengths of these modifier cations. Increasing CaO concentration results in an increase in the packing density and structural rigidity of these glasses and consequently in their glass transition temperature Tg. This apparent role reversal of conventional network-modifying cations in invert alkaline-earth silicate glasses are compared and contrasted with that in their alkali silicate counterparts.
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NASA Astrophysics Data System (ADS)
Tsai, F. T.; Elshall, A. S.; Hanor, J. S.
2012-12-01
Subsurface modeling is challenging because of many possible competing propositions for each uncertain model component. How can we judge that we are selecting the correct proposition for an uncertain model component out of numerous competing propositions? How can we bridge the gap between synthetic mental principles such as mathematical expressions on one hand, and empirical observation such as observation data on the other hand when uncertainty exists on both sides? In this study, we introduce hierarchical Bayesian model averaging (HBMA) as a multi-model (multi-proposition) framework to represent our current state of knowledge and decision for hydrogeological structure modeling. The HBMA framework allows for segregating and prioritizing different sources of uncertainty, and for comparative evaluation of competing propositions for each source of uncertainty. We applied the HBMA to a study of hydrostratigraphy and uncertainty propagation of the Southern Hills aquifer system in the Baton Rouge area, Louisiana. We used geophysical data for hydrogeological structure construction through indictor hydrostratigraphy method and used lithologic data from drillers' logs for model structure calibration. However, due to uncertainty in model data, structure and parameters, multiple possible hydrostratigraphic models were produced and calibrated. The study considered four sources of uncertainties. To evaluate mathematical structure uncertainty, the study considered three different variogram models and two geological stationarity assumptions. With respect to geological structure uncertainty, the study considered two geological structures with respect to the Denham Springs-Scotlandville fault. With respect to data uncertainty, the study considered two calibration data sets. These four sources of uncertainty with their corresponding competing modeling propositions resulted in 24 calibrated models. The results showed that by segregating different sources of uncertainty, HBMA analysis provided insights on uncertainty priorities and propagation. In addition, it assisted in evaluating the relative importance of competing modeling propositions for each uncertain model component. By being able to dissect the uncertain model components and provide weighted representation of the competing propositions for each uncertain model component based on the background knowledge, the HBMA functions as an epistemic framework for advancing knowledge about the system under study.
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NASA Astrophysics Data System (ADS)
Pianosi, Francesca; Lal Shrestha, Durga; Solomatine, Dimitri
2010-05-01
This research presents an extension of UNEEC (Uncertainty Estimation based on Local Errors and Clustering, Shrestha and Solomatine, 2006, 2008 & Solomatine and Shrestha, 2009) method in the direction of explicit inclusion of parameter uncertainty. UNEEC method assumes that there is an optimal model and the residuals of the model can be used to assess the uncertainty of the model prediction. It is assumed that all sources of uncertainty including input, parameter and model structure uncertainty are explicitly manifested in the model residuals. In this research, theses assumptions are relaxed, and the UNEEC method is extended to consider parameter uncertainty as well (abbreviated as UNEEC-P). In UNEEC-P, first we use Monte Carlo (MC) sampling in parameter space to generate N model realizations (each of which is a time series), estimate the prediction quantiles based on the empirical distribution functions of the model residuals considering all the residual realizations, and only then apply the standard UNEEC method that encapsulates the uncertainty of a hydrologic model (expressed by quantiles of the error distribution) in a machine learning model (e.g., ANN). UNEEC-P is applied first to a linear regression model of synthetic data, and then to a real case study of forecasting inflow to lake Lugano in northern Italy. The inflow forecasting model is a stochastic heteroscedastic model (Pianosi and Soncini-Sessa, 2009). The preliminary results show that the UNEEC-P method produces wider uncertainty bounds, which is consistent with the fact that the method considers also parameter uncertainty of the optimal model. In the future UNEEC method will be further extended to consider input and structure uncertainty which will provide more realistic estimation of model predictions.
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A tool for efficient, model-independent management optimization under uncertainty
White, Jeremy; Fienen, Michael N.; Barlow, Paul M.; Welter, Dave E.
2018-01-01
To fill a need for risk-based environmental management optimization, we have developed PESTPP-OPT, a model-independent tool for resource management optimization under uncertainty. PESTPP-OPT solves a sequential linear programming (SLP) problem and also implements (optional) efficient, “on-the-fly” (without user intervention) first-order, second-moment (FOSM) uncertainty techniques to estimate model-derived constraint uncertainty. Combined with a user-specified risk value, the constraint uncertainty estimates are used to form chance-constraints for the SLP solution process, so that any optimal solution includes contributions from model input and observation uncertainty. In this way, a “single answer” that includes uncertainty is yielded from the modeling analysis. PESTPP-OPT uses the familiar PEST/PEST++ model interface protocols, which makes it widely applicable to many modeling analyses. The use of PESTPP-OPT is demonstrated with a synthetic, integrated surface-water/groundwater model. The function and implications of chance constraints for this synthetic model are discussed.
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Speciation in fungal and oomycete plant pathogens
USDA-ARS?s Scientific Manuscript database
The process of speciation by definition involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed ...
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Ruminant-specific multiple duplication events of PRDM9 before speciation
USDA-ARS?s Scientific Manuscript database
Understanding the genetic and evolutionary mechanisms of speciation genes in sexually reproducing organisms would provide important insights into mammalian reproduction and fitness. PRDM9, a widely known speciation gene, has recently gained attention for its important role in meiotic recombination a...
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The Development and Uses of EPA's SPECIATE Database
SPECIATE is the U.S. Environmental Protection Agency's (EPA) repository of volatile organic compounds (VOC) and particulate matter (PM) speciation profiles of air pollution sources. These source profiles can be used to (l) provide input to chemical mass balance (CMB) receptor mod...
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SPECIATION OF ORGANICS IN WATER
We describe herein a method for determining constants for simultaneously occurring, site-specific "microequilibria" (as with tautomers) for organics in water. The method is based in part on modeling temperature-variant Raman spectra according to the van't Hoff equation....
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July 2013 MOVES Model Review Work Group Meeting Materials
Presentations from the Mobile Sources Technical Review Subcommittee (MSTRS) meeting on July 9th of 2013 include MOtor Vehicle Emission Simulator (MOVES) updates; data regarding vehicle populations and activity, PM speciation, and hazardous air pollutants.
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September 2016 MOVES Model Review Work Group Meeting Materials
Presentations from the Mobile Sources Technical Review Subcommittee (MSTRS) meeting on Sep. 14th of 2016 include MOtor Vehicle Emission Simulator (MOVES) updates; data regarding vehicle populations and activity, PM speciation, and hazardous air pollutants.
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The Drosophila flavopilosa species group (Diptera, Drosophilidae)
Robe, Lizandra J.; De Ré, Francine Cenzi; Ludwig, Adriana; Loreto, Elgion L.S.
2013-01-01
The D. flavopilosa group encompasses an ecologically restricted set of species strictly adapted to hosting flowers of Cestrum (Solanaceae). This group presents potential to be used as a model to the study of different questions regarding ecologically restricted species macro and microevolutionary responses, geographical vs. ecological speciation and intra and interspecific competition. This review aims to revisit and reanalyze the patterns and processes that are subjacent to the interesting ecological and evolutionary properties of these species. Biotic and abiotic niche properties of some species were reanalyzed in face of ecological niche modeling approaches in order to get some insights into their ecological evolution. A test of the potential of DNA-Barcoding provided evidences that this technology may be a way of overcoming difficulties related to cryptic species differentiation. The new focus replenishes the scenario with new questions, presenting a case where neither geographical nor ecological speciation may be as yet suggested. PMID:23459119
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Jon Chorover, University of Arizona; Peggy O'ÃÂÃÂDay, University of California, Merced; Karl Mueller, Penn State University
2012-10-01
Hanford sediments impacted by hyperalkaline high level radioactive waste have undergone incongruent silicate mineral weathering concurrent with contaminant uptake. In this project, we studied the impact of background pore water (BPW) on strontium, cesium and iodine desorption and transport in Hanford sediments that were experimentally weathered by contact with simulated hyperalkaline tank waste leachate (STWL) solutions. Using those lab-weathered Hanford sediments (HS) and model precipitates formed during nucleation from homogeneous STWL solutions (HN), we (i) provided detailed characterization of reaction products over a matrix of field-relevant gradients in contaminant concentration, PCO2, and reaction time; (ii) improved molecular-scale understanding of howmore » sorbate speciation controls contaminant desorption from weathered sediments upon removal of caustic sources; and (iii) developed a mechanistic, predictive model of meso- to field-scale contaminant reactive transport under these conditions.« less
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Development of Modal Aerosol Module in CAM5 for Biogeochemical Cycles
DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu, Xiaohong
2017-11-18
This project aims at developing new capabilities for the Modal Aerosol Module in the DOE’s E3SM model with the applications to the global biogeochemical cycle. The impacts of the new developments on model simulations of clouds and climate will be examined. There are thee objectives for this project study: Implementing primary marine organic aerosols into the modal aerosol module (MAM) and investigate effects of primary marine organic aerosols on climate in E3SM; Implementing dust speciation in MAM and investigate the effect of dust species on mixed-phase clouds through indirect effects in E3SM; Writing papers documenting the new MAM developments (e.g.,more » MAM4 documentation paper, marine organic aerosol paper, dust speciation); These objectives will be accomplished in collaborations with Drs. Phil Rasch, Steve Ghan, and Susannah Burrows at Pacific Northwest National Laboratory.« less
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Investigation of uranium binding forms in selected German mineral waters.
Osman, Alfatih A A; Geipel, Gerhard; Bernhard, Gert; Worch, Eckhard
2013-12-01
Cryogenic time-resolved laser-induced fluorescence spectroscopy was successfully used to identify uranium binding forms in selected German mineral waters of extremely low uranium concentrations (<2.0 μg/L). The measurements were performed at a low temperature of 153 K. The spectroscopic data showed a prevalence of aquatic species Ca2UO2(CO3)3 in all investigated waters, while other uranyl-carbonate complexes, viz, UO2CO3(aq) and UO2(CO3)2 (2-), only existed as minor species. The pH value, alkalinity (CO3 (2-)), and the main water inorganic constituents, specifically the Ca(2+) concentration, showed a clear influence on uranium speciation. Speciation modeling was performed using the most recent thermodynamic data for aqueous complexes of uranium. The modeling results for the main uranium binding form in the investigated waters indicated a good agreement with the spectroscopy measurements.
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Kalis, Erwin J J; Weng, Liping; Dousma, Freerk; Temminghoff, Erwin J M; Van Riemsdijk, Willem H
2006-02-01
Metal toxicity is not related to the total but rather to the free or labile metal ion concentration. One of the techniques that can be used to measure several free metal ion concentrations simultaneously is the Donnan Membrane Technique (DMT) in combination with the inductively coupled plasma-mass spectrometer (ICP-MS). However, free metal ion concentrations in natural waters are commonly below the detection limit of ICP-MS. We decreased the detection limit by making use of a ligand, and we developed a field DMT cell that can be applied in situ in natural waters. A kinetic approach can be used to calculate free metal ion concentrations when the equilibrium time becomes too large. The field DMT measured in situ in natural waters a free metal ion concentration ranging from 0.015% (Cu) to 13% (Zn) of a total metal concentration ranging from 0.06 nM (Cd) to 237 nM (Zn). The free metal ion concentrations were difficult to predict using an equilibrium speciation model, probably due to the uncertainty in the nature of the dissolved organic matter or the presence of other reactive colloids. It is shown that DMT can follow changes in the free metal ion concentration on times scales less than a day under certain conditions.
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USDA-ARS?s Scientific Manuscript database
Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road was proposed based on evidence from diverse genomic analyses. Cultiva...
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Arsenic uptake processes were evaluated in a zerovalent iron reactive barrier installed at a lead smelting facility using geochemical modeling, solid-phase analysis, and X-ray absorption spectroscopy techniques. Aqueous speciation of arsenic plays a key role in directing arsenic...
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NASA Astrophysics Data System (ADS)
Migliavacca, M.; Sonnentag, O.; Keenan, T. F.; Cescatti, A.; O'Keefe, J.; Richardson, A. D.
2012-06-01
Phenology, the timing of recurring life cycle events, controls numerous land surface feedbacks to the climate system through the regulation of exchanges of carbon, water and energy between the biosphere and atmosphere. Terrestrial biosphere models, however, are known to have systematic errors in the simulation of spring phenology, which potentially could propagate to uncertainty in modeled responses to future climate change. Here, we used the Harvard Forest phenology record to investigate and characterize sources of uncertainty in predicting phenology, and the subsequent impacts on model forecasts of carbon and water cycling. Using a model-data fusion approach, we combined information from 20 yr of phenological observations of 11 North American woody species, with 12 leaf bud-burst models that varied in complexity. Akaike's Information Criterion indicated support for spring warming models with photoperiod limitations and, to a lesser extent, models that included chilling requirements. We assessed three different sources of uncertainty in phenological forecasts: parameter uncertainty, model uncertainty, and driver uncertainty. The latter was characterized running the models to 2099 using 2 different IPCC climate scenarios (A1fi vs. B1, i.e. high CO2 emissions vs. low CO2 emissions scenario). Parameter uncertainty was the smallest (average 95% Confidence Interval - CI: 2.4 days century-1 for scenario B1 and 4.5 days century-1 for A1fi), whereas driver uncertainty was the largest (up to 8.4 days century-1 in the simulated trends). The uncertainty related to model structure is also large and the predicted bud-burst trends as well as the shape of the smoothed projections varied among models (±7.7 days century-1 for A1fi, ±3.6 days century-1 for B1). The forecast sensitivity of bud-burst to temperature (i.e. days bud-burst advanced per degree of warming) varied between 2.2 days °C-1 and 5.2 days °C-1 depending on model structure. We quantified the impact of uncertainties in bud-burst forecasts on simulated photosynthetic CO2 uptake and evapotranspiration (ET) using a process-based terrestrial biosphere model. Uncertainty in phenology model structure led to uncertainty in the description of forest seasonality, which accumulated to uncertainty in annual model estimates of gross primary productivity (GPP) and ET of 9.6% and 2.9%, respectively. A sensitivity analysis shows that a variation of ±10 days in bud-burst dates led to a variation of ±5.0% for annual GPP and about ±2.0% for ET. For phenology models, differences among future climate scenarios (i.e. driver) represent the largest source of uncertainty, followed by uncertainties related to model structure, and finally, related to model parameterization. The uncertainties we have quantified will affect the description of the seasonality of ecosystem processes and in particular the simulation of carbon uptake by forest ecosystems, with a larger impact of uncertainties related to phenology model structure, followed by uncertainties related to phenological model parameterization.
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Strategies to predict metal mobility in surficial mining environments
Smith, Kathleen S.
2007-01-01
This report presents some strategies to predict metal mobility at mining sites. These strategies are based on chemical, physical, and geochemical information about metals and their interactions with the environment. An overview of conceptual models, metal sources, and relative mobility of metals under different geochemical conditions is presented, followed by a discussion of some important physical and chemical properties of metals that affect their mobility, bioavailability, and toxicity. The physical and chemical properties lead into a discussion of the importance of the chemical speciation of metals. Finally, environmental and geochemical processes and geochemical barriers that affect metal speciation are discussed. Some additional concepts and applications are briefly presented at the end of this report.
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Plummer, Niel; Jones, Blair F.; Truesdell, Alfred Hemingway
1976-01-01
WATEQF is a FORTRAN IV computer program that models the thermodynamic speciation of inorganic ions and complex species in solution for a given water analysis. The original version (WATEQ) was written in 1973 by A. H. Truesdell and B. F. Jones in Programming Language/one (PL/1.) With but a few exceptions, the thermochemical data, speciation, coefficients, and general calculation procedure of WATEQF is identical to the PL/1 version. This report notes the differences between WATEQF and WATEQ, demonstrates how to set up the input data to execute WATEQF, provides a test case for comparison, and makes available a listing of WATEQF. (Woodard-USGS)
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Uncertainty analysis of hydrological modeling in a tropical area using different algorithms
NASA Astrophysics Data System (ADS)
Rafiei Emam, Ammar; Kappas, Martin; Fassnacht, Steven; Linh, Nguyen Hoang Khanh
2018-01-01
Hydrological modeling outputs are subject to uncertainty resulting from different sources of errors (e.g., error in input data, model structure, and model parameters), making quantification of uncertainty in hydrological modeling imperative and meant to improve reliability of modeling results. The uncertainty analysis must solve difficulties in calibration of hydrological models, which further increase in areas with data scarcity. The purpose of this study is to apply four uncertainty analysis algorithms to a semi-distributed hydrological model, quantifying different source of uncertainties (especially parameter uncertainty) and evaluate their performance. In this study, the Soil and Water Assessment Tools (SWAT) eco-hydrological model was implemented for the watershed in the center of Vietnam. The sensitivity of parameters was analyzed, and the model was calibrated. The uncertainty analysis for the hydrological model was conducted based on four algorithms: Generalized Likelihood Uncertainty Estimation (GLUE), Sequential Uncertainty Fitting (SUFI), Parameter Solution method (ParaSol) and Particle Swarm Optimization (PSO). The performance of the algorithms was compared using P-factor and Rfactor, coefficient of determination (R 2), the Nash Sutcliffe coefficient of efficiency (NSE) and Percent Bias (PBIAS). The results showed the high performance of SUFI and PSO with P-factor>0.83, R-factor <0.56 and R 2>0.91, NSE>0.89, and 0.18
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Dissolved organic matter reduces CuO nanoparticle toxicity to duckweed in simulated natural systems.
Rippner, Devin A; Green, Peter G; Young, Thomas M; Parikh, Sanjai J
2018-03-01
With increasing demand for recycled wastewater for irrigation purposes, there is a need to evaluate the potential for manufactured nanomaterials in waste water to impact crop production and agroecosystems. Copper oxide nanoparticles (CuO NPs) have previously been shown to negatively impact the growth of duckweed (Landoltia punctata) a model aquatic plant consumed by water fowl and widely found in agricultural runoff ditches in temperate climates. However, prior studies involving CuO NP toxicity to duckweed have focused on systems without the presence of dissolved organic matter (DOM). In the current study, duckweed growth inhibition was shown to be a function of aqueous Cu 2+ concentration. Growth inhibition was greatest from aqueous CuCl 2 and, for particles, increased with decreasing CuO particle size. The dissolution of CuO NPs in ½ Hoagland's solution was measured to increase with decreasing particle size and in the presence of Suwannee river humic and fulvic acids (HA; FA). However, the current results suggest that HA, and to a lesser extent, FA, decrease the toxicity of both CuO NPs and free ionized Cu to duckweed, likely by inhibiting Cu availability through Cu-DOM complex formation. Such results are consistent with changes to Cu speciation as predicted by speciation modeling software and suggest that DOM changes Cu speciation and therefore toxicity in natural systems. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Studying the genetic basis of speciation in high gene flow marine invertebrates
2016-01-01
A growing number of genes responsible for reproductive incompatibilities between species (barrier loci) exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection diverge early in speciation and commonly cause reproductive incompatibilities has not been systematically investigated on a genome-wide scale. Here, I outline a research program for studying the genetic basis of speciation in broadcast spawning marine invertebrates that uses a priori genome-wide information on a large, unbiased sample of genes tested for positive selection. A targeted sequence capture approach is proposed that scores single-nucleotide polymorphisms (SNPs) in widely separated species populations at an early stage of allopatric divergence. The targeted capture of both coding and non-coding sequences enables SNPs to be characterized at known locations across the genome and at genes with known selective or neutral histories. The neutral coding and non-coding SNPs provide robust background distributions for identifying FST-outliers within genes that can, in principle, identify specific mutations experiencing diversifying selection. If natural hybridization occurs between species, the neutral coding and non-coding SNPs can provide a neutral admixture model for genomic clines analyses aimed at finding genes exhibiting strong blocks to introgression. Strongylocentrotid sea urchins are used as a model system to outline the approach but it can be used for any group that has a complete reference genome available. PMID:29491951
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NASA Astrophysics Data System (ADS)
Mockler, E. M.; Chun, K. P.; Sapriza-Azuri, G.; Bruen, M.; Wheater, H. S.
2016-11-01
Predictions of river flow dynamics provide vital information for many aspects of water management including water resource planning, climate adaptation, and flood and drought assessments. Many of the subjective choices that modellers make including model and criteria selection can have a significant impact on the magnitude and distribution of the output uncertainty. Hydrological modellers are tasked with understanding and minimising the uncertainty surrounding streamflow predictions before communicating the overall uncertainty to decision makers. Parameter uncertainty in conceptual rainfall-runoff models has been widely investigated, and model structural uncertainty and forcing data have been receiving increasing attention. This study aimed to assess uncertainties in streamflow predictions due to forcing data and the identification of behavioural parameter sets in 31 Irish catchments. By combining stochastic rainfall ensembles and multiple parameter sets for three conceptual rainfall-runoff models, an analysis of variance model was used to decompose the total uncertainty in streamflow simulations into contributions from (i) forcing data, (ii) identification of model parameters and (iii) interactions between the two. The analysis illustrates that, for our subjective choices, hydrological model selection had a greater contribution to overall uncertainty, while performance criteria selection influenced the relative intra-annual uncertainties in streamflow predictions. Uncertainties in streamflow predictions due to the method of determining parameters were relatively lower for wetter catchments, and more evenly distributed throughout the year when the Nash-Sutcliffe Efficiency of logarithmic values of flow (lnNSE) was the evaluation criterion.
