Structural determination of individual chemical species in a mixed system by iterative transformation factor analysis-based X-ray absorption spectroscopy combined with UV-visible absorption and quantum chemical calculation.

PubMed

Ikeda, Atsushi; Hennig, Christoph; Rossberg, André; Tsushima, Satoru; Scheinost, Andreas C; Bernhard, Gert

2008-02-15

A multitechnique approach using extended X-ray absorption fine structure (EXAFS) spectroscopy based on iterative transformation factor analysis (ITFA), UV-visible absorption spectroscopy, and density functional theory (DFT) calculations has been performed in order to investigate the speciation of uranium(VI) nitrate species in acetonitrile and to identify the complex structure of individual species in the system. UV-visible spectral titration suggests that there are four different species in the system, that is, pure solvated species, mono-, di-, and trinitrate species. The pure EXAFS spectra of these individual species are extracted by ITFA from the measured spectral mixtures on the basis of the speciation distribution profile calculated from the UV-visible data. Data analysis of the extracted EXAFS spectra, with the help of DFT calculations, reveals the most probable complex structures of the individual species. The pure solvated species corresponds to a uranyl hydrate complex with an equatorial coordination number (CNeq) of 5, [UO2(H2O)5]2+. Nitrate ions tend to coordinate to the uranyl(VI) ion in a bidentate fashion rather than a unidentate one in acetonitrile for all the nitrate species. The mononitrate species forms the complex of [UO2(H2O)3NO3]+ with a CNeq value of 5, while the di- and trinitrate species have a CNeq value of 6, corresponding to [UO2(H2O)2(NO3)2]0 (D2h) and [UO2(NO3)3]- (D3h), respectively.

Uranium chemistry in stack solutions and leachates of phosphogypsum disposed at a coastal area in Cyprus.

PubMed

Lysandrou, M; Pashalidis, I

2008-02-01

The effect of the matrix composition (main constituents) on the concentration and chemical behavior of uranium in phosphogypsum stack solutions and leachates has been investigated. Solid and aqueous samples were taken from three different sub-areas of a phosphogypsum stack at a coastal area in Vasilikos (Cyprus). The sub-areas are characterized whether by their acidity (e.g. "aged" and "non-aged" phosphogypsum) or by their salt content, originating from pulping water during wet stacking or (after deposition) from the adjacent sea. Measurements in stack solutions and leachates showed that phosphogypsum characteristics affect both, the concentration and the chemical behavior of uranium in solution. Uranium concentration in solutions of increased salinity is up to three orders of magnitude higher than in solutions of low salinity and this is attributed to the effect of ionic strength on the solubility of phosphogypsum. Modelling showed that uranium in stack solutions is predominantly present in the form of uranium(VI) phosphate complexes (e.g. UO(2)(H(2)PO(4))(2), UO(2)HPO(4)), whereas in leachates uranium(VI) fluoro complexes (e.g. UO(2)F(2), UO(2)F(3)(-)) are predominant in solution. The latter indicates that elution of uranium from phosphogypsum takes places most probably in the form of fluoro complexes. Both, effective elution by saline water and direct migration of uranium to the sea, where it forms very stable uranium(VI) carbonato complexes, indicate that the adjacent sea will be the final receptor of uranium released from Vasilikos phosphogypsum.

SPECIATE's VOC and PM Speciation Profiles and Their use to Prepare for Air quality Modeling (2017 EIC)

EPA Pesticide Factsheets

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.

Simultaneous extraction and preconcentration of uranium and thorium in aqueous samples by new modified mesoporous silica prior to inductively coupled plasma optical emission spectrometry determination.

PubMed

Yousefi, Seyed Reza; Ahmadi, Seyed Javad; Shemirani, Farzaneh; Jamali, Mohammad Reza; Salavati-Niasari, Masoud

2009-11-15

A new synthesized modified mesoporous silica (MCM-41) using 5-nitro-2-furaldehyde (fural) was applied as an effective sorbent for the solid phase extraction of uranium(VI) and thorium(IV) ions from aqueous solution for the measurement by inductively coupled plasma optical emission spectrometry (ICP OES). The influences of some analytical parameters on the quantitative recoveries of the analyte ions were investigated in batch method. Under optimal conditions, the analyte ions were sorbed by the sorbent at pH 5.5 and then eluted with 1.0 mL of 1.0 mol L(-1) HNO(3). The preconcentration factor was 100 for a 100mL sample volume. The limits of detection (LOD) obtained for uranium(VI) and thorium(IV) were 0.3 microg L(-1). The maximum sorption capacity of the modified MCM-41 was found to be 47 and 49 mg g(-1) for uranium(VI) and thorium(IV), respectively. The sorbent exhibited good stability, reusability, high adsorption capacity and fast rate of equilibrium for sorption/desorption of uranium and thorium ions. The applicability of the synthesized sorbent was examined using CRM and real water samples.

Complexation of uranium(VI) with glutarimidoxioxime: thermodynamic and computational studies.

PubMed

Endrizzi, Francesco; Melchior, Andrea; Tolazzi, Marilena; Rao, Linfeng

2015-08-21

The complex formation between a cyclic ligand glutarimidoxioxime (denoted as HL(III) in this paper) and UO2(2+) is studied by potentiometry and microcalorimetry. Glutarimidoxioxime (HL(III)), together with glutarimidedioxime (H2L(I)) and glutardiamidoxime (H2L(II)), belongs to a family of amidoxime derivatives with prospective applications as binding agents for the recovery of uranium from seawater. An optimized procedure of synthesis that leads to the preparation of glutarimidoxioxime in the absence of other amidoxime byproducts is described in this paper. Speciation models based on the thermodynamic results from this study indicate that, compared with H2L(I) and H2L(II), HL(III) forms a much weaker complex with UO2(2+), UO2(L(III))(+), and cannot effectively compete with the hydrolysis equilibria of UO2(2+) under neutral or alkaline conditions. DFT computations, taking into account the solvation by including discrete hydration water molecules and bulk solvent effects, were performed to evaluate the structures and energies of the possible isomers of UO2(L(III))(+). Differing from the tridentate or η(2)-coordination modes previously found in the U(vi) complexes with amidoxime-related ligands, a bidentate mode, involving the oxygen of the oxime group and the nitrogen of the imino group, is found to be the most probable mode in UO2(L(III))(+). The bidentate coordination mode seems to be stabilized by the formation of a hydrogen bond between the carbonyl group of HL(III) and a water molecule in the hydration sphere of UO2(2+).

SPECIATE and using the Speciation Tool to prepare VOC and PM chemical speciation profiles for air quality modeling

EPA Science Inventory

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.

Trace metal speciation in natural waters: Computational vs. analytical

USGS Publications Warehouse

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.

Effect of Reaction Pathway on the Extent and Mechanism of Uranium(VI) Immobilization with Calcium and Phosphate

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

Mehta, Vrajesh S.; Maillot, Fabien; Wang, Zheming

Phosphate addition to subsurface environments contaminated with uranium can be used as an in situ remediation approach. Batch experiments were conducted to evaluate the dependence of the extent and mechanism of uranium uptake on the pathway for reaction with calcium phosphates. At pH 4.0 and 6.0 uranium uptake occurred via autunite (Ca(UO2)(PO4)3) precipitation irrespective of the starting forms of calcium and phosphate. At pH 7.5, the uptake mechanism depended on the nature of the calcium and phosphate. When dissolved uranium, calcium, and phosphate were added simultaneously, uranium was structurally incorporated into a newly formed amorphous calcium phosphate solid. Adsorption wasmore » the dominant removal mechanism for uranium contacted with pre-formed amorphous calcium phosphate solids,. When U(VI) was added to a suspension containing amorphous calcium phosphate solids as well as dissolved calcium and phosphate, then removal occurred through precipitation (57±4 %) of autunite and adsorption (43±4 %) onto calcium phosphate. The solid phase speciation of the uranium was determined using X-ray absorption spectroscopy and laser induced fluorescence spectroscopy. Dissolved uranium, calcium, and phosphate concentrations with saturation index calculations helped identify removal mechanisms and determine thermodynamically favorable solid phases.« less

Dissolved and labile concentrations of Cd, Cu, Pb, and Zn in the South Fork Coeur d'Alene River, Idaho: Comparisons among chemical equilibrium models and implications for biotic ligand models

USGS Publications Warehouse

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.

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.

MODELING MONOMETHYLMERCURY AND TRIBUTYLTIN SPECIATION WITH EPA'S GEOCHEMICAL SPECIATION MODEL MINTEQA2

EPA Science Inventory

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...

SPECIATE--EPA'S DATABASE OF SPECIATED EMISSION PROFILES

EPA Science Inventory

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. ...

Assessment of Important SPECIATE Profiles in EPA’s Emissions Modeling Platform and Current Data Gaps

EPA Science Inventory

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...

A complex speciation–richness relationship in a simple neutral model

PubMed Central

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

PRECIPITATION OF ZIRCONIUM AND FLUORIDE IONS FROM SOLUTIONS

DOEpatents

Newby, B.J.

1963-06-11

A process is given for removing zirconium and fluorine ions from aqueous solutions also containing uranium(VI). The precipitation is carried out with sodium formate, and the uranium remains in solution. (AEC)

Variation of the NMVOC speciation in the solvent sector and the sensitivity of modelled tropospheric ozone

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.

Assessment of important SPECIATE Profiles in EPA’s Emissions Modeling Platform and Current Data Gaps (US EPA 2017 International Emissions Inventory Conference)

EPA Science Inventory

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...

Frequency-dependent selection predicts patterns of radiations and biodiversity.

PubMed

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.

Uranium removal from a contaminated effluent using a combined microbial and nanoparticle system.

PubMed

Baiget, Mar; Constantí, Magda; López, M Teresa; Medina, Francesc

2013-09-25

Reduction of soluble uranium(VI) to insoluble uranium(IV) for remediating a uranium-contaminated effluent (EF-03) was examined using a biotic and abiotic integrated system. Shewanella putrefaciens was first used and reduced U(VI) in a synthetic medium but not in the EF-03 effluent sample. Subsequently the growth of autochthonous microorganisms was stimulated with lactate. When lactate was supported on active carbon 77% U(VI) was removed in 4 days. Separately, iron nanoparticles that were 50 nm in diameter reduced U(VI) by 60% in 4 hours. The efficiency of uranium(VI) removal was improved to 96% in 30 min by using a system consisting of lactate and iron nanoparticles immobilized on active carbon. Lactate also stimulated the growth of potential uranium-reducing microorganisms in the EF-03 sample. This system can be efficiently used for the bioremediation of uranium-contaminated effluents. Copyright © 2013 Elsevier B.V. All rights reserved.

Interaction between Digestive Strategy and Niche Specialization Predicts Speciation Rates across Herbivorous Mammals.

PubMed

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.

New analytic results for speciation times in neutral models.

PubMed

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.

Biological signatures of dynamic river networks from a coupled landscape evolution and neutral community model

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.

A STUDY OF GAS-PHASE MERCURY SPECIATION USING DETAILED CHEMICAL KINETICS

EPA Science Inventory

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...

Chromosomes, conflict, and epigenetics: chromosomal speciation revisited.

PubMed

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.

Biosorption and Biomineralization of U(VI) by the Marine Bacterium Idiomarina loihiensis MAH1: Effect of Background Electrolyte and pH

PubMed Central

Morcillo, Fernando; González-Muñoz, María T.; Reitz, Thomas; Romero-González, María E.; Arias, José M.; Merroun, Mohamed L.

2014-01-01

The main goal of this study is to compare the effects of pH, uranium concentration, and background electrolyte (seawater and NaClO4 solution) on the speciation of uranium(VI) associated with the marine bacterium Idiomarina loihiensis MAH1. This was done at the molecular level using a multidisciplinary approach combining X-ray Absorption Spectroscopy (XAS), Time-Resolved Laser-Induced Fluorescence Spectroscopy (TRLFS), and High Resolution Transmission Electron Microscopy (HRTEM). We showed that the U(VI)/bacterium interaction mechanism is highly dependent upon pH but also the nature of the used background electrolyte played a role. At neutral conditions and a U concentration ranging from 5·10−4 to 10−5 M (environmentally relevant concentrations), XAS analysis revealed that uranyl phosphate mineral phases, structurally resembling meta-autunite [Ca(UO2)2(PO4)2 2–6H2O] are precipitated at the cell surfaces of the strain MAH1. The formation of this mineral phase is independent of the background solution but U(VI) luminescence lifetime analyses demonstrated that the U(VI) speciation in seawater samples is more intricate, i.e., different complexes were formed under natural conditions. At acidic conditions, pH 2, 3 and 4.3 ([U] = 5·10−4 M, background electrolyte  = 0.1 M NaClO4), the removal of U from solution was due to biosorption to Extracellular Polysaccharides (EPS) and cell wall components as evident from TEM analysis. The L III-edge XAS and TRLFS studies showed that the biosorption process observed is dependent of pH. The bacterial cell forms a complex with U through organic phosphate groups at pH 2 and via phosphate and carboxyl groups at pH 3 and 4.3, respectively. The differences in the complexes formed between uranium and bacteria on seawater compared to NaClO4 solution demonstrates that the actinide/microbe interactions are influenced by the three studied factors, i.e., the pH, the uranium concentration and the chemical composition of the solution. PMID:24618567

SPECIATE 4.4: The Bridge Between Emissions Characterization and Modeling

EPA Science Inventory

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...

Examination of Arsenic Speciation in Sulfidic Solutions Using X-ray Absorption Spectroscopy

EPA Science Inventory

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 ...

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation.

PubMed

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.

Bats (Chiroptera: Noctilionoidea) Challenge a Recent Origin of Extant Neotropical Diversity.

PubMed

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.

Speciation genetics: current status and evolving approaches

PubMed Central

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

Testing founder effect speciation: Divergence population genetics of the Spoonbills Platalea regia and Pl. minor (Threskiornithidae, Aves)

USGS Publications Warehouse

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.

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.

Visualizing speciation in artificial cichlid fish.

PubMed

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.

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.

Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction.

PubMed

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.

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.

Refining the conditions for sympatric ecological speciation.

PubMed

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.

Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization.

PubMed

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.

Comparative tests of the role of dewlap size in Anolis lizard speciation

PubMed Central

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

The reality and importance of founder speciation in evolution.

PubMed

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.

Moran model as a dynamical process on networks and its implications for neutral speciation.

PubMed

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.

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.

A Multivariate Dynamic Spatial Factor Model for Speciated Pollutants and Adverse Birth Outcomes

DOE PAGES

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

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

Speciation and Toxic Emissions from On road Vehicles, and Particulate Matter Emissions from Light-Duty Gasoline Vehicles in MOVES201X

EPA Science Inventory

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...

Influence of dissolved organic matter and manganese oxides on metal speciation in soil solution: A modelling approach.

PubMed

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.

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

Anagenesis, Cladogenesis, and Speciation on Islands.

PubMed

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.

Speciation has a spatial scale that depends on levels of gene flow.

PubMed

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.

Chromosome speciation: Humans, Drosophila, and mosquitoes

PubMed Central

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

In Vitro Model To Assess Arsenic Bioaccessibility and Speciation in Cooked Shrimp.

PubMed

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.

Comparing WHAM 6 and MINEQL+ 4.5 for the chemical speciation of Cu2+ in the rhizosphere of forest soils.

PubMed

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.

Quantitative traits and diversification.

PubMed

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.

Prediction of chemical speciation in stabilized/solidified wastes using a general chemical equilibrium model. Part 1: Chemical representation of cementitious binders

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

Sorption characteristic of uranium(VI) ion onto K-feldspar.

PubMed

Gao, Xiaoqing; Bi, Mingliang; Shi, Keliang; Chai, Zhifang; Wu, Wangsuo

2017-10-01

The effect of pH, contact time, temperature, ionic strength and initial U(VI) concentration on U(VI) sorption onto K-feldspar was investigated using batch techniques. The sorption kinetics was evaluated and the activation energy was obtained based on the rate constants at different temperature. Graphical correlations of sorption isotherm models have been evaluated and applied for U(VI) uptake by K-feldspar. Various thermodynamic parameters, such as, Gibb's free energy, entropy and enthalpy of the on-going sorption process have been calculated and the possible sorption mechanism of U(VI) was deduced. The results are expected to help better understand the migration of uranium in the host materials of granite. Copyright © 2017 Elsevier Ltd. All rights reserved.

Speciation of adsorbates on surface of solids by infrared spectroscopy and chemometrics.

PubMed

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.

Dynamic coupled metal transport-speciation model: application to assess a zinc-contaminated lake.

PubMed

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.

Modeling Non-Steady Isotopologue and Isotopomer Speciation and Fractionation during Denitrification in Soils

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.

Why abundant tropical tree species are phylogenetically old.

PubMed

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.

Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies.

PubMed

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.

Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies.

PubMed

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.

A test of the chromosomal theory of ecotypic speciation in Anopheles gambiae

PubMed Central

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

Mechanisms of rapid sympatric speciation by sex reversal and sexual selection in cichlid fish.

PubMed

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.

A comparative analysis of island floras challenges taxonomy-based biogeographical models of speciation.

PubMed

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.

Detecting cryptic speciation in the widespread and morphologically conservative carpet chameleon (Furcifer lateralis) of Madagascar.

PubMed

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.

Modeling the two-locus architecture of divergent pollinator adaptation: how variation in SAD paralogs affects fitness and evolutionary divergence in sexually deceptive orchids.

PubMed

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.

Assessing when chromosomal rearrangements affect the dynamics of speciation: implications from computer simulations

PubMed Central

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

Ecological speciation in an island snail: evidence for the parallel evolution of a novel ecotype and maintenance by ecologically dependent postzygotic isolation.

PubMed

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.

Speciation in birds: genes, geography, and sexual selection.

PubMed

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.

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.

Sympatric speciation as a consequence of male pregnancy in seahorses

PubMed Central

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

Minimal effects of latitude on present-day speciation rates in New World birds

PubMed Central

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

The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations

PubMed Central

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

Speciation of the trivalent f-elements Eu(III) and Cm(III) in digestive media.

PubMed

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.

A robust framework to predict mercury speciation in combustion flue gases.

PubMed

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.

Phylogenetic evidence for cladogenetic polyploidization in land plants.

PubMed

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.

Adsorption of uranium(VI) to manganese oxides: X-ray absorption spectroscopy and surface complexation modeling.

PubMed

Wang, Zimeng; Lee, Sung-Woo; Catalano, Jeffrey G; Lezama-Pacheco, Juan S; Bargar, John R; Tebo, Bradley M; Giammar, Daniel E

2013-01-15

The mobility of hexavalent uranium in soil and groundwater is strongly governed by adsorption to mineral surfaces. As strong naturally occurring adsorbents, manganese oxides may significantly influence the fate and transport of uranium. Models for U(VI) adsorption over a broad range of chemical conditions can improve predictive capabilities for uranium transport in the subsurface. This study integrated batch experiments of U(VI) adsorption to synthetic and biogenic MnO(2), surface complexation modeling, ζ-potential analysis, and molecular-scale characterization of adsorbed U(VI) with extended X-ray absorption fine structure (EXAFS) spectroscopy. The surface complexation model included inner-sphere monodentate and bidentate surface complexes and a ternary uranyl-carbonato surface complex, which was consistent with the EXAFS analysis. The model could successfully simulate adsorption results over a broad range of pH and dissolved inorganic carbon concentrations. U(VI) adsorption to synthetic δ-MnO(2) appears to be stronger than to biogenic MnO(2), and the differences in adsorption affinity and capacity are not associated with any substantial difference in U(VI) coordination.

A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate

PubMed Central

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

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.

Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis

PubMed Central

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

Assessing element distribution and speciation in a stream at abandoned Pb-Zn mining site by combining classical, in-situ DGT and modelling approaches.

PubMed

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.

Speciation: more likely through a genetic or through a learned habitat preference?

PubMed Central

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

Application of Johnson et al.'s speciation threshold model to apparent colonization times of island biotas.

PubMed

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.

Approaches to surface complexation modeling of Uranium(VI) adsorption on aquifer sediments

NASA Astrophysics Data System (ADS)

Davis, James A.; Meece, David E.; Kohler, Matthias; Curtis, Gary P.

2004-09-01

Uranium(VI) adsorption onto aquifer sediments was studied in batch experiments as a function of pH and U(VI) and dissolved carbonate concentrations in artificial groundwater solutions. The sediments were collected from an alluvial aquifer at a location upgradient of contamination from a former uranium mill operation at Naturita, Colorado (USA). The ranges of aqueous chemical conditions used in the U(VI) adsorption experiments (pH 6.9 to 7.9; U(VI) concentration 2.5 · 10 -8 to 1 · 10 -5 M; partial pressure of carbon dioxide gas 0.05 to 6.8%) were based on the spatial variation in chemical conditions observed in 1999-2000 in the Naturita alluvial aquifer. The major minerals in the sediments were quartz, feldspars, and calcite, with minor amounts of magnetite and clay minerals. Quartz grains commonly exhibited coatings that were greater than 10 nm in thickness and composed of an illite-smectite clay with occluded ferrihydrite and goethite nanoparticles. Chemical extractions of quartz grains removed from the sediments were used to estimate the masses of iron and aluminum present in the coatings. Various surface complexation modeling approaches were compared in terms of the ability to describe the U(VI) experimental data and the data requirements for model application to the sediments. Published models for U(VI) adsorption on reference minerals were applied to predict U(VI) adsorption based on assumptions about the sediment surface composition and physical properties (e.g., surface area and electrical double layer). Predictions from these models were highly variable, with results overpredicting or underpredicting the experimental data, depending on the assumptions used to apply the model. Although the models for reference minerals are supported by detailed experimental studies (and in ideal cases, surface spectroscopy), the results suggest that errors are caused in applying the models directly to the sediments by uncertain knowledge of: 1) the proportion and types of surface functional groups available for adsorption in the surface coatings; 2) the electric field at the mineral-water interface; and 3) surface reactions of major ions in the aqueous phase, such as Ca 2+, Mg 2+, HCO 3-, SO 42-, H 4SiO 4, and organic acids. In contrast, a semi-empirical surface complexation modeling approach can be used to describe the U(VI) experimental data more precisely as a function of aqueous chemical conditions. This approach is useful as a tool to describe the variation in U(VI) retardation as a function of chemical conditions in field-scale reactive transport simulations, and the approach can be used at other field sites. However, the semi-empirical approach is limited by the site-specific nature of the model parameters.

Approaches to surface complexation modeling of Uranium(VI) adsorption on aquifer sediments

USGS Publications Warehouse

Davis, J.A.; Meece, D.E.; Kohler, M.; Curtis, G.P.

