Science.gov

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. Using thermal evolution profiles to infer tritium speciation in nuclear site metals: an aid to decommissioning.

    PubMed

    Croudace, Ian W; Warwick, Phil E; Kim, Daeji

    2014-09-16

    Understanding the association and retention of tritium in metals has significance in nuclear decommissioning programs and can lead to cost benefits through waste reduction and recycling of materials. To develop insights, a range of metals from two nuclear sites and one non-nuclear site were investigated which had different exposure histories. Tritium speciation in metals was inferred through incremental heating experiments over the range of 20-900 °C using a Raddec Pyrolyser instrument. Systematic differences in thermal desorption profiles were found for nonirradiated and irradiated metals. In nonirradiated metals (e.g., stainless steel and copper), it was found that significant tritium had become incorporated following prolonged exposure to tritiated water vapor (HTO) or tritium/hydrogen gas (HT) in nuclear facilities. This externally derived tritium enters metals by diffusion with a rate controlled by the metal composition and whether the surface of the metal had been sealed or coated prior to exposure. The tritium is normally trapped in hydrated oxides lying along grain boundaries. In irradiated metals, an additional type of tritium can form internally through neutron capture reactions. The amount formed depends on the concentration and distribution of trace lithium and boron in the metal as well as the integrated neutron flux. Liberating this kind of tritium typically requires temperatures above 800 °C. The pattern of tritium evolution derived from simple thermal desorption experiments allows reliable inferences to be drawn on the likely origin, location, and phases that trap tritium. Any weakly bound tritium liberated at temperatures of ~100 °C is indicative of mostly HTO interactions in the metal. Any strongly bound tritium liberated over the range of 600-900 °C is indicative of neutrogenic tritium formed via neutron capture by trace Li and B. Neutron capture by lithium is likely to be more significant than for boron based on lithium's higher trace

  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. 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

  6. 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.

  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. A population genetic model to infer allotetraploid speciation and long-term evolution applied to two yarrow species.

    PubMed

    Guo, Yan-Ping; Tong, Xiao-Yuan; Wang, Lan-Wei; Vogl, Claus

    2013-07-01

    Allotetraploid speciation, that is, the generation of a hybrid tetraploid species from two diploid species, and the long-term evolution of tetraploid populations and species are important in plants. We developed a population genetic model to infer population genetic parameters of tetraploid populations from data of the progenitor and descendant species. Two yarrow species, Achillea alpina-4x and A. wilsoniana-4x, arose by allotetraploidization from the diploid progenitors, A. acuminata-2x and A. asiatica-2x. Yet, the population genetic process has not been studied in detail. We applied the model to sequences of three nuclear genes in populations of the four yarrow species and compared their pattern of variability with that in four plastid regions. The plastid data indicated that the two tetraploid species probably originated from multiple independent allopolyploidization events and have accumulated many mutations since. With the nuclear data, we found a low rate of homeologous recombination or gene conversion and a reduction in diversity relative to the level of both diploid species combined. The present analysis with a novel probabilistic model suggests a genetic bottleneck during tetraploid speciation, that the two tetraploid species have a long evolutionary history, and that they have a small amount of genetic exchange between the homeologous genomes. PMID:23574432

  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. 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

  11. 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.

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

    PubMed

    Krause, David J; Whitaker, Rachel J

    2015-11-01

    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.

  13. 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.

  14. 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.

  15. Chromosomal Speciation Revisited: Modes of Diversification in Australian Morabine Grasshoppers (Vandiemenella, viatica Species Group)

    PubMed Central

    Kawakami, Takeshi; Butlin, Roger K.; Cooper, Steven J. B.

    2011-01-01

    Chromosomal rearrangements can alter the rate and patterns of gene flow within or between species through a reduction in the fitness of chromosomal hybrids or by reducing recombination rates in rearranged areas of the genome. This concept, together with the observation that many species have structural variation in chromosomes, has led to the theory that the rearrangements may play a direct role in promoting speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) are an excellent model for studying the role of chromosomal rearrangement in speciation because they show extensive chromosomal variation, parapatric distribution patterns, and narrow hybrid zones at their boundaries. This species group stimulated development of one of the classic chromosomal speciation models, the stasipatric speciation model proposed by White in 1968. Our population genetic and phylogeographic analyses revealed extensive non-monophyly of chromosomal races along with historical and on-going gene introgression between them. These findings suggest that geographical isolation leading to the fixation of chromosomal variants in different geographic regions, followed by secondary contact, resulted in the present day parapatric distributions of chromosomal races. The significance of chromosomal rearrangements in the diversification of the viatica species group can be explored by comparing patterns of genetic differentiation between rearranged and co-linear parts of the genome. PMID:26467499

  16. Correlation between CORSICA inferred magnetic flux surfaces and the onset of toroidal modes in SSPX

    NASA Astrophysics Data System (ADS)