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NASA Astrophysics Data System (ADS)
Sawicka, K.; Breuer, L.; Houska, T.; Santabarbara Ruiz, I.; Heuvelink, G. B. M.
2016-12-01
Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Advances in uncertainty propagation analysis and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the `spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo techniques, as well as several uncertainty visualization functions. Here we will demonstrate that the 'spup' package is an effective and easy-to-use tool to be applied even in a very complex study case, and that it can be used in multi-disciplinary research and model-based decision support. As an example, we use the ecological LandscapeDNDC model to analyse propagation of uncertainties associated with spatial variability of the model driving forces such as rainfall, nitrogen deposition and fertilizer inputs. The uncertainty propagation is analysed for the prediction of emissions of N2O and CO2 for a German low mountainous, agriculturally developed catchment. The study tests the effect of spatial correlations on spatially aggregated model outputs, and could serve as an advice for developing best management practices and model improvement strategies.
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Quantifying radar-rainfall uncertainties in urban drainage flow modelling
NASA Astrophysics Data System (ADS)
Rico-Ramirez, M. A.; Liguori, S.; Schellart, A. N. A.
2015-09-01
This work presents the results of the implementation of a probabilistic system to model the uncertainty associated to radar rainfall (RR) estimates and the way this uncertainty propagates through the sewer system of an urban area located in the North of England. The spatial and temporal correlations of the RR errors as well as the error covariance matrix were computed to build a RR error model able to generate RR ensembles that reproduce the uncertainty associated with the measured rainfall. The results showed that the RR ensembles provide important information about the uncertainty in the rainfall measurement that can be propagated in the urban sewer system. The results showed that the measured flow peaks and flow volumes are often bounded within the uncertainty area produced by the RR ensembles. In 55% of the simulated events, the uncertainties in RR measurements can explain the uncertainties observed in the simulated flow volumes. However, there are also some events where the RR uncertainty cannot explain the whole uncertainty observed in the simulated flow volumes indicating that there are additional sources of uncertainty that must be considered such as the uncertainty in the urban drainage model structure, the uncertainty in the urban drainage model calibrated parameters, and the uncertainty in the measured sewer flows.
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EPA’s SPECIATE 4.4 Database - Development and Uses
SPECIATE is the EPA's repository of TOG, PM, and Other Gases speciation profiles of air pollution sources. It includes weight fractions of both organic species and PM and provides data in consistent units. Species include metals, ions, elements, and organic and inorganic compound...
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Cold Temperature Effects on Speciated VOC Emissions from modern GDI Light Duty Truck
Although gasoline direct injection (GDI) vehicles represent nearly half of the light-duty vehicle market share, few studies have reported speciated volatile organic compounds (VOCs) in GDI vehicle exhaust emissions. In this study, speciated VOC emissions were characterized from t...
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The development of exhaust speciation profiles for commercial jet engines.
DOT National Transportation Integrated Search
2007-10-01
This study reports the emissions of CO, CO2, NOx, Particulate Matter (PM) mass, : speciated PM and speciated hydrocarbons at six thrust settings: 4%, 7%, 30%, 40%, 65% : and 85%, measured from both engines on four parked 737 aircraft at the Oakland :...
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He, L; Huang, G H; Lu, H W
2010-04-15
Solving groundwater remediation optimization problems based on proxy simulators can usually yield optimal solutions differing from the "true" ones of the problem. This study presents a new stochastic optimization model under modeling uncertainty and parameter certainty (SOMUM) and the associated solution method for simultaneously addressing modeling uncertainty associated with simulator residuals and optimizing groundwater remediation processes. This is a new attempt different from the previous modeling efforts. The previous ones focused on addressing uncertainty in physical parameters (i.e. soil porosity) while this one aims to deal with uncertainty in mathematical simulator (arising from model residuals). Compared to the existing modeling approaches (i.e. only parameter uncertainty is considered), the model has the advantages of providing mean-variance analysis for contaminant concentrations, mitigating the effects of modeling uncertainties on optimal remediation strategies, offering confidence level of optimal remediation strategies to system designers, and reducing computational cost in optimization processes. 2009 Elsevier B.V. All rights reserved.
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Geography, assortative mating, and the effects of sexual selection on speciation with gene flow.
Servedio, Maria R
2016-01-01
Theoretical and empirical research on the evolution of reproductive isolation have both indicated that the effects of sexual selection on speciation with gene flow are quite complex. As part of this special issue on the contributions of women to basic and applied evolutionary biology, I discuss my work on this question in the context of a broader assessment of the patterns of sexual selection that lead to, versus inhibit, the speciation process, as derived from theoretical research. In particular, I focus on how two factors, the geographic context of speciation and the mechanism leading to assortative mating, interact to alter the effect that sexual selection through mate choice has on speciation. I concentrate on two geographic contexts: sympatry and secondary contact between two geographically separated populations that are exchanging migrants and two mechanisms of assortative mating: phenotype matching and separate preferences and traits. I show that both of these factors must be considered for the effects of sexual selection on speciation to be inferred.
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Ephemeral ecological speciation and the latitudinal biodiversity gradient.
Cutter, Asher D; Gray, Jeremy C
2016-10-01
The richness of biodiversity in the tropics compared to high-latitude parts of the world forms one of the most globally conspicuous patterns in biology, and yet few hypotheses aim to explain this phenomenon in terms of explicit microevolutionary mechanisms of speciation and extinction. We link population genetic processes of selection and adaptation to speciation and extinction by way of their interaction with environmental factors to drive global scale macroecological patterns. High-latitude regions are both cradle and grave with respect to species diversification. In particular, we point to a conceptual equivalence of "environmental harshness" and "hard selection" as eco-evolutionary drivers of local adaptation and ecological speciation. By describing how ecological speciation likely occurs more readily at high latitudes, with such nascent species especially prone to extinction by fusion, we derive the ephemeral ecological speciation hypothesis as an integrative mechanistic explanation for latitudinal gradients in species turnover and the net accumulation of biodiversity. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.
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Speciation by Symbiosis: the Microbiome and Behavior
Shropshire, J. Dylan
2016-01-01
ABSTRACT Species are fundamental units of comparison in biology. The newly discovered importance and ubiquity of host-associated microorganisms are now stimulating work on the roles that microbes can play in animal speciation. We previously synthesized the literature and advanced concepts of speciation by symbiosis with notable attention to hybrid sterility and lethality. Here, we review recent studies and relevant data on microbes as players in host behavior and behavioral isolation, emphasizing the patterns seen in these analyses and highlighting areas worthy of additional exploration. We conclude that the role of microbial symbionts in behavior and speciation is gaining exciting traction and that the holobiont and hologenome concepts afford an evolving intellectual framework to promote research and intellectual exchange between disciplines such as behavior, microbiology, genetics, symbiosis, and speciation. Given the increasing centrality of microbiology in macroscopic life, microbial symbiosis is arguably the most neglected aspect of animal and plant speciation, and studying it should yield a better understanding of the origin of species. PMID:27034284
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Speciation by Symbiosis: the Microbiome and Behavior.
Shropshire, J Dylan; Bordenstein, Seth R
2016-03-31
Species are fundamental units of comparison in biology. The newly discovered importance and ubiquity of host-associated microorganisms are now stimulating work on the roles that microbes can play in animal speciation. We previously synthesized the literature and advanced concepts of speciation by symbiosis with notable attention to hybrid sterility and lethality. Here, we review recent studies and relevant data on microbes as players in host behavior and behavioral isolation, emphasizing the patterns seen in these analyses and highlighting areas worthy of additional exploration. We conclude that the role of microbial symbionts in behavior and speciation is gaining exciting traction and that the holobiont and hologenome concepts afford an evolving intellectual framework to promote research and intellectual exchange between disciplines such as behavior, microbiology, genetics, symbiosis, and speciation. Given the increasing centrality of microbiology in macroscopic life, microbial symbiosis is arguably the most neglected aspect of animal and plant speciation, and studying it should yield a better understanding of the origin of species. Copyright © 2016 Shropshire and Bordenstein.
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2008-01-01
Background An open, focal issue in evolutionary biology is how reproductive isolation and speciation are initiated; elucidation of mechanisms with empirical evidence has lagged behind theory. Under ecological speciation, reproductive isolation between populations is predicted to evolve incidentally as a by-product of adaptation to divergent environments. The increased genetic diversity associated with interspecific hybridization has also been theorized to promote the development of reproductive isolation among independent populations. Using the fungal model Neurospora, we founded experimental lineages from both intra- and interspecific crosses, and evolved them in one of two sub-optimal, selective environments. We then measured the influence that initial genetic diversity and the direction of selection (parallel versus divergent) had on the evolution of reproductive isolation. Results When assayed in the selective environment in which they were evolved, lineages typically had greater asexual fitness than the progenitors and the lineages that were evolved in the alternate, selective environment. Assays for reproductive isolation showed that matings between lineages that were adapted to the same environment had greater sexual reproductive success than matings between lineages that were adapted to different environments. Evidence of this differential reproductive success was observed at two stages of the sexual cycle. For one of the two observed incompatibility phenotypes, results from genetic analyses were consistent with a two-locus, two-allele model with asymmetric (gender-specific), antagonistic epistasis. The effects of divergent adaptation on reproductive isolation were more pronounced for populations with greater initial genetic variation. Conclusion Divergent selection resulted in divergent adaptation and environmental specialization, consistent with fixation of different alleles in different environments. When brought together by mating, these alleles interacted negatively and had detrimental effects on sexual reproductive success, in agreement with the Dobzhansky-Muller model of genetic incompatibilities. As predicted by ecological speciation, greater reproductive isolation was observed among divergent-adapted lineages than among parallel-adapted lineages. These results support that, given adequate standing genetic variation, divergent adaptation can indirectly cause the evolution of reproductive isolation, and eventually lead to speciation. PMID:18237415
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NASA Astrophysics Data System (ADS)
Haas, Edwin; Santabarbara, Ignacio; Kiese, Ralf; Butterbach-Bahl, Klaus
2017-04-01
Numerical simulation models are increasingly used to estimate greenhouse gas emissions at site to regional / national scale and are outlined as the most advanced methodology (Tier 3) in the framework of UNFCCC reporting. Process-based models incorporate the major processes of the carbon and nitrogen cycle of terrestrial ecosystems and are thus thought to be widely applicable at various conditions and spatial scales. Process based modelling requires high spatial resolution input data on soil properties, climate drivers and management information. The acceptance of model based inventory calculations depends on the assessment of the inventory's uncertainty (model, input data and parameter induced uncertainties). In this study we fully quantify the uncertainty in modelling soil N2O and NO emissions from arable, grassland and forest soils using the biogeochemical model LandscapeDNDC. We address model induced uncertainty (MU) by contrasting two different soil biogeochemistry modules within LandscapeDNDC. The parameter induced uncertainty (PU) was assessed by using joint parameter distributions for key parameters describing microbial C and N turnover processes as obtained by different Bayesian calibration studies for each model configuration. Input data induced uncertainty (DU) was addressed by Bayesian calibration of soil properties, climate drivers and agricultural management practices data. For the MU, DU and PU we performed several hundred simulations each to contribute to the individual uncertainty assessment. For the overall uncertainty quantification we assessed the model prediction probability, followed by sampled sets of input datasets and parameter distributions. Statistical analysis of the simulation results have been used to quantify the overall full uncertainty of the modelling approach. With this study we can contrast the variation in model results to the different sources of uncertainties for each ecosystem. Further we have been able to perform a fully uncertainty analysis for modelling N2O and NO emissions from arable, grassland and forest soils necessary for the comprehensibility of modelling results. We have applied the methodology to a regional inventory to assess the overall modelling uncertainty for a regional N2O and NO emissions inventory for the state of Saxony, Germany.
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Host Model Uncertainty in Aerosol Radiative Effects: the AeroCom Prescribed Experiment and Beyond
NASA Astrophysics Data System (ADS)
Stier, Philip; Schutgens, Nick; Bian, Huisheng; Boucher, Olivier; Chin, Mian; Ghan, Steven; Huneeus, Nicolas; Kinne, Stefan; Lin, Guangxing; Myhre, Gunnar; Penner, Joyce; Randles, Cynthia; Samset, Bjorn; Schulz, Michael; Yu, Hongbin; Zhou, Cheng; Bellouin, Nicolas; Ma, Xiaoyan; Yu, Fangqun; Takemura, Toshihiko
2013-04-01
Anthropogenic and natural aerosol radiative effects are recognized to affect global and regional climate. Multi-model "diversity" in estimates of the aerosol radiative effect is often perceived as a measure of the uncertainty in modelling aerosol itself. However, current aerosol models vary considerably in model components relevant for the calculation of aerosol radiative forcings and feedbacks and the associated "host-model uncertainties" are generally convoluted with the actual uncertainty in aerosol modelling. In the AeroCom Prescribed intercomparison study we systematically isolate and quantify host model uncertainties on aerosol forcing experiments through prescription of identical aerosol radiative properties in eleven participating models. Host model errors in aerosol radiative forcing are largest in regions of uncertain host model components, such as stratocumulus cloud decks or areas with poorly constrained surface albedos, such as sea ice. Our results demonstrate that host model uncertainties are an important component of aerosol forcing uncertainty that require further attention. However, uncertainties in aerosol radiative effects also include short-term and long-term feedback processes that will be systematically explored in future intercomparison studies. Here we will present an overview of the proposals for discussion and results from early scoping studies.
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Uncertainty in tsunami sediment transport modeling
Jaffe, Bruce E.; Goto, Kazuhisa; Sugawara, Daisuke; Gelfenbaum, Guy R.; La Selle, SeanPaul M.
2016-01-01
Erosion and deposition from tsunamis record information about tsunami hydrodynamics and size that can be interpreted to improve tsunami hazard assessment. We explore sources and methods for quantifying uncertainty in tsunami sediment transport modeling. Uncertainty varies with tsunami, study site, available input data, sediment grain size, and model. Although uncertainty has the potential to be large, published case studies indicate that both forward and inverse tsunami sediment transport models perform well enough to be useful for deciphering tsunami characteristics, including size, from deposits. New techniques for quantifying uncertainty, such as Ensemble Kalman Filtering inversion, and more rigorous reporting of uncertainties will advance the science of tsunami sediment transport modeling. Uncertainty may be decreased with additional laboratory studies that increase our understanding of the semi-empirical parameters and physics of tsunami sediment transport, standardized benchmark tests to assess model performance, and development of hybrid modeling approaches to exploit the strengths of forward and inverse models.
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Uncertainty Aware Structural Topology Optimization Via a Stochastic Reduced Order Model Approach
NASA Technical Reports Server (NTRS)
Aguilo, Miguel A.; Warner, James E.
2017-01-01
This work presents a stochastic reduced order modeling strategy for the quantification and propagation of uncertainties in topology optimization. Uncertainty aware optimization problems can be computationally complex due to the substantial number of model evaluations that are necessary to accurately quantify and propagate uncertainties. This computational complexity is greatly magnified if a high-fidelity, physics-based numerical model is used for the topology optimization calculations. Stochastic reduced order model (SROM) methods are applied here to effectively 1) alleviate the prohibitive computational cost associated with an uncertainty aware topology optimization problem; and 2) quantify and propagate the inherent uncertainties due to design imperfections. A generic SROM framework that transforms the uncertainty aware, stochastic topology optimization problem into a deterministic optimization problem that relies only on independent calls to a deterministic numerical model is presented. This approach facilitates the use of existing optimization and modeling tools to accurately solve the uncertainty aware topology optimization problems in a fraction of the computational demand required by Monte Carlo methods. Finally, an example in structural topology optimization is presented to demonstrate the effectiveness of the proposed uncertainty aware structural topology optimization approach.
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Speciation at the Mogollon Rim in the Arizona Mountain Kingsnake (Lampropeltis pyromelana).
Burbrink, Frank T; Yao, Helen; Ingrasci, Matthew; Bryson, Robert W; Guiher, Timothy J; Ruane, Sara
2011-09-01
Studies of speciation and taxon delimitation are usually decoupled. Combining these methods provides a stronger theoretical ground for recognizing new taxa and understanding processes of speciation. Using coalescent methods, we examine speciation, post-speciation population demographics, and taxon delimitation in the Arizona Mountain Kingsnake (Lampropeltis pyromelana), a species restricted to high elevations in southwestern United States and northern Mexico (SW). These methods provide a solid foundation for understanding how biogeographic barriers operate at the regional scale in the SW. Bayesian species delimitation methods, using three loci from samples of L. pyromelana taken throughout their range, show strong support for the existence of two species that are separated by low elevation habitats found between the Colorado Plateau/ Mogollon Rim and the Sierra Madre Occidental. Our results suggest an allopatric mode of speciation given the near absence of gene flow over time, which resulted in two lineages of unequal population sizes. Speciation likely occurred prior to the Pleistocene, during the aridification of the SW and/or the uplift of the Colorado Plateau, and while these species occupy similar high-elevation niches, they are isolated by xeric conditions found in the intervening low deserts. Furthermore, post-speciation demographics suggest that populations of both lineages were not negatively impacted by climate change throughout the Pleistocene. Finally, our results suggest that at least for this group, where divergence is old and gene flow is low, Bayesian species delimitation performs well. Copyright © 2011 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Hand, J. L.; Schichtel, B. A.; Malm, W. C.; Pitchford, M.; Frank, N. H.
2014-11-01
Monthly, seasonal, and annual mean estimates of urban influence on regional concentrations of major aerosol species were computed using speciated aerosol data from the rural IMPROVE network (Interagency Monitoring of Protected Visual Environments) and the United States Environmental Protection Agency's urban Chemical Speciation Network for the 2008 through 2011 period. Aggregated for sites across the continental United States, the annual mean and one standard error in urban excess (defined as the ratio of urban to nearby rural concentrations) was highest for elemental carbon (3.3 ± 0.2), followed by ammonium nitrate (2.5 ± 0.2), particulate organic matter (1.78 ± 0.08), and ammonium sulfate (1.23 ± 0.03). The seasonal variability in urban excess was significant for carbonaceous aerosols and ammonium nitrate in the West, in contrast to the low seasonal variability in the urban influence of ammonium sulfate. Generally for all species, higher excess values in the West were associated with localized urban sources while in the East excess was more regional in extent. In addition, higher excess values in the western United States in winter were likely influenced not only by differences in sources but also by combined meteorological and topographic effects. This work has implications for understanding the spatial heterogeneity of major aerosol species near the interface of urban and rural regions and therefore for designing appropriate air quality management strategies. In addition, the spatial patterns in speciated mass concentrations provide constraints for regional and global models.
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NASA Astrophysics Data System (ADS)
María Yáñez-Serrano, Ana; Nölscher, Anke Christine; Bourtsoukidis, Efstratios; Gomes Alves, Eliane; Ganzeveld, Laurens; Bonn, Boris; Wolff, Stefan; Sa, Marta; Yamasoe, Marcia; Williams, Jonathan; Andreae, Meinrat O.; Kesselmeier, Jürgen
2018-03-01
Speciated monoterpene measurements in rainforest air are scarce, but they are essential for understanding the contribution of these compounds to the overall reactivity of volatile organic compound (VOC) emissions towards the main atmospheric oxidants, such as hydroxyl radicals (OH), ozone (O3) and nitrate radicals (NO3). In this study, we present the chemical speciation of gas-phase monoterpenes measured in the tropical rainforest at the Amazon Tall Tower Observatory (ATTO, Amazonas, Brazil). Samples of VOCs were collected by two automated sampling systems positioned on a tower at 12 and 24 m height and analysed using gas chromatography-flame ionization detection. The samples were collected in October 2015, representing the dry season, and compared with previous wet and dry season studies at the site. In addition, vertical profile measurements (at 12 and 24 m) of total monoterpene mixing ratios were made using proton-transfer-reaction mass spectrometry. The results showed a distinctly different chemical speciation between day and night. For instance, α-pinene was more abundant during the day, whereas limonene was more abundant at night. Reactivity calculations showed that higher abundance does not generally imply higher reactivity. Furthermore, inter- and intra-annual results demonstrate similar chemodiversity during the dry seasons analysed. Simulations with a canopy exchange modelling system show simulated monoterpene mixing ratios that compare relatively well with the observed mixing ratios but also indicate the necessity of more experiments to enhance our understanding of in-canopy sinks of these compounds.