2004-01-01

Uranium(VI) adsorption onto aquifer sediments was studied in batch experiments as a function of pH and U(VI) and dissolved carbonate concentrations in artificial groundwater solutions. The sediments were collected from an alluvial aquifer at a location upgradient of contamination from a former uranium mill operation at Naturita, Colorado (USA). The ranges of aqueous chemical conditions used in the U(VI) adsorption experiments (pH 6.9 to 7.9; U(VI) concentration 2.5 ?? 10-8 to 1 ?? 10-5 M; partial pressure of carbon dioxide gas 0.05 to 6.8%) were based on the spatial variation in chemical conditions observed in 1999-2000 in the Naturita alluvial aquifer. The major minerals in the sediments were quartz, feldspars, and calcite, with minor amounts of magnetite and clay minerals. Quartz grains commonly exhibited coatings that were greater than 10 nm in thickness and composed of an illite-smectite clay with occluded ferrihydrite and goethite nanoparticles. Chemical extractions of quartz grains removed from the sediments were used to estimate the masses of iron and aluminum present in the coatings. Various surface complexation modeling approaches were compared in terms of the ability to describe the U(VI) experimental data and the data requirements for model application to the sediments. Published models for U(VI) adsorption on reference minerals were applied to predict U(VI) adsorption based on assumptions about the sediment surface composition and physical properties (e.g., surface area and electrical double layer). Predictions from these models were highly variable, with results overpredicting or underpredicting the experimental data, depending on the assumptions used to apply the model. Although the models for reference minerals are supported by detailed experimental studies (and in ideal cases, surface spectroscopy), the results suggest that errors are caused in applying the models directly to the sediments by uncertain knowledge of: 1) the proportion and types of surface functional groups available for adsorption in the surface coatings; 2) the electric field at the mineral-water interface; and 3) surface reactions of major ions in the aqueous phase, such as Ca2+, Mg2+, HCO3-, SO42-, H4SiO4, and organic acids. In contrast, a semi-empirical surface complexation modeling approach can be used to describe the U(VI) experimental data more precisely as a function of aqueous chemical conditions. This approach is useful as a tool to describe the variation in U(VI) retardation as a function of chemical conditions in field-scale reactive transport simulations, and the approach can be used at other field sites. However, the semi-empirical approach is limited by the site-specific nature of the model parameters. ?? 2004 Elsevier Ltd.

Modeling bromide effects on yields and speciation of dihaloacetonitriles formed in chlorinated drinking water.

PubMed

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.

Fulvic acid-sulfide ion competition for mercury ion binding in the Florida everglades

USGS Publications Warehouse

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.

Assessing models of speciation under different biogeographic scenarios; An empirical study using multi-locus and RNA-seq analyses

USGS Publications Warehouse

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).

Equilibrium Speciation of Select Lanthanides in the Presence of Acidic Ligands in Homo- and Heterogeneous Solutions

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

Sympatric speciation by sexual selection alone is unlikely.

PubMed

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.

The Origins of Tropical Rainforest Hyperdiversity.

PubMed

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.

Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient.

PubMed

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.

XAS Studies of Se Speciation in Selenite-Fed Rats

PubMed Central

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

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

Mineral solubility and free energy controls on microbial reaction kinetics: Application to contaminant transport in the subsurface

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

Taillefert, Martial; Van Cappellen, Philippe

Recent developments in the theoretical treatment of geomicrobial reaction processes have resulted in the formulation of kinetic models that directly link the rates of microbial respiration and growth to the corresponding thermodynamic driving forces. The overall objective of this project was to verify and calibrate these kinetic models for the microbial reduction of uranium(VI) in geochemical conditions that mimic as much as possible field conditions. The approach combined modeling of bacterial processes using new bioenergetic rate laws, laboratory experiments to determine the bioavailability of uranium during uranium bioreduction, evaluation of microbial growth yield under energy-limited conditions using bioreactor experiments, competitionmore » experiments between metabolic processes in environmentally relevant conditions, and model applications at the field scale. The new kinetic descriptions of microbial U(VI) and Fe(III) reduction should replace those currently used in reactive transport models that couple catabolic energy generation and growth of microbial populations to the rates of biogeochemical redox processes. The above work was carried out in collaboration between the groups of Taillefert (batch reactor experiments and reaction modeling) at Georgia Tech and Van Cappellen (retentostat experiments and reactive transport modeling) at University of Waterloo (Canada).« less

Marsupials as models for understanding the role of chromosome rearrangements in evolution and disease.

PubMed

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.

Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern

PubMed Central

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

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.

Uranium(VI) interactions with mackinawite in the presence and absence of bicarbonate and oxygen.

PubMed

Gallegos, Tanya J; Fuller, Christopher C; Webb, Samuel M; Betterton, William

2013-07-02

Mackinawite, Fe(II)S, samples loaded with uranium (10(-5), 10(-4), and 10(-3) mol U/g FeS) at pH 5, 7, and 9, were characterized using X-ray absorption spectroscopy and X-ray diffraction to determine the effects of pH, bicarbonate, and oxidation on uptake. Under anoxic conditions, a 5 g/L suspension of mackinawite lowered 5 × 10(-5) M uranium(VI) to below 30 ppb (1.26 × 10(-7) M) U. Between 82 and 88% of the uranium removed from solution by mackinawite was U(IV) and was nearly completely reduced to U(IV) when 0.012 M bicarbonate was added. Near-neighbor coordination consisting of uranium-oxygen and uranium-uranium distances indicates the formation of uraninite in the presence and absence of bicarbonate, suggesting reductive precipitation as the dominant removal mechanism. Following equilibration in air, mackinawite was oxidized to mainly goethite and sulfur and about 76% of U(IV) was reoxidized to U(VI) with coordination of uranium to axial and equatorial oxygen, similar to uranyl. Additionally, uranium-iron distances, typical of coprecipitation of uranium with iron oxides, and uranium-sulfur distances indicating bidentate coordination of U(VI) to sulfate were evident. The affinity of mackinawite and its oxidation products for U(VI) provides impetus for further study of mackinawite as a potential reactive medium for remediation of uranium-contaminated water.

A novel benzimidazole-functionalized 2-D COF material: synthesis and application as a selective solid-phase extractant for separation of uranium.

PubMed

Li, Juan; Yang, Xiaodan; Bai, Chiyao; Tian, Yin; Li, Bo; Zhang, Shuang; Yang, Xiaoyu; Ding, Songdong; Xia, Chuanqin; Tan, Xinyu; Ma, Lijian; Li, Shoujian

2015-01-01

A novel COF-based material (COF-COOH) containing large amounts of carboxylic groups was prepared for the first time by using a simple and effective one-step synthetic method, in which the cheap and commercially available raw materials, trimesoyl chloride and p-phenylenediamine, were used. The as-synthesized COF-COOH was modified with previously synthesized 2-(2,4-dihydroxyphenyl)-benzimidazole (HBI) by "grafting to" method, and a new solid-phase extractant (COF-HBI) with highly efficient sorption performance for uranium(VI) was consequently obtained. A series of characterizations demonstrated that COF-COOH and COF-HBI exhibited great thermostabilities and irradiation stabilities. Sorption behavior of the COF-based materials toward U(VI) was compared in simulated nuclear industrial effluent containing UO2(2+) and 11 undesired ions, and the UO2(2+) sorption amount of COF-HBI was 81 mg g(-1), accounting for approximately 58% of the total sorption amount, which was much higher than the sorption selectivity of COF-COOH to UO2(2+) (39%). Batch sorption experiment results indicated that the uranium(VI) sorption on COF-HBI was a pH dependent, rapid (sorption equilibrium was reached in 30 min), endothermic and spontaneous process. In the most favorable conditions, the equilibrium sorption capacity of the adsorbent for uranium could reach 211 mg g(-1). Copyright © 2014 Elsevier Inc. All rights reserved.

Highly Efficient Interception and Precipitation of Uranium(VI) from Aqueous Solution by Iron-Electrocoagulation Combined with Cooperative Chelation by Organic Ligands.

PubMed

Li, Peng; Zhun, Bao; Wang, Xuegang; Liao, PingPing; Wang, Guanghui; Wang, Lizhang; Guo, Yadan; Zhang, Weimin

2017-12-19

A new strategy combining iron-electrocoagulation and organic ligands (OGLs) cooperative chelation was proposed to screen and precipitate low concentrations (0-18.52 μmol/L) of uranium contaminant in aqueous solution. We hypothesized that OGLs with amino, hydroxyl, and carboxyl groups hydrophobically/hydrophilically would realize precuring of uranyl ion at pH < 3.0, and the following iron-electrocoagulation would achieve faster and more efficient uranium precipitation. Experimentally, the strategy demonstrated highly efficient uranium(VI) precipitation efficiency, especially with hydrophilic macromolecular OGLs. The uranium removal efficiency at optimized experimental condition reached 99.65%. The decrease of zeta potential and the lattice enwrapping between U-OGLs chelates and flocculation precursor were ascribed to the enhanced uranium precipitation activity. Uranium was precipitated as oxides of U(VI) or higher valences that were easily captured in aggregated micelles under low operation current potential. The actual uranium tailing wastewater was treated, and a satisfied uranium removal efficiency of 99.02% was discovered. After elution of the precipitated flocs, a concentrated uranium solution (up to 106.52 μmol/L) with very few other metallic impurities was obtained. Therefore, the proposed strategy could remove uranium and concentrate it concurrently. This work could provide new insights into the purification and recovery of uranium from aqueous solutions in a cost-effective and environmentally friendly process.

Uranium(VI) interactions with mackinawite in the presence and absence of bicarbonate and oxygen

USGS Publications Warehouse

Gallegos, Tanya J.; Fuller, Christopher C.; Webb, Samuel M.; Betterton, William J.

2013-01-01

Mackinawite, Fe(II)S, samples loaded with uranium (10-5, 10-4, and 10-3 mol U/g FeS) at pH 5, 7, and 9, were characterized using X-ray absorption spectroscopy and X-ray diffraction to determine the effects of pH, bicarbonate, and oxidation on uptake. Under anoxic conditions, a 5 g/L suspension of mackinawite lowered 5 × 10-5 M uranium(VI) to below 30 ppb (1.26 × 10-7 M) U. Between 82 and 88% of the uranium removed from solution by mackinawite was U(IV) and was nearly completely reduced to U(IV) when 0.012 M bicarbonate was added. Near-neighbor coordination consisting of uranium–oxygen and uranium-uranium distances indicates the formation of uraninite in the presence and absence of bicarbonate, suggesting reductive precipitation as the dominant removal mechanism. Following equilibration in air, mackinawite was oxidized to mainly goethite and sulfur and about 76% of U(IV) was reoxidized to U(VI) with coordination of uranium to axial and equatorial oxygen, similar to uranyl. Additionally, uranium-iron distances, typical of coprecipitation of uranium with iron oxides, and uranium-sulfur distances indicating bidentate coordination of U(VI) to sulfate were evident. The affinity of mackinawite and its oxidation products for U(VI) provides impetus for further study of mackinawite as a potential reactive medium for remediation of uranium-contaminated water.

Including the spatial variability of metal speciation in the effect factor in life cycle impact assessment: Limits of the equilibrium partitioning method.

PubMed

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.

Speciation of heavy metals in landfill leachate: a review.

PubMed

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.

Parapatric speciation in three islands: dynamics of geographical configuration of allele sharing

PubMed Central

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

Development of a database for chemical mechanism assignments for volatile organic emissions.

PubMed

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.

Linking Chaotic Advection with Subsurface Biogeochemical Processes

NASA Astrophysics Data System (ADS)

Mays, D. C.; Freedman, V. L.; White, S. K.; Fang, Y.; Neupauer, R.

2017-12-01

This work investigates the extent to which groundwater flow kinematics drive subsurface biogeochemical processes. In terms of groundwater flow kinematics, we consider chaotic advection, whose essential ingredient is stretching and folding of plumes. Chaotic advection is appealing within the context of groundwater remediation because it has been shown to optimize plume spreading in the laminar flows characteristic of aquifers. In terms of subsurface biogeochemical processes, we consider an existing model for microbially-mediated reduction of relatively mobile uranium(VI) to relatively immobile uranium(IV) following injection of acetate into a floodplain aquifer beneath a former uranium mill in Rifle, Colorado. This model has been implemented in the reactive transport code eSTOMP, the massively parallel version of STOMP (Subsurface Transport Over Multiple Phases). This presentation will report preliminary numerical simulations in which the hydraulic boundary conditions in the eSTOMP model are manipulated to simulate chaotic advection resulting from engineered injection and extraction of water through a manifold of wells surrounding the plume of injected acetate. This approach provides an avenue to simulate the impact of chaotic advection within the existing framework of the eSTOMP code.

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.

Uranium Reduction by Fe(II) in the Presence of Montmorillonite and Nontronite.

PubMed

Tsarev, Sergey; Waite, T David; Collins, Richard N

2016-08-02

Uranium(VI) interactions with three smectites (one montmorillonite and two nontronites - NAu1 and NAu2) were examined with 0, 1, and 2 mM aqueous concentrations of Fe(II) over the pH range of 3-9.5 in a background electrolyte of 100 mM NaCl and 1 mM CaCl2 in equilibration with 400 ppmv CO2(g) ([U(VI)] = 4 μM and 0.5 g smectite/L). In the absence of Fe(II), no differences were observed in the U(VI) sorption curves for the three clay minerals. In the presence of 1 or 2 mM Fe(II), under anoxic conditions, U(VI) uptake by the smectites changed slightly between ∼pH 3 and 6; however, uranium uptake increased significantly above ∼pH 6 and was proportional to the concentration of Fe(II) added to the system, particularly at pH values >8. The uptake of Fe(II) showed a sharp edge starting from ∼pH 6.5 with 95%-100% uptake occurring at pH values >7.5, with no difference observed between the iron-rich nontronites and montmorillonite. After 3 days of reaction at pH 7.6 (i.e., above the Fe(II) "sorption" edge), U(VI) was transformed to a mixture of U(IV) and U(VI) sorption complexes, and after 14 days of reaction, 100% of the U was found to be reduced to U(IV) in the form of nanocrystalline uraninite. In contrast, U remained as sorbed species until 14 days of reaction at pH 6.5. Ferrihydrite (NAu1), lepidocrocite, and magnetite (NAu2) were detected as secondary mineralization products upon reaction of the nontronites with Fe(II) but appeared to have no effect on the partitioning or speciation of uranium.

A Genome-Wide Analysis Reveals No Nuclear Dobzhansky-Muller Pairs of Determinants of Speciation between S. cerevisiae and S. paradoxus, but Suggests More Complex Incompatibilities

PubMed Central

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

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

Uranium(IV) adsorption by natural organic matter in anoxic sediments

DOE PAGES

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

Sorption of uranyl ions from various acido systems by amphoteric epoxy amine ion-exchange resins

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

Rychkov, V.N.; Radionov, B.K.; Molochnikov, L.S.

1995-03-01

Sorption of uranyl ions by epoxy amine ampholytes with N-monomethylenephosphonic acid groups modified with pyridine or quaternary ammonium groups was studied under dynamic conditions. Heterocyclic nitrogen favors sorption of uranyl ion from fluoride, sulfate, and fluoride-sulfate solutions. The ESR studies of mono- and bimetallic forms of nitrogen-containing ampholytes with copper(II) as paramagnetic marker revealed the characteristics of uranium(VI) interaction with cation- and anion-exchange groups and its dependence on the fluoride content in solution.

The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region.

PubMed

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.

A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution

PubMed Central

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

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.

Contributions of natural and sexual selection to the evolution of premating reproductive isolation: a research agenda.

PubMed

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.

Tracking niche variation over millennial timescales in sympatric killer whale lineages

PubMed Central

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

Tracking niche variation over millennial timescales in sympatric killer whale lineages.

PubMed

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.

The importance of ligand speciation in environmental research: a case study.

PubMed

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.

Application of ESI-HRMS for molybdenum speciation in natural waters: An investigation of molybdate-halide reactions.

PubMed

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.

On the distribution of interspecies correlation for Markov models of character evolution on Yule trees.

PubMed

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.

Synthesis and characterization of UO(2)(2+)-ion imprinted polymer for selective extraction of UO(2)(2+).

PubMed

Singh, Dhruv K; Mishra, Shraddha

2009-06-30

Ion-imprinted polymers (IIPs) were prepared for uranyl ion (imprint ion) by formation of binary (salicylaldoxime (SALO) or 4-vinylpyridine (VP)) or ternary (salicylaldoxime and 4-vinylpyridine) complex in 2-methoxy ethanol (porogen) following copolymerization with methacrylic acid (MAA) as a functional monomer and ethylene glycol dimethacrylate (EGDMA) as crosslinking monomer using 2,2'-azobisisobutyronitrile as initiator. Control polymers (CPs) were also prepared under identical experimental conditions without using imprint ion. The above synthesized polymers were characterized by surface area measurement, microanalysis and FT-IR analysis techniques. The imprinted polymer formed with ternary complex of UO(2)(2+)-SALO-VP (1:2:2, IIP3) showed quantitative enrichment of uranyl ion from dilute aqueous solution and hence was chosen for detailed studies. The optimal pH for quantitative enrichment is 3.5-6.5. The adsorbed UO(2)(2+) was completely eluted with 10 mL of 1.0 M HCl. The retention capacity of IIP3 was found to be 0.559 mmol g(-1). Further, the distribution ratio and selectivity coefficients of uranium and other selected inorganic ions were also evaluated. Five replicate determinations of 25 microg L(-1) of uranium(VI) gave a mean absorbance of 0.032 with a relative standard deviation of 2.20%. The detection limit corresponding to three times the standard deviation of the blank was found to be 5 microg L(-1). IIP3 was tested for preconcentration of uranium(VI) from ground, river and sea water samples.

Testing the Underlying Chemical Principles of the Biotic Ligand Model (BLM) to Marine Copper Systems: Measuring Copper Speciation Using Fluorescence Quenching.

PubMed

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.

Whole-cell bioreporters and risk assessment of environmental pollution: A proof-of-concept study using lead.

PubMed

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.

Omnivory in birds is a macroevolutionary sink

PubMed Central

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

Model for macroevolutionary dynamics.

PubMed

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.

Empirical phylogenies and species abundance distributions are consistent with preequilibrium dynamics of neutral community models with gene flow.

PubMed

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.

Uncertainty analysis of the nonideal competitive adsorption-donnan model: effects of dissolved organic matter variability on predicted metal speciation in soil solution.

PubMed

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.

Hybrid Speciation in a Marine Mammal: The Clymene Dolphin (Stenella clymene)

PubMed Central

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

Hybrid speciation in a marine mammal: the clymene dolphin (Stenella clymene).

PubMed

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.

X exceptionalism in Caenorhabditis speciation.

PubMed

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.

SPECIATE 4.3: Addendum to SPECIATE 4.2--Speciation database development documentation

EPA Science Inventory

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...

SPECIATE 4.0: SPECIATION DATABASE DEVELOPMENT DOCUMENTATION--FINAL REPORT

EPA Science Inventory

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 ...

Linking patterns and processes of species diversification in the cone flies Strobilomyia (Diptera: Anthomyiidae).

PubMed

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.

Particulate matter speciation profiles for light-duty gasoline vehicles in the United States.

PubMed

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.

Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles.

PubMed

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.

Diversification dynamics of rhynchostomatian ciliates: the impact of seven intrinsic traits on speciation and extinction in a microbial group.

PubMed

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.

Uranium aqueous speciation in the vicinity of the former uranium mining sites using the diffusive gradients in thin films and ultrafiltration techniques.

PubMed

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.

Mountain Refugia Play a Role in Soil Arthropod Speciation on Madagascar: A Case Study of the Endemic Giant Fire-Millipede Genus Aphistogoniulus

PubMed Central

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

SPECIATE 4.2: speciation Database Development Documentation

EPA Science Inventory

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...

The evolution of sensory divergence in the context of limited gene flow in the bumblebee bat

PubMed Central

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

Ecological Speciation in Nolina parviflora (Asparagaceae): Lacking Spatial Connectivity along of the Trans-Mexican Volcanic Belt

PubMed Central

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

Ecological speciation in Nolina parviflora (Asparagaceae): lacking spatial connectivity along of the Trans-Mexican Volcanic Belt.

PubMed

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.

Model selection in historical biogeography reveals that founder-event speciation is a crucial process in Island Clades.

PubMed

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.

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.

PubMed

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.

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.

Application of aerosol speciation data as an in situ dust proxy for validation of the Dust Regional Atmospheric Model (DREAM)

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.

The biomineralization process of uranium(VI) by Saccharomyces cerevisiae - transformation from amorphous U(VI) to crystalline chernikovite.

PubMed

Shen, Yanghao; Zheng, Xinyan; Wang, Xiaoyu; Wang, Tieshan

2018-05-01

Microorganisms play a significant role in uranium(VI) biogeochemistry and influence U(VI) transformation through biomineralization. In the present work, the process of uranium mineralization was investigated by Saccharomyces cerevisiae. The toxicity experiments showed that the viability of cell was not significantly affected by 100 mg L -1 U(VI) under 4 days of exposure time. The batch experiments showed that the phosphate concentration and pH value increased over time during U(VI) adsorption. Meanwhile, thermodynamic calculations demonstrated that the adsorption system was supersaturated with respect to UO 2 HPO 4 . The X-ray powder diffraction spectroscopy (XRD), field emission scanning electron microscopy (FE-SEM) equipped with energy dispersive spectroscopy (EDX), Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS) analyses indicated that the U(VI) was first attached onto the cell surface and reacted with hydroxyl, carboxyl, and phosphate groups through electrostatic interactions and complexation. As the immobilization of U(VI) transformed it from the ionic to the amorphous state, lamellar uranium precipitate was formed on the cell surface. With the prolongation of time, the amorphous uranium compound disappeared, and there were some crystalline substances observed extracellularly, which were well-characterized as tetragonal-chernikovite. Furthermore, the size of chernikovite was regulated at nano-level by cells, and the perfect crystal was formed finally. These findings provided an understanding of the non-reductive transformation process of U(VI) from the amorphous to crystalline state within microbe systems, which would be beneficial for the U(VI) treatment and reuse of nuclides and heavy metals.

Influence of Organic Matter - Mineral Interfacial Reactions on Metal(loid) Speciation and Bioaccessibility

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.

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.

Assembly processes of gastropod community change with horizontal and vertical zonation in ancient Lake Ohrid: a metacommunity speciation perspective

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.

Quantifying variation in speciation and extinction rates with clade data.

PubMed

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.

Defense Coastal/Estuarine Research Program (DCERP) Baseline Monitoring Plan

DTIC Science & Technology

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

Mimicry on the QT(L): genetics of speciation in Mimulus.

PubMed

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.

Measured solubilities and speciations of neptunium, plutonium, and americium in a typical groundwater (J-13) from the Yucca Mountain region; Milestone report 3010-WBS 1.2.3.4.1.3.1

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

Quantifying the response of the ORAC aerosol optical depth retrieval for MSG SEVIRI to aerosol model assumptions

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%.