    Woodruff, Simon; Hill, David; McLean, Harry; Hooper, Bick; Stallard, Barry; Cohen, Bruce; Umansky, Maxim

    2003-10-01

    The evidence for toroidal modes with m/n<1 is presented for the Sustained Spheromak Physics Experiment, SSPX, which also correlate well with the inferred q-profile from CORSICA (a 2D Grad-Shafranov equilibrium model constrained by many edge magnetic field measurements [1]). Further, the location of the inferred mode-rational surface correlates well with the steepest gradient in the temperature profile, measured with a 10-point Thomson Scattering diagnostic. Under certain instances, the magnetic fluctuation amplitude is suppressed and the core temperature can be quite high (200eV with a top-hat or peaked profile). We examine the possibility that the dominant process causing enhanced transport in SSPX (when confinement is though to be good), is the formation of magnetic islands at mode-rational surfaces. Island formation is explored with the assistance of a perturbed equilibrium model [2], with the use of a perturbing coil [3], and with reference to 3D MHD simulations in the NIMROD code [4]. [1] E. B. Hooper et al Nuclear Fusion 39 863 (1999) [2] M. Umansky et al Proc. Sherwood (2003) [3] J. Goetz this meeting; [4] C. Sovinec et al Phys. Plasmas 8 475 (2001)

  17. Speciation history of the North American funnel web spiders, Agelenopsis (Araneae: Agelenidae): phylogenetic inferences at the population-species interface.

    PubMed

    Ayoub, Nadia A; Riechert, Susan E; Small, Randall L

    2005-07-01

    Intra- and interspecific relationships of 12 out of 13 described species as well as a potential new species in the spider genus Agelenopsis (Araneae: Agelenidae) were analyzed using sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and 16S ribosomal RNA. Approximately half of the species examined formed well-supported monophyletic groups, whereas the rest of the species were part of well-supported monophyletic species groups. Rather than viewing cases where species were not identified as being monophyletic as poor taxonomy, these cases more likely represent recent speciation and offer insights into the process of speciation. The clade with the lowest levels of interspecific sequence divergence was found in eastern North America, whereas western species displayed much higher levels of interspecific divergence. These patterns appear to extend below the species level as well, with southwestern species exhibiting the highest levels of intraspecific sequence divergence and geographic structuring. The relationship between Agelenopsis and Barronopsis, a genus once considered a sub-genus of Agelenopsis, was also examined. The two genera are reciprocally monophyletic but more generic level sampling is needed to confirm an apparent sister relationship between the two.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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...

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. Testing Mendelian inheritance from field-collected parasites: Revealing duplicated loci enables correct inference of reproductive mode and mating system.

    PubMed

    Detwiler, Jillian T; Criscione, Charles D

    2011-09-01

    Cryptic aspects of parasite population biology, e.g., mating systems, are increasingly being inferred from polymorphic and co-dominant genetic markers such as microsatellite loci. Underlying the use of such co-dominant markers is the assumption of Mendelian inheritance. The failure to meet this assumption can lead to artifactual statistics and erroneous population inferences. Here, we illustrate the importance of testing the Mendelian segregation and assortment of genetic markers and demonstrate how field-collected samples can be utilised for this purpose. To examine the reproductive mode and mating system of hermaphroditic parasites, we developed microsatellites for the cestode, Oochoristica javaensis. Among loci, we found a bimodal distribution of F(IS) (a fixation index that quantifies the deviation from Hardy-Weinberg equilibrium within subpopulations) values where loci were either highly negative (close to -1) or highly positive (∼0.8). By conducting tests of Mendelian segregation from natural crosses, we determined that loci with negative F(IS) values were in fact duplicated loci that were amplified by a single primer pair. Genetic crosses also provided linkage data and indicated that the duplicated loci most likely arose via tandem duplications rather than whole genome/chromosome duplications. By correcting for the duplicated loci, we were able to correctly infer that O. javaensis has sexual reproduction, but the mating system is highly inbred. To assist others in testing Mendelian segregation and independent assortment from natural samples, we discuss the benefits and limitations, and provide guidelines for particular parasite systems amenable to the methods employed here.

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

    PubMed Central

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

    2014-01-01

    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

  10. 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

  11. 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...

  12. Multiple player tracking in sports video: a dual-mode two-way bayesian inference approach with progressive observation modeling.