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Towards a global historical biogeography of Palms
NASA Astrophysics Data System (ADS)
Couvreur, Thomas; Baker, William J.; Frigerio, Jean-Marc; Sepulchre, Pierre; Franc, Alain
2017-04-01
Four mechanisms are at work for deciphering historical biogeography of plants : speciation, extinction, migration, and drift (a sort of neutral speciation). The first three mechanisms are under selection pressure of the environment, mainly the climate and connectivity of land masses. Hence, an accurate history of climate and connectivity or non connectivity between landmasses, as well as orogenesis processes, can shed new light on the most likely speciation events and migration routes driven by paleogeography and paleoclimatology. Currently, some models exist (like DIVA) to infer the most parsimonious history (in the number of migration events) knowing the speciation history given by phylogenies (extinction are mostly unknown), in a given setting of climate and landmass connectivity. In a previous project, we have built in collaboration with LSCE a series of paleogeographic and paleoclimatic maps since the Early Cretaceous. We have developed a program, called Aran, which enables to extend DIVA to a time series of varying paleoclimatic and paleogeogarphic conditions. We apply these new methods and data to unravel the biogeographic history of palms (Arecaceae), a pantropical family of 182 genera and >2600 species whose divergence is dated in Late Cretaceous (100 My). Based on a robust dated molecular phylogeny, novel paleoclimatic and paleogeographic maps, we will generate an updated biogeographic history of Arecaceae inferred from the most parsimonious history using Aran. We will discuss the results, and put them in context with what is known and needed to provide a global biogeographic history of tropical palms.
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Soil-solution speciation of Cd as affected by soil characteristics in unpolluted and polluted soils.
Meers, Erik; Unamuno, Virginia; Vandegehuchte, Michiel; Vanbroekhoven, Karolien; Geebelen, Wouter; Samson, Roeland; Vangronsveld, Jaco; Diels, Ludo; Ruttens, Ann; Du Laing, Gijs; Tack, Filip
2005-03-01
Total metal content by itself is insufficient as a measure to indicate actual environmental risk. Understanding the mobility of heavy metals in the soil and their speciation in the soil solution is of great importance for accurately assessing environmental risks posed by these metals. In a first explorative study, the effects of general soil characteristics on Cd mobility were evaluated and expressed in the form of empirical formulations. The most important factors influencing mobility of Cd proved to be pH and total soil content. This may indicate that current legislation expressing the requirement for soil sanitation in Flanders (Belgium) as a function of total soil content, organic matter, and clay does not successfully reflect actual risks. Current legal frameworks focusing on total content, therefore, should be amended with criteria that are indicative of metal mobility and availability and are based on physicochemical soil properties. In addition, soil-solution speciation was performed using two independent software packages (Visual Minteq 2.23 and Windermere Humic Aqueous model VI [WHAM VI]). Both programs largely were in agreement in concern to Cd speciation in all 29 soils under study. Depending on soil type, free ion and the organically complexed forms were the most abundant species. Additional inorganic soluble species were sulfates and chlorides. Minor species in solution were in the form of nitrates, hydroxides, and carbonates, the relative importance of which was deemed insignificant in comparison to the four major species.
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Franchini, Paolo; Xiong, Peiwen; Fruciano, Carmelo; Meyer, Axel
2016-01-01
Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage (Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3′-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3′-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids. PMID:27189980
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Multi-model approach to assess the impact of climate change on runoff
NASA Astrophysics Data System (ADS)
Dams, J.; Nossent, J.; Senbeta, T. B.; Willems, P.; Batelaan, O.
2015-10-01
The assessment of climate change impacts on hydrology is subject to uncertainties related to the climate change scenarios, stochastic uncertainties of the hydrological model and structural uncertainties of the hydrological model. This paper focuses on the contribution of structural uncertainty of hydrological models to the overall uncertainty of the climate change impact assessment. To quantify the structural uncertainty of hydrological models, four physically based hydrological models (SWAT, PRMS and a semi- and fully distributed version of the WetSpa model) are set up for a catchment in Belgium. Each model is calibrated using four different objective functions. Three climate change scenarios with a high, mean and low hydrological impact are statistically perturbed from a large ensemble of climate change scenarios and are used to force the hydrological models. This methodology allows assessing and comparing the uncertainty introduced by the climate change scenarios with the uncertainty introduced by the hydrological model structure. Results show that the hydrological model structure introduces a large uncertainty on both the average monthly discharge and the extreme peak and low flow predictions under the climate change scenarios. For the low impact climate change scenario, the uncertainty range of the mean monthly runoff is comparable to the range of these runoff values in the reference period. However, for the mean and high impact scenarios, this range is significantly larger. The uncertainty introduced by the climate change scenarios is larger than the uncertainty due to the hydrological model structure for the low and mean hydrological impact scenarios, but the reverse is true for the high impact climate change scenario. The mean and high impact scenarios project increasing peak discharges, while the low impact scenario projects increasing peak discharges only for peak events with return periods larger than 1.6 years. All models suggest for all scenarios a decrease of the lowest flows, except for the SWAT model with the mean hydrological impact climate change scenario. The results of this study indicate that besides the uncertainty introduced by the climate change scenarios also the hydrological model structure uncertainty should be taken into account in the assessment of climate change impacts on hydrology. To make it more straightforward and transparent to include model structural uncertainty in hydrological impact studies, there is a need for hydrological modelling tools that allow flexible structures and methods to validate model structures in their ability to assess impacts under unobserved future climatic conditions.
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NASA Astrophysics Data System (ADS)
Li, L.; Xu, C.-Y.; Engeland, K.
2012-04-01
With respect to model calibration, parameter estimation and analysis of uncertainty sources, different approaches have been used in hydrological models. Bayesian method is one of the most widely used methods for uncertainty assessment of hydrological models, which incorporates different sources of information into a single analysis through Bayesian theorem. However, none of these applications can well treat the uncertainty in extreme flows of hydrological models' simulations. This study proposes a Bayesian modularization method approach in uncertainty assessment of conceptual hydrological models by considering the extreme flows. It includes a comprehensive comparison and evaluation of uncertainty assessments by a new Bayesian modularization method approach and traditional Bayesian models using the Metropolis Hasting (MH) algorithm with the daily hydrological model WASMOD. Three likelihood functions are used in combination with traditional Bayesian: the AR (1) plus Normal and time period independent model (Model 1), the AR (1) plus Normal and time period dependent model (Model 2) and the AR (1) plus multi-normal model (Model 3). The results reveal that (1) the simulations derived from Bayesian modularization method are more accurate with the highest Nash-Sutcliffe efficiency value, and (2) the Bayesian modularization method performs best in uncertainty estimates of entire flows and in terms of the application and computational efficiency. The study thus introduces a new approach for reducing the extreme flow's effect on the discharge uncertainty assessment of hydrological models via Bayesian. Keywords: extreme flow, uncertainty assessment, Bayesian modularization, hydrological model, WASMOD
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SPECIATION OF ORGANICS IN WATER WITH RAMAN SPECTROSCOPY: UTILITY OF IONIC STRENGTH VARIATION
We have developed and are applying an experimental and mathematical method for describing the micro-speciation of complex organic contaminants in aqueous media. For our case, micro-speciation can be defined as qualitative and quantitative identification of all discrete forms of ...
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Uncertainty in the Modeling of Tsunami Sediment Transport
NASA Astrophysics Data System (ADS)
Jaffe, B. E.; Sugawara, D.; Goto, K.; Gelfenbaum, G. R.; La Selle, S.
2016-12-01
Erosion and deposition from tsunamis record information about tsunami hydrodynamics and size that can be interpreted to improve tsunami hazard assessment. A recent study (Jaffe et al., 2016) explores sources and methods for quantifying uncertainty in tsunami sediment transport modeling. Uncertainty varies with tsunami properties, study site characteristics, available input data, sediment grain size, and the model used. Although uncertainty has the potential to be large, case studies for both forward and inverse models have shown that sediment transport modeling provides useful information on tsunami inundation and hydrodynamics that can be used to improve tsunami hazard assessment. New techniques for quantifying uncertainty, such as Ensemble Kalman Filtering inversion, and more rigorous reporting of uncertainties will advance the science of tsunami sediment transport modeling. Uncertainty may be decreased with additional laboratory studies that increase our understanding of the semi-empirical parameters and physics of tsunami sediment transport, standardized benchmark tests to assess model performance, and the development of hybrid modeling approaches to exploit the strengths of forward and inverse models. As uncertainty in tsunami sediment transport modeling is reduced, and with increased ability to quantify uncertainty, the geologic record of tsunamis will become more valuable in the assessment of tsunami hazard. Jaffe, B., Goto, K., Sugawara, D., Gelfenbaum, G., and La Selle, S., "Uncertainty in Tsunami Sediment Transport Modeling", Journal of Disaster Research Vol. 11 No. 4, pp. 647-661, 2016, doi: 10.20965/jdr.2016.p0647 https://www.fujipress.jp/jdr/dr/dsstr001100040647/
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Multifidelity, Multidisciplinary Design Under Uncertainty with Non-Intrusive Polynomial Chaos
NASA Technical Reports Server (NTRS)
West, Thomas K., IV; Gumbert, Clyde
2017-01-01
The primary objective of this work is to develop an approach for multifidelity uncertainty quantification and to lay the framework for future design under uncertainty efforts. In this study, multifidelity is used to describe both the fidelity of the modeling of the physical systems, as well as the difference in the uncertainty in each of the models. For computational efficiency, a multifidelity surrogate modeling approach based on non-intrusive polynomial chaos using the point-collocation technique is developed for the treatment of both multifidelity modeling and multifidelity uncertainty modeling. Two stochastic model problems are used to demonstrate the developed methodologies: a transonic airfoil model and multidisciplinary aircraft analysis model. The results of both showed the multifidelity modeling approach was able to predict the output uncertainty predicted by the high-fidelity model as a significant reduction in computational cost.
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Probabilistic accounting of uncertainty in forecasts of species distributions under climate change
Wenger, Seth J.; Som, Nicholas A.; Dauwalter, Daniel C.; Isaak, Daniel J.; Neville, Helen M.; Luce, Charles H.; Dunham, Jason B.; Young, Michael K.; Fausch, Kurt D.; Rieman, Bruce E.
2013-01-01
Forecasts of species distributions under future climates are inherently uncertain, but there have been few attempts to describe this uncertainty comprehensively in a probabilistic manner. We developed a Monte Carlo approach that accounts for uncertainty within generalized linear regression models (parameter uncertainty and residual error), uncertainty among competing models (model uncertainty), and uncertainty in future climate conditions (climate uncertainty) to produce site-specific frequency distributions of occurrence probabilities across a species’ range. We illustrated the method by forecasting suitable habitat for bull trout (Salvelinus confluentus) in the Interior Columbia River Basin, USA, under recent and projected 2040s and 2080s climate conditions. The 95% interval of total suitable habitat under recent conditions was estimated at 30.1–42.5 thousand km; this was predicted to decline to 0.5–7.9 thousand km by the 2080s. Projections for the 2080s showed that the great majority of stream segments would be unsuitable with high certainty, regardless of the climate data set or bull trout model employed. The largest contributor to uncertainty in total suitable habitat was climate uncertainty, followed by parameter uncertainty and model uncertainty. Our approach makes it possible to calculate a full distribution of possible outcomes for a species, and permits ready graphical display of uncertainty for individual locations and of total habitat.
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'spup' - an R package for uncertainty propagation in spatial environmental modelling
NASA Astrophysics Data System (ADS)
Sawicka, Kasia; Heuvelink, Gerard
2016-04-01
Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected static and interactive visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.
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'spup' - an R package for uncertainty propagation analysis in spatial environmental modelling
NASA Astrophysics Data System (ADS)
Sawicka, Kasia; Heuvelink, Gerard
2017-04-01
Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability and being able to deal with case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.
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Field Evaluation Of Arsenic Speciation In Sediments At The Ground Water/Surface Water Interface
The speciation and mineralogy of sediments contaminated with arsenic at the ground water/surface water interface of the Ft. Devens Super Fund Site in Ft. Devens, MA were determined using X-ray absorption fine structure and X-ray diffraction spectroscopy. Speciation and mineralog...
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NASA Astrophysics Data System (ADS)
Szpunar, Joanna; McSheehy, Shona; Połeć, Kasia; Vacchina, Véronique; Mounicou, Sandra; Rodriguez, Isaac; Łobiński, Ryszard
2000-07-01
Recent advances in the coupling of gas chromatography (GC) and high performance liquid chromatography (HPLC) with inductively coupled plasma mass spectrometry (ICP MS) and their role in trace element speciation analysis of environmental materials are presented. The discussion is illustrated with three research examples concerning the following topics: (i) development and coupling of multicapillary microcolumn GC with ICP MS for speciation of organotin in sediment and biological tissue samples; (ii) speciation of arsenic in marine algae by size-exclusion-anion-exchange HPLC-ICP MS; and (iii) speciation of cadmium in plant cell cultures by size-exclusion HPLC-ICP MS. Particular attention is paid to the problem of signal identification in ICP MS chromatograms; the potential of electrospray MS/MS for this purpose is highlighted.
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NASA Astrophysics Data System (ADS)
Pérez-Corona, Teresa; Madrid-Albarrán, Yolanda; Cámara, Carmen; Beceiro, Elisa
1998-02-01
The use of living organisms for metal preconcentration and speciation is discussed. Among substrates, Saccharomyces cerevisiae baker's yeast has been successfully used for the speciation of mercury [Hg(II) and CH 3Hg +], selenium [Se(IV) and Se(VI)] and antimony [Sb(III) and Sb(V)]. To illustrate the capabilities of these organisms, the analytical performance of baker's yeast immobilized on silica gel for on-line preconcentration and speciation of Hg(II) and methylmercury is reported. The immobilized cells were packed in a PTFE microcolumn, through which mixtures of organic and inorganic mercury solutions were passed. Retention of inorganic and organic mercury solutions took place simultaneously, with the former retained in the silica and the latter on the yeast. The efficiency uptake for both species was higher than 95% over a wide pH range. The speciation was carried out by selective and sequential elution with 0.02 mol L -1 HCl for methylmercury and 0.8 mol L -1 CN - for Hg(II). This method allows both preconcentration and speciation of mercury. The preconcentration factors were around 15 and 100 for methylmercury and mercury(II), respectively. The method has been successfully applied to spiked sea water samples.
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NASA Astrophysics Data System (ADS)
Chen, Xinming; Romaniello, Stephen J.; Anbar, Ariel D.
2017-10-01
Natural variations of 238U/235U in marine CaCO3 rocks are being explored as a novel paleoredox proxy to investigate oceanic anoxia events. Although it is generally assumed that U isotopes in CaCO3 directly record 238U/235U of seawater, recently published laboratory experiments demonstrate slight U isotope fractionation during U(VI) incorporation into abiotic calcium carbonates. This fractionation is hypothesized to depend on aqueous U(VI) speciation, which is controlled by pH, ionic strength, pCO2 and Mg2+ and Ca2+ concentrations. Secular variation in seawater chemistry could lead to changes in aqueous U(VI) speciation, and thus, may affect the extent of U isotope fractionation during U(VI) incorporation into CaCO3. In this study, we combine estimates of seawater composition over the Phanerozoic with a model of aqueous U speciation and isotope fractionation to explore variations in the expected offset between the U isotope composition of seawater and primary marine CaCO3 through time. We find that U isotope fractionation between U in primary marine CaCO3 and seawater could have varied between 0.11 and 0.23‰ over the Phanerozoic due to secular variations in seawater chemistry. Such variations would significantly impact estimates of the extent of marine anoxia derived from the U isotope record. For example, at the Permo-Triassic boundary, this effect might imply that the estimated extent of anoxia is ∼32% more extreme than previously inferred. One significant limitation of our model is that the existing experimental database covers only abiotic carbonate precipitation, and does not include a possible range of biological effects which might enhance or suppress the range of isotopic fractionation calculated here. As biotic carbonates dominate the marine carbonate record, more work is need to assess controls on U isotopic fractionation into biotic marine carbonates.
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Identifying influences on model uncertainty: an application using a forest carbon budget model
James E. Smith; Linda S. Heath
2001-01-01
Uncertainty is an important consideration for both developers and users of environmental simulation models. Establishing quantitative estimates of uncertainty for deterministic models can be difficult when the underlying bases for such information are scarce. We demonstrate an application of probabilistic uncertainty analysis that provides for refinements in...
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NASA Astrophysics Data System (ADS)
Hatch, Lindsay E.; Yokelson, Robert J.; Stockwell, Chelsea E.; Veres, Patrick R.; Simpson, Isobel J.; Blake, Donald R.; Orlando, John J.; Barsanti, Kelley C.
2017-01-01
Multiple trace-gas instruments were deployed during the fourth Fire Lab at Missoula Experiment (FLAME-4), including the first application of proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOFMS) and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) for laboratory biomass burning (BB) measurements. Open-path Fourier transform infrared spectroscopy (OP-FTIR) was also deployed, as well as whole-air sampling (WAS) with one-dimensional gas chromatography-mass spectrometry (GC-MS) analysis. This combination of instruments provided an unprecedented level of detection and chemical speciation. The chemical composition and emission factors (EFs) determined by these four analytical techniques were compared for four representative fuels. The results demonstrate that the instruments are highly complementary, with each covering some unique and important ranges of compositional space, thus demonstrating the need for multi-instrument approaches to adequately characterize BB smoke emissions. Emission factors for overlapping compounds generally compared within experimental uncertainty, despite some outliers, including monoterpenes. Data from all measurements were synthesized into a single EF database that includes over 500 non-methane organic gases (NMOGs) to provide a comprehensive picture of speciated, gaseous BB emissions. The identified compounds were assessed as a function of volatility; 6-11 % of the total NMOG EF was associated with intermediate-volatility organic compounds (IVOCs). These atmospherically relevant compounds historically have been unresolved in BB smoke measurements and thus are largely missing from emission inventories. Additionally, the identified compounds were screened for published secondary organic aerosol (SOA) yields. Of the total reactive carbon (defined as EF scaled by the OH rate constant and carbon number of each compound) in the BB emissions, 55-77 % was associated with compounds for which SOA yields are unknown or understudied. The best candidates for future smog chamber experiments were identified based on the relative abundance and ubiquity of the understudied compounds, and they included furfural, 2-methyl furan, 2-furan methanol, and 1,3-cyclopentadiene. Laboratory study of these compounds will facilitate future modeling efforts.
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NASA Astrophysics Data System (ADS)
Goncharov, A. G.; Ionov, D. A.; Doucet, L. S.; Pokhilenko, L. N.
2012-12-01
Oxygen fugacity (fO2) and temperature variations in a complete lithospheric mantle section (70-220 km) of the central Siberian craton are estimated based on 42 peridotite xenoliths in the Udachnaya kimberlite. Pressure and temperature (P-T) estimates for the 70-140 km depth range closely follow the 40 mW/m2 model conductive geotherm but show a bimodal distribution at greater depths. A subset of coarse garnet peridotites at 145-180 km plots near the "cold" 35 mW/m2 geotherm whereas the majority of coarse and sheared rocks at ≥145 km scatter between the 40 and 45 mW/m2 geotherms. This P-T profile may reflect a perturbation of an initially "cold" lithospheric mantle through a combination of (1) magmatic under-plating close to the crust-mantle boundary and (2) intrusion of melts/fluids in the lower lithosphere accompanied by shearing. fO2 values estimated from Fe3+/∑Fe in spinel and/or garnet obtained by Mössbauer spectroscopy decrease from +1 to -4 Δlog fO2 (FMQ) from the top to the bottom of the lithospheric mantle (˜0.25 log units per 10 km) due to pressure effects on Fe2+-Fe3+ equilibria in garnet. Garnet peridotites from Udachnaya appear to be more oxidized than those from the Kaapvaal craton but show fO2 distribution with depth similar to those in the Slave craton. Published fO2 estimates for Udachnaya xenoliths based on C-O-H fluid speciation in inclusions in minerals from gas chromatography are similar to our results at ≤120 km, but are 1-2 orders of magnitude higher for the deeper mantle, possibly due to uncertainties of fO2 estimates based on experimental calibrations at ≤3.5 GPa. Sheared peridotites containing garnets with u-shaped, sinusoidal and humped REE patterns are usually more oxidized than Yb, Lu-rich, melt-equilibrated garnets, which show a continuous decrease from heavy to light REE. This further indicates that mantle redox state may be related to sources and modes of metasomatism.
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NASA Astrophysics Data System (ADS)
Dai, H.; Chen, X.; Ye, M.; Song, X.; Zachara, J. M.