Donnan membrane speciation of Al, Fe, trace metals and REEs in coastal lowland acid sulfate soil-impacted drainage waters.

PubMed

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.

Four groups of new aromatic halogenated disinfection byproducts: effect of bromide concentration on their formation and speciation in chlorinated drinking water.

PubMed

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.

Prediction of the bioavailability of potentially toxic elements in freshwaters. Comparison between speciation models and passive samplers.

PubMed

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.

Volcanic gas composition, metal dispersion and deposition during explosive volcanic eruptions on the Moon

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.

Speciation of High-Pressure Carbon-Saturated COH Fluids at Buffered fO2 Conditions: An Experimental Approach

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.

Particulate-phase mercury emissions from biomass burning ...

EPA Pesticide Factsheets

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

Evaluating EDGARv4.tox2 speciated mercury emissions ex-post scenarios and their impacts on modelled global and regional wet deposition patterns

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.

The telomeric sync model of speciation: species-wide telomere erosion triggers cycles of transposon-mediated genomic rearrangements, which underlie the saltatory appearance of nonadaptive characters

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.

Application of chemometric analysis and self Organizing Map-Artificial Neural Network as source receptor modeling for metal speciation in river sediment.

PubMed

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.

A forecast for extinction debt in the presence of speciation.

PubMed

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.

The impact of seasonality on niche breadth, distribution range and species richness: a theoretical exploration of Janzen's hypothesis.

PubMed

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).

Signatures of microevolutionary processes in phylogenetic patterns.

PubMed

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.

Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus.

PubMed

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.

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.

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

PubMed Central

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

EPA’s SPECIATE 4.4 Database:Development and Uses

EPA Science Inventory

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...

EPA’s SPECIATE 4.4 Database: Development and Uses

EPA Science Inventory

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...

Development of a mercury speciation, fate, and biotic uptake (BIOTRANSPEC) model: Application to Lahontan Reservoir (Nevada, USA)

USGS Publications Warehouse

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.

Sulfur redox chemistry governs diurnal antimony and arsenic cycles at Champagne Pool, Waiotapu, New Zealand

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.

The genetic signature of recent speciation in manta rays (Manta alfredi and M. birostris).

PubMed

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.

Comparison of soil solution speciation and diffusive gradients in thin-films measurement as an indicator of copper bioavailability to plants.

PubMed

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.

US EPA's SPECIATE 4.4 Database: Development and Uses

EPA Science Inventory

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...

EPA’s SPECIATE 4.4 Database: Bridging Data Sources and Data Users

EPA Science Inventory

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...

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

Zhang, Yingjie, E-mail: yzx@ansto.gov.au; Karatchevtseva, Inna; Bhadbhade, Mohan

With the coordination of dimethylformamide (DMF), two new uranium(VI) complexes with either 4-hydroxybenzoic acid (H{sub 2}phb) or terephthalic acid (H{sub 2}tph) have been synthesized under solvothermal conditions and structurally characterized. [(UO{sub 2}){sub 2}(Hphb){sub 2}(phb)(DMF)(H{sub 2}O){sub 3}]·4H{sub 2}O (1) has a dinuclear structure constructed with both pentagonal and hexagonal bipyramidal uranium polyhedra linked through a µ{sub 2}-bridging ligand via both chelating carboxylate arm and alcohol oxygen bonding, first observation of such a coordination mode of 4-hydroxybenzoate for 5 f ions. [(UO{sub 2})(tph)(DMF)] (2) has a three-dimensional (3D) framework built with pentagonal bipyramidal uranium polyhedra linked with µ{sub 4}-terephthalate ligands. The 3Dmore » channeled structure is facilitated by the unique carboxylate bonding with nearly linear C–O–U angles and the coordination of DMF molecules. The presence of phb ligands in different coordination modes, uranyl ions in diverse environments and DMF in complex 1, and tph ligand, DMF and uranyl ion in complex 2 has been confirmed by Raman spectroscopy. In addition, their thermal stability and photoluminescence properties have been investigated. - Graphical abstract: With the coordination of dimethylformamide, two new uranyl complexes with either 4-hydroxybenzoate or terephthalate have been synthesized under solvothermal conditions and structurally characterized. - Highlights: • Solvent facilitates the synthesis of two new uranium(VI) complexes. • A dinuclear complex with both penta- and hexagonal bipyramidal uranium polyhedral. • A unique µ{sub 2}-bridging mode of 4-hydroxybenzoate via alcohol oxygen for 5 f ions. • A 3D framework with uranium polyhedra and µ{sub 4}-terephthalate ligands. • Vibration modes and photoluminescence properties are reported.« less

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

Zhang, Yingjie, E-mail: yzx@ansto.gov.au; Bhadbhade, Mohan; Karatchevtseva, Inna

Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5more » Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.« less

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.

Invasive species and biodiversity crises: testing the link in the late devonian.

PubMed

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.

Quantifying differences in the impact of variable chemistry on equilibrium uranium(VI) adsorption properties of aquifer sediments

USGS Publications Warehouse

Stoliker, Deborah L.; Kent, Douglas B.; Zachara, John M.

2011-01-01

Uranium adsorption-desorption on sediment samples collected from the Hanford 300-Area, Richland, WA varied extensively over a range of field-relevant chemical conditions, complicating assessment of possible differences in equilibrium adsorption properties. Adsorption equilibrium was achieved in 500-1000 h although dissolved uranium concentrations increased over thousands of hours owing to changes in aqueous chemical composition driven by sediment-water reactions. A nonelectrostatic surface complexation reaction, >SOH + UO22+ + 2CO32- = >SOUO2(CO3HCO3)2-, provided the best fit to experimental data for each sediment sample resulting in a range of conditional equilibrium constants (logKc) from 21.49 to 21.76. Potential differences in uranium adsorption properties could be assessed in plots based on the generalized mass-action expressions yielding linear trends displaced vertically by differences in logKc values. Using this approach, logKc values for seven sediment samples were not significantly different. However, a significant difference in adsorption properties between one sediment sample and the fines (Kc uncertainty were improved by capturing all data points within experimental errors. The mass-action expression plots demonstrate that applying models outside the range of conditions used in model calibration greatly increases potential errors.

Dynamics of aluminum speciation in forest-well drainage waters from the Rhode River watershed, Maryland.

PubMed

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.

Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards.

PubMed

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.

The evolution of conditional dispersal and reproductive isolation along environmental gradients

PubMed Central

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

The evolution of conditional dispersal and reproductive isolation along environmental gradients.

PubMed

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.

Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow

USGS Publications Warehouse

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.

Trade-offs drive resource specialization and the gradual establishment of ecotypes

PubMed Central

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

Alleviation of environmental risks associated with severely contaminated mine tailings using amendments: Modeling of trace element speciation, solubility, and plant accumulation.

PubMed

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.

Theoretical size distribution of fossil taxa: analysis of a null model

PubMed Central

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

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.

Arsenic Speciation in Groundwater: Role of Thioanions

EPA Science Inventory

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...

Beryllium chemical speciation in elemental human biological fluids.

PubMed

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.

Solid-phase cadmium speciation in soil using L3-edge XANES spectroscopy with partial least-squares regression.

PubMed

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.

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.

Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses

PubMed Central

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

Evolution, biogeography, and systematics of Puriana: evolution and speciation in Ostracoda, III.

USGS Publications Warehouse

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

Estimating particle speciation concentrations using MISR retrieved aerosol properties in southern California

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.

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%.

Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves).

PubMed

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.

MINTEQA2

EPA Science Inventory

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...

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

PubMed Central

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

Convergent and divergent evolution in carnivorous pitcher plant traps.

PubMed

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.

Energy gradients and the geographic distribution of local ant diversity.

PubMed

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.

BIOCHEM-ORCHESTRA: a tool for evaluating chemical speciation and ecotoxicological impacts of heavy metals on river flood plain systems.

PubMed

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).

Optimisation of the storage of natural freshwaters before organotin speciation.

PubMed

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.

EPAs SPECIATE 4.4 Database: Development and Uses

EPA Science Inventory

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...

SPECIATE Version 4.4 Database Development Documentation

EPA Science Inventory

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...

SPECIATE - EPA'S DATABASE OF SPECIATED EMISSION PROFILES

EPA Science Inventory

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...

The importance of trace element speciation in biomedical science.

PubMed

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.

Theoretical size distribution of fossil taxa: analysis of a null model.

PubMed

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.

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.

Estimating PM2.5 speciation concentrations using prototype 4.4 km-resolution MISR aerosol properties over Southern California

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.

Observations and regional modeling of aerosol optical properties, speciation and size distribution over Northern Africa and western Europe

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.

Age-Dependent and Lineage-Dependent Speciation and Extinction in the Imbalance of Phylogenetic Trees.

PubMed

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.

Geochemical modeling of mercury speciation in surface water and implications on mercury cycling in the everglades wetland.

PubMed

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.

Integrating environmental, molecular, and morphological data to unravel an ice-age radiation of arctic-alpine Campanula in western North America

PubMed Central

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

GEOCHEMICAL MODELING OF ARSENIC SPECIATION AND MOBILIZATION: IMPLICATIONS FOR BIOREMEDIATION

EPA Science Inventory

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...

Plasma-induced grafting of acrylic acid on bentonite for the removal of U(VI) from aqueous solution

NASA Astrophysics Data System (ADS)

Hongshan, ZHU; Shengxia, DUAN; Lei, CHEN; Ahmed, ALSAEDI; Tasawar, HAYAT; Jiaxing, LI

2017-11-01

Fabrication of reusable adsorbents with satisfactory adsorption capacity and using environment-friendly preparation processes is required for the environment-related applications. In this study, acrylic acid (AA) was grafted onto bentonite (BT) to generate an AA-graft-BT (AA-g-BT) composite using a plasma-induced grafting technique considered to be an environment-friendly method. The as-prepared composite was characterized by scanning electron microscopy, x-ray powder diffraction, thermal gravity analysis, Fourier transform infrared spectroscopy and Barrett-Emmett-Teller analysis, demonstrating the successful grafting of AA onto BT. In addition, the removal of uranium(VI) (U(VI)) from contaminated aqueous solutions was examined using the as-prepared composite. The influencing factors, including contact time, pH value, ionic strength, temperature, and initial concentration, for the removal of U(VI) were investigated by batch experiments. The experimental process fitted best with the pseudo-second-order kinetic and the Langmuir models. Moreover, thermodynamic investigation revealed a spontaneous and endothermic process. Compared with previous adsorbents, AA-g-BT has potential practical applications in treating U(VI)-contaminated solutions.

Extraordinarily rapid speciation in a marine fish

PubMed Central

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

A new paradigm for constraining PM2.5 speciation by combining multiangular and polarimetric remote sensing with chemical transport model information

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.

Testing the role of the Red Queen and Court Jester as drivers of the macroevolution of Apollo butterflies.

PubMed

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.

A model of Fe speciation and biogeochemistry at the Tropical Eastern North Atlantic Time-Series Observatory site

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.

SOURCE APPORTIONMENT RESULTS, UNCERTAINTIES, AND MODELING TOOLS

EPA Science Inventory

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 ...

Trait-based diversification shifts reflect differential extinction among fossil taxa.

PubMed

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.

Indian emissions of technology-linked NMVOCs with chemical speciation: An evaluation of the SAPRC99 mechanism with WRF-CAMx simulations

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.

77 FR 69399 - Approval and Promulgation of Air Quality Implementation Plans; Delaware; Attainment Plan for the...

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...

Measured solubilities and speciations from oversaturation experiments of neptunium, plutonium, and americium in UE-25p No. 1 well water from the Yucca Mountain region: Milestone report 3329-WBS1.2.3.4.1.3.1

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

Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China.

PubMed

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.

pH-dependent biotransformation of ionizable organic micropollutants in activated sludge.

PubMed

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.

Detecting local diversity-dependence in diversification.

PubMed

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.

Genome‐wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

PubMed Central

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

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

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

Model-based Analysis of Mixed Uranium(VI) Reduction by Biotic and Abiotic Pathways During in Situ Bioremediation

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

Zhao, Jiao; Scheibe, Timothy D.; Mahadevan, Radhakrishnan

2013-10-24

Uranium bioremediation has emerged as a potential strategy of cleanup of radionuclear contamination worldwide. An integrated geochemical & microbial community model is a promising approach to predict and provide insights into the bioremediation of a complicated natural subsurface. In this study, an integrated column-scale model of uranium bioremediation was developed, taking into account long-term interactions between biotic and abiotic processes. It is also combined with a comprehensive thermodynamic analysis to track the fate and cycling of biogenic species. As compared with other bioremediation models, the model increases the resolution of the connection of microbial community to geochemistry and establishes directmore » quantitative correlation between overall community evolution and geochemical variation, thereby accurately predicting the community dynamics under different sedimentary conditions. The thermodynamic analysis examined a recently identified homogeneous reduction of U(VI) by Fe(II) under dynamic sedimentary conditions across time and space. It shows that the biogenic Fe(II) from Geobacter metabolism can be removed rapidly by the biogenic sulphide from sulfate reducer metabolism, hence constituting one of the reasons that make the abiotic U(VI) reduction thermodynamically infeasible in the subsurface. Further analysis indicates that much higher influent concentrations of both Fe(II) and U(VI) than normal are required to for abiotic U(VI) reduction to be thermodynamically feasible, suggesting that the abiotic reduction cannot be an alternative to the biotic reduction in the remediation of uranium contaminated groundwater.« less

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.

Chemical Mass Balance (CMB) Model

EPA Pesticide Factsheets

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.

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

USGS Publications Warehouse

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.

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species

PubMed Central

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

Slowly dispersing neotenic beetles can speciate on a penny coin and generate space-limited diversity in the tropical mountains

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.

The evolution of recombination rates in finite populations during ecological speciation.

PubMed

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).

Divergence with gene flow across a speciation continuum of Heliconius butterflies.

PubMed

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.

Erosive processes after tectonic uplift stimulate vicariant and adaptive speciation: evolution in an Afrotemperate-endemic paper daisy genus

PubMed Central

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

Extensive range overlap between heliconiine sister species: evidence for sympatric speciation in butterflies?

PubMed

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.

Layered uranium(VI) hydroxides: structural and thermodynamic properties of dehydrated schoepite α-UO₂(OH)₂.

PubMed

Weck, Philippe F; Kim, Eunja

2014-12-07

The structure of dehydrated schoepite, α-UO2(OH)2, was investigated using computational approaches that go beyond standard density functional theory and include van der Waals dispersion corrections (DFT-D). Thermal properties of α-UO2(OH)2, were also obtained from phonon frequencies calculated with density functional perturbation theory (DFPT) including van der Waals dispersion corrections. While the isobaric heat capacity computed from first-principles reproduces available calorimetric data to within 5% up to 500 K, some entropy estimates based on calorimetric measurements for UO3·0.85H2O were found to overestimate by up to 23% the values computed in this study.

The role of Quaternary environmental change in plant macroevolution: the exception or the rule?

PubMed Central

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

NetpathXL - An Excel Interface to the Program NETPATH

USGS Publications Warehouse

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.

Iron Speciation in the Subtropical Waters East of New Zealand using Multi Detection Window CLE-AdCSV Titrations.

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.

Gastropod diversification and community structuring processes in ancient Lake Ohrid: a metacommunity speciation perspective

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.

Effects of aqueous uranyl speciation on the kinetics of microbial uranium reduction

DOE PAGES

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

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.

Temporal assessment of copper speciation, bioavailability and toxicity in UK freshwaters using chemical equilibrium and biotic ligand models: Implications for compliance with copper environmental quality standards.

PubMed

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.

Evolutionary Roots and Diversification of the Genus Aeromonas.

PubMed

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.

Evolutionary Roots and Diversification of the Genus Aeromonas

PubMed Central

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

Rapid and efficient uranium(VI) capture by phytic acid/polyaniline/FeOOH composites.

PubMed

Wei, Xintao; Liu, Qi; Zhang, Hongsen; Liu, Jingyuan; Chen, Rongrong; Li, Rumin; Li, Zhangshuang; Liu, Peili; Wang, Jun

2018-02-01

Uranium plays an indispensable role in nuclear energy, but there are limited land resources to meet the ever growing demand; therefore, a need exists to develop efficient materials for capturing uranium from water. Herein, we synthesize a promising adsorbent of phytic acid/polyaniline/FeOOH composites (PA/PANI/FeOOH) by oxidative polymerization. Phytic acid, acting asa gelator and dopant, plays an important role in the formation of polyaniline (PANI). The PA/PANI/FeOOH exhibites high adsorption capacity (q m =555.8mgg -1 , T=298K), rapid adsorption rate (within 5min), excellent selectivity and cyclic stability. In addition, the results show that the adsorption isotherm is well fitted to the Langmuir isotherm model, and the adsorption kinetics agree with a pseudo-second order model. XPS analysis indicates that the removal of uranium is mainly attributed to abundant amine and imine groups on the surface of PA/PANI/FeOOH. Importantly, the removal of uranium from low concentrations of simulated seawater is highly efficient with a removal rate exceeding 92%. From our study, superior adsorption capacities, along with a low-cost, environmentally friendly and facile synthesis, reveal PA/PANI/FeOOH asa promising material for uranium capture. Copyright © 2017. Published by Elsevier Inc.

Characteristics of uranium biosorption from aqueous solutions on fungus Pleurotus ostreatus.

PubMed

Zhao, Changsong; Liu, Jun; Tu, Hong; Li, Feize; Li, Xiyang; Yang, Jijun; Liao, Jiali; Yang, Yuanyou; Liu, Ning; Sun, Qun

2016-12-01

Uranium(VI) biosorption from aqueous solutions was investigated in batch studies by using fungus Pleurotus ostreatus biomass. The optimal biosorption conditions were examined by investigating the reaction time, biomass dosage, pH, temperature, and uranium initial concentration. The interaction between fungus biomass and uranium was confirmed using Fourier transformed infrared (FT-IR), scanning electronic microscopy energy dispersive X-ray (SEM-EDX), and X-ray photoelectron spectroscopy (XPS) analysis. Results exhibited that the maximum biosorption capacity of uranium on P. ostreatus was 19.95 ± 1.17 mg/g at pH 4.0. Carboxylic, amine, as well as hydroxyl groups were involved in uranium biosorption according to FT-IR analysis. The pseudo-second-order model properly evaluated the U(VI) biosorption on fungus P. ostreatus biomass. The Langmuir equation provided better fitting in comparison with Freundlich isotherm models. The obtained thermodynamic parameters suggested that biosorption is feasible, endothermic, and spontaneous. SEM-EDX and XPS were additionally conducted to comprehend the biosorption process that could be described as a complex process involving several mechanisms of physical adsorption, chemisorptions, and ion exchange. Results obtained from this work indicated that fungus P. ostreatus biomass can be used as potential biosorbent to eliminate uranium or other radionuclides from aqueous solutions.

Solution speciation of plutonium and Americium at an Australian legacy radioactive waste disposal site.

PubMed

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.

Mapping Asian anthropogenic emissions of non-methane volatile organic compounds to multiple chemical mechanisms

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.

Estimation of speciated and total mercury dry deposition at monitoring locations in eastern and central North America

USGS Publications Warehouse

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.

Secondary sympatry caused by range expansion informs on the dynamics of microendemism in a biodiversity hotspot.

PubMed

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.

Selenium Metabolism in Cancer Cells: The Combined Application of XAS and XFM Techniques to the Problem of Selenium Speciation in Biological Systems

PubMed Central

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

The species flocks of East African cichlid fishes: recent advances in molecular phylogenetics and population genetics

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.

Source apportionment of secondary organic aerosol in China using a regional source-oriented chemical transport model and two emission inventories.

PubMed

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.

Can preference for oviposition sites initiate reproductive isolation in Callosobruchus maculatus?

PubMed

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.

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

Chemical fractionation and speciation modelling for optimization of ion-exchange processes to recover palladium from industrial wastewater.

PubMed

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.

Trait-based diversification shifts reflect differential extinction among fossil taxa

PubMed Central

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

Regional Scale Photochemical Model Evaluation of Total Mercury Wet Deposition and Speciated Ambient Mercury

EPA Science Inventory

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...

Speciation of the major inorganic salts in atmospheric aerosols of Beijing, China: Measurements and comparison with model

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.

Issues and Perspectives in Species Delimitation using Phenotypic Data: Atlantean Evolution in Darwin's Finches.

PubMed

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.

Non-local competition drives both rapid divergence and prolonged stasis in a model of speciation in populations with degenerate resource consumption

PubMed Central

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

Biogeography and speciation of terrestrial fauna in the south-western Australian biodiversity hotspot.

PubMed

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.

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.

Phylogenetics and biogeography of the two-wing flyingfish (Exocoetidae: Exocoetus).

PubMed

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.

Aqueous Speciation and Electrochemical Properties of a Water-Soluble Manganese Phthalocyanine Complex#

PubMed Central

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

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species.

PubMed

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.

Shock tube and chemical kinetic modeling study of the oxidation of 2,5-dimethylfuran.

PubMed

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.

New global fire emission estimates and evaluation of volatile organic compounds

Treesearch

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...

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.

Speciation driven by hybridization and chromosomal plasticity in a wild yeast.

PubMed

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.

Speciation in experimental C-O-H fluids produced by the thermal dissociation of oxalic acid dihydrate

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.

Speciation in experimental C-O-H fluids produced by the thermal dissociation of oxalic acid dihydrate

USGS Publications Warehouse

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.

Speciation in Drosophila: from phenotypes to molecules.

PubMed

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.

Molecular Phylogenetics and Temporal Diversification in the Genus Aeromonas Based on the Sequences of Five Housekeeping Genes

PubMed Central

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

How humans drive speciation as well as extinction

PubMed Central

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

How humans drive speciation as well as extinction.

PubMed

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).

Q-Speciation and Network Structure Evolution in Invert Calcium Silicate Glasses.

PubMed

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.

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 ...

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...

The Development and Uses of EPA's SPECIATE Database

EPA Science Inventory

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...

SPECIATION OF ORGANICS IN WATER

EPA Science Inventory

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....

July 2013 MOVES Model Review Work Group Meeting Materials

EPA Pesticide Factsheets

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.

September 2016 MOVES Model Review Work Group Meeting Materials

EPA Pesticide Factsheets

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.

The Drosophila flavopilosa species group (Diptera, Drosophilidae)

PubMed Central

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

Final Project Report: Release of aged contaminants from weathered sediments: Effects of sorbate speciation on scaling of reactive transport

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

Jon Chorover, University of Arizona; Peggy O'€™Day, 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

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

Investigation of uranium binding forms in selected German mineral waters.

PubMed

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.

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

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...

Performance of a Zerovalent Iron Reactive Barrier for the Treatment of Arsenic in Groundwater: Part 2. Geochemical Modeling and Solid Phase Studies

EPA Science Inventory

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...

Strategies to predict metal mobility in surficial mining environments

USGS Publications Warehouse

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.