    PubMed

    Xing, Junliang; Ai, Haizhou; Liu, Liwei; Lao, Shihong

    2011-06-01

    Multiple object tracking (MOT) is a very challenging task yet of fundamental importance for many practical applications. In this paper, we focus on the problem of tracking multiple players in sports video which is even more difficult due to the abrupt movements of players and their complex interactions. To handle the difficulties in this problem, we present a new MOT algorithm which contributes both in the observation modeling level and in the tracking strategy level. For the observation modeling, we develop a progressive observation modeling process that is able to provide strong tracking observations and greatly facilitate the tracking task. For the tracking strategy, we propose a dual-mode two-way Bayesian inference approach which dynamically switches between an offline general model and an online dedicated model to deal with single isolated object tracking and multiple occluded object tracking integrally by forward filtering and backward smoothing. Extensive experiments on different kinds of sports videos, including football, basketball, as well as hockey, demonstrate the effectiveness and efficiency of the proposed method. PMID:21189238

  13. Multiple player tracking in sports video: a dual-mode two-way bayesian inference approach with progressive observation modeling.

    PubMed

    Xing, Junliang; Ai, Haizhou; Liu, Liwei; Lao, Shihong

    2011-06-01

    Multiple object tracking (MOT) is a very challenging task yet of fundamental importance for many practical applications. In this paper, we focus on the problem of tracking multiple players in sports video which is even more difficult due to the abrupt movements of players and their complex interactions. To handle the difficulties in this problem, we present a new MOT algorithm which contributes both in the observation modeling level and in the tracking strategy level. For the observation modeling, we develop a progressive observation modeling process that is able to provide strong tracking observations and greatly facilitate the tracking task. For the tracking strategy, we propose a dual-mode two-way Bayesian inference approach which dynamically switches between an offline general model and an online dedicated model to deal with single isolated object tracking and multiple occluded object tracking integrally by forward filtering and backward smoothing. Extensive experiments on different kinds of sports videos, including football, basketball, as well as hockey, demonstrate the effectiveness and efficiency of the proposed method.

  14. Direct ion speciation analysis with ion-selective membranes operated in a sequential potentiometric/time resolved chronopotentiometric sensing mode.

    PubMed

    Ghahraman Afshar, Majid; Crespo, Gastón A; Bakker, Eric

    2012-10-16

    Ion-selective membranes based on porous polypropylene membranes doped with an ionophore and a lipophilic cation-exchanger are used here in a new tandem measurement mode that combines dynamic electrochemistry and zero current potentiometry into a single protocol. Open circuit potential measurements yield near-nernstian response slopes in complete analogy to established ion-selective electrode methodology. Such measurements are well established to give direct information on the so-called free ion concentration (strictly, activity) in the sample. The same membrane is here also operated in a constant current mode, in which the localized ion depletion at a transition time is visualized by chronopotentiometry. This dynamic electrochemistry methodology gives information on the labile ion concentration in the sample. The sequential protocol is established on potassium and calcium ion-selective membranes. An increase of the ionophore concentration in the membrane to 180 mM makes it possible to determine calcium concentrations as high as 3 mM by chronopotentiometry, thereby making it possible to directly detect total calcium in undiluted blood samples. Recovery times after current perturbation depend on the current amplitude but can be kept to below 1 min for the polypropylene based ion-selective membranes studied here. Plasticized PVC as membrane material is less suited for this protocol, especially when the measurement at elevated concentrations is desired. An analysis of current amplitudes, transition times, and concentrations shows that the data are described by the Sand equation and that migration effects are insignificant. A numerical model describes the experimental findings with good agreement and gives guidance on the required selectivity in order to observe a well-resolved transition time and on the expected errors due to insufficient selectivity. The simulations suggest that the methodology compares well to that of open circuit potentiometry, despite giving

  15. 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…

  16. Allopatric divergence and speciation in coral reef fish: the three-spot dascyllus, Dascyllus trimaculatus, species complex.

    PubMed

    Leray, Matthieu; Beldade, Ricardo; Holbrook, Sally J; Schmitt, Russell J; Planes, Serge; Bernardi, Giacomo

    2010-05-01

    Long pelagic larval phases and the absence of physical barriers impede rapid speciation and contrast the high diversity observed in marine ecosystems such as coral reefs. In this study, we used the three-spot dascyllus (Dascyllus trimaculatus) species complex to evaluate speciation modes at the spatial scale of the Indo-Pacific. The complex includes four recognized species and four main color morphs that differ in distribution. Previous studies of the group using mitochondrial DNA revealed a noncongruence between color morphs and genetic groupings; with two of the color morphs grouped together and one color morph separated into three clades. Using extensive geographic sampling of 563 individuals and a combination of mitochondrial DNA sequences and 13 nuclear microsatellites, we defined population/species boundaries and inferred different speciation modes. The complex is composed of seven genetically distinct entities, some of which are distinct morphologically. Despite extensive dispersal abilities and an apparent lack of barriers, observed genetic partitions are consistent with allopatric speciation. However, ecological pressure, assortative mating, and sexual selection, were likely important during periods of geographical isolation. This study therefore suggests that primarily historical factors later followed by ecological factors caused divergence and speciation in this group of coral reef fish.

