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Sample records for inferring speciation modes

  1. Model inadequacy and mistaken inferences of trait-dependent speciation.

    PubMed

    Rabosky, Daniel L; Goldberg, Emma E

    2015-03-01

    Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the relationships among character states, speciation rates, and extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related models-have been widely used to test hypotheses about character state-dependent diversification rates. Here, we document the disconcerting ease with which neutral traits are inferred to have statistically significant associations with speciation rate. We first demonstrate this unfortunate effect for a known model assumption violation: shifts in speciation rate associated with a character not included in the model. We further show that for many empirical phylogenies, characters simulated in the absence of state-dependent diversification exhibit an even higher Type I error rate, indicating that the method is susceptible to additional, unknown model inadequacies. For traits that evolve slowly, the root cause appears to be a statistical framework that does not require replicated shifts in character state and diversification. However, spurious associations between character state and speciation rate arise even for traits that lack phylogenetic signal, suggesting that phylogenetic pseudoreplication alone cannot fully explain the problem. The surprising severity of this phenomenon suggests that many trait-diversification relationships reported in the literature may not be real. More generally, we highlight the need for diagnosing and understanding the consequences of model inadequacy in phylogenetic comparative methods. PMID:25601943

  2. Inferring Flare Loop Parameters with Measurements of Standing Sausage Modes

    NASA Astrophysics Data System (ADS)

    Guo, Ming-Zhe; Chen, Shao-Xia; Li, Bo; Xia, Li-Dong; Yu, Hui

    2016-03-01

    Standing fast sausage modes in flare loops were suggested to account for a considerable number of quasi-periodic pulsations (QPPs) in the light curves of solar flares. This study continues our investigation into the possibility of inverting the measured periods P and damping times τ of sausage modes to deduce the transverse Alfvén time R/v_{Ai}, density contrast ρi/ρe, and the steepness of the density distribution transverse to flare loops. A generic dispersion relation governing linear sausage modes is derived for pressureless cylinders where density inhomogeneity of arbitrary form takes place within the cylinder. We show that in general the inversion problem is under-determined for QPP events where only a single sausage mode exists, whether the measurements are spatially resolved or unresolved. While R/v_{Ai} can be inferred to some extent, the range of possible steepness parameters may be too broad to be useful. However, for spatially resolved measurements where an additional mode is present, it is possible to deduce self-consistently ρi/ρe, the profile steepness, and the internal Alfvén speed v_{Ai}. We show that at least for a recent QPP event that involves a fundamental kink mode in addition to a sausage one, flare loop parameters are well constrained even if the specific form of the transverse density distribution remains unknown. We conclude that spatially resolved, multi-mode QPP measurements need to be pursued to infer flare loop parameters.

  3. Tempo and mode of speciation in Holacanthus angelfishes based on RADseq markers.

    PubMed

    Tariel, Juliette; Longo, Gary C; Bernardi, Giacomo

    2016-05-01

    In this study we estimated the timing of speciation events in a group of angelfishes using 1186 RADseq markers corresponding to 94,880 base pairs. The genus Holacanthus comprises seven species, including two clades of Panama trans-Isthmian geminates, which diverged approximately 3-3.5Mya. These clades diversified within the Tropical Eastern Pacific (TEP, three species) and Tropical Western Atlantic (TWA, two species) which our data suggest to have occurred within the past 1.5My in both ocean basins, but may have proceeded via different mechanisms. In the TEP, speciation is likely to have followed a peripatric pathway, while in the TWA, sister species are currently partially sympatric, thus raising the possibility of sympatric speciation. This study highlights the use of RADseq markers for estimating both divergence times and modes of speciation at a 1-3My timescale. PMID:26876637

  4. Hawthorn-infesting populations of Rhagoletis pomonella in Mexico and speciation mode plurality.

    PubMed

    Xie, Xianfa; Rull, Juan; Michel, Andrew P; Velez, Sebastian; Forbes, Andrew A; Lobo, Neil F; Aluja, Martin; Feder, Jeffrey L

    2007-05-01

    Categorizing speciation into dichotomous allopatric versus nonallopatric modes may not always adequately describe the geographic context of divergence for taxa. If some of the genetic changes generating inherent barriers to gene flow between populations evolved in geographic isolation, whereas others arose in sympatry, then the mode of divergence would be mixed. The apple maggot fly, Rhagoletis pomonella, has contributed to this emerging concept of a mixed speciation mode "plurality." Genetic studies have implied that a source of diapause life-history variation associated with inversions and contributing to sympatric host race formation and speciation for R. pomonella in the United States may have introgressed from the Eje Volcanico Trans Mexicano (EVTM; a.k.a. the Altiplano) in the past. A critical unresolved issue concerning the introgression hypothesis is how past gene flow occurred given the current 1200-km disjunction in the ranges of hawthorn-infesting flies in the EVTM region of Mexico and the southern extreme of the U.S. population in Texas. Here, we report the discovery of a hawthorn-infesting population of R. pomonella in the Sierra Madre Oriental Mountains (SMO) of Mexico. Sequence data from 15 nuclear loci and mitochondrial DNA imply that the SMO flies are related to, but still different from, U.S. and EVTM flies. The host affiliations, diapause characteristics, and phylogeography of the SMO population are consistent with it having served as a conduit for gene flow between Mexico and the United States. We also present evidence suggesting greater permeability of collinear versus rearranged regions of the genome to introgression, in accord with recent models of chromosomal speciation. We discuss the implications of the results in the context of speciation mode plurality. We do not argue for abandoning the terms sympatry or allopatry, but caution that categorizing divergence into either/or geographic modes may not describe the genetic origins of all

  5. Tempo of speciation in a butterfly genus from the Southeast Asian tropics, inferred from mitochondrial and nuclear DNA sequence data.

    PubMed

    Megens, Hendrik-Jan; van Moorsel, Coline H M; Piel, William H; Pierce, Naomi E; de Jong, Rienk

    2004-06-01

    Molecular systematics is frequently beset with phylogenetic results that are not fully resolved. Researchers either state that the absence of resolution is due to character conflict, explosive speciation, or some combination of the two, but seldom do they carefully examine their data to distinguish between these causes. In this study, we exhaustively analyze a set of nuclear and mitochondrial nucleotide data for the Asian tropical butterfly genus Arhopala so as to highlight the causes of polytomies in the phylogenetic trees, and, as a result, to infer important biological events in the history of this genus. We began by using non-parametric statistical methods to determine whether the ambiguously resolved regions in these trees represent hard or soft polytomies. In addition we determined how this correlated to number of inferred changes on branches, using parametric maximum likelihood estimations. Based on congruent patterns in both mitochondrial and nuclear DNA sequences, we concluded that at two stages in the history of Arhopala there have been accelerated instances of speciation. One event, at the base of the phylogeny, generated many of the groups and subgroups currently recognized in this genus, while a later event generated another major clade consisting of both Oriental and Papuan species groups. Based on comparisons of closely related taxa, the ratio of instantaneous rate of evolution between mitochondrial and nuclear DNA evolution is established at approximately 3:1. The earliest radiation is dated between 7 and 11 Ma by a molecular clock analysis, setting the events generating much of the diversity of Arhopala at well before the Pleistocene. Periodical flooding of the Sunda plateau during interglacial periods was, therefore, not responsible for generating the major divisions in the genus Arhopala. Instead, we hypothesize that large-scale climatic changes taking place in the Miocene have induced the early acceleration in speciation. PMID:15120408

  6. Geographic mode of speciation in a mountain specialist Avian family endemic to the Palearctic

    PubMed Central

    Drovetski, Sergei V; Semenov, Georgy; Drovetskaya, Sofya S; Fadeev, Igor V; Red'kin, Yaroslav A; Voelker, Gary

    2013-01-01

    Mountains host greater avian diversity than lowlands at the same latitude due to their greater diversity of habitats stratified along an elevation gradient. Here we test whether this greater ecological heterogeneity promotes sympatric speciation. We selected accentors (Prunellidae), an avian family associated with mountains of the Palearctic, as a model system. Accentors differ in their habitat/elevation preferences and south-central Siberia and Himalayan regions each host 6 of the 13 species in the family. We used sequences of the mtDNA ND2 gene and the intron 9 of the Z chromosome specific ACO1 gene to reconstruct a complete species-level phylogeny of Prunellidae. The tree based on joint analysis of both loci was used to reconstruct the family's biogeographic history and to date the diversification events. We also analyzed the relationship between the node age and sympatry, to determine the geographic mode of speciation in Prunellidae. Our data suggest a Miocene origin of Prunellidae in the Himalayan region. The major division between alpine species (subgenus Laiscopus) and species associated with shrubs (subgenus Prunella) and initial diversification events within the latter happened within the Himalayan region in the Miocene and Pliocene. Accentors colonized other parts of the Palearctic during the Pliocene-Pleistocene transition. This spread across the Palearctic resulted in rapid diversification of accentors. With only a single exception dating to 0.91 Ma, lineages younger than 1.5 Ma are allopatric. In contrast, sympatry values for older nodes are >0. There was no relationship between node age and range symmetry. Allopatric speciation (not to include peripatric) is the predominant geographic mode of speciation in Prunellidae despite the favorable conditions for ecological diversification in the mountains and range overlaps among species. PMID:23789064

  7. Phylogeny and evolution of the Sulidae (Aves:Pelecaniformes): a test of alternative modes of speciation.

    PubMed

    Friesen, V L; Anderson, D J

    1997-04-01

    Although the allopatric model of speciation is widely accepted, it does not provide a satisfactory explanation for many evolutionary phenomena. Several alternative models exist, but they remain largely untested for vertebrate animals. In the present paper, a molecular phylogeny was used to test competing models of speciation in a seabird family, the Sulidae. A segment including 807 base pairs of the mitochondrial cytochrome b gene was sequenced from all extant sulid species, and phylogenetic methods were used to test model-specific predictions regarding tree topologies, distributions of sister taxa, timing of vicariant events, and comparative biology. Both the neighbor-joining and parsimony analyses placed sequences of gannets (Morus spp.) and boobies of the genus Sula in separate, monophyletic lineages. Sequences of Cape (M. capensis) and Australasian (M. serrator) gannets clustered together, and the sequence of Abbott's booby (Papasula abbotti) was basal to those of the gannets. Sequences of blue-footed (S. nebouxii) and Peruvian (S. variegata) boobies were sisters and formed a monophyletic group with the masked booby (S. dactylatra). The red-footed booby (S. sula) sequence was the most divergent of the Sula boobies. All relationships received strong support from standard-error tests and bootstrap analysis. Substitution rates were similar to those suggested for mammals and suggested that most lineages arose within the last 3 million years. Lineage divergence events for which the mode of speciation could be deduced did not fit the predictions of either allopatric or sympatric models, but apparently involved either peripatric or parapatric processes. PMID:9126567

  8. 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

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

    PubMed

    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

  10. Theoretical studies of speciation and evolutionary inference. Annual progress report, October 1980-September 1981

    SciTech Connect

    Felsenstein, J.

    1981-09-01

    The past year has been a fairly active one, with several pending papers finally being published, along with the Bibliography of Theoretical Population Genetics. The Package for Inferring Phylogenies has enjoyed widespread distribution and popularity. A number of papers submitted in the last part of last year were accepted and are about to be published, and several new projects have resulted in new papers being submitted, in particular a major review article on numerical methods for inferring evolutionary trees. My involvement in development methods for analyzing DNA sequence data has increased.

  11. Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes

    PubMed Central

    Krause, David J.; Whitaker, Rachel J.

    2015-01-01

    Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms. PMID:26316424

  12. INFERRING PHYSICAL PARAMETERS OF COMPACT STARS FROM THEIR f-MODE GRAVITATIONAL WAVE SIGNALS

    SciTech Connect

    Lau, H. K.; Leung, P. T.; Lin, L. M. E-mail: ptleung@phy.cuhk.edu.h

    2010-05-10

    We propose here a robust scheme to infer the physical parameters of compact stars from their f-mode gravitational wave signals. We first show that the frequency and the damping rate of f-mode oscillation of compact stars can be expressed in terms of universal functions of stellar mass and moment of inertia. By employing the universality in the f-mode one can then infer accurate values of the mass, the moment of inertia, and the radius of a compact star. In addition, we demonstrate that our new scheme works well for both realistic neutron stars and quark stars, and hence provides a unifying way to infer the physical parameters of compact stars.

  13. Tempo and mode in fossil molluscs: Investigating organism-environment interactions, species, and speciation

    SciTech Connect

    Geary, D.H. )

    1992-01-01

    After 20 years of investigation into the tempo and mode of species-level change in the fossil record, it is clear that both punctuated equilibrium and phyletic gradualism occur, as do a variety of intermediate patterns. Important questions regarding the maintenance and diversification of species remain, however. The author documents a variety of evolutionary patterns from gastropods and bivalves, and uses these to discuss two basic issues: environment-organism interactions over time, and the importance of information on geographic variation. The tempo of morphological change is an expression of the interaction of organisms and their environment. The initial over which new species appear may be a geologic instant'' (Melanopsis gastropods), or may last 10[sup 4]--10[sup 5] years (Prunum gastropods), or 10[sup 6] years (Melanopsis). This wide range of intervals indicates a variety of tempos of environmental change, and/or different kinds of organismal responses. Analysis of geographic variation is of critical importance in understanding species and speciation, yet is lacking in many paleontological studies. An example of the utility of geographic information is a study of the muricid gastropod Acanthina, which demonstrates how a geographically localized form may spread through a species range. Another example involves a species of Pleuriocardia in stasis: geographic variation among roughly correlative samples greatly exceeds long-term temporal variation. Considerations of the mechanisms for stasis and change must take into account such intraspecific variation.

  14. Inferring the mode of origin of polyploid species from next-generation sequence data.

    PubMed

    Roux, Camille; Pannell, John R

    2015-03-01

    Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels. PMID:25585898

  15. Inference of stress and texture from angular dependence of ultrasonic plate mode velocities

    NASA Technical Reports Server (NTRS)

    Thompson, R. B.; Smith, J. F.; Lee, S. S.

    1986-01-01

    The theory for the angular dependence of the ultrasonic wave velocity in a symmetry plane of an orthorhombic, stressed material is presented. The two waves having polarizations in this plane are shown to have velocities which can be estimated from measurements of the SH sub 0 and S sub 0 guided modes of a thin plate: the relationship being exact for the SH sub 0 mode and requiring a 10% correction for the S sub 0 mode at long wavelength. It is then shown how stress and texture can be independently inferred from various features of the angular dependence of these two velocities. From the SH sub 0 data, the ability to determine the directions and differences in magnitudes of principal stresses is described and supported by experimental data on several materials. From a combination of the SH sub 0 and S sub 0 data, a procedure is proposed for determining the coefficients W sub 400, W sub 420 and W sub 440 of an expansion of the crystallite orientation distribution function in terms of generalized Legendre functions. Possible applications in process control are indicated.

  16. Speciation, diversity, and Mode 1 technologies: the impact of variability selection.

    PubMed

    Grove, Matt

    2011-09-01

    Over geological timescales, organisms encounter periodic shifts in selective conditions driven by environmental change. The variability selection hypothesis suggests that increases in environmental fluctuation have led to the evolution of complex, flexible behaviours able to respond to novel and unpredictable adaptive settings. This hypothesis is tested via the framework of a single locus genetic model in which an invading 'versatilist' allele competes with two opposed specialists in a selection regime driven by a fluctuating environment, modelled initially as a sine wave and subsequently as an empirical climate curve covering the past 5 million years. Results demonstrate that generalist alleles achieve fixation in the sine wave environment, whilst versatilist alleles do so in the empirical environment, even at a range of very low fitness advantages over the basic generalist template. Variability selection is found to be a particularly strong force between approximately 2.5 and 1.2 Ma (millions of years ago). These results are discussed in relation to the spread of Oldowan lithics and the patterns of speciation and extinction documented in the hominin fossil record. It is suggested that the flexibility required for survival in a variable climatic regime may have been a stimulus to the development of the first stone tool technologies, whilst the ecological opportunities provided by heightened variability may have been a factor in prompting the hominin adaptive radiation evidenced during this period. PMID:21664648

  17. Inferring the Mode of Selection from the Transient Response to Demographic Perturbations

    NASA Astrophysics Data System (ADS)

    Balick, Daniel; Do, Ron; Reich, David; Sunyaev, Shamil

    2014-03-01

    Despite substantial recent progress in theoretical population genetics, most models work under the assumption of a constant population size. Deviations from fixed population sizes are ubiquitous in natural populations, many of which experience population bottlenecks and re-expansions. The non-equilibrium dynamics introduced by a large perturbation in population size are generally viewed as a confounding factor. In the present work, we take advantage of the transient response to a population bottleneck to infer features of the mode of selection and the distribution of selective effects. We develop an analytic framework and a corresponding statistical test that qualitatively differentiates between alleles under additive and those under recessive or more general epistatic selection. This statistic can be used to bound the joint distribution of selective effects and dominance effects in any diploid sexual organism. We apply this technique to human population genetic data, and severely restrict the space of allowed selective coefficients in humans. Additionally, one can test a set of functionally or medically relevant alleles for the primary mode of selection, or determine the local regional variation in dominance coefficients along the genome.

  18. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K

    PubMed Central

    Kopelman, Naama M; Mayzel, Jonathan; Jakobsson, Mattias; Rosenberg, Noah A; Mayrose, Itay

    2015-01-01

    The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modeling assumptions, compares results across different pre-determined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the post-processing of results of model-based population structure analyses. For analyzing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp, and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology. PMID:25684545

  19. Standing Sausage Modes in Nonuniform Magnetic Tubes: An Inversion Scheme for Inferring Flare Loop Parameters

    NASA Astrophysics Data System (ADS)

    Chen, Shao-Xia; Li, Bo; Xiong, Ming; Yu, Hui; Guo, Ming-Zhe

    2015-10-01

    Standing sausage modes in flare loops are important for interpreting quasi-periodic pulsations (QPPs) in solar flare light curves. We propose an inversion scheme that consistently uses their periods P and damping times τ to diagnose flare loop parameters. We derive a generic dispersion relation governing linear sausage waves in pressure-less straight tubes, for which the transverse density inhomogeneity takes place in a layer of arbitrary width l and is of arbitrary form. We find that P and τ depend on the combination of [R/{v}{Ai},L/R,l/R,{ρ }{{i}}/{ρ }{{e}}], where R is the loop radius, L is the looplength, vAi is the internal Alfvén speed, and ρi/ρe is the density contrast. For all the density profiles examined, P and τ experience saturation when L/R ≫ 1, yielding an inversion curve in the [R/{v}{Ai},l/R,{ρ }{{i}}/{ρ }{{e}}] space with a specific density profile when L/R is sufficiently large. When applied to a spatially unresolved QPP event, the scheme yields that R/vAi is the best constrained, whereas l/R corresponds to the other extreme. For spatially resolved QPPs, while L/R ≫ 1 cannot be assumed beforehand, an inversion curve remains possible due to additional geometrical constraints. When a spatially resolved QPP event involves another mode, as is the case for a recent event, the full set of [{v}{Ai},l,{ρ }{{i}}/{ρ }{{e}}] can be inferred. We conclude that the proposed scheme provides a useful tool for magneto-seismologically exploiting QPPs.

  20. Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets.

    PubMed

    Shaw, Kerry L

    2002-12-10

    It has been asserted that recent mtDNA phylogenies support the plausibility of sympatric speciation, long considered a controversial mechanism of the origin of species. If such inferences are reliable, mtDNA phylogenies should be congruent with phylogenies based on other data. In previous work, a mtDNA phylogeny suggested that diversification of the Hawaiian cricket genus Laupala was initiated by single invasions into each of several Hawaiian islands, followed by multiple sympatric divergences within each island. In contrast, a systematic hypothesis based on morphology argues that speciation in Laupala has occurred primarily in allopatry, with two independent species radiations diversifying across the archipelago. In this study, I analyze nuclear DNA (nDNA) sequences from Laupala to compare with sequences from the mtDNA. The nDNA phylogeny corroborates the hypothesis of allopatric divergence and multiple invasions, and when compared with mtDNA patterns, suggests that interspecific hybridization is a persistent feature of the history of Laupala. The discrepancy between mtDNA and nDNA phylogenies reveals that speciation histories based on mtDNA alone can be extensively misleading. PMID:12451181

  1. Mode of Action for Reproductive and Hepatic Toxicity Inferred from a Genomic Study of Triazole Antifungals

    EPA Science Inventory

    The mode of action for the reproductive toxicity of triazole antifungals have been previously characterized by an observed increased in serum testosterone, hepatotoxicity, and reduced insemination and fertility indices. In order to refine our mechanistic understanding of these m...

  2. A new description of Earth's wobble modes using Clairaut coordinates 2: results and inferences on the core mode spectrum

    NASA Astrophysics Data System (ADS)

    Crossley, D. J.; Rochester, M. G.

    2014-09-01

    Numerical solutions are presented for the formulation of the linear momentum description of Earth's dynamics using Clairaut coordinates. We have developed a number of methods to integrate the equations of motion, including starting at the Earth's centre of mass, starting at finite radius and separating the displacement associated with the primary rigid rotation. We include rotation and ellipticity to second order up to spherical harmonic T_5^m, starting with the primary displacement T_1^m with m = ±1. We are able to confirm many of the previous results for models PREM (with no surface ocean) and 1066A, both in their original form and with neutrally stratified liquid cores. Our period search ranges from the near-seismic band [0.1 sidereal days (sd)] to 3500 sd, within which we have identified the four well-known wobble-nutation modes: the Free Core Nutation (retrograde) at -456 sd, the Free Inner Core Nutation (FICN, prograde) at 468 sd, the Chandler Wobble (prograde) at 402 sd, and the Inner Core Wobble (ICW, prograde) at about 2842 sd (7.8 yr) for neutral PREM. The latter value varies significantly with earth model and integration method. In addition we have verified to high accuracy the tilt-over mode at 1 sd within a factor 10-6. In an exhaustive search we found no additional near-diurnal wobble modes that could be identified as nutations. We show that the eigenfunctions for the as-yet-unidentified ICW are extremely sensitive to the details of the earth model, especially the core stability profile and there is no well-defined sense of its wobble relative to the mantle. Calculations are also done for a range of models derived from PREM with homogeneous layers, as well as with incompressible cores. For this kind of model the ICW ceases to have just a simple IC rigid motion when the fluid compressibility is either unchanged or multiplied by a factor 10; in this case the outer core exhibits oscillations that arise from an unstable fluid density stratification. For

  3. Adaptive neuro-fuzzy inference system for acoustic analysis of 4-channel phonocardiograms using empirical mode decomposition.

    PubMed

    Becerra, Miguel A; Orrego, Diana A; Delgado-Trejos, Edilson

    2013-01-01

    The heart's mechanical activity can be appraised by auscultation recordings, taken from the 4-Standard Auscultation Areas (4-SAA), one for each cardiac valve, as there are invisible murmurs when a single area is examined. This paper presents an effective approach for cardiac murmur detection based on adaptive neuro-fuzzy inference systems (ANFIS) over acoustic representations derived from Empirical Mode Decomposition (EMD) and Hilbert-Huang Transform (HHT) of 4-channel phonocardiograms (4-PCG). The 4-PCG database belongs to the National University of Colombia. Mel-Frequency Cepstral Coefficients (MFCC) and statistical moments of HHT were estimated on the combination of different intrinsic mode functions (IMFs). A fuzzy-rough feature selection (FRFS) was applied in order to reduce complexity. An ANFIS network was implemented on the feature space, randomly initialized, adjusted using heuristic rules and trained using a hybrid learning algorithm made up by least squares and gradient descent. Global classification for 4-SAA was around 98.9% with satisfactory sensitivity and specificity, using a 50-fold cross-validation procedure (70/30 split). The representation capability of the EMD technique applied to 4-PCG and the neuro-fuzzy inference of acoustic features offered a high performance to detect cardiac murmurs. PMID:24109851

  4. Lightning on Venus inferred from whistler-mode waves in the ionosphere.

    PubMed

    Russell, C T; Zhang, T L; Delva, M; Magnes, W; Strangeway, R J; Wei, H Y

    2007-11-29

    The occurrence of lightning in a planetary atmosphere enables chemical processes to take place that would not occur under standard temperatures and pressures. Although much evidence has been reported for lightning on Venus, some searches have been negative and the existence of lightning has remained controversial. A definitive detection would be the confirmation of electromagnetic, whistler-mode waves propagating from the atmosphere to the ionosphere. Here we report observations of Venus' ionosphere that reveal strong, circularly polarized, electromagnetic waves with frequencies near 100 Hz. The waves appear as bursts of radiation lasting 0.25 to 0.5 s, and have the expected properties of whistler-mode signals generated by lightning discharges in Venus' clouds. PMID:18046401

  5. Evolution of larval life mode of Oecophoridae (Lepidoptera: Gelechioidea) inferred from molecular phylogeny.

    PubMed

    Kim, Sora; Kaila, Lauri; Lee, Seunghwan

    2016-08-01

    Phylogenetic relationships within family Oecophoridae have been poorly understood. Consequently the subfamily and genus level classifications with this family problematic. A comprehensive phylogenetic analysis of Oecophoridae, the concealer moths, was performed based on analysis of 4444 base pairs of mitochondrial COI, nuclear ribosomal RNA genes (18S and 28S) and nuclear protein coding genes (IDH, MDH, Rps5, EF1a and wingless) for 82 taxa. Data were analyzed using maximum likelihood (ML), parsimony (MP) and Bayesian (BP) phylogenetic frameworks. Phylogenetic analyses indicated that (i) genera Casmara, Tyrolimnas and Pseudodoxia did not belong to Oecophoridae, suggesting that Oecophoridae s. authors was not monophyletic; (ii) other oecophorids comprising two subfamilies, Pleurotinae and Oecophorinae, were nested within the same clade, and (iii) Martyringa, Acryptolechia and Periacmini were clustered with core Xyloryctidae. They appeared to be sister lineage with core Oecophoridae. BayesTraits were implemented to explore the ancestral character states to infer historical microhabitat patterns and sheltering strategy of larvae. Reconstruction of ancestral microhabitat of oecophorids indicated that oecophorids might have evolved from dried plant feeders and further convergently specialized. The ancestral larva sheltering strategy of oecophorids might have used a silk tube by making itself, shifting from mining leaves. PMID:27184341

  6. Inferring the degree of incipient speciation in secondary contact zones of closely related lineages of Palearctic green toads (Bufo viridis subgroup).

    PubMed

    Dufresnes, C; Bonato, L; Novarini, N; Betto-Colliard, C; Perrin, N; Stöck, M

    2014-07-01

    Reproductive isolation between lineages is expected to accumulate with divergence time, but the time taken to speciate may strongly vary between different groups of organisms. In anuran amphibians, laboratory crosses can still produce viable hybrid offspring >20 My after separation, but the speed of speciation in closely related anuran lineages under natural conditions is poorly studied. Palearctic green toads (Bufo viridis subgroup) offer an excellent system to address this question, comprising several lineages that arose at different times and form secondary contact zones. Using mitochondrial and nuclear markers, we previously demonstrated that in Sicily, B. siculus and B. balearicus developed advanced reproductive isolation after Plio-Pleistocene divergence (2.6 My, 3.3-1.9), with limited historic mtDNA introgression, scarce nuclear admixture, but low, if any, current gene flow. Here, we study genetic interactions between younger lineages of early Pleistocene divergence (1.9 My, 2.5-1.3) in northeastern Italy (B. balearicus, B. viridis). We find significantly more, asymmetric nuclear and wider, differential mtDNA introgression. The population structure seems to be molded by geographic distance and barriers (rivers), much more than by intrinsic genomic incompatibilities. These differences of hybridization between zones may be partly explained by differences in the duration of previous isolation. Scattered research on other anurans suggests that wide hybrid zones with strong introgression may develop when secondary contacts occur <2 My after divergence, whereas narrower zones with restricted gene flow form when divergence exceeds 3 My. Our study strengthens support for this rule of thumb by comparing lineages with different divergence times within the same radiation. PMID:24713825

  7. Capabilities of mixed-mode liquid chromatography coupled to inductively coupled plasma mass spectrometry for the simultaneous speciation analysis of inorganic and organically-bound selenium.

    PubMed

    Peachey, Emma; Cook, Ken; Castles, Adrian; Hopley, Christopher; Goenaga-Infante, Heidi

    2009-10-16

    This work investigates for the first time the potential of mixed-mode (anion-exchange with reversed-phase) high performance liquid chromatography coupled to inductively coupled plasma mass spectrometry (ICP-MS) for the simultaneous retention and selective separation of a range of inorganic and organically-bound selenium (Se) species. Baseline separation and detection of selenocystine (SeCys(2)), Se-methyl-selenocysteine (SeMC), selenomethionine (SeMet), methylseleninic acid (MSA), selenite, gamma-glutamyl-methyl-selenocysteine (gamma-glutamyl-SeMC), and selenate in a Se standard mixture by mixed-mode HPLC-ICP-MS was achieved by switching between two citrate mobile phases of different pH and ionic strength within a single chromatographic run of 20 min. Limits of detection obtained for these Se species ranged from 80 ng kg(-1) (for SeMC) to 123 ng kg(-1) (for selenate). Using this approach as developed for selenium speciation, an adequate separation of inorganic and organic As compounds was also achieved. These include arsenite, arsenate, arsenobetaine (AsB) and dimethylarsenic acid (DMA), which may coexist with Se species in biological samples. Application of the newly proposed methodology to the investigation of the elemental species distribution in watercress (used as the model sample) after enzymatic hydrolysis or leaching in water by accelerated solvent extraction (ASE) was addressed. Only SeMet, SeMC and selenate could be tentatively identified in watercress extracts by mixed-mode HPLC-ICP-MS and retention time matching with standards. Recoveries (n=3) of these Se species from samples spiked with standards averaged 102% (for SeMC), 94.9% (for SeMet) and 98.3% (for selenate). Verification of the presence of SeMet and SeMC in an enzymatic watercress extract was achieved by on-line HPLC-ESI MS/MS in selected reaction monitoring (SRM) mode. PMID:19758595

  8. Modeling transportation of efavirenz: inference on possibility of mixed modes of transportation and kinetic solubility.

    PubMed

    Nemaura, Tafireyi

    2015-01-01

    Understanding drug transportation mechanisms in the human body is of paramount importance in modeling Pharmacokinetic-Pharmacodynamic relationships. This work gives a novel general model of efavirenz transportation projections based on concentrations simulated from patients on a dose of 600 mg. The work puts forward a proposition that transportation can wholly be modeled by concentration and time in a uniform volumetric space. Furthermore, movement entities are used to inform the state of "kinetic solubility" of a solution. There is use of Ricker's model, and forms of the Hill's equation in modeling transportation. Characterization on the movement rates of solution particle are suggested in relation to advection rate of solution particle. At turning points on the transportation rate of solution particle vs. concentration curve, a suggestion of possibly change of dominance in the mode of transportation and saturation is made. There are four movement rates postulated at primary micro-level transportation, that are attributed to convection, diffusion [passive transportation (EI )] and energy dependent system transportation (ED ) in relation to advection. Furthermore, a new parameter is introduced which is defined as an advection rate constant of solution particle. It is postulated to be dependent on two rate constants of solution particle, that is a convection rate constant of solution particle and a saturable transportation rate constant of solution particle. At secondary micro-level transportation, the results show convection as sum of advection and saturable transportation. The kinetics of dissolution of efavirenz in the solution space is postulated. Relatively, a good level of kinetics of dissolution is projected in the concentration region 0 - 32.82 μg/ml. PMID:26106329

  9. Modeling transportation of efavirenz: inference on possibility of mixed modes of transportation and kinetic solubility

    PubMed Central

    Nemaura, Tafireyi

    2015-01-01

    Understanding drug transportation mechanisms in the human body is of paramount importance in modeling Pharmacokinetic-Pharmacodynamic relationships. This work gives a novel general model of efavirenz transportation projections based on concentrations simulated from patients on a dose of 600 mg. The work puts forward a proposition that transportation can wholly be modeled by concentration and time in a uniform volumetric space. Furthermore, movement entities are used to inform the state of “kinetic solubility” of a solution. There is use of Ricker's model, and forms of the Hill's equation in modeling transportation. Characterization on the movement rates of solution particle are suggested in relation to advection rate of solution particle. At turning points on the transportation rate of solution particle vs. concentration curve, a suggestion of possibly change of dominance in the mode of transportation and saturation is made. There are four movement rates postulated at primary micro-level transportation, that are attributed to convection, diffusion [passive transportation (EI)] and energy dependent system transportation (ED) in relation to advection. Furthermore, a new parameter is introduced which is defined as an advection rate constant of solution particle. It is postulated to be dependent on two rate constants of solution particle, that is a convection rate constant of solution particle and a saturable transportation rate constant of solution particle. At secondary micro-level transportation, the results show convection as sum of advection and saturable transportation. The kinetics of dissolution of efavirenz in the solution space is postulated. Relatively, a good level of kinetics of dissolution is projected in the concentration region 0 − 32.82 μg/ml. PMID:26106329

  10. DOSE RESPONSE FROM HIGH THROUGHPUT GENE EXPRESSION STUDIES AND THE INFLUENCE OF TIME AND CELL LINE ON INFERRED MODE OF ACTION BY ONTOLOGIC ENRICHMENT (SOT)

    EPA Science Inventory

    Gene expression with ontologic enrichment and connectivity mapping tools is widely used to infer modes of action (MOA) for therapeutic drugs. Despite progress in high-throughput (HT) genomic systems, strategies suitable to identify industrial chemical MOA are needed. The L1000 is...

  11. Segmentation of plate coupling, fate of subduction fluids, and modes of arc magmatism in Cascadia, inferred from magnetotelluric resistivity

    NASA Astrophysics Data System (ADS)

    Wannamaker, Philip E.; Evans, Rob L.; Bedrosian, Paul A.; Unsworth, Martyn J.; Maris, Virginie; McGary, R. Shane

    2014-11-01

    magnetotelluric (MT) profiles have been acquired across the Cascadia subduction system and transformed using 2-D and 3-D nonlinear inversion to yield electrical resistivity cross sections to depths of ˜200 km. Distinct changes in plate coupling, subduction fluid evolution, and modes of arc magmatism along the length of Cascadia are clearly expressed in the resistivity structure. Relatively high resistivities under the coasts of northern and southern Cascadia correlate with elevated degrees of inferred plate locking, and suggest fluid- and sediment-deficient conditions. In contrast, the north-central Oregon coastal structure is quite conductive from the plate interface to shallow depths offshore, correlating with poor plate locking and the possible presence of subducted sediments. Low-resistivity fluidized zones develop at slab depths of 35-40 km starting ˜100 km west of the arc on all profiles, and are interpreted to represent prograde metamorphic fluid release from the subducting slab. The fluids rise to forearc Moho levels, and sometimes shallower, as the arc is approached. The zones begin close to clusters of low-frequency earthquakes, suggesting fluid controls on the transition to steady sliding. Under the northern and southern Cascadia arc segments, low upper mantle resistivities are consistent with flux melting above the slab plus possible deep convective backarc upwelling toward the arc. In central Cascadia, extensional deformation is interpreted to segregate upper mantle melts leading to underplating and low resistivities at Moho to lower crustal levels below the arc and nearby backarc. The low- to high-temperature mantle wedge transition lies slightly trenchward of the arc.

  12. Special Speciation

    ERIC Educational Resources Information Center

    Countryman, Lyn L.; Maroo, Jill D.

    2015-01-01

    Considerable anecdotal evidence indicates that some of the most difficult concepts that both high school and undergraduate elementary-education students struggle with are those surrounding evolutionary principles, especially speciation. It's no wonder that entry-level biology students are confused, when biologists have multiple definitions of…

  13. EARLY ASTEROSEISMIC RESULTS FROM KEPLER: STRUCTURAL AND CORE PARAMETERS OF THE HOT B SUBDWARF KPD 1943+4058 AS INFERRED FROM g-MODE OSCILLATIONS

    SciTech Connect

    Van Grootel, V.; Charpinet, S.; Fontaine, G.; Brassard, P.; Green, E. M.; Randall, S. K.; Silvotti, R.; Oestensen, R. H.; Kjeldsen, H.; Christensen-Dalsgaard, J.; Borucki, W. J.; Koch, D. E-mail: stephane.charpinet@ast.obs-mip.f E-mail: brassard@astro.umontreal.c E-mail: srandall@eso.or

    2010-08-01

    We present a seismic analysis of the pulsating hot B subdwarf KPD 1943+4058 (KIC 005807616) on the basis of the long-period, gravity-mode pulsations recently uncovered by Kepler. This is the first time that g-mode seismology can be exploited quantitatively for stars on the extreme horizontal branch, all previous successful seismic analyses having been confined so far to short-period, p-mode pulsators. We demonstrate that current models of hot B subdwarfs can quite well explain the observed g-mode periods, while being consistent with independent constraints provided by spectroscopy. We identify the 18 pulsations retained in our analysis as low-degree (l = 1 and 2), intermediate-order (k = -9 through -58) g-modes. The periods (frequencies) are recovered, on average, at the 0.22% level, which is comparable to the best results obtained for p-mode pulsators. We infer the following structural and core parameters for KPD 1943+4058 (formal fitting uncertainties only): T{sub eff} = 28,050 {+-} 470 K, log g = 5.52 {+-} 0.03, M{sub *} = 0.496 {+-} 0.002 M{sub sun}, log (M{sub env}/M{sub *}) = -2.55 {+-} 0.07, log (1 - M{sub core}/M{sub *}) = -0.37 {+-} 0.01, and X{sub core}(C+O) = 0.261 {+-} 0.008. We additionally derive the age of the star since the zero-age extended horizontal branch 18.4 {+-} 1.0 Myr, the radius R = 0.203 {+-} 0.007 R{sub sun}, the luminosity L = 22.9 {+-} 3.13 L{sub sun}, the absolute magnitude M{sub V} = 4.21 {+-} 0.11, the reddening index E(B - V) = 0.094 {+-} 0.017, and the distance d = 1180 {+-} 95 pc.

  14. 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...

  15. Electron kinetics inferred from observations of microwave bursts during edge localized modes in the mega-amp spherical tokamak.

    PubMed

    Freethy, S J; McClements, K G; Chapman, S C; Dendy, R O; Lai, W N; Pamela, S J P; Shevchenko, V F; Vann, R G L

    2015-03-27

    Recent measurements of microwave and x-ray emission during edge localized mode (ELM) activity in tokamak plasmas provide a fresh perspective on ELM physics. It is evident that electron kinetics, which are not incorporated in standard (fluid) models for the instability that drives ELMs, play a key role in the new observations. These effects should be included in future models for ELMs and the ELM cycle. The observed radiative effects paradoxically imply acceleration of electrons parallel to the magnetic field combined with rapid acquisition of perpendicular momentum. It is shown that this paradox can be resolved by the action of the anomalous Doppler instability which enables fast collective radiative relaxation, in the perpendicular direction, of electrons accelerated in the parallel direction by inductive electric fields generated by the initial ELM instability. PMID:25860751

  16. Inferring Low-Mode Asymmetries from the Elastically Scattered Neutron Spectrum in Layered Cryogenic DT Implosions on OMEGA

    NASA Astrophysics Data System (ADS)

    Forrest, C. J.; Glebov, V. Yu.; Goncharov, V. N.; Sangster, T. C.; Stoeckl, C.; Frenje, J. A.; Gatu Johnson, M.

    2014-10-01

    High-resolution neutron spectroscopy is used to probe the areal density of layered cryogenic DT direct-drive implosions in inertial confinement fusion experiments on OMEGA. Advanced scintillation detectors record the neutron spectrum using time-of-flight techniques. The shape of the energy spectrum is fully determined by the neutron elastic scattering cross-section for spherically symmetric target configurations. Significant differences from the expected shape have been measured for some recent implosions, which indicate a deviation from a spherically symmetric fuel assembly. Neutron scattering with low-mode perturbations in the DT fuel assembly have been simulated in the Monte Carlo n-particle transport code. The experimental data shows good agreement with the model when the mass distribution of the compressed DT shell is highly asymmetric with one side having a factor-of-2 higher areal density. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

  17. Sex-biased gene flow in spectacled eiders (Anatidae): Inferences from molecular markers with contrasting modes of inheritance

    USGS Publications Warehouse

    Scribner, K.T.; Petersen, M.R.; Fields, R.L.; Talbot, S.L.; Pearce, J.M.; Chesser, R.K.

    2001-01-01

    Genetic markers that differ in mode of inheritance and rate of evolution (a sex-linked Z-specific microsatellite locus, five biparentally inherited microsatellite loci, and maternally inherited mitochondrial [mtDNA] sequences) were used to evaluate the degree of spatial genetic structuring at macro- and microgeographic scales, among breeding regions and local nesting populations within each region, respectively, for a migratory sea duck species, the spectacled eider (Somateria fisheri). Disjunct and declining breeding populations coupled with sex-specific differences in seasonal migratory patterns and life history provide a series of hypotheses regarding rates and directionality of gene flow among breeding populations from the Indigirka River Delta, Russia, and the North Slope and Yukon-Kuskokwim Delta, Alaska. The degree of differentiation in mtDNA haplotype frequency among breeding regions and populations within regions was high (??CT = 0.189, P 0.05; biparentally inherited microsatellites: mean ?? = 0.001, P > 0.05) than was observed for mtDNA. Using models explicitly designed for uniparental and biparentally inherited genes, estimates of spatial divergence based on nuclear and mtDNA data together with elements of the species' breeding ecology were used to estimate effective population size and degree of male and female gene flow. Differences in the magnitude and spatial patterns of gene correlations for maternally inherited and nuclear genes revealed that females exhibit greater natal philopatry than do males. Estimates of generational female and male rates of gene flow among breeding regions differed markedly (3.67 ?? 10-4 and 1.28 ?? 10-2, respectively). Effective population size for mtDNA was estimated to be at least three times lower than that for biparental genes (30,671 and 101,528, respectively). Large disparities in population sizes among breeding areas greatly reduces the proportion of total genetic variance captured by dispersal, which may accelerate

  18. 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...

  19. Ecological Inference

    NASA Astrophysics Data System (ADS)

    King, Gary; Rosen, Ori; Tanner, Martin A.

    2004-09-01

    This collection of essays brings together a diverse group of scholars to survey the latest strategies for solving ecological inference problems in various fields. The last half-decade has witnessed an explosion of research in ecological inference--the process of trying to infer individual behavior from aggregate data. Although uncertainties and information lost in aggregation make ecological inference one of the most problematic types of research to rely on, these inferences are required in many academic fields, as well as by legislatures and the Courts in redistricting, by business in marketing research, and by governments in policy analysis.

  20. 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...

  1. What Is Speciation?

    PubMed

    Shapiro, B Jesse; Leducq, Jean-Baptiste; Mallet, James

    2016-03-01

    Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation "in the act" and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent. PMID:27030977

  2. What Is Speciation?

    PubMed Central

    Shapiro, B. Jesse; Leducq, Jean-Baptiste; Mallet, James

    2016-01-01

    Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation “in the act” and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent. PMID:27030977

  3. A genomic perspective on hybridization and speciation

    PubMed Central

    Payseur, Bret A.; Rieseberg, Loren H.

    2016-01-01

    Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns – which may contribute to reproductive barriers – are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation. PMID:26836441

  4. Entropic Inference

    NASA Astrophysics Data System (ADS)

    Caticha, Ariel

    2011-03-01

    In this tutorial we review the essential arguments behing entropic inference. We focus on the epistemological notion of information and its relation to the Bayesian beliefs of rational agents. The problem of updating from a prior to a posterior probability distribution is tackled through an eliminative induction process that singles out the logarithmic relative entropy as the unique tool for inference. The resulting method of Maximum relative Entropy (ME), includes as special cases both MaxEnt and Bayes' rule, and therefore unifies the two themes of these workshops—the Maximum Entropy and the Bayesian methods—into a single general inference scheme.

  5. Perceptual inference.

    PubMed

    Aggelopoulos, Nikolaos C

    2015-08-01

    Perceptual inference refers to the ability to infer sensory stimuli from predictions that result from internal neural representations built through prior experience. Methods of Bayesian statistical inference and decision theory model cognition adequately by using error sensing either in guiding action or in "generative" models that predict the sensory information. In this framework, perception can be seen as a process qualitatively distinct from sensation, a process of information evaluation using previously acquired and stored representations (memories) that is guided by sensory feedback. The stored representations can be utilised as internal models of sensory stimuli enabling long term associations, for example in operant conditioning. Evidence for perceptual inference is contributed by such phenomena as the cortical co-localisation of object perception with object memory, the response invariance in the responses of some neurons to variations in the stimulus, as well as from situations in which perception can be dissociated from sensation. In the context of perceptual inference, sensory areas of the cerebral cortex that have been facilitated by a priming signal may be regarded as comparators in a closed feedback loop, similar to the better known motor reflexes in the sensorimotor system. The adult cerebral cortex can be regarded as similar to a servomechanism, in using sensory feedback to correct internal models, producing predictions of the outside world on the basis of past experience. PMID:25976632

  6. ORGANIC SPECIATION SAMPLING ARTIFACTS

    EPA Science Inventory

    Sampling artifacts for molecular markers from organic speciation of particulate matter were investigated by analyzing forty-one samples collected in Philadelphia as a part of the Northeast Oxidant and Particulate Study (NEOPS). Samples were collected using a high volume sampler ...

  7. Population differentiation without speciation

    PubMed Central

    Magurran, A. E.

    1998-01-01

    Population differentiation is often viewed as an important step towards speciation, and part of the rationale for conserving variation at the intraspecific level is that the potential to generate more biological diversity should be retained. Yet, speciation is not an inevitable consequence of population divergence. This paper reviews recent work on the Trinidadian guppy, Poecilia reticulata, a species that is renowned for its capacity for population differentiation. Guppy populations evolve rapidly, within 101 to 102 generations, as a response to changes in selection exerted by predators. The rates of evolution involved can be up to seven orders of magnitude greater than those seen in the fossil record. Sexual selection, particuarly female choice, appears to reinforce the divergence that natural selection has generated. Perplexingly, however, there is no reproductive isolation (either prezygotic or postzygotic) between populations, even those that have been separated for at least 106 generations. Sexual conflict may be the key to explaining this absence of speciation. Male reproductive behaviour, particularly the high incidence of sneaky mating, may be instrumental in producing sufficient gene flow to prevent reproductive isolation. Sneaky mating has the potential to undermine female choice, and is known to be an important means of sperm transfer in wild populations. Sexual dimorphism, also a result of sexual conflict in guppies, may inhibit speciation in another way. Morphological differences between the sexes, that have arisen for reproductive reasons, mean that males and females are pre-adapted for different foraging niches. This, in turn, reduces the opportunity for the development of feeding polymorphisms, a mechanism that seems to have been important in the sympatric speciation of other fish species.

  8. Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

    PubMed Central

    Marques, David A.; Lucek, Kay; Meier, Joana I.; Mwaiko, Salome; Wagner, Catherine E.; Excoffier, Laurent; Seehausen, Ole

    2016-01-01

    Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this. PMID:26925837

  9. The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly

    SciTech Connect

    Barrack, Keri L.; Fyfe, Paul K.; Hunter, William N.

    2015-04-21

    The structure of a tubulin-binding cofactor from L. major is reported and compared with yeast, plant and human orthologues. Tubulin-binding cofactor A (TBCA) participates in microtubule formation, a key process in eukaryotic biology to create the cytoskeleton. There is little information on how TBCA might interact with β-tubulin en route to microtubule biogenesis. To address this, the protozoan Leishmania major was targeted as a model system. The crystal structure of TBCA and comparisons with three orthologous proteins are presented. The presence of conserved features infers that electrostatic interactions that are likely to involve the C-terminal tail of β-tubulin are key to association. This study provides a reagent and template to support further work in this area.

  10. The evolutionary genetics of speciation.

    PubMed Central

    Coyne, J A; Orr, H A

    1998-01-01

    The last decade has brought renewed interest in the genetics of speciation, yielding a number of new models and empirical results. Defining speciation as 'the origin of reproductive isolation between two taxa', we review recent theoretical studies and relevant data, emphasizing the regular patterns seen among genetic analyses. Finally, we point out some important and tractable questions about speciation that have been neglected. PMID:9533126

  11. 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...

  12. 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. ...

  13. The drivers of tropical speciation.

    PubMed

    Smith, Brian Tilston; McCormack, John E; Cuervo, Andrés M; Hickerson, Michael J; Aleixo, Alexandre; Cadena, Carlos Daniel; Pérez-Emán, Jorge; Burney, Curtis W; Xie, Xiaoou; Harvey, Michael G; Faircloth, Brant C; Glenn, Travis C; Derryberry, Elizabeth P; Prejean, Jesse; Fields, Samantha; Brumfield, Robb T

    2014-11-20

    Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests. PMID:25209666

  14. 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 ...

  15. Environmental speciation of actinides.

    PubMed

    Maher, Kate; Bargar, John R; Brown, Gordon E

    2013-04-01

    Although minor in abundance in Earth's crust (U, 2-4 ppm; Th, 10-15 ppm) and in seawater (U, 0.003 ppm; Th, 0.0007 ppm), light actinides (Th, Pa, U, Np, Pu, Am, and Cm) are important environmental contaminants associated with anthropogenic activities such as the mining and milling of uranium ores, generation of nuclear energy, and storage of legacy waste resulting from the manufacturing and testing of nuclear weapons. In this review, we discuss the abundance, production, and environmental sources of naturally occurring and some man-made light actinides. As is the case with other environmental contaminants, the solubility, transport properties, bioavailability, and toxicity of actinides are dependent on their speciation (composition, oxidation state, molecular-level structure, and nature of the phase in which the contaminant element or molecule occurs). We review the aqueous speciation of U, Np, and Pu as a function of pH and Eh, their interaction with common inorganic and organic ligands in natural waters, and some of the common U-containing minerals. We also discuss the interaction of U, Np, Pu, and Am solution complexes with common Earth materials, including minerals, colloids, gels, natural organic matter (NOM), and microbial organisms, based on simplified model system studies. These surface interactions can inhibit (e.g., sorption to mineral surfaces, formation of insoluble biominerals) or enhance (e.g., colloid-facilitated transport) the dispersal of light actinides in the biosphere and in some cases (e.g., interaction with dissimilatory metal-reducing bacteria, NOM, or Mn- and Fe-containing minerals) can modify the oxidation states and, consequently, the behavior of redox-sensitive light actinides (U, Np, and Pu). Finally, we review the speciation of U and Pu, their chemical transformations, and cleanup histories at several U.S. Department of Energy field sites that have been used to mill U ores, produce fissile materials for reactors and weapons, and store

  16. 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

  17. CORRELATING METAL SPECIATION IN SOILS

    EPA Science Inventory

    Understanding bioavailability of metals from exposure to contaminated soils is a challenging aspect of environmental research. This presentation will examine three areas of research with respect to metal speciation in soils as it relates to bioavailability: 1) Pb immobilization a...

  18. Hybridization Reveals the Evolving Genomic Architecture of Speciation

    PubMed Central

    Kronforst, Marcus R.; Hansen, Matthew E.B.; Crawford, Nicholas G.; Gallant, Jason R.; Zhang, Wei; Kulathinal, Rob J.; Kapan, Durrell D.; Mullen, Sean P.

    2014-01-01

    SUMMARY The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes. Over time, divergence evolves rapidly, due primarily to the origin of new divergent regions. Furthermore, divergent genomic regions display signatures of both selection and adaptive introgression, demonstrating the link between microevolutionary processes acting within species and the origin of species across macroevolutionary timescales. Our results provide a uniquely comprehensive portrait of the evolving species boundary due to the role that hybridization plays in reducing the background accumulation of divergence at neutral sites. PMID:24183670

  19. Sexual conflict and speciation.

    PubMed Central

    Parker, G A; Partridge, L

    1998-01-01

    We review the significance of two forms of sexual conflict (different evolutionary interests of the two sexes) for genetic differentiation of populations and the evolution of reproductive isolation. Conflicting selection on the alleles at a single locus can occur in males and females if the sexes have different optima for a trait, and there are pleiotropic genetic correlations between the sexes for it. There will then be selection for sex limitation and hence sexual dimorphism. This sex limitation could break down in hybrids and reduce their fitness. Pleiotropic genetic correlations between the sexes could also affect the likelihood of mating in interpopulation encounters. Conflict can also occur between (sex-limited) loci that determine behaviour in males and those that determine behaviour in females. Reproductive isolation may occur by rapid coevolution of male trait and female mating preference. This would tend to generate assortative mating on secondary contact, hence promoting speciation. Sexual conflict resulting from sensory exploitation, polyspermy and the cost of mating could result in high levels of interpopulation mating. If females evolve resistance to make pre- and postmating manipulation, males from one population could be more successful with females from the other, because females would have evolved resistance to their own (but not to the allopatric) males. Between-locus sexual conflict could also occur as a result of conflict between males and females of different populations over the production of unfit hybrids. We develop models which show that females are in general selected to resist such matings and males to persist, and this could have a bearing on both the initial level of interpopulation matings and the likelihood that reinforcement will occur. In effect, selection on males usually acts to promote gene flow and to restrict premating isolation, whereas selection on females usually acts in the reverse direction. We review theoretical models

  20. Incipient ring speciation revealed by a migratory divide.

    PubMed

    Irwin, Darren E

    2009-07-01

    Ever since Ernst Mayr (1942) called ring species the 'perfect demonstration of speciation', they have attracted much interest from researchers examining how two species evolve from one. In a ring species, two sympatric and reproductively isolated forms are connected by a long chain of intermediate populations that encircle a geographic barrier. Ring species have the potential to demonstrate that speciation can occur without complete geographic isolation, in contrast to the classic model of allopatric speciation. They also allow researchers to examine the causes of reproductive isolation in the contact zone and to use spatial variation to infer the steps by which speciation occurs. According to the classical definition, a ring species must have (i) gradual variation through a chain of populations connecting two divergent and sympatric forms, and (ii) complete or nearly complete reproductive isolation between the terminal forms. But evolutionary biologists now recognize that the process of speciation might often occur with some periods of geographic contact and hybridization between diverging forms; during these phases, even partial reproductive isolation can limit gene flow and permit further divergence to occur. In this issue Bensch et al. (2009) make an exciting and important contribution by extending the ring species concept to a case in which the divergence is much younger and not yet advanced to full reproductive isolation. Their study of geographic variation in willow warblers (Phylloscopus trochilus; Fig. 1) provides a beautiful example of gradual variation through a ring of populations connecting two forms that are partially reproductively isolated where they meet, possibly due to divergent migratory behaviours of the terminal forms. PMID:19457189

  1. Arabidopsis hybrid speciation processes

    PubMed Central

    Schmickl, Roswitha; Koch, Marcus A.