2016-12-01
Sensitivity analysis has been an important tool in groundwater modeling to identify the influential parameters. Among various sensitivity analysis methods, the variance-based global sensitivity analysis has gained popularity for its model independence characteristic and capability of providing accurate sensitivity measurements. However, the conventional variance-based method only considers uncertainty contribution of single model parameters. In this research, we extended the variance-based method to consider more uncertainty sources and developed a new framework to allow flexible combinations of different uncertainty components. We decompose the uncertainty sources into a hierarchical three-layer structure: scenario, model and parametric. Furthermore, each layer of uncertainty source is capable of containing multiple components. An uncertainty and sensitivity analysis framework was then constructed following this three-layer structure using Bayesian network. Different uncertainty components are represented as uncertain nodes in this network. Through the framework, variance-based sensitivity analysis can be implemented with great flexibility of using different grouping strategies for uncertainty components. The variance-based sensitivity analysis thus is improved to be able to investigate the importance of an extended range of uncertainty sources: scenario, model, and other different combinations of uncertainty components which can represent certain key model system processes (e.g., groundwater recharge process, flow reactive transport process). For test and demonstration purposes, the developed methodology was implemented into a test case of real-world groundwater reactive transport modeling with various uncertainty sources. The results demonstrate that the new sensitivity analysis method is able to estimate accurate importance measurements for any uncertainty sources which were formed by different combinations of uncertainty components. The new methodology can provide useful information for environmental management and decision-makers to formulate policies and strategies.
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Ronald E. McRoberts
2005-01-01
Uncertainty in model-based predictions of individual tree diameter growth is attributed to three sources: measurement error for predictor variables, residual variability around model predictions, and uncertainty in model parameter estimates. Monte Carlo simulations are used to propagate the uncertainty from the three sources through a set of diameter growth models to...
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Aeroservoelastic Uncertainty Model Identification from Flight Data
NASA Technical Reports Server (NTRS)
Brenner, Martin J.
2001-01-01
Uncertainty modeling is a critical element in the estimation of robust stability margins for stability boundary prediction and robust flight control system development. There has been a serious deficiency to date in aeroservoelastic data analysis with attention to uncertainty modeling. Uncertainty can be estimated from flight data using both parametric and nonparametric identification techniques. The model validation problem addressed in this paper is to identify aeroservoelastic models with associated uncertainty structures from a limited amount of controlled excitation inputs over an extensive flight envelope. The challenge to this problem is to update analytical models from flight data estimates while also deriving non-conservative uncertainty descriptions consistent with the flight data. Multisine control surface command inputs and control system feedbacks are used as signals in a wavelet-based modal parameter estimation procedure for model updates. Transfer function estimates are incorporated in a robust minimax estimation scheme to get input-output parameters and error bounds consistent with the data and model structure. Uncertainty estimates derived from the data in this manner provide an appropriate and relevant representation for model development and robust stability analysis. This model-plus-uncertainty identification procedure is applied to aeroservoelastic flight data from the NASA Dryden Flight Research Center F-18 Systems Research Aircraft.
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NASA Astrophysics Data System (ADS)
Wang, Weizong; Berthelot, Antonin; Zhang, Quanzhi; Bogaerts, Annemie
2018-05-01
One of the main issues in plasma chemistry modeling is that the cross sections and rate coefficients are subject to uncertainties, which yields uncertainties in the modeling results and hence hinders the predictive capabilities. In this paper, we reveal the impact of these uncertainties on the model predictions of plasma-based dry reforming in a dielectric barrier discharge. For this purpose, we performed a detailed uncertainty analysis and sensitivity study. 2000 different combinations of rate coefficients, based on the uncertainty from a log-normal distribution, are used to predict the uncertainties in the model output. The uncertainties in the electron density and electron temperature are around 11% and 8% at the maximum of the power deposition for a 70% confidence level. Still, this can have a major effect on the electron impact rates and hence on the calculated conversions of CO2 and CH4, as well as on the selectivities of CO and H2. For the CO2 and CH4 conversion, we obtain uncertainties of 24% and 33%, respectively. For the CO and H2 selectivity, the corresponding uncertainties are 28% and 14%, respectively. We also identify which reactions contribute most to the uncertainty in the model predictions. In order to improve the accuracy and reliability of plasma chemistry models, we recommend using only verified rate coefficients, and we point out the need for dedicated verification experiments.
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Jathar, Shantanu H.; Gordon, Timothy D.; Hennigan, Christopher J.; Pye, Havala O. T.; Pouliot, George; Adams, Peter J.; Donahue, Neil M.; Robinson, Allen L.
2014-01-01
Secondary organic aerosol (SOA) formed from the atmospheric oxidation of nonmethane organic gases (NMOG) is a major contributor to atmospheric aerosol mass. Emissions and smog chamber experiments were performed to investigate SOA formation from gasoline vehicles, diesel vehicles, and biomass burning. About 10–20% of NMOG emissions from these major combustion sources are not routinely speciated and therefore are currently misclassified in emission inventories and chemical transport models. The smog chamber data demonstrate that this misclassification biases model predictions of SOA production low because the unspeciated NMOG produce more SOA per unit mass than the speciated NMOG. We present new source-specific SOA yield parameterizations for these unspeciated emissions. These parameterizations and associated source profiles are designed for implementation in chemical transport models. Box model calculations using these new parameterizations predict that NMOG emissions from the top six combustion sources form 0.7 Tg y−1 of first-generation SOA in the United States, almost 90% of which is from biomass burning and gasoline vehicles. About 85% of this SOA comes from unspeciated NMOG, demonstrating that chemical transport models need improved treatment of combustion emissions to accurately predict ambient SOA concentrations. PMID:25002466
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NASA Astrophysics Data System (ADS)
Touhidul Mustafa, Syed Md.; Nossent, Jiri; Ghysels, Gert; Huysmans, Marijke
2017-04-01
Transient numerical groundwater flow models have been used to understand and forecast groundwater flow systems under anthropogenic and climatic effects, but the reliability of the predictions is strongly influenced by different sources of uncertainty. Hence, researchers in hydrological sciences are developing and applying methods for uncertainty quantification. Nevertheless, spatially distributed flow models pose significant challenges for parameter and spatially distributed input estimation and uncertainty quantification. In this study, we present a general and flexible approach for input and parameter estimation and uncertainty analysis of groundwater models. The proposed approach combines a fully distributed groundwater flow model (MODFLOW) with the DiffeRential Evolution Adaptive Metropolis (DREAM) algorithm. To avoid over-parameterization, the uncertainty of the spatially distributed model input has been represented by multipliers. The posterior distributions of these multipliers and the regular model parameters were estimated using DREAM. The proposed methodology has been applied in an overexploited aquifer in Bangladesh where groundwater pumping and recharge data are highly uncertain. The results confirm that input uncertainty does have a considerable effect on the model predictions and parameter distributions. Additionally, our approach also provides a new way to optimize the spatially distributed recharge and pumping data along with the parameter values under uncertain input conditions. It can be concluded from our approach that considering model input uncertainty along with parameter uncertainty is important for obtaining realistic model predictions and a correct estimation of the uncertainty bounds.
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Kettler, Susanne; Kennedy, Marc; McNamara, Cronan; Oberdörfer, Regina; O'Mahony, Cian; Schnabel, Jürgen; Smith, Benjamin; Sprong, Corinne; Faludi, Roland; Tennant, David
2015-08-01
Uncertainty analysis is an important component of dietary exposure assessments in order to understand correctly the strength and limits of its results. Often, standard screening procedures are applied in a first step which results in conservative estimates. If through those screening procedures a potential exceedance of health-based guidance values is indicated, within the tiered approach more refined models are applied. However, the sources and types of uncertainties in deterministic and probabilistic models can vary or differ. A key objective of this work has been the mapping of different sources and types of uncertainties to better understand how to best use uncertainty analysis to generate more realistic comprehension of dietary exposure. In dietary exposure assessments, uncertainties can be introduced by knowledge gaps about the exposure scenario, parameter and the model itself. With this mapping, general and model-independent uncertainties have been identified and described, as well as those which can be introduced and influenced by the specific model during the tiered approach. This analysis identifies that there are general uncertainties common to point estimates (screening or deterministic methods) and probabilistic exposure assessment methods. To provide further clarity, general sources of uncertainty affecting many dietary exposure assessments should be separated from model-specific uncertainties. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
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Beekhuizen, Johan; Heuvelink, Gerard B M; Huss, Anke; Bürgi, Alfred; Kromhout, Hans; Vermeulen, Roel
2014-11-01
With the increased availability of spatial data and computing power, spatial prediction approaches have become a standard tool for exposure assessment in environmental epidemiology. However, such models are largely dependent on accurate input data. Uncertainties in the input data can therefore have a large effect on model predictions, but are rarely quantified. With Monte Carlo simulation we assessed the effect of input uncertainty on the prediction of radio-frequency electromagnetic fields (RF-EMF) from mobile phone base stations at 252 receptor sites in Amsterdam, The Netherlands. The impact on ranking and classification was determined by computing the Spearman correlations and weighted Cohen's Kappas (based on tertiles of the RF-EMF exposure distribution) between modelled values and RF-EMF measurements performed at the receptor sites. The uncertainty in modelled RF-EMF levels was large with a median coefficient of variation of 1.5. Uncertainty in receptor site height, building damping and building height contributed most to model output uncertainty. For exposure ranking and classification, the heights of buildings and receptor sites were the most important sources of uncertainty, followed by building damping, antenna- and site location. Uncertainty in antenna power, tilt, height and direction had a smaller impact on model performance. We quantified the effect of input data uncertainty on the prediction accuracy of an RF-EMF environmental exposure model, thereby identifying the most important sources of uncertainty and estimating the total uncertainty stemming from potential errors in the input data. This approach can be used to optimize the model and better interpret model output. Copyright © 2014 Elsevier Inc. All rights reserved.
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Flores-Alsina, Xavier; Kazadi Mbamba, Christian; Solon, Kimberly; Vrecko, Darko; Tait, Stephan; Batstone, Damien J; Jeppsson, Ulf; Gernaey, Krist V
2015-11-15
There is a growing interest within the Wastewater Treatment Plant (WWTP) modelling community to correctly describe physico-chemical processes after many years of mainly focusing on biokinetics. Indeed, future modelling needs, such as a plant-wide phosphorus (P) description, require a major, but unavoidable, additional degree of complexity when representing cationic/anionic behaviour in Activated Sludge (AS)/Anaerobic Digestion (AD) systems. In this paper, a plant-wide aqueous phase chemistry module describing pH variations plus ion speciation/pairing is presented and interfaced with industry standard models. The module accounts for extensive consideration of non-ideality, including ion activities instead of molar concentrations and complex ion pairing. The general equilibria are formulated as a set of Differential Algebraic Equations (DAEs) instead of Ordinary Differential Equations (ODEs) in order to reduce the overall stiffness of the system, thereby enhancing simulation speed. Additionally, a multi-dimensional version of the Newton-Raphson algorithm is applied to handle the existing multiple algebraic inter-dependencies. The latter is reinforced with the Simulated Annealing method to increase the robustness of the solver making the system not so dependent of the initial conditions. Simulation results show pH predictions when describing Biological Nutrient Removal (BNR) by the activated sludge models (ASM) 1, 2d and 3 comparing the performance of a nitrogen removal (WWTP1) and a combined nitrogen and phosphorus removal (WWTP2) treatment plant configuration under different anaerobic/anoxic/aerobic conditions. The same framework is implemented in the Benchmark Simulation Model No. 2 (BSM2) version of the Anaerobic Digestion Model No. 1 (ADM1) (WWTP3) as well, predicting pH values at different cationic/anionic loads. In this way, the general applicability/flexibility of the proposed approach is demonstrated, by implementing the aqueous phase chemistry module in some of the most frequently used WWTP process simulation models. Finally, it is shown how traditional wastewater modelling studies can be complemented with a rigorous description of aqueous phase and ion chemistry (pH, speciation, complexation). Copyright © 2015 Elsevier Ltd. All rights reserved.
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Bilcke, Joke; Beutels, Philippe; Brisson, Marc; Jit, Mark
2011-01-01
Accounting for uncertainty is now a standard part of decision-analytic modeling and is recommended by many health technology agencies and published guidelines. However, the scope of such analyses is often limited, even though techniques have been developed for presenting the effects of methodological, structural, and parameter uncertainty on model results. To help bring these techniques into mainstream use, the authors present a step-by-step guide that offers an integrated approach to account for different kinds of uncertainty in the same model, along with a checklist for assessing the way in which uncertainty has been incorporated. The guide also addresses special situations such as when a source of uncertainty is difficult to parameterize, resources are limited for an ideal exploration of uncertainty, or evidence to inform the model is not available or not reliable. for identifying the sources of uncertainty that influence results most are also described. Besides guiding analysts, the guide and checklist may be useful to decision makers who need to assess how well uncertainty has been accounted for in a decision-analytic model before using the results to make a decision.
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NASA Astrophysics Data System (ADS)
Prietzel, Jörg; Dümig, Alexander; Wu, Yanhong; Zhou, Jun; Klysubun, Wantana
2013-05-01
Phosphorus (P) is a crucial element for life on Earth, and the bioavailability of P in terrestrial ecosystems, which is dependent on the soil P stock and its speciation, may limit ecosystem productivity and succession. In our study, for the first time a direct speciation of soil P in two glacier foreland chronosequences has been conducted using synchrotron-based X-ray Absorption Near-Edge Structure (XANES) spectroscopy. The chronosequences are located in the forefields of Hailuogou Glacier (Gongga Shan, China) and Damma Glacier (Swiss Alps). The age since deglaciation of the investigated soils ranges from 0 to 120 years at Hailuogou, and from 15 to >700 years at Damma. Differences in climate conditions (cooler at Damma, in contrast to Hailuogou precluding the establishment of forest in advanced ecosystem succession stages) and in the chemical composition of the parent material result in different soil contents of total P and Fe/Al oxyhydroxides, which are much smaller at Damma than at Hailuogou. Nevertheless, both chronosequences show similar trends of their topsoil P status with increasing soil age. Our study reveals a rapid change of topsoil P speciation in glacier retreat areas already during initial stages of pedogenesis: Initially dominating bedrock-derived apatite-P and Al-bound P is depleted; Fe-bound P and particularly organically-bound P is accumulated. Organic P strongly dominates in the topsoil of the mature soils outside the proglacial area of Damma Glacier (age 700-3000 years), and already 50 years after deglacation in the topsoil of the retreat area of Hailuogou Glacier. A key factor for the change in topsoil P speciation is the establishment of vegetation, resulting in soil organic matter (SOM) accumulation as well as accelerated soil acidification and apatite dissolution by organic acids, which are produced by SOM-degrading micro-organisms, mykorrhiza fungi, and plant roots. Particularly the succession of grassland to forest seems to accelerate the transformation of topsoil P from apatite-P into organic P. The conceptual model developed by Walker and Syers (1976) to explain long-term (millennial) changes of P speciation, availability, and turnover in soils and terrestrial ecosystems seems to be valid to describe short-term changes of P speciation and P availability in proglacial topsoils already within a century of initial soil formation. Because the apatite-depleted topsoil horizons in the young proglacial soils are shallow, the change of topsoil P speciation should not seriously affect P availability and the P acquisition strategy of adult trees, whose roots can easily access apatite-containing C horizons. In contrast, P acquisition strategies of fungi, micro-organisms and plants confined to the topsoil probably change from apatite dissolution to mineralization of organic P already within <3000 years in a proglacial ecosystem succession from bare soil to grassland (Damma Glacier Chronosequence) or even within <100 years in a proglacial ecosystem succession to forest (Hailuogou Glacier Chronosequence).
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Pastene, Luis A; Goto, Mutsuo; Kanda, Naohisa; Zerbini, Alexandre N; Kerem, Dan; Watanabe, Kazuo; Bessho, Yoshitaka; Hasegawa, Masami; Nielsen, Rasmus; Larsen, Finn; Palsbøll, Per J
2007-04-01
How do populations of highly mobile species inhabiting open environments become reproductively isolated and evolve into new species? We test the hypothesis that elevated ocean-surface temperatures can facilitate allopatry among pelagic populations and thus promote speciation. Oceanographic modelling has shown that increasing surface temperatures cause localization and reduction of upwelling, leading to fragmentation of feeding areas critical to pelagic species. We test our hypothesis by genetic analyses of populations of two closely related baleen whales, the Antarctic minke whale (Balaenoptera bonaerensis) and common minke whale (Balaenoptera acutorostrata) whose current distributions and migration patterns extent are largely determined by areas of consistent upwelling with high primary production. Phylogeographic and population genetic analyses of mitochondrial DNA control-region nucleotide sequences collected from 467 whales sampled in four different ocean basins were employed to infer the evolutionary relationship among populations of B. acutorostrata by rooting an intraspecific phylogeny with a population of B. bonaerensis. Our findings suggest that the two species diverged in the Southern Hemisphere less than 5 million years ago (Ma). This estimate places the speciation event during a period of extended global warming in the Pliocene. We propose that elevated ocean temperatures in the period facilitated allopatric speciation by disrupting the continuous belt of upwelling maintained by the Antarctic Circumpolar Current. Our analyses revealed that the current populations of B. acutorostrata likely diverged after the Pliocene some 1.5 Ma when global temperatures had decreased and presumably coinciding with the re-establishment of the polar-equatorial temperature gradient that ultimately drives upwelling. In most population samples, we detected genetic signatures of exponential population expansions, consistent with the notion of increasing carrying capacity after the Pliocene. Our hypothesis that prolonged periods of global warming facilitate speciation in pelagic marine species that depend on upwelling should be tested by comparative analyses in other pelagic species.
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2011-01-01
Background Species generally have a fixed number of chromosomes in the cell nuclei while between-species differences are common and often pronounced. These differences could have evolved through multiple speciation events, each involving the fixation of a single chromosomal rearrangement. Alternatively, marked changes in the karyotype may be the consequence of within-species accumulation of multiple chromosomal fissions/fusions, resulting in highly polymorphic systems with the subsequent extinction of intermediate karyomorphs. Although this mechanism of chromosome number evolution is possible in theory, it has not been well documented. Results We present the discovery of exceptional intraspecific variability in the karyotype of the widespread Eurasian butterfly Leptidea sinapis. We show that within this species the diploid chromosome number gradually decreases from 2n = 106 in Spain to 2n = 56 in eastern Kazakhstan, resulting in a 6000 km-wide cline that originated recently (8,500 to 31,000 years ago). Remarkably, intrapopulational chromosome number polymorphism exists, the chromosome number range overlaps between some populations separated by hundreds of kilometers, and chromosomal heterozygotes are abundant. We demonstrate that this karyotypic variability is intraspecific because in L. sinapis a broad geographical distribution is coupled with a homogenous morphological and genetic structure. Conclusions The discovered system represents the first clearly documented case of explosive chromosome number evolution through intraspecific and intrapopulation accumulation of multiple chromosomal changes. Leptidea sinapis may be used as a model system for studying speciation by means of chromosomally-based suppressed recombination mechanisms, as well as clinal speciation, a process that is theoretically possible but difficult to document. The discovered cline seems to represent a narrow time-window of the very first steps of species formation linked to multiple chromosomal changes that have occurred explosively. This case offers a rare opportunity to study this process before drift, dispersal, selection, extinction and speciation erase the traces of microevolutionary events and just leave the final picture of a pronounced interspecific chromosomal difference. PMID:21507222
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Barluenga, Marta; Meyer, Axel
2010-10-26
Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios. We found that the large lakes contain older and more diverse Midas Cichlid populations, while all crater lakes hold younger and genetically less variable species assemblages. The large lakes appear to have repeatedly acted as source populations for all crater lakes, and our data indicate that faunal exchange among crater lakes is extremely unlikely. Despite their very recent (often only a few thousand years old) and common origin from the two large Nicaraguan lakes, all crater lake Midas Cichlid radiations underwent independent, but parallel, evolution, and comprise distinct genetic units. Indeed several of these crater lakes contain multiple genetically distinct incipient species that most likely arose through sympatric speciation. Several crater lake radiations can be traced back to a single ancestral line, but some appear to have more than one founding lineage. The timing of the colonization(s) of each crater lake differs, although most of them occurred more (probably much more) recently than 20,000 years ago. The genetic differentiation of the crater lake populations is directly related to the number of founding lineages, but independent of the timing of colonization. Interestingly, levels of phenotypic differentiation, and speciation events, appeared independent of both factors.
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Quantum-memory-assisted entropic uncertainty in spin models with Dzyaloshinskii-Moriya interaction
NASA Astrophysics Data System (ADS)
Huang, Zhiming
2018-02-01
In this article, we investigate the dynamics and correlations of quantum-memory-assisted entropic uncertainty, the tightness of the uncertainty, entanglement, quantum correlation and mixedness for various spin chain models with Dzyaloshinskii-Moriya (DM) interaction, including the XXZ model with DM interaction, the XY model with DM interaction and the Ising model with DM interaction. We find that the uncertainty grows to a stable value with growing temperature but reduces as the coupling coefficient, anisotropy parameter and DM values increase. It is found that the entropic uncertainty is closely correlated with the mixedness of the system. The increasing quantum correlation can result in a decrease in the uncertainty, and the robustness of quantum correlation is better than entanglement since entanglement means sudden birth and death. The tightness of the uncertainty drops to zero, apart from slight volatility as various parameters increase. Furthermore, we propose an effective approach to steering the uncertainty by weak measurement reversal.
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Embracing uncertainty in applied ecology.