  17. Shifting distributions and speciation: species divergence during rapid climate change.

    PubMed

    Carstens, Bryan C; Knowles, L Lacey

    2007-02-01

    Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200,000 and 300,000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species

  18. Shifting distributions and speciation: species divergence during rapid climate change.

    PubMed

    Carstens, Bryan C; Knowles, L Lacey

    2007-02-01

    Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200,000 and 300,000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species

  19. 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...

  20. Electron Kinetics Inferred from Observations of Microwave Bursts During Edge Localized Modes in the Mega-Amp Spherical Tokamak

    NASA Astrophysics Data System (ADS)

    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.

    2015-03-01

    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.

  1. 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.

  2. 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

  3. Ecology: is speciation driven by species diversity?

    PubMed

    Cadena, Carlos Daniel; Ricklefs, Robert E; Jiménez, Iván; Bermingham, Eldredge

    2005-11-01

    Emerson and Kolm show that the proportion of species endemic to an island is positively related to its species richness and, assuming that endemism indexes speciation rate, they infer that greater species diversity accelerates diversification. Here we demonstrate that the same correlation between species richness and percentage endemism can arise even if within-island speciation is negligible, particularly when both endemism and species richness depend on attributes of islands (such as area) that influence the average age of resident populations. Island biogeography theory indicates that, where the average time to extinction is relatively long, diversity increases through colonization, irrespective of whether new species are formed; at the same time, islands on which populations persist for longer accumulate more endemic species as local populations differentiate and populations on neighbouring islands become extinct. We therefore suggest that species richness and endemism are correlated fortuitously owing to their mutual dependence on the life spans of populations on islands, which is unrelated to speciation itself.

  4. Biogeography and speciation patterns of the golden orb spider genus Nephila (Araneae: Nephilidae) in Asia.

    PubMed

    Su, Yong-Chao; Chang, Yung-Hau; Smith, Deborah; Zhu, Ming-Sheng; Kuntner, Matjaž; Tso, I-Min

    2011-01-01

    The molecular phylogeny of the globally distributed golden orb spider genus Nephila (Nephilidae) was reconstructed to infer its speciation history, with a focus on SE Asian/W Pacific species. Five Asian, two Australian, four African, and one American species were included in the phylogenetic analyses. Other species in Nephilidae, Araneidae, and Tetragnathidae were included to assess their relationships with the genus Nephila, and one species from Uloboridae was used as the outgroup. Phylogenetic trees were reconstructed from one nuclear (18S) and two mitochondrial (COI and 16S) markers. Our molecular phylogeny shows that the widely distributed Asian/Australian species, N. pilipes, and an African species, N. constricta, form a clade that is sister to all other Nephila species. Nested in this Nephila clade are one clade with tropical and subtropical/temperate Asian/Australian species, and the other containing African and American species. The estimated divergence times suggest that diversification events within Nephila occurred during mid-Miocene to Pliocene (16 Mya-2 Mya), and these time periods were characterized by cyclic global warming/cooling events. According to Dispersal and Vicariance Analysis (DIVA), the ancestral range of the Asian/Australian clade was tropical Asia, and the ancestral range of the genus Nephila was either tropical Asia or Africa. We conclude that the speciation of the Asian/Australian Nephila species was driven by Neogene global cyclic climate changes. However, further population level studies comparing diversification patterns of sister species are needed to determine the mode of speciation of these species.

  5. Hybridization and speciation.

    PubMed

    Abbott, R; Albach, D; Ansell, S; Arntzen, J W; Baird, S J E; Bierne, N; Boughman, J; Brelsford, A; Buerkle, C A; Buggs, R; Butlin, R K; Dieckmann, U; Eroukhmanoff, F; Grill, A; Cahan, S H; Hermansen, J S; Hewitt, G; Hudson, A G; Jiggins, C; Jones, J; Keller, B; Marczewski, T; Mallet, J; Martinez-Rodriguez, P; Möst, M; Mullen, S; Nichols, R; Nolte, A W; Parisod, C; Pfennig, K; Rice, A M; Ritchie, M G; Seifert, B; Smadja, C M; Stelkens, R; Szymura, J M; Väinölä, R; Wolf, J B W; Zinner, D

    2013-02-01

    Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization.

  6. 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...