    2011-01-01

    The genus Arabidopsis provides a unique opportunity to study fundamental biological questions in plant sciences using the diploid model species Arabidopsis thaliana and Arabidopsis lyrata. However, only a few studies have focused on introgression and hybrid speciation in Arabidopsis, although polyploidy is a common phenomenon within this genus. More recently, there is growing evidence of significant gene flow between the various Arabidopsis species. So far, we know Arabidopsis suecica and Arabidopsis kamchatica as fully stabilized allopolyploid species. Both species evolved during Pleistocene glaciation and deglaciation cycles in Fennoscandinavia and the amphi-Beringian region, respectively. These hybrid studies were conducted either on a phylogeographic scale or reconstructed experimentally in the laboratory. In our study we focus at a regional and population level. Our research area is located in the foothills of the eastern Austrian Alps, where two Arabidopsis species, Arabidopsis arenosa and A. lyrata ssp. petraea, are sympatrically distributed. Our hypothesis of genetic introgression, migration, and adaptation to the changing environment during the Pleistocene has been confirmed: We observed significant, mainly unidirectional gene flow between the two species, which has given rise to the tetraploid A. lyrata. This cytotype was able to escape from the narrow ecological niche occupied by diploid A. lyrata ssp. petraea on limestone outcrops by migrating northward into siliceous areas, leaving behind a trail of genetic differentiation. PMID:21825128

  2. Iron Speciation in Urban Dust

    SciTech Connect

    E Elzinga; Y Gao; J Fitts; R Tappero

    2011-12-31

    An improved understanding of anthropogenic impacts on ocean fertility requires knowledge of anthropogenic dust mineralogy and associated Fe speciation as a critical step toward developing Fe solubility models constrained by mineralogical composition. This study explored the utility of micro-focused X-ray absorption spectroscopy ({mu}-XAS) in characterizing the speciation of Fe in urban dust samples. A micro-focused beam of 10 x 7 {micro}m made possible the measurement of the Fe K edge XAS spectra of individual dust particles in the PM5.6 size fraction collected in Newark, New Jersey, USA. Spectral analysis indicated the presence of mixtures of Fe-containing minerals within individual dust particles; we observed significant magnetite content along with other Fe(III)-(hydr)oxide minerals which could not be conclusively identified. Our data indicate that detailed quantitative determination of Fe speciation requires extended energy scans to constrain the types and relative abundance of Fe species present. We observe heterogeneity in Fe speciation at the dust particle level, which underscores the importance of analyzing a statistically adequate number of particles within each dust sample. Where possible, {mu}-XAS measurements should be complemented with additional characterization techniques such as {mu}-XRD and bulk XAS to obtain a comprehensive picture of the Fe speciation in dust materials. X-ray microprobes should be used to complement bulk methods used to determine particle composition, methods that fail to record particle heterogeneity.

  3. Cancer: beyond speciation.

    PubMed

    Vincent, Mark D

    2011-01-01

    A good account of the nature of cancer should provide not only a description of its consistent features, but also how they arise, how they are maintained, why conventional chemotherapy succeeds, and fails, and where to look for better targets. Cancer was once regarded as enigmatic and inexplicable; more recently, the "mutation theory," based on random alterations in a relatively small set of proto-oncogenes and tumor suppressor genes, has enjoyed widespread acceptance. The "mutation theory," however, is noticeable for its failure to explain the basis of differential chemosensitivity, for providing a paucity of targets, especially druggable ones, and for justifying the development of targeted therapies with, in general, disappointingly abbreviated clinical benefit. Furthermore, this theory has mistakenly predicted a widespread commonality of consistent genetic abnormalities across the range of cancers, whereas the opposite, that is, roiling macrogenomic instability, is generally the rule. In contrast, concerning what actually is consistent, that is, the suite of metabolic derangements common to virtually all, especially aggressive, cancers, the "Mutation Theory" has nothing to say. Other hypotheses merit serious consideration "aneuploidy theories" posit whole-genome instability and imbalance as causally responsible for the propagation of the tumor. Another approach, that is, "derepression atavism," suggests cancer results from the release of an ancient survival program, characterized by the emergence of remarkably primitive features such as unicellularity, fermentation, and immortality; existential goals are served by heuristic genomic instability coupled with host-to-tumor biomass interconversion, mediated by the Warburg effect, a major component of the program. Carcinogenesis is here seen as a process of de-speciation; however, genomic nonrestabilization raises issues as to where on the tree of life cancers belong, as a genuinely alternative modus vivendi

  4. 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

  5. Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

    PubMed Central

    2013-01-01

    Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation. PMID:24070215

  6. Mercury speciation modeling using site specific chemical and redox data from the TNXOD OU

    SciTech Connect

    Kaplan, D.I.

    2000-03-22

    The objective of this study was to evaluate mercury speciation under reducing conditions expected in sediments at the TNX Outfall Delta Operable Unit. These changes in speciation would then be used to infer whether mercury toxicity and mobility would be expected to be significantly altered under reducing conditions. The results from this work suggest that mercury would likely become more strongly retained by the solid phase under reducing conditions than under oxidizing conditions at the TNX Outfall Delta Site. Considering that experimental results indicate that mercury is extremely tightly bound to the solid phase under oxidizing conditions, little mercury mobility would therefore be expected under reducing conditions.

  7. PASSENGER CAR HYDROCARBON EMISSIONS SPECIATION

    EPA Science Inventory

    Emission factors for over 60 individual hydrocarbon compounds were determined for four passenger cars. The cars included a 1963 Chevrolet, a 1977 Mustang, and 1978 Monarch, and 1979 LTD II. The speciation data is reported for both tailpipe and evaporative emissions. The tailpipe ...

  8. A PERSONAL PARTICLE SPECIATION SAMPLER

    EPA Science Inventory

    Dr. Susanne Hering of Aerosol Dynamics Inc and her colleagues expect to design and validate a personal monitoring sampler for particles smaller than 2.5 µm (PM2.5) that is suitable for subsequent chemical speciation work. The investigators believe the result will be a...

  9. Inference or Observation?

    ERIC Educational Resources Information Center

    Finson, Kevin D.

    2010-01-01

    Learning about what inferences are, and what a good inference is, will help students become more scientifically literate and better understand the nature of science in inquiry. Students in K-4 should be able to give explanations about what they investigate (NSTA 1997) and that includes doing so through inferring. This article provides some tips…

  10. 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...

  11. 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. PMID:27087841

  12. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.

    PubMed

    FitzJohn, Richard G; Maddison, Wayne P; Otto, Sarah P

    2009-12-01

    Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies. PMID:20525612

  13. Arsenic Speciation of Terrestrial Invertebrates

    SciTech Connect

    Moriarty, M.M.; Koch, I.; Gordon, R.A.; Reimer, K.J. ); )

    2009-07-01

    The distribution and chemical form (speciation) of arsenic in terrestrial food chains determines both the amount of arsenic available to higher organisms, and the toxicity of this metalloid in affected ecosystems. Invertebrates are part of complex terrestrial food webs. This paper provides arsenic concentrations and arsenic speciation profiles for eight orders of terrestrial invertebrates collected at three historical gold mine sites and one background site in Nova Scotia, Canada. Total arsenic concentrations, determined by inductively coupled plasma mass spectrometry (ICP-MS), were dependent upon the classification of invertebrate. Arsenic species were determined by high-performance liquid chromatography (HPLC) ICP-MS and X-ray absorption spectroscopy (XAS). Invertebrates were found by HPLC ICP-MS to contain predominantly arsenite and arsenate in methanol/water extracts, while XAS revealed that most arsenic is bound to sulfur in vivo. Examination of the spatial distribution of arsenic within an ant tissue highlighted the differences between exogenous and endogenous arsenic, as well as the extent to which arsenic is transformed upon ingestion. Similar arsenic speciation patterns for invertebrate groups were observed across sites. Trace amounts of arsenobetaine and arsenocholine were identified in slugs, ants, and spiders.

  14. The geography and ecology of plant speciation: range overlap and niche divergence in sister species

    PubMed Central

    Anacker, Brian L.; Strauss, Sharon Y.

    2014-01-01

    A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under ‘budding’ speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister–non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities

  15. Physical limits of inference

    NASA Astrophysics Data System (ADS)

    Wolpert, David H.

    2008-07-01

    We show that physical devices that perform observation, prediction, or recollection share an underlying mathematical structure. We call devices with that structure “inference devices”. We present a set of existence and impossibility results concerning inference devices. These results hold independent of the precise physical laws governing our universe. In a limited sense, the impossibility results establish that Laplace was wrong to claim that even in a classical, non-chaotic universe the future can be unerringly predicted, given sufficient knowledge of the present. Alternatively, these impossibility results can be viewed as a non-quantum-mechanical “uncertainty principle”. The mathematics of inference devices has close connections to the mathematics of Turing Machines (TMs). In particular, the impossibility results for inference devices are similar to the Halting theorem for TMs. Furthermore, one can define an analog of Universal TMs (UTMs) for inference devices. We call those analogs “strong inference devices”. We use strong inference devices to define the “inference complexity” of an inference task, which is the analog of the Kolmogorov complexity of computing a string. A task-independent bound is derived on how much the inference complexity of an inference task can differ for two different inference devices. This is analogous to the “encoding” bound governing how much the Kolmogorov complexity of a string can differ between two UTMs used to compute that string. However no universe can contain more than one strong inference device. So whereas the Kolmogorov complexity of a string is arbitrary up to specification of the UTM, there is no such arbitrariness in the inference complexity of an inference task. We informally discuss the philosophical implications of these results, e.g., for whether the universe “is” a computer. We also derive some graph-theoretic properties governing any set of multiple inference devices. We also present an

  16. Hierarchical cosmic shear power spectrum inference

    NASA Astrophysics Data System (ADS)

    Alsing, Justin; Heavens, Alan; Jaffe, Andrew H.; Kiessling, Alina; Wandelt, Benjamin; Hoffmann, Till

    2016-02-01

    We develop a Bayesian hierarchical modelling approach for cosmic shear power spectrum inference, jointly sampling from the posterior distribution of the cosmic shear field and its (tomographic) power spectra. Inference of the shear power spectrum is a powerful intermediate product for a cosmic shear analysis, since it requires very few model assumptions and can be used to perform inference on a wide range of cosmological models a posteriori without loss of information. We show that joint posterior for the shear map and power spectrum can be sampled effectively by Gibbs sampling, iteratively drawing samples from the map and power spectrum, each conditional on the other. This approach neatly circumvents difficulties associated with complicated survey geometry and masks that plague frequentist power spectrum estimators, since the power spectrum inference provides prior information about the field in masked regions at every sampling step. We demonstrate this approach for inference of tomographic shear E-mode, B-mode and EB-cross power spectra from a simulated galaxy shear catalogue with a number of important features; galaxies distributed on the sky and in redshift with photometric redshift uncertainties, realistic random ellipticity noise for every galaxy and a complicated survey mask. The obtained posterior distributions for the tomographic power spectrum coefficients recover the underlying simulated power spectra for both E- and B-modes.

  17. SPECIATION OF ELEMENTS IN INCINERATION RESIDUES

    EPA Science Inventory

    Knowledge as to the speciation of elements in incineration residues is important for the successful management and utilization of the residues and for modelling and predicting their leaching behavior. s part of a larger research effort on speciation in combustion residues, ESP as...

  18. Rapid speciation and chromosomal evolution in mammals.

    PubMed Central

    Bush, G L; Case, S M; Wilson, A C; Patton, J L

    1977-01-01

    To test the hypothesis that population subdivision into small demes promotes both rapid speciation and evolutionary changes in gene arrangement by inbreeding and drift, we estimated rates of speciation and rates of chromosomal evolution in 225 genera of vertebrates. Rates of speciation were estimated by considering the number of living species in each genus and the fossil record of each genus as well as information about extinction rates. Speciation rate was strongly correlated with rate of chromosomal evolution and average rates of speciation in lower vertebrate genera were one-fifth those in mammalian genera. Genera with high karyotypic diversity and rapid speciation rates may generally have small effective population size (Ne), whereas large Ne values may be associated with karyotypically uniform genera and slow rates of speciation. Speciation and chromosomal evolution seem fastest in those genera with species organized into clans or harems (e.g., some primates and horses) or with limited adult vagility and juvenile dispersal, patchy distribution, and strong individual territoriality (e.g., some rodents). This is consistent with the above hypothesis regarding the evolutionary importance of demes. PMID:269445

  19. Speciation in fungal and oomycete plant pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  20. 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

  1. Inference in `poor` languages

    SciTech Connect

    Petrov, S.

    1996-10-01

    Languages with a solvable implication problem but without complete and consistent systems of inference rules (`poor` languages) are considered. The problem of existence of finite complete and consistent inference rule system for a ``poor`` language is stated independently of the language or rules syntax. Several properties of the problem arc proved. An application of results to the language of join dependencies is given.

  2. 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.

  3. The speciation of behavior analysis

    PubMed Central

    Rider, David P.

    1991-01-01

    The relationship between the Experimental Analysis of Behavior (EAB) and Applied Behavior Analysis (ABA) has been the subject of several editorials and commentaries in recent years. Various authors have argued that researchers in these two fields (a) have become isolated from each other, (b) face different requirements for survival in their respective fields, and (c) possess different skills to meet those requirements. The present paper provides an allegory for the relationship between EAB and ABA in terms of biological speciation. The conditions that have changed the relationship between EAB and ABA are parallel to those responsible for biological speciation: (a) isolation of some members of a species from the rest of the population, (b) different contingencies of survival for members of the two separate groups, and (c) divergence in the adaptive characteristics displayed by the two groups. When members of two different groups, descendants of common ancestors, no longer are capable of producing viable offspring by interbreeding, the different groups then represent different species. To the extent that members of the EAB group and members of the ABA group interact with each other only trivially, they each represent allegorically different species. Changes in the relationship between EAB and ABA are part of a natural process that takes place in many other sciences, and the course of that process can hardly be reversed by us. PMID:22478096

  4. Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.

    PubMed

    Silvestro, Daniele; Schnitzler, Jan; Liow, Lee Hsiang; Antonelli, Alexandre; Salamin, Nicolas

    2014-05-01

    The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes. PMID:24510972

  5. Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data

    PubMed Central

    Silvestro, Daniele; Schnitzler, Jan; Liow, Lee Hsiang; Antonelli, Alexandre; Salamin, Nicolas

    2015-01-01

    The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes. PMID:24510972

  6. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation.

    PubMed

    Rabosky, Daniel L; Santini, Francesco; Eastman, Jonathan; Smith, Stephen A; Sidlauskas, Brian; Chang, Jonathan; Alfaro, Michael E

    2013-01-01

    Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fishes that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability'-the capacity of organisms to evolve-shapes the dynamics of speciation through time at the largest phylogenetic scales. PMID:23739623

  7. 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, vola...

  8. 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...

  9. Speciation reversal in European whitefish (Coregonus lavaretus (L.)) caused by competitor invasion.

    PubMed

    Bhat, Shripathi; Amundsen, Per-Arne; Knudsen, Rune; Gjelland, Karl Øystein; Fevolden, Svein-Erik; Bernatchez, Louis; Præbel, Kim

    2014-01-01

    Invasion of exotic species has caused the loss of biodiversity and imparts evolutionary and ecological changes in the introduced systems. In northern Fennoscandia, European whitefish (Coregonus lavaretus (L.)) is a highly polymorphic species displaying adaptive radiations into partially reproductively isolated and thus genetically differentiated sympatric morphs utilizing the planktivorous and benthivorous food niche in many lakes. In 1993, Lake Skrukkebukta was invaded by vendace (Coregonus albula (L.)) which is a zooplanktivorous specialist. The vendace displaced the densely rakered whitefish from its preferred pelagic niche to the benthic habitat harbouring the large sparsely rakered whitefish. In this study, we investigate the potential influence of the vendace invasion on the breakdown of reproductive isolation between the two whitefish morphs. We inferred the genotypic and phenotypic differentiation between the two morphs collected at the arrival (1993) and 15 years after (2008) the vendace invasion using 16 microsatellite loci and gill raker numbers, the most distinctive adaptive phenotypic trait between them. The comparison of gill raker number distributions revealed two modes growing closer over 15 years following the invasion. Bayesian analyses of genotypes revealed that the two genetically distinct whitefish morphs that existed in 1993 had collapsed into a single population in 2008. The decline in association between the gill raker numbers and admixture values over 15 years corroborates the findings from the Bayesian analysis. Our study thus suggests an apparent decrease of reproductive isolation in a morph-pair of European whitefish within 15 years (≃ 3 generations) following the invasion of a superior trophic competitor (vendace) in a subarctic lake, reflecting a situation of "speciation in reverse". PMID:24626131

  10. Speciation Reversal in European Whitefish (Coregonus lavaretus (L.)) Caused by Competitor Invasion

    PubMed Central

    Bhat, Shripathi; Amundsen, Per-Arne; Knudsen, Rune; Gjelland, Karl Øystein; Fevolden, Svein-Erik; Bernatchez, Louis; Præbel, Kim

    2014-01-01

    Invasion of exotic species has caused the loss of biodiversity and imparts evolutionary and ecological changes in the introduced systems. In northern Fennoscandia, European whitefish (Coregonus lavaretus (L.)) is a highly polymorphic species displaying adaptive radiations into partially reproductively isolated and thus genetically differentiated sympatric morphs utilizing the planktivorous and benthivorous food niche in many lakes. In 1993, Lake Skrukkebukta was invaded by vendace (Coregonus albula (L.)) which is a zooplanktivorous specialist. The vendace displaced the densely rakered whitefish from its preferred pelagic niche to the benthic habitat harbouring the large sparsely rakered whitefish. In this study, we investigate the potential influence of the vendace invasion on the breakdown of reproductive isolation between the two whitefish morphs. We inferred the genotypic and phenotypic differentiation between the two morphs collected at the arrival (1993) and 15 years after (2008) the vendace invasion using 16 microsatellite loci and gill raker numbers, the most distinctive adaptive phenotypic trait between them. The comparison of gill raker number distributions revealed two modes growing closer over 15 years following the invasion. Bayesian analyses of genotypes revealed that the two genetically distinct whitefish morphs that existed in 1993 had collapsed into a single population in 2008. The decline in association between the gill raker numbers and admixture values over 15 years corroborates the findings from the Bayesian analysis. Our study thus suggests an apparent decrease of reproductive isolation in a morph-pair of European whitefish within 15 years (≃ 3 generations) following the invasion of a superior trophic competitor (vendace) in a subarctic lake, reflecting a situation of “speciation in reverse”. PMID:24626131

  11. Genomic divergence during speciation: causes and consequences

    PubMed Central

    Nosil, Patrik; Feder, Jeffrey L.

    2012-01-01

    Speciation is a fundamental process responsible for the diversity of life. Progress has been made in detecting individual ‘speciation genes’ that cause reproductive isolation. In contrast, until recently, less attention has been given to genome-wide patterns of divergence during speciation. Thus, major questions remain concerning how individual speciation genes are arrayed within the genome, and how this affects speciation. This theme issue is dedicated to exploring this genomic perspective of speciation. Given recent sequencing and computational advances that now allow genomic analyses in most organisms, the goal is to help move the field towards a more integrative approach. This issue draws upon empirical studies in plants and animals, and theoretical work, to review and further document patterns of genomic divergence. In turn, these studies begin to disentangle the role that different processes, such as natural selection, gene flow and recombination rate, play in generating observed patterns. These factors are considered in the context of how genomes diverge as speciation unfolds, from beginning to end. The collective results point to how experimental work is now required, in conjunction with theory and sequencing studies, to move the field from descriptive studies of patterns of divergence towards a predictive framework that tackles the causes and consequences of genome-wide patterns. PMID:22201163

  12. Is ecological speciation a major trend in aphids? Insights from a molecular phylogeny of the conifer-feeding genus Cinara

    PubMed Central

    2013-01-01

    Introduction In the past decade ecological speciation has been recognized as having an important role in the diversification of plant-feeding insects. Aphids are host-specialised phytophagous insects that mate on their host plants and, as such, they are prone to experience reproductive isolation linked with host plant association that could ultimately lead to species formation. The generality of such a scenario remains to be tested through macroevolutionary studies. To explore the prevalence of host-driven speciation in the diversification of the aphid genus Cinara and to investigate alternative modes of speciation, we reconstructed a phylogeny of this genus based on mitochondrial, nuclear and Buchnera aphidicola DNA sequence fragments and applied a DNA-based method of species delimitation. Using a recent software (PhyloType), we explored evolutionary transitions in host-plant genera, feeding sites and geographic distributions in the diversification of Cinara and investigated how transitions in these characters have accompanied speciation events. Results The diversification of Cinara has been constrained by host fidelity to conifer genera sometimes followed by sequential colonization onto different host species and by feeding-site specialisation. Nevertheless, our analyses suggest that, at the most, only half of the speciation events were accompanied by ecological niche shifts. The contribution of geographical isolation in the speciation process is clearly apparent in the occurrence of species from two continents in the same clades in relatively terminal positions in our phylogeny. Furthermore, in agreement with predictions from scenarios in which geographic isolation accounts for speciation events, geographic overlap between species increased significantly with time elapsed since their separation. Conclusions The history of Cinara offers a different perspective on the mode of speciation of aphids than that provided by classic models such as the pea aphid. In this

  13. 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. PMID:24558582

  14. 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

  15. Oxidation-state speciation of

    PubMed

    Hu; Heineman

    2000-06-01

    The analytical utility of chemically modified microelectrodes for oxidation-state speciation of redox couples by cyclic voltammetry has been explored. [Re(I)(DMPE)3]+/[Re(II)(DMPE)3]2+, where DMPE = 1,2-bis(dimethylphosphino)ethane, was studied at carbon-fiber microelectrodes of approximately 5 microm in radius coated with Nafion-entrapped solgel-derived silica (Nafion-silica) composite. The results are compared with cyclic voltammetry of [Fe(CN)6]3-/[Fe(CN)6]4- at bare carbon-fiber microelectrodes. At both microelectrodes, the cathodic and anodic limiting currents are linearly proportional to the concentrations of the reducible and oxidizable species of a redox couple, respectively. The shape of the cyclic voltammogram and the magnitude of the steady-state limiting current are not affected by the potential at which the scan starts. Speciation of both forms of a redox couple could be achieved voltammetrically at the microelectrodes. However, a considerably slower scan rate was required to achieve steady state at the modified electrode because of the smaller diffusion coefficients of [Re(I)(DMPE)3]+ and [Re(II)(DMPE)3]2+ in the Nafion-silica composite. The detection limit at the modified electrode was considerably lower (5 x 10(-9) M for [Re(I)(DMPE)3]+) than at the bare electrode (6 x 10(-5) M for [Fe(CN)6]3- and [Fe(CN)6]4-) because of the substantial preconcentration of [Re(I)(DMPE)3]+ by the Nafion-silica composite. PMID:10857611

  16. 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. PMID:20438362

  17. CORRELATING METAL SPECIATION IN SOILS TO RISK

    EPA Science Inventory

    Understanding bioavailability of metals from exposure to contaminated soils is a challenging aspect of environmental research. This presentation will examine three areas of research with respect to metal speciation in soils as it relates to bioavailability: 1) Pb immobilization a...

  18. Dualism and conflicts in understanding speciation.

    PubMed

    Schilthuizen, M

    2000-12-01

    Speciation is a central but elusive issue in evolutionary biology. Over the past sixty years, the subject has been studied within a framework conceived by Ernst Mayr and Theodosius Dobzhansky and subsequently developed further by numerous other workers. In this "isolation" theory, the evolution of reproductive isolation is a key element of speciation; natural selection is given only secondary importance while gene flow is considered prohibitive to the process. In this paper, I argue that certain elements in this approach have produced confusion and irreconcilability among students of speciation. The more prominent debates in speciation (i.e., the species definition, sympatry/allopatry, and the role of reinforcement) all derive from an inherent conflict between the "isolation" theory and Darwin's "selection" view on species and speciation (in which disruptive selection is crucial). New data, mainly from field ecology, molecular population genetics, laboratory studies with Drosophila and computer analysis, all suggest that the isolation theory may no longer be the most desirable vantage point from which to explore speciation. Instead, environmental selection in large populations, often unimpeded by ongoing gene flow, appears to be the decisive element. The traditional preoccupation with reproductive isolation has created gaps in our knowledge of several crucial issues, mainly regarding the role of environmental selection and its connection with mate selection. PMID:11084629

  19. Neural Correlates of Species-Typical Illogical Cognitive Bias in Human Inference

    ERIC Educational Resources Information Center

    Ogawa, Akitoshi; Yamazaki, Yumiko; Ueno, Kenichi; Cheng, Kang; Iriki, Atsushi

    2010-01-01

    The ability to think logically is a hallmark of human intelligence, yet our innate inferential abilities are marked by implicit biases that often lead to illogical inference. For example, given AB ("if A then B"), people frequently but fallaciously infer the inverse, BA. This mode of inference, called symmetry, is logically invalid because,…

  20. The Bayes Inference Engine

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.

    1996-04-01

    The authors are developing a computer application, called the Bayes Inference Engine, to provide the means to make inferences about models of physical reality within a Bayesian framework. The construction of complex nonlinear models is achieved by a fully object-oriented design. The models are represented by a data-flow diagram that may be manipulated by the analyst through a graphical programming environment. Maximum a posteriori solutions are achieved using a general, gradient-based optimization algorithm. The application incorporates a new technique of estimating and visualizing the uncertainties in specific aspects of the model.

  1. Mental state inference using visual control parameters.

    PubMed

    Oztop, Erhan; Wolpert, Daniel; Kawato, Mitsuo

    2005-02-01

    Although we can often infer the mental states of others by observing their actions, there are currently no computational models of this remarkable ability. Here we develop a computational model of mental state inference that builds upon a generic visuomanual feedback controller, and implements mental simulation and mental state inference functions using circuitry that subserves sensorimotor control. Our goal is (1) to show that control mechanisms developed for manual manipulation are readily endowed with visual and predictive processing capabilities and thus allows a natural extension to the understanding of movements performed by others; and (2) to give an explanation on how cortical regions, in particular the parietal and premotor cortices, may be involved in such dual mechanism. To analyze the model, we simulate tasks in which an observer watches an actor performing either a reaching or a grasping movement. The observer's goal is to estimate the 'mental state' of the actor: the goal of the reaching movement or the intention of the agent performing the grasping movement. We show that the motor modules of the observer can be used in a 'simulation mode' to infer the mental state of the actor. The simulations with different grasping and non-straight line reaching strategies show that the mental state inference model is applicable to complex movements. Moreover, we simulate deceptive reaching, where an actor imposes false beliefs about his own mental state on an observer. The simulations show that computational elements developed for sensorimotor control are effective in inferring the mental states of others. The parallels between the model and cortical organization of movement suggest that primates might have developed a similar resource utilization strategy for action understanding, and thus lead to testable predictions about the brain mechanisms of mental state inference. PMID:15653289

  2. 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. PMID:25142551

  3. Inferring identify from DNA profile evidence.

    PubMed

    Balding, D J; Donnelly, P

    1995-12-01

    The controversy over the interpretation of DNA profile evidence in forensic identification can be attributed in part to confusion over the mode(s) of statistical inference appropriate to this setting. Although there has been substantial discussion in the literature of, for example, the role of population genetics issues, few authors have made explicit the inferential framework which underpins their arguments. This lack of clarity has led both to unnecessary debates over ill-posed or inappropriate questions and to the neglect of some issues which can have important consequences. We argue that the mode of statistical inference which seems to underlie the arguments of some authors, based on a hypothesis testing framework, is not appropriate for forensic identification. We propose instead a logically coherent framework in which, for example, the roles both of the population genetics issues and of the nonscientific evidence in a case are incorporated. Our analysis highlights several widely held misconceptions in the DNA profiling debate. For example, the profile frequency is not directly relevant to forensic inference. Further, very small match probabilities may in some settings be consistent with acquittal. Although DNA evidence is typically very strong, our analysis of the coherent approach highlights situations which can arise in practice where alternative methods for assessing DNA evidence may be misleading. PMID:8524840

  4. Overview of receptor-based source apportionment studies for speciated atmospheric mercury

    NASA Astrophysics Data System (ADS)

    Cheng, I.; Xu, X.; Zhang, L.

    2015-07-01

    Receptor-based source apportionment studies of speciated atmospheric mercury are not only concerned with source contributions but also with the influence of transport, transformation, and deposition processes on speciated atmospheric mercury concentrations at receptor locations. Previous studies applied multivariate receptor models including principal components analysis and positive matrix factorization, and back trajectory receptor models including potential source contribution function, gridded frequency distributions, and concentration-back trajectory models. Combustion sources (e.g., coal combustion, biomass burning, and vehicular, industrial and waste incineration emissions), crustal/soil dust, and chemical and physical processes, such as gaseous elemental mercury (GEM) oxidation reactions, boundary layer mixing, and GEM flux from surfaces were inferred from the multivariate studies, which were predominantly conducted at receptor sites in Canada and the US. Back trajectory receptor models revealed potential impacts of large industrial areas such as the Ohio River valley in the US and throughout China, metal smelters, mercury evasion from the ocean and the Great Lakes, and free troposphere transport on receptor measurements. Input data and model parameters specific to atmospheric mercury receptor models are summarized and model strengths and weaknesses are also discussed. Multivariate models are suitable for receptor locations with intensive air monitoring because they require long-term collocated and simultaneous measurements of speciated atmospheric Hg and ancillary pollutants. The multivariate models provide more insight about the types of Hg emission sources and Hg processes that could affect speciated atmospheric Hg at a receptor location, whereas back trajectory receptor models are mainly ideal for identifying potential regional Hg source locations impacting elevated Hg concentrations. Interpretation of the multivariate model output to sources can be

  5. 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

  6. Speciation by Symbiosis: the Microbiome and Behavior.

    PubMed

    Shropshire, J Dylan; Bordenstein, Seth R

    2016-01-01

    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

  7. Speciation without Pre-Defined Fitness Functions

    PubMed Central

    Gras, Robin; Golestani, Abbas; Hendry, Andrew P.; Cristescu, Melania E.

    2015-01-01

    The forces promoting and constraining speciation are often studied in theoretical models because the process is hard to observe, replicate, and manipulate in real organisms. Most models analyzed to date include pre-defined functions influencing fitness, leaving open the question of how speciation might proceed without these built-in determinants. To consider the process of speciation without pre-defined functions, we employ the individual-based ecosystem simulation platform EcoSim. The environment is initially uniform across space, and an evolving behavioural model then determines how prey consume resources and how predators consume prey. Simulations including natural selection (i.e., an evolving behavioural model that influences survival and reproduction) frequently led to strong and distinct phenotypic/genotypic clusters between which hybridization was low. This speciation was the result of divergence between spatially-localized clusters in the behavioural model, an emergent property of evolving ecological interactions. By contrast, simulations without natural selection (i.e., behavioural model turned off) but with spatial isolation (i.e., limited dispersal) produced weaker and overlapping clusters. Simulations without natural selection or spatial isolation (i.e., behaviour model turned off and high dispersal) did not generate clusters. These results confirm the role of natural selection in speciation by showing its importance even in the absence of pre-defined fitness functions. PMID:26372462

  8. Hydroxyl speciation in felsic magmas

    NASA Astrophysics Data System (ADS)

    Malfait, Wim J.; Xue, Xianyu

    2014-09-01

    The hydroxyl speciation of hydrous, metaluminous potassium and calcium aluminosilicate glasses was investigated by 27Al-1H cross polarization and quantitative 1H MAS NMR spectroscopy. Al-OH is present in both the potassium and the calcium aluminosilicate glasses and its 1H NMR partial spectrum was derived from the 27Al-1H cross polarization data. For the calcium aluminosilicate glasses, the abundance of Al-OH could not be determined because of the low spectral resolution. For the potassium aluminosilicate glasses, the fraction of Al-OH was quantified by fitting its partial spectrum to the quantitative 1H NMR spectra. The degree of aluminum avoidance and the relative tendency for Si-O-Si, Si-O-Al and Al-O-Al bonds to hydrolyze were derived from the measured species abundances. Compared to the sodium, lithium and calcium systems, potassium aluminosilicate glasses display a much stronger degree of aluminum avoidance and a stronger tendency for the Al-O-Al linkages to hydrolyze. Combining our results with those for sodium aluminosilicate glasses (Malfait and Xue, 2010a), we predict that the hydroxyl groups in rhyolitic and phonolitic magmas are predominantly present as Si-OH (84-89% and 68-78%, respectively), but with a significant fraction of Al-OH (11-16% and 22-32%, respectively). For both rhyolitic and phonolitic melts, the AlOH/(AlOH + SiOH) ratio is likely smaller than the Al/(Al + Si) ratio for the lower end of the natural temperature range but may approach the Al/(Al + Si) ratio at higher temperatures.

  9. Complex speciation of humans and chimpanzees.

    PubMed

    Wakeley, John

    2008-03-13

    Genetic data from two or more species provide information about the process of speciation. In their analysis of DNA from humans, chimpanzees, gorillas, orangutans and macaques (HCGOM), Patterson et al. suggest that the apparently short divergence time between humans and chimpanzees on the X chromosome is explained by a massive interspecific hybridization event in the ancestry of these two species. However, Patterson et al. do not statistically test their own null model of simple speciation before concluding that speciation was complex, and--even if the null model could be rejected--they do not consider other explanations of a short divergence time on the X chromosome. These include natural selection on the X chromosome in the common ancestor of humans and chimpanzees, changes in the ratio of male-to-female mutation rates over time, and less extreme versions of divergence with gene flow (see ref. 2, for example). I therefore believe that their claim of hybridization is unwarranted. PMID:18337768

  10. 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.

  11. Speciation on Oceanic Islands: Rapid Adaptive Divergence vs. Cryptic Speciation in a Guadalupe Island Songbird (Aves: Junco)

    PubMed Central

    Aleixandre, Pau; Hernández Montoya, Julio; Milá, Borja

    2013-01-01

    The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis), and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated “cryptic” lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands in driving

  12. 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...

  13. 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...

  14. INFERENCES FROM ROSSI TRACES

    SciTech Connect

    KENNETH M. HANSON; JANE M. BOOKER

    2000-09-08

    The authors an uncertainty analysis of data taken using the Rossi technique, in which the horizontal oscilloscope sweep is driven sinusoidally in time ,while the vertical axis follows the signal amplitude. The analysis is done within a Bayesian framework. Complete inferences are obtained by tilting the Markov chain Monte Carlo technique, which produces random samples from the posterior probability distribution expressed in terms of the parameters.

  15. Motion Information Inferring Scheme for Multi-View Video Coding

    NASA Astrophysics Data System (ADS)

    Koo, Han-Suh; Jeon, Yong-Joon; Jeon, Byeong-Moon

    This letter proposes a motion information inferring scheme for multi-view video coding motivated by the idea that the aspect of motion vector between the corresponding positions in the neighboring view pair is quite similar. The proposed method infers the motion information from the corresponding macroblock in the neighboring view after RD optimization with the existing prediction modes. This letter presents evaluation showing that the method significantly enhances the efficiency especially at high bit rates.

  16. Active inference and learning.

    PubMed

    Friston, Karl; FitzGerald, Thomas; Rigoli, Francesco; Schwartenbeck, Philipp; O'Doherty, John; Pezzulo, Giovanni

    2016-09-01

    This paper offers an active inference account of choice behaviour and learning. It focuses on the distinction between goal-directed and habitual behaviour and how they contextualise each other. We show that habits emerge naturally (and autodidactically) from sequential policy optimisation when agents are equipped with state-action policies. In active inference, behaviour has explorative (epistemic) and exploitative (pragmatic) aspects that are sensitive to ambiguity and risk respectively, where epistemic (ambiguity-resolving) behaviour enables pragmatic (reward-seeking) behaviour and the subsequent emergence of habits. Although goal-directed and habitual policies are usually associated with model-based and model-free schemes, we find the more important distinction is between belief-free and belief-based schemes. The underlying (variational) belief updating provides a comprehensive (if metaphorical) process theory for several phenomena, including the transfer of dopamine responses, reversal learning, habit formation and devaluation. Finally, we show that active inference reduces to a classical (Bellman) scheme, in the absence of ambiguity. PMID:27375276

  17. Bayesian inference in physics

    NASA Astrophysics Data System (ADS)

    von Toussaint, Udo

    2011-07-01

    Bayesian inference provides a consistent method for the extraction of information from physics experiments even in ill-conditioned circumstances. The approach provides a unified rationale for data analysis, which both justifies many of the commonly used analysis procedures and reveals some of the implicit underlying assumptions. This review summarizes the general ideas of the Bayesian probability theory with emphasis on the application to the evaluation of experimental data. As case studies for Bayesian parameter estimation techniques examples ranging from extra-solar planet detection to the deconvolution of the apparatus functions for improving the energy resolution and change point estimation in time series are discussed. Special attention is paid to the numerical techniques suited for Bayesian analysis, with a focus on recent developments of Markov chain Monte Carlo algorithms for high-dimensional integration problems. Bayesian model comparison, the quantitative ranking of models for the explanation of a given data set, is illustrated with examples collected from cosmology, mass spectroscopy, and surface physics, covering problems such as background subtraction and automated outlier detection. Additionally the Bayesian inference techniques for the design and optimization of future experiments are introduced. Experiments, instead of being merely passive recording devices, can now be designed to adapt to measured data and to change the measurement strategy on the fly to maximize the information of an experiment. The applied key concepts and necessary numerical tools which provide the means of designing such inference chains and the crucial aspects of data fusion are summarized and some of the expected implications are highlighted.

  18. Sampling genetic diversity in the sympatrically and allopatrically speciating Midas cichlid species complex over a 16 year time series

    PubMed Central

    Bunje, Paul ME; Barluenga, Marta; Meyer, Axel

    2007-01-01

    Background Speciation often occurs in complex or uncertain temporal and spatial contexts. Processes such as reinforcement, allopatric divergence, and assortative mating can proceed at different rates and with different strengths as populations diverge. The Central American Midas cichlid fish species complex is an important case study for understanding the processes of speciation. Previous analyses have demonstrated that allopatric processes led to species formation among the lakes of Nicaragua as well as sympatric speciation that is occurring within at least one crater lake. However, since speciation is an ongoing process and sampling genetic diversity of such lineages can be biased by collection scheme or random factors, it is important to evaluate the robustness of conclusions drawn on individual time samples. Results In order to assess the validity and reliability of inferences based on different genetic samples, we have analyzed fish from several lakes in Nicaragua sampled at three different times over 16 years. In addition, this time series allows us to analyze the population genetic changes that have occurred between lakes, where allopatric speciation has operated, as well as between different species within lakes, some of which have originated by sympatric speciation. Focusing on commonly used genetic markers, we have analyzed both DNA sequences from the complete mitochondrial control region as well as nuclear DNA variation at ten microsatellite loci from these populations, sampled thrice in a 16 year time period, to develop a robust estimate of the population genetic history of these diversifying lineages. Conclusion The conclusions from previous work are well supported by our comprehensive analysis. In particular, we find that the genetic diversity of derived crater lake populations is lower than that of the source population regardless of when and how each population was sampled. Furthermore, changes in various estimates of genetic diversity within lakes

  19. Arsenic speciation in manufactured seafood products.

    PubMed

    Vélez, D; Montoro, R

    1998-09-01

    The literature on the speciation of arsenic (As) in seafoods was critically reviewed. Most research has been directed toward fresh seafood products with few papers dealing with As speciation in manufactured seafoods. Predictions concerning As species made on the basis of fresh seafood products cannot be extrapolated to manufactured seafoods. Therefore, due to the numerous species of As, the scarcity of data concerning their presence in foods, the transformations each species may undergo during industrial processing and cooking, and the lack of legislation on permitted As levels in seafood products, As species in manufactured seafood products need to be determined and quantified. PMID:9766084

  20. Instrumentation for Aerosol and Gas Speciation

    NASA Technical Reports Server (NTRS)

    Coggiola, Michael J.

    1998-01-01

    Using support from NASA Grant No. NAG 2-963, SRI International successfully completed the project, entitled, 'Instrumentation for Aerosol and Gas Speciation.' This effort (SRI Project 7383) covered the design, fabrication, testing, and deployment of a real-time aerosol speciation instrument in NASA's DC-8 aircraft during the Spring 1996 SUbsonic aircraft: Contrail and Cloud Effects Special Study (SUCCESS) mission. This final technical report describes the pertinent details of the instrument design, its abilities, its deployment during SUCCESS and the data acquired from the mission, and the post-mission calibration, data reduction, and analysis.

  1. Towards Context Sensitive Information Inference.

    ERIC Educational Resources Information Center

    Song, D.; Bruza, P. D.

    2003-01-01

    Discusses information inference from a psychologistic stance and proposes an information inference mechanism that makes inferences via computations of information flow through an approximation of a conceptual space. Highlights include cognitive economics of information processing; context sensitivity; and query models for information retrieval.…

  2. Toxicity, bioavailability and metal speciation.

    PubMed

    Jonnalagadda, S B; Rao, P V

    1993-11-01

    1. Environmental toxicology emphasizes the difference from traditional toxicology in which pure compounds of interest are added to purified diets, or injected into the test animals. When the objective is to study the fate and effects of trace elements in the environment, knowledge of the speciation of the elements and their physico-chemical forms is important. 2. Cadmium salts such as the sulfides, carbonates or oxides, are practically insoluble in water. However, these can be converted to water-soluble salts in nature under the influence of oxygen and acids. Chronic exposure to Cd is associated with renal toxicity in humans once a critical body burden is reached. 3. The solubility of As(III) oxide in water is fairly low, but high in either acid or alkali. In water, arsenic is usually in the form of the arsenate or arsenite. As(III) is systemically more poisonous than the As(V), and As(V) is reduced to the As(III) form before exerting any toxic effects. Organic arsenicals also exert their toxic effects in vivo in animals by first metabolizing to the trivalent arsenoxide form. Some methyl arsenic compounds, such as di- and trimethylarsines, occur naturally as a consequence of biological activity. The toxic effect of arsenite can be potentiated by dithiols, while As has a protective effect against the toxicity of a variety of forms of Se in several species. 4. Selenium occurs in several oxidation states and many selenium analogues of organic sulfur compounds exist in nature. Selenium in selenate form occurs in alkaline soils, where it is soluble and easily available to plants. Selenite binds tightly to iron and aluminum oxides and thus is quite insoluble in soils. Hydrogen selenide is a very toxic gas at room temperature. The methylated forms of Se are much less toxic for the organism than selenite. However, the methylated Se derivatives have strong synergistic toxicity with other minerals such as arsenic. 5. Aquatic organisms absorb and retain Hg in the tissues, as

  3. Overview of receptor-based source apportionment studies for speciated atmospheric mercury

    NASA Astrophysics Data System (ADS)

    Cheng, I.; Xu, X.; Zhang, L.

    2015-02-01

    Receptor-based source apportionment studies of speciated atmospheric mercury are not only concerned with source contributions, but also the influence of transport, transformation, and deposition processes on speciated atmospheric mercury concentrations at receptor locations. Previous studies applied multivariate receptor models including Principal Components Analysis and Positive Matrix Factorization, and back trajectory receptor models including Potential Source Contribution Function, Gridded Frequency Distributions, and Concentration-back trajectory models. Anthropogenic combustion sources, crustal/soil dust, and chemical and physical processes, such as gaseous elemental mercury (GEM) oxidation reactions, boundary layer mixing, and GEM flux from surfaces, were inferred from the multivariate studies, which were predominantly conducted at receptor sites in Canada and the US. Back trajectory receptor models revealed potential impacts of large industrial areas such as the Ohio River Valley in the US and throughout China, metal smelters, mercury evasion from the ocean and Great Lakes, and free troposphere transport on receptor measurements. Input data and model parameters specific to atmospheric mercury receptor models are summarized and model strengths and weaknesses are also discussed. One area of improvement that applies to all receptor models is the greater focus on evaluating the accuracy of receptor models at identifying potential speciated atmospheric mercury sources, source locations, and chemical and physical processes in the atmosphere.

  4. Ecological speciation in tropical reef fishes

    PubMed Central

    Rocha, Luiz A; Robertson, D. Ross; Roman, Joe; Bowen, Brian W

    2005-01-01

    The high biodiversity in tropical seas provides a long-standing challenge to allopatric speciation models. Physical barriers are few in the ocean and larval dispersal is often extensive, a combination that should reduce opportunities for speciation. Yet coral reefs are among the most species-rich habitats in the world, indicating evolutionary processes beyond conventional allopatry. In a survey of mtDNA sequences of five congeneric west Atlantic reef fishes (wrasses, genus Halichoeres) with similar dispersal potential, we observed phylogeographical patterns that contradict expectations of geographical isolation, and instead indicate a role for ecological speciation. In Halichoeres bivittatus and the species pair Halichoeres radiatus/brasiliensis, we observed strong partitions (3.4% and 2.3% divergence, respectively) between adjacent and ecologically distinct habitats, but high genetic connectivity between similar habitats separated by thousands of kilometres. This habitat partitioning is maintained even at a local scale where H. bivittatus lineages are segregated between cold- and warm-water habitats in both Bermuda and Florida. The concordance of evolutionary partitions with habitat types, rather than conventional biogeographical barriers, indicates parapatric ecological speciation, in which adaptation to alternative environmental conditions in adjacent locations overwhelms the homogenizing effect of dispersal. This mechanism can explain the long-standing enigma of high biodiversity in coral reef faunas. PMID:15817431

  5. NICKEL SPECIATION OF RESIDUAL OIL ASH

    EPA Science Inventory

    EPA GRANT NUMBER: R827649C002
    Title: Nickel Speciation Of Residual Oil Ash
    Investigators: Kevin C. Galbreath, John Won, Frank E. Huggins, Gerald P. Huffman, Christopher J. Zygarlicke, Donald L. Toman
    Institution: University of North Dakota<...

  6. Speciation: Genomic Archipelagos in a Crater Lake.

    PubMed

    Ronco, Fabrizia; Salzburger, Walter

    2016-03-01

    The opening stages of speciation remain poorly understood, especially from a genomic perspective. The genomes of newly discovered crater-lake cichlid fish shed light on the early phases of diversification and suggest that selection acts on multiple genomic regions. PMID:26954438

  7. Biosensor for metal analysis and speciation

    DOEpatents

    Aiken, Abigail M.; Peyton, Brent M.; Apel, William A.; Petersen, James N.

    2007-01-30

    A biosensor for metal analysis and speciation is disclosed. The biosensor comprises an electron carrier immobilized to a surface of an electrode and a layer of an immobilized enzyme adjacent to the electrode. The immobilized enzyme comprises an enzyme having biological activity inhibited by a metal to be detected by the biosensor.

  8. 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

  9. Speciation of VOCs from Animal Feeding Operations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Environmental Pollution Agency (EPA) air consent agreement with animal feeding operations (AFO) specifies the use of EPA TO-15 for the speciation of volatile organic compounds (VOC) emitted from these facilities. However, compounds emitted from AFO are often both volatile and highly polar chara...

  10. Characterization of Technetium Speciation in Cast Stone

    SciTech Connect

    Um, Wooyong; Jung, Hun Bok; Wang, Guohui; Westsik, Joseph H.; Peterson, Reid A.

    2013-11-11

    This report describes the results from laboratory tests performed at Pacific Northwest National Laboratory (PNNL) for the U.S. Department of Energy (DOE) EM-31 Support Program (EMSP) subtask, “Production and Long-Term Performance of Low Temperature Waste Forms” to provide additional information on technetium (Tc) speciation characterization in the Cast Stone waste form. To support the use of Cast Stone as an alternative to vitrification for solidifying low-activity waste (LAW) and as the current baseline waste form for secondary waste streams at the Hanford Site, additional understanding of Tc speciation in Cast Stone is needed to predict the long-term Tc leachability from Cast Stone and to meet the regulatory disposal-facility performance requirements for the Integrated Disposal Facility (IDF). Characterizations of the Tc speciation within the Cast Stone after leaching under various conditions provide insights into how the Tc is retained and released. The data generated by the laboratory tests described in this report provide both empirical and more scientific information to increase our understanding of Tc speciation in Cast Stone and its release mechanism under relevant leaching processes for the purpose of filling data gaps and to support the long-term risk and performance assessments of Cast Stone in the IDF at the Hanford Site.

  11. ELEMENTAL SPECIATION IN ENVIRONMENTAL EXPOSURE ASSESSMENT MATRICES

    EPA Science Inventory

    Arsenic and tin are two trace metals where exposure assessments have moved towards a speciation based approach because the toxicity is very chemical form dependent. This toxicity difference can be one of many factors which influence the formulation of certain regulations. For a...

  12. Heavy metal speciation in the composting process.

    PubMed

    Greenway, Gillian M; Song, Qi Jun

    2002-04-01

    Composting is one of the more efficient and environment friendly methods of solid waste disposal and has many advantages when compared with landfill disposal on which the UK and Ireland are currently heavily dependent. Composting is a very complicated process involving intensive microbial activity and the detailed mechanisms of the process have yet to be fully understood. Metal speciation information can provide an insight into the metal-microbial interaction and would help in the evaluation of the quality of compost. This would facilitate the exploitation of composts in remediation of heavy metal contaminated land. In this work a systematic approach to metal speciation in compost has been taken by applying the three-step method for operationally defined metal speciation of soils and sediments, developed by the European Commission's Standards, Measurement and Testing Programme to monitor the change in metal speciation with time (up to 106 days) for four different waste composting processes. The results have shown that in general metals become less available for the first extraction step as the composting process proceeds. This implies that composting tends to redistribute the metals from more labile forms to more fixed forms which may explain why the application of composts could be useful for with heavy metal contaminated land. There are exceptions to this trend and in some cases, certain metals appear to behave differently depending on the source of the compost. PMID:11993774

  13. EFFECT OF SCR CATALYST ON MERCURY SPECIATION

    EPA Science Inventory

    A pilot-scale research study was conducted to investigate the effect of selective catalytic reduction (SCR) on elemental mercury speciation in bituminous and subbituminous coal combustion flue gases. Three different Illinois bituminous coals and one Powder River Basin (PRB) coal...

  14. ARSENIC SPECIATION ANALYSIS IN HUMAN SALIVA

    EPA Science Inventory

    Background: Determination of arsenic species in human saliva is potentially useful for biomonitoring of human exposure to arsenic and for studying arsenic metabolism. However, there is no report on the speciation analysis of arsenic in saliva. Methods: Arsenic species in saliva ...

  15. Visual Inference Programming

    NASA Technical Reports Server (NTRS)

    Wheeler, Kevin; Timucin, Dogan; Rabbette, Maura; Curry, Charles; Allan, Mark; Lvov, Nikolay; Clanton, Sam; Pilewskie, Peter

    2002-01-01

    The goal of visual inference programming is to develop a software framework data analysis and to provide machine learning algorithms for inter-active data exploration and visualization. The topics include: 1) Intelligent Data Understanding (IDU) framework; 2) Challenge problems; 3) What's new here; 4) Framework features; 5) Wiring diagram; 6) Generated script; 7) Results of script; 8) Initial algorithms; 9) Independent Component Analysis for instrument diagnosis; 10) Output sensory mapping virtual joystick; 11) Output sensory mapping typing; 12) Closed-loop feedback mu-rhythm control; 13) Closed-loop training; 14) Data sources; and 15) Algorithms. This paper is in viewgraph form.

  16. Anagenetic speciation in Ullung Island, Korea: genetic diversity and structure in the island endemic species, Acer takesimense (Sapindaceae).

    PubMed

    Takayama, Koji; Sun, Byung-Yun; Stuessy, Tod F

    2013-05-01

    Anagenetic speciation is an important mode of speciation in oceanic islands; one-fourth of the endemic plants are estimated to have been derived via this process. Few studies, however, have critically examined the genetic consequences of anagenesis in comparison with cladogenesis (involved with adaptive radiation). We hypothesize that endemic species originating via anagenetic speciation in a relatively uniform environment should accumulate genetic variation with limited populational differentiation. We undertook a population genetic analysis using nine nuclear microsatellite loci of Acer takesimense, an anagenetically derived species endemic to Ullung Island, Korea, and its continental progenitor A. pseudosieboldianum on the Korean Peninsula. Microsatellite data reveal a clear genetic distinction between the two species. A high F value in the cluster of A. takesimense was found by Bayesian clustering analysis, suggesting a strong episode of genetic drift during colonization and speciation. In comparison with A. pseudosieboldianum, A. takesimense has slightly lower genetic diversity and possesses less than half the number of private and rare alleles. Consistent with predictions, weak geographical genetic structure within the island was found in A. takesimense. These results imply that anagenetic speciation leads to a different pattern of specific and genetic diversity than often seen with cladogenesis. PMID:23090156

  17. 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.

  18. Circular inferences in schizophrenia.

    PubMed

    Jardri, Renaud; Denève, Sophie

    2013-11-01

    A considerable number of recent experimental and computational studies suggest that subtle impairments of excitatory to inhibitory balance or regulation are involved in many neurological and psychiatric conditions. The current paper aims to relate, specifically and quantitatively, excitatory to inhibitory imbalance with psychotic symptoms in schizophrenia. Considering that the brain constructs hierarchical causal models of the external world, we show that the failure to maintain the excitatory to inhibitory balance results in hallucinations as well as in the formation and subsequent consolidation of delusional beliefs. Indeed, the consequence of excitatory to inhibitory imbalance in a hierarchical neural network is equated to a pathological form of causal inference called 'circular belief propagation'. In circular belief propagation, bottom-up sensory information and top-down predictions are reverberated, i.e. prior beliefs are misinterpreted as sensory observations and vice versa. As a result, these predictions are counted multiple times. Circular inference explains the emergence of erroneous percepts, the patient's overconfidence when facing probabilistic choices, the learning of 'unshakable' causal relationships between unrelated events and a paradoxical immunity to perceptual illusions, which are all known to be associated with schizophrenia. PMID:24065721

  19. Moment inference from tomograms

    USGS Publications Warehouse

    Day-Lewis, F. D.; Chen, Y.; Singha, K.

    2007-01-01

    Time-lapse geophysical tomography can provide valuable qualitative insights into hydrologic transport phenomena associated with aquifer dynamics, tracer experiments, and engineered remediation. Increasingly, tomograms are used to infer the spatial and/or temporal moments of solute plumes; these moments provide quantitative information about transport processes (e.g., advection, dispersion, and rate-limited mass transfer) and controlling parameters (e.g., permeability, dispersivity, and rate coefficients). The reliability of moments calculated from tomograms is, however, poorly understood because classic approaches to image appraisal (e.g., the model resolution matrix) are not directly applicable to moment inference. Here, we present a semi-analytical approach to construct a moment resolution matrix based on (1) the classic model resolution matrix and (2) image reconstruction from orthogonal moments. Numerical results for radar and electrical-resistivity imaging of solute plumes demonstrate that moment values calculated from tomograms depend strongly on plume location within the tomogram, survey geometry, regularization criteria, and measurement error. Copyright 2007 by the American Geophysical Union.

  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. PMID:27233437

  1. 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

  2. Choice matters: incipient speciation in Gyrodactylus corydori (Monogenoidea: Gyrodactylidae).

    PubMed

    Bueno-Silva, Marlus; Boeger, Walter A; Pie, Marcio R

    2011-05-01

    unreported mode of adaptive speciation that helps to understand its rate of diversification. PMID:21310159

  3. BIE: Bayesian Inference Engine

    NASA Astrophysics Data System (ADS)

    Weinberg, Martin D.