WATEQF; a FORTRAN IV version of WATEQ : a computer program for calculating chemical equilibrium of natural waters

USGS Publications Warehouse

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)

Dissolved organic matter reduces CuO nanoparticle toxicity to duckweed in simulated natural systems.

PubMed

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.

Studying the genetic basis of speciation in high gene flow marine invertebrates

PubMed Central

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

EPA’s SPECIATE 4.4 Database - Development and Uses

EPA Science Inventory

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...

Cold Temperature Effects on Speciated VOC Emissions from modern GDI Light Duty Truck

EPA Science Inventory

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...

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 :...

Geography, assortative mating, and the effects of sexual selection on speciation with gene flow.

PubMed

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.

Ephemeral ecological speciation and the latitudinal biodiversity gradient.

PubMed

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.

Speciation by Symbiosis: the Microbiome and Behavior

PubMed Central

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

Speciation by Symbiosis: the Microbiome and Behavior.

PubMed

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.

Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach

PubMed Central

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

Divergent adaptation promotes reproductive isolation among experimental populations of the filamentous fungus Neurospora

PubMed Central

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

Speciation at the Mogollon Rim in the Arizona Mountain Kingsnake (Lampropeltis pyromelana).

PubMed

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.

Spatial and seasonal patterns in urban influence on regional concentrations of speciated aerosols across the United States

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.

Monoterpene chemical speciation in a tropical rainforest:variation with season, height, and time of dayat the Amazon Tall Tower Observatory (ATTO)

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.

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.

Soil-solution speciation of Cd as affected by soil characteristics in unpolluted and polluted soils.

PubMed

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.

The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua

PubMed Central

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

SPECIATION OF ORGANICS IN WATER WITH RAMAN SPECTROSCOPY: UTILITY OF IONIC STRENGTH VARIATION

EPA Science Inventory

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 ...

Quantifying Differences in the Impact of Variable Chemistry on Equilibrium Uranium(VI) Adsorption Properties of Aquifer Sediments

PubMed Central

2011-01-01

Uranium adsorption–desorption on sediment samples collected from the Hanford 300-Area, Richland, WA varied extensively over a range of field-relevant chemical conditions, complicating assessment of possible differences in equilibrium adsorption properties. Adsorption equilibrium was achieved in 500–1000 h although dissolved uranium concentrations increased over thousands of hours owing to changes in aqueous chemical composition driven by sediment-water reactions. A nonelectrostatic surface complexation reaction, >SOH + UO22+ + 2CO32- = >SOUO2(CO3HCO3)2–, provided the best fit to experimental data for each sediment sample resulting in a range of conditional equilibrium constants (logKc) from 21.49 to 21.76. Potential differences in uranium adsorption properties could be assessed in plots based on the generalized mass-action expressions yielding linear trends displaced vertically by differences in logKc values. Using this approach, logKc values for seven sediment samples were not significantly different. However, a significant difference in adsorption properties between one sediment sample and the fines (<0.063 mm) of another could be demonstrated despite the fines requiring a different reaction stoichiometry. Estimates of logKc uncertainty were improved by capturing all data points within experimental errors. The mass-action expression plots demonstrate that applying models outside the range of conditions used in model calibration greatly increases potential errors. PMID:21923109

Quantifying differences in the impact of variable chemistry on equilibrium Uranium(VI) adsorption properties of aquifer sediments.

PubMed

Stoliker, Deborah L; Kent, Douglas B; Zachara, John M

2011-10-15

Uranium adsorption-desorption on sediment samples collected from the Hanford 300-Area, Richland, WA varied extensively over a range of field-relevant chemical conditions, complicating assessment of possible differences in equilibrium adsorption properties. Adsorption equilibrium was achieved in 500-1000 h although dissolved uranium concentrations increased over thousands of hours owing to changes in aqueous chemical composition driven by sediment-water reactions. A nonelectrostatic surface complexation reaction, >SOH + UO₂²⁺ + 2CO₃²⁻ = >SOUO₂(CO₃HCO₃)²⁻, provided the best fit to experimental data for each sediment sample resulting in a range of conditional equilibrium constants (logK(c)) from 21.49 to 21.76. Potential differences in uranium adsorption properties could be assessed in plots based on the generalized mass-action expressions yielding linear trends displaced vertically by differences in logK(c) values. Using this approach, logK(c) values for seven sediment samples were not significantly different. However, a significant difference in adsorption properties between one sediment sample and the fines (< 0.063 mm) of another could be demonstrated despite the fines requiring a different reaction stoichiometry. Estimates of logK(c) uncertainty were improved by capturing all data points within experimental errors. The mass-action expression plots demonstrate that applying models outside the range of conditions used in model calibration greatly increases potential errors.

Field Evaluation Of Arsenic Speciation In Sediments At The Ground Water/Surface Water Interface

EPA Science Inventory

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...

Gas and liquid chromatography with inductively coupled plasma mass spectrometry detection for environmental speciation analysis — advances and limitations

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.

Living organisms as an alternative to hyphenated techniques for metal speciation. Evaluation of baker's yeast immobilized on silica gel for Hg speciation*1

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.

Uranium isotope fractionation induced by aqueous speciation: Implications for U isotopes in marine CaCO3 as a paleoredox proxy

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.

Unspeciated organic emissions from combustion sources and their influence on the secondary organic aerosol budget in the United States

PubMed Central

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

A plant-wide aqueous phase chemistry module describing pH variations and ion speciation/pairing in wastewater treatment process models.

PubMed

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.

Synchrotron-based P K-edge XANES spectroscopy reveals rapid changes of phosphorus speciation in the topsoil of two glacier foreland chronosequences

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).

Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata.

PubMed

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.

Unprecedented within-species chromosome number cline in the Wood White butterfly Leptidea sinapis and its significance for karyotype evolution and speciation

PubMed Central

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

Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes.

PubMed

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.

Pollinator-driven ecological speciation in plants: new evidence and future perspectives

PubMed Central

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

Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia

PubMed Central

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

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.

SPECIATION OF COMPLEX ORGANIC CONTAMINANTS IN WATER WITH RAMAN SPECTROSCOPY

EPA Science Inventory

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 ...

THERMODYNAMIC REACTION CONSTANTS FOR MODELING AQUEOUS ENVIRONMENTAL MERCURY SPECIATION

EPA Science Inventory

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...

Sexual selection drives speciation in an Amazonian frog

USGS Publications Warehouse

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.

Metals, Health and the Environment – Emergence of Correlations Between Speciation and Effects

PubMed Central

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

Source Apportionment Using Positive Matrix Factorization on Daily Measurements of Inorganic and Organic Speciated PM2.5

PubMed Central

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

Demonstrated Potential of Ion Mobility Spectrometry for Detection of Adulterated Perfumes and Plant Speciation

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

A thermodynamic model for the prediction of phase equilibria and speciation in the H 2O-CO 2-NaCl-CaCO 3-CaSO 4 system from 0 to 250 °C, 1 to 1000 bar with NaCl concentrations up to halite saturation

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.

Speciation gradients and the distribution of biodiversity.

PubMed

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.

New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds.

PubMed

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.

Ecological Impacts of Reverse Speciation in Threespine Stickleback.

PubMed

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.

Speciation and amphotericin B sensitivity studies on blood isolates of Candida from burned patients

PubMed Central

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

OPTIMIZATION OF MODERN DISPERSIVE RAMAN SPECTROMETERS FOR MOLECULAR SPECIATION OF ORGANICS IN WATER

EPA Science Inventory

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 --...

Approach of the Molten Salt Chemistry for Aluminium Production: High Temperature NMR Measurements, Molecular Dynamics and DFT Calculations

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.

Accelerated and Adaptive Evolution of Yeast Sexual Adhesins

PubMed Central

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

Estimating taxonomic diversity, extinction rates, and speciation rates from fossil data using capture-recapture models

USGS Publications Warehouse

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.

Phytoextraction of cadmium by Ipomoea aquatica (water spinach) in hydroponic solution: effects of cadmium speciation.

PubMed

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.

Relative Bioavailability and Bioaccessability and Speciation of ...

EPA Pesticide Factsheets

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

Climate adaptation and speciation: particular focus on reproductive barriers in Ficedula flycatchers.

PubMed

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.

Effects of sorbate speciation on sorption of selected sulfonamides in three loamy soils

USGS Publications Warehouse

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.

Heterostyly accelerates diversification via reduced extinction in primroses.

PubMed

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.

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.

The Robertsonian phenomenon in the house mouse: mutation, meiosis and speciation.

PubMed

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.

Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species.

PubMed

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).

Heterostyly accelerates diversification via reduced extinction in primroses

PubMed Central

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

Speciation and Bioavailability Measurements of Environmental Plutonium Using Diffusion in Thin Films.

PubMed

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.

Not a simple case - A first comprehensive phylogenetic hypothesis for the Midas cichlid complex in Nicaragua (Teleostei: Cichlidae: Amphilophus).

PubMed

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.

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

PubMed Central

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

[Effects of Low-Molecular-Weight Organic Acids on the Speciation of Pb in Purple Soil and Soil Solution].

PubMed

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.

The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua.

PubMed

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.

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.

Final Report, University of California Merced: Uranium and strontium fate in waste-weathered sediments: Scaling of molecular processes to predict reactive transport

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

Diversification in North American arid lands: niche conservatism, divergence and expansion of habitat explain speciation in the genus Ephedra.

PubMed

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.

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement.

PubMed

Duan, Naibin; Bai, Yang; Sun, Honghe; Wang, Nan; Ma, Yumin; Li, Mingjun; Wang, Xin; Jiao, Chen; Legall, Noah; Mao, Linyong; Wan, Sibao; Wang, Kun; He, Tianming; Feng, Shouqian; Zhang, Zongying; Mao, Zhiquan; Shen, Xiang; Chen, Xiaoliu; Jiang, Yuanmao; Wu, Shujing; Yin, Chengmiao; Ge, Shunfeng; Yang, Long; Jiang, Shenghui; Xu, Haifeng; Liu, Jingxuan; Wang, Deyun; Qu, Changzhi; Wang, Yicheng; Zuo, Weifang; Xiang, Li; Liu, Chang; Zhang, Daoyuan; Gao, Yuan; Xu, Yimin; Xu, Kenong; Chao, Thomas; Fazio, Gennaro; Shu, Huairui; Zhong, Gan-Yuan; Cheng, Lailiang; Fei, Zhangjun; Chen, Xuesen

2017-08-15

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 is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an "ancient" isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.Apple is one of the most important fruit crops. Here, the authors perform deep genome resequencing of 117 diverse accessions and reveal comprehensive models of apple origin, speciation, domestication, and fruit size evolution as well as candidate genes associated with important agronomic traits.

Zinc complexation in chloride-rich hydrothermal fluids (25-600 °C): A thermodynamic model derived from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël

2015-02-01

The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized gradient approximation for exchange-correlation. We caution, however, that simulations are mostly reliable at high T where ligand exchange is fast enough to yield thermodynamic averages over the timescales of the simulations.

Recent Developments in the Speciation and Determination of Mercury Using Various Analytical Techniques

PubMed Central

Suvarapu, Lakshmi Narayana; Baek, Sung-Ok

2015-01-01

This paper reviews the speciation and determination of mercury by various analytical techniques such as atomic absorption spectrometry, voltammetry, inductively coupled plasma techniques, spectrophotometry, spectrofluorometry, high performance liquid chromatography, and gas chromatography. Approximately 126 research papers on the speciation and determination of mercury by various analytical techniques published in international journals since 2013 are reviewed. PMID:26236539

Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest

Treesearch

Ryan R. Bracewell; Barbara J. Bentz; Brian T. Sullivan; Jeffrey M. Good

2017-01-01

Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine...

Presumptive speciation of Streptococcus bovis and other group D streptococci from human sources by using arginine and pyruvate tests.

PubMed Central

Gross, K C; Houghton, M P; Senterfit, L B

1975-01-01

A simplified method for speciation of group D streptococci is described. A total of 4,156 streptococcal isolates from human clinical material was tested for ability to hydrolyze esculin in the presence of 40% bile, ferment pyruvate, hydrolyze arginine, and grow in media containing 40% bile or 6.5% NaCl. Streptococci which hydrolyzed esculin in 40% bile, but which did not hydrolyze arginine, were also tested for their ability to ferment raffinose or sorbose. Sixty percent (2,503) of the isolates hydrolyzed esculin in the presence of 40% bile and were thus presumptively identified as group D. By application of the other criteria, 84% of these were speciated as Streptococcus faecalis, 7% were speciated as S. faecium, 6% were speciated as S. bovis, 2% were speciated as S. avium, and 1% were not identified. This scheme was shown to be both reliable and practical for use in the diagnostic laboratory. S. avium and S. bovis isolates were characterized, and 18 S. bovis isolates from patients with bacterial endocarditis were compared physiologically with 151 isolates of this species from other sources. PMID:1176592

Pleistocene phylogeographic effects on avian populations and the speciation process.

PubMed Central

Avise, J C; Walker, D

1998-01-01

Pleistocene biogeographic events have traditionally been ascribed a major role in promoting speciations and in sculpting the present-day diversity and distributions of vertebrate taxa. However, this paradigm has recently come under challenge from a review of interspecific mtDNA genetic distances in birds: most sister-species separations dated to the Pliocene. Here we summarize the literature on intraspecific mtDNA phylogeographic patterns in birds and reinterpret the molecular evidence bearing on Pleistocene influences. At least 37 of the 63 avian species surveyed (59%) are sundered into recognizable phylogeographic units, and 28 of these separations (76%) trace to the Pleistocene. Furthermore, use of phylogroup separation times within species as minimum estimates of 'speciation durations' also indicates that many protracted speciations, considered individually, probably extended through time from Pliocene origins to Pleistocene completions. When avian speciation is viewed properly as an extended temporal process rather than as a point event, Pleistocene conditions appear to have played an active role both in initiating major phylogeographic separations within species, and in completing speciations that had been inaugurated earlier. Whether the Pleistocene was exceptional in these regards compared with other geological times remains to be determined. PMID:9569664

Prevalence of disruptive selection predicts extent of species differentiation in Lake Victoria cichlids.

PubMed

van Rijssel, Jacco C; Moser, Florian N; Frei, David; Seehausen, Ole

2018-01-31

Theory suggests that speciation with gene flow is most likely when both sexual and ecological selection are divergent or disruptive. Divergent sexual and natural selection on the visual system have been demonstrated before in sympatric, morphologically similar sister species of Lake Victoria cichlids, but this does not explain the subtle morphological differences between them. To investigate the significance of natural selection on morphology during speciation, we here ask whether the prevalence of disruptive ecological selection differs between sympatric sister species that are at different stages of speciation. Some of our species pairs do ( Pundamilia ) and others do not ( Neochromis ) differ distinctively in sexually selected male nuptial coloration. We find that (i) evidence for disruptive selection, and for evolutionary response to it, is prevalent in traits that are differentiated between sister species; (ii) prevalence of both predicts the extent of genetic differentiation; and (iii) genetic differentiation is weaker in species pairs with conserved male nuptial coloration. Our results speak to the existence of two different mechanisms of speciation with gene flow: speciation mainly by sexual selection tightly followed by ecological character displacement in some cases and speciation mainly by divergent ecological selection in others. © 2018 The Author(s).

Comparative study of adaptive radiations with an example using parasitic flatworms (Platyhelminthes): Cercomeria

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

Brooks, D.R.; McLennan, D.A.

1993-11-01

Studies of adaptive radiations require robust phylogenies, estimates of species numbers for monophyletic groups within clades, assessments of the adaptive value of putative key innovations, and estimates of the frequency of speciation modes. Four criteria are necessary to identify an adaptive radiation within the parasitic platyhelminths: (1) a group contains significantly more species than its sister group, (2) species richness is apomorphic, (3) apomorphic traits enhance the potential for adaptively driven modes of speciation (sympatric speciation and speciation by peripheral isolation via host switching), and (4) the frequency of adaptively driven speciation modes is high within the group when comparedmore » with data from free-living groups. Only the species-rich Monogenea fulfill all four criteria. The Digenea and Eucestoda also are more species rich than their sister groups, their species richness is derived, and they possess unique characters that increase the potential for host switching to occur. However, because there is not enough information to determine whether the frequency of adaptive modes of speciation is high for those groups, we cannot yet assert that their radiations have been adaptive. 102 refs., 3 figs., 1 tab.« less

OPTIMIZATION OF RAMAN SPECTROSCOPY FOR SPECIATION OF ORGANICS IN WATER

EPA Science Inventory

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. Spectra a...

Arsenic Metabolism by Human Gut Microbiota upon in Vitro Digestion of Contaminated Soils

EPA Science Inventory

Speciation analysis is essential when evaluating risks from, arsenic (As) exposure. In an oral exposure scenario, the importance of presystemic metabolism by gut microorganisms has been evidenced with in vivo animal models and in vitro experiments with animal microbiota. Howeve...

Interactions between hydrated cement paste and organic acids: Thermodynamic data and speciation modeling

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

De Windt, Laurent, E-mail: laurent.dewindt@mines-paristech.fr; Bertron, Alexandra; Larreur-Cayol, Steeves

2015-03-15

Interactions of short-chain organic acids with hydrated cement phases affect structure durability in the agro-food and nuclear waste industries but can also be used to modify cement properties. Most previous studies have been experimental, performed at fixed concentrations and pH, without quantitatively discriminating among polyacidity effects, or complexation and salt precipitation processes. This paper addresses such issues by thermodynamic equilibrium calculations for acetic, citric, oxalic, succinic acids and a simplified hydrated CEM-I. The thermodynamic constants collected from the literature allow the speciation to be modeled over a wide range of pH and concentrations. Citric and oxalic had a stronger chelatingmore » effect than acetic acid, while succinic acid was intermediate. Similarly, Ca-citrate and Ca-oxalate salts were more insoluble than Ca-acetate and Ca-succinate salts. Regarding aluminium complexation, hydroxyls, sulfates, and acid competition was highlighted. The exploration of acid mixtures showed the preponderant effect of oxalate and citrate over acetate and succinate.« less

Limited by the roof of the world: mountain radiations of Apollo swallowtails controlled by diversity-dependence processes.

PubMed

Condamine, Fabien L

2018-03-01

Mountainous areas contain a substantial part of the world species richness, but the evolutionary origins and diversification of this biodiversity remain elusive. Diversification may result from differences in clade age (longer time to diversify), net diversification rates (faster speciation rate) or carrying capacities (number of niches). The likelihood of these macroevolutionary scenarios was assessed for six clades of Apollo swallowtails ( Parnassius ) that diversified mainly in the Himalayan-Tibetan region. The analyses suggest that neither the clade age nor the speciation rate could explain the mountain butterfly diversification. Instead diversity-dependence models were strongly supported for each group. Models further estimated clades' carrying capacities, which approximate to the current number of species, indicating that diversity equilibrium has been reached (or close to being reached). The results suggest that diversification of mountain butterflies was controlled by ecological limits, which governed the number of niches, and provide macroevolutionary justification for regarding mountains as islands. © 2018 The Author(s).

Geological and climatic forces driving speciation in the continentally distributed trilling chorus frogs (Pseudacris).

PubMed

Lemmon, Emily Moriarty; Lemmon, Alan R; Cannatella, David C

2007-09-01

Tertiary geological events and Quaternary climatic fluctuations have been proposed as important factors of speciation in the North American flora and fauna. Few studies, however, have rigorously tested hypotheses regarding the specific factors driving divergence of taxa. Here, we test explicit speciation hypotheses by correlating geologic events with divergence times among species in the continentally distributed trilling chorus frogs (Pseudacris). In particular, we ask whether marine inundation of the Mississippi Embayment, uplift of the Appalachian Mountains, or modification of the ancient Teays-Mahomet River system contributed to speciation. To examine the plausibility of ancient rivers causing divergence, we tested whether modern river systems inhibit gene flow. Additionally, we compared the effects of Quaternary climatic factors (glaciation and aridification) on levels of genetic variation. Divergence time estimates using penalized likelihood and coalescent approaches indicate that the major lineages of chorus frogs diversified during the Tertiary, and also exclude Quaternary climate change as a factor in speciation of chorus frogs. We show the first evidence that inundation of the Mississippi Embayment contributed to speciation. We reject the hypotheses that Cenozoic uplift of the Appalachians and that diversion of the Teays-Mahomet River contributed to speciation in this clade. We find that by reducing gene flow, rivers have the potential to cause divergence of lineages. Finally, we demonstrate that populations in areas affected by Quaternary glaciation and aridification have reduced levels of genetic variation compared to those from more equable regions, suggesting recent colonization.

Uptake of elements from seawater by ferromanganese crusts: Solid-phase associations and seawater speciation

USGS Publications Warehouse

Koschinsky, A.; Hein, J.R.

2003-01-01

Marine Fe-Mn oxyhydroxide crusts form by precipitation of dissolved components from seawater. Three hydrogenetic crust samples (one phosphatized) and two hydrothermal Mn-oxide samples were subjected to a sequential-leaching procedure in order to determine the host phases of 40 elements. Those host-phase associations are discussed with respect to element speciation in seawater. The partitioning of elements between the two major phases, Mn oxide and Fe oxyhydroxide, can in a first-order approximation be explained by a simple sorption model related to the inorganic speciation of the elements in seawater, as has been proposed in earlier models. Free and weakly complexed cations, such as alkali and alkaline earth metals, Mn, Co, Ni, Zn, T1(I), and partly Y, are sorbed preferentially on the negatively charged surface of the MnO2 in hydrogenetic crusts. The driving force is a strong coulombic interaction. All neutral or negatively charged chloro (Cd, Hg, T1), carbonate (Cu, Y, Pb, and U), and hydroxide (Be, Sc, Ti, Fe, Zr, Nb, In, Sn, Sb, Te, Hf, Ta, Bi, Th, and T1(III)) complexes and oxyanions (V, Cr, As, Se, Mo, and W) bind to the slightly positively charged surface of the amorphous FeOOH phase. While coulombic interaction can explain the sorption of the negatively charged species, the binding of neutral species is based on specific chemical interaction. Organic complexation of elements in deep-ocean water seems to be at most of minor importance. Surface oxidation can explain some strong metal associations, e.g. of Co and T1 with the MnO2 and Te with the FeOOH. Sorption reactions initially driven by coulombic forces are often followed by the formation of specific bonds between the adsorbate and the atoms of the oxide surface. Differences in the associations of some metals between the non-phosphatized and phosphatized hydrogenetic crusts and between the hydrogenetic and the hydrothermal samples reflect the different physico-chemical environments of formation and speciations in oxic seawater vs. less-oxic fluids, especially for the redox-sensitive metals such as Mo and V. These environmental-related differences indicate that the methodology of chemical speciation used here in combination with spectroscopic methods may allow for the detection of changes in paleoceanographic conditions recorded during the several tens of millions of years of crust growth. ?? 2003 Elsevier Science B.V. All rights reserved.