  7. Sympatric speciation by allochrony in a seabird.

    PubMed

    Friesen, V L; Smith, A L; Gómez-Díaz, E; Bolton, M; Furness, R W; González-Solís, J; Monteiro, L R

    2007-11-20

    The importance of sympatric speciation (the evolution of reproductive isolation between codistributed populations) in generating biodiversity is highly controversial. Whereas potential examples of sympatric speciation exist for plants, insects, and fishes, most theoretical models suggest that it requires conditions that are probably not common in nature, and only two possible cases have been described for tetrapods. One mechanism by which it could occur is through allochronic isolation-separation of populations by breeding time. Oceanodroma castro (the Madeiran or band-rumped storm-petrel) is a small seabird that nests on tropical and subtropical islands throughout the Atlantic and Pacific Oceans. In at least five archipelagos, different individuals breed on the same islands in different seasons. We compared variation in five microsatellite loci and the mitochondrial control region among 562 O. castro from throughout the species' range. We found that sympatric seasonal populations differ genetically within all five archipelagos and have ceased to exchange genes in two. Population and gene trees all indicate that seasonal populations within four of the archipelagos are more closely related to each other than to populations from the same season from other archipelagos; divergence of the fifth sympatric pair is too ancient for reliable inference. Thus, seasonal populations appear to have arisen sympatrically at least four times. This is the first evidence for sympatric speciation by allochrony in a tetrapod, and adds to growing indications that population differentiation and speciation can occur without geographic barriers to gene flow. PMID:18006662

  8. 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...

  9. Theory and speciation.

    PubMed

    Turelli, M; Barton, N H.; Coyne, J A.

    2001-07-01

    The study of speciation has become one of the most active areas of evolutionary biology, and substantial progress has been made in documenting and understanding phenomena ranging from sympatric speciation and reinforcement to the evolutionary genetics of postzygotic isolation. This progress has been driven largely by empirical results, and most useful theoretical work has concentrated on making sense of empirical patterns. Given the complexity of speciation, mathematical theory is subordinate to verbal theory and generalizations about data. Nevertheless, mathematical theory can provide a useful classification of verbal theories; can help determine the biological plausibility of verbal theories; can determine whether alternative mechanisms of speciation are consistent with empirical patterns; and can occasionally provide predictions that go beyond empirical generalizations. We discuss recent examples of progress in each of these areas.

  10. 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

  11. 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

  12. 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

  13. Speciation and bifurcations.

    PubMed

    Volkenstein, M V; Livshits, M A

    1989-01-01

    The interrelations of physics and biology are discussed. It is shown that Darwin can be considered as one of the founders of the important field of contemporary physics called physics of dissipative structures or synergetics. The theories of gradual and punctual evolution are presented. The contradiction between these theories can be solved on the basis of molecular theory of evolution and on the basis of the phenomenological physical treatment. The general physical properties of living systems, considered as open systems being far from equilibrium, are listed and simple non-linear mathematical models describing gradual and punctual speciation are suggested. The usual pictures which present these two kinds of speciation can possess physico-mathematical sense. Punctuated speciation means bifurcation, a kind of non-equilibrium phase transition.

  14. Sexual selection and speciation.

    PubMed

    Panhuis, T M.; Butlin, R; Zuk, M; Tregenza, T

    2001-07-01

    The power of sexual selection to drive changes in mate recognition traits gives it the potential to be a potent force in speciation. Much of the evidence to support this possibility comes from comparative studies that examine differences in the number of species between clades that apparently differ in the intensity of sexual selection. We argue that more detailed studies are needed, examining extinction rates and other sources of variation in species richness. Typically, investigations of extant natural populations have been too indirect to convincingly conclude speciation by sexual selection. Recent empirical work, however, is beginning to take a more direct approach and rule out confounding variables.

  15. Phylogenetics and speciation.

    PubMed

    Barraclough, T G.; Nee, S

    2001-07-01

    Species-level phylogenies derived from molecular data provide an indirect record of the speciation events that have led to extant species. This offers enormous potential for investigating the general causes and rates of speciation within clades. To make the most of this potential, we should ideally sample all the species in a higher group, such as a genus, ensure that those species reflect evolutionary entities within the group, and rule out the effects of other processes, such as extinction, as explanations for observed patterns. We discuss recent practical and theoretical advances in this area and outline how future work should benefit from incorporating data from genealogical and phylogeographical scales.

  16. 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 ...

  17. 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.

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

    PubMed

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

    2015-05-01

    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.

  19. 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.

  20. 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

  1. 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

  2. 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...

  3. 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. ...

  4. Speciation in granitic melts

    SciTech Connect

    Burnham, C.W.; Nekvasil, H.

    1985-01-01

    Refinement of the cryoscopic equations for the major granitic melt components, NaAlSi/sub 3/O/sub 8/(ab), CaAl/sub 2/O/sub 8/(an), KAlSi/sub 3/O/sub 8/(or), and Si/sub 4/O/sub 8/(qz), has led to the recognition of several major speciation reactions in anhydrous and hydrous melts of the system Ab-An-Or-Qz-H/sub 2/O. These reactions involve either dissociation of the feldspar-like components, as in incongruent melting, or interaction between them and qz. In all cases of interaction, one of the speciation products has the stoichiometry of dpy or py (pyrophyllite) (Al/sub 1.455/Si/sub 2.91/O/sub 8/ +/- 0.73H/sub 2/O), in which Al is presumed to be in either fivefold (dpy) or sixfold (py) coordination. The py component also is a major product of speciation by interaction between sil (Al/sub 3.2/Si/sub 1.6/O/sub 8/) and qz in peraluminous melts of the system Ab-Or-Qz-Sil-H/sub 2/O; as a consequence, the quartz liquidus field boundary is shifted to lower temperatures and toward qz. There is no evidence in peraluminous haplogranite melts for the existence of a muscovite-like species. Application of the refined thermodynamic model to the system Ab-Qz-Eu - H/sub 2/O at 2.0 kbar predicts the occurrence of a eu and qz-consuming reaction that produces a petalite-like species and a consequent dramatic shift in liquidus field boundaries. Higher pressures favor conversion of pe to qz + sp. In the spodumene-like species, sp, Al presumably is six-coordinated.