    2013-12-01

    The Bayesian Inference Engine (BIE) is an object-oriented library of tools written in C++ designed explicitly to enable Bayesian update and model comparison for astronomical problems. To facilitate "what if" exploration, BIE provides a command line interface (written with Bison and Flex) to run input scripts. The output of the code is a simulation of the Bayesian posterior distribution from which summary statistics e.g. by taking moments, or determine confidence intervals and so forth, can be determined. All of these quantities are fundamentally integrals and the Markov Chain approach produces variates heta distributed according to P( heta|D) so moments are trivially obtained by summing of the ensemble of variates.

  4. Bayesian inference in geomagnetism

    NASA Technical Reports Server (NTRS)

    Backus, George E.

    1988-01-01

    The inverse problem in empirical geomagnetic modeling is investigated, with critical examination of recently published studies. Particular attention is given to the use of Bayesian inference (BI) to select the damping parameter lambda in the uniqueness portion of the inverse problem. The mathematical bases of BI and stochastic inversion are explored, with consideration of bound-softening problems and resolution in linear Gaussian BI. The problem of estimating the radial magnetic field B(r) at the earth core-mantle boundary from surface and satellite measurements is then analyzed in detail, with specific attention to the selection of lambda in the studies of Gubbins (1983) and Gubbins and Bloxham (1985). It is argued that the selection method is inappropriate and leads to lambda values much larger than those that would result if a reasonable bound on the heat flow at the CMB were assumed.

  5. Bayes factors and multimodel inference

    USGS Publications Warehouse

    Link, W.A.; Barker, R.J.

    2009-01-01

    Multimodel inference has two main themes: model selection, and model averaging. Model averaging is a means of making inference conditional on a model set, rather than on a selected model, allowing formal recognition of the uncertainty associated with model choice. The Bayesian paradigm provides a natural framework for model averaging, and provides a context for evaluation of the commonly used AIC weights. We review Bayesian multimodel inference, noting the importance of Bayes factors. Noting the sensitivity of Bayes factors to the choice of priors on parameters, we define and propose nonpreferential priors as offering a reasonable standard for objective multimodel inference.

  6. SERIES - Satellite Emission Range Inferred Earth Surveying

    NASA Technical Reports Server (NTRS)

    Macdoran, P. F.; Spitzmesser, D. J.; Buennagel, L. A.

    1983-01-01

    The Satellite Emission Range Inferred Earth Surveying (SERIES) concept is based on the utilization of NAVSTAR Global Positioning System (GPS) radio transmissions without any satellite modifications and in a totally passive mode. The SERIES stations are equipped with lightweight 1.5 m diameter dish antennas mounted on trailers. A series baseline measurement accuracy demonstration is considered, taking into account a 100 meter baseline estimation from approximately one hour of differential Doppler data. It is planned to conduct the next phase of experiments on a 150 m baseline. Attention is given to details regarding future baseline measurement accuracy demonstrations, aspects of ionospheric calibration in connection with subdecimeter baseline accuracy requirements of geodesy, and advantages related to the use of the differential Doppler or pseudoranging mode.

  7. Speciation in aqueous solutions of nitric acid.

    PubMed

    Hlushak, S; Simonin, J P; De Sio, S; Bernard, O; Ruas, A; Pochon, P; Jan, S; Moisy, P

    2013-02-28

    In this study, speciation in aqueous solutions of nitric acid at 25 °C was assessed in two independent ways. First, Raman experiments were carried out and interpreted in terms of free nitrate ions, ion pairs and neutral HNO(3) molecules. In parallel, a model was developed to account for the formation of these two kinds of pairs. It was based on an extension of the binding mean spherical approximation (BiMSA), or associative MSA (AMSA), in which the size and the charge of the ions in the chemical pair may differ from those of the free ions. A simultaneous fit of the osmotic coefficient and of the proportion of free ions (obtained from Raman spectroscopy experiments) led to an estimation of the speciation in nitric acid solutions. The result obtained using this procedure was compared with the estimation obtained from the Raman experiments. PMID:23258765

  8. Is There a Free Lunch in Inference?

    PubMed

    Rouder, Jeffrey N; Morey, Richard D; Verhagen, Josine; Province, Jordan M; Wagenmakers, Eric-Jan

    2016-07-01

    The field of psychology, including cognitive science, is vexed by a crisis of confidence. Although the causes and solutions are varied, we focus here on a common logical problem in inference. The default mode of inference is significance testing, which has a free lunch property where researchers need not make detailed assumptions about the alternative to test the null hypothesis. We present the argument that there is no free lunch; that is, valid testing requires that researchers test the null against a well-specified alternative. We show how this requirement follows from the basic tenets of conventional and Bayesian probability. Moreover, we show in both the conventional and Bayesian framework that not specifying the alternative may lead to rejections of the null hypothesis with scant evidence. We review both frequentist and Bayesian approaches to specifying alternatives, and we show how such specifications improve inference. The field of cognitive science will benefit because consideration of reasonable alternatives will undoubtedly sharpen the intellectual underpinnings of research. PMID:27489199

  9. Interactions among quantitative traits in the course of sympatric speciation

    NASA Astrophysics Data System (ADS)

    Kondrashov, Alexey S.; Kondrashov, Fyodor A.

    1999-07-01

    Sympatric speciation, the origin of two or more species from a single local population, has almost certainly been involved in formation of several species flocks, and may be fairly common in nature. The most straightforward scenario for sympatric speciation requires disruptive selection favouring two substantially different phenotypes, and consists of the evolution of reproductive isolation between them followed by the elimination of all intermediate phenotypes. Here we use the hypergeometric phenotypic model to show that sympatric speciation is possible even when fitness and mate choice depend on different quantitative traits, so that speciation must involve formation of covariance between these traits. The increase in the number of variable lociaffecting fitness facilitates sympatric speciation, whereas the increase in the number of variable loci affecting mate choice has the opposite effect. These predictions may enable more cases of sympatric speciation to be identified.

  10. Floral symmetry affects speciation rates in angiosperms.

    PubMed Central

    Sargent, Risa D.

    2004-01-01

    Despite much recent activity in the field of pollination biology, the extent to which animal pollinators drive the formation of new angiosperm species remains unresolved. One problem has been identifying floral adaptations that promote reproductive isolation. The evolution of a bilaterally symmetrical corolla restricts the direction of approach and movement of pollinators on and between flowers. Restricting pollinators to approaching a flower from a single direction facilitates specific placement of pollen on the pollinator. When coupled with pollinator constancy, precise pollen placement can increase the probability that pollen grains reach a compatible stigma. This has the potential to generate reproductive isolation between species, because mutations that cause changes in the placement of pollen on the pollinator may decrease gene flow between incipient species. I predict that animal-pollinated lineages that possess bilaterally symmetrical flowers should have higher speciation rates than lineages possessing radially symmetrical flowers. Using sister-group comparisons I demonstrate that bilaterally symmetric lineages tend to be more species rich than their radially symmetrical sister lineages. This study supports an important role for pollinator-mediated speciation and demonstrates that floral morphology plays a key role in angiosperm speciation. PMID:15156918

  11. Chiral Speciation in Terrestrial Pulmonate Snails

    PubMed Central

    Gittenberger, Edmund; Hamann, Thomas D.; Asami, Takahiro

    2012-01-01

    On the basis of data in the literature, the percentages of dextral versus sinistral species of snails have been calculated for western Europe, Turkey, North America (north of Mexico), and Japan. When the family of Clausiliidae is represented, about a quarter of all snail species may be sinistral, whereas less than one per cent of the species may be sinistral where that family does not occur. The number of single-gene speciation events on the basis of chirality, resulting in the origin of mirror image species, is not closely linked to the percentage of sinistral versus dextral species in a particular region. Turkey is nevertheless exceptional by both a high percentage of sinistral species and a high number of speciation events resulting in mirror image species. Shell morphology and genetic background may influence the ease of chirality-linked speciation, whereas sinistrality may additionally be selected against by internal selection. For the Clausiliidae, the fossil record and the recent fauna suggest that successful reversals in coiling direction occurred with a frequency of once every three to four million years. PMID:22532825

  12. 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

  13. Causal Inference in Retrospective Studies.

    ERIC Educational Resources Information Center

    Holland, Paul W.; Rubin, Donald B.

    1988-01-01

    The problem of drawing causal inferences from retrospective case-controlled studies is considered. A model for causal inference in prospective studies is applied to retrospective studies. Limitations of case-controlled studies are formulated concerning relevant parameters that can be estimated in such studies. A coffee-drinking/myocardial…

  14. Improving Inferences from Multiple Methods.

    ERIC Educational Resources Information Center

    Shotland, R. Lance; Mark, Melvin M.

    1987-01-01

    Multiple evaluation methods (MEMs) can cause an inferential challenge, although there are strategies to strengthen inferences. Practical and theoretical issues involved in the use by social scientists of MEMs, three potential problems in drawing inferences from MEMs, and short- and long-term strategies for alleviating these problems are outlined.…

  15. Causal Inference and Developmental Psychology

    ERIC Educational Resources Information Center

    Foster, E. Michael

    2010-01-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether…

  16. Learning to Observe "and" Infer

    ERIC Educational Resources Information Center

    Hanuscin, Deborah L.; Park Rogers, Meredith A.

    2008-01-01

    Researchers describe the need for students to have multiple opportunities and social interaction to learn about the differences between observation and inference and their role in developing scientific explanations (Harlen 2001; Simpson 2000). Helping children develop their skills of observation and inference in science while emphasizing the…

  17. INFERRING THE ECCENTRICITY DISTRIBUTION

    SciTech Connect

    Hogg, David W.; Bovy, Jo; Myers, Adam D.

    2010-12-20

    Standard maximum-likelihood estimators for binary-star and exoplanet eccentricities are biased high, in the sense that the estimated eccentricity tends to be larger than the true eccentricity. As with most non-trivial observables, a simple histogram of estimated eccentricities is not a good estimate of the true eccentricity distribution. Here, we develop and test a hierarchical probabilistic method for performing the relevant meta-analysis, that is, inferring the true eccentricity distribution, taking as input the likelihood functions for the individual star eccentricities, or samplings of the posterior probability distributions for the eccentricities (under a given, uninformative prior). The method is a simple implementation of a hierarchical Bayesian model; it can also be seen as a kind of heteroscedastic deconvolution. It can be applied to any quantity measured with finite precision-other orbital parameters, or indeed any astronomical measurements of any kind, including magnitudes, distances, or photometric redshifts-so long as the measurements have been communicated as a likelihood function or a posterior sampling.

  18. Inferring the Eccentricity Distribution

    NASA Astrophysics Data System (ADS)

    Hogg, David W.; Myers, Adam D.; Bovy, Jo

    2010-12-01

    Standard maximum-likelihood estimators for binary-star and exoplanet eccentricities are biased high, in the sense that the estimated eccentricity tends to be larger than the true eccentricity. As with most non-trivial observables, a simple histogram of estimated eccentricities is not a good estimate of the true eccentricity distribution. Here, we develop and test a hierarchical probabilistic method for performing the relevant meta-analysis, that is, inferring the true eccentricity distribution, taking as input the likelihood functions for the individual star eccentricities, or samplings of the posterior probability distributions for the eccentricities (under a given, uninformative prior). The method is a simple implementation of a hierarchical Bayesian model; it can also be seen as a kind of heteroscedastic deconvolution. It can be applied to any quantity measured with finite precision—other orbital parameters, or indeed any astronomical measurements of any kind, including magnitudes, distances, or photometric redshifts—so long as the measurements have been communicated as a likelihood function or a posterior sampling.

  19. Social Inference Through Technology

    NASA Astrophysics Data System (ADS)

    Oulasvirta, Antti

    Awareness cues are computer-mediated, real-time indicators of people’s undertakings, whereabouts, and intentions. Already in the mid-1970 s, UNIX users could use commands such as “finger” and “talk” to find out who was online and to chat. The small icons in instant messaging (IM) applications that indicate coconversants’ presence in the discussion space are the successors of “finger” output. Similar indicators can be found in online communities, media-sharing services, Internet relay chat (IRC), and location-based messaging applications. But presence and availability indicators are only the tip of the iceberg. Technological progress has enabled richer, more accurate, and more intimate indicators. For example, there are mobile services that allow friends to query and follow each other’s locations. Remote monitoring systems developed for health care allow relatives and doctors to assess the wellbeing of homebound patients (see, e.g., Tang and Venables 2000). But users also utilize cues that have not been deliberately designed for this purpose. For example, online gamers pay attention to other characters’ behavior to infer what the other players are like “in real life.” There is a common denominator underlying these examples: shared activities rely on the technology’s representation of the remote person. The other human being is not physically present but present only through a narrow technological channel.

  20. Inference from aging information.

    PubMed

    de Oliveira, Evaldo Araujo; Caticha, Nestor

    2010-06-01

    For many learning tasks the duration of the data collection can be greater than the time scale for changes of the underlying data distribution. The question we ask is how to include the information that data are aging. Ad hoc methods to achieve this include the use of validity windows that prevent the learning machine from making inferences based on old data. This introduces the problem of how to define the size of validity windows. In this brief, a new adaptive Bayesian inspired algorithm is presented for learning drifting concepts. It uses the analogy of validity windows in an adaptive Bayesian way to incorporate changes in the data distribution over time. We apply a theoretical approach based on information geometry to the classification problem and measure its performance in simulations. The uncertainty about the appropriate size of the memory windows is dealt with in a Bayesian manner by integrating over the distribution of the adaptive window size. Thus, the posterior distribution of the weights may develop algebraic tails. The learning algorithm results from tracking the mean and variance of the posterior distribution of the weights. It was found that the algebraic tails of this posterior distribution give the learning algorithm the ability to cope with an evolving environment by permitting the escape from local traps. PMID:20421181

  1. Phylogeny and historical biogeography of ancient assassin spiders (Araneae: Archaeidae) in the Australian mesic zone: evidence for Miocene speciation within Tertiary refugia.

    PubMed

    Rix, Michael G; Harvey, Mark S

    2012-01-01

    The rainforests, wet sclerophyll forests and temperate heathlands of the Australian mesic zone are home to a diverse and highly endemic biota, including numerous old endemic lineages restricted to refugial, mesic biomes. A growing number of phylogeographic studies have attempted to explain the origins and diversification of the Australian mesic zone biota, in order to test and better understand the mode and tempo of historical speciation within Australia. Assassin spiders (family Archaeidae) are a lineage of iconic araneomorph spiders, characterised by their antiquity, remarkable morphology and relictual biogeography on the southern continents. The Australian assassin spider fauna is characterised by a high diversity of allopatric species, many of which are restricted to individual mountains or montane systems, and all of which are closely tied to mesic and/or refugial habitats in the east and extreme south-west of mainland Australia. We tested the phylogeny and vicariant biogeography of the Australian Archaeidae (genus Austrarchaea Forster & Platnick), using a multi-locus molecular approach. Fragments from six mitochondrial genes (COI, COII, tRNA-K, tRNA-D, ATP8, ATP6) and one nuclear protein-coding gene (Histone H3) were used to infer phylogenetic relationships and to explore the phylogeographic origins of the diverse Australian fauna. Bayesian analyses of the complete molecular dataset, along with differentially-partitioned Bayesian and parsimony analyses of a smaller concatenated dataset, revealed the presence of three major Australian lineages, each with non-overlapping distributions in north-eastern Queensland, mid-eastern Australia and southern Australia, respectively. Divergence date estimation using mitochondrial data and a rate-calibrated relaxed molecular clock revealed that major lineages diverged in the early Tertiary period, prior to the final rifting of Australia from East Antarctica. Subsequent speciation occurred during the Miocene (23-5.3 million

  2. Evaluation of Regenerated Catalyst for Mercury Speciation

    SciTech Connect

    Dennis Laudal

    2007-06-01

    In March of 2005, U.S. Environmental Protection Agency (EPA) promulgated the Clean Air Mercury Rule (CAMR). Mercury from coal-fired power plants was to be reduced from the current 48 to 38 tons/yr by 2010 and then 15 tons/yr by 2018. It is expected that the first phase reduction of {approx}21% will be achieved by cobenefits that will occur as a result of installing additional selective catalytic reduction (SCR) and flue gas desulfurization (FGD) systems to meet the new Clean Air Interstate Rule (CAIR). Detroit Edison (DTE) is installing SCR at all four units at its Monroe Station and will eventually install wet-FGD systems. As such, the Electric Power Research Institute (EPRI), the U.S. Department of Energy (DOE), and DTE have contracted with the Energy & Environmental Research Center (EERC) to determine the extent of mercury oxidation that occurs at Monroe Station. The EERC originally did mercury speciation sampling at Monroe Station in 2004 and then went back in 2005 to determine if any changes occurred as a result of catalyst aging. During the second test, in addition to measuring the mercury speciation at the inlet and outlet of the SCR, the EERC also completed sampling at a location between the catalyst layers. The results are shown in Table 1. In Table 1, the results show that {approx}40% of the Hg was in oxidized form (Hg{sup 2+}) at the inlet and nearly 100% Hg{sup 2+} at the outlet. The results at the midpoint were between 40% and 100%. As part of their overall strategy to reduce SCR costs, utilities and SCR vendors are attempting to regenerate catalyst layers that have degenerated over time. If these regenerated catalysts are used, the question remains as to the effect this process will have on the ability of these catalysts to oxidize mercury as well as reduce NO{sub x}. The current project is designed to measure the Hg speciation across an SCR using a regenerated catalyst. The results were compared to previous results to determine what, if any, changes

  3. Phylogenetic relationships in the coral family acroporidae, reassessed by inference from mitochondrial genes.

    PubMed

    Fukami, H; Omori, M; Hatta, M

    2000-07-01

    Phylogenetic relationships within the dominant reef coral family Acroporidae were inferred from the mitochondrial genes cytochrome b and ATPase 6. The rate of nucleotide substitution in the genes gave proper resolution to deduce genetic relationships between the genera in this family. The molecular phylogeny divided this family into three major lineages: the genera Astreopora, Montipora and Acropora. The genus Anacropora was included in the same clade as the genus Montipora, suggesting its recent speciation from Montipora. The subgenus Isopora was significantly distant from the subgenus Acropora. Taken together with morphological and reproductive differences, we propose that these two subgenera be classified as independent genera. The divergence times deduced from the genetic distances were consistent with the fossil record for the major genera. The results also suggest that the extant reef corals speciated and expanded very recently, probably after the Miocene, from single lineage which survived repeated extinction by climate changes during the Cenozoic era. PMID:18517306

  4. 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

  5. Testing gradual and speciational models of evolution in extant taxa: the example of ratites.

    PubMed

    Laurin, M; Gussekloo, S W S; Marjanović, D; Legendre, L; Cubo, J

    2012-02-01

    Ever since Eldredge and Gould proposed their model of punctuated equilibria, evolutionary biologists have debated how often this model is the best description of nature and how important it is compared to the more gradual models of evolution expected from natural selection and the neo-Darwinian paradigm. Recently, Cubo proposed a method to test whether morphological data in extant ratites are more compatible with a gradual or with a speciational model (close to the punctuated equilibrium model). As shown by our simulations, a new method to test the mode of evolution of characters (involving regression of standardized contrasts on their expected standard deviation) is easier to implement and more powerful than the previously proposed method, but the Mesquite module comet (aimed at investigating evolutionary models using comparative data) performs better still. Uncertainties in branch length estimates are probably the largest source of potential error. Cubo hypothesized that heterochronic mechanisms may underlie morphological changes in bone shape during the evolution of ratites. He predicted that the outcome of these changes may be consistent with a speciational model of character evolution because heterochronic changes can be instantaneous in terms of geological time. Analysis of a more extensive data set confirms his prediction despite branch length uncertainties: evolution in ratites has been mostly speciational for shape-related characters. However, it has been mostly gradual for size-related ones. PMID:22107024

  6. Viviparity-driven conflict: more to speciation than meets the fly.

    PubMed

    Zeh, Jeanne A; Zeh, David W

    2008-01-01

    Equipped with Mendel's laws and only rudimentary knowledge of genes and genomes, the architects of the Modern Synthesis provided key insights into the dynamics of gene frequency change within populations. Extension of population genetic models to speciation identified Dobzhansky-Muller incompatibilities (negative epistatic interactions between genes from isolated populations) as the primary cause of hybrid inviability and sterility, a view consistent with empirical findings on the genetics of reproductive isolation in Drosophila. Although speciation models have become increasingly mathematically sophisticated, many remain based on an overly static concept of the genome, grounded in Mendelian genetics and devoid of potentially important biological details. A unifying theory of speciation therefore remains elusive, with debate over the relative importance of natural selection, sexual selection, sexual conflict, genetic drift, and selfish genetic elements in the evolution of reproductive isolation. Drawing on recent findings in molecular genetics and comparative genomics, we revisit, update, and extend the theory that reproductive mode plays a crucial role in shaping the speciation process. By providing a direct conduit for manipulation of the mother's physiology by genes expressed in the embryo, viviparity creates a postfertilization arena for genomic conflicts absent in species that lay eggs. In polyandrous species, viviparity-driven conflict (VDC) is likely to generate perpetual antagonistic coevolution between genes expressed during embryonic development and those involved in maternal reproductive physiology, thereby accelerating the rate at which postzygotic isolation evolves between populations. Moreover, in mammals and flowering plants, VDC has favored the evolution of genomic imprinting and a central role for epigenetic mechanisms in the regulation of antagonistic patterns of gene expression by maternally and paternally inherited genomes. VDC can account for

  7. Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax.

    PubMed

    Li, Kexin; Hong, Wei; Jiao, Hengwu; Wang, Guo-Dong; Rodriguez, Karl A; Buffenstein, Rochelle; Zhao, Yang; Nevo, Eviatar; Zhao, Huabin

    2015-09-22

    important mode of speciation as first envisaged by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection]. PMID:26340990

  8. Capillary microextraction (CME) and its application to trace elements analysis and their speciation.

    PubMed

    Hu, Bin; Zheng, Fei; He, Man; Zhang, Nan

    2009-09-14

    As a solvent-free miniaturized sample preparation technique, capillary microextraction (CME) has been hyphenated with different analytical instruments for trace elements analysis of environmental, biological, food and pharmaceutical samples. This review discusses the fundamentals and recent development of CME, including the theoretical basis, extraction modes (packed, open-tubular and monolithic CME) and capillary materials for CME. The emphasis is placed on the application of CME to trace/ultra-trace elements analysis and their speciation. Existing coating/monolithic materials used for CME are summarized together with a detailed overview of their preparation methods. PMID:19720168

  9. Case studies and mathematical models of ecological speciation. 4. Hybrid speciation in butterflies in a jungle.

    PubMed

    Duenez-Guzman, Edgar A; Mavárez, Jesus; Vose, Michael D; Gavrilets, Sergey

    2009-10-01

    We build a spatial individual-based multilocus model of homoploid hybrid speciation tailored for a tentative case of hybrid origin of Heliconius heurippa from H. melpomene and H. cydno in South America. Our model attempts to account for empirical patterns and data on genetic incompatibility, mating preferences and selection by predation (both based on coloration patterns), habitat preference, and local adaptation for all three Heliconius species. Using this model, we study the likelihood of recombinational speciation and identify the effects of various ecological and genetic parameters on the dynamics, patterns, and consequences of hybrid ecological speciation. Overall, our model supports the possibility of hybrid origin of H. heurippa under certain conditions. The most plausible scenario would include hybridization between H. melpomene and H. cydno in an area geographically isolated from the rest of both parental species with subsequent long-lasting geographic isolation of the new hybrid species, followed by changes in the species ranges, the secondary contact, and disappearance of H. melpomene-type ecomorph in the hybrid species. However, much more work (both empirical and theoretical) is necessary to be able to make more definite conclusions on the importance of homoploid hybrid speciation in animals. PMID:19545268

  10. Diversification of the silverspot butterflies (Nymphalidae) in the Neotropics inferred from multi-locus DNA sequences.

    PubMed

    Massardo, Darli; Fornel, Rodrigo; Kronforst, Marcus; Gonçalves, Gislene Lopes; Moreira, Gilson Rudinei Pires

    2015-01-01

    The tribe Heliconiini (Lepidoptera: Nymphalidae) is a diverse group of butterflies distributed throughout the Neotropics, which has been studied extensively, in particular the genus Heliconius. However, most of the other lineages, such as Dione, which are less diverse and considered basal within the group, have received little attention. Basic information, such as species limits and geographical distributions remain uncertain for this genus. Here we used multilocus DNA sequence data and the geographical distribution analysis across the entire range of Dione in the Neotropical region in order to make inferences on the evolutionary history of this poorly explored lineage. Bayesian time-tree reconstruction allows inferring two major diversification events in this tribe around 25mya. Lineages thought to be ancient, such as Dione and Agraulis, are as recent as Heliconius. Dione formed a monophyletic clade, sister to the genus Agraulis. Dione juno, D. glycera and D. moneta were reciprocally monophyletic and formed genetic clusters, with the first two more close related than each other in relation to the third. Divergence time estimates support the hypothesis that speciation in Dione coincided with both the rise of Passifloraceae (the host plants) and the uplift of the Andes. Since the sister species D. glycera and D. moneta are specialized feeders on passion-vine lineages that are endemic to areas located either within or adjacent to the Andes, we inferred that they co-speciated with their host plants during this vicariant event. PMID:25300455

  11. Ensemble Inference and Inferability of Gene Regulatory Networks

    PubMed Central

    Ud-Dean, S. M. Minhaz; Gunawan, Rudiyanto

    2014-01-01

    The inference of gene regulatory network (GRN) from gene expression data is an unsolved problem of great importance. This inference has been stated, though not proven, to be underdetermined implying that there could be many equivalent (indistinguishable) solutions. Motivated by this fundamental limitation, we have developed new framework and algorithm, called TRaCE, for the ensemble inference of GRNs. The ensemble corresponds to the inherent uncertainty associated with discriminating direct and indirect gene regulations from steady-state data of gene knock-out (KO) experiments. We applied TRaCE to analyze the inferability of random GRNs and the GRNs of E. coli and yeast from single- and double-gene KO experiments. The results showed that, with the exception of networks with very few edges, GRNs are typically not inferable even when the data are ideal (unbiased and noise-free). Finally, we compared the performance of TRaCE with top performing methods of DREAM4 in silico network inference challenge. PMID:25093509

  12. Mercury speciation analysis in terrestrial animal tissues.

    PubMed

    Berzas Nevado, J J; Rodríguez Martín-Doimeadios, R C; Guzmán Bernardo, F J; Rodríguez Fariñas, N; Patiño Ropero, M J

    2012-09-15

    No previous analytical procedures are available and validated for mercury speciation analysis in terrestrial animal tissues. This analysis is a difficult task both because the expected concentrations are low, since important accumulation process are not likely to occur, and also because there are not commercially available certified reference material. Thus, an analytical methodology has been developed and validated for mercury speciation for the specific case of terrestrial animal tissues. The proposed method is based on the quantitative extraction of the species by closed-vessel microwave assisted heating with an alkaline reagent, followed by ethylation. The ethylated derivatives were then submitted to head-space solid phase microextraction with a 100 μm polidimethylsiloxane-coated fiber, and desorbed onto a gas chromatograph coupled to atomic fluorescence detection via pyrolysis unit (HS-SPME-GC-pyro-AFS). Procedural detection limits were 31.8 ng g(-1) and 52.5 ng g(-1) for CH(3)Hg(+) and Hg(2+), respectively, for liver and 35.3 ng g(-1) and 58.1 ng g(-1) for CH(3)Hg(+) and Hg(2+), respectively, for kidney. These limits of detection are 5.5 and 6 times better than the obtained without solid phase microextraction for CH(3)Hg(+) and Hg(2+), respectively. The methodology was found linear up to 120 μg L(-1) and reproducible from one day to the following. It was validated with certified reference materials NCS ZC 71001 (beef liver) and BCR No 186 (pig kidney) for total mercury, calculated as the sum of species, and with spiked red deer liver and kidney for speciation. Finally, it was applied to the analysis of samples of red deer liver, red deer kidney and wild boar kidney coming from the Almadén's mercury mining area (Ciudad Real, Spain), the longest and largest producer of mercury in the world until its closure in 2002. PMID:22967634

  13. Complementary arsenic speciation methods: A review

    NASA Astrophysics Data System (ADS)

    Nearing, Michelle M.; Koch, Iris; Reimer, Kenneth J.

    2014-09-01

    The toxicity of arsenic greatly depends on its chemical form and oxidation state (speciation) and therefore accurate determination of arsenic speciation is a crucial step in understanding its chemistry and potential risk. High performance liquid chromatography with inductively coupled mass spectrometry (HPLC-ICP-MS) is the most common analysis used for arsenic speciation but it has two major limitations: it relies on an extraction step (usually from a solid sample) that can be incomplete or alter the arsenic compounds; and it provides no structural information, relying on matching sample peaks to standard peaks. The use of additional analytical methods in a complementary manner introduces the ability to address these disadvantages. The use of X-ray absorption spectroscopy (XAS) with HPLC-ICP-MS can be used to identify compounds not extracted for HPLC-ICP-MS and provide minimal processing steps for solid state analysis that may help preserve labile compounds such as those containing arsenicsbnd sulfur bonds, which can degrade under chromatographic conditions. On the other hand, HPLC-ICP-MS is essential in confirming organoarsenic compounds with similar white line energies seen by using XAS, and identifying trace arsenic compounds that are too low to be detected by XAS. The complementary use of electrospray mass spectrometry (ESI-MS) with HPLC-ICP-MS provides confirmation of arsenic compounds identified during the HPLC-ICP-MS analysis, identification of unknown compounds observed during the HPLC-ICP-MS analysis and further resolves HPLC-ICP-MS by identifying co-eluting compounds. In the complementary use of HPLC-ICP-MS and ESI-MS, HPLC-ICP-MS helps to focus the ESI-MS selection of ions. Numerous studies have shown that the information obtained from HPLC-ICP-MS analysis can be greatly enhanced by complementary approaches.

  14. Speciation and release kinetics of zinc in contaminated paddy soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Zinc is an important nutrient for plants, but it can be toxic at high concentrations. The solubility and speciation of Zn is controlled by many factors, especially soil pH and Eh, which can vary in lowland rice culture. This study determined Zn speciation and release kinetics in Cd-Zn co-contamina...

  15. 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...

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

    PubMed

    Gottscho, Andrew D; Marks, Sharyn B; Jennings, W Bryan

    2014-06-01

    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

  17. 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

  18. Passenger car hydrocarbon emissions speciation. Final report

    SciTech Connect

    Black, F.; High, L.

    1980-05-01

    Emission factors for over 60 individual hydrocarbon compounds were determined for four passenger cars. The cars included a 1963 Chevrolet, a 1977 Mustang, and 1978 Monarch, and 1979 LTD II. The speciation data is reported for both tailpipe and evaporative emissions. The tailpipe emissions were for the urban driving conditions of the Federal Test Procedure used in motor vehicle certification. The evaporative emissions were for both diurnal and hot soak conditions, also prescribed in the Federal Test Procedure for certification. The vehicle tests involved four gasoline fuels of varying composition.

  19. Plutonium Speciation, Solubilization and Migration in Soils

    SciTech Connect

    Neu, M.; Runde, W.

    1999-06-01

    This report summarizes research completed in the first half of a three-year project. As outlined in the authors' proposal they are focusing on (1) characterizing the plutonium at an actinide contaminated site, RFETS, including determining the origin, dispersion, and speciation of the plutonium, (2) studying environmentally important plutonium complexes, primarily hydroxides and carbonates, and (3) examining the interactions of plutonium species with manganese minerals. In the first year the authors focused on site based studies. This year they continue to characterize samples from the RFETS, study the formation and structural and spectroscopic features of environmentally relevant Pu species, and begin modeling the environmental behavior of plutonium.

  20. Arsenic speciation in natural sulfidic geothermal waters

    NASA Astrophysics Data System (ADS)

    Keller, Nicole S.; Stefánsson, Andri; Sigfússon, Bergur

    2014-10-01

    The speciation of arsenic in natural sulfidic geothermal waters was studied using chemical analyses and thermodynamic aqueous speciation calculations. Samples were collected in three geothermal systems in Iceland, having contrasting H2S concentrations in the reservoir (high vs. low). The sampled waters contained 7-116 ppb As and <0.01-77.6 ppm H2S with pH of 8.56-9.60. The analytical setup used for the determination of arsenic species (Ion Chromatography-Hydride Generation Atomic Fluorescence Spectrometry, IC-HG-AFS) was field-deployed and the samples analyzed within ∼5 min of sampling in order to prevent changes upon storage, which were shown to be considerable regardless of the sample storage method used. Nine aqueous arsenic species were detected, among others arsenite (HnAsO3n-3), thioarsenite (HnAsS3n-3), arsenate (HnAsO4n-3), monothioarsenate (HnAsSO3n-3), dithioarsenate (HnAsS2O2n-3), trithioarsenate (HnAsS3O) and tetrathioarsenate (HnAsS4n-3). The results of the measured aqueous arsenic speciation in the natural geothermal waters and comparison with thermodynamic calculations reveal that the predominant factors determining the species distribution are sulfide concentration and pH. In alkaline waters with low sulfide concentrations the predominant species are AsIII oxyanions. This can be seen in samples from a liquid-only well, tapping water that is H2S-poor and free of oxygen. At intermediate sulfide concentration AsIII and AsV thio species become important and predominate at high sulfide concentration, as seen in two-phase well waters, which have high H2S concentrations in the reservoir. Upon oxidation, for instance due to mixing of the reservoir fluid with oxygenated water upon ascent to the surface, AsV oxyanions form, as well as AsV thio complexes if the sulfide concentration is intermediate to high. This oxidation process can be seen in samples from hot springs in the Geysir geothermal area. While the thermodynamic modeling allows for a first

  1. Chemoselective Boronic Ester Synthesis by Controlled Speciation**

    PubMed Central

    Fyfe, James W B; Seath, Ciaran P; Watson, Allan J B

    2014-01-01

    Control of boronic acid solution speciation is presented as a new strategy for the chemoselective synthesis of boronic esters. Manipulation of the solution equilibria within a cross-coupling milieu enables the formal homologation of aryl and alkenyl boronic acid pinacol esters. The generation of a new, reactive boronic ester in the presence of an active palladium catalyst also facilitates streamlined iterative catalytic C=C bond formation and provides a method for the controlled oligomerization of sp2-hybridized boronic esters. PMID:25267096

  2. Homoploid hybrid speciation and genome evolution via chromosome sorting

    PubMed Central

    Lukhtanov, Vladimir A.; Shapoval, Nazar A.; Anokhin, Boris A.; Saifitdinova, Alsu F.; Kuznetsova, Valentina G.

    2015-01-01

    Genomes of numerous diploid plant and animal species possess traces of interspecific crosses, and many researches consider them as support for homoploid hybrid speciation (HHS), a process by which a new reproductively isolated species arises through hybridization and combination of parts of the parental genomes, but without an increase in ploidy. However, convincing evidence for a creative role of hybridization in the origin of reproductive isolation between hybrid and parental forms is extremely limited. Here, through studying Agrodiaetus butterflies, we provide proof of a previously unknown mode of HHS based on the formation of post-zygotic reproductive isolation via hybridization of chromosomally divergent parental species and subsequent fixation of a novel combination of chromosome fusions/fissions in hybrid descendants. We show that meiotic segregation, operating in the hybrid lineage, resulted in the formation of a new diploid genome, drastically rearranged in terms of chromosome number. We also demonstrate that during the heterozygous stage of the hybrid species formation, recombination was limited between rearranged chromosomes of different parental origin, representing evidence that the reproductive isolation was a direct consequence of hybridization. PMID:25925097

  3. Global Population Genetic Structure of Caenorhabditis remanei Reveals Incipient Speciation

    PubMed Central

    Dey, Alivia; Jeon, Yong; Wang, Guo-Xiu; Cutter, Asher D.

    2012-01-01

    Mating system transitions dramatically alter the evolutionary trajectories of genomes that can be revealed by contrasts of species with disparate modes of reproduction. For such transitions in Caenorhabditis nematodes, some major causes of genome variation in selfing species have been discerned. And yet, we have only limited understanding of species-wide population genetic processes for their outcrossing relatives, which represent the reproductive state of the progenitors of selfing species. Multilocus–multipopulation sequence polymorphism data provide a powerful means to uncover the historical demography and evolutionary processes that shape genomes. Here we survey nucleotide polymorphism across the X chromosome for three populations of the outcrossing nematode Caenorhabditis remanei and demonstrate its divergence from a fourth population describing a closely related new species from China, C. sp. 23. We find high genetic variation globally and within each local population sample. Despite geographic barriers and moderate genetic differentiation between Europe and North America, considerable gene flow connects C. remanei populations. We discovered C. sp. 23 while investigating C. remanei, observing strong genetic differentiation characteristic of reproductive isolation that was confirmed by substantial F2 hybrid breakdown in interspecific crosses. That C. sp. 23 represents a distinct biological species provides a cautionary example of how standard practice can fail for mating tests of species identity in this group. This species pair permits full application of divergence population genetic methods to obligately outcrossing species of Caenorhabditis and also presents a new focus for interrogation of the genetics and evolution of speciation with the Caenorhabditis model system. PMID:22649079

  4. Homoploid hybrid speciation and genome evolution via chromosome sorting.

    PubMed

    Lukhtanov, Vladimir A; Shapoval, Nazar A; Anokhin, Boris A; Saifitdinova, Alsu F; Kuznetsova, Valentina G

    2015-05-22

    Genomes of numerous diploid plant and animal species possess traces of interspecific crosses, and many researches consider them as support for homoploid hybrid speciation (HHS), a process by which a new reproductively isolated species arises through hybridization and combination of parts of the parental genomes, but without an increase in ploidy. However, convincing evidence for a creative role of hybridization in the origin of reproductive isolation between hybrid and parental forms is extremely limited. Here, through studying Agrodiaetus butterflies, we provide proof of a previously unknown mode of HHS based on the formation of post-zygotic reproductive isolation via hybridization of chromosomally divergent parental species and subsequent fixation of a novel combination of chromosome fusions/fissions in hybrid descendants. We show that meiotic segregation, operating in the hybrid lineage, resulted in the formation of a new diploid genome, drastically rearranged in terms of chromosome number. We also demonstrate that during the heterozygous stage of the hybrid species formation, recombination was limited between rearranged chromosomes of different parental origin, representing evidence that the reproductive isolation was a direct consequence of hybridization. PMID:25925097

  5. Linking emergence of fungal plant diseases and ecological speciation

    PubMed Central

    Giraud, Tatiana; Gladieux, Pierre; Gavrilets, Sergey

    2010-01-01

    Emerging diseases represent a growing worldwide problem accompanying global environmental changes, and there is tremendous interest in identifying the factors controlling the appearance and spread of these diseases. Here, we discuss emerging fungal plant diseases, and argue that they often result from host shift speciation, a particular case of ecological speciation. We consider the factors controlling local adaptation and ecological speciation and show that certain life-history traits of many fungal plant pathogens are conducive for rapid ecological speciation, thus favoring the emergence of novel pathogen species adapted to new hosts. We argue that placing the problem of emerging fungal diseases of plants within the context of ecological speciation can significantly improve our understanding of the biological mechanisms governing emergence of such diseases. PMID:20434790

  6. 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

  7. Age-dependent speciation can explain the shape of empirical phylogenies.

    PubMed

    Hagen, Oskar; Hartmann, Klaas; Steel, Mike; Stadler, Tanja

    2015-05-01

    Tens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees, inferences can be made about the underlying macroevolutionary processes, yet remarkably these processes are still poorly understood. Simple and widely used evolutionary null models are problematic: Empirical trees show very different imbalance between the sizes of the daughter clades of ancestral taxa compared to what models predict. Obtaining a simple evolutionary model that is both biologically plausible and produces the imbalance seen in empirical trees is a challenging problem, to which none of the existing models provide a satisfying answer. Here we propose a simple, biologically plausible macroevolutionary model in which the rate of speciation decreases with species age, whereas extinction rates can vary quite generally. We show that this model provides a remarkable fit to the thousands of trees stored in the online database TreeBase. The biological motivation for the identified age-dependent speciation process may be that recently evolved taxa often colonize new regions or niches and may initially experience little competition. These new taxa are thus more likely to give rise to further new taxa than a taxon that has remained largely unchanged and is, therefore, well adapted to its niche. We show that age-dependent speciation may also be the result of different within-species populations following the same laws of lineage splitting to produce new species. As the fit of our model to the tree database shows, this simple biological motivation provides an explanation for a long standing problem in macroevolution. PMID:25575504

  8. Localization and speciation of mercury in brown rice with implications for pan-Asian public health.

    PubMed

    Meng, Bo; Feng, Xinbin; Qiu, Guangle; Anderson, Christopher W N; Wang, Jianxu; Zhao, Lei

    2014-07-15

    Cultivation of paddy rice for human consumption is a dominant agricultural activity throughout Asia. High levels of mercury (Hg) in rice grain pose a potential threat to human health, although the extent of risk is dependent on the chemical speciation of Hg inside the grain. We have investigated the speciation and localization of Hg in three fractions of rice grain (hull, bran, and white rice) collected from a Hg-contaminated region in China. On a mass basis, the majority of inorganic mercury (IHg) in a rice grain is found in hull and bran. However, the majority of the more toxic species methyl mercury (MeHg) is found in edible white rice. Our data show that during grain processing, most of the IHg (∼78%) is eliminated, but the majority of the MeHg remains in the food product (∼80%). Synchrotron radiation microscopic X-ray fluorescence (SR-μXRF) mapping shows strong localization of Hg at the surface of brown rice grains, corresponding to the pericarp and aleurone layer. We infer that this Hg is predominantly IHg absorbed from the atmosphere. Based on X-ray absorption near-edge spectroscopy (XANES) data we propose that IHg in bran is primarily bound to cysteine, and is associated with phytochelatins. Consequently, IHg is largely immobile and restricted to the outer layers of rice grain. MeHg in bran is primarily bound to cysteine and is associated with proteins. However, this MeHg-cysteine association behaves like a mobile nutrient and is actively transported to the endosperm during seed ripening. Concentration of MeHg-cysteine in white rice has implications for public health. There is growing evidence for Hg contamination of rice throughout Asia due to point and diffuse sources of Hg pollution. The magnitude of the associated risk must be quantified through better understanding of the localization and speciation of mercury in rice. Our work makes an effort to contribute to this understanding. PMID:24925231

  9. Degradation monitoring using probabilistic inference

    NASA Astrophysics Data System (ADS)

    Alpay, Bulent

    In order to increase safety and improve economy and performance in a nuclear power plant (NPP), the source and extent of component degradations should be identified before failures and breakdowns occur. It is also crucial for the next generation of NPPs, which are designed to have a long core life and high fuel burnup to have a degradation monitoring system in order to keep the reactor in a safe state, to meet the designed reactor core lifetime and to optimize the scheduled maintenance. Model-based methods are based on determining the inconsistencies between the actual and expected behavior of the plant, and use these inconsistencies for detection and diagnostics of degradations. By defining degradation as a random abrupt change from the nominal to a constant degraded state of a component, we employed nonlinear filtering techniques based on state/parameter estimation. We utilized a Bayesian recursive estimation formulation in the sequential probabilistic inference framework and constructed a hidden Markov model to represent a general physical system. By addressing the problem of a filter's inability to estimate an abrupt change, which is called the oblivious filter problem in nonlinear extensions of Kalman filtering, and the sample impoverishment problem in particle filtering, we developed techniques to modify filtering algorithms by utilizing additional data sources to improve the filter's response to this problem. We utilized a reliability degradation database that can be constructed from plant specific operational experience and test and maintenance reports to generate proposal densities for probable degradation modes. These are used in a multiple hypothesis testing algorithm. We then test samples drawn from these proposal densities with the particle filtering estimates based on the Bayesian recursive estimation formulation with the Metropolis Hastings algorithm, which is a well-known Markov chain Monte Carlo method (MCMC). This multiple hypothesis testing

  10. Bayesian Inference: with ecological applications

    USGS Publications Warehouse

    Link, William A.; Barker, Richard J.

    2010-01-01

    This text provides a mathematically rigorous yet accessible and engaging introduction to Bayesian inference with relevant examples that will be of interest to biologists working in the fields of ecology, wildlife management and environmental studies as well as students in advanced undergraduate statistics.. This text opens the door to Bayesian inference, taking advantage of modern computational efficiencies and easily accessible software to evaluate complex hierarchical models.

  11. Active inference, communication and hermeneutics.

    PubMed

    Friston, Karl J; Frith, Christopher D

    2015-07-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others--during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions--both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then--in principle--they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa. PMID:25957007

  12. Causal inference and developmental psychology.

    PubMed

    Foster, E Michael

    2010-11-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether the risk factor actually causes outcomes. Random assignment is not possible in many instances, and for that reason, psychologists must rely on observational studies. Such studies identify associations, and causal interpretation of such associations requires additional assumptions. Research in developmental psychology generally has relied on various forms of linear regression, but this methodology has limitations for causal inference. Fortunately, methodological developments in various fields are providing new tools for causal inference-tools that rely on more plausible assumptions. This article describes the limitations of regression for causal inference and describes how new tools might offer better causal inference. This discussion highlights the importance of properly identifying covariates to include (and exclude) from the analysis. This discussion considers the directed acyclic graph for use in accomplishing this task. With the proper covariates having been chosen, many of the available methods rely on the assumption of "ignorability." The article discusses the meaning of ignorability and considers alternatives to this assumption, such as instrumental variables estimation. Finally, the article considers the use of the tools discussed in the context of a specific research question, the effect of family structure on child development. PMID:20677855

  13. Active inference, communication and hermeneutics☆

    PubMed Central

    Friston, Karl J.; Frith, Christopher D.

    2015-01-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others – during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions – both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then – in principle – they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa. PMID:25957007

  14. Correcting for Sequencing Error in Maximum Likelihood Phylogeny Inference

    PubMed Central

    Kuhner, Mary K.; McGill, James

    2014-01-01

    Accurate phylogenies are critical to taxonomy as well as studies of speciation processes and other evolutionary patterns. Accurate branch lengths in phylogenies are critical for dating and rate measurements. Such accuracy may be jeopardized by unacknowledged sequencing error. We use simulated data to test a correction for DNA sequencing error in maximum likelihood phylogeny inference. Over a wide range of data polymorphism and true error rate, we found that correcting for sequencing error improves recovery of the branch lengths, even if the assumed error rate is up to twice the true error rate. Low error rates have little effect on recovery of the topology. When error is high, correction improves topological inference; however, when error is extremely high, using an assumed error rate greater than the true error rate leads to poor recovery of both topology and branch lengths. The error correction approach tested here was proposed in 2004 but has not been widely used, perhaps because researchers do not want to commit to an estimate of the error rate. This study shows that correction with an approximate error rate is generally preferable to ignoring the issue. PMID:25378476

  15. Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida)

    PubMed Central

    2014-01-01

    Introduction Many marine planktonic crustaceans such as copepods have been considered as widespread organisms. However, the growing evidence for cryptic and pseudo-cryptic speciation has emphasized the need of re-evaluating the status of copepod species complexes in molecular and morphological studies to get a clearer picture about pelagic marine species as evolutionary units and their distributions. This study analyses the molecular diversity of the ecologically important Paracalanus parvus species complex. Its seven currently recognized species are abundant and also often dominant in marine coastal regions worldwide from temperate to tropical oceans. Results COI and Cytochrome b sequences of 160 specimens of the Paracalanus parvus complex from all oceans were obtained. Furthermore, 42 COI sequences from GenBank were added for the genetic analyses. Thirteen distinct molecular operational taxonomic units (MOTU) and two single sequences were revealed with cladistic analyses (Maximum Likelihood, Bayesian Inference), of which seven were identical with results from species delimitation methods (barcode gaps, ABDG, GMYC, Rosenberg’s P(AB)). In total, 10 to 12 putative species were detected and could be placed in three categories: (1) temperate geographically isolated, (2) warm-temperate to tropical wider spread and (3) circumglobal warm-water species. Conclusions The present study provides evidence of cryptic or pseudocryptic speciation in the Paracalanus parvus complex. One major insight is that the species Paracalanus parvus s.s. is not panmictic, but may be restricted in its distribution to the northeastern Atlantic. PMID:24581044

  16. Magadi tilapia ecological specialization: filling the early gap in the speciation continuum.

    PubMed

    Pinho, Catarina; Faria, Rui

    2016-04-01

    Cichlid fish are well known for their high speciation rates, which are usually accompanied by spectacular and rapid diversification in eco-morphological and secondary sexual traits. This is best illustrated by the famous repeated explosive radiations in the African Great Lakes Tanganyika, Malawi and Victoria, each lake harbouring several hundreds of mostly endemic species. Correspondingly, cichlids diversified very rapidly in many other lakes across their range. Although the larger radiations, unparalleled in vertebrates, are certainly the most intriguing, they are also the most intricate and difficult to address because of their complex nature. This is where smaller, simpler systems may prove to be the most useful. In this issue of Molecular Ecology, Kavembe et al. (2016) report very recent genetic diversification accompanied by ecological specialization in cichlids of the small and ecologically extreme Lake Magadi, in Kenya. Combining geometric morphometrics, stable isotope analysis, population genomics using RADSeq data and coalescent-based modelling techniques, the authors characterize the eco-morphological differences between genetically distinct populations of Magadi tilapia (Alcolapia grahami), which are consistent with the different environmental conditions they experience, and infer their history of divergence. The simplicity of the focal system and the use of a multidisciplinary approach make this work particularly important for our understanding of the early stages of speciation, in both cichlids and other organisms. PMID:27012820

  17. Global patterns of speciation and diversity.

    PubMed

    de Aguiar, M A M; Baranger, M; Baptestini, E M; Kaufman, L; Bar-Yam, Y

    2009-07-16

    In recent years, strikingly consistent patterns of biodiversity have been identified over space, time, organism type and geographical region. A neutral theory (assuming no environmental selection or organismal interactions) has been shown to predict many patterns of ecological biodiversity. This theory is based on a mechanism by which new species arise similarly to point mutations in a population without sexual reproduction. Here we report the simulation of populations with sexual reproduction, mutation and dispersal. We found simulated time dependence of speciation rates, species-area relationships and species abundance distributions consistent with the behaviours found in nature. From our results, we predict steady speciation rates, more species in one-dimensional environments than two-dimensional environments, three scaling regimes of species-area relationships and lognormal distributions of species abundance with an excess of rare species and a tail that may be approximated by Fisher's logarithmic series. These are consistent with dependences reported for, among others, global birds and flowering plants, marine invertebrate fossils, ray-finned fishes, British birds and moths, North American songbirds, mammal fossils from Kansas and Panamanian shrubs. Quantitative comparisons of specific cases are remarkably successful. Our biodiversity results provide additional evidence that species diversity arises without specific physical barriers. This is similar to heavy traffic flows, where traffic jams can form even without accidents or barriers. PMID:19606148

  18. Gene regulation and speciation in house mice.

    PubMed

    Mack, Katya L; Campbell, Polly; Nachman, Michael W

    2016-04-01

    One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproductive isolation. Here, we take advantage of a cross between house mouse subspecies, where hybrid dysfunction is largely unidirectional, to test several key predictions about regulatory divergence and reproductive isolation. Regulatory divergence betweenMus musculus musculusandM. m. domesticuswas characterized by studying allele-specific expression in fertile hybrid males using mRNA-sequencing of whole testes. We found extensive regulatory divergence betweenM. m. musculusandM. m. domesticus, largely attributable tocis-regulatory changes. When bothcisandtranschanges occurred, they were observed in opposition much more often than expected under a neutral model, providing strong evidence of widespread compensatory evolution. We also found evidence for lineage-specific positive selection on a subset of genes related to transcriptional regulation. Comparisons of fertile and sterile hybrid males identified a set of genes that were uniquely misexpressed in sterile individuals. Lastly, we discovered a nonrandom association between these genes and genes showing evidence of compensatory evolution, consistent with the idea that regulatory interactions might contribute to Dobzhansky-Muller incompatibilities and be important in speciation. PMID:26833790

  19. Pleistocene Speciation in the Genus Populus (Salicaceae)

    PubMed Central

    Levsen, Nicholas D.; Tiffin, Peter; Olson, Matthew S.

    2012-01-01

    The macroevolutionary consequences of recent climate change remain controversial, and there is little paleobotanical or morphological evidence that Pleistocene (1.8–0.12 Ma) glacial cycles acted as drivers of speciation, especially among lineages with long generation times, such as trees. We combined genetic and ecogeographic data from 2 closely related North American tree species, Populus balsamifera and P. trichocarpa (Salicacaeae), to determine if their divergence coincided with and was possibly caused by Pleistocene climatic events. We analyzed 32 nuclear loci from individuals of P. balsamifera and P. trichocarpa to produce coalescent-based estimates of the divergence time between the 2 species. We coupled the coalescent analyses with paleodistribution models to assess the influence of climate change on species' range. Furthermore, measures of niche overlap were used to investigate patterns of ecological differentiation between species. We estimated the divergence date of P. balsamifera and P. trichocarpa at approximately 75 Ka, which corresponds closely with the onset of Marine Isotope Stage 4 (∼76 Ka) and a rapid increase in global ice volume. Significance tests of niche overlap, in conjunction with genetic estimates of migration, suggested that speciation occurred in allopatry, possibly resulting from the environmental effects of Pleistocene glacial cycles. Our results indicate that the divergence of keystone tree species, which have shaped community diversity in northern North American ecosystems, was recent and may have been a consequence of Pleistocene-era glaciation and climate change. PMID:22213709

  20. Raman study of aluminum speciation in simulated alkaline nuclear waste.

    PubMed

    Johnston, Cliff T; Agnew, Stephen F; Schoonover, Jon R; Kenney, John W; Page, Bobbi; Osborn, Jill; Corbin, Rob

    2002-06-01

    The chemistry of concentrated sodium aluminate solutions stored in many of the large, underground storage tanks containing high-level waste (HLW) at the Hanford and Savannah River Nuclear Reservations is an area of recent research interest. Not only is the presence of aluminate in solution important for continued safe storage of these wastes, the nature of both solid and solution aluminum oxyhydroxides is important for waste pretreatment. Moreover, for many tanks that have leaked high aluminum waste in the past, little is known about the speciation of Al in the soil. In this study, Raman spectroscopy has been used to investigate the speciation of the aqueous species in the Al2O3-Na2O-H2O system over a wide range of solution compositions and hydration. A ternary phase diagram has been used to correlate the observed changes in the spectra with the composition of the solution and with dimerization of aluminate that occurs at elevated aluminate concentrations (>1.5 M). Dimerization is evidenced by growth of new Al-O stretching bands at 535 and 695 cm(-1) at the expense of the aluminate monomer band at 620 cm(-1). The spectrum of water was strongly influenced by the high concentrations of Na+ and OH- (>17 M). Upon increasing the concentration of NaOH in solution, the delta-(H-O-H) bending band of water (v2 mode) increased in frequency to 1663 cm(-1), indicating that the water contained in the concentrated caustic solution was more strongly hydrogen bonded at the higher base content. In addition, the sharp, well-resolved band at 3610 cm(-1), assigned to the v(O-H) of free OH-, increased in intensity with increasing NaOH. Analysis of the v(O-H) bands in the 3800-2600 cm(-1) region supported the overall increase in hydrogen bonding as evidenced by the increase in relative intensity of a strongly hydrated water band at 3118 cm(-1). Taking into consideration the activity of water, the molar concentrations of the monomeric and dimeric aluminate species were estimated using

  1. Optimal inference with suboptimal models: Addiction and active Bayesian inference

    PubMed Central

    Schwartenbeck, Philipp; FitzGerald, Thomas H.B.; Mathys, Christoph; Dolan, Ray; Wurst, Friedrich; Kronbichler, Martin; Friston, Karl

    2015-01-01

    When casting behaviour as active (Bayesian) inference, optimal inference is defined with respect to an agent’s beliefs – based on its generative model of the world. This contrasts with normative accounts of choice behaviour, in which optimal actions are considered in relation to the true structure of the environment – as opposed to the agent’s beliefs about worldly states (or the task). This distinction shifts an understanding of suboptimal or pathological behaviour away from aberrant inference as such, to understanding the prior beliefs of a subject that cause them to behave less ‘optimally’ than our prior beliefs suggest they should behave. Put simply, suboptimal or pathological behaviour does not speak against understanding behaviour in terms of (Bayes optimal) inference, but rather calls for a more refined understanding of the subject’s generative model upon which their (optimal) Bayesian inference is based. Here, we discuss this fundamental distinction and its implications for understanding optimality, bounded rationality and pathological (choice) behaviour. We illustrate our argument using addictive choice behaviour in a recently described ‘limited offer’ task. Our simulations of pathological choices and addictive behaviour also generate some clear hypotheses, which we hope to pursue in ongoing empirical work. PMID:25561321

  2. Rice genomes recorded ancient pararetrovirus activities: Virus genealogy and multiple origins of endogenization during rice speciation.