Milner-Gulland, E J; Shea, K
2017-12-01
Applied ecologists often face uncertainty that hinders effective decision-making.Common traps that may catch the unwary are: ignoring uncertainty, acknowledging uncertainty but ploughing on, focussing on trivial uncertainties, believing your models, and unclear objectives.We integrate research insights and examples from a wide range of applied ecological fields to illustrate advances that are generally underused, but could facilitate ecologists' ability to plan and execute research to support management.Recommended approaches to avoid uncertainty traps are: embracing models, using decision theory, using models more effectively, thinking experimentally, and being realistic about uncertainty. Synthesis and applications . Applied ecologists can become more effective at informing management by using approaches that explicitly take account of uncertainty.
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Pollinator-driven ecological speciation in plants: new evidence and future perspectives
Van der Niet, Timotheüs; Peakall, Rod; Johnson, Steven D.
2014-01-01
Background The hypothesis that pollinators have been important drivers of angiosperm diversity dates back to Darwin, and remains an important research topic today. Mounting evidence indicates that pollinators have the potential to drive diversification at several different stages of the evolutionary process. Microevolutionary studies have provided evidence for pollinator-mediated floral adaptation, while macroevolutionary evidence supports a general pattern of pollinator-driven diversification of angiosperms. However, the overarching issue of whether, and how, shifts in pollination system drive plant speciation represents a critical gap in knowledge. Bridging this gap is crucial to fully understand whether pollinator-driven microevolution accounts for the observed macroevolutionary patterns. Testable predictions about pollinator-driven speciation can be derived from the theory of ecological speciation, according to which adaptation (microevolution) and speciation (macroevolution) are directly linked. This theory is a particularly suitable framework for evaluating evidence for the processes underlying shifts in pollination systems and their potential consequences for the evolution of reproductive isolation and speciation. Scope This Viewpoint paper focuses on evidence for the four components of ecological speciation in the context of plant-pollinator interactions, namely (1) the role of pollinators as selective agents, (2) floral trait divergence, including the evolution of ‘pollination ecotypes‘, (3) the geographical context of selection on floral traits, and (4) the role of pollinators in the evolution of reproductive isolation. This Viewpoint also serves as the introduction to a Special Issue on Pollinator-Driven Speciation in Plants. The 13 papers in this Special Issue range from microevolutionary studies of ecotypes to macroevolutionary studies of historical ecological shifts, and span a wide range of geographical areas and plant families. These studies further illustrate innovative experimental approaches, and they employ modern tools in genetics and floral trait quantification. Future advances to the field require better quantification of selection through male fitness and pollinator isolation, for instance by exploiting next-generation sequencing technologies. By combining these new tools with strategically chosen study systems, and smart experimental design, we predict that examples of pollinator-driven speciation will be among the most widespread and compelling of all cases of ecological speciation. PMID:24418954
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On the Directional Dependence and Null Space Freedom in Uncertainty Bound Identification
NASA Technical Reports Server (NTRS)
Lim, K. B.; Giesy, D. P.
1997-01-01
In previous work, the determination of uncertainty models via minimum norm model validation is based on a single set of input and output measurement data. Since uncertainty bounds at each frequency is directionally dependent for multivariable systems, this will lead to optimistic uncertainty levels. In addition, the design freedom in the uncertainty model has not been utilized to further reduce uncertainty levels. The above issues are addressed by formulating a min- max problem. An analytical solution to the min-max problem is given to within a generalized eigenvalue problem, thus avoiding a direct numerical approach. This result will lead to less conservative and more realistic uncertainty models for use in robust control.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Marcus, Matthew A.; Edwards, Katrina J.; Gueguen, Bleuenn
Deep-sea ferromanganese nodules accumulate trace elements from seawater and underlying sediment porewaters during the growth of concentric mineral layers over millions of years. These trace elements have the potential to record past ocean geochemical conditions. The goal of this study was to determine whether Fe mineral alteration occurs and how the speciation of trace elements responds to alteration over ~3.7Ma of marine ferromanganese nodule (MFN) formation, a timeline constrained by estimates from 9 Be/ 10 Be concentrations in the nodule material. We determined Fe-bearing phases and Fe isotope composition in a South Pacific Gyre (SPG) nodule. Specifically, the distribution patternsmore » and speciation of trace element uptake by these Fe phases were investigated. The time interval covered by the growth of our sample of the nodule was derived from 9 Be/ 10 Be accelerator mass spectrometry (AMS). The composition and distribution of major and trace elements were mapped at various spatial scales, using micro-X-ray fluorescence (μXRF), electron microprobe analysis (EMPA), and inductively coupled plasma mass spectrometry (ICP-MS). Fe phases were characterized by micro-extended X-ray absorption fine structure (μEXAFS) spectroscopy and micro-X-ray diffraction (μXRD). Speciation of Ti and V, associated with Fe, was measured using micro-X-ray absorption near edge structure (μXANES) spectroscopy. Iron isotope composition (δ 56/54 Fe) in subsamples of 1-3mm increments along the radius of the nodule was determined with multiple-collector ICP-MS (MC-ICP-MS). The SPG nodule formed through primarily hydrogeneous inputs at a rate of 4.0±0.4mm/Ma. The nodule exhibited a high diversity of Fe mineral phases: feroxyhite (δ-FeOOH), goethite (α-FeOOH), lepidocrocite (γ-FeOOH), and poorly ordered ferrihydrite-like phases. These findings provide evidence that Fe oxyhydroxides within the nodule undergo alteration to more stable phases over millions of years. Trace Ti and V were spatially correlated with Fe and found to be adsorbed to Fe-bearing minerals. Ti/Fe and V/Fe ratios, and Ti and V speciation, did not vary along the nodule radius. The δ 56/54 Fe values, when averaged over sample increments representing 0.25-0.75Ma, were homogeneous within uncertainty along the nodule radius, at -0.12±0.07‰ (2sd, n=10). Our results indicate that the Fe isotope composition of the nodule remained constant during nodule growth and that mineral alteration did not affect the primary Fe isotope composition of the nodule. Furthermore, the average δ 56/54 Fe value of -0.12‰ we find is consistent with Fe sourced from continental eolian particles (dust). Despite mineral alteration, the trace element partitioning of Ti and V, and Fe isotope composition, do not appear to change within the sensitivity of our measurements. These findings suggest that Fe oxyhydroxides within hydrogenetic ferromanganese nodules are out of geochemical contact with seawater once they are covered by subsequent concentric mineral layers. Even though Fe-bearing minerals are altered, trace element ratios, speciation and Fe isotope composition are preserved within the nodule.« less
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Marcus, Matthew A.; Edwards, Katrina J.; Gueguen, Bleuenn; ...
2015-09-05
Deep-sea ferromanganese nodules accumulate trace elements from seawater and underlying sediment porewaters during the growth of concentric mineral layers over millions of years. These trace elements have the potential to record past ocean geochemical conditions. The goal of this study was to determine whether Fe mineral alteration occurs and how the speciation of trace elements responds to alteration over ~3.7Ma of marine ferromanganese nodule (MFN) formation, a timeline constrained by estimates from 9 Be/ 10 Be concentrations in the nodule material. We determined Fe-bearing phases and Fe isotope composition in a South Pacific Gyre (SPG) nodule. Specifically, the distribution patternsmore » and speciation of trace element uptake by these Fe phases were investigated. The time interval covered by the growth of our sample of the nodule was derived from 9 Be/ 10 Be accelerator mass spectrometry (AMS). The composition and distribution of major and trace elements were mapped at various spatial scales, using micro-X-ray fluorescence (μXRF), electron microprobe analysis (EMPA), and inductively coupled plasma mass spectrometry (ICP-MS). Fe phases were characterized by micro-extended X-ray absorption fine structure (μEXAFS) spectroscopy and micro-X-ray diffraction (μXRD). Speciation of Ti and V, associated with Fe, was measured using micro-X-ray absorption near edge structure (μXANES) spectroscopy. Iron isotope composition (δ 56/54 Fe) in subsamples of 1-3mm increments along the radius of the nodule was determined with multiple-collector ICP-MS (MC-ICP-MS). The SPG nodule formed through primarily hydrogeneous inputs at a rate of 4.0±0.4mm/Ma. The nodule exhibited a high diversity of Fe mineral phases: feroxyhite (δ-FeOOH), goethite (α-FeOOH), lepidocrocite (γ-FeOOH), and poorly ordered ferrihydrite-like phases. These findings provide evidence that Fe oxyhydroxides within the nodule undergo alteration to more stable phases over millions of years. Trace Ti and V were spatially correlated with Fe and found to be adsorbed to Fe-bearing minerals. Ti/Fe and V/Fe ratios, and Ti and V speciation, did not vary along the nodule radius. The δ 56/54 Fe values, when averaged over sample increments representing 0.25-0.75Ma, were homogeneous within uncertainty along the nodule radius, at -0.12±0.07‰ (2sd, n=10). Our results indicate that the Fe isotope composition of the nodule remained constant during nodule growth and that mineral alteration did not affect the primary Fe isotope composition of the nodule. Furthermore, the average δ 56/54 Fe value of -0.12‰ we find is consistent with Fe sourced from continental eolian particles (dust). Despite mineral alteration, the trace element partitioning of Ti and V, and Fe isotope composition, do not appear to change within the sensitivity of our measurements. These findings suggest that Fe oxyhydroxides within hydrogenetic ferromanganese nodules are out of geochemical contact with seawater once they are covered by subsequent concentric mineral layers. Even though Fe-bearing minerals are altered, trace element ratios, speciation and Fe isotope composition are preserved within the nodule.« less
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Relating Data and Models to Characterize Parameter and Prediction Uncertainty
Applying PBPK models in risk analysis requires that we realistically assess the uncertainty of relevant model predictions in as quantitative a way as possible. The reality of human variability may add a confusing feature to the overall uncertainty assessment, as uncertainty and v...
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Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia
Beheregaray, Luciano B.; Cooke, Georgina M.; Chao, Ning L.; Landguth, Erin L.
2015-01-01
Evolution creates and sustains biodiversity via adaptive changes in ecologically relevant traits. Ecologically mediated selection contributes to genetic divergence both in the presence or absence of geographic isolation between populations, and is considered an important driver of speciation. Indeed, the genetics of ecological speciation is becoming increasingly studied across a variety of taxa and environments. In this paper we review the literature of ecological speciation in the tropics. We report on low research productivity in tropical ecosystems and discuss reasons accounting for the rarity of studies. We argue for research programs that simultaneously address biogeographical and taxonomic questions in the tropics, while effectively assessing relationships between reproductive isolation and ecological divergence. To contribute toward this goal, we propose a new framework for ecological speciation that integrates information from phylogenetics, phylogeography, population genomics, and simulations in evolutionary landscape genetics (ELG). We introduce components of the framework, describe ELG simulations (a largely unexplored approach in ecological speciation), and discuss design and experimental feasibility within the context of tropical research. We then use published genetic datasets from populations of five codistributed Amazonian fish species to assess the performance of the framework in studies of tropical speciation. We suggest that these approaches can assist in distinguishing the relative contribution of natural selection from biogeographic history in the origin of biodiversity, even in complex ecosystems such as Amazonia. We also discuss on how to assess ecological speciation using ELG simulations that include selection. These integrative frameworks have considerable potential to enhance conservation management in biodiversity rich ecosystems and to complement historical biogeographic and evolutionary studies of tropical biotas. PMID:25653668
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H2O in rhyolitic glasses and melts: Measurement, speciation, solubility, and diffusion
NASA Astrophysics Data System (ADS)
Zhang, Youxue
1999-11-01
Dissolved H2O in silicate melts and glasses plays a crucial role in volcanic eruptions on terrestrial planets and affects glass properties and magma evolution. In this paper, major progress on several aspects of the H2O-melt (or glass) system is reviewed, consistency among a variety of data is investigated, discrepancies are evaluated, and confusion is clarified. On the infrared measurement of total H2O and species concentrations, calibration for a variety of glasses has been carried out at room temperature. The measurements for H2O in rhyolitic glasses have undergone the most scrutiny, resulting in the realization that absorptivities for the near-infrared bands depend on total H2O content. Although the variation of the absorptivities does not seem to significantly affect the determination of total H2O, it does affect the determination of molecular H2O and OH species concentrations. Calibration of the infrared technique for H2O in rhyolitic glasses still needs much improvement, especially at high total H2O. Furthermore, it is now almost certain that the molar absorptivities also depend on the measurement temperature in in situ studies. Hence it will be necessary to carry out calibrations in situ at high temperatures. On H2O speciation, results from two experimental approaches, the quench technique and the in situ technique, are very different, leading to controversy in our understanding of true speciation. A solution is presented to reconcile this controversy. It is almost certain that the quench technique does not suffer from a quench problem, but interpretation of in situ results suffered from ignoring the dependence of the molar absorptivities on measurement temperature. Accurate calibration at high temperatures is necessary for the quantitative application of the in situ technique to H2O speciation in silicate melts and glasses. On H2O solubility in silicate melts, recent experimental work has significantly expanded the T-P range of solubility measurements, and recent solubility models fill a gap for predicting solubility for a wide range of melt compositions. I present a solubility model for rhyolitic and quasi-rhyolitic melts over a wide range of T and P (500°-1350°C, 0-8 kbar) by incorporating the role of speciation. The solubility model is able to recover the experimental solubility data and has extrapolative value, although the partial molar volume of H2O derived from the solubility model differs from that derived from density measurements. On H2O diffusion, recent studies on H2O diffusion in a quasi-rhyolitic melt at 800°-1200°C, 0.5-5 kbar, and up to 7% total H2O not only provide important new diffusion data, but are also challenging earlier understanding of H2O diffusion based on data in rhyolitic glasses at 400°-550°C, 1 bar, and 0.2-1.8% total H2O. A comparison between the earlier model and recent data is made. The recent high-temperature diffusivities at total H2O ≤ 2% can be predicted by the earlier model. However, at higher total H2O, the earlier model fails. New work is under way to understand the diffusion mechanisms at high H2O contents.
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SPECIATION OF COMPLEX ORGANIC CONTAMINANTS IN WATER WITH RAMAN SPECTROSCOPY
Pesticides and industrial chemicals are typically complex organic molecules with multiple heteroatoms that can ionize, tautomerize, and form various types of hydrates in water. However, conceptual models for predicting the fate of these chemicals in the environment ignore these ...
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THERMODYNAMIC REACTION CONSTANTS FOR MODELING AQUEOUS ENVIRONMENTAL MERCURY SPECIATION
Unacceptably high fish tissue mercury residues are responsible for the majority of fish consumption advisories issued in 48 states of the United States of America. Mercury also has emerged as a transboundary contaminant of global concern. Although monomethylmercury is generally...
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Sexual selection drives speciation in an Amazonian frog
Boul, K.E.; Funk, W.C.; Darst, C.R.; Cannatella, D.C.; Ryan, M.J.
2007-01-01
One proposed mechanism of speciation is divergent sexual selection, whereby divergence in female preferences and male signals results in behavioural isolation. Despite the appeal of this hypothesis, evidence for it remains inconclusive. Here, we present several lines of evidence that sexual selection is driving behavioural isolation and speciation among populations of an Amazonian frog (Physalaemus petersi). First, sexual selection has promoted divergence in male mating calls and female preferences for calls between neighbouring populations, resulting in strong behavioural isolation. Second, phylogenetic analysis indicates that populations have become fixed for alternative call types several times throughout the species' range, and coalescent analysis rejects genetic drift as a cause for this pattern, suggesting that this divergence is due to selection. Finally, gene flow estimated with microsatellite loci is an average of 30 times lower between populations with different call types than between populations separated by a similar geographical distance with the same call type, demonstrating genetic divergence and incipient speciation. Taken together, these data provide strong evidence that sexual selection is driving behavioural isolation and speciation, supporting sexual selection as a cause for speciation in the wild. ?? 2006 The Royal Society.
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Metals, Health and the Environment – Emergence of Correlations Between Speciation and Effects
Williams, David R.
2004-01-01
Over the last half-century both the identification of the causes of diseases and the use of inorganic compounds to treat such conditions have been considerably enlightened through our emerging capabilities to identify the pivotal chemical species involved. The ‘duty of care’ placed upon scientists to protect the environment from manufactured chemicals and to limit their effects upon humans therefrom is best realised from a speciation knowledge database. This paper discusses categorising chemicals in terms of their persistence, bioaccumulation, and toxicities and uses speciation information to optimise desirable effects of chemicals in several applications such as the manufacture of pulp for paper and in the foliar nutrition of crops. Simultaneously, the chemical wasting side effects of industrial overdosing is easily avoided if speciation approaches are used. The move towards new environmentally friendly ligand agents is described and methods of finding substitute agents (often combinations of two or more chemicals) to replace nonbiodegradable EDTA. The geosphere migration of metals through the environment is discussed in terms of speciation. Future objectives discussed include improved means of communicating speciation-based recommendations to decision makers. PMID:18365083
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Uncertainties in Past and Future Global Water Availability
NASA Astrophysics Data System (ADS)
Sheffield, J.; Kam, J.
2014-12-01
Understanding how water availability changes on inter-annual to decadal time scales and how it may change in the future under climate change are a key part of understanding future stresses on water and food security. Historic evaluations of water availability on regional to global scales are generally based on large-scale model simulations with their associated uncertainties, in particular for long-term changes. Uncertainties are due to model errors and missing processes, parameter uncertainty, and errors in meteorological forcing data. Recent multi-model inter-comparisons and impact studies have highlighted large differences for past reconstructions, due to different simplifying assumptions in the models or the inclusion of physical processes such as CO2 fertilization. Modeling of direct anthropogenic factors such as water and land management also carry large uncertainties in their physical representation and from lack of socio-economic data. Furthermore, there is little understanding of the impact of uncertainties in the meteorological forcings that underpin these historic simulations. Similarly, future changes in water availability are highly uncertain due to climate model diversity, natural variability and scenario uncertainty, each of which dominates at different time scales. In particular, natural climate variability is expected to dominate any externally forced signal over the next several decades. We present results from multi-land surface model simulations of the historic global availability of water in the context of natural variability (droughts) and long-term changes (drying). The simulations take into account the impact of uncertainties in the meteorological forcings and the incorporation of water management in the form of reservoirs and irrigation. The results indicate that model uncertainty is important for short-term drought events, and forcing uncertainty is particularly important for long-term changes, especially uncertainty in precipitation due to reduced gauge density in recent years. We also discuss uncertainties in future projections from these models as driven by bias-corrected and downscaled CMIP5 climate projections, in the context of the balance between climate model robustness and climate model diversity.
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Holistic uncertainty analysis in river basin modeling for climate vulnerability assessment
NASA Astrophysics Data System (ADS)
Taner, M. U.; Wi, S.; Brown, C.
2017-12-01
The challenges posed by uncertain future climate are a prominent concern for water resources managers. A number of frameworks exist for assessing the impacts of climate-related uncertainty, including internal climate variability and anthropogenic climate change, such as scenario-based approaches and vulnerability-based approaches. While in many cases climate uncertainty may be dominant, other factors such as future evolution of the river basin, hydrologic response and reservoir operations are potentially significant sources of uncertainty. While uncertainty associated with modeling hydrologic response has received attention, very little attention has focused on the range of uncertainty and possible effects of the water resources infrastructure and management. This work presents a holistic framework that allows analysis of climate, hydrologic and water management uncertainty in water resources systems analysis with the aid of a water system model designed to integrate component models for hydrology processes and water management activities. The uncertainties explored include those associated with climate variability and change, hydrologic model parameters, and water system operation rules. A Bayesian framework is used to quantify and model the uncertainties at each modeling steps in integrated fashion, including prior and the likelihood information about model parameters. The framework is demonstrated in a case study for the St. Croix Basin located at border of United States and Canada.
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Uncertainty in simulating wheat yields under climate change
NASA Astrophysics Data System (ADS)
Asseng, S.; Ewert, F.; Rosenzweig, C.; Jones, J. W.; Hatfield, J. L.; Ruane, A. C.; Boote, K. J.; Thorburn, P. J.; Rötter, R. P.; Cammarano, D.; Brisson, N.; Basso, B.; Martre, P.; Aggarwal, P. K.; Angulo, C.; Bertuzzi, P.; Biernath, C.; Challinor, A. J.; Doltra, J.; Gayler, S.; Goldberg, R.; Grant, R.; Heng, L.; Hooker, J.; Hunt, L. A.; Ingwersen, J.; Izaurralde, R. C.; Kersebaum, K. C.; Müller, C.; Naresh Kumar, S.; Nendel, C.; O'Leary, G.; Olesen, J. E.; Osborne, T. M.; Palosuo, T.; Priesack, E.; Ripoche, D.; Semenov, M. A.; Shcherbak, I.; Steduto, P.; Stöckle, C.; Stratonovitch, P.; Streck, T.; Supit, I.; Tao, F.; Travasso, M.; Waha, K.; Wallach, D.; White, J. W.; Williams, J. R.; Wolf, J.