  5. 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.

  6. 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

  7. Relationships and genetic consequences of contrasting modes of speciation among endemic species of Robinsonia (Asteraceae, Senecioneae) of the Juan Fernández Archipelago, Chile, based on AFLPs and SSRs.

    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

    This study analyses and compares the genetic signatures of anagenetic and cladogenetic speciation in six species of the genus Robinsonia (Asteraceae, Senecioneae), endemic to the Juan Fernández Islands, Chile. Population genetic structure was analyzed by amplified fragment length polymorphism (AFLP) and microsatellite (simple sequence repeat, SSR) markers from 286 and 320 individuals, respectively, in 28 populations. Each species is genetically distinct. Previous hypotheses of classification among these species into subgenera and sections, via morphological, phytochemical, isozymic and internal transcribed spacer (ITS) data, have been confirmed, except that R. saxatilis appears to be related to R. gayana rather than R. evenia. Analysis of phylogenetic results and biogeographic context suggests that five of these species have originated by cladogenesis and adaptive radiation on the older Robinson Crusoe Island. The sixth species, R. masafuerae, restricted to the younger Alejandro Selkirk Island, is closely related to and an anagenetic derivative of R. evenia from Robinson Crusoe. Microsatellite and AFLP data reveal considerable genetic variation among the cladogenetically derived species of Robinsonia, but within each the genetic variation is lower, highlighting presumptive genetic isolation and rapid radiation. The anagenetically derived R. masafuerae harbors a level of genetic variation similar to that of its progenitor, R. evenia. This is the first direct comparison of the genetic consequences of anagenetic and cladogenetic speciation in plants of an oceanic archipelago.

  8. 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 ...

  9. 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

  10. 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

  11. Female mate-choice behavior and sympatric speciation.

    PubMed

    Verzijden, Machteld N; Lachlan, Robert F; Servedio, Maria R

    2005-10-01

    Many models have investigated how the process of speciation may occur in sympatry. In these models, individuals are either asexual or mate choice is determined by very simple rules. Females, for example, may be assumed either to compare their phenotype to that of a potential mate, preferring to mate with similar males (phenotype matching), or to possess preference genes that determine which male phenotype they prefer. These rules often do not reflect the mate-choice rules found in empirical studies. In this paper, we compare these two modes of female choice with various types of sexual imprinting. We examine the efficacy of different mate-choice behavior in causing divergence in male traits under simple deterministic one-locus population genetic models as well as under polygenic, individual-based simulations based on the models of Dieckmann and Doebeli (1999). We find that the inheritance mechanism of mate choice can have a large effect on the ease of sympatric speciation. When females imprint on their mothers, the result of the model is similar to phenotype matching, where speciation can occur fairly easily. When females imprint on their fathers or imprint obliquely, speciation becomes considerably less likely. Finally, when females rely on preference genes, male trait evolution occurs easily, but the correlation between trait and preference can be weak, and interpreting these results as speciation may be suspect.

  12. 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...

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

    PubMed

    Igea, Javier; Bogarín, Diego; Papadopulos, Alexander S T; Savolainen, Vincent

    2015-02-01

    Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy-based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation. PMID:25522772

  14. 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

  15. 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

  16. Arsenic Speciation in Geothermal Waters

    NASA Astrophysics Data System (ADS)

    Keller, N. S.; Stefansson, A.; Sigfusson, B.