    PubMed

    Chen, Sunlu; Liu, Ruifang; Koyanagi, Kanako O; Kishima, Yuji

    2014-12-01

    Viral fossils in rice genomes are a best entity to understand ancient pararetrovirus activities through host plant history because of our advanced knowledge of the genomes and evolutionary history with rice and its related species. Here, we explored organization, geographic origins and genealogy of rice pararetroviruses, which were turned into endogenous rice tungro bacilliform virus-like (eRTBVL) sequences. About 300 eRTBVL sequences from three representative rice genomes were clearly classified into six families. Most of the endogenization events of the eRTBVLs were initiated before differentiation of the rice progenitor (> 160,000 years ago). We successfully followed the genealogy of old relic viruses during rice speciation, and inferred the geographical origins for these viruses. Possible virus genomic sequences were explained mostly by recombinations between different virus families. Interestingly, we discovered that only a few recombination events among the numerous occasions had determined the virus genealogy. PMID:25461539

  3. Genetic consequences of cladogenetic vs. anagenetic speciation in endemic plants of oceanic islands.

    PubMed

    Takayama, Koji; López-Sepúlveda, Patricio; Greimler, Josef; Crawford, Daniel J; Peñailillo, Patricio; Baeza, Marcelo; Ruiz, Eduardo; Kohl, Gudrun; Tremetsberger, Karin; Gatica, Alejandro; Letelier, Luis; Novoa, Patricio; Novak, Johannes; Stuessy, Tod F

    2015-01-01

    Adaptive radiation is a common mode of speciation among plants endemic to oceanic islands. This pattern is one of cladogenesis, or splitting of the founder population, into diverse lineages in divergent habitats. In contrast, endemic species have also evolved primarily by simple transformations from progenitors in source regions. This is anagenesis, whereby the founding population changes genetically and morphologically over time primarily through mutation and recombination. Gene flow among populations is maintained in a homogeneous environment with no splitting events. Genetic consequences of these modes of speciation have been examined in the Juan Fernández Archipelago, which contains two principal islands of differing geological ages. This article summarizes population genetic results (nearly 4000 analyses) from examination of 15 endemic species, involving 1716 and 1870 individuals in 162 and 163 populations (with amplified fragment length polymorphisms and simple sequence repeats, respectively) in the following genera: Drimys (Winteraceae), Myrceugenia (Myrtaceae), Rhaphithamnus (Verbenaceae), Robinsonia (Asteraceae, Senecioneae) and Erigeron (Asteraceae, Astereae). The results indicate that species originating anagenetically show high levels of genetic variation within the island population and no geographic genetic partitioning. This contrasts with cladogenetic species that show less genetic diversity within and among populations. Species that have been derived anagenetically on the younger island (1-2 Ma) contain less genetic variation than those that have anagenetically speciated on the older island (4 Ma). Genetic distinctness among cladogenetically derived species on the older island is greater than among similarly derived species on the younger island. An important point is that the total genetic variation within each genus analysed is comparable, regardless of whether adaptive divergence occurs. PMID:26311732

  4. Genetic consequences of cladogenetic vs. anagenetic speciation in endemic plants of oceanic islands

    PubMed Central

    Takayama, Koji; López-Sepúlveda, Patricio; Greimler, Josef; Crawford, Daniel J.; Peñailillo, Patricio; Baeza, Marcelo; Ruiz, Eduardo; Kohl, Gudrun; Tremetsberger, Karin; Gatica, Alejandro; Letelier, Luis; Novoa, Patricio; Novak, Johannes; Stuessy, Tod F.

    2015-01-01

    Adaptive radiation is a common mode of speciation among plants endemic to oceanic islands. This pattern is one of cladogenesis, or splitting of the founder population, into diverse lineages in divergent habitats. In contrast, endemic species have also evolved primarily by simple transformations from progenitors in source regions. This is anagenesis, whereby the founding population changes genetically and morphologically over time primarily through mutation and recombination. Gene flow among populations is maintained in a homogeneous environment with no splitting events. Genetic consequences of these modes of speciation have been examined in the Juan Fernández Archipelago, which contains two principal islands of differing geological ages. This article summarizes population genetic results (nearly 4000 analyses) from examination of 15 endemic species, involving 1716 and 1870 individuals in 162 and 163 populations (with amplified fragment length polymorphisms and simple sequence repeats, respectively) in the following genera: Drimys (Winteraceae), Myrceugenia (Myrtaceae), Rhaphithamnus (Verbenaceae), Robinsonia (Asteraceae, Senecioneae) and Erigeron (Asteraceae, Astereae). The results indicate that species originating anagenetically show high levels of genetic variation within the island population and no geographic genetic partitioning. This contrasts with cladogenetic species that show less genetic diversity within and among populations. Species that have been derived anagenetically on the younger island (1–2 Ma) contain less genetic variation than those that have anagenetically speciated on the older island (4 Ma). Genetic distinctness among cladogenetically derived species on the older island is greater than among similarly derived species on the younger island. An important point is that the total genetic variation within each genus analysed is comparable, regardless of whether adaptive divergence occurs. PMID:26311732

  5. 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...

  6. 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...

  7. 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...

  8. Statistical inference and string theory

    NASA Astrophysics Data System (ADS)

    Heckman, Jonathan J.

    2015-09-01

    In this paper, we expose some surprising connections between string theory and statistical inference. We consider a large collective of agents sweeping out a family of nearby statistical models for an M-dimensional manifold of statistical fitting parameters. When the agents making nearby inferences align along a d-dimensional grid, we find that the pooled probability that the collective reaches a correct inference is the partition function of a nonlinear sigma model in d dimensions. Stability under perturbations to the original inference scheme requires the agents of the collective to distribute along two dimensions. Conformal invariance of the sigma model corresponds to the condition of a stable inference scheme, directly leading to the Einstein field equations for classical gravity. By summing over all possible arrangements of the agents in the collective, we reach a string theory. We also use this perspective to quantify how much an observer can hope to learn about the internal geometry of a superstring compactification. Finally, we present some brief speculative remarks on applications to the AdS/CFT correspondence and Lorentzian signature space-times.

  9. PM2.5 speciation -- objectives, requirements, and approach

    SciTech Connect

    Homolya, J.B.; Rice, J.; Scheffe, R.D.

    1998-12-31

    Chemical speciation of selected PM2.5 monitor samples is included in the discussion of major monitoring requirements and principles described in the Part 58 Rule. The regulation requires the implementation of a modest chemical speciation network of 50 PM2.5 sites that provides a first order characterization of the metals, ions, and carbon constituents of PM2.5. These data are to be used to support several areas of interest, including: (1) Helping to implement the PM2.5 standard through the use of speciated data as inputs to air quality modeling analyses and as indicators to track progress of controls; (2) Aiding the interpretation of health studies by linking effects to PM2.5 constituents; (3) Understanding the effects of atmospheric constituents on visibility impairment; and (4) Using speciated particulate data to aid in monitoring network design and siting adjustment. For these reasons, EPA has developed plans for the initial 50-site speciation monitoring network that include collocating at least 25 monitors within the Photochemical Air Monitoring System (PAMS) which collect data for a range of volatile hazardous air pollutants and ozone. Therefore these initial speciation sites will provide EPA and the research community a baseline of gaseous and particulate atmospheric characterization information. Current plans include the outfitting of up to 300 PM2.5 speciation monitoring sites. The speciation monitors are currently being fabricated under EPA National Federal Reference Method monitor procurement contracts and are projected to begin to be deployed in 10/98. This paper will present a detailed discussion of the design and implementation of the speciation monitoring network and explain EPA`s approach to implementation of the monitoring activities which includes siting, target analytes of interest, sample handling, analytical SOPs, and data reduction, validation and reporting.

  10. Lead Speciation in remote Mountain Lakes

    NASA Astrophysics Data System (ADS)

    Plöger, A.; van den Berg, C. M. G.

    2003-04-01

    In natural waters trace metals can become complexed by organic matter. This complexation can change the geochemistry of the metals by preventing them being scavenged, thereby increasing their residence time in the water column. The chemical speciation of trace metals also affects the bioavalability and their toxicological impact on organisms. It is therefore important to determine the chemical speciation of trace metals as well as their concentrations. Mountain lakes have been less studied in the past than other lakes- partly because of their remoteness and partly because they were perceived to be unpolluted and undisturbed. But work so far on mountain lakes has shown that most sites are affected and threatened, for example by transboundary air pollutants like trace metals. One of the important features that distinguishes these lakes from lowland lakes at similar latitudes is the fact that they may be isolated from the atmosphere for six months or more during the winter by a thick ice cover. Also, as these lakes are remote from direct anthropogenic influences, they reflect the regional distribution of pollutants transferred via the atmosphere. For this work, under the framework of the EMERGE (European Mountain lake Ecosystems: Regionalisation, diaGnostic and socio-economic Evaluation) programme, two remote mountain lakes have been studied in detail, with water sampling taking place at different times of the year to investigate possible seasonal differences in lead concentrations and speciation. Results so far have shown that lead-complexing ligand concentrations are in excess to dissolved lead concentrations, indicating that dissolved lead probably occurs fully complexed in these lakes. Therefore the toxic fraction is likely to be less than the dissolved lead concentration. Also, lead concentrations at the time of the spring thaw are higher than autumn concentrations just before ice cover, indicating that a significant proportion of fallout onto the lake catchment

  11. Genome-wide congealing and rapid transitions across the speciation continuum during speciation with gene flow.

    PubMed

    Feder, Jeffrey L; Nosil, Patrik; Wacholder, Aaron C; Egan, Scott P; Berlocher, Stewart H; Flaxman, Samuel M

    2014-01-01

    Our current understanding of speciation is often based on considering a relatively small number of genes, sometimes in isolation of one another. Here, we describe a possible emergent genome process involving the aggregate effect of many genes contributing to the evolution of reproductive isolation across the speciation continuum. When a threshold number of divergently selected mutations of modest to low fitness effects accumulate between populations diverging with gene flow, nonlinear transitions can occur in which levels of adaptive differentiation, linkage disequilibrium, and reproductive isolation dramatically increase. In effect, the genomes of the populations start to "congeal" into distinct entities representing different species. At this stage, reproductive isolation changes from being a characteristic of specific, divergently selected genes to a property of the genome. We examine conditions conducive to such genome-wide congealing (GWC), describe how to empirically test for GWC, and highlight a putative empirical example involving Rhagoletis fruit flies. We conclude with cautious optimism that the models and concepts discussed here, once extended to large numbers of neutral markers, may provide a framework for integrating information from genome scans, selection experiments, quantitative trait loci mapping, association studies, and natural history to develop a deeper understanding of the genomics of speciation. PMID:25149256

  12. Genome-wide characterization of adaptation and speciation in tiger swallowtail butterflies using de novo transcriptome assemblies.

    PubMed

    Zhang, Wei; Kunte, Krushnamegh; Kronforst, Marcus R

    2013-01-01

    Hybrid speciation appears to be rare in animals, yet characterization of possible examples offers to shed light on the genomic consequences of this unique phenomenon, as well as more general processes such as the role of adaptation in speciation. Here, we first generate transcriptome assemblies for a putative hybrid butterfly species, Papilio appalachiensis, its parental species, P. glaucus and P. canadensis, and an outgroup, P. polytes. Then, we use these data to infer genome-wide patterns of introgression and genomic mosaicism using both phylogenetic and population genetic approaches. Our results reveal that there is little genetic divergence among all three of the focal species, but the subset of gene trees that strongly support a specific tree topology suggest widespread sharing of genetic variation between P. appalachiensis and both parental species, likely as a result of hybrid speciation. We also find evidence for substantial shared genetic variation between P. glaucus and P. canadensis, which may be due to gene flow or ancestral variation. Consistent with previous work, we show that P. applachiensis is more similar to P. canadensis at Z-linked genes and more similar to P. glaucus at mitochondrial genes. We also identify a variety of targets of adaptive evolution, which appear to be enriched for traits that are likely to be important in the evolution of this butterfly system, such as pigmentation, hormone sensitivity, developmental processes, and cuticle formation. Overall, our results provide a genome-wide portrait of divergence and introgression associated with adaptation and speciation in an iconic butterfly radiation. PMID:23737327

  13. Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards.

    PubMed

    Lavretsky, Philip; Dacosta, Jeffrey M; Hernández-Baños, Blanca E; Engilis, Andrew; Sorenson, Michael D; Peters, Jeffrey L

    2015-11-01

    Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (ΦST  = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST  = 0.017) but comparable to mtDNA (ΦST  = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST ) and absolute (dXY ) estimates of divergence. In contrast, the ratio of Z-linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST  = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation. PMID:26414437

  14. 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).

  15. Thermodynamics of cellular statistical inference

    NASA Astrophysics Data System (ADS)

    Lang, Alex; Fisher, Charles; Mehta, Pankaj

    2014-03-01

    Successful organisms must be capable of accurately sensing the surrounding environment in order to locate nutrients and evade toxins or predators. However, single cell organisms face a multitude of limitations on their accuracy of sensing. Berg and Purcell first examined the canonical example of statistical limitations to cellular learning of a diffusing chemical and established a fundamental limit to statistical accuracy. Recent work has shown that the Berg and Purcell learning limit can be exceeded using Maximum Likelihood Estimation. Here, we recast the cellular sensing problem as a statistical inference problem and discuss the relationship between the efficiency of an estimator and its thermodynamic properties. We explicitly model a single non-equilibrium receptor and examine the constraints on statistical inference imposed by noisy biochemical networks. Our work shows that cells must balance sample number, specificity, and energy consumption when performing statistical inference. These tradeoffs place significant constraints on the practical implementation of statistical estimators in a cell.

  16. Causal inference from observational data.

    PubMed

    Listl, Stefan; Jürges, Hendrik; Watt, Richard G

    2016-10-01

    Randomized controlled trials have long been considered the 'gold standard' for causal inference in clinical research. In the absence of randomized experiments, identification of reliable intervention points to improve oral health is often perceived as a challenge. But other fields of science, such as social science, have always been challenged by ethical constraints to conducting randomized controlled trials. Methods have been established to make causal inference using observational data, and these methods are becoming increasingly relevant in clinical medicine, health policy and public health research. This study provides an overview of state-of-the-art methods specifically designed for causal inference in observational data, including difference-in-differences (DiD) analyses, instrumental variables (IV), regression discontinuity designs (RDD) and fixed-effects panel data analysis. The described methods may be particularly useful in dental research, not least because of the increasing availability of routinely collected administrative data and electronic health records ('big data'). PMID:27111146

  17. We infer light in space.

    PubMed

    Schirillo, James A

    2013-10-01

    In studies of lightness and color constancy, the terms lightness and brightness refer to the qualia corresponding to perceived surface reflectance and perceived luminance, respectively. However, what has rarely been considered is the fact that the volume of space containing surfaces appears neither empty, void, nor black, but filled with light. Helmholtz (1866/1962) came closest to describing this phenomenon when discussing inferred illumination, but previous theoretical treatments have fallen short by restricting their considerations to the surfaces of objects. The present work is among the first to explore how we infer the light present in empty space. It concludes with several research examples supporting the theory that humans can infer the differential levels and chromaticities of illumination in three-dimensional space. PMID:23435628

  18. Genetics of ecological divergence during speciation

    PubMed Central

    Arnegard, Matthew E.; McGee, Matthew D.; Matthews, Blake; Marchinko, Kerry B.; Conte, Gina L.; Kabir, Sahriar; Bedford, Nicole; Bergek, Sara; Chan, Yingguang Frank; Jones, Felicity C.; Kingsley, David M.; Peichel, Catherine L.; Schluter, Dolph

    2014-01-01

    Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Though this process is a major generator of biodiversity, its genetic basis remains poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but that depend on the ecological context. PMID:24909991

  19. NICKEL SPECIATION OF URBAN PARTICULATE MATTER

    SciTech Connect

    Kevin C. Galbreath; Charlene R. Crocker; Carolyn M. Nyberg; Frank E. Huggins; Gerald P. Huffman

    2003-10-01

    A four-step sequential Ni extraction method, summarized in Table AB-1, was evaluated for identifying and quantifying the Ni species occurring in urban total suspended particulate (TSP) matter and fine particulate matter (<10 {micro}m [PM{sub 10}] and <2.5 {micro}m [PM{sub 2.5}] in aerodynamic diameter). The extraction method was originally developed for quantifying soluble, sulfidic, elemental, and oxidic forms of Ni that may occur in industrial atmospheres. X-ray diffraction (XRD) and x-ray absorption fine structure (XAFS) spectroscopy were used to evaluate the Ni species selectivity of the extraction method. Uncertainties in the chemical speciation of Ni in urban PM{sub 10} and PM{sub 2.5} greatly affect inhalation health risk estimates, primarily because of the large variability in acute, chronic, and cancer-causing effects for different Ni compounds.

  20. Chemical speciation of radionuclides migrating in groundwaters

    SciTech Connect

    Robertson, D.; Schilk, A.; Abel, K.; Lepel, E.; Thomas, C.; Pratt, S.; Cooper, E.; Hartwig, P.; Killey, R.

    1994-04-01

    In order to more accurately predict the rates and mechanisms of radionuclide migration from low-level waste disposal facilities via groundwater transport, ongoing studies are being conducted at field sites at Chalk River Laboratories to identify and characterize the chemical speciation of mobile, long-lived radionuclides migrating in groundwaters. Large-volume water sampling techniques are being utilized to separate and concentrate radionuclides into particular, cationic, anionic, and nonionic chemical forms. Most radionuclides are migrating as soluble, anionic species that appear to be predominantly organoradionuclide complexes. Laboratory studies utilizing anion exchange chromatography have separated several anionically complexed radionuclides, e.g., {sup 60}Co and {sup 106}Ru, into a number of specific compounds or groups of compounds. Further identification of the anionic organoradionuclide complexes is planned utilizing high resolution mass spectrometry. Large-volume ultra-filtration experiments are characterizing the particulate forms of radionuclides being transported in these groundwaters.

  1. Speciation of arsenic in sulfidic waters

    PubMed Central

    Wilkin, Richard T; Wallschläger, Dirk; Ford, Robert G

    2003-01-01

    Formation constants for thioarsenite species have been determined in dilute solutions at 25°C, ΣH2S from 10-7.5 to 10-3.0 M, ΣAs from 10-5.6 to 10-4.8 M, and pH 7 and 10. The principal inorganic arsenic species in anoxic aquatic systems are arsenite, As(OH)30, and a mononuclear thioarsenite with an S/As ratio of 3:1. Thioarsenic species with S/As ratios of 1 : 1,2 : 1, and 4 : 1 are lesser components in sulfidic solutions that might be encountered in natural aquatic environments. Thioarsenites dominate arsenic speciation at sulfide concentrations > 10-4.3 M at neutral pH. Conversion from neutral As(OH)30 to anionic thioarsenite species may regulate the transport and fate of arsenic in sulfate-reducing environments by governing sorption and mineral precipitation reactions.

  2. Carbon speciation and surface tension of fog

    USGS Publications Warehouse

    Capel, P.D.; Gunde, R.; Zurcher, F.; Giger, W.

    1990-01-01

    The speciation of carbon (dissolved/particulate, organic/inorganic) and surface tension of a number of radiation fogs from the urban area of Zurich, Switzerland, were measured. The carbon species were dominated by "dissolved" organic carbon (DOC; i.e., the fraction that passes through a filter), which was typically present at levels of 40-200 mg/L. Less than 10% of the DOC was identified as specific individual organic compounds. Particulate organic carbon (POC) accounted for 26-41% of the mass of the particles, but usually less than 10% of the total organic carbon mass. Inorganic carbon species were relatively minor. The surface tensions of all the measured samples were less than pure water and were correlated with their DOC concentrations. The combination of high DOC and POC and low surface tension suggests a mechanism for the concentration of hydrophobic organic contaminants in the fog droplet, which have been observed by numerous investigators. ?? 1990 American Chemical Society.

  3. Mercury speciation in the Adriatic Sea.

    PubMed

    Kotnik, Jože; Horvat, Milena; Ogrinc, Nives; Fajon, Vesna; Žagar, Dušan; Cossa, Daniel; Sprovieri, Francesca; Pirrone, Nicola

    2015-07-15

    Mercury and its speciation were studied in surface and deep waters of the Adriatic Sea. Several mercury species (i.e. DGM – dissolved gaseous Hg, RHg – reactive Hg, THg – total Hg, MeHg – monomethyl Hg and DMeHg – dimethylmercury) together with other water parameters were measured in coastal and open sea deep water profiles. THg concentrations in the water column, as well as in sediments and pore waters, were the highest in the northern, most polluted part of the Adriatic Sea as the consequence of Hg mining in Idrija and the heavy industry of northern Italy. Certain profiles in the South Adriatic Pit exhibit an increase of DGM just over the bottom due to its diffusion from sediment as a consequence of microbial and/or tectonic activity. Furthermore, a Hg mass balance for the Adriatic Sea was calculated based on measurements and literature data. PMID:26013591

  4. Competitive speciation in quantitative genetic models.

    PubMed

    Drossel, B; Mckane, A

    2000-06-01

    We study sympatric speciation due to competition in an environment with a broad distribution of resources. We assume that the trait under selection is a quantitative trait, and that mating is assortative with respect to this trait. Our model alternates selection according to Lotka-Volterra-type competition equations, with reproduction using the ideas of quantitative genetics. The recurrence relations defined by these equations are studied numerically and analytically. We find that when a population enters a new environment, with a broad distribution of unexploited food sources, the population distribution broadens under a variety of conditions, with peaks at the edge of the distribution indicating the formation of subpopulations. After a long enough time period, the population can split into several subpopulations with little gene flow between them. PMID:10816369

  5. Horizontal Gene Transfer, Dispersal and Haloarchaeal Speciation

    PubMed Central

    Papke, R. Thane; Corral, Paulina; Ram-Mohan, Nikhil; de la Haba, Rafael R.; Sánchez-Porro, Cristina; Makkay, Andrea; Ventosa, Antonio

    2015-01-01

    The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria. PMID:25997110

  6. Eight challenges in phylodynamic inference

    PubMed Central

    Frost, Simon D.W.; Pybus, Oliver G.; Gog, Julia R.; Viboud, Cecile; Bonhoeffer, Sebastian; Bedford, Trevor

    2015-01-01

    The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data. PMID:25843391

  7. Inferring biotic interactions from proxies.

    PubMed

    Morales-Castilla, Ignacio; Matias, Miguel G; Gravel, Dominique; Araújo, Miguel B

    2015-06-01

    Inferring biotic interactions from functional, phylogenetic and geographical proxies remains one great challenge in ecology. We propose a conceptual framework to infer the backbone of biotic interaction networks within regional species pools. First, interacting groups are identified to order links and remove forbidden interactions between species. Second, additional links are removed by examination of the geographical context in which species co-occur. Third, hypotheses are proposed to establish interaction probabilities between species. We illustrate the framework using published food-webs in terrestrial and marine systems. We conclude that preliminary descriptions of the web of life can be made by careful integration of data with theory. PMID:25922148

  8. Nitrogen speciation in mantle and crustal fluids

    NASA Astrophysics Data System (ADS)

    Li, Yuan; Keppler, Hans

    2014-03-01

    Seventy-nine experiments have been carried out at 600-1400 °C, 2-35 kbar, and oxygen fugacities ranging from the Fe-FeO to the Re-ReO2 buffer to investigate the nitrogen speciation in mantle and crustal N-H-O fluids. Laser Raman analyses of fluid inclusions trapped in situ in quartz and olivine crystals show that N2 and/or NH3 are the only detectable nitrogen species in the fluids at the conditions of the present study. The results further show that in the fluids of the oxidized shallow upper mantle, nitrogen is mostly present as N2, while in the deep reduced upper mantle, NH3 is the dominant nitrogen species. Nitrogen speciation in subduction zone fluids is also calculated from the experimental data to constrain the efficiency of nitrogen recycling. The data show that a hot, oxidized slab is an efficient barrier for deep nitrogen subduction, while a cold, reduced slab would favor recycling nitrogen into the deep mantle. The nitrogen species in magmatic fluids of mid-ocean ridge basalt and arc magmas are predominantly N2, but a significant fraction of nitrogen can be NH3 at certain conditions. The nitrogen species in fluids released from the solidifying magma ocean and the reduced young mantle may have been mostly NH3. The release of such fluids may have created a reduced atmosphere on the every early Earth, with an elevated concentration of NH3. This may not only resolve the faint young Sun paradox but may also have created favorable conditions for the formation of biomolecules through Miller-Urey type reactions.

  9. Polyploidy in relation to plant evolution and speciation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Polyploidy is a dominant force in plant evolution and speciation. Allopolyploids, resulting from interspecific or intergeneric hybridization coupled with chromosome doubling, are preponderant in nature. For the meiotic and reproductive stability of the allopolyploids, a precise genetic control of ...

  10. ACTINIDE-ALUMINATE SPECIATION IN ALKALINE RADIOACTIVE WASTE

    EPA Science Inventory

    Highly alkaline radioactive waste tanks contain a number of transuranic species, in particular U, Np, Pu, and Am - the exact forms of which are currently unknown. Knowledge of actinide speciation under highly alkaline conditions is essential towards understanding and predicting ...

  11. Male competition fitness landscapes predict both forward and reverse speciation.

    PubMed

    Keagy, Jason; Lettieri, Liliana; Boughman, Janette W

    2016-01-01

    Speciation is facilitated when selection generates a rugged fitness landscape such that populations occupy different peaks separated by valleys. Competition for food resources is a strong ecological force that can generate such divergent selection. However, it is unclear whether intrasexual competition over resources that provide mating opportunities can generate rugged fitness landscapes that foster speciation. Here we use highly variable male F2 hybrids of benthic and limnetic threespine sticklebacks, Gasterosteus aculeatus Linnaeus, 1758, to quantify the male competition fitness landscape. We find that disruptive sexual selection generates two fitness peaks corresponding closely to the male phenotypes of the two parental species, favouring divergence. Most surprisingly, an additional region of high fitness favours novel hybrid phenotypes that correspond to those observed in a recent case of reverse speciation after anthropogenic disturbance. Our results reveal that sexual selection through male competition plays an integral role in both forward and reverse speciation. PMID:26612568

  12. PARTICLE SPECIATION AND EMISSION PROFILES OF SMALL 2-STROKE ENGINES

    EPA Science Inventory

    The Human Exposure and Atmospheric Sciences Division (HEASD) conducts studies designed to acquire information from emission sources for use in source apportionment studies. The objective of this work is to characterize a complete, speciated emission profile (PM and air toxics) ...

  13. Science Shorts: Observation versus Inference

    ERIC Educational Resources Information Center

    Leager, Craig R.

    2008-01-01

    When you observe something, how do you know for sure what you are seeing, feeling, smelling, or hearing? Asking students to think critically about their encounters with the natural world will help to strengthen their understanding and application of the science-process skills of observation and inference. In the following lesson, students make…

  14. Sample Size and Correlational Inference

    ERIC Educational Resources Information Center

    Anderson, Richard B.; Doherty, Michael E.; Friedrich, Jeff C.

    2008-01-01

    In 4 studies, the authors examined the hypothesis that the structure of the informational environment makes small samples more informative than large ones for drawing inferences about population correlations. The specific purpose of the studies was to test predictions arising from the signal detection simulations of R. B. Anderson, M. E. Doherty,…

  15. Word Learning as Bayesian Inference

    ERIC Educational Resources Information Center

    Xu, Fei; Tenenbaum, Joshua B.

    2007-01-01

    The authors present a Bayesian framework for understanding how adults and children learn the meanings of words. The theory explains how learners can generalize meaningfully from just one or a few positive examples of a novel word's referents, by making rational inductive inferences that integrate prior knowledge about plausible word meanings with…

  16. The mechanisms of temporal inference

    NASA Technical Reports Server (NTRS)

    Fox, B. R.; Green, S. R.

    1987-01-01

    The properties of a temporal language are determined by its constituent elements: the temporal objects which it can represent, the attributes of those objects, the relationships between them, the axioms which define the default relationships, and the rules which define the statements that can be formulated. The methods of inference which can be applied to a temporal language are derived in part from a small number of axioms which define the meaning of equality and order and how those relationships can be propagated. More complex inferences involve detailed analysis of the stated relationships. Perhaps the most challenging area of temporal inference is reasoning over disjunctive temporal constraints. Simple forms of disjunction do not sufficiently increase the expressive power of a language while unrestricted use of disjunction makes the analysis NP-hard. In many cases a set of disjunctive constraints can be converted to disjunctive normal form and familiar methods of inference can be applied to the conjunctive sub-expressions. This process itself is NP-hard but it is made more tractable by careful expansion of a tree-structured search space.

  17. Perceptual Inference and Autistic Traits

    ERIC Educational Resources Information Center

    Skewes, Joshua C; Jegindø, Else-Marie; Gebauer, Line

    2015-01-01

    Autistic people are better at perceiving details. Major theories explain this in terms of bottom-up sensory mechanisms or in terms of top-down cognitive biases. Recently, it has become possible to link these theories within a common framework. This framework assumes that perception is implicit neural inference, combining sensory evidence with…

  18. Improving Explanatory Inferences from Assessments

    ERIC Educational Resources Information Center

    Diakow, Ronli Phyllis

    2013-01-01

    This dissertation comprises three papers that propose, discuss, and illustrate models to make improved inferences about research questions regarding student achievement in education. Addressing the types of questions common in educational research today requires three different "extensions" to traditional educational assessment: (1)…

  19. Speciation, Ecological Opportunity, and Latitude (American Society of Naturalists Address).

    PubMed

    Schluter, Dolph

    2016-01-01

    Evolutionary hypotheses to explain the greater numbers of species in the tropics than the temperate zone include greater age and area, higher temperature and metabolic rates, and greater ecological opportunity. These ideas make contrasting predictions about the relationship between speciation processes and latitude, which I elaborate and evaluate. Available data suggest that per capita speciation rates are currently highest in the temperate zone and that diversification rates (speciation minus extinction) are similar between latitudes. In contrast, clades whose oldest analyzed dates precede the Eocene thermal maximum, when the extent of the tropics was much greater than today, tend to show highest speciation and diversification rates in the tropics. These findings are consistent with age and area, which is alone among hypotheses in predicting a time trend. Higher recent speciation rates in the temperate zone than the tropics suggest an additional response to high ecological opportunity associated with low species diversity. These broad patterns are compelling but provide limited insights into underlying mechanisms, arguing that studies of speciation processes along the latitudinal gradient will be vital. Using threespine stickleback in depauperate northern lakes as an example, I show how high ecological opportunity can lead to rapid speciation. The results support a role for ecological opportunity in speciation, but its importance in the evolution of the latitudinal gradient remains uncertain. I conclude that per capita evolutionary rates are no longer higher in the tropics than the temperate zone. Nevertheless, the vast numbers of species that have already accumulated in the tropics ensure that total rate of species production remains highest there. Thus, tropical evolutionary momentum helps to perpetuate the steep latitudinal biodiversity gradient. PMID:26814593

  20. Inferring gene duplications, transfers and losses can be done in a discrete framework.

    PubMed

    Ranwez, Vincent; Scornavacca, Celine; Doyon, Jean-Philippe; Berry, Vincent

    2016-06-01

    In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree-whose internal nodes represent speciation events-while the evolutionary history of a gene family is depicted by a gene tree-whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family. This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees. In the past decade, several parsimony-based methods have been developed to infer such reconciliations, accounting for gene duplications ([Formula: see text]), transfers ([Formula: see text]) and losses ([Formula: see text]). The main contribution of this paper is to formally prove an important assumption implicitly made by previous works on these reconciliations, namely that solving the (maximum) parsimony [Formula: see text] reconciliation problem in the discrete framework is equivalent to finding a most parsimonious [Formula: see text] scenario in the continuous framework. In the process, we also prove several intermediate results that are useful on their own and constitute a theoretical toolbox that will likely facilitate future theoretical contributions in the field. PMID:26337177

  1. 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

  2. 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. PMID:26804556

  3. 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. PMID:27358365

  4. Speciation in birds: Genes, geography, and sexual selection

    PubMed Central

    Edwards, Scott V.; Kingan, Sarah B.; Calkins, Jennifer D.; Balakrishnan, Christopher N.; Jennings, W. Bryan; Swanson, Willie J.; Sorenson, Michael D.

    2005-01-01

    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. PMID:15851678

  5. Chemical PM2.5 Speciation in Major Cities Worldwide

    NASA Astrophysics Data System (ADS)

    Snider, Graydon; Weagle, Crystal; Brauer, Michael; Cohen, Aaron; Gibson, Mark; Liu, Yang; Martins, Vanderlei; Rudich, Yinon; Martin, Randall

    2016-04-01

    We examined the chemical composition of fine particulate matter (PM2.5) across 13 globally dispersed urban locations (including Atlanta, Buenos Aires, Beijing, Manila, and Dhaka), as part of the Surface PARTiculate mAtter Network (SPARTAN). At each site sampling was conducted over 4 to 24 months for the years 2013 to 2015. Analysis of filter samples revealed that several PM2.5 chemical components varied by more than an order of magnitude between sites. Ammonium sulfate ranged from 2 μg m‑3 (Ilorin) to 17 μg m‑3 (Kanpur). Ammonium nitrate ranged from 0.2 μg m‑3 (Atlanta) to 6.7 μg m‑3 (Kanpur). Effective black carbon ranged from 0.4 μg m‑3 (Atlanta) to 5 μg m‑3 (Dhaka and Kanpur). The all-site mean values of major PM2.5 constituents were ammonium sulfate (20 ± 10 %), crustal material (12 ± 6.5%), effective black carbon (10 ± 7.4 %), ammonium nitrate (3.7 ± 2.5%), sea salt (2.2 ± 1.5%), trace element oxides (0.9 ± 0.7 %), water (7.2 ± 3.0%) and residue materials (44 ± 24%). Based on the evaluation with collocated studies we treated residue material as mostly organic. Major ions generally agreed well with previous studies at the same urban locations (e.g. sulfate fractions agreed within 4% for eight out of 11 collocation comparisons). Enhanced crustal material (CM) concentrations with high Zn:Al ratios at large cities (e.g. Hanoi, Dhaka, Manila) imply significant anthropogenic CM contributions that deserve more attention. Detailed chemical speciation also aided our characterization of site-specific PM2.5 water retention. The expected water contribution to aerosols was calculated via the hygroscopicity parameter for each filter. Hourly PM2.5 at specified relative humidity (35%) was inferred from nephelometer measurements of light scatter at ambient relative humidity and 9-day filter measurements of PM2.5 mass. Our PM2.5 estimates compared favorably with a beta attenuation monitor (BAM) at the nearby US embassy in Beijing, with a coefficient of

  6. Competitive release leads to range expansion and rampant speciation in malagasy dung beetles.

    PubMed

    Miraldo, Andreia; Hanski, Ilkka A

    2014-07-01

    Competition is often thought to promote ecological diversification and thereby to facilitate the coexistence of competitors during evolutionary radiations. At large spatial scales, species may also coexist by having allopatric distributions, which raises the question about the role of range expansion in the proliferation of species during radiations. Here, we integrate a well-sampled (50 out of 74 species) and timed phylogeny of Nanos and Apotolamprus dung beetles (Canthonini) in Madagascar with data on species' geographical ranges, abundances, and body sizes. There is an overall decline in lineage accumulation through time since the colonization of northern Madagascar in the mid Miocene (24-13 Ma). A clade of 24 extant Nanos species (clade L) originating 6.0 Ma exhibits an increase in speciation rate, which is associated with a significant increase in body size and strikingly allopatric distributions of the species. Large body size typically confers a competitive advantage in dung beetles, which is here reflected by strong numerical dominance of clade L species in local communities. We suggest that the "key innovation" of large body size has allowed range expansion due to competitive release, which has created extensive opportunities for allopatric speciation and differentiation along environmental gradients. Most theories to explain diversification patterns in Madagascar rely on allopatric modes of speciation, but they fail to explain how ancestral species became widespread in the first place. The mechanism proposed here, involving range expansion following competitive release via a "key innovation", may have operated in other Malagasy taxa with large numbers of species with small geographic ranges. [biodiversity hotspot; competition; Madagascar; microendemism; radiation.]. PMID:24578226

  7. The variability in iron speciation in size fractionated residual oil fly ash particulate matter (ROFA PM).

    PubMed

    Pattanaik, Sidhartha; Huggins, Frank E; Huffman, Gerald P

    2016-08-15

    Ambient particulate matter (PM) containing iron can catalyze Fenton reaction leading to the production of reactive oxygen species in cells. It can also catalyze atmospheric redox reaction. These reactions are governed by the physicochemical characteristics of iron in ambient PM. As a surrogate for ambient PM, we prepared residual oil fly ash PM (ROFA PM) in a practical fire tube boiler firing residual oils with varying sulfur and ash contents. The ROFA particles were resolved into fine PM or PM2.5 (aerodynamic diameter (AD)<2.5μm) and coarse PM or PM2.5+ (AD between 2.5μm and 50μm). The iron speciation in PM2.5+ was ascertained using X-ray absorption spectroscopy and leaching method while that in PM2.5 was reported earlier. The results of both studies are compared to get an insight into the variability in the iron speciation in different size fractions. The results show the predominance of ferric sulfate, with a minor spinal ferrite in both PM (i.e. ZnxNi1-xFe2O4 in PM2.5, ZnFe2O4 in PM2.5+). The iron solubility in ROFA PM depends on its speciation, mode of incorporation of iron into particle's carbonaceous matrix, the grade and composition of oils, and pH of the medium. The soluble fraction of iron in PM is critical in assessing its interaction with the biological systems and its toxic potential. PMID:27125683

  8. Iodine speciation in rain, snow and aerosols

    NASA Astrophysics Data System (ADS)

    Gilfedder, B. S.; Lai, S. C.; Petri, M.; Biester, H.; Hoffmann, T.

    2008-10-01

    Iodine oxides, such as iodate, should be the only thermodynamically stable sink species for iodine in the troposphere. However, field observations have increasingly found very little iodate and significant amounts of iodide and soluble organically bound iodine (SOI) in precipitation and aerosols. The aim of this study was to investigate iodine speciation, including the organic fraction, in rain, snow, and aerosols in an attempt to further clarify aqueous phase iodine chemistry. Diurnal aerosol samples were taken with a 5 stage cascade impactor and a virtual impactor (PM2.5) from the Mace Head research station, Ireland, during summer 2006. Rain was collected from Australia, New Zealand, Patagonia, Germany, Ireland, and Switzerland and snow was obtained from Greenland, Germany, Switzerland, and New Zealand. Aerosols were extracted from the filters with water and all samples were analysed for total soluble iodine (TSI) by inductively coupled plasma mass spectrometry (ICP-MS) and iodine speciation was determined by coupling an ion chromatography unit to the ICP-MS. The median concentration of TSI in aerosols from Mace Head was 222 pmol m-3 (summed over all impactor stages) of which the majority was associated with the SOI fraction (median day: 90±4%, night: 94±2% of total iodine). Iodide exhibited higher concentrations than iodate (median 6% vs. 1.2% of total iodine), and displayed significant enrichment during the day compared to the night. Interestingly, up to 5 additional, presumably anionic iodo-organic peaks were observed in all IC-ICP-MS chromatograms, composing up to 15% of the TSI. Soluble organically bound iodine was also the dominant fraction in all rain and snow samples, with lesser amounts of iodide and iodate (iodate was particularly low in snow). Two of the same unidentified peaks found in aerosols were also observed in precipitation from both Southern and Northern Hemispheres. This suggests that these species are transferred from the aerosols into

  9. Inference of Population History by Coupling Exploratory and Model-Driven Phylogeographic Analyses

    PubMed Central

    Garrick, Ryan C.; Caccone, Adalgisa; Sunnucks, Paul

    2010-01-01

    Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions. PMID:20480016

  10. Bayesian Inference on Proportional Elections

    PubMed Central

    Brunello, Gabriel Hideki Vatanabe; Nakano, Eduardo Yoshio

    2015-01-01

    Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software. PMID:25786259

  11. Bayesian inference on proportional elections.

    PubMed

    Brunello, Gabriel Hideki Vatanabe; Nakano, Eduardo Yoshio

    2015-01-01

    Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software. PMID:25786259

  12. System Support for Forensic Inference

    NASA Astrophysics Data System (ADS)

    Gehani, Ashish; Kirchner, Florent; Shankar, Natarajan

    Digital evidence is playing an increasingly important role in prosecuting crimes. The reasons are manifold: financially lucrative targets are now connected online, systems are so complex that vulnerabilities abound and strong digital identities are being adopted, making audit trails more useful. If the discoveries of forensic analysts are to hold up to scrutiny in court, they must meet the standard for scientific evidence. Software systems are currently developed without consideration of this fact. This paper argues for the development of a formal framework for constructing “digital artifacts” that can serve as proxies for physical evidence; a system so imbued would facilitate sound digital forensic inference. A case study involving a filesystem augmentation that provides transparent support for forensic inference is described.

  13. Statistical learning and selective inference

    PubMed Central

    Taylor, Jonathan; Tibshirani, Robert J.

    2015-01-01

    We describe the problem of “selective inference.” This addresses the following challenge: Having mined a set of data to find potential associations, how do we properly assess the strength of these associations? The fact that we have “cherry-picked”—searched for the strongest associations—means that we must set a higher bar for declaring significant the associations that we see. This challenge becomes more important in the era of big data and complex statistical modeling. The cherry tree (dataset) can be very large and the tools for cherry picking (statistical learning methods) are now very sophisticated. We describe some recent new developments in selective inference and illustrate their use in forward stepwise regression, the lasso, and principal components analysis. PMID:26100887

  14. Network Plasticity as Bayesian Inference

    PubMed Central

    Legenstein, Robert; Maass, Wolfgang

    2015-01-01

    General results from statistical learning theory suggest to understand not only brain computations, but also brain plasticity as probabilistic inference. But a model for that has been missing. We propose that inherently stochastic features of synaptic plasticity and spine motility enable cortical networks of neurons to carry out probabilistic inference by sampling from a posterior distribution of network configurations. This model provides a viable alternative to existing models that propose convergence of parameters to maximum likelihood values. It explains how priors on weight distributions and connection probabilities can be merged optimally with learned experience, how cortical networks can generalize learned information so well to novel experiences, and how they can compensate continuously for unforeseen disturbances of the network. The resulting new theory of network plasticity explains from a functional perspective a number of experimental data on stochastic aspects of synaptic plasticity that previously appeared to be quite puzzling. PMID:26545099

  15. Causal inference based on counterfactuals

    PubMed Central

    Höfler, M

    2005-01-01

    Background The counterfactual or potential outcome model has become increasingly standard for causal inference in epidemiological and medical studies. Discussion This paper provides an overview on the counterfactual and related approaches. A variety of conceptual as well as practical issues when estimating causal effects are reviewed. These include causal interactions, imperfect experiments, adjustment for confounding, time-varying exposures, competing risks and the probability of causation. It is argued that the counterfactual model of causal effects captures the main aspects of causality in health sciences and relates to many statistical procedures. Summary Counterfactuals are the basis of causal inference in medicine and epidemiology. Nevertheless, the estimation of counterfactual differences pose several difficulties, primarily in observational studies. These problems, however, reflect fundamental barriers only when learning from observations, and this does not invalidate the counterfactual concept. PMID:16159397

  16. Speciation and phylogeography of giant petrels Macronectes.

    PubMed

    Techow, N M S M; O'Ryan, C; Phillips, R A; Gales, R; Marin, M; Patterson-Fraser, D; Quintana, F; Ritz, M S; Thompson, D R; Wanless, R M; Weimerskirch, H; Ryan, P G

    2010-02-01

    We examine global phylogeography of the two forms of giant petrel Macronectes spp. Although previously considered to be a single taxon, and despite debate over the status of some populations and the existence of minimal genetic data (one mitochondrial cytochrome b sequence per form), the current consensus based on morphology is that there are two species, Northern Giant Petrel M. halli and Southern Giant Petrel M. giganteus. This study examined genetic variation at cytochrome b as well as six microsatellite loci in giant petrels from 22 islands, representing most island groups at which the two species breed. Both markers support separate species status, although sequence divergence in cytochrome b was only 0.42% (corrected). Divergence was estimated to have occurred approximately 0.2mya, but with some colonies apparently separated for longer (up to 0.5 my). Three clades were found within giant petrels, which separated approximately 0.7mya, with the Southern Giant Petrel paraphyletic to a monophyletic Northern Giant Petrel. There was evidence of past fragmentation during the Pleistocene, with subsequent secondary contact within Southern Giant Petrels. The analysis also suggested a period of past population expansion that corresponded roughly to the timing of speciation and the separation of an ancestral giant petrel population from the fulmar Fulmarus clade. PMID:19755164

  17. The biological speciation and toxicokinetics of aluminum.

    PubMed Central

    DeVoto, E; Yokel, R A

    1994-01-01

    This review discusses recent literature on the chemical and physiological factors that influence the absorption, distribution, and excretion of aluminum in mammals, with particular regard to gastrointestinal absorption and speciation in plasma. Humans encounter aluminum, a ubiquitous yet highly insoluble element in most forms, in foods, drinking water, and pharmaceuticals. Exposure also occurs by inhalation of dust and aerosols, particularly in occupational settings. Absorption from the gut depends largely on pH and the presence of complexing ligands, particularly carboxylic acids, with which the metal can form absorbable neutral aluminum species. Uremic animals and humans experience higher than normal body burdens of aluminum despite increased urinary clearance of the metal. In plasma, 80-90% of aluminum binds to transferrin, an iron-transport protein for which receptors exist in many tissue. The remaining fraction of plasma aluminum takes the form of small-molecule hydroxy species and small complexes with carboxylic acids, phosphate, and, to a much lesser degree, amino acids. Most of these species have not been observed in vivo but are predicted from equilibrium models derived from potentiometric methods and NMR investigations. These models predict that the major small-molecule aluminum species under plasma conditions are charged and hence unavailable for uptake into tissues. PMID:9738208

  18. Selenium speciation in flue desulfurization residues.

    PubMed

    Zhong, Liping; Cao, Yan; Li, Wenying; Xie, Kechang; Pan, Wei-Ping

    2011-01-01

    Flue gas from coal combustion contains significant amounts of volatile selenium (Se). The capture of Se in the flue gas desulfurization (FGD) scrubber unit has resulted in a generation of metal-laden residues. It is important to determine Se speciation to understand the environmental impact of its disposal. A simple method has been developed for selective inorganic Se(IV), Se(VI) and organic Se determination in the liquid-phase FGD residues by hydride generation atomic fluorescence spectrometry (AFS). It has been determined that Se(IV), Se(VI) and organic Se can be accurately determined with detection limits (DL) of 0.05, 0.06 and 0.06 microg/L, respectively. The accuracy of the proposed method was evaluated by analyzing the certified reference material, NIST CRM 1632c, and also by analyzing spiked tap-water samples. Analysis indicates that the concentration of Se is high in FGD liquid residues and primarily exists in a reduced state as selenite (Se(IV)). The toxicity of Se(IV) is the strongest of all Se species. Flue gas desulfurization residues pose a serious environmental risk. PMID:21476358

  19. Geographically multifarious phenotypic divergence during speciation

    PubMed Central

    Gompert, Zachariah; Lucas, Lauren K; Nice, Chris C; Fordyce, James A; Alex Buerkle, C; Forister, Matthew L

    2013-01-01

    Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference). PMID:23532669

  20. Speciation of triphenyltin compounds using Moessbauer spectroscopy. Final report

    SciTech Connect

    Eng, G.

    1993-11-01

    Organotin compounds have been used widely as the active agent in antifouling marine paints. Organotin compounds, i.e., tributyltin compounds (TBTs) and triphenyltin compounds (TPTs) have been found to be effective in preventing the unwanted attachment and development of aquatic organisms such as barnacles, sea grass and hydroids on ships, hulls and underwater surfaces. However, these organotin compounds have been found to be toxic to non-targeted marine species as well. While speciation of tributyltins in environmental water systems has received much attention in the literature, little information concerning the speciation of triphenyltins is found. Therefore, it would be important to study the fate of TPTs in the aquatic environment, particularly in sediments, both oxic and anoxic, in order to obtain speciation data. Since marine estuaries consist of areas with varying salinity and pH, it is important to investigate the speciation of these compounds under varying salinity conditions. In addition, evaluation of the speciation of these compounds as a function of pH would give an insight into how these compounds might interact with sediments in waters where industrial chemical run-offs can affect the pH of the estuarine environment. Finally, since organotins are present in both salt and fresh water environments, the speciation of the organotins in seawater and distilled water should also be studied. Moessbauer spectroscopy would provide a preferred method to study the speciation of triphenyltins as they leach from marine paints into the aquatic environment. Compounds used in this study are those triphenyltin compounds that are commonly incorporated into marine paints such as triphenyltin fluoride (TPTF), triphenyltin acetate (TPTOAc), triphenyltin chloride (TPTCl) and triphenyltin hydroxide (TPTOH).

  1. Self-enforcing Private Inference Control

    NASA Astrophysics Data System (ADS)

    Yang, Yanjiang; Li, Yingjiu; Weng, Jian; Zhou, Jianying; Bao, Feng

    Private inference control enables simultaneous enforcement of inference control and protection of users' query privacy. Private inference control is a useful tool for database applications, especially when users are increasingly concerned about individual privacy nowadays. However, protection of query privacy on top of inference control is a double-edged sword: without letting the database server know the content of user queries, users can easily launch DoS attacks. To assuage DoS attacks in private inference control, we propose the concept of self-enforcing private inference control, whose intuition is to force users to only make inference-free queries by enforcing inference control themselves; otherwise, penalty will inflict upon the violating users.

  2. Inter-locus antagonistic coevolution as an engine of speciation: Assessment with hemiclonal analysis

    PubMed Central

    Rice, William R.; Linder, Jodell E.; Friberg, Urban; Lew, Timothy A.; Morrow, Edward H.; Stewart, Andrew D.

    2005-01-01

    One of Ernst Mayr's legacies is the consensus that the allopatry model is the predominant mode of speciation in most sexually reproducing lineages. In this model, reproductive isolation develops as a pleiotropic byproduct of the genetic divergence that develops among physically isolated populations. Presently, there is no consensus concerning which, if any, evolutionary process is primarily responsible for driving the specific genetic divergence that leads to reproductive isolation. Here, we focus on the hypothesis that inter-locus antagonistic coevolution drives rapid genetic divergence among allopatric populations and thereby acts as an important “engine” of speciation. We assert that only data from studies of experimental evolution, rather than descriptive patterns of molecular evolution, can provide definitive evidence for this hypothesis. We describe and use an experimental approach, called hemiclonal analysis, that can be used in the Drosophila melanogaster laboratory model system to simultaneously screen nearly the entire genome for both standing genetic variation within a population and the net-selection gradient acting on the variation. Hemiclonal analysis has four stages: (i) creation of a laboratory “island population”; (ii) cytogenetic cloning of nearly genome-wide haplotypes to construct hemiclones; (iii) measurement of additive genetic variation among hemiclones; and (iv) measurement of the selection gradient acting on phenotypic variation among hemiclones. We apply hemiclonal analysis to test the hypothesis that there is ongoing antagonistic coevolution between the sexes in the D. melanogaster laboratory model system and then discuss the relevance of this analysis to natural systems. PMID:15851669

  3. [Influence of Dissimilatory Iron Reduction on the Speciation and Bioavailability of Heavy Metals in Soil].

    PubMed

    Si, You-bin; Wang, Juan

    2015-09-01

    Fe(III) dissimilatory reduction by microbes is an important process of producing energy in the oxidation of organic compounds under anaerobic condition with Fe(III) as the terminal electron acceptor and Fe(II) as the reduction product. This process is of great significance in element biogeochemical cycle. Iron respiration has been described as one of the most ancient forms of microbial metabolism on the earth, which is bound up with material cycle in water, soil and sediments. Dissimilatory iron reduction plays important roles in heavy metal form transformation and the remediation of heavy metal and radionuclide contaminated soils. In this paper, we summarized the research progress of iron reduction in the natural environment, and discussed the influence and the mechanism of dissimilatory iron reduction on the speciation and bioavailability of heavy metals in soil. The effects of dissimilatory iron reduction on the speciation of heavy metals may be attributed to oxidation and reduction, methytation and immobilization of heavy metals in relation to their bioavailability in soils. The mechanisms of Fe(III) dissimilatory reduction on heavy metal form transformation contain biological and chemical interactions, but the mode of interaction remains to be further investigated. PMID:26717720

  4. The genetic basis of speciation in the Giliopsis lineage of Ipomopsis (Polemoniaceae)

    USGS Publications Warehouse

    Nakazato, Takuya; Rieseberg, Loren H.; Wood, Troy E.

    2013-01-01

    One of the most powerful drivers of speciation in plants is pollinator-mediated disruptive selection, which leads to the divergence of floral traits adapted to the morphology and behavior of different pollinators. Despite the widespread importance of this speciation mechanism, its genetic basis has been explored in only a few groups. Here, we characterize the genetic basis of pollinator-mediated divergence of two species in genus Ipomopsis, I. guttata and I. tenuifolia, using quantitative trait locus (QTL) analyses of floral traits and other variable phenotypes. We detected one to six QTLs per trait, with each QTL generally explaining small to modest amounts of the phenotypic variance of a backcross hybrid population. In contrast, flowering time and anthocyanin abundance (a metric of color variation) were controlled by a few QTLs of relatively large effect. QTLs were strongly clustered within linkage groups, with 26 of 37 QTLs localized to six marker-interval ‘hotspots,’ all of which harbored pleiotropic QTLs. In contrast to other studies that have examined the genetic basis of pollinator shifts, our results indicate that, in general, mutations of small to modest effect on phenotype were involved. Thus, the evolutionary transition between the distinct pollination modes of I. guttata and I. tenuifolia likely proceeded incrementally, rather than saltationally.