Detailed Modelling of Kinetic Biodegradation Processes in a Laboratory Mmicrocosm

NASA Astrophysics Data System (ADS)

Watson, I.; Oswald, S.; Banwart, S.; Mayer, U.

2003-04-01

Biodegradation of organic contaminants in soil and groundwater usually takes places via different redox processes happening sequentially as well as simultaneously. We used numerical modelling of a long-term lab microcosm experiment to simulate the dynamic behaviour of fermentation and respiration in the aqueous phase in contact with the sandstone material, and to develop a conceptual model describing these processes. Aqueous speciation, surface complexation, mineral dissolution and precipitation were taken into account also. Fermentation can be the first step of the degradation process producing intermediate species, which are subsequently consumed by TEAPs. Microbial growth and substrate utilisation kinetics are coupled via a formulation that also includes aqueous speciation and other geochemical reactions including surface complexation, mineral dissolution and precipitation. Competitive exclusion between TEAPs is integral to the conceptual model of the simulation, and the results indicate that exclusion is not complete, but some overlap is found between TEAPs. The model was used to test approaches like the partial equilibrium approach that currently make use of hydrogen levels to diagnose prevalent TEAPs in groundwater. The observed pattern of hydrogen and acetate concentrations were reproduced well by the simulations, and the results show the relevance of kinetics, lag times and inhibition, and especially that intermediate products play a key role.

A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution.

PubMed

Blanquart, Samuel; Lartillot, Nicolas

2006-11-01

Variations of nucleotidic composition affect phylogenetic inference conducted under stationary models of evolution. In particular, they may cause unrelated taxa sharing similar base composition to be grouped together in the resulting phylogeny. To address this problem, we developed a nonstationary and nonhomogeneous model accounting for compositional biases. Unlike previous nonstationary models, which are branchwise, that is, assume that base composition only changes at the nodes of the tree, in our model, the process of compositional drift is totally uncoupled from the speciation events. In addition, the total number of events of compositional drift distributed across the tree is directly inferred from the data. We implemented the method in a Bayesian framework, relying on Markov Chain Monte Carlo algorithms, and applied it to several nucleotidic data sets. In most cases, the stationarity assumption was rejected in favor of our nonstationary model. In addition, we show that our method is able to resolve a well-known artifact. By Bayes factor evaluation, we compared our model with 2 previously developed nonstationary models. We show that the coupling between speciations and compositional shifts inherent to branchwise models may lead to an overparameterization, resulting in a lesser fit. In some cases, this leads to incorrect conclusions, concerning the nature of the compositional biases. In contrast, our compound model more flexibly adapts its effective number of parameters to the data sets under investigation. Altogether, our results show that accounting for nonstationary sequence evolution may require more elaborate and more flexible models than those currently used.

Determining Spatial Variability in PM2.5 Source Impacts across Detroit, MI

EPA Science Inventory

Intra-urban variability in air pollution source impacts was investigated using receptor modeling of daily speciated PM_2.5 measurements collected at residential outdoor locations across Detroit, MI (Wayne County) as part of the Detroit Exposure and Aerosol Research Stud...

SOILSOLN: A Program for Teaching Equilibria Modeling of Soil Solution Composition.

ERIC Educational Resources Information Center

Wolt, Jeffrey D.

1989-01-01

Presents a computer program for use in teaching ion speciation in soil solutions. Provides information on the structure of the program, execution, and software specifications. The program estimates concentrations of ion pairs, hydrolytic species, metal-organic complexes, and free ions in solutions. (Author/RT)

Arsenic Metabolism by Human Gut Microbiota upon In Vitro Digestion of Contaminated Soils

EPA Science Inventory

Background: Speciation analysis is essential when evaluating risks from arsenic (As) exposure. In an oral exposure scenario, the importance of presystemic metabolism by gut microorganisms has been evidenced with in vivo animal models and in vitro experiments with ...

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

PubMed Central

Nadachowska-Brzyska, Krystyna; Burri, Reto; Olason, Pall I.; Kawakami, Takeshi; Smeds, Linnéa; Ellegren, Hans

2013-01-01

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000–80,000) and census sizes (5–50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species. PMID:24244198

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data.

PubMed

Nadachowska-Brzyska, Krystyna; Burri, Reto; Olason, Pall I; Kawakami, Takeshi; Smeds, Linnéa; Ellegren, Hans

2013-11-01

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000-80,000) and census sizes (5-50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.

Theoretical estimation of equilibrium sulfur isotope fractionations among aqueous sulfite species: Implications for isotope models of microbial sulfate reduction

NASA Astrophysics Data System (ADS)

Eldridge, D. L.; Farquhar, J.; Guo, W.

2015-12-01

Sulfite (sensu lato), an intermediate in a variety sulfur redox processes, plays a particularly important role in microbial sulfate reduction. It exists intracellularly as multiple species between sets of enzymatic reactions that transform sulfate to sulfide, with the exact speciation depending on pH, T, and ionic strength. However, the complex speciation of sulfite is ignored in current isotope partitioning models of microbial sulfate reduction and simplified solely to the pyramidal SO32- (sulfite sensu stricto), due to a lack of appropriate constraints. We theoretically estimated the equilibrium sulfur isotope fractionations (33S/32S, 34S/32S, 36S/32S) among all documented sulfite species in aqueous solution, including sulfite (SO32-), bisulfite isomers and dimers ((HS)O3-, (HO)SO2-, S2O52-), and SO2(aq), through first principles quantum mechanical calculations. The calculations were performed at B3LYP/6-31+G(d,p) level using cluster models with 30-40 water molecules surrounding the solute. Our calculated equilibrium fractionation factors compare well to the available experimental constraints and suggest that the minor and often-ignored tetrahedral (HS)O3- isomer of bisulfite strongly influences isotope partitioning behavior in the sulfite system under most environmentally relevant conditions, particularly fractionation magnitudes and unusual temperature dependence. For example, we predict that sulfur isotope fractionation between sulfite and bulk bisulfite in solution should have an apparent inverse temperature dependence due to the influence of (HS)O3- and its increased stability at higher temperatures. Our findings highlight the need to appropriately account for speciation/isomerization of sulfur species in sulfur isotope studies. We will also present similar calculation results of other aqueous sulfur compounds (e.g., H2S/HS-, SO42-, S2O32-, S3O62-, and poorly documented SO22- species), and discuss the implication of our results for microbial sulfate reduction models and other sulfur-redox processes in nature.

'Geo'chemical research: a key building block for nuclear waste disposal safety cases.

PubMed

Altmann, Scott

2008-12-12

Disposal of high level radioactive waste in deep underground repositories has been chosen as solution by several countries. Because of the special status this type waste has in the public mind, national implementation programs typically mobilize massive R&D efforts, last decades and are subject to extremely detailed and critical social-political scrutiny. The culminating argument of each program is a 'Safety Case' for a specific disposal concept containing, among other elements, the results of performance assessment simulations whose object is to model the release of radionuclides to the biosphere. Public and political confidence in performance assessment results (which generally show that radionuclide release will always be at acceptable levels) is based on their confidence in the quality of the scientific understanding in the processes included in the performance assessment model, in particular those governing radionuclide speciation and mass transport in the geological host formation. Geochemistry constitutes a core area of research in this regard. Clay-mineral rich formations are the subjects of advanced radwaste programs in several countries (France, Belgium, Switzerland...), principally because of their very low permeabilities and demonstrated capacities to retard by sorption most radionuclides. Among the key processes which must be represented in performance assessment models are (i) radioelement speciation (redox state, speciation, reactions determining radionuclide solid-solution partitioning) and (ii) diffusion-driven transport. The safety case must therefore demonstrate a detailed understanding of the physical-chemical phenomena governing the effects of these two aspects, for each radionuclide, within the geological barrier system. A wide range of coordinated (and internationally collaborated) research has been, and is being, carried out in order to gain the detailed scientific understanding needed for constructing those parts of the Safety Case supporting how radionuclide transfer is represented in the performance assessment model. The objective here is to illustrate how geochemical research contributes to this process and, above all, to identify a certain number of subjects which should be treated in priority.

Great Salt Lake Composition and Rare Earth Speciation Analysis

DOE Data Explorer

Jiao, Yongqin; Lammers, Laura; Brewer, Aaron

2017-04-19

We have conducted aqueous speciation analyses of the Great Salt Lake (GSL) brine sample (Table 1) and a mock geo sample (Table 2) spiked with 1 ppb Tb and 100 ppb Tb. The GSL speciation (Figure 1) aligns with our basic speciation expectations that strong carbonate complexes would form at mid to higher pH's. Although we expected strong aqueous complexes with fluorides at neutral pH and with chlorides, and hydroxides at low pH, we observe that the dominant species in the low to mid pH range to be Tb3+ as a free ion. Still, we do see the presence of fluoride and chloride complexes within the expected low to mid pH range.

Arsenic, Antimony, Chromium, and Thallium Speciation in Water and Sediment Samples with the LC-ICP-MS Technique

PubMed Central

Jabłońska-Czapla, Magdalena

2015-01-01

Chemical speciation is a very important subject in the environmental protection, toxicology, and chemical analytics due to the fact that toxicity, availability, and reactivity of trace elements depend on the chemical forms in which these elements occur. Research on low analyte levels, particularly in complex matrix samples, requires more and more advanced and sophisticated analytical methods and techniques. The latest trends in this field concern the so-called hyphenated techniques. Arsenic, antimony, chromium, and (underestimated) thallium attract the closest attention of toxicologists and analysts. The properties of those elements depend on the oxidation state in which they occur. The aim of the following paper is to answer the question why the speciation analytics is so important. The paper also provides numerous examples of the hyphenated technique usage (e.g., the LC-ICP-MS application in the speciation analysis of chromium, antimony, arsenic, or thallium in water and bottom sediment samples). An important issue addressed is the preparation of environmental samples for speciation analysis. PMID:25873962

Transformation of heavy metal speciation during sludge drying: mechanistic insights

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

Weng, Huanxin; Ma, Xue-Wen; Fu, Feng-Xia

2014-01-30

Speciation can fundamentally affect on the stability and toxicity of heavy metals in sludge from wastewater treatment plants. This research investigated the speciation of heavy metals in sludge from both municipal and industrial sources, and metal speciation change as a result of drying process to reduce sludge volume. The changes in sludge properties including sludge moisture content, temperature, density, and electrical conductivity were also monitored to provide insights into the mechanisms causing the change in heavy metal speciation. The results show that the drying process generally stabilized the Cr, Cu, Cd and Pb in sludge by transforming acid-soluble, reducible andmore » oxidizable species into structurally stable forms. Such transformation and stabilization occurred regardless of the sludge source and type, and were primarily caused by the changes in sludge properties associated with decomposition of organic matter and sulfide. The results enhanced our understanding of the geochemical behavior of heavy metals in municipal sludge, and are useful for designing a treatment system for environment-friendly disposal of sludge.« less

Multielemental speciation analysis by advanced hyphenated technique - HPLC/ICP-MS: A review.

PubMed

Marcinkowska, Monika; Barałkiewicz, Danuta

2016-12-01

Speciation analysis has become an invaluable tool in human health risk assessment, environmental monitoring or food quality control. Another step is to develop reliable multielemental speciation methodologies, to reduce costs, waste and time needed for the analysis. Separation and detection of species of several elements in a single analytical run can be accomplished by high performance liquid chromatography hyphenated to inductively coupled plasma mass spectrometry (HPLC/ICP-MS). Our review assembles articles concerning multielemental speciation determination of: As, Se, Cr, Sb, I, Br, Pb, Hg, V, Mo, Te, Tl, Cd and W in environmental, biological, food and clinical samples analyzed with HPLC/ICP-MS. It addresses the procedures in terms of following issues: sample collection and pretreatment, selection of optimal conditions for elements species separation by HPLC and determination using ICP-MS as well as metrological approach. The presented work is the first review article concerning multielemental speciation analysis by advanced hyphenated technique HPLC/ICP-MS. Copyright © 2016 Elsevier B.V. All rights reserved.

Biodegradation and speciation of residual SS-ethylenediaminedisuccinic acid (EDDS) in soil solution left after soil washing.

PubMed

Tandy, Susan; Ammann, Adrian; Schulin, Rainer; Nowack, Bernd

2006-07-01

This paper aims to investigate the degradation and speciation of EDDS-complexes (SS-ethylenediaminedisuccinic acid) in soil following soil washing. The changes in soil solution metal and EDDS concentrations were investigated for three polluted soils. EDDS was degraded after a lag phase of 7-11 days with a half-life of 4.18-5.60 days. No influence of EDDS-speciation on the reaction was observed. The decrease in EDDS resulted in a corresponding decrease in solubilized metals. Changes in EDDS speciation can be related to (1) initial composition of the soil, (2) temporarily anoxic conditions in the soil slurry after soil washing, (3) exchange of EDDS complexes with Cu even in soils without elevated Cu and (4) formation of NiEDDS. Dissolved organic matter is important for metal speciation at low EDDS concentrations. Our results show that even in polluted soils EDDS is degraded from a level of several hundred micromoles to below 1 microM within 50 days.

Genomic islands of divergence are not affected by geography of speciation in sunflowers.

PubMed

Renaut, S; Grassa, C J; Yeaman, S; Moyers, B T; Lai, Z; Kane, N C; Bowers, J E; Burke, J M; Rieseberg, L H

2013-01-01

Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert

PubMed Central

Luebert, Federico; Jacobs, Pit; Hilger, Hartmut H; Muller, Ludo A H

2014-01-01

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (FST = 0.35), and FST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times. PMID:24558582

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert.

PubMed

Luebert, Federico; Jacobs, Pit; Hilger, Hartmut H; Muller, Ludo A H

2014-02-01

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (F ST = 0.35), and F ST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.

Song evolution, speciation, and vocal learning in passerine birds.

PubMed

Mason, Nicholas A; Burns, Kevin J; Tobias, Joseph A; Claramunt, Santiago; Seddon, Nathalie; Derryberry, Elizabeth P

2017-03-01

Phenotypic divergence can promote reproductive isolation and speciation, suggesting a possible link between rates of phenotypic evolution and the tempo of speciation at multiple evolutionary scales. To date, most macroevolutionary studies of diversification have focused on morphological traits, whereas behavioral traits─including vocal signals─are rarely considered. Thus, although behavioral traits often mediate mate choice and gene flow, we have a limited understanding of how behavioral evolution contributes to diversification. Furthermore, the developmental mode by which behavioral traits are acquired may affect rates of behavioral evolution, although this hypothesis is seldom tested in a phylogenetic framework. Here, we examine evidence for rate shifts in vocal evolution and speciation across two major radiations of codistributed passerines: one oscine clade with learned songs (Thraupidae) and one suboscine clade with innate songs (Furnariidae). We find that evolutionary bursts in rates of speciation and song evolution are coincident in both thraupids and furnariids. Further, overall rates of vocal evolution are higher among taxa with learned rather than innate songs. Taken together, these findings suggest an association between macroevolutionary bursts in speciation and vocal evolution, and that the tempo of behavioral evolution can be influenced by variation in developmental modes among lineages. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

REE speciation in low-temperature acidic waters and the competitive effects of aluminum

USGS Publications Warehouse

Gimeno, Serrano M.J.; Auque, Sanz L.F.; Nordstrom, D. Kirk

2000-01-01

The effect of simultaneous competitive speciation of dissolved rare earth elements (REEs) in acidic waters (pH 3.3 to 5.2) has been evaluated by applying the PHREEQE code to the speciation of water analyses from Spain, Brazil, USA, and Canada. The main ions that might affect REE are Al3+, F-, SO42-, and PO43-. Fluoride, normally a significant complexer of REEs, is strongly associated with Al3+ in acid waters and consequently has little influence on REEs. The inclusion of aluminum concentrations in speciation calculations for acidic waters is essential for reliable speciation of REEs. Phosphate concentrations are too low (10-4 to 10-7 m) to affect REE speciation. Consequently, SO42- is the only important complexing ligand for REEs under these conditions. According to Millero [Millero, F.J., 1992. Stability constants for the formation of rare earth inorganic complexes as a function of ionic strength. Geochim. Cosmochim. Acta, 56, 3123-3132], the lanthanide sulfate stability constants are nearly constant with increasing atomic number so that no REE fractionation would be anticipated from aqueous complexation in acidic waters. Hence, REE enrichments or depletions must arise from mass transfer reactions. (C) 2000 Elsevier Science B.V. All rights reserved.

Primate diversification inferred from phylogenies and fossils.

PubMed

Herrera, James P

2017-12-01

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana

PubMed Central

MacLeod, Amy; Rodríguez, Ariel; Vences, Miguel; Orozco-terWengel, Pablo; García, Carolina; Trillmich, Fritz; Gentile, Gabriele; Caccone, Adalgisa; Quezada, Galo; Steinfartz, Sebastian

2015-01-01

The effects of the direct interaction between hybridization and speciation—two major contrasting evolutionary processes—are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within-island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50 000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island—ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole. PMID:26041359

Bromine speciation in hydrous haplogranitic melts up to 7 GPa

NASA Astrophysics Data System (ADS)

Cochain, B.; de Grouchy, C.; Crepisson, C.; Kantor, I.; Irifune, T.; Sanloup, C.

2013-12-01

Halogens are minor volatiles in the Earth's mantle and crust, but they have significant and specific influences on magmatic and degassing processes. They also provide insights about subsurface magma movement and eruption likelihood in subduction-related volcanism. Their speciation in silicate melts affects volatile exsolution, rheology, and the thermodynamic properties of the melts but still remains relatively unknown. A few studies have explored halogen speciation at room conditions, i.e. in glasses but no firm conclusion has yet been reached. Furthermore, halogen speciation remains unexplored at high pressures and temperatures. In this work we investigate the speciation of Br in subduction-related melt (hydrous haplogranite melt) up to 1200°C and 7 GPa using X-ray absorption spectroscopy (XANES and EXAFS) at the Br K-edge. High P-T conditions were generated by the Paris-Edinburgh press. The use of nanocrystalline diamond capsules enabled us to avoid glitches in the EXAFS spectra. The results provide valuable information on Br speciation and its evolution with pressure. It gives insights into solubility mechanisms for halogens in magmas at depth and on their degassing from the melt. In addition, we were able to identify quench effects on the atomic environment of Br by comparison of high P-T in-situ spectra and ex-situ spectra recorded on quenched samples.

Speciation on a local geographic scale: the evolution of a rare rock outcrop specialist in Mimulus.

PubMed

Ferris, Kathleen G; Sexton, Jason P; Willis, John H

2014-08-05

Speciation can occur on both large and small geographical scales. In plants, local speciation, where small populations split off from a large-ranged progenitor species, is thought to be the dominant mode, yet there are still few examples to verify speciation has occurred in this manner. A recently described morphological species in the yellow monkey flowers, Mimulus filicifolius, is an excellent candidate for local speciation because of its highly restricted geographical range. Mimulus filicifolius was formerly identified as a population of M. laciniatus due to similar lobed leaf morphology and rocky outcrop habitat. To investigate whether M. filicifolius is genetically divergent and reproductively isolated from M. laciniatus, we examined patterns of genetic diversity in ten nuclear and eight microsatellite loci, and hybrid fertility in M. filicifolius and its purported close relatives: M. laciniatus, M. guttatus and M. nasutus. We found that M. filicifolius is genetically divergent from the other species and strongly reproductively isolated from M. laciniatus. We conclude that M. filicifolius is an independent rock outcrop specialist despite being morphologically and ecologically similar to M. laciniatus, and that its small geographical range nested within other wide-ranging members of the M. guttatus species complex is consistent with local speciation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

The single species hypothesis: truly dead and pushing up bushes, or still twitching and ripe for resuscitation?

PubMed

Hunt, Kevin D

2003-08-01

Frank Livingstone proclaims himself to be the last living proponent of the single species hypothesis. In sharp contrast, a species-rich, bushy phylogeny is favored by most human paleontologists. Is Livingstone's proclamation merely contrarian posturing, or does closer inspection warrant reconsideration of just how speciose the hominin lineage is? The high-speciation perspective draws on evidence of speciosity in the Cercopithecoidea and punctuated equilibria theory for support. If blue monkeys and redtail monkeys are indistinguishable skeletally, this reasoning goes, or if red colobus and black and white colobus are likewise indistinguishable, should we not expect that there are more species of hominin than is apparent from skeletal evidence alone? A contrarian perspective notes that not all monkey taxa are speciose. Importantly, two broadly distributed, partly terrestrial monkeys have not speciated at all: vervets and baboons. Nor are monkeys the first choice as a hominin speciation model. If expectations of species numbers are based on the Hominoidea, a taxon more closely related to hominins, more similar in body size, and found in more hominin-like habitats than monkeys, a single-species perspective is more appealing. No great ape genus has even two sympatric species. Moreover, despite a separation of 1.6 Ma, West African chimpanzees have not speciated from Pt. troglodytes nor Pt. schweinfurthii. It is notable that no two contemporaneous species of hominin were separated by significantly more than this interval. A biological--as opposed to an ecological or geographical--species definition would place all hominins in a single, phenotypically diverse species. Since divergence from the chimpanzee, "species" distinctness in hominins may have been maintained by temporary allopatry and centripetal niche separation. The hominin lineage may have evolved as a single, phenotypically diverse, reticulately evolving species.

Multiscale Speciation of U and Pu at Chernobyl, Hanford, Los Alamos, McGuire AFB, Mayak, and Rocky Flats.

PubMed

Batuk, Olga N; Conradson, Steven D; Aleksandrova, Olga N; Boukhalfa, Hakim; Burakov, Boris E; Clark, David L; Czerwinski, Ken R; Felmy, Andrew R; Lezama-Pacheco, Juan S; Kalmykov, Stepan N; Moore, Dean A; Myasoedov, Boris F; Reed, Donald T; Reilly, Dallas D; Roback, Robert C; Vlasova, Irina E; Webb, Samuel M; Wilkerson, Marianne P

2015-06-02

The speciation of U and Pu in soil and concrete from Rocky Flats and in particles from soils from Chernobyl, Hanford, Los Alamos, and McGuire Air Force Base and bottom sediments from Mayak was determined by a combination of X-ray absorption fine structure (XAFS) spectroscopy and X-ray fluorescence (XRF) element maps. These experiments identify four types of speciation that sometimes may and other times do not exhibit an association with the source terms and histories of these samples: relatively well ordered PuO2+x and UO2+x that had equilibrated with O2 and H2O under both ambient conditions and in fires or explosions; instances of small, isolated particles of U as UO2+x, U3O8, and U(VI) species coexisting in close proximity after decades in the environment; alteration phases of uranyl with other elements including ones that would not have come from soils; and mononuclear Pu-O species and novel PuO2+x-type compounds incorporating additional elements that may have occurred because the Pu was exposed to extreme chemical conditions such as acidic solutions released directly into soil or concrete. Our results therefore directly demonstrate instances of novel complexity in the Å and μm-scale chemical speciation and reactivity of U and Pu in their initial formation and after environmental exposure as well as occasions of unexpected behavior in the reaction pathways over short geological but significant sociological times. They also show that incorporating the actual disposal and site conditions and resultant novel materials such as those reported here may be necessary to develop the most accurate predictive models for Pu and U in the environment.