2013-09-01
Projections of climate change impacts on crop yields are inherently uncertain. Uncertainty is often quantified when projecting future greenhouse gas emissions and their influence on climate. However, multi-model uncertainty analysis of crop responses to climate change is rare because systematic and objective comparisons among process-based crop simulation models are difficult. Here we present the largest standardized model intercomparison for climate change impacts so far. We found that individual crop models are able to simulate measured wheat grain yields accurately under a range of environments, particularly if the input information is sufficient. However, simulated climate change impacts vary across models owing to differences in model structures and parameter values. A greater proportion of the uncertainty in climate change impact projections was due to variations among crop models than to variations among downscaled general circulation models. Uncertainties in simulated impacts increased with CO2 concentrations and associated warming. These impact uncertainties can be reduced by improving temperature and CO2 relationships in models and better quantified through use of multi-model ensembles. Less uncertainty in describing how climate change may affect agricultural productivity will aid adaptation strategy development andpolicymaking.
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Confronting the Uncertainty in Aerosol Forcing Using Comprehensive Observational Data
NASA Astrophysics Data System (ADS)
Johnson, J. S.; Regayre, L. A.; Yoshioka, M.; Pringle, K.; Sexton, D.; Lee, L.; Carslaw, K. S.
2017-12-01
The effect of aerosols on cloud droplet concentrations and radiative properties is the largest uncertainty in the overall radiative forcing of climate over the industrial period. In this study, we take advantage of a large perturbed parameter ensemble of simulations from the UK Met Office HadGEM-UKCA model (the aerosol component of the UK Earth System Model) to comprehensively sample uncertainty in aerosol forcing. Uncertain aerosol and atmospheric parameters cause substantial aerosol forcing uncertainty in climatically important regions. As the aerosol radiative forcing itself is unobservable, we investigate the potential for observations of aerosol and radiative properties to act as constraints on the large forcing uncertainty. We test how eight different theoretically perfect aerosol and radiation observations can constrain the forcing uncertainty over Europe. We find that the achievable constraint is weak unless many diverse observations are used simultaneously. This is due to the complex relationships between model output responses and the multiple interacting parameter uncertainties: compensating model errors mean there are many ways to produce the same model output (known as model equifinality) which impacts on the achievable constraint. However, using all eight observable quantities together we show that the aerosol forcing uncertainty can potentially be reduced by around 50%. This reduction occurs as we reduce a large sample of model variants (over 1 million) that cover the full parametric uncertainty to around 1% that are observationally plausible.Constraining the forcing uncertainty using real observations is a more complex undertaking, in which we must account for multiple further uncertainties including measurement uncertainties, structural model uncertainties and the model discrepancy from reality. Here, we make a first attempt to determine the true potential constraint on the forcing uncertainty from our model that is achievable using a comprehensive set of real aerosol and radiation observations taken from ground stations, flight campaigns and satellite. This research has been supported by the UK-China Research & Innovation Partnership Fund through the Met Office Climate Science for Service Partnership (CSSP) China as part of the Newton Fund, and by the NERC funded GASSP project.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Clark, Jared Matthew; Daum, Keith Alvin; Kalival, J. H.
2003-01-01
This initial study evaluates the use of ion mobility spectrometry (IMS) as a rapid test procedure for potential detection of adulterated perfumes and speciation of plant life. Sample types measured consist of five genuine perfumes, two species of sagebrush, and four species of flowers. Each sample type is treated as a separate classification problem. It is shown that discrimination using principal component analysis with K-nearest neighbors can distinguish one class from another. Discriminatory models generated using principal component regressions are not as effective. Results from this examination are encouraging and represent an initial phase demonstrating that perfumes and plants possessmore » characteristic chemical signatures that can be used for reliable identification.« less
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Toward Scientific Numerical Modeling
NASA Technical Reports Server (NTRS)
Kleb, Bil
2007-01-01
Ultimately, scientific numerical models need quantified output uncertainties so that modeling can evolve to better match reality. Documenting model input uncertainties and verifying that numerical models are translated into code correctly, however, are necessary first steps toward that goal. Without known input parameter uncertainties, model sensitivities are all one can determine, and without code verification, output uncertainties are simply not reliable. To address these two shortcomings, two proposals are offered: (1) an unobtrusive mechanism to document input parameter uncertainties in situ and (2) an adaptation of the Scientific Method to numerical model development and deployment. Because these two steps require changes in the computational simulation community to bear fruit, they are presented in terms of the Beckhard-Harris-Gleicher change model.
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When 1+1 can be >2: Uncertainties compound when simulating climate, fisheries and marine ecosystems
NASA Astrophysics Data System (ADS)
Evans, Karen; Brown, Jaclyn N.; Sen Gupta, Alex; Nicol, Simon J.; Hoyle, Simon; Matear, Richard; Arrizabalaga, Haritz
2015-03-01
Multi-disciplinary approaches that combine oceanographic, biogeochemical, ecosystem, fisheries population and socio-economic models are vital tools for modelling whole ecosystems. Interpreting the outputs from such complex models requires an appreciation of the many different types of modelling frameworks being used and their associated limitations and uncertainties. Both users and developers of particular model components will often have little involvement or understanding of other components within such modelling frameworks. Failure to recognise limitations and uncertainties associated with components and how these uncertainties might propagate throughout modelling frameworks can potentially result in poor advice for resource management. Unfortunately, many of the current integrative frameworks do not propagate the uncertainties of their constituent parts. In this review, we outline the major components of a generic whole of ecosystem modelling framework incorporating the external pressures of climate and fishing. We discuss the limitations and uncertainties associated with each component of such a modelling system, along with key research gaps. Major uncertainties in modelling frameworks are broadly categorised into those associated with (i) deficient knowledge in the interactions of climate and ocean dynamics with marine organisms and ecosystems; (ii) lack of observations to assess and advance modelling efforts and (iii) an inability to predict with confidence natural ecosystem variability and longer term changes as a result of external drivers (e.g. greenhouse gases, fishing effort) and the consequences for marine ecosystems. As a result of these uncertainties and intrinsic differences in the structure and parameterisation of models, users are faced with considerable challenges associated with making appropriate choices on which models to use. We suggest research directions required to address these uncertainties, and caution against overconfident predictions. Understanding the full impact of uncertainty makes it clear that full comprehension and robust certainty about the systems themselves are not feasible. A key research direction is the development of management systems that are robust to this unavoidable uncertainty.
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NASA Astrophysics Data System (ADS)
Li, Jun; Duan, Zhenhao
2011-08-01
A thermodynamic model is developed for the calculation of both phase and speciation equilibrium in the H 2O-CO 2-NaCl-CaCO 3-CaSO 4 system from 0 to 250 °C, and from 1 to 1000 bar with NaCl concentrations up to the saturation of halite. The vapor-liquid-solid (calcite, gypsum, anhydrite and halite) equilibrium together with the chemical equilibrium of H+,Na+,Ca, CaHCO3+,Ca(OH)+,OH-,Cl-, HCO3-,HSO4-,SO42-, CO32-,CO,CaCO and CaSO 4(aq) in the aqueous liquid phase as a function of temperature, pressure and salt concentrations can be calculated with accuracy close to the experimental results. Based on this model validated from experimental data, it can be seen that temperature, pressure and salinity all have significant effects on pH, alkalinity and speciations of aqueous solutions and on the solubility of calcite, halite, anhydrite and gypsum. The solubility of anhydrite and gypsum will decrease as temperature increases (e.g. the solubility will decrease by 90% from 360 K to 460 K). The increase of pressure may increase the solubility of sulphate minerals (e.g. gypsum solubility increases by about 20-40% from vapor pressure to 600 bar). Addition of NaCl to the solution may increase mineral solubility up to about 3 molality of NaCl, adding more NaCl beyond that may slightly decrease its solubility. Dissolved CO 2 in solution may decrease the solubility of minerals. The influence of dissolved calcite on the solubility of gypsum and anhydrite can be ignored, but dissolved gypsum or anhydrite has a big influence on the calcite solubility. Online calculation is made available on www.geochem-model.org/model.
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Inter-sectoral comparison of model uncertainty of climate change impacts in Africa
NASA Astrophysics Data System (ADS)
van Griensven, Ann; Vetter, Tobias; Piontek, Franzisca; Gosling, Simon N.; Kamali, Bahareh; Reinhardt, Julia; Dinkneh, Aklilu; Yang, Hong; Alemayehu, Tadesse
2016-04-01
We present the model results and their uncertainties of an inter-sectoral impact model inter-comparison initiative (ISI-MIP) for climate change impacts in Africa. The study includes results on hydrological, crop and health aspects. The impact models used ensemble inputs consisting of 20 time series of daily rainfall and temperature data obtained from 5 Global Circulation Models (GCMs) and 4 Representative concentration pathway (RCP). In this study, we analysed model uncertainty for the Regional Hydrological Models, Global Hydrological Models, Malaria models and Crop models. For the regional hydrological models, we used 2 African test cases: the Blue Nile in Eastern Africa and the Niger in Western Africa. For both basins, the main sources of uncertainty are originating from the GCM and RCPs, while the uncertainty of the regional hydrological models is relatively low. The hydrological model uncertainty becomes more important when predicting changes on low flows compared to mean or high flows. For the other sectors, the impact models have the largest share of uncertainty compared to GCM and RCP, especially for Malaria and crop modelling. The overall conclusion of the ISI-MIP is that it is strongly advised to use ensemble modeling approach for climate change impact studies throughout the whole modelling chain.
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NASA Astrophysics Data System (ADS)
Mannina, Giorgio; Cosenza, Alida; Viviani, Gaspare
In the last few years, the use of mathematical models in WasteWater Treatment Plant (WWTP) processes has become a common way to predict WWTP behaviour. However, mathematical models generally demand advanced input for their implementation that must be evaluated by an extensive data-gathering campaign, which cannot always be carried out. This fact, together with the intrinsic complexity of the model structure, leads to model results that may be very uncertain. Quantification of the uncertainty is imperative. However, despite the importance of uncertainty quantification, only few studies have been carried out in the wastewater treatment field, and those studies only included a few of the sources of model uncertainty. Seeking the development of the area, the paper presents the uncertainty assessment of a mathematical model simulating biological nitrogen and phosphorus removal. The uncertainty assessment was conducted according to the Generalised Likelihood Uncertainty Estimation (GLUE) methodology that has been scarcely applied in wastewater field. The model was based on activated-sludge models 1 (ASM) and 2 (ASM2). Different approaches can be used for uncertainty analysis. The GLUE methodology requires a large number of Monte Carlo simulations in which a random sampling of individual parameters drawn from probability distributions is used to determine a set of parameter values. Using this approach, model reliability was evaluated based on its capacity to globally limit the uncertainty. The method was applied to a large full-scale WWTP for which quantity and quality data was gathered. The analysis enabled to gain useful insights for WWTP modelling identifying the crucial aspects where higher uncertainty rely and where therefore, more efforts should be provided in terms of both data gathering and modelling practises.
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Speciation gradients and the distribution of biodiversity.
Schluter, Dolph; Pennell, Matthew W
2017-05-31
Global patterns of biodiversity are influenced by spatial and environmental variations in the rate at which new species form. We relate variations in speciation rates to six key patterns of biodiversity worldwide, including the species-area relationship, latitudinal gradients in species and genetic diversity, and between-habitat differences in species richness. Although they sometimes mirror biodiversity patterns, recent rates of speciation, at the tip of the tree of life, are often highest where species richness is low. Speciation gradients therefore shape, but are also shaped by, biodiversity gradients and are often more useful for predicting future patterns of biodiversity than for interpreting the past.
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An uncertainty analysis of wildfire modeling [Chapter 13
Karin Riley; Matthew Thompson
2017-01-01
Before fire models can be understood, evaluated, and effectively applied to support decision making, model-based uncertainties must be analyzed. In this chapter, we identify and classify sources of uncertainty using an established analytical framework, and summarize results graphically in an uncertainty matrix. Our analysis facilitates characterization of the...
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Climate data induced uncertainty in model-based estimations of terrestrial primary productivity
NASA Astrophysics Data System (ADS)
Wu, Zhendong; Ahlström, Anders; Smith, Benjamin; Ardö, Jonas; Eklundh, Lars; Fensholt, Rasmus; Lehsten, Veiko
2017-06-01
Model-based estimations of historical fluxes and pools of the terrestrial biosphere differ substantially. These differences arise not only from differences between models but also from differences in the environmental and climatic data used as input to the models. Here we investigate the role of uncertainties in historical climate data by performing simulations of terrestrial gross primary productivity (GPP) using a process-based dynamic vegetation model (LPJ-GUESS) forced by six different climate datasets. We find that the climate induced uncertainty, defined as the range among historical simulations in GPP when forcing the model with the different climate datasets, can be as high as 11 Pg C yr-1 globally (9% of mean GPP). We also assessed a hypothetical maximum climate data induced uncertainty by combining climate variables from different datasets, which resulted in significantly larger uncertainties of 41 Pg C yr-1 globally or 32% of mean GPP. The uncertainty is partitioned into components associated to the three main climatic drivers, temperature, precipitation, and shortwave radiation. Additionally, we illustrate how the uncertainty due to a given climate driver depends both on the magnitude of the forcing data uncertainty (climate data range) and the apparent sensitivity of the modeled GPP to the driver (apparent model sensitivity). We find that LPJ-GUESS overestimates GPP compared to empirically based GPP data product in all land cover classes except for tropical forests. Tropical forests emerge as a disproportionate source of uncertainty in GPP estimation both in the simulations and empirical data products. The tropical forest uncertainty is most strongly associated with shortwave radiation and precipitation forcing, of which climate data range contributes higher to overall uncertainty than apparent model sensitivity to forcing. Globally, precipitation dominates the climate induced uncertainty over nearly half of the vegetated land area, which is mainly due to climate data range and less so due to the apparent model sensitivity. Overall, climate data ranges are found to contribute more to the climate induced uncertainty than apparent model sensitivity to forcing. Our study highlights the need to better constrain tropical climate, and demonstrates that uncertainty caused by climatic forcing data must be considered when comparing and evaluating carbon cycle model results and empirical datasets.
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Escudero, Marcial
2015-07-01
• Fahrenholz's rule states that common ancestors of extant parasites were parasites of the common ancestors of extant hosts. Consequently, parasite phylogeny should mirror host phylogeny. The smut fungi genus Anthracoidea (Anthracoideaceae) is mainly hosted by species of the genus Carex (Cyperaceae). Whether smut fungi phylogeny mirrors sedge phylogeny is still under debate.• The nuclear large subunit DNA region (LSU; 57 accessions) from 31 Anthracoidea species and the ITS, ETS, and trnL-F spacer-trnL intron complex from 41 Carex species were used to infer the phylogenetic history of parasites and their hosts using a maximum likelihood approach. Event-based and distance-based cophylogenetic methods were used to test the hypothesis of whether the phylogeny of smut fungi from the genus Anthracoidea matches the phylogeny of the sedge Carex species they host.• Cophylogenetic reconstructions taking into account phylogenetic uncertainties based on event-based analyses demonstrated that the Anthracoidea phylogeny has significant topological congruence with the phylogeny of their Carex hosts. A distance-based test was also significant; therefore, the phylogenies of Anthracoide and Carex are partially congruent.• The phylogenetic congruence of Anthracoidea and Carex is partially based on smut fungi species being preferentially hosted by closely related sedges (host conservatism). In addition, many different events rather than only codivergence events are inferred. All of this evidence suggests that host-shift speciation rather than cospeciation seems to explain the cophylogenetic patterns of Anthracoidea and Carex. © 2015 Botanical Society of America, Inc.
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Development of a Prototype Model-Form Uncertainty Knowledge Base
NASA Technical Reports Server (NTRS)
Green, Lawrence L.
2016-01-01
Uncertainties are generally classified as either aleatory or epistemic. Aleatory uncertainties are those attributed to random variation, either naturally or through manufacturing processes. Epistemic uncertainties are generally attributed to a lack of knowledge. One type of epistemic uncertainty is called model-form uncertainty. The term model-form means that among the choices to be made during a design process within an analysis, there are different forms of the analysis process, which each give different results for the same configuration at the same flight conditions. Examples of model-form uncertainties include the grid density, grid type, and solver type used within a computational fluid dynamics code, or the choice of the number and type of model elements within a structures analysis. The objectives of this work are to identify and quantify a representative set of model-form uncertainties and to make this information available to designers through an interactive knowledge base (KB). The KB can then be used during probabilistic design sessions, so as to enable the possible reduction of uncertainties in the design process through resource investment. An extensive literature search has been conducted to identify and quantify typical model-form uncertainties present within aerospace design. An initial attempt has been made to assemble the results of this literature search into a searchable KB, usable in real time during probabilistic design sessions. A concept of operations and the basic structure of a model-form uncertainty KB are described. Key operations within the KB are illustrated. Current limitations in the KB, and possible workarounds are explained.
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Incorporating uncertainty in predictive species distribution modelling.
Beale, Colin M; Lennon, Jack J
2012-01-19
Motivated by the need to solve ecological problems (climate change, habitat fragmentation and biological invasions), there has been increasing interest in species distribution models (SDMs). Predictions from these models inform conservation policy, invasive species management and disease-control measures. However, predictions are subject to uncertainty, the degree and source of which is often unrecognized. Here, we review the SDM literature in the context of uncertainty, focusing on three main classes of SDM: niche-based models, demographic models and process-based models. We identify sources of uncertainty for each class and discuss how uncertainty can be minimized or included in the modelling process to give realistic measures of confidence around predictions. Because this has typically not been performed, we conclude that uncertainty in SDMs has often been underestimated and a false precision assigned to predictions of geographical distribution. We identify areas where development of new statistical tools will improve predictions from distribution models, notably the development of hierarchical models that link different types of distribution model and their attendant uncertainties across spatial scales. Finally, we discuss the need to develop more defensible methods for assessing predictive performance, quantifying model goodness-of-fit and for assessing the significance of model covariates.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sig Drellack, Lance Prothro
2007-12-01
The Underground Test Area (UGTA) Project of the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office is in the process of assessing and developing regulatory decision options based on modeling predictions of contaminant transport from underground testing of nuclear weapons at the Nevada Test Site (NTS). The UGTA Project is attempting to develop an effective modeling strategy that addresses and quantifies multiple components of uncertainty including natural variability, parameter uncertainty, conceptual/model uncertainty, and decision uncertainty in translating model results into regulatory requirements. The modeling task presents multiple unique challenges to the hydrological sciences as a result ofmore » the complex fractured and faulted hydrostratigraphy, the distributed locations of sources, the suite of reactive and non-reactive radionuclides, and uncertainty in conceptual models. Characterization of the hydrogeologic system is difficult and expensive because of deep groundwater in the arid desert setting and the large spatial setting of the NTS. Therefore, conceptual model uncertainty is partially addressed through the development of multiple alternative conceptual models of the hydrostratigraphic framework and multiple alternative models of recharge and discharge. Uncertainty in boundary conditions is assessed through development of alternative groundwater fluxes through multiple simulations using the regional groundwater flow model. Calibration of alternative models to heads and measured or inferred fluxes has not proven to provide clear measures of model quality. Therefore, model screening by comparison to independently-derived natural geochemical mixing targets through cluster analysis has also been invoked to evaluate differences between alternative conceptual models. Advancing multiple alternative flow models, sensitivity of transport predictions to parameter uncertainty is assessed through Monte Carlo simulations. The simulations are challenged by the distributed sources in each of the Corrective Action Units, by complex mass transfer processes, and by the size and complexity of the field-scale flow models. An efficient methodology utilizing particle tracking results and convolution integrals provides in situ concentrations appropriate for Monte Carlo analysis. Uncertainty in source releases and transport parameters including effective porosity, fracture apertures and spacing, matrix diffusion coefficients, sorption coefficients, and colloid load and mobility are considered. With the distributions of input uncertainties and output plume volumes, global analysis methods including stepwise regression, contingency table analysis, and classification tree analysis are used to develop sensitivity rankings of parameter uncertainties for each model considered, thus assisting a variety of decisions.« less
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New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds.
Johnson, Ned K; Cicero, Carla
2004-05-01
The timing of origin of modern North American bird species in relation to Pleistocene glaciations has long been the topic of significant discussion and disagreement. Recently, Klicka and Zink (1997) and Avise and Walker (1998) enlivened this debate by using calibrated molecular distance values to estimate timing of speciations. Here we use new molecular studies to test their conclusions. Molecular distance values for 39 pairs of proven sister species, 27 of which are based on new data, alter the currently perceived pattern that avian species splits occurred mainly in the Pliocene and early-mid-Pleistocene. Mitochondrial DNA divergence values for this set of taxa showed a skewed distribution pointing toward relatively young speciation times, in contrast to the pattern presented by Klicka and Zink (1997) for 35 sister plus non-sister species pairs. Our pattern was not significantly different from that of Avise and Walker (1998) for "intraspecific phylogroups," some of which are species. We conclude that the entire Pleistocene, including the last two glacial cycles (<250,000 years ago), was important in speciations of modern North American birds. A substantial number of speciations were both initiated and completed in the last 250,000 years. Simultaneously, many taxa began to diverge in the Pleistocene but their speciations are not yet complete (per Avise and Walker 1998). The suggestion that durations of speciations average two million years is probably a substantial overestimate.