  5. How sympatric is speciation in the Howea palms of Lord Howe Island?

    PubMed

    Babik, Wiesław; Butlin, Roger K; Baker, William J; Papadopulos, Alexander S T; Boulesteix, Matthieu; Anstett, Marie-Charlotte; Lexer, Christian; Hutton, Ian; Savolainen, Vincent

    2009-09-01

    The two species of the palm genus Howea (Arecaceae) from Lord Howe Island, a minute volcanic island in the Tasman Sea, are now regarded as one of the most compelling examples of sympatric speciation, although this view is still disputed by some authors. Population genetic and ecological data are necessary to provide a more coherent and comprehensive understanding of this emerging model system. Here, we analyse data on abundance, juvenile recruitment, pollination mode and genetic variation and structure in both species. We find that Howea forsteriana is less abundant than Howea belmoreana. The genetic data based on amplified fragment length polymorphisms markers indicate similar levels of variation in the two species, despite the estimated census population size of H. belmoreana being three times larger than that of H. forsteriana. Genetic structure within species is low although some weak isolation by distance is detectable. Gene flow between species appears to be extremely limited and restricted to early-generation hybrids - only three admixed individuals, classified as F2s or first generation backcrosses to a parental species, were found among sampled palms. We conclude that speciation in Howea was indeed sympatric, although under certain strict definitions it may be called parapatric. PMID:19674301

  6. Did pollination shifts drive diversification in southern African Gladiolus? Evaluating the model of pollinator-driven speciation.

    PubMed

    Valente, Luis M; Manning, John C; Goldblatt, Peter; Vargas, Pablo

    2012-07-01

    The pollinator-driven ecological speciation model has frequently been invoked to explain plant richness in biodiversity hotspots. Here, by focusing on Gladiolus (260 species), a flagship example of a clade with diverse pollination biology, we test the hypothesis that high species diversity in southern Africa, one of the world's most floristically rich regions, has primarily been driven by ecological shifts in pollination systems. We use phylogenetic methods to estimate rates of transition between the seven highly specialized pollination strategies in Gladiolus. We find that pollination systems have evolved multiple times and that some pollination strategies arose by a variety of evolutionary pathways. Pollination shifts account for up to one-third of all lineage splitting events in the genus, providing partial support for the pollinator-driven speciation model. Transitions from the ancestral pollination mode to derived systems have also resulted in increased rates of diversification, suggesting that certain pollination systems may speed up speciation processes, independently of pollination shifts per se. This study suggests that frequent pollination shifts have played a role in driving high phenotypic and species diversity but indicates that additional factors need to be invoked to account for the spectacular diversification in southern African Gladiolus. PMID:22673653

  7. Host shift and speciation in a coral-feeding nudibranch.

    PubMed

    Faucci, Anuschka; Toonen, Robert J; Hadfield, Michael G

    2007-01-01

    While the role of host preference in ecological speciation has been investigated extensively in terrestrial systems, very little is known in marine environments. Host preference combined with mate choice on the preferred host can lead to population subdivision and adaptation leading to host shifts. We use a phylogenetic approach based on two mitochondrial genetic markers to disentangle the taxonomic status and to investigate the role of host specificity in the speciation of the nudibranch genus Phestilla (Gastropoda, Opisthobranchia) from Guam, Palau and Hawaii. Species of the genus Phestilla complete their life cycle almost entirely on their specific host coral (species of Porites, Goniopora and Tubastrea). They reproduce on their host coral and their planktonic larvae require a host-specific chemical cue to metamorphose and settle onto their host. The phylogenetic trees of the combined cytochrome oxidase I and ribosomal 16S gene sequences clarify the relationship among species of Phestilla identifying most of the nominal species as monophyletic clades. We found a possible case of host shift from Porites to Goniopora and Tubastrea in sympatric Phestilla spp. This represents one of the first documented cases of host shift as a mechanism underlying speciation in a marine invertebrate. Furthermore, we found highly divergent clades within Phestilla sp. 1 and Phestilla minor (8.1-11.1%), suggesting cryptic speciation. The presence of a strong phylogenetic signal for the coral host confirms that the tight link between species of Phestilla and their host coral probably played an important role in speciation within this genus. PMID:17134995

  8. Speciation with gene flow on Lord Howe Island

    PubMed Central

    Papadopulos, Alexander S. T.; Baker, William J.; Crayn, Darren; Butlin, Roger K.; Kynast, Ralf G.; Hutton, Ian; Savolainen, Vincent

    2011-01-01

    Understanding the processes underlying the origin of species is a fundamental goal of biology. It is widely accepted that speciation requires an interruption of gene flow between populations: ongoing gene exchange is considered a major hindrance to population divergence and, ultimately, to the evolution of new species. Where a geographic barrier to reproductive isolation is lacking, a biological mechanism for speciation is required to counterbalance the homogenizing effect of gene flow. Speciation with initially strong gene flow is thought to be extremely rare, and few convincing empirical examples have been published. However, using phylogenetic, karyological, and ecological data for the flora of a minute oceanic island (Lord Howe Island, LHI), we demonstrate that speciation with gene flow may, in fact, be frequent in some instances and could account for one in five of the endemic plant species of LHI. We present 11 potential instances of species divergence with gene flow, including an in situ radiation of five species of Coprosma (Rubiaceae, the coffee family). These results, together with the speciation of Howea palms on LHI, challenge current views on the origin of species diversity. PMID:21730151

  9. 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.

  10. On the origin of species by sympatric speciation

    NASA Astrophysics Data System (ADS)

    Dieckmann, Ulf; Doebeli, Michael

    1999-07-01

    Understanding speciation is a fundamental biological problem. It is believed that many species originated through allopatric divergence, where new species arise from geographically isolated populations of the same ancestral species. In contrast, the possibility of sympatric speciation (in which new species arise without geographical isolation) has often been dismissed, partly because of theoretical difficulties,. Most previous models analysing sympatric speciation concentrated on particular aspects of the problem while neglecting others. Here we present a model that integrates a novel combination of different features and show that sympatric speciation is a likely outcome of competition for resources. We use multilocus genetics to describe sexual reproduction in an individual-based model, and we consider the evolution of assortative mating (where individuals mate preferentially with like individuals) depending either on an ecological character affecting resource use or on a selectively neutral marker trait. In both cases, evolution of assortative mating often leads to reproductive isolation between ecologically diverging subpopulations. When assortative mating depends on a marker trait, and is therefore not directly linked to resource competition, speciation occurs when genetic drift breaks the linkage equilibrium between the marker and the ecological trait. Our theory conforms well with mounting empirical evidence for the sympatric origin of many species.

  11. Pollinator shifts as triggers of speciation in painted petal irises (Lapeirousia: Iridaceae)

    PubMed Central

    Forest, Félix; Goldblatt, Peter; Manning, John C.; Baker, David; Colville, Jonathan F.; Devey, Dion S.; Jose, Sarah; Kaye, Maria; Buerki, Sven

    2014-01-01

    Background and Aims Adaptation to different pollinators has been hypothesized as one of the main factors promoting the formation of new species in the Cape region of South Africa. Other researchers favour alternative causes such as shifts in edaphic preferences. Using a phylogenetic framework and taking into consideration the biogeographical scenario explaining the distribution of the group as well as the distribution of pollinators, this study compares pollination strategies with substrate adaptations to develop hypotheses of the primary factors leading to speciation in Lapeirousia (Iridaceae), a genus of corm-bearing geophytes well represented in the Cape and presenting an important diversity of pollination syndromes and edaphic preferences. Methods Phylogenetic relationships are reconstructed within Lapeirousia using nuclear and plastid DNA sequence data. State-of-the-art methods in biogeography, divergence time estimation, character optimization and diversification rate assessments are used to examine the evolution of pollination syndromes and substrate shifts in the history of the group. Based on the phylogenetic results, ecological factors are compared for nine sister species pairs in Lapeirousia. Key Results Seventeen pollinator shifts and ten changes in substrate types were inferred during the evolution of the genus Lapeirousia. Of the nine species pairs examined, all show divergence in pollination syndromes, while only four pairs present different substrate types. Conclusions The available evidence points to a predominant influence of pollinator shifts over substrate types on the speciation process within Lapeirousia, contrary to previous studies that favoured a more important role for edaphic factors in these processes. This work also highlights the importance of biogeographical patterns in the study of pollination syndromes. PMID:24323246

  12. Speciation and rapid phenotypic differentiation in the yellow-rumped warbler Dendroica coronata complex.

    PubMed

    Milá, Borja; Smith, Thomas B; Wayne, Robert K

    2007-01-01

    The relative importance of the Pleistocene glacial cycles in driving avian speciation remains controversial, partly because species limits in many groups remain poorly understood, and because current taxonomic designations are often based on phenotypic characteristics of uncertain phylogenetic significance. We use mtDNA sequence data to examine patterns of genetic variation, sequence divergence and phylogenetic relationships between phenotypically distinct groups of the yellow-rumped warbler complex. Currently classified as a single species, the complex is composed of two North American migratory forms (myrtle warbler Dendroica coronata coronata and Audubon's warbler Dendroica coronata auduboni), and two largely sedentary forms: Dendroica coronata nigrifrons of Mexico, and Dendroica coronata goldmani of Guatemala. The latter are typically considered to be races of the Audubon's warbler based on plumage characteristics. However, mtDNA sequence data reveal that sedentary Mesoamerican forms are reciprocally monophyletic to each other and to migratory forms, from which they show a long history of isolation. In contrast, migratory myrtle and Audubon's warblers form a single cluster due to high levels of shared ancestral polymorphism as evidenced by widespread sharing of mtDNA haplotypes despite marked phenotypic differentiation. Sedentary and migratory forms diverged in the early Pleistocene, whereas phenotypic differentiation between the two migratory forms has occurred in the Holocene and is likely the result of geographical isolation and subsequent range expansion since the last glaciation. Our results underscore the importance of Quaternary climatic events in driving songbird speciation and indicate that plumage traits can evolve remarkably fast, thus rendering them potentially misleading for inferring systematic relationships. PMID:17181728

  13. Mitochondrial and Allozyme Genetics of Incipient Speciation in a Landlocked Population of Galaxias Truttaceus (Pisces: Galaxiidae)

    PubMed Central

    Ovenden, J. R.; White, RWG.

    1990-01-01

    Galaxias truttaceus is found in coastal rivers and streams in south-eastern Australia. It spawns at the head of estuaries in autumn and the larvae spend 3 months of winter at sea before returning to fresh water. In Tasmania there are landlocked populations of G. truttaceus in a cluster of geologically young lakes on the recently glaciated Central Plateau. These populations have no marine larval stage and spawn in the lakes in spring. Speciation due to land locking is thought to be a frequent occurrence within Galaxias. To investigate the nature of the speciation event which may be occurring within lake populations of G. truttaceus we studied the mitochondrial DNA (mtDNA) and allozyme diversity of both lake and stream populations. Using the presence or absence of restriction sites recognized by 13 six-base restriction endonucleases, we found 58 mtDNA haplotypes among 150 fish collected from 13 Tasmanian and one south-east Australian mainland stream populations. The most parsimonious network relating the haplotypes by site loss or gain was starlike in shape. We argue that this arrangement is best explained by selection upon slightly beneficial mutations within the mitochondrial genome. Gene diversity analysis under Wright's island model showed that the populations in each drainage were not genetically subdivided. Only two of these stream haplotypes were found among the 66 fish analyzed from four lake populations. Despite the extreme lack of mtDNA diversity in lake populations, the observed nuclear DNA heterozygosity of 40 lake fish (0.10355) was only slightly less than that of 82 stream fish (0.11635). In the short time (3000-7000 years) that the lake fish have been landlocked, random genetic drift in a finite, stable-sized population was probably not responsible for the lack of mtDNA diversity in the lake populations. We infer the lake populations have probably experienced at least one, severe, but transitory bottleneck possibly induced by natural selection for life

  14. Neptunium redox speciation at the illite surface

    NASA Astrophysics Data System (ADS)

    Marsac, Rémi; Banik, Nidhu lal; Lützenkirchen, Johannes; Marquardt, Christian Michael; Dardenne, Kathy; Schild, Dieter; Rothe, Joerg; Diascorn, Alexandre; Kupcik, Tomas; Schäfer, Thorsten; Geckeis, Horst

    2015-03-01

    Neptunium (Np(V)) sorption onto a purified illite is investigated as a function of pH (3-10) and [NpVO2+]tot(3 × 10-8-3 × 10-4 M) in 0.1 M NaCl under Ar atmosphere. After about one week reaction time, only insignificant variation of Np sorption is observed and the establishment of reaction equilibrium can be assumed. Surprisingly, solid-liquid distribution ratios (Rd) are clearly higher than those measured for Np(V) sorption onto illite under aerobic conditions. The observation that Rd increases with decreasing pe (pe = -log ae-) suggests partial reduction to Np(IV), although measured redox potentials (pe values) at a first glance suggest the predominance of Np(V). Reduction to Np(IV) at the illite surface could indeed be confirmed by X-ray absorption near-edge spectroscopy (XANES). Np speciation in presence of the purified Na-illite under given conditions is consistently described by applying the 2 sites protolysis non-electrostatic surface complexation and cation exchange model. Measured pe data are taken to calculate Np redox state and surface complexation constants for Np(IV) are derived by applying a data fitting procedure. Constants are very consistent with results obtained by applying an existing linear free energy relationship (LFER). Taking Np(IV) surface complexation constants into account shifts the calculated Np(V)/Np(IV) redox borderline in presence of illite surfaces by 3-5 pe units (0.2-0.3 V) towards redox neutral conditions. Our study suggests that Np(V) reduction in presence of a sorbing mineral phase is thermodynamically favored.

  15. Arsenic speciation and reactivity in poultry litter

    USGS Publications Warehouse

    Arai, Y.; Lanzirotti, A.; Sutton, S.; Davis, J.A.; Sparks, D.L.

    2003-01-01

    Recent U.S. government action to lower the maximum concentration levels (MCL) of total arsenic (As) (10 ppb) in drinking water has raised serious concerns about the agricultural use of As-containing biosolids such as poultry litter (PL). In this study, solid-state chemical speciation, desorbability, and total levels of As in PL and long-term amended soils were investigated using novel synchrotronbased probing techniques (microfocused (??) synchrotron X-ray fluorescence (SXRF) and ??-X-ray absorption near-edge structure (XANES) spectroscopies) coupled with chemical digestion and batch experiments. The total As levels in the PL were as high as ???50 mg kg-1, and As(II/III and V) was always concentrated in abundant needle-shaped microscopic particles (???20/ ??m x 850 ??m) associated with Ca, Cu, and Fe and to a lesser extent with S, CI, and Zn. Postedge XANES features of litter particles are dissimilar to those of the organo-As(V) compound in poultry feed (i.e., roxarsone), suggesting possible degradation/transformation of roxarsone in the litter and/or in poultry digestive tracts. The extent of As desorption from the litter increased with increasing time and pH from 4.5 to 7, but at most 15% of the total As was released after 5 d at pH 7, indicating the presence of insoluble phases and/or strongly retained soluble compounds. No significant As accumulation (< 15 mg kg-1) was found in long-term PL-a mended agricultural surface soils. This suggests that As in the PL may have undergone surface and subsurface transport processes. Our research results raise concerns about long-term PL amendment effects on As contamination in surrounding soilwater environments.

  16. sick: The Spectroscopic Inference Crank

    NASA Astrophysics Data System (ADS)

    Casey, Andrew R.

    2016-03-01

    There exists an inordinate amount of spectral data in both public and private astronomical archives that remain severely under-utilized. The lack of reliable open-source tools for analyzing large volumes of spectra contributes to this situation, which is poised to worsen as large surveys successively release orders of magnitude more spectra. In this article I introduce sick, the spectroscopic inference crank, a flexible and fast Bayesian tool for inferring astrophysical parameters from spectra. sick is agnostic to the wavelength coverage, resolving power, or general data format, allowing any user to easily construct a generative model for their data, regardless of its source. sick can be used to provide a nearest-neighbor estimate of model parameters, a numerically optimized point estimate, or full Markov Chain Monte Carlo sampling of the posterior probability distributions. This generality empowers any astronomer to capitalize on the plethora of published synthetic and observed spectra, and make precise inferences for a host of astrophysical (and nuisance) quantities. Model intensities can be reliably approximated from existing grids of synthetic or observed spectra using linear multi-dimensional interpolation, or a Cannon-based model. Additional phenomena that transform the data (e.g., redshift, rotational broadening, continuum, spectral resolution) are incorporated as free parameters and can be marginalized away. Outlier pixels (e.g., cosmic rays or poorly modeled regimes) can be treated with a Gaussian mixture model, and a noise model is included to account for systematically underestimated variance. Combining these phenomena into a scalar-justified, quantitative model permits precise inferences with credible uncertainties on noisy data. I describe the common model features, the implementation details, and the default behavior, which is balanced to be suitable for most astronomical applications. Using a forward model on low-resolution, high signal

  17. Plutonium Speciation in Support of Oxidative-Leaching Demonstration Test

    SciTech Connect

    Sinkov, Sergey I.

    2007-10-31

    Bechtel National, Inc. (BNI) is evaluating the plutonium speciation in caustic solutions that reasonably represent the process streams from the oxidative-leaching demonstration test. Battelle—Pacific Northwest Division (PNWD) was contracted to develop a spectrophotometric method to measure plutonium speciation at submicromolar (< 10-6 M) concentrations in alkaline solutions in the presence of chromate and carbonate. Data obtained from the testing will be used to identify the oxidation state of Pu(IV), Pu(V), and Pu(VI) species, which potentially could exist in caustic leachates. Work was initially conducted under contract number 24590-101-TSA-W000-00004 satisfying the needs defined in Appendix C of the Research and Technology Plan TSS A-219 to evaluate the speciation of chromium, plutonium, and manganese before and after oxidative leaching. In February 2007, the contract mechanism was switched to Pacific Northwest National Laboratory (PNNL) Operating Contract MOA: 24590-QL-HC9-WA49-00001.

  18. Rapid acceleration of plant speciation during the Anthropocene.

    PubMed

    Thomas, Chris D

    2015-08-01

    Speciation rates need to be considered when estimating human impacts on the numbers of species on Earth, given that past mass extinctions have been followed by the accelerated origination of new taxa. Here, I suggest that the Anthropocene is already exhibiting a greatly accelerated plant speciation rate due to agriculture, horticulture, and the human-mediated transport of species, followed by hybridisation. For example, more new plant species have come into existence in Europe over the past three centuries than have been documented as becoming extinct over the same period, even though most new hybrid-origin species are likely to remain undetected. Current speciation rates are unusually high and they could be higher than during or after previous mass extinctions. PMID:26115931

  19. The relationship of selenium tolerance and speciation in Lecythidaceae species.

    PubMed

    Németh, Anikó; García Reyes, Juan Francisco; Kosáry, Judit; Dernovics, Mihály

    2013-12-01

    Comparative study of selenium (Se) speciation in hyperaccumulator plants offers an interesting challenge from the analytical point of view. In our study the application of a sophisticated sample clean-up procedure and the combination of elemental and molecular mass spectrometric methods led to the identification of several new selenocompounds. The difference between the Se speciation of the primary accumulator Lecythis minor and the secondary accumulator Bertholletia excelsa confirmed the current opinion that the speciation pattern in hyperaccumulator plants is principally related to the mechanism of accumulation and not to taxonomy. The most abundant new selenocompounds were found to be the derivatives of selenohomocysteine (SeHCy) and selenomethionine (SeMet), including fatty acid metabolism related compounds. A series of SeHCy derived species containing multiple Se atoms (>2) was also detected and their structures were validated by the synthesis of their S-Se analogues. PMID:24136350

  20. 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...

  1. 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 ...

  2. Quantum Inference on Bayesian Networks

    NASA Astrophysics Data System (ADS)

    Yoder, Theodore; Low, Guang Hao; Chuang, Isaac

    2014-03-01

    Because quantum physics is naturally probabilistic, it seems reasonable to expect physical systems to describe probabilities and their evolution in a natural fashion. Here, we use quantum computation to speedup sampling from a graphical probability model, the Bayesian network. A specialization of this sampling problem is approximate Bayesian inference, where the distribution on query variables is sampled given the values e of evidence variables. Inference is a key part of modern machine learning and artificial intelligence tasks, but is known to be NP-hard. Classically, a single unbiased sample is obtained from a Bayesian network on n variables with at most m parents per node in time (nmP(e) - 1 / 2) , depending critically on P(e) , the probability the evidence might occur in the first place. However, by implementing a quantum version of rejection sampling, we obtain a square-root speedup, taking (n2m P(e) -1/2) time per sample. The speedup is the result of amplitude amplification, which is proving to be broadly applicable in sampling and machine learning tasks. In particular, we provide an explicit and efficient circuit construction that implements the algorithm without the need for oracle access.

  3. A Global Phylogeny of Leafmining Ectoedemia Moths (Lepidoptera: Nepticulidae): Exploring Host Plant Family Shifts and Allopatry as Drivers of Speciation

    PubMed Central

    Doorenweerd, Camiel; van Nieukerken, Erik J.; Menken, Steph B. J.

    2015-01-01

    Background Host association patterns in Ectoedemia (Lepidoptera: Nepticulidae) are also encountered in other insect groups with intimate plant relationships, including a high degree of monophagy, a preference for ecologically dominant plant families (e.g. Fagaceae, Rosaceae, Salicaceae, and Betulaceae) and a tendency for related insect species to feed on related host plant species. The evolutionary processes underlying these patterns are only partly understood, we therefore assessed the role of allopatry and host plant family shifts in speciation within Ectoedemia. Methodology Six nuclear and mitochondrial DNA markers with a total aligned length of 3692 base pairs were used to infer phylogenetic relationships among 92 species belonging to the subgenus Ectoedemia of the genus Ectoedemia, representing a thorough taxon sampling with a global coverage. The results support monophyletic species groups that are congruent with published findings based on morphology. We used the obtained phylogeny to explore host plant family association and geographical distribution to investigate if host shifts and allopatry have been instrumental in the speciation of these leafmining insects. Significance We found that, even though most species within species groups commonly feed on plants from one family, shifts to a distantly related host family have occasionally occurred throughout the phylogeny and such shifts are most commonly observed towards Betulaceae. The largest radiations have occurred within species groups that feed on Fagaceae, Rosaceae, and Salicaceae. Most species are restricted to one of the seven global biogeographic regions, but within species groups representatives are commonly found in different biogeographic regions. Although we find general patterns with regard to host use and biogeography, there are differences between clades that suggest that different drivers of speciation, and perhaps drivers that we did not examine, have shaped diversity patterns in different

  4. Solubility and speciation of carbonate in aqueous fluids at HP-HT

    NASA Astrophysics Data System (ADS)

    Daniel, Isabelle

    2013-06-01

    We report an integrated experimental and theoretical study of the equilibration of CaCO3 minerals with aqueous solutions (pure H2O or NaCl solutions) at HP-HT (0.5 to 8 GPa, 250 to 500° C). The fluid speciation was studied using in situ Raman spectroscopy in an externally heated membrane-type diamond anvil cell. The aqueous fluid and a calcite crystal were loaded in a rhenium gasket. P was determined from the calibrated shift of the carbonate ν1 symmetric stretching mode of aragonite and the T measured with a K-type thermocouple. Spectra were recorded using a LabRam HR800 Raman spectrometer (Horiba Jobin-Yvon) coupled to a Spectra Physics Ar+ laser. At equilibrium with an aragonite crystal, the Raman data show that bicarbonate is the most abundant species in low-pressure fluids below 4 GPa whereas carbonate becomes progressively dominant at higher pressure. After correction from their Raman cross-sections, the relative amounts of dissolved carbonate and bicarbonate were estimated from the areas of the ν1 and ν5 symmetric stretching Raman modes of the carbonate and bicarbonate ions, respectively. The presence of sodium chloride extends the pressure range of predominance for bicarbonate species in the fluid. The Raman data were also used to constrain a theoretical thermodynamic model of the fluid speciation in equilibrium with CaCO3. Revised thermodynamic properties of aqueous CO2 and HCO3-,data for the aqueous CaHCO3+complex from 4 to 90° C, and estimated dielectric constants of water, enabled an equation of state characterization of the standard Gibbs free energy of CaHCO3+at the conditions of the Raman study. At 300-400° C, the Raman speciation results were used to constrain equilibrium constants involving the carbonate ion. The results indicate that CO2 is a minor species in fluids in equilibrium with aragonite at 300-500° C and P >1 GPa. Instead, the CaHCO3+species becomes important at high pressures until carbonate ion becomes the dominant C-species. The

  5. XANES Identification of Plutonium Speciation in RFETS Samples

    SciTech Connect

    LoPresti, V.; Conradson, S.D.; Clark, D.L.

    2009-06-03

    Using primarily X-ray absorption near edge spectroscopy (XANES) with standards run in tandem with samples, probable plutonium speciation was determined for 13 samples from contaminated soil, acid-splash or fire-deposition building interior surfaces, or asphalt pads from the Rocky Flats Environmental Technology Site (RFETS). Save for extreme oxidizing situations, all other samples were found to be of Pu(IV) speciation, supporting the supposition that such contamination is less likely to show mobility off site. EXAFS analysis conducted on two of the 13 samples supported the validity of the XANES features employed as determinants of the plutonium valence.

  6. Actinide speciation in glass leach-layers: An EXAFS study

    SciTech Connect

    Biwer, B.M.; Soderholm, L.; Greegor, R.B.; Lytle, F.W.

    1996-12-31

    Uranium L{sub 3} X-ray absorption data were obtained from two borosilicate glasses, which are considered as models for radioactive wasteforms, both before and after leaching. Surface sensitivity to uranium speciation was attained by a novel application of simultaneous fluorescence and electron-yield detection. Changes in speciation are clearly discernible, from U(VI) in the bulk to (UO{sub 2}){sup 2+}-uranyl in the leach layer. The leach-layer uranium concentration variations with leaching times are also determined from the data.

  7. [Speciation and its mechanisms: conceptual background and recent advances].

    PubMed

    Colley, Eduardo; Fischer, Marta Luciane

    2013-10-01

    This paper presents a historical approach on general concepts of speciation and its mechanisms, from the primordial ideas to the most recent theories that seek to elucidate the origin of biodiversity. It is common knowledge that speciation is a controversial and complex issue that encompasses virtually all the lines of research of biology, in addition to geology and paleontology. The main objective of the paper is to clarify the theoretical concepts on the origin of the animal species, in the chronological order in which they became established throughout the whole of the development of evolutionary biology as a science. PMID:24473657

  8. Hybrid speciation and independent evolution in lineages of alpine butterflies.

    PubMed

    Nice, Chris C; Gompert, Zachariah; Fordyce, James A; Forister, Matthew L; Lucas, Lauren K; Buerkle, C Alex

    2013-04-01

    The power of hybridization between species to generate variation and fuel adaptation is poorly understood despite long-standing interest. There is, however, increasing evidence that hybridization often generates biodiversity, including via hybrid speciation. We tested the hypothesis of hybrid speciation in butterflies occupying extreme, high-altitude habitats in four mountain ranges in western North America with an explicit, probabilistic model, and genome-wide DNA sequence data. Using this approach, in concert with ecological experiments and observations and morphological data, we document three lineages of hybrid origin. These lineages have different genome admixture proportions and distinctive trait combinations that suggest unique and independent evolutionary histories. PMID:23550755

  9. Uranium speciation in glass corrosion layers: An XAFS study

    SciTech Connect

    Biwer, B.M.; Soderholm, L.; Greegor, R.B.; Lytle, F.W.

    1997-12-31

    Uranium L{sub 3} X-ray absorption data were obtained from two borosilicate glasses, which are considered as models for radioactive wasteforms, both before and after leaching. Surface sensitivity to uranium speciation was attained by a novel application of simultaneous fluorescence and electron-yield detection. Changes in speciation are clearly discernible, from U(VI) in the bulk to (UO{sub 2}){sup 2+}-uranyl in the corrosion layer. The uranium concentrations within the corrosion layer also show variations with leaching times that can be determined from the data.

  10. Inhibited emission of electromagnetic modes confined in subwavelength cavities

    SciTech Connect

    Le Thomas, N.; Houdre, R.

    2011-07-15

    We experimentally demonstrate the active inhibition of subwavelength confined cavity modes emission and quality factor enhancement by controlling the cavity optical surrounding. The intrinsic radiation angular spectrum of modes confined in planar photonics crystal cavities as well as its modifications depending on the environment are inferred via a transfer matrix modeling and k-space imaging.

  11. Mercury speciation on three European mining districts by XANES techniques

    NASA Astrophysics Data System (ADS)

    Esbri, J. M.; Garcia-Noguero, E. M.; Guerrero, B.; Kocman, D.; Bernaus, A.; Gaona, X.; Higueras, P.; Alvarez, R.; Loredo, J.; Horvat, M.; Ávila, M.

    2009-04-01

    The mobility, bioavailability and toxicity of mercury in the environment depend on the chemical species in which is present in soil, sediments, water or air. In this work we used synchrotron radiation to determine mercury species in geological samples of three mercury mining districts: Almadén (Spain), Idria (Slovenia) and Asturias (Spain). The aim of this study was to find differences on mobility and bioavailability of mercury on three mining districts with different type of mineralization. For this porpoises we selected samples of ore, calcines, soils and stream sediments from the three sites, completely characterized by the Almadén School of Mines, Josef Stefan Institute of Ljubljana and Oviedo School of Mines. Speciation of mercury was carried out on Synchrotron Laboratories of Hamburg (HASYLAB) by XANES techniques. Spectra of pure compounds [HgCl2, HgSO4, HgO, CH3HgCl, Hg2Cl2 (calomel), HgSred (cinnabar), HgSblack (metacinnabar), Hg2NCl0.5(SO4)0.3(MoO4)0.1(CO3)0.1(H2O) (mosesite), Hg3S2Cl2 (corderoite), Hg3(SO4)O2 (schuetteite) y Hg2ClO (terlinguaite)] were obtained on transmittance mode. The number and type of the compounds required to reconstruct experimental spectra for each sample was obtained by PCA analysis and linear fitting of minimum quadratics of the pure compounds spectra. This offers a semiquantitative approach to the mineralogical constitution of each analyzed sample. The results put forward differences on the efficiency of roasting furnaces from the three studied sites, evidenced by the presence of metacinnabar on the less efficient (Almadén and Asturias) and absence on the most efficient (Idria). For the three studied sites, sulfide species (cinnabar and metacinnabar) were largely more abundant than soluble species (chlorides and sulfates). On the other hand, recent results on the mobility of both Hg and As on the target sites will be presented. These results correlate with the related chemical species found by XANES techniques.

  12. Tracing the first step to speciation: ecological and genetic differentiation of a salamander population in a small forest.

    PubMed

    Steinfartz, Sebastian; Weitere, Markus; Tautz, Diethard

    2007-11-01

    Mechanisms and processes of ecologically driven adaptive speciation are best studied in natural situations where the splitting process is still occurring, i.e. before complete reproductive isolation is achieved. Here, we present a case of an early stage of adaptive differentiation under sympatric conditions in the fire salamander, Salamandra salamandra, that allows inferring the underlying processes for the split. Larvae of S. salamandra normally mature in small streams until metamorphosis, but in an old, continuous forest area near Bonn (the Kottenforst), we found salamander larvae not only in small streams but also in shallow ponds, which are ecologically very different from small streams. Common-environment experiments with larvae from both habitat types reveal specific adaptations to these different ecological conditions. Mitochondrial and microsatellite analyses show that the two ecologically differentiated groups also show signs of genetic differentiation. A parallel analysis of animals from a neighbouring much larger forest area (the Eifel), in which larvae mature only in streams, shows no signs of genetic differentiation, indicating that gene flow between ecologically similar types can occur over large distances. Hence, geographical factors cannot explain the differential larval habitat adaptations in the Kottenforst, in particular since adult life and mating of S. salamandra is strictly terrestrial and not associated with larval habitats. We propose therefore that the evolution of these adaptations was coupled with the evolution of cues for assortative mating which would be in line with models of sympatric speciation that suggest a co-evolution of habitat adaptations and associated mating signals. PMID:17877714

  13. Bayesian Inference of Tumor Hypoxia

    NASA Astrophysics Data System (ADS)

    Gunawan, R.; Tenti, G.; Sivaloganathan, S.

    2009-12-01

    Tumor hypoxia is a state of oxygen deprivation in tumors. It has been associated with aggressive tumor phenotypes and with increased resistance to conventional cancer therapies. In this study, we report on the application of Bayesian sequential analysis in estimating the most probable value of tumor hypoxia quantification based on immunohistochemical assays of a biomarker. The `gold standard' of tumor hypoxia assessment is a direct measurement of pO2 in vivo by the Eppendorf polarographic electrode, which is an invasive technique restricted to accessible sites and living tissues. An attractive alternative is immunohistochemical staining to detect proteins expressed by cells during hypoxia. Carbonic anhydrase IX (CAIX) is an enzyme expressed on the cell membrane during hypoxia to balance the immediate extracellular microenvironment. CAIX is widely regarded as a surrogate marker of chronic hypoxia in various cancers. The study was conducted with two different experimental procedures. The first data set was a group of three patients with invasive cervical carcinomas, from which five biopsies were obtained. Each of the biopsies was fully sectioned and from each section, the proportion of CAIX-positive cells was estimated. Measurements were made by image analysis of multiple deep sections cut through these biopsies, labeled for CAIX using both immunofluorescence and immunohistochemical techniques [1]. The second data set was a group of 24 patients, also with invasive cervical carcinomas, from which two biopsies were obtained. Bayesian parameter estimation was applied to obtain a reliable inference about the proportion of CAIX-positive cells within the carcinomas, based on the available biopsies. From the first data set, two to three biopsies were found to be sufficient to infer the overall CAIX percentage in the simple form: best estimate±uncertainty. The second data-set led to a similar result in 70% of the cases. In the remaining cases Bayes' theorem warned us

  14. Infering Networks From Collective Dynamics

    NASA Astrophysics Data System (ADS)

    Timme, Marc

    How can we infer direct physical interactions between pairs of units from only knowing the units' time series? Here we present a dynamical systems' view on collective network dynamics, and propose the concept of a dynamics' space to reveal interaction networks from time series. We present two examples: one, where the time series stem from standard ordinary differential equations, and a second, more abstract, where the time series exhibits only partial information about the units' states. We apply the latter to neural circuit dynamics where the observables are spike timing data, i.e. only a discrete, state-dependent outputs of the neurons. These results may help revealing network structure for systems where direct access to dynamics is simpler than to connectivity, cf.. This is work with Jose Casadiego, Srinivas Gorur Shandilya, Mor Nitzan, Hauke Haehne and Dimitra Maoutsa. Supported by Grants of the BMBF (Future Compliant Power Grids - CoNDyNet) and by the Max Planck Society to MT.

  15. Inferred properties of stellar granulation

    SciTech Connect

    Gray, D.F.; Toner, C.G.

    1985-06-01

    Apparent characteristics of stellar granulation in F and G main-sequence stars are inferred directly from observed spectral-line asymmetries and from comparisons of numerical simulations with the observations: (1) the apparent granulation velocity increases with effective temperature, (2) the dispersion of granule velocities about their mean velocity of rise increases with the apparent granulation velocity, (3) the mean velocity of rise of granules must be less than the total line broadening, (4) the apparent velocity difference between granules and dark lanes corresponds to the granulation velocity deduced from stellar line bisectors, (5) the dark lanes show velocities of fall approximately twice as large as the granule rise velocities, (6) the light contributed to the stellar flux by the granules is four to ten times more than the light from the dark lanes. Stellar rotation is predicted to produce distortions in the line bisectors which may give information on the absolute velocity displacements of the line bisectors. 37 references.

  16. Structural inference for uncertain networks

    NASA Astrophysics Data System (ADS)

    Martin, Travis; Ball, Brian; Newman, M. E. J.

    2016-01-01

    In the study of networked systems such as biological, technological, and social networks the available data are often uncertain. Rather than knowing the structure of a network exactly, we know the connections between nodes only with a certain probability. In this paper we develop methods for the analysis of such uncertain data, focusing particularly on the problem of community detection. We give a principled maximum-likelihood method for inferring community structure and demonstrate how the results can be used to make improved estimates of the true structure of the network. Using computer-generated benchmark networks we demonstrate that our methods are able to reconstruct known communities more accurately than previous approaches based on data thresholding. We also give an example application to the detection of communities in a protein-protein interaction network.

  17. Transdimensional inference in the geosciences.

    PubMed

    Sambridge, M; Bodin, T; Gallagher, K; Tkalcic, H

    2013-02-13

    Seismologists construct images of the Earth's interior structure using observations, derived from seismograms, collected at the surface. A common approach to such inverse problems is to build a single 'best' Earth model, in some sense. This is despite the fact that the observations by themselves often do not require, or even allow, a single best-fit Earth model to exist. Interpretation of optimal models can be fraught with difficulties, particularly when formal uncertainty estimates become heavily dependent on the regularization imposed. Similar issues occur across the physical sciences with model construction in ill-posed problems. An alternative approach is to embrace the non-uniqueness directly and employ an inference process based on parameter space sampling. Instead of seeking a best model within an optimization framework, one seeks an ensemble of solutions and derives properties of that ensemble for inspection. While this idea has itself been employed for more than 30 years, it is now receiving increasing attention in the geosciences. Recently, it has been shown that transdimensional and hierarchical sampling methods have some considerable benefits for problems involving multiple parameter types, uncertain data errors and/or uncertain model parametrizations, as are common in seismology. Rather than being forced to make decisions on parametrization, the level of data noise and the weights between data types in advance, as is often the case in an optimization framework, the choice can be informed by the data themselves. Despite the relatively high computational burden involved, the number of areas where sampling methods are now feasible is growing rapidly. The intention of this article is to introduce concepts of transdimensional inference to a general readership and illustrate with particular seismological examples. A growing body of references provide necessary detail. PMID:23277604

  18. Peripatric speciation of an endemic species driven by Pleistocene climate change: The case of the Mexican prairie dog (Cynomys mexicanus).

    PubMed

    Castellanos-Morales, Gabriela; Gámez, Niza; Castillo-Gámez, Reyna A; Eguiarte, Luis E

    2016-01-01

    The hypothesis that endemic species could have originated by the isolation and divergence of peripheral populations of widespread species can be tested through the use of ecological niche models (ENMs) and statistical phylogeography. The joint use of these tools provides complementary perspectives on historical dynamics and allows testing hypotheses regarding the origin of endemic taxa. We used this approach to infer the historical processes that have influenced the origin of a species endemic to the Mexican Plateau (Cynomys mexicanus) and its divergence from a widespread ancestor (Cynomys ludovicianus), and to test whether this endemic species originated through peripatric speciation. We obtained genetic data for 295 individuals for two species of black-tailed prairie dogs (C. ludovicianus and C. mexicanus). Genetic data consisted of mitochondrial DNA sequences (cytochrome b and control region), and 10 nuclear microsatellite loci. We estimated dates of divergence between species and between lineages within each species and performed ecological niche modelling (Present, Last Glacial Maximum and Last Interglacial) to determine changes in the distribution range of both species during the Pleistocene. Finally, we used Bayesian inference methods (DIYABC) to test different hypotheses regarding the divergence and demographic history of these species. Data supported the hypothesis of the origin of C. mexicanus from a peripheral population isolated during the Pleistocene [∼230,000 years ago (0.1-0.43 Ma 95% HPD)], with a Pleistocene-Holocene (∼9,000-11,000 years ago) population expansion (∼10-fold increase in population size). We identified the presence of two possible refugia in the southern area of the distribution range of C. ludovicianus and another, consistent with the distribution range of C. mexicanus. Our analyses suggest that Pleistocene climate change had a strong impact in the distribution of these species, promoting peripatric speciation for the origin of

  19. F-Mode Eikonal Heliotomography

    NASA Astrophysics Data System (ADS)

    de Ridder, S.; Zhao, J.

    2014-12-01

    We investigate 5 days of Doppler measurements geo-tracked for a sunspot. The data is cross -correlated to create time-distance impulse responses of wave propagation in the plasma. We focus on imaging the f-mode (surface gravity mode), which is separated from the other modes by k-ω filtering. Recent developments for surface wave imaging in earth-seismology include the development of an eikonal tomography technique. Eikonal tomography relies on evaluation of the local spatial derivatives of a traveltime surface to directly infer the slowness of wave-propagation. Whereas earth-seismology relies on increasing high signal-to-noise ratio (SNR) by cross-correlating long-time series, helioseismology relies on stacking over geometrically similar virtual sources. We assume there are two symmetries in the geometry of virtual sources around a sunspot. The first is a radial symmetry centered at the sunspot. The second is a radial symmetry of propagation around each virtual source. Because we are interested in the effect of sunspots on wave-propagation, we keep the averaging along the second symmetry axis to a minimum, and rely heavily on averaging each virtual source with equal distance from the sunspot. We will investigate the spatial variation of f-mode dispersion in a radial geometry with the sunspot at the center by creating f-mode velocity maps at different frequencies.

  20. Microscale characterization of sulfur speciation in lake sediments.

    PubMed

    Zeng, Teng; Arnold, William A; Toner, Brandy M

    2013-02-01

    Prairie pothole lakes (PPLs) are naturally sulfur-enriched wetlands in the glaciated prairie region of North America. High sulfate levels and dynamic hydrogeochemistry in combination render PPLs a unique environment to explore the speciation of sedimentary sulfur (S). The goals of this research were to define and quantify the solid-phase S pools in PPL sediments and track seasonal dynamics of S speciation. A quantitative X-ray microprobe method was developed based on S 1s X-ray absorption near-edge structure (XANES) spectroscopy and multienergy X-ray fluorescence mapping. Three S pools-pyritic S, reduced organic S (organic mono- and disulfide), and oxidized S (inorganic sulfate, ester sulfate, and sulfonate)-were identified in PPL sediments. No significant seasonal variation was evident for total S, but S speciation showed a seasonal response. During the spring-summer transition, the reduced organic S decreased from 55 to 15 mol %, with a concomitant rise in the oxidized S. During the summer-fall transition, the trend reversed and the reduced organic S grew to 75 mol % at the expense of the oxidized S. The pyritic S, on the other hand, remained relatively constant (∼22 mol %) over time. The seasonal changes in S speciation have strong potential to force the cycling of elements such as mercury in prairie wetlands. PMID:23282039

  1. PM 2.5 ORGANIC SPECIATION INTERCOMPARISON RESULTS

    EPA Science Inventory

    This abstract describes a poster on results to a laboratory intercomparison of organic aerosol speciation analysis to be presented at the 2006 International Aerosol Conference sponsored by the American Association for Aerosol Research in St. Paul, Minnesota on September 10-15. T...

  2. Latitude, elevational climatic zonation and speciation in New World vertebrates.

    PubMed

    Cadena, Carlos Daniel; Kozak, Kenneth H; Gómez, Juan Pablo; Parra, Juan Luis; McCain, Christy M; Bowie, Rauri C K; Carnaval, Ana C; Moritz, Craig; Rahbek, Carsten; Roberts, Trina E; Sanders, Nathan J; Schneider, Christopher J; VanDerWal, Jeremy; Zamudio, Kelly R; Graham, Catherine H

    2012-01-01

    Many biodiversity hotspots are located in montane regions, especially in the tropics. A possible explanation for this pattern is that the narrow thermal tolerances of tropical species and greater climatic stratification of tropical mountains create more opportunities for climate-associated parapatric or allopatric speciation in the tropics relative to the temperate zone. However, it is unclear whether a general relationship exists among latitude, climatic zonation and the ecology of speciation. Recent taxon-specific studies obtained different results regarding the role of climate in speciation in tropical versus temperate areas. Here, we quantify overlap in the climatic distributions of 93 pairs of sister species of mammals, birds, amphibians and reptiles restricted to either the New World tropics or to the Northern temperate zone. We show that elevational ranges of tropical- and temperate-zone species do not differ from one another, yet the temperature range experienced by species in the temperate zone is greater than for those in the tropics. Moreover, tropical sister species tend to exhibit greater similarity in their climatic distributions than temperate sister species. This pattern suggests that evolutionary conservatism in the thermal niches of tropical taxa, coupled with the greater thermal zonation of tropical mountains, may result in increased opportunities for allopatric isolation, speciation and the accumulation of species in tropical montane regions. Our study exemplifies the power of combining phylogenetic and spatial datasets of global climatic variation to explore evolutionary (rather than purely ecological) explanations for the high biodiversity of tropical montane regions. PMID:21632626

  3. Speciation Mapping of Environmental Samples Using XANES Imaging

    EPA Science Inventory

    Fast X-ray detectors with large solid angles and high dynamic ranges open the door to XANES imaging, in which millions of spectra are collected to image the speciation of metals at micrometre resolution, over areas up to several square centimetres. This paper explores how such mu...

  4. LINKING WATERFOWL WITH CONTAMINANT SPECIATION IN RIPARIAN SOILS

    EPA Science Inventory

    This report summarizes the results of Mine Waste Technology Program (MWTP) Activity III, Project 38, Linking Waterfowl with Contaminant Speciation in Riparian Soils, implemented and funded by the U.S. Environmental Protection Agency (EPA) and jointly administered by EPA and the U...

  5. Capillary electrophoresis application in metal speciation and complexation characterization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Capillary electrophoresis is amenable to the separation of metal ionic species and the characterization of metal-ligand interactions. This book chapter reviews and discusses three representative case studies in applications of CE technology in speciation and reactions of metal with organic molecules...

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

    SciTech Connect

    Weng, Huanxin; 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 the 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.

  7. FINE PARTICULATE MATTER (PM) AND ORGANIC SPECIATION OF FIREPLACE EMISSIONS

    EPA Science Inventory

    This paper presents a summary of fireplace particle size and organic speciation data gathered to date in an on-going project. Tests are being conducted in a residential wood combustion (RWC) laboratory on three factory-built fireplaces. RWC wood smoke particles <10?m (PM10) con...

  8. Lead Speciation And Bioavailability In Apatite-Amended Sediments

    EPA Science Inventory

    The in situ sequestration of lead (Pb) in sediment with a phosphate amendment was investigated by Pb speciation and bioavailability. Sediment Pb in preamendment samples was identified as galena (PbS) with trace amounts of absorbed Pb. Sediment exposed to atmospheric conditions ...

  9. Speciation And Bioavailability Of Zinc In Amended Sediments

    EPA Science Inventory

    The speciation and bioavailability of zinc (Zn) in smelter-contaminated sediments was investigated as a function of phosphate (apatite) and organic amendment loading rate. Zinc species identified in preamendment sediment were zinc hydroxide-like phases, sphalerite, and zinc sorbe...

  10. The role of gene expression in ecological speciation

    PubMed Central

    Pavey, Scott A; Collin, Hélène; Nosil, Patrik; Rogers, Sean M

    2010-01-01

    Ecological speciation is the process by which barriers to gene flow between populations evolve due to adaptive divergence via natural selection. A relatively unexplored area in ecological speciation is the role of gene expression. Gene expression may be associated with ecologically important phenotypes not evident from morphology and play a role during colonization of new environments. Here we review two potential roles of gene expression in ecological speciation: (1) its indirect role in facilitating population persistence and (2) its direct role in contributing to genetically based reproductive isolation. We find indirect evidence that gene expression facilitates population persistence, but direct tests are lacking. We also find clear examples of gene expression having effects on phenotypic traits and adaptive genetic divergence, but links to the evolution of reproductive isolation itself remain indirect. Gene expression during adaptive divergence seems to often involve complex genetic architectures controlled by gene networks, regulatory regions, and “eQTL hotspots.” Nonetheless, we review how approaches for isolating the functional mutations contributing to adaptive divergence are proving to be successful. The study of gene expression has promise for increasing our understanding ecological speciation, particularly when integrative approaches are applied. PMID:20860685

  11. A recombination suppressor contributes to ecological speciation in OSTRINIA moths.

    PubMed

    Wadsworth, C B; Li, X; Dopman, E B

    2015-06-01

    Despite unparalleled access to species' genomes in our post-genomic age, we often lack adequate biological explanations for a major hallmark of the speciation process-genetic divergence. In the presence of gene flow, chromosomal rearrangements such as inversions are thought to promote divergence and facilitate speciation by suppressing recombination. Using a combination of genetic crosses, phenotyping of a trait underlying ecological isolation, and population genetic analysis of wild populations, we set out to determine whether evidence supports a role for recombination suppressors during speciation between the Z and E strains of European corn borer moth (Ostrinia nubilalis). Our results are consistent with the presence of an inversion that has contributed to accumulation of ecologically adaptive alleles and genetic differentiation across roughly 20% of the Ostrinia sex chromosome (~4 Mb). Patterns in Ostrinia suggest that chromosomal divergence may involve two separate phases-one driving its transient origin through local adaptation and one determining its stable persistence through differential introgression. As the evolutionary rate of rearrangements in lepidopteran genomes appears to be one of the fastest among eukaryotes, structural mutations may have had a disproportionate role during adaptive divergence and speciation in Ostrinia and in other moths and butterflies. PMID:25626887

  12. A recombination suppressor contributes to ecological speciation in OSTRINIA moths

    PubMed Central

    Wadsworth, C B; Li, X; Dopman, E B

    2015-01-01

    Despite unparalleled access to species' genomes in our post-genomic age, we often lack adequate biological explanations for a major hallmark of the speciation process—genetic divergence. In the presence of gene flow, chromosomal rearrangements such as inversions are thought to promote divergence and facilitate speciation by suppressing recombination. Using a combination of genetic crosses, phenotyping of a trait underlying ecological isolation, and population genetic analysis of wild populations, we set out to determine whether evidence supports a role for recombination suppressors during speciation between the Z and E strains of European corn borer moth (Ostrinia nubilalis). Our results are consistent with the presence of an inversion that has contributed to accumulation of ecologically adaptive alleles and genetic differentiation across roughly 20% of the Ostrinia sex chromosome (~4 Mb). Patterns in Ostrinia suggest that chromosomal divergence may involve two separate phases—one driving its transient origin through local adaptation and one determining its stable persistence through differential introgression. As the evolutionary rate of rearrangements in lepidopteran genomes appears to be one of the fastest among eukaryotes, structural mutations may have had a disproportionate role during adaptive divergence and speciation in Ostrinia and in other moths and butterflies. PMID:25626887

  13. Speciation dynamics and biogeography of Neotropical spiral gingers (Costaceae).

    PubMed

    André, Thiago; Salzman, Shayla; Wendt, Tânia; Specht, Chelsea D

    2016-10-01

    Species can arise via the divisive effects of allopatry as well as due to ecological and/or reproductive character displacement within sympatric populations. Two separate lineages of Costaceae are native to the Neotropics; an early-diverging clade endemic to South America (consisting of ca. 16 species in the genera Monocostus, Dimerocostus and Chamaecostus); and the Neotropical Costus clade (ca. 50 species), a diverse assemblage of understory herbs comprising nearly half of total familial species richness. We use a robust dated molecular phylogeny containing most of currently known species to inform macroevolutionary reconstructions, enabling us to examine the context of speciation in Neotropical lineages. Analyses of speciation rate revealed a significant variation among clades, with a rate shift at the most recent common ancestor of the Neotropical Costus clade. There is an overall predominance of allopatric speciation in the South American clade, as most species display little range overlap. In contrast, sympatry is much higher within the Neotropical Costus clade, independent of node age. Our results show that speciation dynamics during the history of Costaceae is strongly heterogeneous, and we suggest that the Costus radiation in the Neotropics arose at varied geographic contexts. PMID:27400627

  14. Speciational view of macroevolution: Are micro and macroevolution decoupled?

    NASA Astrophysics Data System (ADS)

    Schwämmle, V.; Brigatti, E.

    2006-07-01

    We introduce a simple computational model that, with microscopic dynamics driven by natural selection and mutation alone, allows the description of true speciation events. A statistical analysis of the evolutionary tree so generated captures realistic features showing power laws for frequency distributions in time and size. Finally, some possible interpretations of the absence of punctuated dynamics with mass extinctions are worked out.

  15. Speciation of volatile organic compounds from poultry production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The air consent agreement between EPA and large animal feeding operations (AFO) is designed to determine at what level compounds are being emitted from these facilities. However, the methodology used for quantifying total non-methane hydrocarbons and speciation of volatile organic compounds (VOC) n...

  16. Screening of rice cultivars for grain arsenic concentration and speciation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recently, there has been growing interest in the concentration and speciation of arsenic in rice grain because of concerns with food quality and interest in minimizing any potential risk from dietary exposure. Our objective was to screen a range of rice varieties from the USDA world collection for ...

  17. ANNUAL REPORT. ACTINIDE-ALUMINATE SPECIATION IN ALKALINE RADIOACTIVE WASTE

    EPA Science Inventory

    Highly alkaline radioactive waste tanks contain a number of transuranic species, in particular U, Np, Pu, and Am-the exact forms of which are currently unknown. Knowledge of actinide speciation under highly alkaline conditions is essential towards understanding and predicting the...

  18. EXAMINATION OF CHANGES IN AS SPECIATION IN SULFIDIC SOLUTIONS

    EPA Science Inventory

    The fate of arsenic (As) in the environment, its bioavailability and toxicity is fundamentally linked to its speciation. As in aerobic environments is predominantly arsenate (As(V)), however under reducing conditions arsenite (As(III)) species dominate. In sulfidic environments t...

  19. Bayesian Nonparametric Inference – Why and How

    PubMed Central

    Müller, Peter; Mitra, Riten

    2013-01-01

    We review inference under models with nonparametric Bayesian (BNP) priors. The discussion follows a set of examples for some common inference problems. The examples are chosen to highlight problems that are challenging for standard parametric inference. We discuss inference for density estimation, clustering, regression and for mixed effects models with random effects distributions. While we focus on arguing for the need for the flexibility of BNP models, we also review some of the more commonly used BNP models, thus hopefully answering a bit of both questions, why and how to use BNP. PMID:24368932

  20. Inference engine using optical array logic

    NASA Astrophysics Data System (ADS)

    Iwata, Masaya; Tanida, Jun; Ichioka, Yoshiki

    1990-07-01

    An implementation method for an inference engine using optical array logic is presented. Optical array logic is a technique for parallel neighborhood operation using spatial coding and 2-D correlation. For efficient execution of inference in artificial intelligence problems, a large number of data must be searched effectively. To achieve this demand, a template matching technique is applied to the inference operation. By introducing a new function of data conversion, the inference operation can be implemented with optical array logic, which utilizes parallelism in optical techniques.

  1. Inference-Based Teacher Professionalism: How Professional Practitioners in Religious Education Reflect in Action

    ERIC Educational Resources Information Center

    Heil, Stefan; Ziebertz, Hans-Georg

    2004-01-01

    A theory of professional action is developed based on the 3 modes of inference: abduction, induction, and deduction. The theory explains how professionals reflect in action by combining a single case to their professional repertoire. With teachers in religious education (RE), the problem is focused on how they link students' new and individual…

  2. MultiNest: Efficient and Robust Bayesian Inference

    NASA Astrophysics Data System (ADS)

    Feroz, F.; Hobson, M. P.; Bridges, M.