    2011-12-01

    Various arsenic species have been observed or inferred in geothermal waters in recent years, in particular thio- and oxyanions. However their exact stoechiometry and their oxidation state has been subjected to a sustained debate over the last decade. Most of the As species seen in geothermal waters are unstable under laboratory conditions, thus it is crucial that appropriate sampling and analytical techniques are used in order to minimise post-sampling changes. The goals of this study were to determine how many As species can be seen in geothermal systems and how geochemical parameters control the number and relative abundance of the species. Furthermore, we tested the stability of the As-S compounds after sampling, in particular whether the traditionally used flash-freezing method quantitatively preserves the species. Samples were collected from wells at the Hellisheidi Power Plant and from natural hot springs in the Geysir Geothermal Area in SW Iceland. The samples were analysed on-site immediately after sampling by first separating the various As species by Ion Chromatography followed by quantification by Hydride-Generation Atomic Fluorescence Spectrometer (HG-AFS). Preliminary results show that analysis of the samples immediately after sampling is crucial, as sample storage and flash-freezing/thawing appear to modify the As speciation. Using the retention times of the analytes through the chromatographic column, a minimum of seven As species were observed. Two of the species are oxides of AsIII and AsV, based on the comparison of their retention times with standards. The other five species have yet to be unequivocally identified, but based on prior studies it is assumed that at least some of them are thioarsenic species with various S:O ratios, with longer retention times for increasing S:O. Clear differences can be seen between samples from Hellisheidi and Geysir. In the case of the oxyanions, only AsIII is present at Hellisheidi whereas both oxidation states

  17. Possible incipient sympatric ecological speciation in blind mole rats (Spalax).

    PubMed

    Hadid, Yarin; Tzur, Shay; Pavlícek, Tomáš; Šumbera, Radim; Šklíba, Jan; Lövy, Matěj; Fragman-Sapir, Ori; Beiles, Avigdor; Arieli, Ran; Raz, Shmuel; Nevo, Eviatar

    2013-02-12

    Sympatric speciation has been controversial since it was first proposed as a mode of speciation. Subterranean blind mole rats (Spalacidae) are considered to speciate allopatrically or peripatrically. Here, we report a possible incipient sympatric adaptive ecological speciation in Spalax galili (2n = 52). The study microsite (0.04 km(2)) is sharply subdivided geologically, edaphically, and ecologically into abutting barrier-free ecologies divergent in rock, soil, and vegetation types. The Pleistocene Alma basalt abuts the Cretaceous Senonian Kerem Ben Zimra chalk. Only 28% of 112 plant species were shared between the soils. We examined mitochondrial DNA in the control region and ATP6 in 28 mole rats from basalt and in 14 from chalk habitats. We also sequenced the complete mtDNA (16,423 bp) of four animals, two from each soil type. Remarkably, the frequency of all major haplotype clusters (HC) was highly soil-biased. HCI and HCII are chalk biased. HC-III was abundant in basalt (36%) but absent in chalk; HC-IV was prevalent in basalt (46.5%) but was low (20%) in chalk. Up to 40% of the mtDNA diversity was edaphically dependent, suggesting constrained gene flow. We identified a homologous recombinant mtDNA in the basalt/chalk studied area. Phenotypically significant divergences differentiate the two populations, inhabiting different soils, in adaptive oxygen consumption and in the amount of outside-nest activity. This identification of a possible incipient sympatric adaptive ecological speciation caused by natural selection indirectly refutes the allopatric alternative. Sympatric ecological speciation may be more prevalent in nature because of abundant and sharply abutting divergent ecologies.

  18. Metallomics for drug development: an integrated CE-ICP-MS and ICP-MS approach reveals the speciation changes for an investigational ruthenium(III) drug bound to holo-transferrin in simulated cancer cytosol.

    PubMed

    Aleksenko, Svetlana S; Matczuk, Magdalena; Lu, Xifeng; Foteeva, Lidia S; Pawlak, Katarzyna; Timerbaev, Andrei R; Jarosz, Maciej

    2013-08-01

    A method based on combining inductively coupled plasma mass spectrometry (ICP-MS) with capillary electrophoresis (CE) or an ultrafiltration step was developed to study the speciation of the serum-protein adducts of a ruthenium anticancer drug under in vitro intracellular conditions. The formation of a reactive Ru species in the cell, following the metal release from the protein, is thought to play an important role in the drug's mode of action. Glutathione and ascorbic acid at their cancer cytosol concentrations were shown to be capable of altering the metal speciation in the drug adduct with holo-transferrin but not that with albumin. The appearance of the additional peaks in ICP-MS electropherograms (by recording both Ru- and Fe-specific signals) was found to be dependent on time which allowed for kinetic assessment of the evolution of novel metal species. On the contrary, after the addition of citric acid the ruthenium ion (within the appropriately complexed scaffold) remained sequestered in the adduct. This was inferred as a proof of the speciation changes taking place by a virtue of a redox mechanism rather than due to ligand-exchange transformations. The protein-bound metallodrug was further characterized by direct ICP-MS assaying so as to confirm a partial release of ruthenium induced by glutathione.

  19. 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.

  20. Sulfur speciation in individual aerosol particles

    NASA Astrophysics Data System (ADS)

    Neubauer, Kenneth R.; Sum, Stephen T.; Johnston, Murray V.; Wexler, Anthony S.