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

PubMed

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

2018-01-01

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

Phenotypic disparity in Iberian short-horned grasshoppers (Acrididae): the role of ecology and phylogeny.

PubMed

García-Navas, Vicente; Noguerales, Víctor; Cordero, Pedro J; Ortego, Joaquín

2017-05-04

The combination of model-based comparative techniques, disparity analyses and ecomorphological correlations constitutes a powerful method to gain insight into the evolutionary mechanisms that shape morphological variation and speciation processes. In this study, we used a time-calibrated phylogeny of 70 Iberian species of short-horned grasshoppers (Acrididae) to test for patterns of morphological disparity in relation to their ecology and phylogenetic history. Specifically, we examined the role of substrate type and level of ecological specialization in driving different aspects of morphological evolution (locomotory traits, chemosensitive organs and cranial morphology) in this recent radiation. We found a bimodal distribution of locomotory attributes corresponding to the two main substrate type guilds (plant vs. ground); plant-perching species tend to exhibit larger wings and thicker femora than those that remain on the ground. This suggests that life form (i.e., substrate type) is an important driving force in the evolution of morphological traits in short-horned grasshoppers, irrespective of ancestry. Substrate type and ecological specialization had no significant influence on head shape, a trait that showed a strong phylogenetic conservatism. Finally, we also found a marginal significant association between the length of antennae and the level of ecological specialization, suggesting that the development of sensory organs may be favored in specialist species. Our results provide evidence that even in taxonomic groups showing limited morphological and ecological disparity, natural selection seems to play a more important role than genetic drift in driving the speciation process. Overall, this study suggests that morphostatic radiations should not necessarily be considered as "non-adaptive" and that the speciation process can bind both adaptive divergence mechanisms and neutral speciation processes related with allopatric and/or reproductive isolation.

Pleistocene climate change promoted rapid diversification of aquatic invertebrates in Southeast Australia

PubMed Central

2012-01-01

Background The Pleistocene Ice Ages were the most recent geohistorical event of major global impact, but their consequences for most parts of the Southern hemisphere remain poorly known. We investigate a radiation of ten species of Sternopriscus, the most species-rich genus of epigean Australian diving beetles. These species are distinct based on genital morphology but cannot be distinguished readily by mtDNA and nDNA because of genotype sharing caused by incomplete lineage sorting. Their genetic similarity suggests a Pleistocene origin. Results We use a dataset of 3858 bp of mitochondrial and nuclear DNA to reconstruct a phylogeny of Sternopriscus using gene and species trees. Diversification analyses support the finding of a recent rapid speciation event with estimated speciation rates of up to 2.40 species per MY, which is considerably higher than the proposed average rate of 0.16 species per MY for insects. Additionally, we use ecological niche modeling and analyze data on habitat preferences to test for niche divergence between species of the recent Sternopriscus radiation. These analyses show that the species can be characterized by a set of ecological variables referring to habitat, climate and altitude. Conclusions Our results suggest that the repeated isolation of populations in glacial refugia might have led to divergent ecological adaptations and the fixation of morphological traits supporting reproductive isolation and therefore may have promoted speciation. The recent Sternopriscus radiation fulfills many characteristics of a species flock and would be the first described example of an aquatic insect species flock. We argue that the species of this group may represent a stage in speciation past the species flock condition because of their mostly broad and often non-overlapping ranges and preferences for different habitat types. PMID:22873814

The Phylogeny and Biogeographic History of Ashes (Fraxinus, Oleaceae) Highlight the Roles of Migration and Vicariance in the Diversification of Temperate Trees

PubMed Central

Hinsinger, Damien Daniel; Basak, Jolly; Gaudeul, Myriam; Cruaud, Corinne; Bertolino, Paola; Frascaria-Lacoste, Nathalie; Bousquet, Jean

2013-01-01

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees. PMID:24278282

The phylogeny and biogeographic history of ashes (fraxinus, oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees.

PubMed

Hinsinger, Damien Daniel; Basak, Jolly; Gaudeul, Myriam; Cruaud, Corinne; Bertolino, Paola; Frascaria-Lacoste, Nathalie; Bousquet, Jean

2013-01-01

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.

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.

Charging Properties of Cassiterite (alpha-SnO2) surfaces in NaCl and RbCl Ionic Media.

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

Rosenqvist, Jorgen K; Machesky, Michael L.; Vlcek, Lukas

2009-01-01

The acid-base properties of cassiterite (alpha-SnO2) surfaces at 10-50 degrees C were studied using potentiometric titrations of powder suspensions in aqueous NaCl and RbCl media. The proton sorption isotherms exhibited common intersection points in the pH range of 4.0-4.5 under all conditions, and the magnitude of charging was similar but not identical in NaCl and RbCl. The hydrogen bonding configuration at the oxide-water interface, obtained from classical molecular dynamics (MD) simulations, was analyzed in detail, and the results were explicitly incorporated in calculations of protonation constants for the reactive surface sites using the revised MUSIC model. The calculations indicated thatmore » the terminal SnOH2 group is more acidic than the bridging Sn2OH group, with protonation constants (log KH) of 3.60 and 5.13 at 25 degrees C, respectively. This is contrary to the situation on the isostructural alpha-TiO2 (rutile), apparently because of the difference in electronegativity between Ti and Sn. MD simulations and speciation calculations indicated considerable differences in the speciation of Na+ and Rb+, despite the similarities in overall charging. Adsorbed sodium ions are almost exclusively found in bidentate surface complexes, whereas adsorbed rubidium ions form comparable numbers of bidentate and tetradentate complexes. Also, the distribution of adsorbed Na+ between the different complexes shows a considerable dependence on the surface charge density (pH), whereas the distribution of adsorbed Rb+ is almost independent of pH. A surface complexation model (SCM) capable of accurately describing both the measured surface charge and the MD-predicted speciation of adsorbed Na+/Rb+ was formulated. According to the SCM, the deprotonated terminal group (SnOH(-0.40)) and the protonated bridging group (Sn2OH+0.36) dominate the surface speciation over the entire pH range of this study (2.7-10). The complexation of medium cations increases significantly with increasing negative surface charge, and at pH 10, roughly 40% of the terminal sites are predicted to form cation complexes, whereas anion complexation is minor throughout the studied pH range.« less

Charging properties of cassiterite (alfa-SnO2) surfaces

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

Rosenqvist, Jorgen K; Machesky, Michael L.; Vlcek, L.

The acid-base properties of cassiterite (alfa-SnO2) surfaces at 10 50 C were studied using potentiometric titrations of powder suspensions in aqueous NaCl and RbCl media. The proton sorption isotherms exhibited common intersection points in the pH-range 4.0 to 4.5 at all conditions and the magnitude of charging was similar but not identical in NaCl and RbCl. The hydrogen bonding configuration at the oxide-water interface, obtained from classical Molecular Dynamics (MD) simulations, was analyzed in detail and the results were explicitly incorporated in calculations of protonation constants for the reactive surface sites using the revised MUSIC model. The calculations indicated thatmore » the terminal SnOH2 group is more acidic than the bridging Sn2OH group, with protonation constants (log KH) of 3.60 and 5.13 at 25 C, respectively. This is contrary to the situation on the isostructural alfa-TiO2 (rutile), apparently due to the difference in electronegativity between Ti and Sn. MD simulations and speciation calculations indicated considerable differences in the speciation of Na+ and Rb+, despite the similarities in overall charging. Adsorbed sodium ions are almost exclusively found in bidentate surface complexes, while adsorbed rubidium ions form comparable amounts of bidentate and tetradentate complexes. Also, the distribution of adsorbed Na+ between the different complexes shows a considerable dependence on surface charge density (pH), while the distribution of adsorbed Rb+ is almost independent of pH. A Surface Complexation Model (SCM) capable of accurately describing both the measured surface charge and the MD predicted speciation of adsorbed Na+/Rb+ was formulated. According to the SCM, the deprotonated terminal group (SnOH-0.40) and the protonated bridging group (Sn2OH+0.36) dominate the surface speciation over the entire pH-range (2.7 10), illustrating the ability of positively and negatively charged surface groups to coexist. Complexation of the medium cations increases significantly with increasing negative surface charge and at pH 10 roughly 40 percent of the terminal sites are predicted to form cation complexes, while anion complexation is minor throughout the studied pH-range.« less

Prediction of toxicity of zinc and nickel mixtures to Artemia sp. at various salinities: From additivity to antagonism.

PubMed

Damasceno, Évila Pinheiro; de Figuerêdo, Lívia Pitombeira; Pimentel, Marcionília Fernandes; Loureiro, Susana; Costa-Lotufo, Letícia Veras

2017-08-01

Few studies have examined the toxicity of metal mixtures to marine organisms exposed to different salinities. The aim of the present study was to investigate the acute toxicity of zinc and nickel exposures singly and in combination to Artemia sp. under salinities of 10, 17, and 35 psu. The mixture concentrations were determined according to individual toxic units (TUs) to follow a fixed ratio design. Zinc was more toxic than nickel, and both their individual toxicities were higher at lower salinities. These changes in toxicity can be attributed to the Biotic Ligand Model (BLM) rather than to metal speciation. To analyze the mixture effect, the observed data were compared with the expected mixture effects predicted by the concentration addition (CA) model and by deviations for synergistic/antagonistic interactions and dose-level and dose-ratio dependencies. For a salinity of 35 psu, the mixture had no deviations; therefore, the effects were additive. After decreasing the salinity to 17 psu, the toxicity pattern changed to antagonism at low concentrations and synergism at higher equivalent LC 50 levels. For the lowest salinity tested (10 psu), antagonism was observed. The speciations of both metals were similar when in a mixture and when isolated, and changes in toxicity patterns are more related to the organism's physiology than metal speciation. Therefore, besides considering chemical interactions in real-world scenarios, where several chemicals can be present, the influence of abiotic factors, such as salinity, should also be considered. Copyright © 2017 Elsevier Inc. All rights reserved.

Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC.

PubMed

Dellicour, Simon; Flot, Jean-François

2015-11-01

Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Assessing the Selectivity of Extractant Solutions for Recovering Labile Arsenic Associated with Iron (Hydr)oxides and Sulfides in Sediments

EPA Science Inventory

Sequential extractions can provide analytical constraints on the identification of mineral phases that control arsenic speciation in sediments. Model solids were used in this study to evaluate different solutions designed to extract arsenic from relatively labile solid phases. ...

Speciation modeling of ammonia and other major solutes in anaerobic digesters

USDA-ARS?s Scientific Manuscript database

Anaerobic digestion of high-nitrogen wastes can be inhibited by high concentrations of un-ionized ammonia, NH**3 (aq). Understanding the toxicity of NH**3 (aq) to anaerobic digestion requires an understanding of the mechanisms controlling its concentration. Previous work on ammonia toxicity in an...

Source-receptor reconciliation of fine-particulate emissions from residential wood combustion in the southeastern United States

EPA Science Inventory

An extensive collection of speciated PM2.5 measurements including organic tracers permitted a detailed examination of the emissions from residential wood combustion (RWC) in the southeastern United States over an entire year (2007). The Community Multiscale Air Quality model-base...

Gas and aerosol carbon in California: comparison of measurements and model predictions in Pasadena and Bakersfield.

EPA Science Inventory

Co-located measurements of fine particulate matter (PM2.5) organic carbon (OC), elemental carbon, radiocarbon (14C), speciated volatile organic compounds (VOCs),and OH radicals during the CalNex field campaign provide a unique opportunity to evaluate the Community Multiscale Air ...

Particulate Matter Speciation Profiles for Light-duty Gasoline Vehicles in the United States

EPA Science Inventory

Representative particulate matter (PM2.5) profiles for particles less than or equal to 2.5 micrometers are estimated from the Kansas City Light-Duty Vehicle Emissions Study for use in the US EPA’s vehicle emission model, the Motor Vehicle Emission Simulator (MOVES). The profiles ...

Diversification amongst the South American fire ants: how when and why species barriers break down

USDA-ARS?s Scientific Manuscript database

Fire ants (Solenopsis) are an ideal model system for studying speciation and coexistence. Based on preliminary mitochondrial work, they appear to be a relatively recent radiation, and possibly a species swarm (ancient hybridization among young species). We are using a variety of phylogenetic, phylog...

MEASUREMENT AND MODELING OF ATMOSPHERIC MERCURY SPECIES AND RELATED POLLUTANTS IN SOUTH FLORIDA FROM 2000-2005

EPA Science Inventory

In 2000, Florida DEP, USEPA, and Broward EPD located an atmospheric mercury monitoring site adjacent to the Everglades in southeast Florida for the purposes of field testing the Tekran mercury speciation system under long-term operational conditions and evaluating the impact of e...

EMISSIONS INVENTORY OF PM 2.5 TRACE ELEMENTS ACROSS THE U.S.

EPA Science Inventory

This abstract describes work done to speciate PM_2.5 emissions into emissions of trace metals to enable concentrations of metal species to be predicted by air quality models. Methods are described and initial results are presented. A technique for validating the resul...

A null model for microbial diversification

PubMed Central

Straub, Timothy J.

2017-01-01

Whether prokaryotes (Bacteria and Archaea) are naturally organized into phenotypically and genetically cohesive units comparable to animal or plant species remains contested, frustrating attempts to estimate how many such units there might be, or to identify the ecological roles they play. Analyses of gene sequences in various closely related prokaryotic groups reveal that sequence diversity is typically organized into distinct clusters, and processes such as periodic selection and extensive recombination are understood to be drivers of cluster formation (“speciation”). However, observed patterns are rarely compared with those obtainable with simple null models of diversification under stochastic lineage birth and death and random genetic drift. Via a combination of simulations and analyses of core and phylogenetic marker genes, we show that patterns of diversity for the genera Escherichia, Neisseria, and Borrelia are generally indistinguishable from patterns arising under a null model. We suggest that caution should thus be taken in interpreting observed clustering as a result of selective evolutionary forces. Unknown forces do, however, appear to play a role in Helicobacter pylori, and some individual genes in all groups fail to conform to the null model. Taken together, we recommend the presented birth−death model as a null hypothesis in prokaryotic speciation studies. It is only when the real data are statistically different from the expectations under the null model that some speciation process should be invoked. PMID:28630293

Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes.

PubMed

Höhna, Sebastian

2013-06-01

Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birth-death process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit. In the present article, I consider as the model a global time-dependent birth-death process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birth-death process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae). The methods described in this manuscript are implemented in the R package TESS, available from the repository CRAN (http://cran.r-project.org/web/packages/TESS/). Supplementary data are available at Bioinformatics online.

Use of Mössbauer spectroscopy to determine the effect of salinity on the speciation of triorganotins in Anacostia River sediments

NASA Astrophysics Data System (ADS)

Eng, George; Song, Xueqing; May, Leopold

2006-06-01

The speciation of several tributyltin and triphenyltin compounds under varying salinity conditions (0, 20, 40 and 60%) was studied by Mössbauer spectroscopy in both anaerobic and aerobic Anacostia River sediments. The Mössbauer spectral parameters of the spiked sediments indicated that changes in the salinity did not affect the speciation of the tin compounds in either aerobic or anaerobic sediments.

Use of Mössbauer spectroscopy to determine the effect of salinity on the speciation of triorganotins in Anacostia River sediments

NASA Astrophysics Data System (ADS)

Eng, George; Song, Xueqing; May, Leopold

The speciation of several tributyltin and triphenyltin compounds under varying salinity conditions (0, 20, 40 and 60%) was studied by Mössbauer spectroscopy in both anaerobic and aerobic Anacostia River sediments. The Mössbauer spectral parameters of the spiked sediments indicated that changes in the salinity did not affect the speciation of the tin compounds in either aerobic or anaerobic sediments.

Considerations in As analysis and speciation

USGS Publications Warehouse

Edwards, M.; Patel, S.; McNeil, L.; Chen, H.W.; Frey, M.; Eaton, A.D.; Antweiler, Ronald C.; Taylor, Howard E.

1998-01-01

This article summarizes recent experiences in arsenic (As) quantification, preservation, and speciation developed during AWWA Research Foundation (AWWARF) and Water Industry Technical Action Fund (WITAF) projects. The goal of this article is to alert analysts and decision-makers to potential problems in As analysis and speciation, because there appear to be several unresolved problems with routine analytical approaches. In true split drinking water samples As was quantified by three accepted analytical methods in three laboratories. The techniques used were graphite furnace atomic absorption spectrometry (GFAAS), inductively coupled plasma mass spectrometry (ICP-MS), and hydride generation inductively coupled plasma-emission spectrometry (HG-ICP-AES). Experimental findings are organized into sections on As analysis, particulate As in water supplies, and examination of As speciation methods.

Biology and toxicology of tellurium explored by speciation analysis.

PubMed

Ogra, Yasumitsu

2017-05-24

Tellurium (Te) is widely used in industry because it has unique physicochemical properties. Although Te is a non-essential element in animals and plants, it is expected to be metabolized to organometallic compounds having a carbon-Te bond in living organisms exposed to inorganic Te compounds. Thus, the speciation and identification of tellurometabolites are expected to contribute to the depiction of the metabolic chart of Te. Speciation by elemental mass spectrometry and identification by molecular mass spectrometry coupled with separation techniques have significantly contributed to the discovery of tellurometabolites in animals and plants. The aim of this mini review is to present recent advances in the biology and toxicology of tellurium as revealed by speciation and identification by molecular mass spectrometry.

Dinosaurs in decline tens of millions of years before their final extinction

PubMed Central

Sakamoto, Manabu; Benton, Michael J.; Venditti, Chris

2016-01-01

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous–Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event. PMID:27092007

Dinosaurs in decline tens of millions of years before their final extinction.

PubMed

Sakamoto, Manabu; Benton, Michael J; Venditti, Chris

2016-05-03

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous-Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event.

Inferring phylogeny and speciation of Gymnosporangium species, and their coevolution with host plants

PubMed Central

Zhao, Peng; Liu, Fang; Li, Ying-Ming; Cai, Lei

2016-01-01

Gymnosporangium species (Pucciniaceae, Pucciniales) cause serious diseases and significant economic losses to apple cultivars. Most of the reported species are heteroecious and complete their life cycles on two different plant hosts belonging to two unrelated genera, i.e. Juniperus and Malus. However, the phylogenetic relationships among Gymnosporangium species and the evolutionary history of Gymnosporangium on its aecial and telial hosts were still undetermined. In this study, we recognized species based on rDNA sequence data by using coalescent method of generalized mixed Yule-coalescent (GMYC) and Poisson Tree Processes (PTP) models. The evolutionary relationships of Gymnosporangium species and their hosts were investigated by comparing the cophylogenetic analyses of Gymnosporangium species with Malus species and Juniperus species, respectively. The concordant results of GMYC and PTP analyses recognized 14 species including 12 known species and two undescribed species. In addition, host alternations of 10 Gymnosporangium species were uncovered by linking the derived sequences between their aecial and telial stages. This study revealed the evolutionary process of Gymnosporangium species, and clarified that the aecial hosts played more important roles than telial hosts in the speciation of Gymnosporangium species. Host switch, losses, duplication and failure to divergence all contributed to the speciation of Gymnosporangium species. PMID:27385413

Dinosaurs in decline tens of millions of years before their final extinction

NASA Astrophysics Data System (ADS)

Sakamoto, Manabu; Benton, Michael J.

2016-05-01

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous-Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event.

The Secondary Contact Zone of Phylogenetic Lineages of the Philaenus spumarius (Hemiptera: Aphrophoridae): An Example of Incomplete Allopatric Speciation

PubMed Central

Lis, Agata; Maryańska-Nadachowska, Anna; Lachowska-Cierlik, Dorota; Kajtoch, Łukasz

2014-01-01

Abstract Previous studies on the phylogeography of the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) suggest the existence of a contact zone of its main phylogenetic lineages along mountain chains in Europe and western Asia. This study presents a detailed examination of the population genetics of P. spumarius within the Carpathian Mountains. The main objective was to determine whether the populations inhabiting that area consist of individuals belonging to different genetic units and whether the observed pattern could be an example of secondary contact zone which formed after incomplete allopatric speciation. Specimens from six transects across the Carpathian arc were examined. The mitochondrial phylogeography of the meadow spittlebug in the examined area clearly shows that individuals from both main clades meet and mix there. Representatives of all three main EF1-α clades were also found. The present distribution of the main clades with a zone of overlap along the mountain ranges may suggest that these phylogenetic lineages form a young hybrid zone. Moreover, a limited number of individuals were shown to possess heteroplasmic mitochondrial DNA, which gives additional support to intraspecific hybridization. P. spumarius could be used in future work as an excellent model species in investigating population genetics, intraspecific hybridization, and speciation in progress. PMID:25500280

Interspecific geographic range size-body size relationship and the diversification dynamics of Neotropical furnariid birds.

PubMed

Inostroza-Michael, Oscar; Hernández, Cristián E; Rodríguez-Serrano, Enrique; Avaria-Llautureo, Jorge; Rivadeneira, Marcelo M

2018-05-01

Among the earliest macroecological patterns documented, is the range and body size relationship, characterized by a minimum geographic range size imposed by the species' body size. This boundary for the geographic range size increases linearly with body size and has been proposed to have implications in lineages evolution and conservation. Nevertheless, the macroevolutionary processes involved in the origin of this boundary and its consequences on lineage diversification have been poorly explored. We evaluate the macroevolutionary consequences of the difference (hereafter the distance) between the observed and the minimum range sizes required by the species' body size, to untangle its role on the diversification of a Neotropical species-rich bird clade using trait-dependent diversification models. We show that speciation rate is a positive hump-shaped function of the distance to the lower boundary. The species with highest and lowest distances to minimum range size had lower speciation rates, while species close to medium distances values had the highest speciation rates. Further, our results suggest that the distance to the minimum range size is a macroevolutionary constraint that affects the diversification process responsible for the origin of this macroecological pattern in a more complex way than previously envisioned. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Does sex speed up evolutionary rate and increase biodiversity?

PubMed

Melián, Carlos J; Alonso, David; Allesina, Stefano; Condit, Richard S; Etienne, Rampal S

2012-01-01

Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity.

Comparative Evolution of an Archetypal Adaptive Radiation: Innovation and Opportunity in Anolis Lizards.