    2011-09-01

    We present further development and the first public release of our multimodal nested sampling algorithm, called MultiNest. This Bayesian inference tool calculates the evidence, with an associated error estimate, and produces posterior samples from distributions that may contain multiple modes and pronounced (curving) degeneracies in high dimensions. The developments presented here lead to further substantial improvements in sampling efficiency and robustness, as compared to the original algorithm presented in Feroz & Hobson (2008), which itself significantly outperformed existing MCMC techniques in a wide range of astrophysical inference problems. The accuracy and economy of the MultiNest algorithm is demonstrated by application to two toy problems and to a cosmological inference problem focusing on the extension of the vanilla LambdaCDM model to include spatial curvature and a varying equation of state for dark energy. The MultiNest software is fully parallelized using MPI and includes an interface to CosmoMC. It will also be released as part of the SuperBayeS package, for the analysis of supersymmetric theories of particle physics, at this http URL.

  3. Strategies in Seismic Inference of Supergranular Flows on the Sun

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Jishnu; Hanasoge, Shravan M.

    2016-08-01

    Observations of the solar surface reveal the presence of flows with length scales of around 35 Mm, commonly referred to as supergranules. Inferring the subsurface flow profile of supergranules from measurements of the surface and photospheric wavefield is an important challenge faced by helioseismology. Traditionally, the inverse problem has been approached by studying the linear response of seismic waves in a horizontally translationally invariant background to the presence of the supergranule; following an iterative approach that does not depend on horizontal translational invariance might perform better, since the misfit can be analyzed post iterations. In this work, we construct synthetic observations using a reference supergranule and invert for the flow profile using surface measurements of travel times of waves belonging to modal ridges f (surface gravity) and p 1 through p 7 (acoustic). We study the extent to which individual modes and their combinations contribute to infer the flow. We show that this method of nonlinear iterative inversion tends to underestimate the flow velocities, as well as inferring a shallower flow profile, with significant deviations from the reference supergranule near the surface. We carry out a similar analysis for a sound-speed perturbation and find that analogous near-surface deviations persist, although the iterations converge faster and more accurately. We conclude that a better approach to inversion would be to expand the supergranule profile in an appropriate basis, thereby reducing the number of parameters being inverted for and appropriately regularizing them.

  4. Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts

    PubMed Central

    Pool, John E.; Nielsen, Rasmus

    2009-01-01

    After migrant chromosomes enter a population, they are progressively sliced into smaller pieces by recombination. Therefore, the length distribution of “migrant tracts” (chromosome segments with recent migrant ancestry) contains information about historical patterns of migration. Here we introduce a theoretical framework describing the migrant tract length distribution and propose a likelihood inference method to test demographic hypotheses and estimate parameters related to a historical change in migration rate. Applying this method to data from the hybridizing subspecies Mus musculus domesticus and M. m. musculus, we find evidence for an increase in the rate of hybridization. Our findings could indicate an evolutionary trajectory toward fusion rather than speciation in these taxa. PMID:19087958

  5. Protein inference: A protein quantification perspective.

    PubMed

    He, Zengyou; Huang, Ting; Liu, Xiaoqing; Zhu, Peijun; Teng, Ben; Deng, Shengchun

    2016-08-01

    In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis. In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/. PMID:26935399

  6. Speciation with gene flow in whiptail lizards from a Neotropical xeric biome.

    PubMed

    Oliveira, Eliana F; Gehara, Marcelo; São-Pedro, Vinícius A; Chen, Xin; Myers, Edward A; Burbrink, Frank T; Mesquita, Daniel O; Garda, Adrian A; Colli, Guarino R; Rodrigues, Miguel T; Arias, Federico J; Zaher, Hussam; Santos, Rodrigo M L; Costa, Gabriel C

    2015-12-01

    Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well-delimited lineages (Northeast and Southwest) that have diverged along the Cerrado-Caatinga border during the Mid-Late Miocene (6-14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado-Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process. PMID:26502084

  7. Abundance and Speciation of Water and Sulfate at Gusev Crater and Meridiani Planum

    NASA Technical Reports Server (NTRS)

    Ming, D. W.; Clark, B. C.; Klingelhoefer, G.; Gellert, R.; Rodionov, D.; Schroeder, C.; deSouza, P.; Yen, A.

    2005-01-01

    A major science goal of the Mars Exploration Rover (MER) mission is to search for evidence of water activity, and direct mineralogical evidence for aqueous activity has been reported for Meridiani Planum in the form of the iron sulfate hydroxide mineral jarosite and at Gusev crater in the form of goethite. The Spirit and Opportunity rovers have each collected 110+ Moessbauer (MB) and 75+ Alpha Particle X-Ray Spectrometer (APXS) spectra from Gusev crater and Meridiani Planum [1 - 4]. In this abstract, we use mineralogical and elemental data, primarily from the Moessbauer and APXS instruments, to infer the speciation and estimate the abundance of sulfate and water (as either the H2O molecule or the hydroxyl anion) at Gusev crater and Meridiani Planum. Throughout the abstract, we adopt a format for mineral formulas that shows water explicitly rather than the usual practice of structure-based formulas (e.g., for goethite we write Fe2O3xH2O instead of FeOOH).

  8. Speciation and domestication in maize and its wild relatives: evidence from the globulin-1 gene.

    PubMed Central

    Hilton, H; Gaut, B S

    1998-01-01

    The grass genus Zea contains the domesticate maize and several wild taxa indigenous to Central and South America. Here we study the genetic consequences of speciation and domestication in this group by sampling DNA sequences from four taxa-maize (Zea mays ssp. mays), its wild progenitor (Z. mays ssp. parviglumis), a more distant species within the genus (Z. luxurians), and a representative of the sister genus (Tripsacum dactyloides). We sampled a total of 26 sequences from the glb1 locus, which encodes a nonessential seed storage protein. Within the Zea taxa sampled, the progenitor to maize contains the most sequence diversity. Maize contains 60% of the level of genetic diversity of its progenitor, and Z. luxurians contains even less diversity (32% of the level of diversity of Z. mays ssp. parviglumis). Sequence variation within the glb1 locus is consistent with neutral evolution in all four taxa. The glb1 data were combined with adh1 data from a previous study to make inferences about the population genetic histories of these taxa. Comparisons of sequence data between the two morphologically similar wild Zea taxa indicate that the species diverged approximately 700, 000 years ago from a common ancestor of intermediate size to their present populations. Conversely, the domestication of maize was a recent event that could have been based on a very small number of founding individuals. Maize retained a substantial proportion of the genetic variation of its progenitor through this founder event, but diverged rapidly in morphology. PMID:9755214

  9. Forward and Backward Inference in Spatial Cognition

    PubMed Central

    Penny, Will D.; Zeidman, Peter; Burgess, Neil

    2013-01-01

    This paper shows that the various computations underlying spatial cognition can be implemented using statistical inference in a single probabilistic model. Inference is implemented using a common set of ‘lower-level’ computations involving forward and backward inference over time. For example, to estimate where you are in a known environment, forward inference is used to optimally combine location estimates from path integration with those from sensory input. To decide which way to turn to reach a goal, forward inference is used to compute the likelihood of reaching that goal under each option. To work out which environment you are in, forward inference is used to compute the likelihood of sensory observations under the different hypotheses. For reaching sensory goals that require a chaining together of decisions, forward inference can be used to compute a state trajectory that will lead to that goal, and backward inference to refine the route and estimate control signals that produce the required trajectory. We propose that these computations are reflected in recent findings of pattern replay in the mammalian brain. Specifically, that theta sequences reflect decision making, theta flickering reflects model selection, and remote replay reflects route and motor planning. We also propose a mapping of the above computational processes onto lateral and medial entorhinal cortex and hippocampus. PMID:24348230

  10. Inferring Learners' Knowledge from Their Actions

    ERIC Educational Resources Information Center

    Rafferty, Anna N.; LaMar, Michelle M.; Griffiths, Thomas L.

    2015-01-01

    Watching another person take actions to complete a goal and making inferences about that person's knowledge is a relatively natural task for people. This ability can be especially important in educational settings, where the inferences can be used for assessment, diagnosing misconceptions, and providing informative feedback. In this paper, we…

  11. Local and Global Thinking in Statistical Inference

    ERIC Educational Resources Information Center

    Pratt, Dave; Johnston-Wilder, Peter; Ainley, Janet; Mason, John

    2008-01-01

    In this reflective paper, we explore students' local and global thinking about informal statistical inference through our observations of 10- to 11-year-olds, challenged to infer the unknown configuration of a virtual die, but able to use the die to generate as much data as they felt necessary. We report how they tended to focus on local changes…

  12. The Impact of Disablers on Predictive Inference

    ERIC Educational Resources Information Center

    Cummins, Denise Dellarosa

    2014-01-01

    People consider alternative causes when deciding whether a cause is responsible for an effect (diagnostic inference) but appear to neglect them when deciding whether an effect will occur (predictive inference). Five experiments were conducted to test a 2-part explanation of this phenomenon: namely, (a) that people interpret standard predictive…

  13. Causal Inferences during Text Comprehension and Production.

    ERIC Educational Resources Information Center

    Kemper, Susan

    As comprehension failure results whenever readers are unable to infer missing causal connections, recent comprehension research has focused both on assessing the inferential complexity of texts and on investigating students' developing ability to infer causal relationships. Studies have demonstrated that texts rely on four types of causal…

  14. Scalar Inferences in Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Chevallier, Coralie; Wilson, Deirdre; Happe, Francesca; Noveck, Ira

    2010-01-01

    On being told "John or Mary will come", one might infer that "not both" of them will come. Yet the semantics of "or" is compatible with a situation where both John and Mary come. Inferences of this type, which enrich the semantics of "or" from an "inclusive" to an "exclusive" interpretation, have been extensively studied in linguistic pragmatics.…

  15. Genetic Network Inference Using Hierarchical Structure.

    PubMed

    Kimura, Shuhei; Tokuhisa, Masato; Okada-Hatakeyama, Mariko

    2016-01-01

    Many methods for inferring genetic networks have been proposed, but the regulations they infer often include false-positives. Several researchers have attempted to reduce these erroneous regulations by proposing the use of a priori knowledge about the properties of genetic networks such as their sparseness, scale-free structure, and so on. This study focuses on another piece of a priori knowledge, namely, that biochemical networks exhibit hierarchical structures. Based on this idea, we propose an inference approach that uses the hierarchical structure in a target genetic network. To obtain a reasonable hierarchical structure, the first step of the proposed approach is to infer multiple genetic networks from the observed gene expression data. We take this step using an existing method that combines a genetic network inference method with a bootstrap method. The next step is to extract a hierarchical structure from the inferred networks that is consistent with most of the networks. Third, we use the hierarchical structure obtained to assign confidence values to all candidate regulations. Numerical experiments are also performed to demonstrate the effectiveness of using the hierarchical structure in the genetic network inference. The improvement accomplished by the use of the hierarchical structure is small. However, the hierarchical structure could be used to improve the performances of many existing inference methods. PMID:26941653

  16. The Reasoning behind Informal Statistical Inference

    ERIC Educational Resources Information Center

    Makar, Katie; Bakker, Arthur; Ben-Zvi, Dani

    2011-01-01

    Informal statistical inference (ISI) has been a frequent focus of recent research in statistics education. Considering the role that context plays in developing ISI calls into question the need to be more explicit about the reasoning that underpins ISI. This paper uses educational literature on informal statistical inference and philosophical…

  17. Reinforcement learning or active inference?

    PubMed

    Friston, Karl J; Daunizeau, Jean; Kiebel, Stefan J

    2009-01-01

    This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain. PMID:19641614

  18. Reinforcement Learning or Active Inference?

    PubMed Central

    Friston, Karl J.; Daunizeau, Jean; Kiebel, Stefan J.

    2009-01-01

    This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain. PMID:19641614

  19. Causal Inference in Public Health

    PubMed Central

    Glass, Thomas A.; Goodman, Steven N.; Hernán, Miguel A.; Samet, Jonathan M.

    2014-01-01

    Causal inference has a central role in public health; the determination that an association is causal indicates the possibility for intervention. We review and comment on the long-used guidelines for interpreting evidence as supporting a causal association and contrast them with the potential outcomes framework that encourages thinking in terms of causes that are interventions. We argue that in public health this framework is more suitable, providing an estimate of an action’s consequences rather than the less precise notion of a risk factor’s causal effect. A variety of modern statistical methods adopt this approach. When an intervention cannot be specified, causal relations can still exist, but how to intervene to change the outcome will be unclear. In application, the often-complex structure of causal processes needs to be acknowledged and appropriate data collected to study them. These newer approaches need to be brought to bear on the increasingly complex public health challenges of our globalized world. PMID:23297653

  20. Active inference and epistemic value.

    PubMed

    Friston, Karl; Rigoli, Francesco; Ognibene, Dimitri; Mathys, Christoph; Fitzgerald, Thomas; Pezzulo, Giovanni

    2015-01-01

    We offer a formal treatment of choice behavior based on the premise that agents minimize the expected free energy of future outcomes. Crucially, the negative free energy or quality of a policy can be decomposed into extrinsic and epistemic (or intrinsic) value. Minimizing expected free energy is therefore equivalent to maximizing extrinsic value or expected utility (defined in terms of prior preferences or goals), while maximizing information gain or intrinsic value (or reducing uncertainty about the causes of valuable outcomes). The resulting scheme resolves the exploration-exploitation dilemma: Epistemic value is maximized until there is no further information gain, after which exploitation is assured through maximization of extrinsic value. This is formally consistent with the Infomax principle, generalizing formulations of active vision based upon salience (Bayesian surprise) and optimal decisions based on expected utility and risk-sensitive (Kullback-Leibler) control. Furthermore, as with previous active inference formulations of discrete (Markovian) problems, ad hoc softmax parameters become the expected (Bayes-optimal) precision of beliefs about, or confidence in, policies. This article focuses on the basic theory, illustrating the ideas with simulations. A key aspect of these simulations is the similarity between precision updates and dopaminergic discharges observed in conditioning paradigms. PMID:25689102

  1. Speciation of mercury and mode of transport from placer gold mine tailings

    USGS Publications Warehouse

    Slowey, A.J.; Rytuba, J.J.; Brown, Gordon E., Jr.

    2005-01-01

    Historic placer gold mining in the Clear Creek tributary to the Sacramento River (Redding, CA) has highly impacted the hydrology and ecology of an important salmonid spawning stream. Restoration of the watershed utilized dredge tailings contaminated with mercury (Hg) introduced during gold mining, posing the possibility of persistent Hg release to the surrounding environment, including the San Francisco Bay Delta. Column experiments have been performed to evaluate the extent of Hg transport under chemical conditions potentially similar to those in river restoration projects utilizing dredge tailings such as at Clear Creek. Physicochemical perturbations, in the form of shifts in column influent ionic strength and the presence of a low molecular weight organic acid, were applied to coarse and fine sand placer tailings containing 109-194 and 69-90 ng of Hg/g, respectively. Significant concentrations of mercury, up to 16 ??g/L, leach from these sediments in dissolved and particle-associated forms. Sequential chemical extractions (SCE) of these tailings indicate that elemental Hg initially introduced during gold mining has been transformed to readily soluble species, such as mercury oxides and chlorides (3-4%), intermediately extractable phases that likely include (in)organic sorption complexes and amalgams (75-87%), and fractions of highly insoluble forms such as mercury sulfides (6-20%; e.g., cinnabar and metacinnabar). Extended X-ray absorption fine structure (EXAFS) spectroscopic analysis of colloids obtained from column effluent identified cinnabar particles as the dominant mobile mercury-bearing phase. The fraction of intermediately extractable Hg phases also likely includes mobile colloids to which Hg is adsorbed. ?? 2005 American Chemical Society.

  2. Inference-based constraint satisfaction supports explanation

    SciTech Connect

    Sqalli, M.H.; Freuder, E.C.

    1996-12-31

    Constraint satisfaction problems are typically solved using search, augmented by general purpose consistency inference methods. This paper proposes a paradigm shift in which inference is used as the primary problem solving method, and attention is focused on special purpose, domain specific inference methods. While we expect this approach to have computational advantages, we emphasize here the advantages of a solution method that is more congenial to human thought processes. Specifically we use inference-based constraint satisfaction to support explanations of the problem solving behavior that are considerably more meaningful than a trace of a search process would be. Logic puzzles are used as a case study. Inference-based constraint satisfaction proves surprisingly powerful and easily extensible in this domain. Problems drawn from commercial logic puzzle booklets are used for evaluation. Explanations are produced that compare well with the explanations provided by these booklets.

  3. The Inference of Gene Trees with Species Trees

    PubMed Central

    Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

    2015-01-01

    This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

  4. Speciation of mercury compounds by differential atomization - atomic absorption spectroscopy

    SciTech Connect

    Robinson, J.W.; Skelly, E.M.

    1982-01-01

    This paper describes the dual stage atomization technique which allows speciation of several mercury-containing compounds in aqueous solution and in biological fluids. The technique holds great promise for further speciation studies. Accurate temperature control, expecially at temperatures less than 200/sup 0/C, is needed to separate the extremely volatile mercury halides and simple organomercurials from each other. Studies with mercury salts and EDTA, L-cysteine and dithioxamide demonstrate that this technique may be used to study the extent of complex formation. Investigations of biological fluids indicate that there is a single predominant form of mercury in sweat and a single predominant form of mercury in urine. The mercury compound in urine is more volatile than that in sweat. Both quantitative and qualitative analyses are possible with this technique.

  5. Speciation of uranium(VI) sorption complexes on montmorillonite

    SciTech Connect

    Chisholm-Brause, C.J.; Morris, D.E.; Richard, R.E.

    1992-05-01

    Environmental contaminant releases that contain uranium are among the most serious problems that must be confronted by restoration programs. To facilitate restoration, information concerning the speciation of uranium is needed. Under oxidizing conditions, dissolved uranium is predominantly in the U(VI) (uranyl) form and is quite mobile in the environment, however sorption onto soils may retard its movement. In this study, we have investigated the effects of changes in solution speciation on the nature of uranyl sorption complexes on montmorillonite, a common soil constituent. Aqueous U(VI) solutions between pH 3 to 7 were batch-equilibrated with montmorillonite for several days; specific pH values were selected such that the solutions consisted of dominantly monomeric, oligomeric, or a mix of monomeric and oligomeric aqueous uranyl species. Emission spectroscopy was used to investigate the nature of U(VI) sorbed to montmorillonite.

  6. Speciation of Fe in ambient aerosol and cloudwater

    SciTech Connect

    Siefert, L.

    1996-08-15

    Atmospheric iron (Fe) is thought to play an important role in cloudwater chemistry (e.g., S(IV) oxidation, oxidant production, etc.), and is also an important source of Fe to certain regions of the worlds oceans where Fe is believed to be a rate-limiting nutrient for primary productivity. This thesis focuses on understanding the chemistry, speciation and abundance of Fe in cloudwater and aerosol in the troposphere, through observations of Fe speciation in the cloudwater and aerosol samples collected over the continental United States and the Arabian Sea. Different chemical species of atmospheric Fe were measured in aerosol and cloudwater samples to help assess the role of Fe in cloudwater chemistry.

  7. SUBSURFACE MOBILE PLUTONIUM SPECIATION: SAMPLING ARTIFACTS FOR GROUNDWATER COLLOIDS

    SciTech Connect

    Kaplan, D.; Buesseler, K.

    2010-06-29

    A recent review found several conflicting conclusions regarding colloid-facilitated transport of radionuclides in groundwater and noted that colloids can both facilitate and retard transport. Given these contrasting conclusions and the profound implications even trace concentrations of plutonium (Pu) have on the calculated risk posed to human health, it is important that the methodology used to sample groundwater colloids be free of artifacts. The objective of this study was: (1) to conduct a field study and measure Pu speciation, ({sup 239}Pu and {sup 240}Pu for reduced-Pu{sub aq}, oxidized-Pu{sub aq}, reduced-Pu{sub colloid}, and oxidized-Pu{sub colloid}), in a Savannah River Site (SRS) aquifer along a pH gradient in F-Area, (2) to determine the impact of pumping rate on Pu concentration, Pu speciation, and Pu isotopic ratios, (3) determine the impact of delayed sample processing (as opposed to processing directly from the well).

  8. Sexual selection accelerates signal evolution during speciation in birds

    PubMed Central

    Seddon, Nathalie; Botero, Carlos A.; Tobias, Joseph A.; Dunn, Peter O.; MacGregor, Hannah E. A.; Rubenstein, Dustin R.; Uy, J. Albert C.; Weir, Jason T.; Whittingham, Linda A.; Safran, Rebecca J.

    2013-01-01

    Sexual selection is proposed to be an important driver of diversification in animal systems, yet previous tests of this hypothesis have produced mixed results and the mechanisms involved remain unclear. Here, we use a novel phylogenetic approach to assess the influence of sexual selection on patterns of evolutionary change during 84 recent speciation events across 23 passerine bird families. We show that elevated levels of sexual selection are associated with more rapid phenotypic divergence between related lineages, and that this effect is restricted to male plumage traits proposed to function in mate choice and species recognition. Conversely, we found no evidence that sexual selection promoted divergence in female plumage traits, or in male traits related to foraging and locomotion. These results provide strong evidence that female choice and male–male competition are dominant mechanisms driving divergence during speciation in birds, potentially linking sexual selection to the accelerated evolution of pre-mating reproductive isolation. PMID:23864596

  9. Speciation of uranium in compartments of living cells.

    PubMed

    Geipel, Gerhard; Viehweger, Katrin

    2015-06-01

    Depleted uranium used as ammunition corrodes in the environment forming mineral phases and then dissolved uranium species like uranium carbonates (Schimmack et al., in Radiat Environ Biophys 46:221-227, 2007) and hydroxides. These hydroxide species were contacted with plant cells (canola). After 24 h contact time the cells were fractionated and the uranium speciation in the fraction was determined by time resolved laser-induced fluorescence spectroscopy at room temperature as well at 150 K. It could be shown that the uranium speciation in the fractions is different to that in the nutrient solution. Comparison of the emission bands with literature data allows assignment of the uranium binding forms. PMID:25724950

  10. Inferring genetic networks from microarray data.

    SciTech Connect

    May, Elebeoba Eni; Davidson, George S.; Martin, Shawn Bryan; Werner-Washburne, Margaret C.; Faulon, Jean-Loup Michel

    2004-06-01

    In theory, it should be possible to infer realistic genetic networks from time series microarray data. In practice, however, network discovery has proved problematic. The three major challenges are: (1) inferring the network; (2) estimating the stability of the inferred network; and (3) making the network visually accessible to the user. Here we describe a method, tested on publicly available time series microarray data, which addresses these concerns. The inference of genetic networks from genome-wide experimental data is an important biological problem which has received much attention. Approaches to this problem have typically included application of clustering algorithms [6]; the use of Boolean networks [12, 1, 10]; the use of Bayesian networks [8, 11]; and the use of continuous models [21, 14, 19]. Overviews of the problem and general approaches to network inference can be found in [4, 3]. Our approach to network inference is similar to earlier methods in that we use both clustering and Boolean network inference. However, we have attempted to extend the process to better serve the end-user, the biologist. In particular, we have incorporated a system to assess the reliability of our network, and we have developed tools which allow interactive visualization of the proposed network.

  11. Linguistic Markers of Inference Generation While Reading.

    PubMed

    Clinton, Virginia; Carlson, Sarah E; Seipel, Ben

    2016-06-01

    Words can be informative linguistic markers of psychological constructs. The purpose of this study is to examine associations between word use and the process of making meaningful connections to a text while reading (i.e., inference generation). To achieve this purpose, think-aloud data from third-fifth grade students ([Formula: see text]) reading narrative texts were hand-coded for inferences. These data were also processed with a computer text analysis tool, Linguistic Inquiry and Word Count, for percentages of word use in the following categories: cognitive mechanism words, nonfluencies, and nine types of function words. Findings indicate that cognitive mechanisms were an independent, positive predictor of connections to background knowledge (i.e., elaborative inference generation) and nonfluencies were an independent, negative predictor of connections within the text (i.e., bridging inference generation). Function words did not provide unique variance towards predicting inference generation. These findings are discussed in the context of a cognitive reflection model and the differences between bridging and elaborative inference generation. In addition, potential practical implications for intelligent tutoring systems and computer-based methods of inference identification are presented. PMID:25833811

  12. Statistical Physics of High Dimensional Inference

    NASA Astrophysics Data System (ADS)

    Advani, Madhu; Ganguli, Surya

    To model modern large-scale datasets, we need efficient algorithms to infer a set of P unknown model parameters from N noisy measurements. What are fundamental limits on the accuracy of parameter inference, given limited measurements, signal-to-noise ratios, prior information, and computational tractability requirements? How can we combine prior information with measurements to achieve these limits? Classical statistics gives incisive answers to these questions as the measurement density α =N/P --> ∞ . However, modern high-dimensional inference problems, in fields ranging from bio-informatics to economics, occur at finite α. We formulate and analyze high-dimensional inference analytically by applying the replica and cavity methods of statistical physics where data serves as quenched disorder and inferred parameters play the role of thermal degrees of freedom. Our analysis reveals that widely cherished Bayesian inference algorithms such as maximum likelihood and maximum a posteriori are suboptimal in the modern setting, and yields new tractable, optimal algorithms to replace them as well as novel bounds on the achievable accuracy of a large class of high-dimensional inference algorithms. Thanks to Stanford Graduate Fellowship and Mind Brain Computation IGERT grant for support.

  13. Possible method for dissolved organic carbon speciation in forest soils

    NASA Astrophysics Data System (ADS)

    Drabek, O.; Tejnecký, V.; Ash, C.; Hubova, P.; Boruvka, L.

    2013-12-01

    Dissolved organic carbon (DOC) is a natural part of dissolved organic matter and it plays an important role in the biogeochemistry of soil processes. Low Molecular Mass Organic Acids (LMMOA) are an essential part of DOC. These acids play a key role in chemical processes that affect the entire soil environment. Knowing the amount of DOC and the speciation of LMMOA is required for realistic equilibrium modelling of soil chemical processes and transport mechanisms. There have been a number of proposed methods for the quantitative analysis of DOC and for speciation of LMMOA. The first aim of this contribution is to introduce and test a modified spectroscopic method for the determination of water-extractable organic carbon (WEOC) from forest soils. In general this method is based on the oxidization of WEOC by chromium-sulphuric acid. The presented method can be used as an economical alternative to the classical, more financially demanding elemental analysis. However, the main aim is to test the reliability of the method for LMMOA speciation. Ion exchange chromatography (IC) with hydroxide elution has proven to be a useful tool for the determination of LMMOA in many different water-based samples. However, the influence of multivalent cations (often present in environmental samples) on IC results has not yet been sufficiently studied. In order to assess the influence of Al, Fe, Mn, Mg and Ca on the amount of LMMOA determined by IC, an extensive set of model solutions was prepared and immediately analysed by means of IC. Moreover, the influence of pH on determined amounts of LMMOA in model solutions and representative soil aqueous extracts was investigated. These experimental results were compared to expected values and also to results provided by the chemical equilibrium model - PHREEQC. Based on the above listed research, some modifications to the common IC method for LMMOA speciation are presented.

  14. Plutonium speciation in water from Mono Lake, California

    USGS Publications Warehouse

    Cleveland, J.M.; Rees, T.F.; Nash, K.L.

    1983-01-01

    The solubility of plutonium in Mono Lake water is enhanced by the presence of large concentrations of indigenous carbonate ions and moderate concentrations of fluoride ions. In spite of the complex chemical composition of this water, only a few ions govern the behavior of plutonium, as demonstrated by the fact that it was possible to duplicate plutonium speciation in a synthetic water containing only the principal components of Mono Lake water.

  15. Pu speciation in actual and simulated aged wastes

    SciTech Connect

    Lezama-pacheco, Juan S; Conradson, Steven D

    2008-01-01

    X-ray Absorption Fine Structure Spectroscopy (XAFS) at the Pu L{sub II/III} edge was used to determine the speciation of this element in (1) Hanford Z-9 Pu crib samples, (2) deteriorated waste resins from a chloride process ion-exchange purification line, and (3) the sediments from two Waste Isolation Pilot Plant Liter Scale simulant brine systems. The Pu speciation in all of these samples except one is within the range previously displayed by PuO{sub 2+x-2y}(OH){sub y}{center_dot}zH{sub 2}O compounds, which is expected based on the putative thermodynamic stability of this system for Pu equilibrated with excess H{sub 2}O and O{sub 2} under environmental conditions. The primary exception was a near neutral brine experiment that displayed evidence for partial substitution of the normal O-based ligands with Cl{sup -} and a concomitant expansion of the Pu-Pu distance relative to the much more highly ordered Pu near neighbor shell in PuO{sub 2}. However, although the Pu speciation was not necessarily unusual, the Pu chemistry identified via the history of these samples did exhibit unexpected patterns, the most significant of which may be that the presence of the Pu(V)-oxo species may decrease rather than increase the overall solubility of these compounds. Several additional aspects of the Pu speciation have also not been previously observed in laboratory-based samples. The molecular environmental chemistry of Pu is therefore likely to be more complicated than would be predicted based solely on the behavior of PuO{sub 2} under laboratory conditions.

  16. Sulfur Speciation in the Martian Regolith Component in Shergottite Glasses

    NASA Technical Reports Server (NTRS)

    Rao, M. N.; Nyquist, Laurence E.; Sutton, S.; Huth, J.

    2009-01-01

    We have shown that Gas-Rich Impact-Melt (GRIM) glasses in Shergotty, Zagami, and EET79001 (Lith A and Lith B) contain Martian regolith components that were molten during impact and quenched into glasses in voids of host rock materials based on neutron-capture isotopes, i.e., Sm-150 excesses and Sm-149 deficits in Sm, and Kr-80 excesses produced from Br [1, 2]. These GRIM glasses are rich in S-bearing secondary minerals [3.4]. Evidence for the occurrence of CaSO4 and S-rich aluminosilicates in these glasses is provided by CaO-SO3 and Al2O3-SO3 correlations, which are consistent with the finding of gypsum laths protruding from the molten glass in EET79001 (Lith A) [5]. However, in the case of GRIM glasses from EET79001 (Lith B), Shergotty and Zagami, we find a different set of secondary minerals that show a FeO-SO3 correlation (but no MgOSO3 correlation), instead of CaO-SO3 and Al2O3-SO3 correlations observed in Lith A. These results might indicate different fluidrock interactions near the shergottite source region on Mars. The speciation of sulfur in these salt assemblages was earlier studied by us using XANES techniques [6], where we found that Lith B predominantly contains Fe-sulfide globules (with some sulfate). On the other hand, Lith A showed predominantly Casulfite/ sulfate with some FeS. Furthermore, we found Fe to be present as Fe2+ indicating little oxidation, if any, in these glasses. To examine the sulfide-sulfate association in these glasses, we studied their Fe/Ni ratios with a view to find diagnostic clues for the source fluid. The Fe-sulfide mineral (Fe(0.93)Ni(0.3)S) in EET79001, Lith A is pyrrhotite [7, 8]. It yields an Fe/Ni ratio of 31. In Shergotty, pyrrhotite occurs with a molar ratio of Fe:S of 0.94 and a Ni abundance of 0.12% yielding a Fe/Ni ratio of approx.500 [8]. In this study, we determined a NiO content of approx.0.1% and FeO/NiO ratio of approx.420 in S-rich globules in #507 (EET79001, Lith B) sample using FE-SEM. In the same sample

  17. Inference and the introductory statistics course

    NASA Astrophysics Data System (ADS)

    Pfannkuch, Maxine; Regan, Matt; Wild, Chris; Budgett, Stephanie; Forbes, Sharleen; Harraway, John; Parsonage, Ross

    2011-10-01

    This article sets out some of the rationale and arguments for making major changes to the teaching and learning of statistical inference in introductory courses at our universities by changing from a norm-based, mathematical approach to more conceptually accessible computer-based approaches. The core problem of the inferential argument with its hypothetical probabilistic reasoning process is examined in some depth. We argue that the revolution in the teaching of inference must begin. We also discuss some perplexing issues, problematic areas and some new insights into language conundrums associated with introducing the logic of inference through randomization methods.

  18. Selenium speciation in framboidal and euhedral pyrites in shales.

    PubMed

    Matamoros-Veloza, Adriana; Peacock, Caroline L; Benning, Liane G

    2014-08-19

    The release of Se from shales is poorly understood because its occurrence, distribution, and speciation in the various components of shale are unknown. To address this gap we combined bulk characterization, sequential extractions, and spatially resolved μ-focus spectroscopic analyses and investigated the occurrence and distribution of Se and other associated elements (Fe, As, Cr, Ni, and Zn) and determined the Se speciation at the μ-scale in typical, low bulk Se containing shales. Our results revealed Se primarily correlated with the pyrite fraction with exact Se speciation highly dependent on pyrite morphology. In euhedral pyrites, we found Se(-II) substitutes for S in the mineral structure. However, we also demonstrate that Se is associated with framboidal pyrite grains as a discrete, independent FeSex phase. The presence of this FeSex species has major implications for Se release, because FeSex species oxidize much faster than Se substituted in the euhedral pyrite lattice. Thus, such an FeSex species will enhance and control the dynamics of Se weathering and release into the aqueous environment. PMID:25032506

  19. Arsenic concentration and speciation in infant formulas and first foods

    PubMed Central

    Jackson, Brian P.; Taylor, Vivien F.; Punshon, Tracy; Cottingham, Kathryn L.

    2012-01-01

    Arsenic exposure to humans is pervasive, and, increasingly, studies are revealing adverse health effects at ever lower doses. Drinking water is the main route of exposure for many individuals; however, food can be a significant source of arsenic to an individual, especially if their diet is rice-based. Infants are particularly susceptible to dietary exposure, since many first foods contain rice and they have a low body mass. Here we report on arsenic concentration and speciation in infant formulas and first foods. Speciation is essential for food analysis because of the much greater toxicity of inorganic arsenic species and the possibility that arsenic in food (unlike water) may be present in either inorganic or organic forms. Infant milk formulas were low in total arsenic (2.2–12.6 ng g−1, n=15). Non-dairy formulas were significantly higher in arsenic than dairy-based formulas. Arsenic in formula was almost exclusively inorganic and predominantly arsenic(V). Arsenic concentration in purees (n=41) and stage 3 foods (n=18) ranged from 0.3–22 ng g−1. Rice-fortified foods had significantly higher total arsenic concentrations than non rice-based foods. Again arsenic speciation was predominantly inorganic; arsenic(III) was the main species with lower concentrations of DMA and arsenic(V) also present. These data confirm that infants are exposed to arsenic via diet, and suggest that careful attention to diet choices may limit this. PMID:22701232

  20. Silver speciation in wastewater effluent, surface waters, and pore waters

    SciTech Connect

    Adams, N.W.H.; Kramer, J.R.

    1999-12-01

    Silver, inorganic sulfide, and thiol compounds were measured in municipal wastewater effluent, receiving waters, and pore waters from an anoxic lake sediment in order to predict silver speciation in these systems. The authors found submicromolar concentrations of inorganic sulfide even in fully oxic surface water. This inorganic sulfide is likely to exist in the form of colloidal metal sulfides, which have been shown to be stable under oxidizing conditions for periods of several hours. Inorganic sulfide in both the wastewater effluent and receiving waters was found to be 200 to 300 times in excess of silver concentrations, whereas inorganic sulfide in pore waters was 1,000 to 15,000 times in excess of silver concentrations. With sulfide in excess of silver, the authors predict silver sulfide complexes to dominate silver speciation. Thiols were present at low nanomolar levels in pore waters but were not detectable in wastewater effluent or receiving waters. Thiols do not appear to be important to silver speciation in these freshwater systems. Partitioning of silver into particular, colloidal, and dissolved size fractions showed that a significant proportion of silver is in the colloidal and dissolved phases. Dissolved phase concentrations were relatively constant in the treatment plant effluent and receiving waters, suggesting that silver in the <10-kDa size fraction is strongly complexed by ligands that are not significantly affected by aggregation or sorption processes.

  1. Recent advances in arsenic bioavailability, transport, and speciation in rice.

    PubMed

    Wang, Xin; Peng, Bo; Tan, Changyin; Ma, Lena; Rathinasabapathi, Bala

    2015-04-01

    Widespread arsenic (As) contamination in paddy rice (Oryza sativa) from both geologic and anthropogenic origins is an increasing concern globally. Substantial efforts have been made to elucidate As transformation and uptake processes in rhizosphere and metabolism in rice plant, which provides an essential foundation for the development of mitigation strategies. However, a range of crucial mechanisms from As mobilization in rhizosphere to transport to grains remain poorly understood. To provide new insight into the underlying mechanisms of As accumulation in rice, a range of new perspectives on As bioavailability, transport pathways, and in situ speciation are reviewed here. Specifically, the prominent effects of water regime, Fe plaque, and biochar on As mobilization in rice rhizosphere are discussed critically. An updated understanding of arsenite (AsIII) and methylated As transport from root to vascular bundle and grain is integrated and discussed in detail. Special attention is given to As speciation and distribution in rice grain with potential coping strategies being provided and discussed. Future research priorities are also identified. The new insight into As bioavailability, transport and speciation in rice would lead to a better understanding of As contamination in rice. They would also provide useful strategies from agronomic measures to genetic engineering for more effective restriction of As transport and accumulation in food chain. PMID:25827791

  2. Tree of Life Reveals Clock-Like Speciation and Diversification

    PubMed Central

    Hedges, S. Blair; Marin, Julie; Suleski, Michael; Paymer, Madeline; Kumar, Sudhir

    2015-01-01

    Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process. PMID:25739733

  3. The genetics of speciation: Insights from Fisher's geometric model.

    PubMed

    Fraïsse, Christelle; Gunnarsson, P Alexander; Roze, Denis; Bierne, Nicolas; Welch, John J

    2016-07-01

    Research in speciation genetics has uncovered many robust patterns in intrinsic reproductive isolation, and fitness landscape models have been useful in interpreting these patterns. Here, we examine fitness landscapes based on Fisher's geometric model. Such landscapes are analogous to models of optimizing selection acting on quantitative traits, and have been widely used to study adaptation and the distribution of mutational effects. We show that, with a few modifications, Fisher's model can generate all of the major findings of introgression studies (including "speciation genes" with strong deleterious effects, complex epistasis and asymmetry), and the major patterns in overall hybrid fitnesses (including Haldane's Rule, the speciation clock, heterosis, hybrid breakdown, and male-female asymmetry in the F1). We compare our approach to alternative modeling frameworks that assign fitnesses to genotypes by identifying combinations of incompatible alleles. In some cases, the predictions are importantly different. For example, Fisher's model can explain conflicting empirical results about the rate at which incompatibilities accumulate with genetic divergence. In other cases, the predictions are identical. For example, the quality of reproductive isolation is little affected by the manner in which populations diverge. PMID:27252049

  4. Signals and speciation in plant-feeding insects

    NASA Astrophysics Data System (ADS)

    Cocroft, Reginald; Rodriguez, Rafael; Hunt, Randy

    2003-04-01

    Communication can play a role in speciation when differences in signaling systems reduce gene flow between diverging lineages. However, the observation that closely related species have different signals leaves open the question of cause and effect, because divergence in signals can also occur after speciation is completed. The relationship of signals and divergence is being investigated in the Enchenopa binotata species complex of treehoppers, a group of plant-feeding insects that communicate using substrate-borne vibrational signals. Speciation in the E. binotata complex is hypothesized to have resulted from repeated shifts to novel host plants. Sources of selection on the signals of these treehoppers can be studied not only in fully differentiated species, but also in experimental populations in the early stages of divergence. Some unique features of vibrational communication through plant stems will be discussed, as well as how shifts to novel host plants may influence signaling systems, and what role(s) communication may have played in the process of evolutionary divergence in this group.

  5. Speciation with gene flow and the genetics of habitat transitions.

    PubMed

    Cristescu, Melania E; Constantin, Anna; Bock, Dan G; Cáceres, Carla E; Crease, Teresa J

    2012-03-01

    Whether speciation can advance to completion in the face of initially high levels of gene flow is a very controversial topic in evolutionary biology. Extensive gene exchange is generally considered to homogenize populations and counteract divergence. Moreover, the role of introgressive hybridization in evolution remains largely unexplored in animals, particularly in freshwater zooplankton in which allopatric speciation is considered to be the norm. Our work investigates the genetic structure of two young ecological species: the pond species, Daphnia pulex and the lake species, Daphnia pulicaria. Phylogenetic and population genetics analyses were conducted on mitochondrial NADH dehydrogenase 5 (ND5) gene, the nuclear Lactate dehydrogenase (Ldh) gene and 21 nuclear microsatellite markers in 416 individuals from habitats with various degrees of permanence. The strong and consistent phylogenetic discordance between nuclear and mitochondrial markers suggests a complex evolutionary history of multiple independent habitat transition events that involved hybridization and introgression between lake and pond Daphnia. On the other hand, the low level of contemporary gene flow between adjacent populations indicates the presence of effective habitat isolating barriers. The Daphnia system provides strong evidence for a divergence-with-gene flow speciation model that involves multiple habitat transition events. PMID:22269101

  6. Introduction. Speciation in plants and animals: pattern and process.

    PubMed

    Abbott, Richard J; Ritchie, Michael G; Hollingsworth, Peter M

    2008-09-27

    Although approximately 150 years have passed since the publication of On the origin of species by means of natural selection, the definition of what species are and the ways in which species originate remain contentious issues in evolutionary biology. The biological species concept, which defines species as groups of interbreeding natural populations that are reproductively isolated from other such groups, continues to draw support. However, there is a growing realization that many animal and plant species can hybridize with their close relatives and exchange genes without losing their identity. On occasion, such hybridization can lead to the origin of new species. A key to understanding what species are and the ways in which they originate rests to a large extent on a detailed knowledge of the nature and genetics of factors that limit gene flow between species and the conditions under which such isolation originates. The collection of papers in this issue addresses these topics and deals as well with some specific issues of hybrid speciation and the causes of species radiations. The papers included arise from a 1-day symposium on speciation held during the Sixth Biennial Meeting of the Systematics Association at Edinburgh in August 2007. In this introduction, we provide some background to these papers and highlight some key points made. The papers make clear that highly significant advances to our understanding of animal and plant speciation are currently being made across the range of this topic. PMID:18583278

  7. Parallel Elemental and Molecular Mass Spectrometry (PEMMS) for Speciation of Metals in Complex Matrices

    NASA Astrophysics Data System (ADS)

    Derry, L. A.; Sacks, G. L.; Brenna, J. T.

    2006-12-01

    The mobility, bioavailability, and toxicity of many metals are strongly influenced by their molecular form, or speciation. Many metals (M) in the environment are complexed with organic ligands (L); in some cases such complexed forms comprise virtually all of the dissolved metal. When available, stability constants can be used to model speciation, but only when the identities of species can be known or assumed. In other cases, coupling a separation tool such as HPLC to a metal detection system like ICP-MS can provide information on speciation. But because ICP-MS destroys molecular information the complexing L must be identified by retention time matching of standards. The assumptions inherent in these approaches preclude investigation of unknown compounds. Electrochemical methods can determine conditional stability constants for unknown L but do not provide information on their molecular structure or composition. Molecular MS allows characterization of molecular mass and structure and is a powerful tool for identifying unknown organic compounds. However, sensitivity for M and precision for isotope ratios are often low. We combined HPLC separation with simultaneous parallel detection of metals (M) and ligands (L) by ICP-MS and API-QTOF-MS-MS. The basis of our approach is that the shape of a chromatographic peak is essentially set by interactions with the LC column. The signal of a metal M determined by the ICP-MS in chromatographic mode is fit using an exponentially modified Gaussian function. Peak parameters including retention time, peak width and skew are determined for the M peak. The parallel QTOF signal in full scan mode may show hundreds of peaks in the same time window. The acquired peak library is searched for L peaks that match the parameters determined for the M peak on the ICP-MS. We have found that our system can correctly identify M-L pairs and L in complex samples and generates few false positives. Unknown L can be further interrogated by using the MS

  8. ISSUES IN SIMULATING ELEMENTAL MERCURY AIR/WATER EXCHANGE AND AQUEOUS MONOMETHYLMERCURY SPECIATION

    EPA Science Inventory

    This presentation focuses on two areas relevant to assessing the global fate and bioavailability of mercury: elemental mercury air/water exchange and aqueous environmental monomethylmercury speciation.

  9. An inference engine for embedded diagnostic systems

    NASA Technical Reports Server (NTRS)

    Fox, Barry R.; Brewster, Larry T.

    1987-01-01

    The implementation of an inference engine for embedded diagnostic systems is described. The system consists of two distinct parts. The first is an off-line compiler which accepts a propositional logical statement of the relationship between facts and conclusions and produces data structures required by the on-line inference engine. The second part consists of the inference engine and interface routines which accept assertions of fact and return the conclusions which necessarily follow. Given a set of assertions, it will generate exactly the conclusions which logically follow. At the same time, it will detect any inconsistencies which may propagate from an inconsistent set of assertions or a poorly formulated set of rules. The memory requirements are fixed and the worst case execution times are bounded at compile time. The data structures and inference algorithms are very simple and well understood. The data structures and algorithms are described in detail. The system has been implemented on Lisp, Pascal, and Modula-2.

  10. Metamodel-Driven Evolution with Grammar Inference

    NASA Astrophysics Data System (ADS)

    Bryant, Barrett R.; Liu, Qichao; Mernik, Marjan

    2010-10-01

    Domain-specific modeling (DSM) has become one of the most popular techniques for incorporating model-driven engineering (MDE) into software engineering. In DSM, domain experts define metamodels to describe the essential problems in a domain. A model conforms to a schema definition represented by a metamodel in a similar manner to a programming language conforms to a grammar. Metamodel-driven evolution is when a metamodel undergoes evolutions to incorporate new concerns in the domain. However, this results in losing the ability to use existing model instances. Grammar inference is the problem of inferring a grammar from sample strings which the grammar should generate. This paper describes our work in solving the problem of metamodel-driven evolution with grammar inference, by inferring the metamodel from model instances.

  11. Critical Thinking: Distinguishing between Inferences and Assumptions.

    ERIC Educational Resources Information Center

    Elder, Linda; Paul, Richard

    2002-01-01

    Outlines the differences between inferences and assumptions in critical thinking processes. Explains that as students develop critical intuitions, they increasingly notice how their point of view shapes their experiences. (AUTH/NB)

  12. Are Evaluations Inferred Directly From Overt Actions?

    ERIC Educational Resources Information Center

    Brown, Donald; And Others

    1975-01-01

    The operation of a covert information processing mechanism was investigated in two experiments of the self-persuasion phenomena; i. e., making an inference about a stimulus on the basis of one's past behavior. (Editor)

  13. Multisensory causal inference in the brain.

    PubMed

    Kayser, Christoph; Shams, Ladan

    2015-02-01

    At any given moment, our brain processes multiple inputs from its different sensory modalities (vision, hearing, touch, etc.). In deciphering this array of sensory information, the brain has to solve two problems: (1) which of the inputs originate from the same object and should be integrated and (2) for the sensations originating from the same object, how best to integrate them. Recent behavioural studies suggest that the human brain solves these problems using optimal probabilistic inference, known as Bayesian causal inference. However, how and where the underlying computations are carried out in the brain have remained unknown. By combining neuroimaging-based decoding techniques and computational modelling of behavioural data, a new study now sheds light on how multisensory causal inference maps onto specific brain areas. The results suggest that the complexity of neural computations increases along the visual hierarchy and link specific components of the causal inference process with specific visual and parietal regions. PMID:25710476

  14. Zn Speciation in two Fe-Mn Banded Systems

    NASA Astrophysics Data System (ADS)

    Marcus, M.; Manceau, A.; Kersten, M.; Tazaki, K.

    2002-12-01

    We have used micro-EXAFS spectroscopy to study the speciation of Zn in two shallow-water Fe-Mn banded structures. One of the samples is from the Baltic Sea and contains anthropogenic Zn in a matrix which is believed to be banded due to annual oscillations in oxygen content, pH and other variables of water chemistry (Hlawatsch, et. al., 2002). The other sample, from Akayu Hot Springs off the coast of a volcanic island (Satsuma-Iwo Jima) at the southern tip of Japan, is a hardened biomat in which the compositional oscillations are at least partly due to bacterial action, and in which the Zn content is natural (Tazaki, 2000). By using a beam as small as 5μm in diameter, we can look at details of metal distribution and speciation on a spatial scale much finer than the banding, which has wavelengths of order 100μm. In both samples, the Zn is associated with the high-Mn layers, though the layer-to-layer contrast is lower in the Japan sample. However, the speciation of Zn is different in the two samples. The Baltic sample shows Zn only in one form - sorbed on a layered phyllomanganate resembling birnessite with Zn tetrahedrally coordinated and sorbed to vacant octahedral sites of the Mn layer. This species was also found in soil (Manceau et. al., 2000). The Japan sample also has tetrahedral Zn in birnessite-like phyllomanganate as well as Zn in at least two other forms. The phyllomanganate species is thus seen to be a ubiquitous sink for Zn in the environment. We will discuss some possible reasons for the differences and similarities of Zn speciation in these two systems. Hlawatsch, S., Garbe-Schönberg, C.D., Lechtenberg, F., Manceau, A., Tamura, N., Kulik, D.A., Kersten, M. (2002) Trace metal fluxes to ferromanganese nodules from the western Baltic Sea as a record for long-term environmental changes. Chemical Geology, 182 697-709. Manceau A., Lanson B., Schlegel M.L., Hargé J.C., Musso M., Eybert-Bérard L., Hazemann J.L., Chateigner D., Lamble G.M. (2000

  15. Atmospheric speciation of mercury in two contrasting Southeastern US airsheds

    NASA Astrophysics Data System (ADS)

    Gabriel, Mark C.; Williamson, Derek G.; Brooks, Steve; Lindberg, Steve

    Simultaneous measurement of gaseous elemental, reactive gaseous, and fine particulate mercury took place in Tuscaloosa AL, (urban airshed) and Cove Mountain, TN (non-urban airshed) during the summers of 2002 and 2003. The objective of this research was to (1) summarize the temporal distribution of each mercury specie at each site and compare to other speciation data sets developed by other researchers and (2) provide insight into urban and non-urban mercury speciation effects using various statistical methods. Average specie concentrations were as follows: 4.05 ng m -3 (GEM), 13.6 pg m -3 (RGM), 16.4 pg m -3 (Hg-p) for Tuscaloosa; 3.20 ng m -3 (GEM), 13.6 pg m -3 (RGM), 9.73 pg m -3 (Hg-p) for Cove Mountain. As a result of urban airshed impacts, short periods of high concentration for all mercury species was common in Tuscaloosa. At Cove Mountain a consistent mid-day rise and evening drop for mercury species was found. This pattern was primarily the result of un-impacted physical boundary layer movement, although, other potential impacts were ambient photochemistry and air-surface exchange of mercury. Meteorological parameters that are known to heavily impact mercury speciation were similar for the study period for Tuscaloosa and Cove Mountain except for wind speed (m s -1), which was higher at Cove Mountain. For both sites statistically significant ( p<0.0001), inverse relationships existed between wind speed and Hg 0 concentration. A weaker windspeed-Hg 0 correlation existed for Tuscaloosa. By analyzing Hg concentration—wind speed magnitude change at both sites it was found that wind speed at Cove Mountain had a greater influence on Hg 0 concentration variability than Tuscaloosa by a factor of 3. Using various statistical tests, we concluded that the nature of Tuscaloosa's atmospheric mercury speciation was the result of typical urban airshed impacts. Cove Mountain showed atmospheric mercury speciation characteristics indicative of a non-urban area along with

  16. Mercury Speciation by X-ray Absorption Fine Structure Spectroscopy and Sequential Chemical Extractions: A Comparison of Speciation Methods

    USGS Publications Warehouse

    Kim, C.S.; Bloom, N.S.; Rytuba, J.J.; Brown, Gordon E., Jr.

    2003-01-01

    Determining the chemical speciation of mercury in contaminated mining and industrial environments is essential for predicting its solubility, transport behavior, and potential bioavailability as well as for designing effective remediation strategies. In this study, two techniques for determining Hg speciation-X-ray absorption fine structure (XAFS) spectroscopy and sequential chemical extractions (SCE)-are independently applied to a set of samples with Hg concentrations ranging from 132 to 7539 mg/kg to determine if the two techniques provide comparable Hg speciation results. Generally, the proportions of insoluble HgS (cinnabar, metacinnabar) and HgSe identified by XAFS correlate well with the proportion of Hg removed in the aqua regia extraction demonstrated to remove HgS and HgSe. Statistically significant (> 10%) differences are observed however in samples containing more soluble Hg-containing phases (HgCl2, HgO, Hg3S2O 4). Such differences may be related to matrix, particle size, or crystallinity effects, which could affect the apparent solubility of Hg phases present. In more highly concentrated samples, microscopy techniques can help characterize the Hg-bearing species in complex multiphase natural samples.

  17. Probabilistic inferences related to the measurement process

    NASA Astrophysics Data System (ADS)

    Rossi, G. B.

    2010-07-01

    In measurement indications from a measuring system are acquired and, on the basis of them, some inference about the measurand is made. The final result may be the assignment of a probability distribution for the possible values of the measurand. We discuss the logical structure of such an inference and some of its epistemological consequences. In particular, we propose a new solution to the problem of systematic effects in measurement.

  18. Causal inference in economics and marketing.

    PubMed

    Varian, Hal R

    2016-07-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual-a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  19. Symbolic transfer entropy: inferring directionality in biosignals.

    PubMed

    Staniek, Matthäus; Lehnertz, Klaus

    2009-12-01

    Inferring directional interactions from biosignals is of crucial importance to improve understanding of dynamical interdependences underlying various physiological and pathophysiological conditions. We here present symbolic transfer entropy as a robust measure to infer the direction of interactions between multidimensional dynamical systems. We demonstrate its performance in quantifying driver-responder relationships in a network of coupled nonlinear oscillators and in the human epileptic brain. PMID:19938889

  20. Causal inference in economics and marketing

    PubMed Central

    Varian, Hal R.

    2016-01-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual—a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  1. Operation of the Bayes Inference Engine

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.

    1998-07-27

    The authors have developed a computer application, called the Bayes Inference Engine, to enable one to make inferences about models of a physical object from radiographs taken of it. In the BIE calculational models are represented by a data-flow diagram that can be manipulated by the analyst in a graphical-programming environment. The authors demonstrate the operation of the BIE in terms of examples of two-dimensional tomographic reconstruction including uncertainty estimation.