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Ecological Impacts of Reverse Speciation in Threespine Stickleback.
Rudman, Seth M; Schluter, Dolph
2016-02-22
Young species are highly prone to extinction via increased gene flow after human-caused environmental changes. This mechanism of biodiversity loss, often termed reverse speciation or introgressive extinction, is of exceptional interest because the parent species are typically highly differentiated ecologically. Reverse speciation events are potentially powerful case studies for the role of evolution in driving ecological changes, as the phenotypic shifts associated with introgressive extinction can be large and they occur over particularly short timescales. Furthermore, reverse speciation can lead to novel phenotypes, which may in turn produce novel ecological effects. Here we investigate the ecological shift associated with reverse speciation in threespine stickleback fish using a field study and a replicated experiment. We find that an instance of introgressive extinction had cascading ecological consequences that altered the abundance of both aquatic prey and the pupating aquatic insects that emerged into the terrestrial ecosystem. The community and ecosystem impacts of reverse speciation were novel, and yet they were also predictable based on ecological and morphological considerations. The study suggests that knowledge about the community ecology and changes in functional morphology of a dominant species may lead to some predictive power for the ecological effects of evolutionary change. Moreover, the rapid nature and resultant ecological impacts associated with reverse speciation demonstrates the interplay between biodiversity, evolutionary change, and ecosystem function. Copyright © 2016 Elsevier Ltd. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Johnson, J. D.; Oberkampf, William Louis; Helton, Jon Craig
2006-10-01
Evidence theory provides an alternative to probability theory for the representation of epistemic uncertainty in model predictions that derives from epistemic uncertainty in model inputs, where the descriptor epistemic is used to indicate uncertainty that derives from a lack of knowledge with respect to the appropriate values to use for various inputs to the model. The potential benefit, and hence appeal, of evidence theory is that it allows a less restrictive specification of uncertainty than is possible within the axiomatic structure on which probability theory is based. Unfortunately, the propagation of an evidence theory representation for uncertainty through a modelmore » is more computationally demanding than the propagation of a probabilistic representation for uncertainty, with this difficulty constituting a serious obstacle to the use of evidence theory in the representation of uncertainty in predictions obtained from computationally intensive models. This presentation describes and illustrates a sampling-based computational strategy for the representation of epistemic uncertainty in model predictions with evidence theory. Preliminary trials indicate that the presented strategy can be used to propagate uncertainty representations based on evidence theory in analysis situations where naive sampling-based (i.e., unsophisticated Monte Carlo) procedures are impracticable due to computational cost.« less
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Shock Layer Radiation Modeling and Uncertainty for Mars Entry
NASA Technical Reports Server (NTRS)
Johnston, Christopher O.; Brandis, Aaron M.; Sutton, Kenneth
2012-01-01
A model for simulating nonequilibrium radiation from Mars entry shock layers is presented. A new chemical kinetic rate model is developed that provides good agreement with recent EAST and X2 shock tube radiation measurements. This model includes a CO dissociation rate that is a factor of 13 larger than the rate used widely in previous models. Uncertainties in the proposed rates are assessed along with uncertainties in translational-vibrational relaxation modeling parameters. The stagnation point radiative flux uncertainty due to these flowfield modeling parameter uncertainties is computed to vary from 50 to 200% for a range of free-stream conditions, with densities ranging from 5e-5 to 5e-4 kg/m3 and velocities ranging from of 6.3 to 7.7 km/s. These conditions cover the range of anticipated peak radiative heating conditions for proposed hypersonic inflatable aerodynamic decelerators (HIADs). Modeling parameters for the radiative spectrum are compiled along with a non-Boltzmann rate model for the dominant radiating molecules, CO, CN, and C2. A method for treating non-local absorption in the non-Boltzmann model is developed, which is shown to result in up to a 50% increase in the radiative flux through absorption by the CO 4th Positive band. The sensitivity of the radiative flux to the radiation modeling parameters is presented and the uncertainty for each parameter is assessed. The stagnation point radiative flux uncertainty due to these radiation modeling parameter uncertainties is computed to vary from 18 to 167% for the considered range of free-stream conditions. The total radiative flux uncertainty is computed as the root sum square of the flowfield and radiation parametric uncertainties, which results in total uncertainties ranging from 50 to 260%. The main contributors to these significant uncertainties are the CO dissociation rate and the CO heavy-particle excitation rates. Applying the baseline flowfield and radiation models developed in this work, the radiative heating for the Mars Pathfinder probe is predicted to be nearly 20 W/cm2. In contrast to previous studies, this value is shown to be significant relative to the convective heating.
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NASA Astrophysics Data System (ADS)
Ricciuto, Daniel M.; King, Anthony W.; Dragoni, D.; Post, Wilfred M.
2011-03-01
Many parameters in terrestrial biogeochemical models are inherently uncertain, leading to uncertainty in predictions of key carbon cycle variables. At observation sites, this uncertainty can be quantified by applying model-data fusion techniques to estimate model parameters using eddy covariance observations and associated biometric data sets as constraints. Uncertainty is reduced as data records become longer and different types of observations are added. We estimate parametric and associated predictive uncertainty at the Morgan Monroe State Forest in Indiana, USA. Parameters in the Local Terrestrial Ecosystem Carbon (LoTEC) are estimated using both synthetic and actual constraints. These model parameters and uncertainties are then used to make predictions of carbon flux for up to 20 years. We find a strong dependence of both parametric and prediction uncertainty on the length of the data record used in the model-data fusion. In this model framework, this dependence is strongly reduced as the data record length increases beyond 5 years. If synthetic initial biomass pool constraints with realistic uncertainties are included in the model-data fusion, prediction uncertainty is reduced by more than 25% when constraining flux records are less than 3 years. If synthetic annual aboveground woody biomass increment constraints are also included, uncertainty is similarly reduced by an additional 25%. When actual observed eddy covariance data are used as constraints, there is still a strong dependence of parameter and prediction uncertainty on data record length, but the results are harder to interpret because of the inability of LoTEC to reproduce observed interannual variations and the confounding effects of model structural error.
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Analytic uncertainty and sensitivity analysis of models with input correlations
NASA Astrophysics Data System (ADS)
Zhu, Yueying; Wang, Qiuping A.; Li, Wei; Cai, Xu
2018-03-01
Probabilistic uncertainty analysis is a common means of evaluating mathematical models. In mathematical modeling, the uncertainty in input variables is specified through distribution laws. Its contribution to the uncertainty in model response is usually analyzed by assuming that input variables are independent of each other. However, correlated parameters are often happened in practical applications. In the present paper, an analytic method is built for the uncertainty and sensitivity analysis of models in the presence of input correlations. With the method, it is straightforward to identify the importance of the independence and correlations of input variables in determining the model response. This allows one to decide whether or not the input correlations should be considered in practice. Numerical examples suggest the effectiveness and validation of our analytic method in the analysis of general models. A practical application of the method is also proposed to the uncertainty and sensitivity analysis of a deterministic HIV model.
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Speciation and amphotericin B sensitivity studies on blood isolates of Candida from burned patients
Stieritz, Donald D.; Law, Edward J.; Holder, Ian Alan
1973-01-01
Methods of speciating Candida isolates from clinical specimens are described and the necessity of speciation is emphasized. Differences in susceptibility of C. albicans and C. tropicalis to amphotericin B were observed and the implications of this in relation to treatment with amphotericin B and the development of resistance are discussed. PMID:4578160
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Uncertainty evaluation of dead zone of diagnostic ultrasound equipment
NASA Astrophysics Data System (ADS)
Souza, R. M.; Alvarenga, A. V.; Braz, D. S.; Petrella, L. I.; Costa-Felix, R. P. B.
2016-07-01
This paper presents a model for evaluating measurement uncertainty of a feature used in the assessment of ultrasound images: dead zone. The dead zone was measured by two technicians of the INMETRO's Laboratory of Ultrasound using a phantom and following the standard IEC/TS 61390. The uncertainty model was proposed based on the Guide to the Expression of Uncertainty in Measurement. For the tested equipment, results indicate a dead zone of 1.01 mm, and based on the proposed model, the expanded uncertainty was 0.17 mm. The proposed uncertainty model contributes as a novel way for metrological evaluation of diagnostic imaging by ultrasound.
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Incorporating parametric uncertainty into population viability analysis models
McGowan, Conor P.; Runge, Michael C.; Larson, Michael A.
2011-01-01
Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models.
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OPTIMIZATION OF MODERN DISPERSIVE RAMAN SPECTROMETERS FOR MOLECULAR SPECIATION OF ORGANICS IN WATER
Pesticides and industrial chemicals are typically complex organic molecules with multiple heteroatoms that can ionize in water. However, models for understanding the behavior of these chemicals in the environment typically assume that they exist exclusively as neutral species --...
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NASA Astrophysics Data System (ADS)
Machado, Kelly; Zanghi, Didier; Sarou-Kanian, Vincent; Cadars, Sylvian; Burbano, Mario; Salanne, Mathieu; Bessada, Catherine
In aluminum production, the electrolyte is a molten fluorides mixture typically around 1000°C. In order to have a better understanding of the industrial process, it is necessary to have a model which will describe the molten salts on a wide range of compositions and temperatures, to accurately cover all the combinations that may be encountered in an operating electrolysis vessel. The aim of this study is to describe the speciation in the electrolyte in terms of anionic species in the bulk materials far from electrodes. To determine the speciation in situ at high temperature in the absence of an electrical field, we develop an original approach combining experimental methods such as Nuclear Magnetic Resonance spectroscopy (NMR) at high temperature with Molecular Dynamics (MD) simulation coupled with first principle calculations based on Density Functional Theory (DFT). This approach allows the calculation of NMR parameters and the comparison with the experimental ones. It will be provide an additional validation and constraint of the model used for MD. We test this approach on the model NaF-AlF3 system.
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Accelerated and Adaptive Evolution of Yeast Sexual Adhesins
Xie, Xianfa; Qiu, Wei-Gang; Lipke, Peter N.
2011-01-01
There is a recent emergence of interest in the genes involved in gametic recognition as drivers of reproductive isolation. The recent population genomic sequencing of two species of sexually primitive yeasts (Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V et al. [23 co-authors]. 2009. Population genomics of domestic and wild yeasts. Nature 458:337–341.) has provided data for systematic study of the roles these genes play in the early evolution of sex and speciation. Here, we discovered that among genes encoding cell surface proteins, the sexual adhesin genes have evolved significantly more rapidly than others, both within and between Saccharomyces cerevisiae and its closest relative S. paradoxus. This result was supported by analyses using the PAML pairwise model, a modified McDonald–Kreitman test, and the PAML branch model. Moreover, using a combination of a new statistic of neutrality, an information theory–based measure of evolutionary variability, and functional characterization of amino acid changes, we found that a higher proportion of amino acid changes are fixed in the sexual adhesins than in other proteins and a greater proportion of the fixed amino acid changes either between the two species or the two subgroups of S. paradoxus are functionally dissimilar or radically different. These results suggest that the accelerated evolution of sexual adhesin genes may facilitate speciation, or incipient speciation, and promote sexual selection in general. PMID:21633112
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Nichols, J.D.; Pollock, K.H.
1983-01-01
Capture-recapture models can be used to estimate parameters of interest from paleobiological data when encouter probabilities are unknown and variable over time. These models also permit estimation of sampling variances and goodness-of-fit tests are available for assessing the fit of data to most models. The authors describe capture-recapture models which should be useful in paleobiological analyses and discuss the assumptions which underlie them. They illustrate these models with examples and discuss aspects of study design.
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Zajac, Zuzanna; Stith, Bradley M.; Bowling, Andrea C.; Langtimm, Catherine A.; Swain, Eric D.
2015-01-01
Habitat suitability index (HSI) models are commonly used to predict habitat quality and species distributions and are used to develop biological surveys, assess reserve and management priorities, and anticipate possible change under different management or climate change scenarios. Important management decisions may be based on model results, often without a clear understanding of the level of uncertainty associated with model outputs. We present an integrated methodology to assess the propagation of uncertainty from both inputs and structure of the HSI models on model outputs (uncertainty analysis: UA) and relative importance of uncertain model inputs and their interactions on the model output uncertainty (global sensitivity analysis: GSA). We illustrate the GSA/UA framework using simulated hydrology input data from a hydrodynamic model representing sea level changes and HSI models for two species of submerged aquatic vegetation (SAV) in southwest Everglades National Park: Vallisneria americana (tape grass) and Halodule wrightii (shoal grass). We found considerable spatial variation in uncertainty for both species, but distributions of HSI scores still allowed discrimination of sites with good versus poor conditions. Ranking of input parameter sensitivities also varied spatially for both species, with high habitat quality sites showing higher sensitivity to different parameters than low-quality sites. HSI models may be especially useful when species distribution data are unavailable, providing means of exploiting widely available environmental datasets to model past, current, and future habitat conditions. The GSA/UA approach provides a general method for better understanding HSI model dynamics, the spatial and temporal variation in uncertainties, and the parameters that contribute most to model uncertainty. Including an uncertainty and sensitivity analysis in modeling efforts as part of the decision-making framework will result in better-informed, more robust decisions.
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Wang, Kai-Sung; Huang, Lung-Chiu; Lee, Hong-Shen; Chen, Pai-Ye; Chang, Shih-Hsien
2008-06-01
Phytoextraction is a promising technique to remediate heavy metals from contaminated wastewater. However, the interactions of multi-contaminants are not fully clear. This study employed cadmium, Triton X-100 (TX-100), and EDTA to investigate their interactions on phytotoxicity and Cd phytoextraction of Ipomoea aquatica (water spinach) in simulated wastewater. The Cd speciation was estimated by a chemical equilibrium model and MINEQL+. Statistic regression was applied to evaluate Cd speciation on Cd uptake in shoots and stems of I. aquatica. Results indicated that the root length was a more sensitive parameter than root weight and shoot weight. Root elongation was affected by Cd in the Cd-EDTA solution and TX-100 in the Cd-TX-100 solution. Both the root length and the root biomass were negatively correlated with the total soluble Cd ions. In contrast, Cd phytoextraction of I. aquatic was correlated with the aqueous Cd ions in the free and complex forms rather than in the chelating form. Additionally, the high Cd bioconcentration factors of I. aquatica (375-2227 l kg(-1) for roots, 45-144 l kg(-1) for shoots) imply that I. aquatica is a potential aquatic plant to remediate Cd-contaminated wastewater.
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Relative Bioavailability and Bioaccessability and Speciation of ...
Background: Assessment of soil arsenic (As) bioavailability may profoundly affect the extent of remediation required at contaminated sites by improving human exposure estimates. Because small adjustments in soil As bioavailability estimates can significantly alter risk assessments and remediation goals, convenient, rapid, reliable, and inexpensive tools are needed to determine soil As bioavailability. Objectives: We evaluated inexpensive methods for assessing As bioavailability in soil as a means to improve human exposure estimates and potentially reduce remediation costs. Methods: Nine soils from residential sites affected by mining or smelting activity and two National Institute of Standards and Technology standard reference materials were evaluated for As bioavailability, bioaccessibility, and speciation. Arsenic bioavailability was determined using an in vivo mouse model, and As bioaccessibility was determined using the Solubility/Bioavailability Research Consortium in vitro assay. Arsenic speciation in soil and selected soil physicochemical properties were also evaluated to determine whether these parameters could be used as predictors of As bio¬availability and bioaccessibility. Results: In the mouse assay, we compared bioavailabilities of As in soils with that for sodium arsenate. Relative bioavailabilities (RBAs) of soil As ranged from 11% to 53% (mean, 33%). In vitro soil As bioaccessibility values were strongly correlated with soil As RBAs (R
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Qvarnström, Anna; Ålund, Murielle; McFarlane, S Eryn; Sirkiä, Päivi M
2016-01-01
Climate adaptation is surprisingly rarely reported as a cause for the build-up of reproductive isolation between diverging populations. In this review, we summarize evidence for effects of climate adaptation on pre- and postzygotic isolation between emerging species with a particular focus on pied (Ficedula hypoleuca) and collared (Ficedula albicollis) flycatchers as a model for research on speciation. Effects of climate adaptation on prezygotic isolation or extrinsic selection against hybrids have been documented in several taxa, but the combined action of climate adaptation and sexual selection is particularly well explored in Ficedula flycatchers. There is a general lack of evidence for divergent climate adaptation causing intrinsic postzygotic isolation. However, we argue that the profound effects of divergence in climate adaptation on the whole biochemical machinery of organisms and hence many underlying genes should increase the likelihood of genetic incompatibilities arising as side effects. Fast temperature-dependent co-evolution between mitochondrial and nuclear genomes may be particularly likely to lead to hybrid sterility. Thus, how climate adaptation relates to reproductive isolation is best explored in relation to fast-evolving barriers to gene flow, while more research on later stages of divergence is needed to achieve a complete understanding of climate-driven speciation.
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Effects of sorbate speciation on sorption of selected sulfonamides in three loamy soils
Kurwadkar , Sudarshan T.; Adams, Craig D.; Meyer, Michael T.; Kolpin, Dana W.
2007-01-01
Sorption of sulfamethazine (SMN) and sulfathiazole (STZ) was investigated in three soils, a North Carolina loamy sand, an Iowa sandy loam, and a Missouri loam, under various pH conditions. A significant increase in the sorption coefficient (KD) was observed in all three soils, as the sulfonamides converted from an anionic form at higher pH to a neutral/cationic form at lower pH. Above pH 7.5, sulfonamides exist primarily in anionic form and have higher aqueous solubility and no cationic character, thereby consequently leading to lower sorption to soils. The effect of speciation on sorption is not the same for all sulfonamides; it is a function of the pH of the soil and the pKa of the sulfonamides. The results indicate that, for the soils under investigation, SMN has comparatively lower KD values than STZ. The pH-dependent sorption of sulfonamides was observed to be consistent in all three soils investigated. The KD values for each speciated formcationic, neutral, and anionicwere calculated using an empirical model in which the species-specific sorption coefficients (KD0, KD1, and KD2) were weighted with their respective fractions present at any given pH.
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Heterostyly accelerates diversification via reduced extinction in primroses.
de Vos, Jurriaan M; Hughes, Colin E; Schneeweiss, Gerald M; Moore, Brian R; Conti, Elena
2014-06-07
The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower-pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin's model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification.
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Rapid biological speciation driven by tectonic evolution in New Zealand
NASA Astrophysics Data System (ADS)
Craw, Dave; Upton, Phaedra; Burridge, Christopher P.; Wallis, Graham P.; Waters, Jonathan M.
2016-02-01
Collisions between tectonic plates lead to the rise of new mountain ranges that can separate biological populations and ultimately result in new species. However, the identification of links between tectonic mountain-building and biological speciation is confounded by environmental and ecological factors. Thus, there are surprisingly few well-documented examples of direct tectonic controls on terrestrial biological speciation. Here we present examples from New Zealand, where the rapid evolution of 18 species of freshwater fishes has resulted from parallel tectonic landscape evolution. We use numerical models to reconstruct changes in the deep crustal structure and surface drainage catchments of the southern island of New Zealand over the past 25 million years. We show that the island and mountain topography evolved in six principal tectonic zones, which have distinct drainage catchments that separated fish populations. We use new and existing phylogenetic analyses of freshwater fish populations, based on over 1,000 specimens from more than 400 localities, to show that fish genomes can retain evidence of this tectonic landscape development, with a clear correlation between geologic age and extent of DNA sequence divergence. We conclude that landscape evolution has controlled on-going biological diversification over the past 25 million years.
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The Robertsonian phenomenon in the house mouse: mutation, meiosis and speciation.
Garagna, Silvia; Page, Jesus; Fernandez-Donoso, Raul; Zuccotti, Maurizio; Searle, Jeremy B
2014-12-01
Many different chromosomal races with reduced chromosome number due to the presence of Robertsonian fusion metacentrics have been described in western Europe and northern Africa, within the distribution area of the western house mouse Mus musculus domesticus. This subspecies of house mouse has become the ideal model for studies to elucidate the processes of chromosome mutation and fixation that lead to the formation of chromosomal races and for studies on the impact of chromosome heterozygosities on reproductive isolation and speciation. In this review, we briefly describe the history of the discovery of the first and subsequent metacentric races in house mice; then, we focus on the molecular composition of the centromeric regions involved in chromosome fusion to examine the molecular characteristics that may explain the great variability of the karyotype that house mice show. The influence that metacentrics exert on the nuclear architecture of the male meiocytes and the consequences on meiotic progression are described to illustrate the impact that chromosomal heterozygosities exert on fertility of house mice-of relevance to reproductive isolation and speciation. The evolutionary significance of the Robertsonian phenomenon in the house mouse is discussed in the final section of this review.