PubMed

Poe, Steven; de Oca, Adrián Nieto-Montes; Torres-Carvajal, Omar; de Queiroz, Kevin; Velasco, Julián A; Truett, Brad; Gray, Levi N; Ryan, Mason J; Köhler, Gunther; Ayala-Varela, Fernando; Latella, Ian

2018-06-01

Adaptive radiation is a widely recognized pattern of evolution wherein substantial phenotypic change accompanies rapid speciation. Adaptive radiation may be triggered by environmental opportunities resulting from dispersal to new areas or via the evolution of traits, called key innovations, that allow for invasion of new niches. Species sampling is a known source of bias in many comparative analyses, yet classic adaptive radiations have not been studied comparatively with comprehensively sampled phylogenies. In this study, we use unprecedented comprehensive phylogenetic sampling of Anolis lizard species to examine comparative evolution in this well-studied adaptive radiation. We compare adaptive radiation models within Anolis and in the Anolis clade and a potential sister lineage, the Corytophanidae. We find evidence for island (i.e., opportunity) effects and no evidence for trait (i.e., key innovation) effects causing accelerated body size evolution within Anolis. However, island effects are scale dependent: when Anolis and Corytophanidae are analyzed together, no island effect is evident. We find no evidence for an island effect on speciation rate and tenuous evidence for greater speciation rate due to trait effects. These results suggest the need for precision in treatments of classic adaptive radiations such as Anolis and further refinement of the concept of adaptive radiation.

Distribution and speciation of mercury affected by humic acid in mariculture sites at the Pearl River estuary.

PubMed

Ding, Lingyun; Zhao, Kaiyun; Zhang, Lijuan; Liang, Peng; Wu, Shengchun; Wong, Ming Hung; Tao, Huchun

2018-05-14

At the Pearl River Estuary of southern China, mercury and its environmental problems have long been a great concern. This study investigated the distribution and speciation of mercury compounds that are significantly influenced by the increasing content of humic acid (HA, a model natural organic matter) in this region. The inorganic mercury and methyl mercury, being adsorbed and converted at different HA levels, were studied in sediments and surface water at both mariculture and their reference sites. In mariculture sediments with higher HA content (up to 4.5%), more mercury were adsorbed at different compound levels, promoting the methylation and accumulation of mercury (P < 0.05) at the sediment-water interface. Seasonal shift in environmental temperature might control the HA content, subsequently favouring mercury methylation (maximum 1.75 ± 0.08 mg L -1 d -1 ) under warm weather conditions. In reference sites received less HA wastes, lower adsorption capacity and methylation rate were observed for mercury in sediments and surface water. Our work points to the significant roles of HA on mercury distribution and speciation both spatially and seasonally, thus addressing the impacts of mariculture activities on estuary eco-system. Copyright © 2018 Elsevier Ltd. All rights reserved.

Sensory specificity and speciation: a potential neuronal pathway for host fruit odour discrimination in Rhagoletis pomonella

PubMed Central

Batra, Srishti; Ramaswamy, Sree Subha; Feder, Jeffrey L.

2016-01-01

Behavioural changes in habitat or mate choice can trigger population divergence, leading to speciation. However, little is known about the neurological bases for such changes. Rhagoletis pomonella (Diptera: Tephritidae) is a model for ecological speciation via host plant shifts. Within the past 180 years, Rhagoletis flies infesting hawthorn (Crataegus spp.) shifted to attack domesticated apple (Malus pumila). The two populations differ in their olfactory preferences for apple versus hawthorn fruit. Here, we looked for patterns of sensory organization that may have contributed to this shift by characterizing the morphology, specificity and distribution of olfactory sensory neurons (OSNs) on the antennae of Rhagoletis responding to host fruit and non-host volatiles. Of 28 OSN classes identified, two colocalized OSN pairs were found that specifically responded to the major behavioural attractant and antagonist volatiles for each fly population. A reversal in the response of these OSNs to fruit volatiles, either through a switch in receptor expression between these paired neurons or changes in neuronal projections in the brain, could therefore account for the behavioural difference between apple and hawthorn flies. The finding supports the hypothesis that relatively minor changes in olfactory sensory pathways may contribute to rapid host shifting and divergence in Rhagoletis. PMID:28003447

Facilitation of environmental adaptation and evolution by epigenetic phenotype variation: insights from clonal, invasive, polyploid, and domesticated animals

PubMed Central

Vogt, Günter

2017-01-01

Abstract There is increasing evidence, particularly from plants, that epigenetic mechanisms can contribute to environmental adaptation and evolution. The present article provides an overview on this topic for animals and highlights the special suitability of clonal, invasive, hybrid, polyploid, and domesticated species for environmental and evolutionary epigenetics. Laboratory and field studies with asexually reproducing animals have shown that epigenetically diverse phenotypes can be produced from the same genome either by developmental stochasticity or environmental induction. The analysis of invasions revealed that epigenetic phenotype variation may help to overcome genetic barriers typically associated with invasions such as bottlenecks and inbreeding. Research with hybrids and polyploids established that epigenetic mechanisms are involved in consolidation of speciation by contributing to reproductive isolation and restructuring of the genome in the neo-species. Epigenetic mechanisms may even have the potential to trigger speciation but evidence is still meager. The comparison of domesticated animals and their wild ancestors demonstrated heritability and selectability of phenotype modulating DNA methylation patterns. Hypotheses, model predictions, and empirical results are presented to explain how epigenetic phenotype variation could facilitate adaptation and speciation. Clonal laboratory lineages, monoclonal invaders, and adaptive radiations of different evolutionary age seem particularly suitable to empirically test the proposed ideas. A respective research agenda is presented. PMID:29492304

First field-based atmospheric observation of the reduction of reactive mercury driven by sunlight

NASA Astrophysics Data System (ADS)

de Foy, Benjamin; Tong, Yindong; Yin, Xiufeng; Zhang, Wei; Kang, Shichang; Zhang, Qianggong; Zhang, Guoshuai; Wang, Xuejun; Schauer, James J.

2016-06-01

Hourly speciated measurements of atmospheric mercury made in a remote, high-altitude site in the Tibetan Plateau revealed the first field observations of the reduction of reactive mercury in the presence of sunlight in the atmosphere. Measurements were collected over four winter months on the shore of Nam Co Lake in the inland Tibetan Plateau. The data was analyzed to identify sources and atmospheric transformations of the speciated mercury compounds. The absence of local anthropogenic sources provided a unique opportunity to examine chemical transformations of mercury. An optimization algorithm was used to determine the parameters of a chemical box model that would match the measured reactive mercury concentrations. This required the presence of a photolytic reduction reaction previously observed in laboratory studies and in power plant plumes. In addition, the model estimated the role of vertical mixing in diluting reactive gaseous mercury during the day, and the role of bromine chemistry in oxidizing gaseous elemental mercury to produce reactive gaseous mercury. This work provides further evidence of the need to add the photolytic reduction reaction of oxidized mercury into atmospheric transport models in order to better simulate mercury deposition.

Influence of soil pH on the sorption of ionizable chemicals: modeling advances.

PubMed

Franco, Antonio; Fu, Wenjing; Trapp, Stefan

2009-03-01

The soil-water distribution coefficient of ionizable chemicals (K(d)) depends on the soil acidity, mainly because the pH governs speciation. Using pH-specific K(d) values normalized to organic carbon (K(OC)) from the literature, a method was developed to estimate the K(OC) of monovalent organic acids and bases. The regression considers pH-dependent speciation and species-specific partition coefficients, calculated from the dissociation constant (pK(a)) and the octanol-water partition coefficient of the neutral molecule (log P(n)). Probably because of the lower pH near the organic colloid-water interface, the optimal pH to model dissociation was lower than the bulk soil pH. The knowledge of the soil pH allows calculation of the fractions of neutral and ionic molecules in the system, thus improving the existing regression for acids. The same approach was not successful with bases, for which the impact of pH on the total sorption is contrasting. In fact, the shortcomings of the model assumptions affect the predictive power for acids and for bases differently. We evaluated accuracy and limitations of the regressions for their use in the environmental fate assessment of ionizable chemicals.

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.

A new approach to estimate parameters of speciation models with application to apes.

PubMed

Becquet, Celine; Przeworski, Molly

2007-10-01

How populations diverge and give rise to distinct species remains a fundamental question in evolutionary biology, with important implications for a wide range of fields, from conservation genetics to human evolution. A promising approach is to estimate parameters of simple speciation models using polymorphism data from multiple loci. Existing methods, however, make a number of assumptions that severely limit their applicability, notably, no gene flow after the populations split and no intralocus recombination. To overcome these limitations, we developed a new Markov chain Monte Carlo method to estimate parameters of an isolation-migration model. The approach uses summaries of polymorphism data at multiple loci surveyed in a pair of diverging populations or closely related species and, importantly, allows for intralocus recombination. To illustrate its potential, we applied it to extensive polymorphism data from populations and species of apes, whose demographic histories are largely unknown. The isolation-migration model appears to provide a reasonable fit to the data. It suggests that the two chimpanzee species became reproductively isolated in allopatry approximately 850 Kya, while Western and Central chimpanzee populations split approximately 440 Kya but continued to exchange migrants. Similarly, Eastern and Western gorillas and Sumatran and Bornean orangutans appear to have experienced gene flow since their splits approximately 90 and over 250 Kya, respectively.

Allochronic speciation, secondary contact, and reproductive character displacement in periodical cicadas (Hemiptera: Magicicada spp.): genetic, morphological, and behavioural evidence.

PubMed

Cooley, J R; Simon, C; Marshall, D C; Slon, K; Ehrhardt, C

2001-03-01

Periodical cicadas have proven useful in testing a variety of ecological and evolutionary hypotheses because of their unusual life history, extraordinary abundance, and wide geographical range. Periodical cicadas provide the best examples of synchronous periodicity and predator satiation in the animal kingdom, and are excellent illustrations of habitat partitioning (by the three morphologically distinct species groups), incipient species (the year classes or broods), and cryptic species (a newly discovered 13-year species, Magicicada neotredecim). They are particularly useful for exploring questions regarding speciation via temporal isolation, or allochronic speciation. Recently, data were presented that provided strong support for an instance of allochronic speciation by life-cycle switching. This speciation event resulted in the formation of a new 13-year species from a 17-year species and led to secondary contact between two formerly separated lineages, one represented by the new 13-year cicadas (and their 17-year ancestors), and the other represented by the pre-existing 13-year cicadas. Allozyme frequency data, mitochondrial DNA (mtDNA), and abdominal colour were shown to be correlated genetic markers supporting the life-cycle switching/allochronic speciation hypothesis. In addition, a striking pattern of reproductive character displacement in male call pitch and female pitch preference between the two 13-year species was discovered. In this paper we report a strong association between calling song pitch and mtDNA haplotype for 101 individuals from a single locality within the M. tredecim/M. neotredecim contact zone and a strong association between abdomen colour and mtDNA haplotype. We conclude by reviewing proposed mechanisms for allochronic speciation and reproductive character displacement.

Sample preparation and storage can change arsenic speciation in human urine.

PubMed

Feldmann, J; Lai, V W; Cullen, W R; Ma, M; Lu, X; Le, X C

1999-11-01

Stability of chemical speciation during sample handling and storage is a prerequisite to obtaining reliable results of trace element speciation analysis. There is no comprehensive information on the stability of common arsenic species, such as inorganic arsenite [As(III)], arsenate [As(V)], monomethylarsonic acid, dimethylarsinic acid, and arsenobetaine, in human urine. We compared the effects of the following storage conditions on the stability of these arsenic species: temperature (25, 4, and -20 degrees C), storage time (1, 2, 4, and 8 months), and the use of additives (HCl, sodium azide, benzoic acid, benzyltrimethylammonium chloride, and cetylpyridinium chloride). HPLC with both inductively coupled plasma mass spectrometry and hydride generation atomic fluorescence detection techniques were used for the speciation of arsenic. We found that all five of the arsenic species were stable for up to 2 months when urine samples were stored at 4 and -20 degrees C without any additives. For longer period of storage (4 and 8 months), the stability of arsenic species was dependent on urine matrices. Whereas the arsenic speciation in some urine samples was stable for the entire 8 months at both 4 and -20 degrees C, other urine samples stored under identical conditions showed substantial changes in the concentration of As(III), As(V), monomethylarsonic acid, and dimethylarsinic acid. The use of additives did not improve the stability of arsenic speciation in urine. The addition of 0.1 mol/L HCl (final concentration) to urine samples produced relative changes in inorganic As(III) and As(V) concentrations. Low temperature (4 and -20 degrees C) conditions are suitable for the storage of urine samples for up to 2 months. Untreated samples maintain their concentration of arsenic species, and additives have no particular benefit. Strong acidification is not appropriate for speciation analysis.

The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

PubMed

Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

2018-05-01

Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

Speciation distribution and mass balance of copper and zinc in urban rain, sediments, and road runoff.

PubMed

Zuo, Xiaojun; Fu, Dafang; Li, He

2012-11-01

Heavy metal pollution in road runoff had caused widespread concern since the last century. However, there are little references on metal speciation in multiple environmental media (e.g., rain, road sediments, and road runoff). Our research targeted the investigation of metal speciation in rain, road sediments, and runoff; the analysis of speciation variation and mass balance of metals among rain, road sediments, and runoff; the selection of main factors by principal component analysis (PCA); and the establishment of equation to evaluate the impact of rain and road sediments to metals in road runoff. Sequential extraction procedure contains five steps for the chemical fractionation of metals. Flame atomic absorption spectrometry (Shimadzu, AA-6800) was used to determine metal speciation concentration, as well as the total and dissolved fractions. The dissolved fractions for both Cu and Zn were dominant in rain. The speciation distribution of Zn was different from that of Cu in road sediments, while speciation distribution of Zn is similar to that of Cu in runoff. The bound to carbonates for both Cu and Zn in road sediments were prone to be dissolved by rain. The levels of Cu and Zn in runoff were not obviously influenced by rain, but significantly influenced by road sediments. The masses for both Cu and Zn among rain, road sediments, and road runoff approximately meet the mass balance equation for all rainfall patterns. Five principal factors were selected for metal regression equation based on PCA, including rainfall, average rainfall intensity, antecedent dry periods, total suspended particles, and temperature. The established regression equations could be used to predict the effect of road runoff on receiving environments.

Speciation of Reactive Sulfur Species and their Reactions with Alkylating Agents: Do we have any clue about what is present inside the cell?

PubMed

Bogdándi, Virág; Ida, Tomoaki; Sutton, Thomas R; Bianco, Christopher; Ditrói, Tamás; Koster, Grielof; Henthorn, Hillary A; Minnion, Magda; Toscano, John P; van der Vliet, Albert; Pluth, Michael D; Feelisch, Martin; Fukuto, Jon M; Akaike, Takaaki; Nagy, Péter

2018-06-17

Posttranslational modifications of cysteine (Cys) residues represent a major aspect of redox biology, and their reliable detection is key in providing mechanistic insights. The metastable character of these modifications and cell lysis-induced artifactual oxidation render current state-of-the-art protocols to rely on alkylation-based stabilization of labile Cys derivatives before cell/tissue rupture. An untested assumption in these procedures is that for all Cys derivatives alkylation rates are faster than their dynamic interchange. However, when the interconversion of Cys derivatives is not rate-limiting, then electrophilic labeling is under Curtin-Hammett control and hence the final alkylated mixture may not represent the speciation that prevailed before alkylation. We here present evidence that in the majority of cases, the speciation of alkylated polysulfide/thiol derivatives indeed depends on the experimental conditions. Our results reveal that alkylation perturbs sulfur speciation in both a concentration- and time-dependent manner, and that strong alkylating agents can cleave polysulfur chains. Moreover, we show that labeling of sulfenic acids with dimedone also affects Cys speciation, suggesting that part of the endogenous pool of products previously believed to represent sulfenic acid species may in fact represent polysulfides. These observations were obtained using buffered aqueous solutions of inorganic-, organic-, cysteine-, glutathione- and GAPDH-polysulfide species. Additional experiments in human plasma and serum revealed that monobromobimane can extract sulfide from the endogenous sulfur pool by shifting speciation equilibria, suggesting caution should be exercised when interpreting experimental results using this tool. We highlight methodological caveats potentially arising from these pitfalls and conclude that current derivatization strategies often fail to adequately capture physiologic speciation of sulfur species. This article is protected by copyright. All rights reserved.

Chemical Speciation and Metallomics.

PubMed

de Jesus, Jemmyson Romário; da Costa, Luana Ferreira; Lehmann, Eraldo Luiz; Galazzi, Rodrigo Moretto; Madrid, Katherine Chacón; Arruda, Marco Aurélio Zezzi

2018-01-01

Chemical speciation approaches is an inherent part of metallomics, once metals/metalloids and organic structures need to be currently evaluated for attaining metallomics studies. Then, this chapter focuses on the applications of the chemical speciation applied to the human health risk, food and human diet, drugs, forensic, nanoscience, and geological metallomics, also pointing out the advances in such area. Some aspects regarding sample preparation is commented along this chapter, and some strategies for maintaining the integrity of the metallomics information are also emphasized.

The phosphorus speciations in the sediments up- and down-stream of cascade dams along the middle Lancang River.

PubMed

Liu, Qi; Liu, Shiliang; Zhao, Haidi; Deng, Li; Wang, Cong; Zhao, Qinghe; Dong, Shikui

2015-02-01

We detected the longitudinal variability of phosphorus speciations and its relation to metals and grain size distribution of sediments in three cascade canyon reservoirs (Xiaowan, Manwan and Dachaoshan) along Lancang River, China. Five phosphorus speciations including loosely bound P (ex-P), reductant soluble P (BD-P), metal oxide-bound P (NaOH-P) calcium-bound P (HCl-P) and residual-P were extracted and quantified. Results showed that in Manwan Reservoir HCl-P accounted for the largest part of total phosphorus (TP) (49.69%), while in Xiaowan and Dachaoshan reservoirs, NaOH-P was the most abundant speciation which accounted for 57.21% and 55.19% of total phosphorus respectively. Higher contents of bio-available phosphorus in Xiaowan and Dachaoshan reservoirs suggested a high rate of P releasing from sediments. Results also showed ex-P and HCl-P had positive correlation with Ca. Total phosphorus was positively correlated with Fe. The silt/clay contents of the sediments had close relationship with ex-P (r=0.413, p<0.05), NaOH-P (r=0.428, p<0.05) and BAP (r=0.458, p<0.05). The concentration of Ca, Mn and silt/clay speciation in the sediments explained 40%, 10% and 4% of the spatial variation of phosphorus speciations, respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ancient islands and modern invasions: disparate phylogeographic histories among Hispaniola's endemic birds.

PubMed

Sly, Nicholas D; Townsend, Andrea K; Rimmer, Christopher C; Townsend, Jason M; Latta, Steven C; Lovette, Irby J

2011-12-01

With its large size, complex topography and high number of avian endemics, Hispaniola appears to be a likely candidate for the in situ speciation of its avifauna, despite the worldwide rarity of avian speciation within single islands. We used multilocus comparative phylogeography techniques to examine the pattern and history of divergence in 11 endemic birds representing potential within-island speciation events. Haplotype and allele networks from mitochondrial ND2 and nuclear intron loci reveal a consistent pattern: phylogeographic divergence within or between closely related species is correlated with the likely distribution of ancient sea barriers that once divided Hispaniola into several smaller paleo-islands. Coalescent and mitochondrial clock dating of divergences indicate species-specific response to different geological events over the wide span of the island's history. We found no evidence that ecological or topographical complexity generated diversity, either by creating open niches or by restricting long-term gene flow. Thus, no true within-island speciation appears to have occurred among the species sampled on Hispaniola. Divergence events predating the merging of Hispaniola's paleo-island blocks cannot be considered in situ divergence, and postmerging divergence in response to episodic island segmentation by marine flooding probably represents in situ vicariance or interarchipelago speciation by dispersal. Our work highlights the necessity of considering island geologic history while investigating the speciation-area relationship in birds and other taxa. © 2011 Blackwell Publishing Ltd.

Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages

PubMed Central

2010-01-01

Background A positive relationship between diversification (i.e., speciation) and nucleotide substitution rates is commonly reported for angiosperm clades. However, the underlying cause of this relationship is often unknown because multiple intrinsic and extrinsic factors can affect the relationship, and these have confounded previous attempts infer causation. Determining which factor drives this oft-reported correlation can lend insight into the macroevolutionary process. Results Using a new database of 13 time-calibrated angiosperm phylogenies based on internal transcribed spacer (ITS) sequences, and controlling for extrinsic variables of life history and habitat, I evaluated several potential intrinsic causes of this correlation. Speciation rates (λ) and relative extinction rates (ε) were positively correlated with mean substitution rates, but were uncorrelated with substitution rate heterogeneity. It is unlikely that the positive diversification-substitution correlation is due to accelerated molecular evolution during speciation (e.g., via enhanced selection or drift), because punctuated increases in ITS rate (i.e., greater mean and variation in ITS rate for rapidly speciating clades) were not observed. Instead, fast molecular evolution likely increases speciation rate (via increased mutational variation as a substrate for selection and reproductive isolation) but also increases extinction (via mutational genetic load). Conclusions In general, these results predict that clades with higher background substitution rates may undergo successful diversification under new conditions while clades with lower substitution rates may experience decreased extinction during environmental stasis. PMID:20515493

Selenium speciation in seleniferous agricultural soils under different cropping systems using sequential extraction and X-ray absorption spectroscopy.

PubMed

Qin, Hai-Bo; Zhu, Jian-Ming; Lin, Zhi-Qing; Xu, Wen-Po; Tan, De-Can; Zheng, Li-Rong; Takahashi, Yoshio

2017-06-01

Selenium (Se) speciation in soil is critically important for understanding the solubility, mobility, bioavailability, and toxicity of Se in the environment. In this study, Se fractionation and chemical speciation in agricultural soils from seleniferous areas were investigated using the elaborate sequential extraction and X-ray absorption near-edge structure (XANES) spectroscopy. The speciation results quantified by XANES technique generally agreed with those obtained by sequential extraction, and the combination of both approaches can reliably characterize Se speciation in soils. Results showed that dominant organic Se (56-81% of the total Se) and lesser Se(IV) (19-44%) were observed in seleniferous agricultural soils. A significant decrease in the proportion of organic Se to the total Se was found in different types of soil, i.e., paddy soil (81%) > uncultivated soil (69-73%) > upland soil (56-63%), while that of Se(IV) presented an inverse tendency. This suggests that Se speciation in agricultural soils can be significantly influenced by different cropping systems. Organic Se in seleniferous agricultural soils was probably derived from plant litter, which provides a significant insight for phytoremediation in Se-laden ecosystems and biofortification in Se-deficient areas. Furthermore, elevated organic Se in soils could result in higher Se accumulation in crops and further potential chronic Se toxicity to local residents in seleniferous areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

Derivation of Pitzer Interaction Parameters for an Aqueous Species Pair of Sodium and Iron(II)-Citrate Complex

NASA Astrophysics Data System (ADS)

Jang, J. H.; Nemer, M.