  2. Coronal Seismology: Inferring Magnetic Fields and Exploring Damping Mechanisms

    NASA Astrophysics Data System (ADS)

    McAteer, R. T. James; Ireland, Jack

    2015-08-01

    Recent observations in extreme ultra-violet wavelengths have shown that the solar corona oscillates at many different spatial sizes and temporal size scales. However, much remains unknown about many of these oscillations; they are intermittent for unknown reasons, appear on some coronal features and not on other, similar, neighboring features, and may (or may not) be magnetohydrodynamic (MHD) wave modes. Definitive causes of the structure and origins of these oscillations are still largely lacking. Here, we use automated oscillation detection routines to study a large sample of oscillations, inferring physical mechanisms as to how and why the corona varies.First, we measure the oscillation content of different physical regions on the Sun in SDO AIA data, using two different automated oscillation detection algorithms. This shows a power-law distribution in oscillatory frequency, disagreeing with strong historical assumptions about the nature of coronal heating and coronal seismology. We show how such disagreements can be reconciled by using a power-law background for oscillatory signals.Second we use coronal seismology to provide a means to infer coronal plasma parameters and to differentiate between potential damping mechanisms. Recent sets of kink-mode observations (usually 5-8 loops) have come insights into how the coronal is structured and how it evolves. We present a complex set of flare-induced, off-limb, coronal kink-mode oscillations of almost 100 loops. These display a spread of periods, amplitudes, and damping times, allowing us to probe the spatial distribution of these parameters for the first time. Both Fourier and Wavelet routines are used to automatically extract and characterize these oscillations. An initial period of P~500s, results in an inferred coronal magnetic field of B~20G. The decrease in the oscillation period of the loop position corresponds to a drop in number density inside the coronal loop, as predicted by MHD. As the the period drops

  3. On the criticality of inferred models

    NASA Astrophysics Data System (ADS)

    Mastromatteo, Iacopo; Marsili, Matteo

    2011-10-01

    Advanced inference techniques allow one to reconstruct a pattern of interaction from high dimensional data sets, from probing simultaneously thousands of units of extended systems—such as cells, neural tissues and financial markets. We focus here on the statistical properties of inferred models and argue that inference procedures are likely to yield models which are close to singular values of parameters, akin to critical points in physics where phase transitions occur. These are points where the response of physical systems to external perturbations, as measured by the susceptibility, is very large and diverges in the limit of infinite size. We show that the reparameterization invariant metrics in the space of probability distributions of these models (the Fisher information) are directly related to the susceptibility of the inferred model. As a result, distinguishable models tend to accumulate close to critical points, where the susceptibility diverges in infinite systems. This region is the one where the estimate of inferred parameters is most stable. In order to illustrate these points, we discuss inference of interacting point processes with application to financial data and show that sensible choices of observation time scales naturally yield models which are close to criticality.

  4. Subsurface conditions in hydrothermal vents inferred from diffuse flow composition, and models of reaction and transport

    NASA Astrophysics Data System (ADS)

    Larson, B. I.; Houghton, J. L.; Lowell, R. P.; Farough, A.; Meile, C. D.

    2015-08-01

    Chemical gradients in the subsurface of mid-ocean ridge hydrothermal systems create an environment where minerals precipitate and dissolve and where chemosynthetic organisms thrive. However, owing to the lack of easy access to the subsurface, robust knowledge of the nature and extent of chemical transformations remains elusive. Here, we combine measurements of vent fluid chemistry with geochemical and transport modeling to give new insights into the under-sampled subsurface. Temperature-composition relationships from a geochemical mixing model are superimposed on the subsurface temperature distribution determined using a heat flow model to estimate the spatial distribution of fluid composition. We then estimate the distribution of Gibb's free energies of reaction beneath mid oceanic ridges and by combining flow simulations with speciation calculations estimate anhydrite deposition rates. Applied to vent endmembers observed at the fast spreading ridge at the East Pacific Rise, our results suggest that sealing times due to anhydrite formation are longer than the typical time between tectonic and magmatic events. The chemical composition of the neighboring low temperature flow indicates relatively uniform energetically favorable conditions for commonly inferred microbial processes such as methanogenesis, sulfate reduction and numerous oxidation reactions, suggesting that factors other than energy availability may control subsurface microbial biomass distribution. Thus, these model simulations complement fluid-sample datasets from surface venting and help infer the chemical distribution and transformations in subsurface flow.

  5. Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data.

    PubMed

    Cahill, James A; Soares, André E R; Green, Richard E; Shapiro, Beth

    2016-07-19

    Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. PMID:27325835

  6. Inferring host range dynamics from comparative data: the protozoan parasites of new world monkeys.

    PubMed

    Waxman, David; Weinert, Lucy A; Welch, John J

    2014-07-01

    Uncovering the ecological determinants of parasite host range is a central goal of comparative parasitology and infectious disease ecology. But while parasites are often distributed nonrandomly across the host phylogeny, such patterns are difficult to interpret without a genealogy for the parasite samples and without knowing what sorts of ecological dynamics might lead to what sorts of nonrandomness. We investigated inferences from comparative data, using presence/absence records from protozoan parasites of the New World monkeys. We first demonstrate several distinct types of phylogenetic signal in these data, showing, for example, that parasite species are clustered on the host tree and that closely related host species harbor similar numbers of parasite species. We then show that all of these patterns can be generated by a single, simple dynamical model, in which parasite host range changes more rapidly than host speciation/extinction and parasites preferentially colonize uninfected host species that are closely related to their existing hosts. Fitting this model to data, we then estimate its parameters. Finally, we caution that quite different ecological processes can lead to similar signatures but show how phylogenetic variation in host susceptibility can be distinguished from a tendency for parasites to colonize closely related hosts. Our new process-based analyses, which estimate meaningful parameters, should be useful for inferring the determinants of parasite host range and transmission success. PMID:24921601

  7. Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks.

    PubMed

    Bunnefeld, Lynsey; Frantz, Laurent A F; Lohse, Konrad

    2015-11-01

    The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks--extreme population size changes of short duration--not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference. Finally, we apply our method to genomic data from a species of pig (Sus cebifrons) endemic to islands in the center and west of the Philippines to estimate whether a bottleneck occurred upon island colonization and compare our scheme to Li and Durbin's pairwise sequentially Markovian coalescent (PSMC) both for the pig data and using simulations. PMID:26341659

  8. Prions, Radionuclides and Clays: Impact of clay interlayer "acidity" on toxic compound speciation

    NASA Astrophysics Data System (ADS)

    Charlet, L.; Hureau, C.; Sobolev, O.; Cuello, G.; Chapron, Y.

    2007-05-01

    The physical and chemical processes that are the basis of contaminant retardation in clay rich medium, such as soil or nuclear waste repository, have been studied at the molecular level by a combination of molecular dynamics (MD), electron paramagnetic spectroscopy (EPR) and neutron diffraction with isotopic substitution (NDIS). The speciation of contaminants such as Sm, a radionuclide analogue, and Cu, bound to Prion protein (PrP), has been studied upon adsorption in clay interlayers. We used as molecular probe the P5-Cu(II) complex, where the P5 pentapeptide(92-96 PrP residues) represents one of the five Cu(II) binding site present in PrP, the key protein involved in diseases known as transmissible spongiform encephalopathies. In both cases, the pH of the interlayer has been inferred from the metal ion coordination, here used as a molecular reporter. In circum neutral pH waters, samarium is present as Sm(OH)3° species and should not be adsorbed in clay interlayer by "cation exchange" unless its hydrolysis is altered. Samarium NDIS results indicate that whether the number of oxygen nearest neighbours varies only from 8.5 to 7, as Sm penetrates the interlayer, the number of hydrogen nearest neighbours drops from 12 to 6. The high affinity of clay for Sm shows that a change in Sm hydrolysis occurs in the clay interlayer, but is directly followed by the formation of a surface complex with montmorillonite siloxane plane functional groups which prevents the determination of a "local pH". Conversely, has been found to be a much more sensitive interlayer water pH probe. and this peptide domain is involved in the misfolding of the protein,a transconformation which may lead to the pathogenic PrPSc form. We have therefore studied by EPR spectroscopy the adsorption of Cu(II)-P5 complexes on montmorillonite, and found the clay to have a large and selective adsorption capacity for the various [Cu(P5)H-n](2-n)+ complexes where n is the number of deprotonated amido function

  9. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae).

    PubMed

    Daïnou, K; Mahy, G; Duminil, J; Dick, C W; Doucet, J-L; Donkpégan, A S L; Pluijgers, M; Sinsin, B; Lejeune, P; Hardy, O J

    2014-07-01

    The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically. PMID:24549110

  10. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)

    PubMed Central

    Daïnou, K; Mahy, G; Duminil, J; Dick, C W; Doucet, J-L; Donkpégan, A S L; Pluijgers, M; Sinsin, B; Lejeune, P; Hardy, O J

    2014-01-01

    The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically. PMID:24549110

  11. Inference of Isoforms from Short Sequence Reads

    NASA Astrophysics Data System (ADS)

    Feng, Jianxing; Li, Wei; Jiang, Tao

    Due to alternative splicing events in eukaryotic species, the identification of mRNA isoforms (or splicing variants) is a difficult problem. Traditional experimental methods for this purpose are time consuming and cost ineffective. The emerging RNA-Seq technology provides a possible effective method to address this problem. Although the advantages of RNA-Seq over traditional methods in transcriptome analysis have been confirmed by many studies, the inference of isoforms from millions of short sequence reads (e.g., Illumina/Solexa reads) has remained computationally challenging. In this work, we propose a method to calculate the expression levels of isoforms and infer isoforms from short RNA-Seq reads using exon-intron boundary, transcription start site (TSS) and poly-A site (PAS) information. We first formulate the relationship among exons, isoforms, and single-end reads as a convex quadratic program, and then use an efficient algorithm (called IsoInfer) to search for isoforms. IsoInfer can calculate the expression levels of isoforms accurately if all the isoforms are known and infer novel isoforms from scratch. Our experimental tests on known mouse isoforms with both simulated expression levels and reads demonstrate that IsoInfer is able to calculate the expression levels of isoforms with an accuracy comparable to the state-of-the-art statistical method and a 60 times faster speed. Moreover, our tests on both simulated and real reads show that it achieves a good precision and sensitivity in inferring isoforms when given accurate exon-intron boundary, TSS and PAS information, especially for isoforms whose expression levels are significantly high.

  12. Ultrasensitive Speciation Analysis of Mercury in Rice by Headspace Solid Phase Microextraction Using Porous Carbons and Gas Chromatography-Dielectric Barrier Discharge Optical Emission Spectrometry.

    PubMed

    Lin, Yao; Yang, Yuan; Li, Yuxuan; Yang, Lu; Hou, Xiandeng; Feng, Xinbin; Zheng, Chengbin

    2016-03-01

    Rice consumption is a primary pathway for human methylmercury (MeHg) exposure in inland mercury mining areas of Asia. In addition, the use of iodomethane, a common fumigant that significantly accelerates the methylation of mercury in soil under sunlight, could increase the MeHg exposure from rice. Conventional hyphenated techniques used for mercury speciation analysis are usually too costly for most developing countries. Consequently, there is an increased interest in the development of sensitive and inexpensive methods for the speciation of mercury in rice. In this work, gas chromatography (GC) coupled to dielectric barrier discharge optical emission spectrometry (DBD-OES) was developed for the speciation analysis of mercury in rice. Prior to GC-DBD-OES analysis, mercury species were derivatized to their volatile species with NaBPh4 and preconcentrated by headspace solid phase microextraction using porous carbons. Limits of detection of 0.5 μg kg(-1) (0.16 ng), 0.75 μg kg(-1) (0.24 ng), and 1.0 μg kg(-1) (0.34 ng) were obtained for Hg(2+), CH3Hg(+), and CH3CH2Hg(+), respectively, with relative standard deviations (RSDs) better than 5.2% and 6.8% for one fiber or fiber-to-fiber mode, respectively. Recoveries of 90-105% were obtained for the rice samples, demonstrating the applicability of the proposed technique. Owing to the small size, low power, and low gas consumption of DBD-OES as well as efficient extraction of mercury species by porous carbons headspace solid phase micro-extraction, the proposed technique provides several advantages including compactness, cost-effectiveness, and potential to couple with miniature GC to accomplish the field speciation of mercury in rice compared to conventional hyphenated techniques. PMID:26828416

  13. Inference of random walk models to describe leukocyte migration

    NASA Astrophysics Data System (ADS)

    Jones, Phoebe J. M.; Sim, Aaron; Taylor, Harriet B.; Bugeon, Laurence; Dallman, Magaret J.; Pereira, Bernard; Stumpf, Michael P. H.; Liepe, Juliane

    2015-12-01

    While the majority of cells in an organism are static and remain relatively immobile in their tissue, migrating cells occur commonly during developmental processes and are crucial for a functioning immune response. The mode of migration has been described in terms of various types of random walks. To understand the details of the migratory behaviour we rely on mathematical models and their calibration to experimental data. Here we propose an approximate Bayesian inference scheme to calibrate a class of random walk models characterized by a specific, parametric particle re-orientation mechanism to observed trajectory data. We elaborate the concept of transition matrices (TMs) to detect random walk patterns and determine a statistic to quantify these TM to make them applicable for inference schemes. We apply the developed pipeline to in vivo trajectory data of macrophages and neutrophils, extracted from zebrafish that had undergone tail transection. We find that macrophage and neutrophils exhibit very distinct biased persistent random walk patterns, where the strengths of the persistence and bias are spatio-temporally regulated. Furthermore, the movement of macrophages is far less persistent than that of neutrophils in response to wounding.

  14. Inference of random walk models to describe leukocyte migration.

    PubMed

    Jones, Phoebe J M; Sim, Aaron; Taylor, Harriet B; Bugeon, Laurence; Dallman, Magaret J; Pereira, Bernard; Stumpf, Michael P H; Liepe, Juliane

    2015-12-01

    While the majority of cells in an organism are static and remain relatively immobile in their tissue, migrating cells occur commonly during developmental processes and are crucial for a functioning immune response. The mode of migration has been described in terms of various types of random walks. To understand the details of the migratory behaviour we rely on mathematical models and their calibration to experimental data. Here we propose an approximate Bayesian inference scheme to calibrate a class of random walk models characterized by a specific, parametric particle re-orientation mechanism to observed trajectory data. We elaborate the concept of transition matrices (TMs) to detect random walk patterns and determine a statistic to quantify these TM to make them applicable for inference schemes. We apply the developed pipeline to in vivo trajectory data of macrophages and neutrophils, extracted from zebrafish that had undergone tail transection. We find that macrophage and neutrophils exhibit very distinct biased persistent random walk patterns, where the strengths of the persistence and bias are spatio-temporally regulated. Furthermore, the movement of macrophages is far less persistent than that of neutrophils in response to wounding. PMID:26403334

  15. Intent Inference and Syntactic Tracking with GMTI Measurements

    NASA Astrophysics Data System (ADS)

    Wang, Alex; Krishnamurthy, Vikram; Balaji, Bhashyam

    In conventional target tracking systems, human operators use the estimated target tracks to make higher level inference of the target behaviour/intent. This paper develops syntactic filtering algorithms that assist human operators by extracting spatial patterns from target tracks to identify suspicious/anomalous spatial trajectories. The targets' spatial trajectories are modeled by a stochastic context free grammar (SCFG) and a switched mode state space model. Bayesian filtering algorithms for stochastic context free grammars are presented for extracting the syntactic structure and illustrated for a ground moving target indicator (GMTI) radar example. The performance of the algorithms is tested with the experimental data collected using DRDC Ottawa's X-band Wideband Experimental Airborne Radar (XWEAR).

  16. Power deposition by mode converted electron Bernstein waves in the DIII-D heat pinch experiments

    SciTech Connect

    Forest, C.B.; Harvey, R.W.; Smirnov, A.P.

    2001-05-01

    Mode converted electron Bernstein waves are shown to play an important role in power deposition in the off-axis electron cyclotron heating experiments on the DIII-D tokamak in which the effect known as the 'heat pinch' was inferred. Ray tracing shows that the mode converted Bernstein modes (generated when the launched X mode reflects from an outboard upper hybrid layer) are damped in the central region where the previous analysis had assumed no power was being deposited.

  17. Selenium Speciation and Management in Wet FGD Systems

    SciTech Connect

    Searcy, K; Richardson, M; Blythe, G; Wallschlaeger, D; Chu, P; Dene, C

    2012-02-29

    This report discusses results from bench- and pilot-scale simulation tests conducted to determine the factors that impact selenium speciation and phase partitioning in wet FGD systems. The selenium chemistry in wet FGD systems is highly complex and not completely understood, thus extrapolation and scale-up of these results may be uncertain. Control of operating parameters and application of scrubber additives have successfully demonstrated the avoidance or decrease of selenite oxidation at the bench and pilot scale. Ongoing efforts to improve sample handling methods for selenium speciation measurements are also discussed. Bench-scale scrubber tests explored the impacts of oxidation air rate, trace metals, scrubber additives, and natural limestone on selenium speciation in synthetic and field-generated full-scale FGD liquors. The presence and concentration of redox-active chemical species as well as the oxidation air rate contribute to the oxidation-reduction potential (ORP) conditions in FGD scrubbers. Selenite oxidation to the undesirable selenate form increases with increasing ORP conditions, and decreases with decreasing ORP conditions. Solid-phase manganese [Mn(IV)] appeared to be the significant metal impacting the oxidation of selenite to selenate. Scrubber additives were tested for their ability to inhibit selenite oxidation. Although dibasic acid and other scrubber additives showed promise in early clear liquor (sodium based and without calcium solids) bench-scale tests, these additives did not show strong inhibition of selenite oxidation in tests with higher manganese concentrations and with slurries from full-scale wet FGD systems. In bench-tests with field liquors, addition of ferric chloride at a 250:1 iron-to-selenium mass ratio sorbed all incoming selenite to the solid phase, although addition of ferric salts had no impact on native selenate that already existed in the field slurry liquor sample. As ORP increases, selenite may oxidize to selenate more

  18. Estimating uncertainty of inference for validation

    SciTech Connect

    Booker, Jane M; Langenbrunner, James R; Hemez, Francois M; Ross, Timothy J

    2010-09-30

    We present a validation process based upon the concept that validation is an inference-making activity. This has always been true, but the association has not been as important before as it is now. Previously, theory had been confirmed by more data, and predictions were possible based on data. The process today is to infer from theory to code and from code to prediction, making the role of prediction somewhat automatic, and a machine function. Validation is defined as determining the degree to which a model and code is an accurate representation of experimental test data. Imbedded in validation is the intention to use the computer code to predict. To predict is to accept the conclusion that an observable final state will manifest; therefore, prediction is an inference whose goodness relies on the validity of the code. Quantifying the uncertainty of a prediction amounts to quantifying the uncertainty of validation, and this involves the characterization of uncertainties inherent in theory/models/codes and the corresponding data. An introduction to inference making and its associated uncertainty is provided as a foundation for the validation problem. A mathematical construction for estimating the uncertainty in the validation inference is then presented, including a possibility distribution constructed to represent the inference uncertainty for validation under uncertainty. The estimation of inference uncertainty for validation is illustrated using data and calculations from Inertial Confinement Fusion (ICF). The ICF measurements of neutron yield and ion temperature were obtained for direct-drive inertial fusion capsules at the Omega laser facility. The glass capsules, containing the fusion gas, were systematically selected with the intent of establishing a reproducible baseline of high-yield 10{sup 13}-10{sup 14} neutron output. The deuterium-tritium ratio in these experiments was varied to study its influence upon yield. This paper on validation inference is the

  19. Deep Learning for Population Genetic Inference

    PubMed Central

    Sheehan, Sara; Song, Yun S.

    2016-01-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  20. Scene Construction, Visual Foraging, and Active Inference

    PubMed Central

    Mirza, M. Berk; Adams, Rick A.; Mathys, Christoph D.; Friston, Karl J.

    2016-01-01

    This paper describes an active inference scheme for visual searches and the perceptual synthesis entailed by scene construction. Active inference assumes that perception and action minimize variational free energy, where actions are selected to minimize the free energy expected in the future. This assumption generalizes risk-sensitive control and expected utility theory to include epistemic value; namely, the value (or salience) of information inherent in resolving uncertainty about the causes of ambiguous cues or outcomes. Here, we apply active inference to saccadic searches of a visual scene. We consider the (difficult) problem of categorizing a scene, based on the spatial relationship among visual objects where, crucially, visual cues are sampled myopically through a sequence of saccadic eye movements. This means that evidence for competing hypotheses about the scene has to be accumulated sequentially, calling upon both prediction (planning) and postdiction (memory). Our aim is to highlight some simple but fundamental aspects of the requisite functional anatomy; namely, the link between approximate Bayesian inference under mean field assumptions and functional segregation in the visual cortex. This link rests upon the (neurobiologically plausible) process theory that accompanies the normative formulation of active inference for Markov decision processes. In future work, we hope to use this scheme to model empirical saccadic searches and identify the prior beliefs that underwrite intersubject variability in the way people forage for information in visual scenes (e.g., in schizophrenia). PMID:27378899

  1. Scene Construction, Visual Foraging, and Active Inference.

    PubMed

    Mirza, M Berk; Adams, Rick A; Mathys, Christoph D; Friston, Karl J

    2016-01-01

    This paper describes an active inference scheme for visual searches and the perceptual synthesis entailed by scene construction. Active inference assumes that perception and action minimize variational free energy, where actions are selected to minimize the free energy expected in the future. This assumption generalizes risk-sensitive control and expected utility theory to include epistemic value; namely, the value (or salience) of information inherent in resolving uncertainty about the causes of ambiguous cues or outcomes. Here, we apply active inference to saccadic searches of a visual scene. We consider the (difficult) problem of categorizing a scene, based on the spatial relationship among visual objects where, crucially, visual cues are sampled myopically through a sequence of saccadic eye movements. This means that evidence for competing hypotheses about the scene has to be accumulated sequentially, calling upon both prediction (planning) and postdiction (memory). Our aim is to highlight some simple but fundamental aspects of the requisite functional anatomy; namely, the link between approximate Bayesian inference under mean field assumptions and functional segregation in the visual cortex. This link rests upon the (neurobiologically plausible) process theory that accompanies the normative formulation of active inference for Markov decision processes. In future work, we hope to use this scheme to model empirical saccadic searches and identify the prior beliefs that underwrite intersubject variability in the way people forage for information in visual scenes (e.g., in schizophrenia). PMID:27378899

  2. Computationally efficient Bayesian inference for inverse problems.

    SciTech Connect

    Marzouk, Youssef M.; Najm, Habib N.; Rahn, Larry A.

    2007-10-01

    Bayesian statistics provides a foundation for inference from noisy and incomplete data, a natural mechanism for regularization in the form of prior information, and a quantitative assessment of uncertainty in the inferred results. Inverse problems - representing indirect estimation of model parameters, inputs, or structural components - can be fruitfully cast in this framework. Complex and computationally intensive forward models arising in physical applications, however, can render a Bayesian approach prohibitive. This difficulty is compounded by high-dimensional model spaces, as when the unknown is a spatiotemporal field. We present new algorithmic developments for Bayesian inference in this context, showing strong connections with the forward propagation of uncertainty. In particular, we introduce a stochastic spectral formulation that dramatically accelerates the Bayesian solution of inverse problems via rapid evaluation of a surrogate posterior. We also explore dimensionality reduction for the inference of spatiotemporal fields, using truncated spectral representations of Gaussian process priors. These new approaches are demonstrated on scalar transport problems arising in contaminant source inversion and in the inference of inhomogeneous material or transport properties. We also present a Bayesian framework for parameter estimation in stochastic models, where intrinsic stochasticity may be intermingled with observational noise. Evaluation of a likelihood function may not be analytically tractable in these cases, and thus several alternative Markov chain Monte Carlo (MCMC) schemes, operating on the product space of the observations and the parameters, are introduced.

  3. Deep Learning for Population Genetic Inference.

    PubMed

    Sheehan, Sara; Song, Yun S

    2016-03-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  4. Inferring learners' knowledge from their actions.

    PubMed

    Rafferty, Anna N; LaMar, Michelle M; Griffiths, Thomas L

    2015-04-01

    Watching another person take actions to complete a goal and making inferences about that person's knowledge is a relatively natural task for people. This ability can be especially important in educational settings, where the inferences can be used for assessment, diagnosing misconceptions, and providing informative feedback. In this paper, we develop a general framework for automatically making such inferences based on observed actions; this framework is particularly relevant for inferring student knowledge in educational games and other interactive virtual environments. Our approach relies on modeling action planning: We formalize the problem as a Markov decision process in which one must choose what actions to take to complete a goal, where choices will be dependent on one's beliefs about how actions affect the environment. We use a variation of inverse reinforcement learning to infer these beliefs. Through two lab experiments, we show that this model can recover people's beliefs in a simple environment, with accuracy comparable to that of human observers. We then demonstrate that the model can be used to provide real-time feedback and to model data from an existing educational game. PMID:25155381

  5. Cluster Mass Inference via Random Field Theory

    PubMed Central

    Zhang, Hui; Nichols, Thomas E.; Johnson, Timothy D.

    2009-01-01

    Cluster extent and voxel intensity are two widely used statistics in neuroimaging inference. Cluster extent is sensitive to spatially extended signals while voxel intensity is better for intense but focal signals. In order to leverage strength from both statistics, several nonparametric permutation methods have been proposed to combine the two methods. Simulation studies have shown that of the different cluster permutation methods, the cluster mass statistic is generally the best. However, to date, there is no parametric cluster mass inference method available. In this paper, we propose a cluster mass inference method based on random field theory (RFT). We develop this method for Gaussian images, evaluate it on Gaussian and Gaussianized t-statistic images and investigate its statistical properties via simulation studies and real data. Simulation results show that the method is valid under the null hypothesis and demonstrate that it can be more powerful than the cluster extent inference method. Further, analyses with a single-subject and a group fMRI dataset demonstrate better power than traditional cluster extent inference, and good accuracy relative to a gold-standard permutation test. PMID:18805493

  6. Reliability of the Granger causality inference

    NASA Astrophysics Data System (ADS)

    Zhou, Douglas; Zhang, Yaoyu; Xiao, Yanyang; Cai, David

    2014-04-01

    How to characterize information flows in physical, biological, and social systems remains a major theoretical challenge. Granger causality (GC) analysis has been widely used to investigate information flow through causal interactions. We address one of the central questions in GC analysis, that is, the reliability of the GC evaluation and its implications for the causal structures extracted by this analysis. Our work reveals that the manner in which a continuous dynamical process is projected or coarse-grained to a discrete process has a profound impact on the reliability of the GC inference, and different sampling may potentially yield completely opposite inferences. This inference hazard is present for both linear and nonlinear processes. We emphasize that there is a hazard of reaching incorrect conclusions about network topologies, even including statistical (such as small-world or scale-free) properties of the networks, when GC analysis is blindly applied to infer the network topology. We demonstrate this using a small-world network for which a drastic loss of small-world attributes occurs in the reconstructed network using the standard GC approach. We further show how to resolve the paradox that the GC analysis seemingly becomes less reliable when more information is incorporated using finer and finer sampling. Finally, we present strategies to overcome these inference artifacts in order to obtain a reliable GC result.

  7. Habitat preference and the marine-speciation paradox.

    PubMed Central

    Bierne, Nicolas; Bonhomme, François; David, Patrice

    2003-01-01

    Marine organisms challenge the classical theories of local adaptation and speciation because their planktonic larvae have the potential to maintain high gene flow. The marine-speciation paradox is illustrated by contact zones between incipient species that are so large that allopatric divergence seems unlikely. For this reason any mechanism preventing sympatric larvae of two incipient species from coexisting in the same habitats can be a powerful promoter of speciation. The contact zone between two hybridizing taxa of mussel, Mytilus edulis and M. galloprovincialis, in Europe provides an excellent example. Although the zone itself extends over thousands of kilometres, the opportunities for interbreeding are considerably reduced by the small-scale mosaic structure of the zone, where local patches of each taxon alternate at scales of kilometres or less, in response to locally variable ecological factors. Habitat choice by settling larvae would be a less costly mechanism than post-settlement selection to maintain such a mosaic structure. Unfortunately the role of selective settlement has remained hypothetical because larvae could not be scored by classical genetic markers. PCR markers allowed us to study larvae and settlement in ecologically contrasting sites within the zone. We show that only a subset of the genotypes present in the plankton settle in some sites, and that the adults on these sites show the same genetic bias. Genetically based variation in pre-settlement processes therefore accounts for the ecological segregation observed, though it is not the only factor involved in limiting successful interbreeding. The present dataset also supports previous reports of partial spawning asynchrony. PMID:12965032

  8. Speciation And Colloid Transport of Arsenic From Mine Tailings

    SciTech Connect

    Slowey, A.J.; Johnson, S.B.; Newville, M.; Brown, G.E., Jr.

    2007-07-13

    In addition to affecting biogeochemical transformations, the speciation of As also influences its transport from tailings at inoperative mines. The speciation of As in tailings from the Sulfur Bank Mercury Mine site in Clear Lake, California (USA) (a hot-spring Hg deposit) and particles mobilized from these tailings have been examined during laboratory-column experiments. Solutions containing two common, plant-derived organic acids (oxalic and citric acid) were pumped at 13 pore volumes d{sup -1} through 25 by 500 mm columns of calcined Hg ore, analogous to the pedogenesis of tailings. Chemical analysis of column effluent indicated that all of the As mobilized was particulate (1.5 mg, or 6% of the total As in the column through 255 pore volumes of leaching). Arsenic speciation was evaluated using X-ray absorption spectroscopy (XAS), indicating the dominance of arsenate [As(V)] sorbed to poorly crystalline Fe(III)-(hydr)oxides and coprecipitated with jarosite [KFe{sub 3}(SO{sub 4}, AsO{sub 4}){sub 2}(OH){sub 6}] with no detectable primary or secondary minerals in the tailings and mobilized particles. Sequential chemical extractions (SCE) of <45 {micro}m mine tailings fractions also suggest that As occurs adsorbed to Fe (hydr)oxides (35%) and coprecipitated within poorly crystalline phases (45%). In addition, SCEs suggest that As is associated with 1 N acid-soluble phases such as carbonate minerals (20%) and within crystalline Fe-(hydr)oxides (10%). The finding that As is transported from these mine tailings dominantly as As(V) adsorbed to Fe (hydr)oxides or coprecipitated within hydroxysulfates such as jarosite suggests that As release from soils and sediments contaminated with tailings will be controlled by either organic acid-promoted dissolution or reductive dissolution of host phases.

  9. Genetic Evidence for Hybrid Trait Speciation in Heliconius Butterflies

    PubMed Central

    Salazar, Camilo; Baxter, Simon W.; Pardo-Diaz, Carolina; Wu, Grace; Surridge, Alison; Linares, Mauricio; Bermingham, Eldredge; Jiggins, Chris D.

    2010-01-01

    Homoploid hybrid speciation is the formation of a new hybrid species without change in chromosome number. So far, there has been a lack of direct molecular evidence for hybridization generating novel traits directly involved in animal speciation. Heliconius butterflies exhibit bright aposematic color patterns that also act as cues in assortative mating. Heliconius heurippa has been proposed as a hybrid species, and its color pattern can be recreated by introgression of the H. m. melpomene red band into the genetic background of the yellow banded H. cydno cordula. This hybrid color pattern is also involved in mate choice and leads to reproductive isolation between H. heurippa and its close relatives. Here, we provide molecular evidence for adaptive introgression by sequencing genes across the Heliconius red band locus and comparing them to unlinked wing patterning genes in H. melpomene, H. cydno, and H. heurippa. 670 SNPs distributed among 29 unlinked coding genes (25,847bp) showed H. heurippa was related to H. c. cordula or the three species were intermixed. In contrast, among 344 SNPs distributed among 13 genes in the red band region (18,629bp), most showed H. heurippa related with H. c. cordula, but a block of around 6,5kb located in the 3′ of a putative kinesin gene grouped H. heurippa with H. m. melpomene, supporting the hybrid introgression hypothesis. Genealogical reconstruction showed that this introgression occurred after divergence of the parental species, perhaps around 0.43Mya. Expression of the kinesin gene is spatially restricted to the distal region of the forewing, suggesting a mechanism for pattern regulation. This gene therefore constitutes the first molecular evidence for adaptive introgression during hybrid speciation and is the first clear candidate for a Heliconius wing patterning locus. PMID:20442862

  10. Berreman mode and epsilon near zero mode.

    PubMed

    Vassant, Simon; Hugonin, Jean-Paul; Marquier, Francois; Greffet, Jean-Jacques

    2012-10-01

    In this paper, we discuss the existence of an electromagnetic mode propagating in a thin dielectric film deposited on a metallic film at the particular frequency such that the dielectric permittivity vanishes. We discuss the remarkable properties of this mode in terms of extreme subwavelength mode confinment and its potential applications. We also discuss the link between this mode, the IR absorption peak on a thin dielectric film known as Berreman effect and the surface phonon polariton mode at the air/dielectric interface. Finally, we establish a connection with the polarization shift occuring in quantum wells. PMID:23188363

  11. 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...

  12. 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

  13. 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...

  14. 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...

  15. GEOCHEM-EZ: a chemical speciation program with greater power and flexibility

    Technology Transfer Automated Retrieval System (TEKTRAN)

    GEOCHEM –EZ is a multi-functional chemical speciation program, which was designed to replace the existing GEOCHEM-PC, a program that can only be used on DOS consoles. Chemical speciation programs, such as GEOCHEM (Sposito and Mattigod, 1980) and GEOCHEM-PC (Parker et al., 1995), have been excellent ...

  16. 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 ...

  17. EFFECTS OF PH AND COMPETING ANIONS ON THE SOLUTION SPECIATION OF ARSENIC BY ION EXCHANGE RESINS

    EPA Science Inventory

    Anion-exchange resins (AER) are used to differentiate As(V) and As(III) by retaining As(V) and allowing As(III) to pass through. AERs allow rapid speciation of As in the field which precludes the effects sample preservation on As speciation. Aqueous environmental samples contai...

  18. ISOTOPIC COMPOSITION, SPECIATION AND MOBILITY OF PU IN THE GROUNDWATER AT DOE SAVANNAH RIVER SITE

    EPA Science Inventory

    Prior studies have revealed that speciation and/ or complexation chemistry have dramatic effect on the mobility of many elements in aquifers because sorption onto any solid phase will depend upon the speciation in solution (Choppin, 1988; Choppin, 1992; Moulin and Ouzounian, 1992...

  19. Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria).

    PubMed

    Geml, J; Laursen, G A; O'neill, K; Nusbaum, H C; Taylor, D L

    2006-01-01

    Amanita muscaria sensu lato has a wide geographic distribution, occurring in Europe, Asia, Africa, Australia, New Zealand, and North, Central and South America. Previous phylogenetic work by others indicates three geographic clades (i.e. 'Eurasian', 'Eurasian-alpine' and 'North American' groups) within A. muscaria. However, the historical dispersal patterns of A. muscaria remained unclear. In our project, we collected specimens from arctic, boreal and humid temperate regions in Alaska, and generated DNA sequence data from the protein-coding beta-tubulin gene and the internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA repeat. Homologous sequences from additional A. muscaria isolates were downloaded from GenBank. We conducted phylogenetic and nested clade analyses (NCA) to reveal the phylogeographic history of the species complex. Although phylogenetic analyses confirmed the existence of the three above-mentioned clades, representatives of all three groups were found to occur sympatrically in Alaska, suggesting that they represent cryptic phylogenetic species with partially overlapping geographic distributions rather than being allopatric populations. All phylogenetic species share at least two morphological varieties with other species, suggesting ancestral polymorphism in pileus and wart colour pre-dating their speciations. The ancestral population of A. muscaria likely evolved in the Siberian-Beringian region and underwent fragmentation as inferred from NCA and the coalescent analyses. The data suggest that these populations later evolved into species, expanded their range in North America and Eurasia. In addition to range expansions, populations of all three species remained in Beringia and adapted to the cooling climate. PMID:16367842

  20. Speciation and dissolution of hydrogen in the proto-lunar disk

    NASA Astrophysics Data System (ADS)

    Pahlevan, Kaveh; Karato, Shun-ichiro; Fegley, Bruce

    2016-07-01

    Despite very high temperatures accompanying lunar origin, indigenous water in the form of OH has been unambiguously observed in Apollo samples in recent years. Such observations have prompted questions about the abundance and distribution of lunar hydrogen. Here, we investigate the related question of the origin of lunar H: is the hydrogen observed a remnant of a much larger initial inventory that was inherited from a "wet" Earth but partly depleted during the process of origin, or was primordial hydrogen quantitatively lost from the lunar material, with water being delivered to lunar reservoirs via subsequent impacts after the origins sequence? Motivated by recent results pointing to a limited extent of hydrogen escape from the gravity field of the Earth during lunar origin, we apply a newly developed thermodynamic model of liquid-vapor silicates to the proto-lunar disk to interrogate the behavior of H as a trace element in the energetic aftermath of the giant impact. We find that: (1) pre-existing H-bearing molecules are rapidly dissociated at the temperatures considered (3100-4200 K) and vaporized hydrogen predominantly exists as OH(v), H(v) and MgOH(v) for nearly the full range of thermal states encountered in the proto-lunar disk, (2) despite such a diversity in the vapor speciation - which reduces the water fugacity and favors hydrogen exsolution from co-existing liquids - the equilibration of the vapor atmosphere with the disk liquid results in significant dissolution of H into proto-lunar magmas, and (3) equilibrium H isotopic fractionation in this setting is limited to <10 per mil and the "terrestrial" character of lunar D/H recently inferred should extend to such a precision if liquid-vapor equilibration in the proto-lunar disk is the process that gave rise to lunar hydrogen. Taken together, these results implicate dissolution as the process responsible for establishing lunar H abundances.

  1. Plasma mass spectrometry as a detector for chemical speciation studies.

    PubMed

    Tomlinson, M J; Lin, L; Caruso, J A

    1995-03-01

    Inductively coupled plasma mass spectrometry (ICP-MS), when coupled with the unique separating power of various chromatographic techniques, allows the detection of various elements at ultra-trace levels. The investigation of various toxic elements of environmental concern coupling relatively recent techniques, such as supercritical fluid chromatography (SFC) and capillary zone electrophoresis (CZE), to ICP-MS, is discussed. Comparisons have been made with detection limits obtained by using the flame ionization detector. The conventional technique of liquid chromatography for the speciation of vanadium, chromium and nickel is also discussed. PMID:7741220

  2. Iron speciation and its biological availability in seawater: A workshop

    SciTech Connect

    Wells, M.L.; Bruland, K.W.

    1995-09-08

    This workshop brought together marine chemists with expertise in iron chemistry and biologists with expertise in the role of iron in phytoplankton production to discuss controversies regarding the role of iron in oceanic primary productivity and global climatic change. A new paradigm for marine iron biogeochemistry was generated. The five major new items within this paradigm included (1) the nature of iron inputs to the sea, (2) chemical speciation of iron in seawater, (3) relationships between iron chemistry and marine microbial community dynamics, (4) adaptations of marine microbes to iron input, and (5) ecological and biogeochemical implications of changes in iron supply to the sea.

  3. Colonization and speciation of cave animals in the Philippines

    NASA Astrophysics Data System (ADS)

    Husana, D.; Yamamuro, M.; Kase, T.

    2012-12-01

    Island-like situation of caves resulted to species isolation while organism's phenotypic plasticity allows the animal to cope with the cave's environment. These conditions eventually lead to organism's speciation through genetic differentiation. Combined morphological and molecular analyses provided insights on the speciation events and colonization of the subterranean ecosystem. Morphological analysis of hypogean species, known as troglobite, and its epigean congeners showed the interesting differences in their characters. Troglobite exhibited cave adaptations such as degenerated eyesight, enlargement or elongation of ambulatory organs, loss of pigmentation and development of other useful organs that favors their survival in the dark cave environment. Molecular clock estimation based on the substitution rate of 0.88% per million years established for 16S rRNA for the grapsid crab genus Sesarma suggested that the troglobitic Sundathelphusa species colonized the cave habitat in Samar Island in the late Miocene epoch and started to diverge from its epigean ancestor ca. 5.92 mya. Interestingly, the five species of the genus Sundathelphusa from Bohol Island comprising of both hypogean and epigean species (S. cavernicola, S. sottoae, S. vediniki, S. urichi and S. boex) occupy a single clade with divergence time from its sister clade ca. 2.58 mya. This phenomenon suggests two possible interpretations of the existence of Bohol species: (1) they belong to a single species with regular genetic flow from their surface relative and that their character differences can be best interpreted as ecophenotypic, or, (2) the speciation event was very rapid and quite recent. Mitochondrial DNA sequences of 430 base pairs of the large subunit rRNA (16S rRNA) revealed the phylogenetic relationships of the genus Sundathelphusa suggesting a multiple colonizations of caves. The speciation events coincided with the timing of the eustatic sea level fluctuation and geologic changes in the

  4. Fe, Ni and Zn speciation, in airborne particulate matter

    NASA Astrophysics Data System (ADS)

    Thiodjio Sendja, Bridinette; Aquilanti, Giuliana; Vassura, Ivano; Giorgetti, Marco

    2016-05-01

    The study of elemental speciation in atmospheric particulate matter is important for the assessment of the source of the particle as well for the evaluation of its toxicity. XANES data at Fe, Ni, and Zn K-edges are recorded on a sample of urban dust (from the Rimini area of Emilia Romagna region, Italy) deposited on a filter and on the NIST standard reference material 1648. Using linear combination fitting we give an indication of the chemical species of the three metals present in the samples.

  5. Children's and Adults' Judgments of the Certainty of Deductive Inferences, Inductive Inferences, and Guesses

    ERIC Educational Resources Information Center

    Pillow, Bradford H.; Pearson, RaeAnne M.; Hecht, Mary; Bremer, Amanda

    2010-01-01

    Children and adults rated their own certainty following inductive inferences, deductive inferences, and guesses. Beginning in kindergarten, participants rated deductions as more certain than weak inductions or guesses. Deductions were rated as more certain than strong inductions beginning in Grade 3, and fourth-grade children and adults…

  6. The Observation/Inference Chart: Improving Students' Abilities to Make Inferences while Reading Nontraditional Texts

    ERIC Educational Resources Information Center

    Nokes, Jeffery D.

    2008-01-01

    The Observation/Inference (OI) Chart is a strategy that can help students learn to make observations and inferences when reading nontraditional texts such as artifacts, paintings or movies. Nontraditional texts can be highly engaging and provide authentic thinking experiences for students, but they can also be difficult to comprehend. Teachers can…

  7. Carbon dioxide binding at dry FeOOH mineral surfaces: evidence for structure-controlled speciation.

    PubMed

    Song, Xiaowei; Boily, Jean-François

    2013-08-20

    Interactions between CO2(g) and mineral surfaces are important to atmospheric and terrestrial settings. This study provides detailed evidence on how differences in mineral surface structure impact carbonate speciation resulting from CO2(g) adsorption reactions. It was achieved by resolving the identity of adsorption sites and geometries of (bi)carbonate species at surfaces of nanosized goethite (α-FeOOH) and lepidocrocite (γ-FeOOH) particles. Fourier transform infrared spectroscopy was used to obtain this information on particles contacted with atmospheres of CO2(g). Vibrational modes of surface hydroxo groups covering these particles were first monitored. These showed that only one type of the surface groups that are singly coordinated to Fe atoms (-OH) are involved in the formation of (bi)carbonate species. Those of higher coordination numbers (μ-OH, μ3-OH) do not participate. Adsorption geometries were then resolved by investigating the C-O stretching region, assisted by density functional theoretical calculations. These efforts provided indications leaning toward a predominance of monodentate mononuclear species, -O-CO2Hx=[0,1]. In contrast, monodentate binuclear species of (-O)2-COHx=[0,1], are expected to form at particle terminations and surface defects. Finally, calculations suggested that bicarbonate is the dominant species on goethite, while a mixture of bicarbonate and carbonate species is present on lepidocrocite, a result stemming from different hydrogen bonding patterns at these mineral surfaces. PMID:23885755

  8. Using Alien Coins to Test Whether Simple Inference Is Bayesian

    ERIC Educational Resources Information Center

    Cassey, Peter; Hawkins, Guy E.; Donkin, Chris; Brown, Scott D.

    2016-01-01

    Reasoning and inference are well-studied aspects of basic cognition that have been explained as statistically optimal Bayesian inference. Using a simplified experimental design, we conducted quantitative comparisons between Bayesian inference and human inference at the level of individuals. In 3 experiments, with more than 13,000 participants, we…

  9. 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

    2016-01-01

    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. PMID:27571751

  10. Dynamical inference of hidden biological populations

    NASA Astrophysics Data System (ADS)

    Luchinsky, D. G.; Smelyanskiy, V. N.; Millonas, M.; McClintock, P. V. E.

    2008-10-01

    Population fluctuations in a predator-prey system are analyzed for the case where the number of prey could be determined, subject to measurement noise, but the number of predators was unknown. The problem of how to infer the unmeasured predator dynamics, as well as the model parameters, is addressed. Two solutions are suggested. In the first of these, measurement noise and the dynamical noise in the equation for predator population are neglected; the problem is reduced to a one-dimensional case, and a Bayesian dynamical inference algorithm is employed to reconstruct the model parameters. In the second solution a full-scale Markov Chain Monte Carlo simulation is used to infer both the unknown predator trajectory, and also the model parameters, using the one-dimensional solution as an initial guess.

  11. Inferences from counterfactual threats and promises.

    PubMed

    Egan, Suzanne M; Byrne, Ruth M J

    2012-01-01

    We examine how people understand and reason from counterfactual threats, for example, "if you had hit your sister, I would have grounded you" and counterfactual promises, for example, "if you had tidied your room, I would have given you ice-cream." The first experiment shows that people consider counterfactual threats, but not counterfactual promises, to have the illocutionary force of an inducement. They also make the immediate inference that the action mentioned in the "if" part of the counterfactual threat and promise did not occur. The second experiment shows that people make more negative inferences (modus tollens and denial of the antecedent) than affirmative inferences (modus ponens and affirmation of the consequent) from counterfactual threats and promises, unlike indicative threats and promises. We discuss the implications of the results for theories of the mental representations and cognitive processes that underlie conditional inducements. PMID:22580411

  12. Identification and Inference for Econometric Models

    NASA Astrophysics Data System (ADS)

    Andrews, Donald W. K.; Stock, James H.

    2005-07-01

    This volume contains the papers presented in honor of the lifelong achievements of Thomas J. Rothenberg on the occasion of his retirement. The authors of the chapters include many of the leading econometricians of our day, and the chapters address topics of current research significance in econometric theory. The chapters cover four themes: identification and efficient estimation in econometrics, asymptotic approximations to the distributions of econometric estimators and tests, inference involving potentially nonstationary time series, such as processes that might have a unit autoregressive root, and nonparametric and semiparametric inference. Several of the chapters provide overviews and treatments of basic conceptual issues, while others advance our understanding of the properties of existing econometric procedures and/or propose new ones. Specific topics include identification in nonlinear models, inference with weak instruments, tests for nonstationary in time series and panel data, generalized empirical likelihood estimation, and the bootstrap.

  13. Parameter inference with estimated covariance matrices

    NASA Astrophysics Data System (ADS)

    Sellentin, Elena; Heavens, Alan F.

    2016-02-01

    When inferring parameters from a Gaussian-distributed data set by computing a likelihood, a covariance matrix is needed that describes the data errors and their correlations. If the covariance matrix is not known a priori, it may be estimated and thereby becomes a random object with some intrinsic uncertainty itself. We show how to infer parameters in the presence of such an estimated covariance matrix, by marginalizing over the true covariance matrix, conditioned on its estimated value. This leads to a likelihood function that is no longer Gaussian, but rather an adapted version of a multivariate t-distribution, which has the same numerical complexity as the multivariate Gaussian. As expected, marginalization over the true covariance matrix improves inference when compared with Hartlap et al.'s method, which uses an unbiased estimate of the inverse covariance matrix but still assumes that the likelihood is Gaussian.

  14. Single board system for fuzzy inference

    NASA Technical Reports Server (NTRS)

    Symon, James R.; Watanabe, Hiroyuki

    1991-01-01

    The very large scale integration (VLSI) implementation of a fuzzy logic inference mechanism allows the use of rule-based control and decision making in demanding real-time applications. Researchers designed a full custom VLSI inference engine. The chip was fabricated using CMOS technology. The chip consists of 688,000 transistors of which 476,000 are used for RAM memory. The fuzzy logic inference engine board system incorporates the custom designed integrated circuit into a standard VMEbus environment. The Fuzzy Logic system uses Transistor-Transistor Logic (TTL) parts to provide the interface between the Fuzzy chip and a standard, double height VMEbus backplane, allowing the chip to perform application process control through the VMEbus host. High level C language functions hide details of the hardware system interface from the applications level programmer. The first version of the board was installed on a robot at Oak Ridge National Laboratory in January of 1990.

  15. Automatic transformations in the inference process

    SciTech Connect

    Veroff, R. L.

    1980-07-01

    A technique for incorporating automatic transformations into processes such as the application of inference rules, subsumption, and demodulation provides a mechanism for improving search strategies for theorem proving problems arising from the field of program verification. The incorporation of automatic transformations into the inference process can alter the search space for a given problem, and is particularly useful for problems having broad rather than deep proofs. The technique can also be used to permit the generation of inferences that might otherwise be blocked and to build some commutativity or associativity into the unification process. Appropriate choice of transformations, and new literal clashing and unification algorithms for applying them, showed significant improvement on several real problems according to several distinct criteria. 22 references, 1 figure.

  16. Combined Application of QEM-SEM and Hard X-ray Microscopy to Determine Mineralogical Associations and Chemcial Speciation of Trace Metals

    SciTech Connect

    M Grafe; M Landers; R Tappero; P Austin; B Gan; A Grabsch; C Klauber

    2011-12-31

    We describe the application of quantitative evaluation of mineralogy by scanning electron microscopy in combination with techniques commonly available at hard X-ray microprobes to define the mineralogical environment of a bauxite residue core segment with the more specific aim of determining the speciation of trace metals (e.g., Ti, V, Cr, and Mn) within the mineral matrix. Successful trace metal speciation in heterogeneous matrices, such as those encountered in soils or mineral residues, relies on a combination of techniques including spectroscopy, microscopy, diffraction, and wet chemical and physical experiments. Of substantial interest is the ability to define the mineralogy of a sample to infer redox behavior, pH buffering, and mineral-water interfaces that are likely to interact with trace metals through adsorption, coprecipitation, dissolution, or electron transfer reactions. Quantitative evaluation of mineralogy by scanning electron microscopy coupled with micro-focused X-ray diffraction, micro-X-ray fluorescence, and micro-X-ray absorption near edge structure (mXANES) spectroscopy provided detailed insights into the composition of mineral assemblages and their effect on trace metal speciation during this investigation. In the sample investigated, titanium occurs as poorly ordered ilmenite, as rutile, and is substituted in iron oxides. Manganese's spatial correlation to Ti is closely linked to ilmenite, where it appears to substitute for Fe and Ti in the ilmenite structure based on its mXANES signature. Vanadium is associated with ilmenite and goethite but always assumes the +4 oxidation state, whereas chromium is predominantly in the +3 oxidation state and solely associated with iron oxides (goethite and hematite) and appears to substitute for Fe in the goethite structure.

  17. A formal model of interpersonal inference

    PubMed Central

    Moutoussis, Michael; Trujillo-Barreto, Nelson J.; El-Deredy, Wael; Dolan, Raymond J.; Friston, Karl J.

    2014-01-01

    Introduction: We propose that active Bayesian inference—a general framework for decision-making—can equally be applied to interpersonal exchanges. Social cognition, however, entails special challenges. We address these challenges through a novel formulation of a formal model and demonstrate its psychological significance. Method: We review relevant literature, especially with regards to interpersonal representations, formulate a mathematical model and present a simulation study. The model accommodates normative models from utility theory and places them within the broader setting of Bayesian inference. Crucially, we endow people's prior beliefs, into which utilities are absorbed, with preferences of self and others. The simulation illustrates the model's dynamics and furnishes elementary predictions of the theory. Results: (1) Because beliefs about self and others inform both the desirability and plausibility of outcomes, in this framework interpersonal representations become beliefs that have to be actively inferred. This inference, akin to “mentalizing” in the psychological literature, is based upon the outcomes of interpersonal exchanges. (2) We show how some well-known social-psychological phenomena (e.g., self-serving biases) can be explained in terms of active interpersonal inference. (3) Mentalizing naturally entails Bayesian updating of how people value social outcomes. Crucially this includes inference about one's own qualities and preferences. Conclusion: We inaugurate a Bayes optimal framework for modeling intersubject variability in mentalizing during interpersonal exchanges. Here, interpersonal representations are endowed with explicit functional and affective properties. We suggest the active inference framework lends itself to the study of psychiatric conditions where mentalizing is distorted. PMID:24723872

  18. To speciate, or not to speciate? Resource heterogeneity, the subjectivity of similarity, and the macroevolutionary consequences of niche-width shifts in plant-feeding insects.

    PubMed

    Nyman, Tommi

    2010-05-01

    Coevolutionary studies on plants and plant-feeding insects have significantly improved our understanding of the role of niche shifts in the generation of new species. Evolving plant lineages essentially constitute moving islands and archipelagoes in resource space, and host shifts by insects are usually preceded by colonizations of novel resources. Critical to hypotheses concerning ecological speciation is what happens immediately before and after colonization attempts: if an available plant is too similar to the current host(s), it simply will be incorporated into the existing diet, but if it is too different, it will not be colonized in the first place. It thus seems that the probability of speciation is maximized when alternative hosts are at an 'intermediate' distance in resource space. In this review, I wish to highlight the possibility that resource similarity and, thus, the definition of 'intermediate', are subjective concepts that depend on the herbivore lineage's tolerance to dietary variation. This subjectivity of similarity means that changes in tolerance can either decrease or increase speciation probabilities depending on the distribution of plants in resource space: insect lineages with narrow tolerances are likely to speciate by 'island-hopping' on young, species-rich plant groups, whereas more generalized lineages could speciate by shifting among resource archipelagoes formed by higher plant taxa. Repeated and convergent origins of traits known to broaden or to restrict host-plant use in multiple different insect groups provide opportunities for studying how tolerance and resource heterogeneity may interact to determine speciation rates. PMID:20002390

  19. Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest

    PubMed Central

    Staggemeier, Vanessa Graziele; Diniz-Filho, José Alexandre Felizola; Forest, Félix; Lucas, Eve

    2015-01-01

    Background and Aims Myrcia section Aulomyrcia includes ∼120 species that are endemic to the Neotropics and disjunctly distributed in the moist Amazon and Atlantic coastal forests of Brazil. This paper presents the first comprehensive phylogenetic study of this group and this phylogeny is used as a basis to evaluate recent classification systems and to test alternative hypotheses associated with the history of this clade. Methods Fifty-three taxa were sampled out of the 120 species currently recognized, plus 40 outgroup taxa, for one nuclear marker (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, trnL-trnF, trnQ-rpS16 and ndhF). The relationships were reconstructed based on Bayesian and maximum likelihood analyses. Additionally, a likelihood approach, ‘geographic state speciation and extinction’, was used to estimate region- dependent rates of speciation, extinction and dispersal, comparing historically climatic stable areas (refugia) and unstable areas. Key Results Maximum likelihood and Bayesian inferences indicate that Myrcia and Marlierea are polyphyletic, and the internal groupings recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Amazonian and north-eastern species and between north-eastern and south-eastern species. Lower extinction rates within glacial refugia suggest that these areas were important in maintaining diversity in the Atlantic forest biodiversity hotspot. Conclusions This study provides a robust phylogenetic framework to address important ecological questions for Myrcia s.l. within an evolutionary context, and supports the need to unite taxonomically the two traditional genera Myrcia and Marlierea in an expanded Myrcia s.l. Furthermore, this study offers valuable insights into the diversification of plant species in the highly impacted Atlantic forest of South America; evidence is presented that the lowest extinction rates are found inside

  20. Evolutionary site-number changes of ribosomal DNA loci during speciation: complex scenarios of ancestral and more recent polyploid events

    PubMed Central

    Rosato, Marcela; Moreno-Saiz, Juan C.; Galián, José A.; Rosselló, Josep A.