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Gompert, Zachariah; Lucas, Lauren K; Nice, Chris C; Fordyce, James A; Forister, Matthew L; Buerkle, C Alex
2012-07-01
Speciation is the process by which reproductively isolated lineages arise, and is one of the fundamental means by which the diversity of life increases. Whereas numerous studies have documented an association between ecological divergence and reproductive isolation, relatively little is known about the role of natural selection in genome divergence during the process of speciation. Here, we use genome-wide DNA sequences and Bayesian models to test the hypothesis that loci under divergent selection between two butterfly species (Lycaeides idas and L. melissa) also affect fitness in an admixed population. Locus-specific measures of genetic differentiation between L. idas and L. melissa and genomic introgression in hybrids varied across the genome. The most differentiated genetic regions were characterized by elevated L. idas ancestry in the admixed population, which occurs in L. idas-like habitat, consistent with the hypothesis that local adaptation contributes to speciation. Moreover, locus-specific measures of genetic differentiation (a metric of divergent selection) were positively associated with extreme genomic introgression (a metric of hybrid fitness). Interestingly, concordance of differentiation and introgression was only partial. We discuss multiple, complementary explanations for this partial concordance. © 2012 The Author(s).
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Heterostyly accelerates diversification via reduced extinction in primroses
de Vos, Jurriaan M.; Hughes, Colin E.; Schneeweiss, Gerald M.; Moore, Brian R.; Conti, Elena
2014-01-01
The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower–pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin's model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification. PMID:24759859
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Cusnir, Ruslan; Steinmann, Philipp; Christl, Marcus; Bochud, François; Froidevaux, Pascal
2015-11-09
The biological uptake of plutonium (Pu) in aquatic ecosystems is of particular concern since it is an alpha-particle emitter with long half-life which can potentially contribute to the exposure of biota and humans. The diffusive gradients in thin films technique is introduced here for in-situ measurements of Pu bioavailability and speciation. A diffusion cell constructed for laboratory experiments with Pu and the newly developed protocol make it possible to simulate the environmental behavior of Pu in model solutions of various chemical compositions. Adjustment of the oxidation states to Pu(IV) and Pu(V) described in this protocol is essential in order to investigate the complex redox chemistry of plutonium in the environment. The calibration of this technique and the results obtained in the laboratory experiments enable to develop a specific DGT device for in-situ Pu measurements in freshwaters. Accelerator-based mass-spectrometry measurements of Pu accumulated by DGTs in a karst spring allowed determining the bioavailability of Pu in a mineral freshwater environment. Application of this protocol for Pu measurements using DGT devices has a large potential to improve our understanding of the speciation and the biological transfer of Pu in aquatic ecosystems.
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Geiger, Matthias F; McCrary, Jeffrey K; Schliewen, Ulrich K
2010-09-01
Nicaraguan Midas cichlids from crater lakes have recently attracted attention as potential model systems for speciation research, but no attempt has been made to comprehensively reconstruct phylogenetic relationships of this highly diverse and recently evolved species complex. We present a first AFLP (2793 loci) and mtDNA based phylogenetic hypothesis including all described and several undescribed species from six crater lakes (Apoyeque, Apoyo, Asososca Leon, Masaya, Tiscapa and Xiloá), the two great Lakes Managua and Nicaragua and the San Juan River. Our analyses demonstrate that the relationships between the Midas cichlid members are complex, and that phylogenetic information from different markers and methods do not always yield congruent results. Nevertheless, monophyly support for crater lake assemblages from Lakes Apoyeque, Apoyo, A. Leon is high as compared to those from L. Xiloá indicating occurrence of sympatric speciation. Further, we demonstrate that a 'three species' concept for the Midas cichlid complex is inapplicable and consequently that an individualized and voucher based approach in speciation research of the Midas cichlid complex is necessary at least as long as there is no comprehensive revision of the species complex available. Copyright 2010 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Dong, Xinyi; Fu, Joshua S.; Huang, Kan; Tong, Daniel; Zhuang, Guoshun
2016-07-01
The Community Multiscale Air Quality (CMAQ) model has been further developed in terms of simulating natural wind-blown dust in this study, with a series of modifications aimed at improving the model's capability to predict the emission, transport, and chemical reactions of dust. The default parameterization of initial threshold friction velocity constants are revised to correct the double counting of the impact of soil moisture in CMAQ by the reanalysis of field experiment data; source-dependent speciation profiles for dust emission are derived based on local measurements for the Gobi and Taklamakan deserts in East Asia; and dust heterogeneous chemistry is also implemented. The improved dust module in the CMAQ is applied over East Asia for March and April from 2006 to 2010. The model evaluation result shows that the simulation bias of PM10 and aerosol optical depth (AOD) is reduced, respectively, from -55.42 and -31.97 % by the original CMAQ to -16.05 and -22.1 % by the revised CMAQ. Comparison with observations at the nearby Gobi stations of Duolun and Yulin indicates that applying a source-dependent profile helps reduce simulation bias for trace metals. Implementing heterogeneous chemistry also results in better agreement with observations for sulfur dioxide (SO2), sulfate (SO42-), nitric acid (HNO3), nitrous oxides (NOx), and nitrate (NO3-). The investigation of a severe dust storm episode from 19 to 21 March 2010 suggests that the revised CMAQ is capable of capturing the spatial distribution and temporal variation of dust. The model evaluation also indicates potential uncertainty within the excessive soil moisture used by meteorological simulation. The mass contribution of fine-mode particles in dust emission may be underestimated by 50 %. The revised CMAQ model provides a useful tool for future studies to investigate the emission, transport, and impact of wind-blown dust over East Asia and elsewhere.
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Zhang, Jie; Li, Jingyi; Wang, Peng; Chen, Gang; Mendola, Pauline; Sherman, Seth; Ying, Qi
2017-02-01
PAHs (polycyclic aromatic hydrocarbons) in the environment are of significant concern due to their negative impact on human health. PAH measurements at the air toxics monitoring network stations alone are not sufficient to provide a complete picture of ambient PAH levels or to allow accurate assessment of public exposure in the United States. In this study, speciation profiles for PAHs were prepared using data assembled from existing emission profile data bases, and the Sparse Matrix Operator Kernel Emissions (SMOKE) model was used to generate the gridded national emissions of 16 priority PAHs in the US. The estimated emissions were applied to simulate ambient concentration of PAHs for January, April, July and October 2011, using a modified Community Multiscale Air Quality (CMAQ) model (v5.0.1) that treats the gas and particle phase partitioning of PAHs and their reactions in the gas phase and on particle surface. Predicted daily PAH concentrations at 61 air toxics monitoring sites generally agreed with observations, and averaging the predictions over a month reduced the overall error. The best model performance was obtained at rural sites, with an average mean fractional bias (MFB) of -0.03 and mean fractional error (MFE) of 0.70. Concentrations at suburban and urban sites were underestimated with overall MFB=-0.57 and MFE=0.89. Predicted PAH concentrations were highest in January with better model performance (MFB=0.12, MFE=0.69; including all sites), and lowest in July with worse model performance (MFB=-0.90, MFE=1.08). Including heterogeneous reactions of several PAHs with O 3 on particle surface reduced the over-prediction bias in winter, although significant uncertainties were expected due to relative simple treatment of the heterogeneous reactions in the current model. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Quantitative body DW-MRI biomarkers uncertainty estimation using unscented wild-bootstrap.
Freiman, M; Voss, S D; Mulkern, R V; Perez-Rossello, J M; Warfield, S K
2011-01-01
We present a new method for the uncertainty estimation of diffusion parameters for quantitative body DW-MRI assessment. Diffusion parameters uncertainty estimation from DW-MRI is necessary for clinical applications that use these parameters to assess pathology. However, uncertainty estimation using traditional techniques requires repeated acquisitions, which is undesirable in routine clinical use. Model-based bootstrap techniques, for example, assume an underlying linear model for residuals rescaling and cannot be utilized directly for body diffusion parameters uncertainty estimation due to the non-linearity of the body diffusion model. To offset this limitation, our method uses the Unscented transform to compute the residuals rescaling parameters from the non-linear body diffusion model, and then applies the wild-bootstrap method to infer the body diffusion parameters uncertainty. Validation through phantom and human subject experiments shows that our method identify the regions with higher uncertainty in body DWI-MRI model parameters correctly with realtive error of -36% in the uncertainty values.
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Watson, John G; Chow, Judith C; Lowenthal, Douglas H; Antony Chen, L-W; Shaw, Stephanie; Edgerton, Eric S; Blanchard, Charles L
2015-09-01
Positive matrix factorization (PMF) and effective variance (EV) solutions to the chemical mass balance (CMB) were applied to PM(2.5) (particulate matter with an aerodynamic diameter <2.5 μm) mass and chemically speciated measurements for samples taken from 2008 to 2010 at the Atlanta, Georgia, and Birmingham, Alabama, sites. Commonly measured PM(2.5) mass, elemental, ionic, and thermal carbon fraction concentrations were supplemented with detailed nonpolar organic speciation by thermal desorption-gas chromatography/mass spectrometry (TD-GC/MS). Source contribution estimates were calculated for motor vehicle exhaust, biomass burning, cooking, coal-fired power plants, road dust, vegetative detritus, and secondary sulfates and nitrates for Atlanta. Similar sources were found for Birmingham, with the addition of an industrial source and the separation of biomass burning into open burning and residential wood combustion. EV-CMB results based on conventional species were qualitatively similar to those estimated by PMF-CMB. Secondary ammonium sulfate was the largest contributor, accounting for 27-38% of PM(2.5), followed by biomass burning (21-24%) and motor vehicle exhaust (9-24%) at both sites, with 4-6% of PM(2.5) attributed to coal-fired power plants by EV-CMB. Including organic compounds in the EV-CMB reduced the motor vehicle exhaust and biomass burning contributions at both sites, with a 13-23% deficit for PM(2.5) mass. The PMF-CMB solution showed mixing of sources within the derived factors, both with and without the addition of speciated organics, as is often the case with complex source mixtures such as those at these urban-scale sites. The nonpolar TD-GC/MS compounds can be obtained from existing filter samples and are a useful complement to the elements, ions, and carbon fractions. However, they should be supplemented with other methods, such as TD-GC/MS on derivitized samples, to obtain a wider range of polar compounds such as sterols, sugars, and organic acids. The PMF and EV solutions to the CMB equations are complementary to, rather than replacements for, each other, as comparisons of their results reveal uncertainties that are not otherwise evident. Organic markers can be measured on currently acquired PM(2.5) filter samples by thermal methods. These markers can complement element, ion, and carbon fraction measurements from long-term speciation networks. Applying the positive matrix factorization and effective variance solutions for the chemical mass balance equations provides useful information on the accuracy of the source contribution estimates. Nonpolar compounds need to be complemented with polar compounds to better apportion cooking and secondary organic aerosol contributors.
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Hobolth, Asger; Dutheil, Julien Y.; Hawks, John; Schierup, Mikkel H.; Mailund, Thomas
2011-01-01
We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent hidden Markov model (HMM) framework. We find ILS present in ∼1% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. The existence of ILS is validated with simulations, site pattern analysis, and analysis of rare genomic events. The existence of ILS allows us to disentangle the time of isolation of humans and orangutans (the speciation time) from the genetic divergence time, and we find speciation to be as recent as 9–13 million years ago (Mya; contingent on the calibration point). The analyses provide further support for a recent speciation of human and chimpanzee at ∼4 Mya and a diverse ancestor of human and chimpanzee with an effective population size of about 50,000 individuals. Posterior decoding infers ILS for each nucleotide in the genome, and we use this to deduce patterns of selection in the ancestral species. We demonstrate the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS was found to be reduced in exons and gene-dense regions when we control for confounding factors such as GC content and recombination rate. Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny. PMID:21270173
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Liu, Jiang; Jiang, Tao; Huang, Rong; Zhang, Jin-zhong; Chen, Hong
2016-04-15
Lead (Pb) in purple soil was selected as the research target, using one-step extraction method with 0.01 mol · L⁻¹ sodium nitrate as the background electrolyte to study the release effect of citric acid (CA), tartaric acid (TA) and acetic acid (AC) with different concentrations. Sequential extraction and geochemical model (Visual Minteq v3.0) were applied to analyze and predict the speciation of Pb in soil solid phase and soil solution phase. Then the ebvironmental implications and risks of low-molecule weight organic acid (LMWOA) on soil Pb were analyzed. The results indicated that all three types of LMWOA increased the desorption capacity of Pb in purple soil, and the effect followed the descending order of CA > TA > AC. After the action of LMWOAs, the exchangeable Pb increased; the carbonate-bound Pb and Fe-Mn oxide bound Pb dropped in soil solid phase. Organic bound Pb was the main speciation in soil solution phase, accounting for 45.16%-75.05%. The following speciation of Pb in soil solution was free Pb, accounting for 22.71%-50.25%. For CA and TA treatments, free Pb ions and inorganic bound Pb in soil solution increased with increasing LMWOAs concentration, while organic bound Pb suffered a decrease in this process. An opposite trend for AC treatment was observed compared with CA and TA treatments. Overall, LMWOAs boosted the bioavailability of Pb in purple soil and had a potential risk to contaminate underground water. Among the three LMWOAs in this study, CA had the largest potential to activate soil Pb.
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Franchini, Paolo; Xiong, Peiwen; Fruciano, Carmelo; Meyer, Axel
2016-06-03
Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage (Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3'-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3'-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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NASA Astrophysics Data System (ADS)
Shoaib, Syed Abu; Marshall, Lucy; Sharma, Ashish
2018-06-01
Every model to characterise a real world process is affected by uncertainty. Selecting a suitable model is a vital aspect of engineering planning and design. Observation or input errors make the prediction of modelled responses more uncertain. By way of a recently developed attribution metric, this study is aimed at developing a method for analysing variability in model inputs together with model structure variability to quantify their relative contributions in typical hydrological modelling applications. The Quantile Flow Deviation (QFD) metric is used to assess these alternate sources of uncertainty. The Australian Water Availability Project (AWAP) precipitation data for four different Australian catchments is used to analyse the impact of spatial rainfall variability on simulated streamflow variability via the QFD. The QFD metric attributes the variability in flow ensembles to uncertainty associated with the selection of a model structure and input time series. For the case study catchments, the relative contribution of input uncertainty due to rainfall is higher than that due to potential evapotranspiration, and overall input uncertainty is significant compared to model structure and parameter uncertainty. Overall, this study investigates the propagation of input uncertainty in a daily streamflow modelling scenario and demonstrates how input errors manifest across different streamflow magnitudes.
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NASA Astrophysics Data System (ADS)
Pathiraja, S. D.; Moradkhani, H.; Marshall, L. A.; Sharma, A.; Geenens, G.
2016-12-01
Effective combination of model simulations and observations through Data Assimilation (DA) depends heavily on uncertainty characterisation. Many traditional methods for quantifying model uncertainty in DA require some level of subjectivity (by way of tuning parameters or by assuming Gaussian statistics). Furthermore, the focus is typically on only estimating the first and second moments. We propose a data-driven methodology to estimate the full distributional form of model uncertainty, i.e. the transition density p(xt|xt-1). All sources of uncertainty associated with the model simulations are considered collectively, without needing to devise stochastic perturbations for individual components (such as model input, parameter and structural uncertainty). A training period is used to derive the distribution of errors in observed variables conditioned on hidden states. Errors in hidden states are estimated from the conditional distribution of observed variables using non-linear optimization. The theory behind the framework and case study applications are discussed in detail. Results demonstrate improved predictions and more realistic uncertainty bounds compared to a standard perturbation approach.
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Role of natural nanoparticles on the speciation of Ni in andosols of la Reunion
NASA Astrophysics Data System (ADS)
Levard, Clément; Doelsch, Emmanuel; Rose, Jérôme; Masion, Armand; Basile-Doelsch, Isabelle; Proux, Olivier; Hazemann, Jean-Louis; Borschneck, Daniel; Bottero, Jean-Yves
2009-08-01
Andosols on the island of Réunion have high nickel (Ni) concentrations due to the natural pedo-geochemical background. Enhanced knowledge of Ni speciation is necessary to predict the bioavailability and potential toxicity of this element. Ni speciation in these andosols, marked by the presence of high amounts of natural aluminosilicate nanoparticles, was investigated in two complementary systems: (i) In a soil sample—densimetric fractionation was first performed in order to separate the potential bearing phases, prior to Ni speciation characterization. (ii) In a synthetic sample—Ni reactivity with synthetic aluminosilicate nanoparticle analogs were studied. In both cases, Ni speciation was determined using X-ray absorption spectroscopy (XAS). The results revealed that Ni had the same local environment in both systems (natural and synthetic systems), and Ni was chemically linked to natural short-range ordered aluminosilicates or analogs. This complex represented about 75% of the total Ni in the studied soil.
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Using CV-GLUE procedure in analysis of wetland model predictive uncertainty.
Huang, Chun-Wei; Lin, Yu-Pin; Chiang, Li-Chi; Wang, Yung-Chieh
2014-07-01
This study develops a procedure that is related to Generalized Likelihood Uncertainty Estimation (GLUE), called the CV-GLUE procedure, for assessing the predictive uncertainty that is associated with different model structures with varying degrees of complexity. The proposed procedure comprises model calibration, validation, and predictive uncertainty estimation in terms of a characteristic coefficient of variation (characteristic CV). The procedure first performed two-stage Monte-Carlo simulations to ensure predictive accuracy by obtaining behavior parameter sets, and then the estimation of CV-values of the model outcomes, which represent the predictive uncertainties for a model structure of interest with its associated behavior parameter sets. Three commonly used wetland models (the first-order K-C model, the plug flow with dispersion model, and the Wetland Water Quality Model; WWQM) were compared based on data that were collected from a free water surface constructed wetland with paddy cultivation in Taipei, Taiwan. The results show that the first-order K-C model, which is simpler than the other two models, has greater predictive uncertainty. This finding shows that predictive uncertainty does not necessarily increase with the complexity of the model structure because in this case, the more simplistic representation (first-order K-C model) of reality results in a higher uncertainty in the prediction made by the model. The CV-GLUE procedure is suggested to be a useful tool not only for designing constructed wetlands but also for other aspects of environmental management. Copyright © 2014 Elsevier Ltd. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chorover, Jon; Mueller, Karl; O'Day, Peggy Anne
2016-06-30
Objectives of the Project: 1. Determine the process coupling that occurs between mineral transformation and contaminant (U and Sr) speciation in acid-uranium waste weathered Hanford sediments. 2. Establish linkages between molecular-scale contaminant speciation and meso-scale contaminant lability, release and reactive transport. 3. Make conjunctive use of molecular- to bench-scale data to constrain the development of a mechanistic, reactive transport model that includes coupling of contaminant sorption-desorption and mineral transformation reactions. Hypotheses Tested: Uranium and strontium speciation in legacy sediments from the U-8 and U-12 Crib sites can be reproduced in bench-scale weathering experiments conducted on unimpacted Hanford sediments from themore » same formations; Reactive transport modeling of future uranium and strontium releases from the vadose zone of acid-waste weathered sediments can be effectively constrained by combining molecular-scale information on contaminant bonding environment with grain-scale information on contaminant phase partitioning, and meso-scale kinetic data on contaminant release from the waste-weathered porous media; Although field contamination and laboratory experiments differ in their diagenetic time scales (decades for field vs. months to years for lab), sediment dissolution, neophase nucleation, and crystal growth reactions that occur during the initial disequilibrium induced by waste-sediment interaction leave a strong imprint that persists over subsequent longer-term equilibration time scales and, therefore, give rise to long-term memory effects. Enabling Capabilities Developed: Our team developed an iterative measure-model approach that is broadly applicable to elucidate the mechanistic underpinnings of reactive contaminant transport in geomedia subject to active weathering.« less
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Loera, Israel; Sosa, Victoria; Ickert-Bond, Stefanie M
2012-11-01
A lineage of 12 arid land shrubby species in the gymnosperm genus Ephedra (Gnetales) from North America is used to evaluate the influence of climate on speciation. With a long evolutionary history, and a well documented fossil record this lineage is an ideal model for understanding the process of speciation under a niche conservatism scenario. Using seven DNA molecular markers, Bayesian inference is carried out to uncover sister species and to estimate time of divergence of the lineages. Ecological niche models are generated for four parapatric and sympatric sister species and two analyses of niche evolution are performed, one based on ecological niche models and another using raw data and multivariate analysis. As previous analyses suggest, the diversification of North America Ephedra species may be the result of a recent secondary radiation. Both parapatric and sympatric species diverged mostly in a scenario of climatic niche conservatism. However, we also found strong evidence for niche divergence for one of the sister species pairs (E. californica-E. trifurca). Moreover, the multivariate analysis found environmental differences for some variables between sister species. The estimated divergence time of three pairs of sister species distributed in southwestern North America (E. cutleri-E. aspera, E. californica-E. trifurca and E. torreyana-E. viridis) is inferred to have occurred in the Late Miocene to Pliocene and for the sister species pair E. antisyphilitica-E. coryi distributed in the southern United States and northeastern Mexico, it was inferred from the Pliocene to Pleistocene. The orogenetic and climatic changes documented for these regions related to expansion of arid lands, may have contributed to the diversification in North American Ephedra, rather than adaptations to new climatic conditions. Copyright © 2012 Elsevier Inc. All rights reserved.