2015-12-01

The U.S. DOE Waste Isolation Pilot Plant (WIPP) is a deep underground repository for the permanent disposal of transuranic (TRU) radioactive waste. The WIPP is located in the Permian Delaware Basin near Carlsbad, New Mexico, U.S.A. The TRU waste includes, but is not limited to, iron-based alloys and the complexing agent, citric acid. Iron is also present from the steel used in the waste containers. The objective of this analysis is to derive the Pitzer activity coefficients for the pair of Na+ and FeCit- complex to expand current WIPP thermodynamic database. An aqueous model for the dissolution of Fe(OH)2(s) in a Na3Cit solution was fitted to the experimentally measured solubility data. The aqueous model consists of several chemical reactions and related Pitzer interaction parameters. Specifically, Pitzer interaction parameters for the Na+ and FeCit- pair (β(0), β(1), and Cφ) plus the stability constant for species of FeCit- were fitted to the experimental data. Anoxic gloveboxes were used to keep the oxygen level low (<1 ppm) throughout the experiments due to redox sensitivity. EQ3NR, a computer program for geochemical aqueous speciation-solubility calculations, packaged in EQ3/6 v.8.0a, calculates the aqueous speciation and saturation index using an aqueous model addressed in EQ3/6's database. The saturation index indicates how far the system is from equilibrium with respect to the solid of interest. Thus, the smaller the sum of squared saturation indices that the aqueous model calculates for the given number of experiments, the more closely the model attributes equilibrium to each individual experiment with respect to the solid of interest. The calculation of aqueous speciation and saturation indices was repeated by adjusting stability constant of FeCit-, β(0), β(1), and Cφ in the database until the values are found that make the sum of squared saturation indices the smallest for the given number of experiments. Results will be presented at the time of conference.

SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT

PubMed Central

Baker, Robert J.; Bradley, Robert D.

2009-01-01

We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson–Dobzhansky–Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these “morphologically cryptic genetic species” are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F1s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is “reproductively isolated species.” Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen–based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum. PMID:19890476

Speciation through the lens of biomechanics: locomotion, prey capture and reproductive isolation.

PubMed

Higham, Timothy E; Rogers, Sean M; Langerhans, R Brian; Jamniczky, Heather A; Lauder, George V; Stewart, William J; Martin, Christopher H; Reznick, David N

2016-09-14

Speciation is a multifaceted process that involves numerous aspects of the biological sciences and occurs for multiple reasons. Ecology plays a major role, including both abiotic and biotic factors. Whether populations experience similar or divergent ecological environments, they often adapt to local conditions through divergence in biomechanical traits. We investigate the role of biomechanics in speciation using fish predator-prey interactions, a primary driver of fitness for both predators and prey. We highlight specific groups of fishes, or specific species, that have been particularly valuable for understanding these dynamic interactions and offer the best opportunities for future studies that link genetic architecture to biomechanics and reproductive isolation (RI). In addition to emphasizing the key biomechanical techniques that will be instrumental, we also propose that the movement towards linking biomechanics and speciation will include (i) establishing the genetic basis of biomechanical traits, (ii) testing whether similar and divergent selection lead to biomechanical divergence, and (iii) testing whether/how biomechanical traits affect RI. Future investigations that examine speciation through the lens of biomechanics will propel our understanding of this key process. © 2016 The Author(s).

250 years of hybridization between two biennial herb species without speciation.

PubMed

Matthews, Andrew; Emelianova, Katie; Hatimy, Abubakar A; Chester, Michael; Pellicer, Jaume; Ahmad, Khawaja Shafique; Guignard, Maité S; Rouhan, Germinal; Soltis, Douglas E; Soltis, Pamela S; Leitch, Ilia J; Leitch, Andrew R; Mavrodiev, Evgeny V; Buggs, Richard J A

2015-07-17

Hybridization between plant species can generate novel morphological diversity and lead to speciation at homoploid or polyploid levels. Hybrids between biennial herbs Tragopogon pratensis and T. porrifolius have been studied in experimental and natural populations for over 250 years. Here we examine their current status in natural populations in southeast England. All hybrids found were diploid; they tended to grow taller and with more buds than their parental species; many showed partial fertility; a few showed evidence of backcrossing. However, we found no evidence to suggest that the hybrids are establishing as a new species, nor can we find literature documenting speciation of these hybrids elsewhere. This lack of speciation despite at least 250 years of hybridization contrasts with the fact that both parental species have formed new allopolyploid species through hybridization with another diploid, T. dubius. Understanding why hybrids often do not speciate, despite repeated opportunities, would enhance our understanding of both the evolutionary process and risk assessments of invasive species. Published by Oxford University Press on behalf of the Annals of Botany Company.

Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence

PubMed Central

Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K.; Otwinowski, Zbyszek; Grishin, Nick V.

2016-01-01

Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies. PMID:27120974

Transformation of heavy metal speciation during sludge drying: mechanistic insights.

PubMed

Weng, Huan-Xin; Ma, Xue-Wen; Fu, Feng-Xia; Zhang, Jin-Jun; Liu, Zan; Tian, Li-Xun; Liu, Chongxuan

2014-01-30

Speciation can fundamentally affect on the stability and toxicity of heavy metals in sludge from wastewater treatment plants. This research investigated the speciation of heavy metals in sludge from both municipal and industrial sources, and metal speciation change as a result of drying process to reduce sludge volume. The changes in sludge properties including sludge moisture content, temperature, density, and electrical conductivity were also monitored to provide insights into the mechanisms causing the change in heavy metal speciation. The results show that the drying process generally stabilized Cr, Cu, Cd, and Pb in sludge by transforming acid-soluble, reducible, and oxidizable species into structurally stable forms. Such transformation and stabilization occurred regardless of the sludge source and type, and were primarily caused by the changes in sludge properties associated with decomposition of organic matter and sulfide. The results enhanced our understanding of the geochemical behavior of heavy metals in municipal sludge, and are useful for designing a treatment system for environment-friendly disposal of sludge. Copyright © 2013 Elsevier B.V. All rights reserved.

A review of recent developments in the speciation and location of arsenic and selenium in rice grain

PubMed Central

Carey, Anne-Marie; Lombi, Enzo; Donner, Erica; de Jonge, Martin D.; Punshon, Tracy; Jackson, Brian P.; Guerinot, Mary Lou; Price, Adam H.; Meharg, Andrew A.

2014-01-01

Rice is a staple food yet is a significant dietary source of inorganic arsenic, a class 1, nonthreshold carcinogen. Establishing the location and speciation of arsenic within the edible rice grain is essential for understanding the risk and for developing effective strategies to reduce grain arsenic concentrations. Conversely, selenium is an essential micronutrient and up to 1 billion people worldwide are selenium-deficient. Several studies have suggested that selenium supplementation can reduce the risk of some cancers, generating substantial interest in biofortifying rice. Knowledge of selenium location and speciation is important, because the anti-cancer effects of selenium depend on its speciation. Germanic acid is an arsenite/silicic acid analogue, and location of germanium may help elucidate the mechanisms of arsenite transport into grain. This review summarises recent discoveries in the location and speciation of arsenic, germanium, and selenium in rice grain using state-of-the-art mass spectrometry and synchrotron techniques, and illustrates both the importance of high-sensitivity and high-resolution techniques and the advantages of combining techniques in an integrated quantitative and spatial approach. PMID:22159463

Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence.

PubMed

Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K; Otwinowski, Zbyszek; Grishin, Nick V

2016-04-28

Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies.

Speciation through the lens of biomechanics: locomotion, prey capture and reproductive isolation

PubMed Central

Rogers, Sean M.; Langerhans, R. Brian; Jamniczky, Heather A.; Lauder, George V.; Stewart, William J.; Martin, Christopher H.; Reznick, David N.

2016-01-01

Speciation is a multifaceted process that involves numerous aspects of the biological sciences and occurs for multiple reasons. Ecology plays a major role, including both abiotic and biotic factors. Whether populations experience similar or divergent ecological environments, they often adapt to local conditions through divergence in biomechanical traits. We investigate the role of biomechanics in speciation using fish predator–prey interactions, a primary driver of fitness for both predators and prey. We highlight specific groups of fishes, or specific species, that have been particularly valuable for understanding these dynamic interactions and offer the best opportunities for future studies that link genetic architecture to biomechanics and reproductive isolation (RI). In addition to emphasizing the key biomechanical techniques that will be instrumental, we also propose that the movement towards linking biomechanics and speciation will include (i) establishing the genetic basis of biomechanical traits, (ii) testing whether similar and divergent selection lead to biomechanical divergence, and (iii) testing whether/how biomechanical traits affect RI. Future investigations that examine speciation through the lens of biomechanics will propel our understanding of this key process. PMID:27629033

Anaerobic Digestion Alters Copper and Zinc Speciation.

PubMed

Legros, Samuel; Levard, Clément; Marcato-Romain, Claire-Emmanuelle; Guiresse, Maritxu; Doelsch, Emmanuel

2017-09-19

Anaerobic digestion is a widely used organic waste treatment process. However, little is known on how it could alter the speciation of contaminants in organic waste. This study was focused on determining the influence of anaerobic digestion on the speciation of copper and zinc, two metals that generally occur at high concentration in organic waste. Copper and zinc speciation was investigated by X-ray absorption spectroscopy in four different raw organic wastes (predigestion) and their digested counterparts (postdigestion, i.e., digestates). The results highlighted an increase in the digestates of the proportion of amorphous or nanostructured copper sulfides as well as amorphous or nanostructured zinc sulfides and zinc phosphate as compared to raw waste. We therefore suggest that the environmental fate of these elements would be different when spreading either digestates or raw waste on cropland.

Analytical methodologies for aluminium speciation in environmental and biological samples--a review.

PubMed

Bi, S P; Yang, X D; Zhang, F P; Wang, X L; Zou, G W

2001-08-01

It is recognized that aluminium (Al) is a potential environmental hazard. Acidic deposition has been linked to increased Al concentrations in natural waters. Elevated levels of Al might have serious consequences for biological communities. Of particular interest is the speciation of Al in aquatic environments, because Al toxicity depends on its forms and concentrations. In this paper, advances in analytical methodologies for Al speciation in environmental and biological samples during the past five years are reviewed. Concerns about the specific problems of Al speciation and highlights of some important methods are elucidated in sections devoted to hybrid techniques (HPLC or FPLC coupled with ET-AAS, ICP-AES, or ICP-MS), flow-injection analysis (FIA), nuclear magnetic resonance (27Al NMR), electrochemical analysis, and computer simulation. More than 130 references are cited.

Application of the WRF-Chem model for the simulation of air quality over Cyprus

NASA Astrophysics Data System (ADS)

Kushta, Jonilda; Proestos, Yiannis; Georgiou, George; Christoudias, Theodoros; Lelieveld, Jos

2017-04-01

The fully coupled WRF-Chem (Weather Research and Forecasting with Chemistry) model is used to simulate air quality over Cyprus. Cyprus is an island country with complex topography, located in the eastern corner of East Mediterranean region, affected year-long by local, regional and long range transported pollution. An extensive sensitivity analysis of the model performance has been performed over the area of interest with three domains of respective grid spacing of 40, 8 and 2 km. Different configurations have been deployed regarding horizontal resolution, simulation timestep, boundary conditions, NOx emissions and speciation method of emitted NMVOCs (Non Methane Volatile Organic Compounds). The WRF-Chem model simulated hourly concentrations of air pollutants for a month-long period (July 2014) during which measurements are available over 13 stations (4 of which background stations, 1 industrial and 8 urban/traffic stations). The model was initialized with meteorological initial and boundary conditions (ICBC) using NCAR-NCEP's F Global Forecast System output (GFS) at a 1o x1o spatial resolution. The ICBC for the chemical species are derived from the MOZART global model results (2.5o x 2.5o). Both ICBCs datasets are updated every 6 hours. The emission inventory used in the study is the EDGAR-HTAP v2 dataset with a horizontal grid resolution of 0.1o × 0.1o, while an additional dataset with speciated NMVOCs (instead of summed volatile species) is also tested. The diurnal cycle of the atmospheric concentrations of ozone averaged over the island, exhibits a maximum of 114 μg/m3 when the boundary conditions are derived from MOZART and 94 μg/m3 when the boundary conditions are not included (local background and production), suggesting a constant inflow of ozone from long range transport of about 20 μg/m3. The contribution of pollution from regional sources is more pronounced at the western border due to the characteristic summer time north-northeasterly etesian flow that brings southward the pollution produced or accumulated over Eastern Europe, the Black sea and major upwind megacities (Istanbul, Athens etc). Ozone concentrations are overestimated in all stations indicating a possible overestimation of ozone from the global model (MOZART) that has also been discussed in other studies over neighbouring countries, or an excess of ozone production in the parent domain that includes all Eastern Mediterranean. Model results are influenced by the speciation of NMVOCs with the pre-speciated emission dataset resulting in lower ozone values by an average of 5 μg/m3. Lowering NOx emission brings ozone levels closer to observations; however this does not account for the overestimation of ozone since the respective comparison of NOx levels reveals strong underestimation of NOx (both NO and NO2) even before reducing them. Horizontal, vertical and temporal resolutions show smaller impact on changing the modelled patterns of ozone concentrations. The discrepancies between modelled and observed ozone over the main Cypriot urban areas point at the need for more detailed emission inventories, either in terms of spatial resolution and/or validation of absolute emitted values, and adjustments in the use of boundary conditions from global models.

SPECIATION OF MERCURY IN THE PRESENCE OF COAL AND WASTE COMBUSTION FLY ASHES

EPA Science Inventory

The paper gives results of a study that focused on the oxidation of elemental mercury (Hgo) in the presence of both complex, four-component, model fly ashes, and actual coal combustion fly ashes collected from a pilot plant. Steady-state oxidation of Hgo promoted by the four-com...

THE IMPACT OF GROUND WATER-SURFACE WATER INTERACTIONS ON CONTAMINANT TRANSPORT AT CONTAMINATED SITES

EPA Science Inventory

The purpose of this document is to provide an overview of the dynamics of chemical processes that govern contaminant transport and speciation during water exchange across the GW/SW transition zone. A conceptual model of the GW/SW transition zone is defined to serve as a starting...

LINKING SOLID PHASE SPECIATION OF PB SEQUESTERED TO BIRNESSITE TO ORAL PB BIOACCESSIBLITY: IMPLICATIONS FOR SOIL REMEDIATION

EPA Science Inventory

Lead (Pb) sorption onto oxide surfaces in soils may strongly influence the risk posed from incidental ingestion of lead-contaminated soils. In this study, Pb was sorbed to a model soil mineral, birnessite, and was placed in a simulated gastrointestinal tract (in vitro) to simula...

An Evaluation of the Role of Sensory Drive in the Evolution of Lake Malawi Cichlid Fishes

PubMed Central

Smith, Adam R.; van Staaden, Moira J.; Carleton, Karen L.

2012-01-01

Although the cichlids of Lake Malawi are an important model system for the study of sensory evolution and sexual selection, the evolutionary processes linking these two phenomena remain unclear. Prior works have proposed that evolutionary divergence is driven by sensory drive, particularly as it applies to the visual system. While evidence suggests that sensory drive has played a role in the speciation of Lake Victoria cichlids, the findings from several lines of research on cichlids of Lake Malawi are not consistent with the primary tenets of this hypothesis. More specifically, three observations make the sensory drive model implausible in Malawi: (i) a lack of environmental constraint due to a broad and intense ambient light spectrum in species rich littoral habitats, (ii) pronounced variation in receiver sensory characteristics, and (iii) pronounced variability in male courtship signal characteristics. In the following work, we synthesize the results from recent studies to draw attention to the importance of sensory variation in cichlid evolution and speciation, and we suggest possible avenues of future research. PMID:22779029

Release of aged contaminants from weathered sediments: Effects of sorbate speciation on scaling of reactive transport

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

Chorover, Jon; Perdrial, Nico; Mueller, Karl

2012-11-05

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 thorough characterization of reaction products over a matrix of field-relevant gradients in contaminant concentration, partial pressure of carbon dioxide, and reaction time; (ii) improvedmore » molecular-scale understanding of how 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. In this final report, we provide detailed descriptions of our results from this three-year study, completed in 2012 following a one-year no cost extension.« less

Release of Aged Contaminants from weathered sediments: Effects of sorbate speciation on scaling of reactive transport

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

Chorover, Jon; Perdrial, Nico; Mueller, Karl

2012-08-14

Hanford sediments impacted by hyperalkaline high level radioactive waste have undergone incongruent silicate mineral weathering concurrent with contaminant uptake (Chorover et al., 2008). 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 thorough characterization of reaction products over a matrix of field-relevant gradients in contaminant concentration, P CO2, and reaction time; (ii)more » improved molecular-scale understanding of how 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. Below, we provide some detailed descriptions of our results from this three year study, recently completed following a one-year no cost extension.« less

Distinct Processes Drive Diversification in Different Clades of Gesneriaceae.

PubMed

Roalson, Eric H; Roberts, Wade R

2016-07-01

Using a time-calibrated phylogenetic hypothesis including 768 Gesneriaceae species (out of [Formula: see text]3300 species) and more than 29,000 aligned bases from 26 gene regions, we test Gesneriaceae for diversification rate shifts and the possible proximal drivers of these shifts: geographic distributions, growth forms, and pollination syndromes. Bayesian Analysis of Macroevolutionary Mixtures analyses found five significant rate shifts in Beslerieae, core Nematanthus, core Columneinae, core Streptocarpus, and Pacific Cyrtandra These rate shifts correspond with shifts in diversification rates, as inferred by Binary State Speciation and Extinction Model and Geographic State Speciation and Extinction model, associated with hummingbird pollination, epiphytism, unifoliate growth, and geographic area. Our results suggest that diversification processes are extremely variable across Gesneriaceae clades with different combinations of characters influencing diversification rates in different clades. Diversification patterns between New and Old World lineages show dramatic differences, suggesting that the processes of diversification in Gesneriaceae are very different in these two geographic regions. © 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.

An introgressed wing pattern acts as a mating cue.

PubMed

Sánchez, Angela P; Pardo-Diaz, Carolina; Enciso-Romero, Juan; Muñoz, Astrid; Jiggins, Chris D; Salazar, Camilo; Linares, Mauricio

2015-06-01

Heliconius butterflies provide good examples of both homoploid hybrid speciation and ecological speciation. In particular, examples of adaptive introgression have been detected among the subspecies of Heliconius timareta, which acquired red color pattern elements from H. melpomene. We tested whether the introgression of red wing pattern elements into H. timareta florencia might also be associated with incipient reproductive isolation (RI) from its close relative, H. timareta subsp. nov., found in the eastern Andes. No choice experiments show a 50% reduction in mating between females of H. t. subsp. nov. and males of H .t. florencia, but not in the reciprocal direction. In choice experiments using wing models, males of H. timareta subsp. nov. approach and court red phenotypes less than their own, whereas males of H. t. florencia prefer models with a red phenotype. Intrinsic postzygotic isolation was not detected in crosses between these H. timareta races. These results suggest that a color pattern trait gained by introgression is triggering RI between H. timareta subsp. nov. and H. t. florencia. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

A counterflow diffusion flame study of branched octane isomers

DOE PAGES

Sarathy, S. Mani; Niemann, Ulrich; Yeung, Coleman; ...

2012-09-25

Conventional petroleum, Fischer–Tropsch (FT), and other alternative hydrocarbon fuels typically contain a high concentration of lightly methylated iso-alkanes. However, until recently little work has been done on this important class of hydrocarbon components. In order to better understand the combustion characteristics of real fuels, this study presents new experimental data for 3-methylheptane and 2,5-dimethylhexane in counterflow diffusion flames. This new dataset includes flame ignition, extinction, and speciation profiles. The high temperature oxidation of these fuels has been modeled using an extended transport database and a high temperature skeletal chemical kinetic model. The skeletal model is generated from a detailed modelmore » reduced using the directed relation graph with expert knowledge (DRG-X) methodology. The proposed skeletal model contains sufficient chemical fidelity to accurately predict the experimental speciation data in flames. The predictions are compared to elucidate the effects of number and location of the methyl substitutions. The location is found to have little effect on ignition and extinction in these counterflow diffusion flames. However, increasing the number of methyl substitutions was found to inhibit ignition and promote extinction. Chemical kinetic modelling simulations were used to correlate a fuel’s extinction propensity with its ability to populate the H radical concentration. In conclusion, species composition measurements indicate that the location and number of methyl substitutions was found to particularly affect the amount and type of alkenes observed.« less

Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow.

PubMed

Sachdeva, Himani; Barton, Nicholas H

2017-06-01

Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Quantification of Cation Sorption to Engineered Barrier Materials Under Extreme Conditions

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

Powell, Brian; Schlautman, Mark; Rao, Linfeng

The objective of this research is to examine mechanisms and thermodynamics of actinide sorption to engineered barrier materials (iron (oxyhydr)oxides and bentonite clay) for nuclear waste repositories under high temperature and high ionic strength conditions using a suite of macroscopic and microscopic techniques which will be coupled with interfacial reaction models. Gaining a mechanistic understanding of interfacial processes governing the sorption/sequestration of actinides at mineral-water interfaces is fundamental for the accurate prediction of actinide behavior in waste repositories. Although macroscale sorption data and various spectroscopic techniques have provided valuable information regarding speciation of actinides at solid-water interfaces, significant knowledge gapsmore » still exist with respect to sorption mechanisms and the ability to quantify sorption, particularly at high temperatures and ionic strengths. This objective is addressed through three major tasks: (1) influence of oxidation state on actinide sorption to iron oxides and clay minerals at elevated temperatures and ionic strengths; (2) calorimetric titrations of actinide-mineral suspensions; (3) evaluation of bentonite performance under repository conditions. The results of the work will include a qualitative conceptual model and a quantitative thermodynamic speciation model describing actinide partitioning to minerals and sediments, which is based upon a mechanistic understanding of specific sorption processes as determined from both micro-scale and macroscale experimental techniques. The speciation model will be a thermodynamic aqueous and surface complexation model of actinide interactions with mineral surfaces that is self-consistent with macroscopic batch sorption data, calorimetric and potentiometric titrations, X-ray absorption Spectroscopy (XAS, mainly Extended X-ray Absorption Fine Structure (EXAFS)), and electron microscopy analyses. The novelty of the proposed work lies largely in the unique system conditions which will be examined (i.e. elevated temperature and ionic strength) and the manner in which the surface complexation model will be developed in terms of specific surface species identified using XAS. These experiments will thus provide a fundamental understanding of the chemical and physical processes occurring at the solid-solution interface under expected repository conditions. Additionally, the focus on thermodynamic treatment of actinide ion interactions with minerals as proposed will provide information on the driving forces involved and contribute to the overall understanding of the high affinity many actinide ions have for oxide surfaces. The utility of this model will be demonstrated in this work through a series of advective and diffusive flow experiments.« less