    2015-01-01

    Several genome duplications have been identified in the evolution of seed plants, providing unique systems for studying karyological processes promoting diversification and speciation. Knowledge about the number of ribosomal DNA (rDNA) loci, together with their chromosomal distribution and structure, provides clues about organismal and molecular evolution at various phylogenetic levels. In this work, we aim to elucidate the evolutionary dynamics of karyological and rDNA site-number variation in all known taxa of subtribe Vellinae, showing a complex scenario of ancestral and more recent polyploid events. Specifically, we aim to infer the ancestral chromosome numbers and patterns of chromosome number variation, assess patterns of variation of both 45S and 5S rDNA families, trends in site-number change of rDNA loci within homoploid and polyploid series, and reconstruct the evolutionary history of rDNA site number using a phylogenetic hypothesis as a framework. The best-fitting model of chromosome number evolution with a high likelihood score suggests that the Vellinae core showing x = 17 chromosomes arose by duplication events from a recent x = 8 ancestor. Our survey suggests more complex patterns of polyploid evolution than previously noted for Vellinae. High polyploidization events (6x, 8x) arose independently in the basal clade Vella castrilensis–V. lucentina, where extant diploid species are unknown. Reconstruction of ancestral rDNA states in Vellinae supports the inference that the ancestral number of loci in the subtribe was two for each multigene family, suggesting that an overall tendency towards a net loss of 5S rDNA loci occurred during the splitting of Vellinae ancestors from the remaining Brassiceae lineages. A contrasting pattern for rDNA site change in both paleopolyploid and neopolyploid species was linked to diversification of Vellinae lineages. This suggests dynamic and independent changes in rDNA site number during speciation processes and a

  1. Gene-network inference by message passing

    NASA Astrophysics Data System (ADS)

    Braunstein, A.; Pagnani, A.; Weigt, M.; Zecchina, R.

    2008-01-01

    The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.

  2. Inference System Integration Via Logic Morphisms

    NASA Technical Reports Server (NTRS)

    Bjorner, Nikolaj S.; Espinosa, David

    2000-01-01

    This is a final report on the accomplishments during the period of the NASA grant. The work on inference servers accomplished the integration of the SLANG logic (Specware's default specification logic) with a number of inference servers in order to make their complementary strengths available. These inverence servers are (1) SNARK. (2) Gandalf, Setheo, and Spass, (3) the Prototype Verification System (PVS) from SRI. (4) HOL98. We designed and implemented MetaSlang, an ML-like language, which we are using to specify and implement all our logic morphisms.

  3. Modes and origins of mechanical and ethological isolation in angiosperms.

    PubMed Central

    Grant, V

    1994-01-01

    Mechanical and ethological isolation between species is widespread in angiosperms with specialized animal-pollinated flowers, being recorded in 29 species groups belonging to 27 genera and 16 families. Mechanical isolation occurs in two forms. (i) The common type, designated the Salvia type, operates when two or more species of flowers are adapted for different groups of pollinators with different body sizes and shapes. (ii) In the Pedicularis type two flower species have the same species of pollinator but pick up pollen from different parts of the pollinator's body. Four forms of ethological isolation are recognized. (i) In the Aquilegia type, which is widespread, ethological isolation is a side effect of mechanical isolation. (ii) The flower-constancy type, as the name suggests, is based on flower-constant foraging behavior. (iii) In the Ophrys type, floral scents attract male bees or wasps and play a role in their mating behavior; different species of flowers, often orchids, have different scents and attract different sets of hymenopteran species. (iv) The monotropy type occurs in plants pollinated by hymenopterans with species-specific or group-specific flower preferences for nutritive purposes (monotropic and oligotropic bees and fig wasps). Three modes of origin of floral isolation are confirmed by evidence: (i) mechanical and ethological isolation arising as a by-product of allopatric speciation, (ii) ethological isolation developing by selection for reproductive isolation per se, and (iii) mechanical isolation arising as a by-product of character displacement. Mode of origin i accounts for the Salvia and Aquilegia types of isolation in nine known species groups and for the Ophrys type in one group. Mode of origin ii accounts for the flower-constancy type of ethological isolation in two species groups. Mode of origin iii explains mechanical isolation in two groups. Sympatric origin of floral isolation by hybrid speciation and by flower constancy has been

  4. Speciation of nanoscale objects by nanoparticle imprinted matrices.

    PubMed

    Hitrik, Maria; Pisman, Yamit; Wittstock, Gunther; Mandler, Daniel

    2016-08-01

    The toxicity of nanoparticles is not only a function of the constituting material but depends largely on their size, shape and stabilizing shell. Hence, the speciation of nanoscale objects, namely, their detection and separation based on the different species, similarly to heavy metals, is of outmost importance. Here we demonstrate the speciation of gold nanoparticles (AuNPs) and their electrochemical detection using the concept of "nanoparticles imprinted matrices" (NAIM). Negatively charged AuNPs are adsorbed as templates on a conducting surface previously modified with polyethylenimine (PEI). The selective matrix is formed by the adsorption of either oleic acid (OA) or poly(acrylic acid) (PAA) on the non-occupied areas. The AuNPs are removed by electrooxidation to form complementary voids. These voids are able to recognize the AuNPs selectively based on their size. Furthermore, the selectivity could be improved by adsorbing an additional layer of 1-hexadecylamine, which deepened the voids. Interestingly, silver nanoparticles (AgNPs) were also recognized if their size matched those of the template AuNPs. The steps in assembling the NAIMs and the reuptake of the nanoparticles were characterized carefully. The prospects for the analytical use of NAIMs, which are simple, of small dimension, cost-efficient and portable, are in the sensing and separation of nanoobjects. PMID:26955908

  5. Assortative flocking in crossbills and implications for ecological speciation

    PubMed Central

    Smith, Julie W.; Sjoberg, Stephanie M.; Mueller, Matthew C.; Benkman, Craig W.

    2012-01-01

    How reproductive isolation is related to divergent natural selection is a central question in speciation. Here, we focus on several ecologically specialized taxa or ‘call types’ of red crossbills (Loxia curvirostra complex), one of the few groups of birds providing much evidence for ecological speciation. Call types differ in bill sizes and feeding capabilities, and also differ in vocalizations, such that contact calls provide information on crossbill phenotype. We found that two call types of red crossbills were more likely to approach playbacks of their own call type than those of heterotypics, and that their propensity to approach heterotypics decreased with increasing divergence in bill size. Although call similarity also decreased with increasing divergence in bill size, comparisons of responses to familiar versus unfamiliar call types indicate that the decrease in the propensity to approach heterotypics with increasing divergence in bill size was a learned response, and not a by-product of calls diverging pleiotropically as bill size diverged. Because crossbills choose mates while in flocks, assortative flocking could lead indirectly to assortative mating as a by-product. These patterns of association therefore provide a mechanism by which increasing divergent selection can lead to increasing reproductive isolation. PMID:22915674

  6. Assortative flocking in crossbills and implications for ecological speciation.

    PubMed

    Smith, Julie W; Sjoberg, Stephanie M; Mueller, Matthew C; Benkman, Craig W

    2012-10-22

    How reproductive isolation is related to divergent natural selection is a central question in speciation. Here, we focus on several ecologically specialized taxa or 'call types' of red crossbills (Loxia curvirostra complex), one of the few groups of birds providing much evidence for ecological speciation. Call types differ in bill sizes and feeding capabilities, and also differ in vocalizations, such that contact calls provide information on crossbill phenotype. We found that two call types of red crossbills were more likely to approach playbacks of their own call type than those of heterotypics, and that their propensity to approach heterotypics decreased with increasing divergence in bill size. Although call similarity also decreased with increasing divergence in bill size, comparisons of responses to familiar versus unfamiliar call types indicate that the decrease in the propensity to approach heterotypics with increasing divergence in bill size was a learned response, and not a by-product of calls diverging pleiotropically as bill size diverged. Because crossbills choose mates while in flocks, assortative flocking could lead indirectly to assortative mating as a by-product. These patterns of association therefore provide a mechanism by which increasing divergent selection can lead to increasing reproductive isolation. PMID:22915674

  7. Allopatric speciation within a cryptic species complex of Australasian octopuses.

    PubMed

    Amor, Michael D; Norman, Mark D; Cameron, Hayley E; Strugnell, Jan M

    2014-01-01

    Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the 'tetricus complex'. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide. PMID:24964133

  8. Effects of dispersal plasticity on population divergence and speciation.

    PubMed

    Arendt, J D

    2015-10-01

    Phenotypic plasticity is thought to have a role in driving population establishment, local adaptation and speciation. However, dispersal plasticity has been underappreciated in this literature. Plasticity in the decision to disperse is taxonomically widespread and I provide examples for insects, molluscs, polychaetes, vertebrates and flowering plants. Theoretical work is limited but indicates an interaction between dispersal distance and plasticity in the decision to disperse. When dispersal is confined to adjacent patches, dispersal plasticity may enhance local adaptation over unconditional (non-plastic) dispersal. However, when dispersal distances are greater, plasticity in dispersal decisions strongly reduces the potential for local adaptation and population divergence. Upon dispersal, settlement may be random, biased but genetically determined, or biased but plastically determined. Theory shows that biased settlement of either type increases population divergence over random settlement. One model suggests that plasticity further enhances chances of speciation. However, there are many strategies for deciding on where to settle such as a best-of-N strategy, sequential sampling with a threshold for acceptance or matching with natal habitat. To date, these strategies do not seem to have been compared within a single model. Although we are just beginning to explore evolutionary effects of dispersal plasticity, it clearly has the potential to enhance as well as inhibit population divergence. Additional work should pay particular attention to dispersal distance and the strategy used to decide on where to settle. PMID:25806544

  9. Parallel speciation in Astyanax cave fish (Teleostei) in Northern Mexico.

    PubMed

    Strecker, Ulrike; Hausdorf, Bernhard; Wilkens, Horst

    2012-01-01

    We investigated differentiation processes in the Neotropical fish Astyanax that represents a model system for examining adaptation to caves, including regressive evolution. In particular, we analyzed microsatellite and mitochondrial data of seven cave and seven surface populations from Mexico to test whether the evolution of the cave fish represents a case of parallel evolution. Our data revealed that Astyanax invaded northern Mexico across the Trans-Mexican Volcanic Belt at least three times and that populations of all three invasions adapted to subterranean habitats. Significant differentiation was found between the cave and surface populations. We did not observe gene flow between the strongly eye and pigment reduced old cave populations (Sabinos, Tinaja, Pachon) and the surface fish, even when syntopically occurring like in Yerbaniz cave. Little gene flow, if any, was found between cave populations, which are variable in eye and pigmentation (Micos, Chica, Caballo Moro caves), and surface fish. This suggests that the variability is due to their more recent origin rather than to hybridization. Finally, admixture of the young Chica cave fish population with nuclear markers from older cave fish demonstrates that gene flow between populations that independently colonized caves occurs. Thus, all criteria of parallel speciation are fulfilled. Moreover, the microsatellite data provide evidence that two co-occurring groups with small sunken eyes and externally visible eyes, respectively, differentiated within the partly lightened Caballo Moro karst window cave and might represent an example for incipient sympatric speciation. PMID:21963344

  10. Technetium Inventory, Distribution, and Speciation in Hanford Tanks

    SciTech Connect

    Serne, R. Jeffrey; Rapko, Brian M.; Pegg, Ian L.

    2014-11-13

    The purpose of this report is three fold: 1) assemble the available information regarding Tc inventory, distribution between phases, and speciation in Hanford’s 177 storage tanks into a single, detailed, comprehensive assessment; 2) discuss the fate (distribution/speciation) of Tc once retrieved from the storage tanks and processed into final waste forms; and 3) discuss/document in less detail the available data on the inventory of Tc in other “pools” such as the vadose zone below inactive cribs and trenches, below single-shell tanks (SSTs) that have leaked, and in the groundwater below the Hanford Site. This report was revised in September 2014 to add detail and correct inaccuracies in Section 5.0 on the fate of technetium (Tc) recycle from the off-gas systems downstream of the low-activity waste (LAW) melters back to the melters, based on several reports that were not found in the original literature search on the topic. The newly provided reports, from experts active in the Hanford Tank Waste Treatment and Immobilization Plant (WTP) glass studies, the Vitreous State Laboratory at The Catholic University of America (VSL) melter and off-gas system demonstrations and overall WTP systems analysis, were not originally found on electronic databases commonly searched. The major revisions to Section 5.0 also required changes to Section 7.0 (Summary and Conclusions) and this executive summary.

  11. Allopatric Speciation within a Cryptic Species Complex of Australasian Octopuses

    PubMed Central

    Amor, Michael D.; Norman, Mark D.; Cameron, Hayley E.; Strugnell, Jan M.

    2014-01-01

    Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the ‘tetricus complex’. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide. PMID:24964133

  12. Thiolated eggshell membranes sorb and speciate inorganic selenium.

    PubMed

    Yang, Ting; Chen, Ming-Li; Hu, Xian-Wei; Wang, Zhao-Wen; Wang, Jian-Hua; Dasgupta, Purnendu K

    2011-01-01

    Eggshell membranes (ESMs) provide a unique, disulfide bond-rich surface. Thioglycolate reduction was used to generate thiol (-SH) groups on the ESM surface by S-S bond cleavage. The thiol-bearing ESMs (TESMs) were characterized by scanning electron microscopy and Raman spectroscopy. The fibrous network structure of the ESM is retained in the TESMs. TESMs adsorb both Se(IV) and Se(VI) but by different mechanisms: Se(VI) is retained reversibly, possibly via ionic interactions, while Se(IV) is reduced to Se(0) and deposited. We thus demonstrate speciation of selenium species, by using samples (a) as such and after prior oxidation to Se(VI), (b) preconcentration on a TESM microcolumn, (c) elution by 0.5 M HNO(3) that only elutes Se(VI) and (d) detection by graphite furnace atomic absorption spectrometry (GFAAS). The Se(IV) amount is determined by difference. For a 1.0 mL sample, the enrichment factor was 17.2, the S/N = 3 detection limit was 0.06 μg L(-1) and the precision was 3.3% at 0.50 μg L(-1). The linear range was 0.25-2.50 μg L(-1). The procedure was validated by analyzing selenium in certified reference materials of human hair (GBW 09101) and rice (GBW 10010). We further demonstrate utility by speciation of inorganic selenium in a series of water samples. PMID:20877887

  13. Evaluation of mercury speciation by EPA (Draft) Method 29

    SciTech Connect

    Laudal, D.L.; Heidt, M.K.; Nott, B.

    1995-11-01

    The 1990 Clean Air Act Amendments require that the U.S. Environmental protection Agency (EPA) assess the health risks associated with mercury emissions. Also, the law requires a separate assessment of health risks posed by the emission of 189 tract chemicals (including mercury) for electric utility steam-generating units. In order to conduct a meaningful assessment of health and environmental effects, we must have, among other things, a reliable and accurate method to measure mercury emissions. In addition, the rate of mercury deposition and the type of control strategies used may depend upon the type of mercury emitted (i.e., whether it is in the oxidized or elemental form). It has been speculated that EPA (Draft) Method 29 can speciate mercury by selective absorption; however, this claim has yet to be proven. The Electric Power Research Institute (EPRI) and the U.S. Department of Energy (DOE) have contracted with the Energy & Environmental Research Center (EERC) at University of North Dakota to evaluate EPA (Draft) Method 29 at the pilot-scale level. The objective of the work is to determine whether EPA (Draft) Method 29 can reliably quantify and speciate mercury in the flue gas from coal-fired boilers.

  14. Thermal enrichment and speciation of copper in rice husk ashes.

    PubMed

    Wei, Yu-Ling; Hu, Ming-Jan; Peng, Yen-Hsun

    2010-12-15

    Copper(II) was considerably enriched in the residual ash via thermal treatment of copper-sorbed rice husk at 700-1100°C for 2h, and the copper speciation was quantitatively determined with X-ray absorption spectroscopy. After the thermal process, the resulting ash only represents by weight 18.7-26.4% of the pre-heated samples. Copper content in the ashes is >7% which is far above the required minimum copper content in copper ores for the copper smelting sector, 0.5%. Crystalline SiO(2) is observed only in the ash generated at 1100°C, with more copper in this ash being available for leaching in acidic solution. It is suggested that this is due to the considerable dissimilarity in crystalline structure between copper compounds and crystalline SiO(2). No chemical reaction between copper and SiO(2) is observed in any ash. In fact, we suggest that the SiO(2) crystalline phase repels copper during the thermal process; this would make it easy to extract copper from the ashes. For copper speciation in the ashes, CuO merely represents 0-12% of the total copper, while Cu(2)O and Cu(0) represent 34-42% and 46-63%, respectively. The lower copper oxidation state would be beneficial for the copper smelting process due to less usage of coke. PMID:20869164

  15. 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.

  16. Arsenic speciation in humans and food products: a review.

    PubMed

    Benramdane, L; Bressolle, F; Vallon, J J

    1999-09-01

    Although acute intoxication has become rare, arsenic (As) is still a dangerous pollution agent for industrial workers and people living in the vicinity of emission sources. In humans, only inorganic As is toxic; organic forms present in large amounts in the environment are nontoxic. It is therefore important to be able to differentiate one group from the other using appropriate speciation methods. The authors review the present knowledge of the distribution of As in humans and food products. The three steps of the speciation methods (sample preparation, species separation, and detection) are described. For liquid samples, a clean-up step (C18 cartridge extraction, dilution, or freezing) is necessary to eliminate proteins and salts from the matrix. For solid organic samples, the first step consists of the digestion of tissues followed by solvent extraction sometimes coupled with a C18 extraction. The separation of As species is accomplished by different high-performance liquid chromatography (HPLC) methods (ion-exchange, ion-pairing, and micellar liquid chromatography). The detection methods are compatible with HPLC and are able to detect As species in the microgram-per-liter range. Inductively coupled plasma (ICP) atomic emission spectrometry is more frequently used, but suffers from interference by organic solvents in the mobile phases. Atomic absorption spectrometry methods give sensitivities of the same order. ICP-mass spectrometry has the advantage of specificity and can be 100- to 1000-fold more sensitive than previous methods. PMID:10497786

  17. Iron(III) citrate speciation in aqueous solution.

    PubMed

    Silva, Andre M N; Kong, XiaoLe; Parkin, Mark C; Cammack, Richard; Hider, Robert C

    2009-10-28

    Citrate is an iron chelator and it has been shown to be the major iron ligand in the xylem sap of plants. Furthermore, citrate has been demonstrated to be an important ligand for the non-transferrin bound iron (NTBI) pool occurring in the plasma of individuals suffering from iron-overload. However, ferric citrate chemistry is complicated and a definitive description of its aqueous speciation at neutral pH remains elusive. X-Ray crystallography data indicates that the alcohol function of citrate (Cit4-) is involved in Fe(III) coordination and that deprotonation of this functional group occurs upon complex formation. The inability to include this deprotonation in the affinity constant calculations has been a major source of divergence between various reports of iron(III)-citrate affinity constants. However the recent determination of the alcoholic pKa of citric acid (H4Cit) renders the reassessment of the ferric citrate system possible. The aqueous speciation of ferric citrate has been investigated by mass spectrometry and EPR spectroscopy. It was observed that the most relevant species are a monoiron dicitrate species and dinuclear and trinuclear oligomeric complexes, the relative concentration of which depends on the solution pH value and the iron : citric acid molar ratio. Spectrophotometric titration was utilized for affinity constant determination and the formation constant for the biologically relevant [Fe(Cit)2]5- is reported for the first time. PMID:19809738

  18. Speciation reversal and biodiversity dynamics with hybridization in changing environments.

    PubMed

    Seehausen, Ole; Takimoto, Gaku; Roy, Denis; Jokela, Jukka

    2008-01-01

    A considerable fraction of the world's biodiversity is of recent evolutionary origin and has evolved as a by-product of, and is maintained by, divergent adaptation in heterogeneous environments. Conservationists have paid attention to genetic homogenization caused by human-induced translocations (e.g. biological invasions and stocking), and to the importance of environmental heterogeneity for the ecological coexistence of species. However, far less attention has been paid to the consequences of loss of environmental heterogeneity to the genetic coexistence of sympatric species. Our review of empirical observations and our theoretical considerations on the causes and consequences of interspecific hybridization suggest that a loss of environmental heterogeneity causes a loss of biodiversity through increased genetic admixture, effectively reversing speciation. Loss of heterogeneity relaxes divergent selection and removes ecological barriers to gene flow between divergently adapted species, promoting interspecific introgressive hybridization. Since heterogeneity of natural environments is rapidly deteriorating in most biomes, the evolutionary ecology of speciation reversal ought to be fully integrated into conservation biology. PMID:18034800

  19. Speciation and bioavailability of zinc in amended sediments

    SciTech Connect

    Williams, Aaron G.B.; Scheckel, Kirk G.; McDermott, Gregory; Gratson, David; Neptune, Dean; Ryan, James A.

    2011-12-09

    The speciation and bioavailability of zinc (Zn) in smelter-contaminated sediments were investigated as a function of phosphate (apatite) and organic amendment loading rate. Zinc species identified in preamendment sediment were zinc hydroxide-like phases, sphalerite, and zinc sorbed to an iron oxide via X-ray adsorption near edge structure (XANES) spectroscopy. Four months after adding the amendments to the contaminated sediment, hopeite, a Zn phosphate mineral, was identified indicating phosphate was binding and sequestering available Zn and Zn pore water concentrations were decreased at levels of 90% or more. Laboratory experiments indicate organic amendments exhibit a limited effect and may hinder sequestration of pore water Zn when mixed with apatite. The acute toxicity of the sediment Zn was evaluated with Hyalella azteca, and bioaccumulation of Zn with Lumbriculus variegates. The survivability of H. azteca increased as a function of phosphate (apatite) loading rate. In contaminated sediment without apatite, no specimens of H. azteca survived. The bioaccumulation of Zn in L. variegates also followed a trend of decreased bioaccumulation with increased phosphate loading in the contaminated sediment. The research supports an association between Zn speciation and bioavailability.

  20. Mercury speciation during in situ thermal desorption in soil.

    PubMed

    Park, Chang Min; Katz, Lynn E; Liljestrand, Howard M

    2015-12-30

    Metallic mercury (Hg(0)) and its compounds are highly mobile and toxic environmental pollutants at trace level. In situ thermal desorption (ISTD) is one of the soil remediation processes applying heat and vacuum simultaneously. Knowledge of thermodynamic mercury speciation is imperative to understand the fate and transport of mercury during thermal remediation and operate the treatment processes in a cost-effective manner. Hence, speciation model for inorganic mercury was developed over a range of environmental conditions to identify distribution of dissolved mercury species and potential transformations of mercury at near source environment. Simulation of phase transitions for metallic mercury, mercury(II) chloride and mercury sulfide with temperature increase showed that complete vaporization of metallic mercury and mercury(II) chloride were achieved below the boiling point of water. The effect of soil compositions on mercury removal was also evaluated to better understand thermal remediation process. Higher vapor pressures expected both from soil pore water and inorganic carbonate minerals in soil as well as creation of permeability were significant for complete vaporization and removal of mercury. PMID:26275352

  1. Speciation of aluminum in aqueous solutions using ion chromatography.

    PubMed

    Bertsch, P M; Anderson, M A

    1989-03-15

    An ion chromatographic method in which aluminum (AI) is quantitatively determined via postcolumn derivatization with Tiron (4,5-dihydroxy-m-benzenedisulfonic acid) was evaluated for its utility as a method for speciating AI in aqueous solutions. Fluro-, oxalato-, and citratoaluminum complexes were identified by distinct peaks within chromatograms of AI solutions when the appropriate ligand was added. Excellent quantitative agreement between predicted species concentrations (via the thermodynamic speciation model GEOCHEM) and those determined by ion chromatography was obtained for samples prepared in the eluent matrix. The predominantly outer sphere sulfatoaluminum complexes were not observed to elute as singly charged species, but rather exhibited a retention time indistinguishable from the AI(H2O)6(3+) species. It is concluded that inner sphere AI complexes (generally possessing relatively high association constants) possess adequate kinetic stability to withstand degradation during the ion exchange process, whereas outer sphere complexes apparently readily dissociate in the presence of the sulfonate exchange sites. Deviations in sample ionic strength (mu) and pH from that of the eluent resulted in some redistribution among species, the degree of which was ligand specific. PMID:2729589

  2. Multivariate sexual selection in a rapidly evolving speciation phenotype.

    PubMed

    Oh, Kevin P; Shaw, Kerry L

    2013-06-22

    Estimating the fitness surface of rapidly evolving secondary sexual traits can elucidate the origins of sexual isolation and thus speciation. Evidence suggests that sexual selection is highly complex in nature, often acting on multivariate sexual characters that sometimes include non-heritable components of variation, thus presenting a challenge for predicting patterns of sexual trait evolution. Laupala crickets have undergone an explosive species radiation marked by divergence in male courtship song and associated female preferences, yet patterns of sexual selection that might explain this diversification remain unknown. We used female phonotaxis trials to estimate the fitness surface for acoustic characters within one population of Laupala cerasina, a species with marked geographical variation in male song and female preferences. Results suggested significant directional sexual selection on three major song traits, while canonical rotation of the matrix of nonlinear selection coefficients (γ) revealed the presence of significant convex (stabilizing) sexual selection along combinations of characters. Analysis of song variation within and among males indicated significantly higher repeatability along the canonical axis of greatest stabilizing selection than along the axis of greatest linear selection. These results are largely consistent with patterns of song divergence that characterize speciation and suggest that different song characters have the potential to indicate distinct information to females during courtship. PMID:23760640

  3. Astatine standard redox potentials and speciation in acidic medium.

    PubMed

    Champion, J; Alliot, C; Renault, E; Mokili, B M; Chérel, M; Galland, N; Montavon, G

    2010-01-14

    A combined experimental and theoretical approach is used to define astatine (At) speciation in acidic aqueous solution and to answer the two main questions raised from literature data: does At(0) exist in aqueous solution and what is the chemical form of At(+III), if it exists. The experimental approach considers that a given species is characterized by its distribution coefficient (D) experimentally determined in a biphasic system. The change in speciation arising from a change in experimental conditions is observed by a change in D value. The theoretical approach involves quasi-relativistic quantum chemistry calculations. The results show that At at the oxidation state 0 cannot exist in aqueous solution. The three oxidation states present in the range of water stability are At(-I), At(+I), and At(+III) and exist as At(-), At(+), and AtO(+), respectively, in the 1-2 pH range. The standard redox potentials of the At(+)/At(-) and AtO(+)/At(+) couples have been determined, the respective values being 0.36 +/- 0.01 and 0.74 +/- 0.01 V vs NHE. PMID:20014840

  4. Trace metal speciation and bioavailability in anaerobic digestion: A review.

    PubMed

    Thanh, Pham Minh; Ketheesan, Balachandran; Yan, Zhou; Stuckey, David

    2016-01-01

    Trace metals are essential for the growth of anaerobic microorganisms, however, in practice they are often added to anaerobic digesters in excessive amounts, which can lead to inhibition. The concept of bioavailability of metals in anaerobic digestion has been poorly understood in the past, and a lack of deep understanding of the relationship between trace metal speciation and bioavailability can result in ineffective metal dosing strategies for anaerobic digesters. Sequential extraction schemes are useful for fractionating trace metals into their different forms, and metal sulfides can serve as a store and source for trace metals during anaerobic digestion, while natural/synthetic chelating agents (soluble microbial products-SMPs, extracellular polysaccharides-EPS, and EDTA/NTA) are capable of controlling trace metal bioavailability. Nevertheless, more work is needed to: investigate the speciation and bioavailability of Ca, Mg, Mn, W, and Se; compare the bioavailability of different forms of trace metals e.g. carbonates, sulfides, phosphates to different anaerobic trophic groups; determine what factors influence metal sulfide dissolution; investigate whether chelating agents can increase trace metal bioavailability; develop and adapt specialized analytical techniques, and; determine how trace metal dynamics change in an anaerobic membrane bioreactor (AnMBR). PMID:26707985

  5. Submicrometer particle formation and mercury speciation under O{sub 2}-CO{sub 2} coal combustion

    SciTech Connect

    Achariya Suriyawong; Michael Gamble; Myong-Hwa Lee; Richard Axelbaum; Pratim Biswas

    2006-12-15

    The characteristics of the submicrometer mode of ash and mercury speciation on combustion of coal in an oxygen-carbon dioxide and air (conventional) system were compared. The experiments were conducted at different O{sub 2}:CO{sub 2} and O{sub 2}:N{sub 2}:CO{sub 2} mixing ratios. On replacing the nitrogen in air with carbon dioxide, the total mass of the particles in the submicrometer mode ({lt}0.5 {mu}m) of ash was smaller. Correspondingly, the geometric mean size (d{sub pg}) of the submicrometer aerosol was smaller by approximately 28%. When the O{sub 2}:CO{sub 2} ratio was increased from 1:4 to 4:4, the geometric mean size of the submicrometer mode increased from 29 to 54 nm because of a faster vaporization rate as a result of a higher coal particle temperature. An increase in the geometric mean size was observed on increasing the N{sub 2}:CO{sub 2} ratio at a fixed O{sub 2} concentration because of the same reasons. The shape of the primary particles was spherical in all the tests, indicating that a vapor to particle transformation pathway was prevalent. The ratios of elemental to oxidized mercury (approximately 4:1) were similar for O{sub 2}-CO{sub 2} and air combustion. 31 refs., 8 figs., 2 tabs.

  6. Manganese speciation in Diplodon chilensis patagonicus shells: a XANES study

    NASA Astrophysics Data System (ADS)

    Soldati, A. L.; Vicente-Vilas, V.; Goettlicher, J.; Jacob, D. E.

    2009-04-01

    century, resolving the environmental signal annually and even seasonally (Soldati et al., 2008b). High resolution trace elemental analysis by LA-ICPMS and EPMA in the shells show that elements like Mg and Mn are related to the seasonal pattern and can be enriched along the organic-rich annual shell growth lines. Thus, these elements could possibly be bound organically instead of occupying a defined site in the crystal lattice of the calcium carbonate phase. LA-ICP-MS results show that Mn concentrations in these Diplodon shells range between 1000-300 g/g and 100-10 g/g and that the areas of enrichment are in the micrometer range. Raman and XRD measurements at high spatial resolution failed in recognizing whether the Mn is in carbonate solid solution or not. Therefore, speciation techniques like X-ray absorption fine structure (XAFS) spectroscopy with a high lateral resolution are required to address this question. Prior to XAFS spectroscopy the samples were mapped with the intensity of the Mn Kα fluorescence emission line in order to locate the Mn rich areas of interest. Because of the Mn concentrations in the sub % range the XAFS spectra at the positions of interest have been recorded in fluorescence mode using a 7 element Si(Li) detector. This study focuses on the near edge (XANES: X-ray absorption near edge structure) part of the spectra. For data evaluation, XANES spectra of reference substances were additionally measured in order to get first hints to Mn valence and bonding. As standards were used Mn and Mn rich carbonates, Mn oxides with Mn in different oxidation states, and Mn in organic compounds (Mn-porphyrin and Mn-acetate). The XAFS measurements have been carried out at the SUL-X beamline of the synchrotron radiation source ANKA of the Forschungszentrum Karlsruhe. Data evaluation is ongoing. References MEIBOM, A., CUIF, J.P., HOULBREQUE, F., MOSTEFAOUI, S., DAUPHIN, Y., MEIBOM; K.L. & DUNBAR, R. (2008). Compositional variations at ultra-structure length scales

  7. Influence of the hydration by the environmental humidity on the metallic speciation and the photocatalytic activity of Cr/MCM-41

    NASA Astrophysics Data System (ADS)

    Elías, Verónica R.; Sabre, Ema V.; Winkler, Elin L.; Andrini, Leandro; Requejo, Félix G.; Casuscelli, Sandra G.; Eimer, Griselda A.

    2014-05-01

    The influence of the environmental humidity on the Cr species deposited on inorganic supports like MCM-41 silicates was analyzed by UV-vis Diffuse Reflectance (UV-vis RD), Electronic Spin Resonance (ESR) and X-ray near-edge (XANES) spectroscopy. Metal speciation could be inferred, finding that prolonged exposure periods under environmental humidity provoked the reduction of the active Cr6+ species and thus, the decrease of the Cr/MCM-41 photoactivity. After the Ti loading over the Cr modified samples, Cr species and the photoactivity were not notably influenced by the humidity exposure. Thus, it could be concluded that the presence of Ti is important because the TiO2 cover protects the oxidized Cr species, stabilizing them.

  8. SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT.

    PubMed

    Baker, Robert J; Bradley, Robert D

    2006-08-01

    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

  9. Inferring Orthologs: Open Questions and Perspectives

    PubMed Central

    Tekaia, Fredj

    2016-01-01

    With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. Yet, the dynamic remodeling of genome content through gain, loss, transfer of genes, and segmental and whole-genome duplication hinders reliable orthology detection. Moreover, the lack of direct functional evidence and the questionable quality of some available genome sequences and annotations present additional difficulties to assess orthology. This article reviews the existing computational methods and their potential accuracy in the high-throughput era of genome sequencing and anticipates open questions in terms of methodology, reliability, and computation. Appropriate taxon sampling together with combination of methods based on similarity, phylogeny, synteny, and evolutionary knowledge that may help detecting speciation events appears to be the most accurate strategy. This review also raises perspectives on the potential determination of orthology throughout the whole species phylogeny. PMID:26966373

  10. The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation.

    PubMed

    Melo-Ferreira, José; Seixas, Fernando A; Cheng, Ellen; Mills, L Scott; Alves, Paulo C

    2014-09-01

    Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America - the snowshoe hare (Lepus americanus), the white-tailed jackrabbit (L. townsendii) and the black-tailed jackrabbit (L. californicus) - by analysing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6240 bp; 94 specimens). A multilocus-multispecies coalescent-based phylogeny suggests that L. americanus diverged ~2.7 Ma and that L. californicus and L. townsendii split more recently (~1.2 Ma). Within L. americanus, a deep history of cryptic divergence (~2.0 Ma) was inferred, which coincides with major speciation events in other North American species. While the isolation-with-migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change. PMID:25113393

  11. List mode multichannel analyzer

    DOEpatents

    Archer, Daniel E.; Luke, S. John; Mauger, G. Joseph; Riot, Vincent J.; Knapp, David A.

    2007-08-07

    A digital list mode multichannel analyzer (MCA) built around a programmable FPGA device for onboard data analysis and on-the-fly modification of system detection/operating parameters, and capable of collecting and processing data in very small time bins (<1 millisecond) when used in histogramming mode, or in list mode as a list mode MCA.

  12. Inferring magnetospheric heavy ion density using EMIC waves

    NASA Astrophysics Data System (ADS)

    Kim, Eun-Hwa; Johnson, Jay R.; Kim, Hyomin; Lee, Dong-Hun

    2015-08-01

    We present a method to infer heavy ion concentration ratios from electromagnetic ion cyclotron (EMIC) wave observations that result from ion-ion hybrid (IIH) resonance. A key feature of the IIH resonance is the concentration of wave energy in a field-aligned resonant mode that exhibits linear polarization. These mode-converted waves at the IIH resonance are localized at the location where the frequency of a compressional wave driver matches the IIH resonance condition, which depends sensitively on the heavy ion concentration. This dependence makes it possible to estimate the heavy ion concentration ratio. In this paper, we evaluate the absorption coefficients at the IIH resonance at Earth's geosynchronous orbit for variable concentrations of He+ and wave frequencies using a dipole magnetic field model. We find that the resonance only occurs over a limited range of wave frequency such that the IIH resonance frequency is close to but not exactly the same as the crossover frequency. Using the wave absorption and EMIC waves observed from the GOES 12 satellite, we demonstrate how this technique can be used to estimate the He+ concentration of around 4% near L = 6.6 assuming electron-H+-He+ plasma.

  13. Inferring Magnetospheric Heavy Ion Density using EMIC Waves

    SciTech Connect

    Kim, Eun-Hwa; Johnson, Jay R.; Kim, Hyomin; Lee, Dong-Hun

    2014-05-01

    We present a method to infer heavy ion concentration ratios from EMIC wave observations that result from ionion hybrid (IIH) resonance. A key feature of the ion-ion hybrid resonance is the concentration of wave energy in a field-aligned resonant mode that exhibits linear polarization. This mode converted wave is localized at the location where the frequency of a compressional wave driver matches the IIH resonance condition, which depends sensitively on the heavy ion concentration. This dependence makes it possible to estimate the heavy ion concentration ratio. In this letter, we evaluate the absorption coefficients at the IIH resonance at Earth's geosynchronous orbit for variable concentrations of He+ and field-aligned wave numbers using a dipole magnetic field. Although wave absorption occurs for a wide range of heavy ion concentrations, it only occurs for a limited range of field-aligned wave numbers such that the IIH resonance frequency is close to, but not exactly the same as the crossover frequency. Using the wave absorption and observed EMIC waves from GOES-12 satellite, we demonstrate how this technique can be used to estimate that the He+ concentration is around 4% near L = 6.6.

  14. Causal Inferences with Group Based Trajectory Models

    ERIC Educational Resources Information Center

    Haviland, Amelia M.; Nagin, Daniel S.

    2005-01-01

    A central theme of research on human development and psychopathology is whether a therapeutic intervention or a turning-point event, such as a family break-up, alters the trajectory of the behavior under study. This paper lays out and applies a method for using observational longitudinal data to make more confident causal inferences about the…

  15. What Children Infer from Social Categories

    ERIC Educational Resources Information Center

    Diesendruck, Gil; Eldror, Ehud

    2011-01-01

    Children hold the belief that social categories have essences. We investigated what kinds of properties children feel licensed to infer about a person based on social category membership. Seventy-two 4-6-year-olds were introduced to novel social categories defined as having one internal--psychological or biological--and one external--behavioral or…

  16. Inference and the Introductory Statistics Course

    ERIC Educational Resources Information Center

    Pfannkuch, Maxine; Regan, Matt; Wild, Chris; Budgett, Stephanie; Forbes, Sharleen; Harraway, John; Parsonage, Ross

    2011-01-01

    This article sets out some of the rationale and arguments for making major changes to the teaching and learning of statistical inference in introductory courses at our universities by changing from a norm-based, mathematical approach to more conceptually accessible computer-based approaches. The core problem of the inferential argument with its…

  17. Making statistical inferences about software reliability

    NASA Technical Reports Server (NTRS)

    Miller, Douglas R.

    1988-01-01

    Failure times of software undergoing random debugging can be modelled as order statistics of independent but nonidentically distributed exponential random variables. Using this model inferences can be made about current reliability and, if debugging continues, future reliability. This model also shows the difficulty inherent in statistical verification of very highly reliable software such as that used by digital avionics in commercial aircraft.

  18. Making statistical inferences about software reliability

    NASA Technical Reports Server (NTRS)

    Miller, Douglas R.

    1986-01-01

    Failure times of software undergoing random debugging can be modeled as order statistics of independent but nonidentically distributed exponential random variables. Using this model inferences can be made about current reliability and, if debugging continues, future reliability. This model also shows the difficulty inherent in statistical verification of very highly reliable software such as that used by digital avionics in commercial aircraft.

  19. Elaborative Inferences on an Expository Text.

    ERIC Educational Resources Information Center

    Durgunoglu, Aydin Y.; Jehng, Jihn-Chang J.

    1991-01-01

    The distinction between remembering text information and applying the acquired knowledge (making inferences) was studied with a dissociation paradigm, using 110 undergraduates who performed verification and recognition tasks. The same variables did not affect performance on the two tasks. Text organization affected recognition but not verification…

  20. Inverse Ising inference with correlated samples

    NASA Astrophysics Data System (ADS)

    Obermayer, Benedikt; Levine, Erel

    2014-12-01

    Correlations between two variables of a high-dimensional system can be indicative of an underlying interaction, but can also result from indirect effects. Inverse Ising inference is a method to distinguish one from the other. Essentially, the parameters of the least constrained statistical model are learned from the observed correlations such that direct interactions can be separated from indirect correlations. Among many other applications, this approach has been helpful for protein structure prediction, because residues which interact in the 3D structure often show correlated substitutions in a multiple sequence alignment. In this context, samples used for inference are not independent but share an evolutionary history on a phylogenetic tree. Here, we discuss the effects of correlations between samples on global inference. Such correlations could arise due to phylogeny but also via other slow dynamical processes. We present a simple analytical model to address the resulting inference biases, and develop an exact method accounting for background correlations in alignment data by combining phylogenetic modeling with an adaptive cluster expansion algorithm. We find that popular reweighting schemes are only marginally effective at removing phylogenetic bias, suggest a rescaling strategy that yields better results, and provide evidence that our conclusions carry over to the frequently used mean-field approach to the inverse Ising problem.

  1. Inference and Children's Comprehension of Pronouns.

    ERIC Educational Resources Information Center

    Wykes, Til

    1981-01-01

    Investigated five-year-olds' abilities to determine the reference of anaphoric pronouns. Children had difficulty when a sentence contained more than one pronoun, especially when assigning the reference of a pronoun requiring an inference. The children's difficulties stemmed from forgetting premise information and from having problems in carrying…

  2. Efficient Bayesian inference for ARFIMA processes

    NASA Astrophysics Data System (ADS)

    Graves, T.; Gramacy, R. B.; Franzke, C. L. E.; Watkins, N. W.

    2015-03-01

    Many geophysical quantities, like atmospheric temperature, water levels in rivers, and wind speeds, have shown evidence of long-range dependence (LRD). LRD means that these quantities experience non-trivial temporal memory, which potentially enhances their predictability, but also hampers the detection of externally forced trends. Thus, it is important to reliably identify whether or not a system exhibits LRD. In this paper we present a modern and systematic approach to the inference of LRD. Rather than Mandelbrot's fractional Gaussian noise, we use the more flexible Autoregressive Fractional Integrated Moving Average (ARFIMA) model which is widely used in time series analysis, and of increasing interest in climate science. Unlike most previous work on the inference of LRD, which is frequentist in nature, we provide a systematic treatment of Bayesian inference. In particular, we provide a new approximate likelihood for efficient parameter inference, and show how nuisance parameters (e.g. short memory effects) can be integrated over in order to focus on long memory parameters, and hypothesis testing more directly. We illustrate our new methodology on the Nile water level data, with favorable comparison to the standard estimators.

  3. Tactile length contraction as Bayesian inference.

    PubMed

    Tong, Jonathan; Ngo, Vy; Goldreich, Daniel

    2016-08-01

    To perceive, the brain must interpret stimulus-evoked neural activity. This is challenging: The stochastic nature of the neural response renders its interpretation inherently uncertain. Perception would be optimized if the brain used Bayesian inference to interpret inputs in light of expectations derived from experience. Bayesian inference would improve perception on average but cause illusions when stimuli violate expectation. Intriguingly, tactile, auditory, and visual perception are all prone to length contraction illusions, characterized by the dramatic underestimation of the distance between punctate stimuli delivered in rapid succession; the origin of these illusions has been mysterious. We previously proposed that length contraction illusions occur because the brain interprets punctate stimulus sequences using Bayesian inference with a low-velocity expectation. A novel prediction of our Bayesian observer model is that length contraction should intensify if stimuli are made more difficult to localize. Here we report a tactile psychophysical study that tested this prediction. Twenty humans compared two distances on the forearm: a fixed reference distance defined by two taps with 1-s temporal separation and an adjustable comparison distance defined by two taps with temporal separation t ≤ 1 s. We observed significant length contraction: As t was decreased, participants perceived the two distances as equal only when the comparison distance was made progressively greater than the reference distance. Furthermore, the use of weaker taps significantly enhanced participants' length contraction. These findings confirm the model's predictions, supporting the view that the spatiotemporal percept is a best estimate resulting from a Bayesian inference process. PMID:27121574

  4. John Updike and Norman Mailer: Sport Inferences.

    ERIC Educational Resources Information Center

    Upshaw, Kathryn Jane

    The phenomenon of writer use of sport inferences in the literary genre of the novel is examined in the works of Updike and Mailer. Novels of both authors were reviewed in order to study the pattern of usage in each novel. From these patterns, concepts which illustrated the sport philosophies of each author were used for general comparisons of the…

  5. Campbell's and Rubin's Perspectives on Causal Inference

    ERIC Educational Resources Information Center

    West, Stephen G.; Thoemmes, Felix

    2010-01-01

    Donald Campbell's approach to causal inference (D. T. Campbell, 1957; W. R. Shadish, T. D. Cook, & D. T. Campbell, 2002) is widely used in psychology and education, whereas Donald Rubin's causal model (P. W. Holland, 1986; D. B. Rubin, 1974, 2005) is widely used in economics, statistics, medicine, and public health. Campbell's approach focuses on…

  6. Investigating Mathematics Teachers' Thoughts of Statistical Inference

    ERIC Educational Resources Information Center

    Yang, Kai-Lin

    2012-01-01

    Research on statistical cognition and application suggests that statistical inference concepts are commonly misunderstood by students and even misinterpreted by researchers. Although some research has been done on students' misunderstanding or misconceptions of confidence intervals (CIs), few studies explore either students' or mathematics…

  7. Decision generation tools and Bayesian inference

    NASA Astrophysics Data System (ADS)

    Jannson, Tomasz; Wang, Wenjian; Forrester, Thomas; Kostrzewski, Andrew; Veeris, Christian; Nielsen, Thomas

    2014-05-01

    Digital Decision Generation (DDG) tools are important software sub-systems of Command and Control (C2) systems and technologies. In this paper, we present a special type of DDGs based on Bayesian Inference, related to adverse (hostile) networks, including such important applications as terrorism-related networks and organized crime ones.

  8. Linguistic Markers of Inference Generation While Reading

    ERIC Educational Resources Information Center

    Clinton, Virginia; Carlson, Sarah E.; Seipel, Ben

    2016-01-01

    Words can be informative linguistic markers of psychological constructs. The purpose of this study is to examine associations between word use and the process of making meaningful connections to a text while reading (i.e., inference generation). To achieve this purpose, think-aloud data from third-fifth grade students (N = 218) reading narrative…

  9. Evolutionary inference via the Poisson Indel Process.

    PubMed

    Bouchard-Côté, Alexandre; Jordan, Michael I

    2013-01-22

    We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments. PMID:23275296

  10. Rates inferred from the space debris catalog

    SciTech Connect

    Canavan, G.H.

    1996-08-01

    Collision and fragmentation rates are inferred from the AFSPC space debris catalog and compare with estimates from other treatments. The collision rate is evaluated without approximation. The fragmentation rate requires additional empirical assessments. The number of fragments per collision is low compared to analytic and numerical treatments, is peaked low, and falls rapidly with altitude.

  11. Causal Inferences in the Campbellian Validity System

    ERIC Educational Resources Information Center

    Lund, Thorleif

    2010-01-01

    The purpose of the present paper is to critically examine causal inferences and internal validity as defined by Campbell and co-workers. Several arguments are given against their counterfactual effect definition, and this effect definition should be considered inadequate for causal research in general. Moreover, their defined independence between…

  12. An evaluation of explanations of probabilistic inference.

    PubMed Central

    Suermondt, H. J.; Cooper, G. F.

    1992-01-01

    Providing explanations of the conclusions of decision-support systems can be viewed as presenting inference results in a manner that enhances the user's insight into how these results were obtained. The ability to explain inferences has been demonstrated to be an important factor in making medical decision-support systems acceptable for clinical use. Although many researchers in artificial intelligence have explored the automatic generation of explanations for decision-support systems based on symbolic reasoning, research in automated explanation of probabilistic results has been limited. We present the results of an an evaluation study of INSITE, a program that explains the reasoning of decision-support systems based on Bayesian belief networks. In the domain of anesthesia, we compared subjects who had access to a belief network with explanations of the inference results, to control subjects who used the same belief network without explanations. We show that, compared to control subjects, the explanation subjects demonstrated greater diagnostic accuracy, were more confident about their conclusions, were more critical of the belief network, and found the presentation of the inference results more clear. PMID:1482939

  13. Connecting Scientific Reasoning and Causal Inference

    ERIC Educational Resources Information Center

    Kuhn, Deanna; Dean, David, Jr.

    2004-01-01

    Literature on multivariable causal inference (MCI) and literature on scientific reasoning (SR) have proceeded almost entirely independently, although they in large part address the same phenomena. An effort is made to bring these paradigms into close enough alignment with one another to compare implications of the two lines of work and examine how…

  14. Statistical Inference in Retrieval Effectiveness Evaluation.

    ERIC Educational Resources Information Center

    Savoy, Jacques

    1997-01-01

    Discussion of evaluation methodology in information retrieval focuses on the average precision over a set of fixed recall values in an effort to evaluate the retrieval effectiveness of a search algorithm. Highlights include a review of traditional evaluation methodology with examples; and a statistical inference methodology called bootstrap.…

  15. Pediatric Pain, Predictive Inference, and Sensitivity Analysis.

    ERIC Educational Resources Information Center

    Weiss, Robert

    1994-01-01

    Coping style and effects of counseling intervention on pain tolerance was studied for 61 elementary school students through immersion of hands in cold water. Bayesian predictive inference tools are able to distinguish between subject characteristics and manipulable treatments. Sensitivity analysis strengthens the certainty of conclusions about…

  16. Double jeopardy in inferring cognitive processes

    PubMed Central

    Fific, Mario

    2014-01-01

    Inferences we make about underlying cognitive processes can be jeopardized in two ways due to problematic forms of aggregation. First, averaging across individuals is typically considered a very useful tool for removing random variability. The threat is that averaging across subjects leads to averaging across different cognitive strategies, thus harming our inferences. The second threat comes from the construction of inadequate research designs possessing a low diagnostic accuracy of cognitive processes. For that reason we introduced the systems factorial technology (SFT), which has primarily been designed to make inferences about underlying processing order (serial, parallel, coactive), stopping rule (terminating, exhaustive), and process dependency. SFT proposes that the minimal research design complexity to learn about n number of cognitive processes should be equal to 2n. In addition, SFT proposes that (a) each cognitive process should be controlled by a separate experimental factor, and (b) The saliency levels of all factors should be combined in a full factorial design. In the current study, the author cross combined the levels of jeopardies in a 2 × 2 analysis, leading to four different analysis conditions. The results indicate a decline in the diagnostic accuracy of inferences made about cognitive processes due to the presence of each jeopardy in isolation and when combined. The results warrant the development of more individual subject analyses and the utilization of full-factorial (SFT) experimental designs. PMID:25374545

  17. Reliability of inferred age, and coincidence between inferred age and chronological age.

    PubMed

    Kataoka, J; Ohara, S; Shibata, S; Maie, K

    1996-06-01

    Outdoor research is restricted by many factors. The age inference was one of the biggest problems for the outdoor researchers. We have investigated the reliability of inferred age for the Japanese people, and took out the estimation formula for the age, even if it was based on the inferred age. The age classification was the most popular method for this purpose, and there were many classifications. We took the classification of young, middle aged, and elderly groups, in which classification of the SDs were rather small, that is, 4, 5, and 7 years for the young, middle aged, and elderly age groups, respectively. PMID:9551138

  18. Density-dependent speciation alters the structure and dynamics of neutral communities.

    PubMed

    Wang, Shaopeng; Chen, Anping; Pacala, Stephen W; Fang, Jingyun

    2015-05-01

    The neutral theory of biodiversity (NTB) provides an individual-based modeling framework to study eco-evolutionary dynamics. Previous NTB models usually assumed the same per capita rate of speciation across lineages. However, population dynamics may induce macroevolutionary feedbacks that can result in variable per capita speciation rates across lineages. In this paper, with analytical and simulation approaches, we explore how different scenarios of density-dependent speciation may impact the diversity and phylogenetic patterns of neutral communities, and compare the results to predictions of the original NTB model with an invariant speciation rate. Our results show that positive per capita speciation rate-abundance relationships could result in higher species richness and evenness, enhanced stability (evidenced by higher post-disturbance recovery rates and lower temporal variability in species diversity), and higher imbalance in phylogenetic trees. The opposite patterns are predicted when per capita speciation rates decrease with abundance. Particularly, strong negative speciation rate-abundance relationships can generate a positive correlation between phylogenetic age and abundance, which has been observed in Panamanian tree species. Our findings demonstrate the importance of eco-evolutionary feedbacks for understanding long-term diversity and phylogenetic patterns in ecological communities. PMID:25701450

  19. Geographic variation in animal colour polymorphisms and its role in speciation.

    PubMed

    McLean, Claire A; Stuart-Fox, Devi

    2014-11-01

    Polymorphic species, in which multiple variants coexist within a population, are often used as model systems in evolutionary biology. Recent research has been dominated by the hypothesis that polymorphism can be a precursor to speciation. To date, the majority of research regarding polymorphism and speciation has focused on whether polymorphism is maintained within a population or whether morphs within populations may diverge to form separate species (sympatric speciation); however, the geographical context of speciation in polymorphic systems is likely to be both diverse and complex. In this review, we draw attention to the geographic variation in morph composition and frequencies that characterises many, if not most polymorphic species. Recent theoretical and empirical developments suggest that such variation in the number, type and frequency of morphs present among populations can increase the probability of speciation. Thus, the geographical context of a polymorphism requires a greater research focus. Here, we review the prevalence, causes and evolutionary consequences of geographic variation in polymorphism in colour-polymorphic animal species. The prevalence and nature of geographic variation in polymorphism suggests that polymorphism may be a precursor to and facilitate speciation more commonly than appreciated previously. We argue that a better understanding of the processes generating geographic variation in polymorphism is vital to understanding how polymorphism can promote speciation. PMID:24528520

  20. The genomics of an adaptive radiation: insights across the Heliconius speciation continuum.

    PubMed

    Supple, Megan; Papa, Riccardo; Counterman, Brian; McMillan, W Owen

    2014-01-01

    Fueled by new technologies that allow rapid and inexpensive assessment of fine scale individual genomic variation, researchers are making transformational discoveries at the interface between genomes and biological complexity. Here we review genomic research in Heliconius butterflies - a radiation characterized by extraordinary phenotypic diversity in warningly colored wing patterns and composed of a continuum of taxa across the stages of speciation. These characteristics, coupled with a 50-year legacy of ecological and behavioral research, offer exceptional prospects for genomic studies into the nature of adaptive differences and the formation of new species. Research in Heliconius provides clear connections between genotype, phenotype, and fitness of wing color patterns shown to underlie adaptation and speciation. This research is challenging our perceptions about how speciation occurs in the presence of gene flow and the role of hybridization in generating adaptive novelty. With the release of the first Heliconius genome assembly, emerging genomic studies are painting a dynamic picture of the evolving species boundary. As the field of speciation genomics moves beyond describing patterns, towards a more integrated understanding of the process of speciation, groups such as Heliconius, where there is a clear speciation continuum and the traits underlying adaptation and speciation are known, will provide a roadmap for identifying variation crucial in the origins of biodiversity. PMID:24277304