    1996-08-01

    Sulfur aerosols play an important role in acid deposition and the Earth's energy balance. Important species in these aerosols include methanesulfonates, hydroxymethanesulfonates, sulfates, and sulfites. Because the relative amounts of these species indicate different sources and atmospheric processes, it is important to distinguish them in single-aerosol particles. To accomplish this task, we use rapid single-particle mass spectrometry (RSMS), a technique that permits individual particles to be analyzed in an online mode. Each sulfur species produces a characteristic set of ions in the mass spectra. In simulated marine and urban aerosols the relative amounts of methanesulfonic acid (MSA) and sodium hydroxymethanesulfonate (NaHMSA) in a single particle can be determined from peak area ratios in the mass spectra. Improved quantitation is possible by application of the classification and regression tree (CART) algorithm to distinguish the mass spectra of particles having different compositions. Factors that influence speciation include particle size, morphology, and laser fluence.

  1. 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

  2. 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

  3. Iron speciation in urban dust

    SciTech Connect

    Elzinga, E.J.; Fitts, J.; Gao, Y.; Tappero, R.

    2011-08-01

    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 {mu}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. Keywords - Urban dust; Iron; Speciation; Micro-focused X-ray absorption spectroscopy.

  4. 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.

  5. How common is homoploid hybrid speciation?

    PubMed

    Schumer, Molly; Rosenthal, Gil G; Andolfatto, Peter

    2014-06-01

    Hybridization has long been considered a process that prevents divergence between species. In contrast to this historical view, an increasing number of empirical studies claim to show evidence for hybrid speciation without a ploidy change. However, the importance of hybridization as a route to speciation is poorly understood, and many claims have been made with insufficient evidence that hybridization played a role in the speciation process. We propose criteria to determine the strength of evidence for homoploid hybrid speciation. Based on an evaluation of the literature using this framework, we conclude that although hybridization appears to be common, evidence for an important role of hybridization in homoploid speciation is more circumscribed.

  6. The phylogenetic pattern of speciation and wing pattern change in neotropical Ithomia butterflies (Lepidoptera: nymphalidae).

    PubMed

    Jiggins, Chris D; Mallarino, Ricardo; Willmott, Keith R; Bermingham, Eldredge

    2006-07-01

    Species level phylogenetic hypotheses can be used to explore patterns of divergence and speciation. In the tropics, speciation is commonly attributed to either vicariance, perhaps within climate-induced forest refugia, or ecological speciation caused by niche adaptation. Mimetic butterflies have been used to identify forest refugia as well as in studies of ecological speciation, so they are ideal for discriminating between these two models. The genus Ithomia contains 24 species of warningly colored mimetic butterflies found in South and Central America, and here we use a phylogenetic hypothesis based on seven genes for 23 species to investigate speciation in this group. The history of wing color pattern evolution in the genus was reconstructed using both parsimony and likelihood. The ancestral pattern for the group was almost certainly a transparent butterfly, and there is strong evidence for convergent evolution due to mimicry. A punctuationist model of pattern evolution was a significantly better fit to the data than a gradualist model, demonstrating that pattern changes above the species level were associated with cladogenesis and supporting a model of ecological speciation driven by mimicry adaptation. However, there was only one case of sister species unambiguously differing in pattern, suggesting that some recent speciation events have occurred without pattern shifts. The pattern of geographic overlap between clades over time shows that closely related species are mostly sympatric or, in one case, parapatric. This is consistent with modes of speciation with ongoing gene flow, although rapid range changes following allopatric speciation could give a similar pattern. Patterns of lineage accumulation through time differed significantly from that expected at random, and show that most of the extant species were present by the beginning of the Pleistocene at the latest. Hence Pleistocene refugia are unlikely to have played a major role in Ithomia diversification.

  7. Homoploid hybrid speciation in animals.

    PubMed

    Mavárez, Jesús; Linares, Mauricio

    2008-10-01

    Among animals, evidence for homoploid hybrid speciation (HHS, i.e. the creation of a hybrid lineage without a change in chromosome number) was limited until recently to the virgin chub, Gila seminuda, and some controversial data in support of hybrid status for the red wolf, Canis rufus. This scarcity of evidence, together with pessimistic attitudes among zoologists about the evolutionary importance of hybridisation, prompted the view that HHS is extremely rare among animals, especially as compared with plants. However, in recent years, the literature on animal HHS has expanded to include several new putative examples in butterflies, ants, flies and fishes. We argue that this evidence suggests that HHS is far more common than previously thought and use it to provide insights into some of the genetic and ecological aspects associated with this type of speciation among animals.

  8. 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...

  9. 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.

  10. 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

  11. Sexual behaviour: rapid speciation in an arthropod.

    PubMed

    Mendelson, Tamra C; Shaw, Kerry L

    2005-01-27

    Theory predicts that sexual behaviour in animals can evolve rapidly, accelerating the rate of species formation. Here we estimate the rate of speciation in Laupala, a group of forest-dwelling Hawaiian crickets that is characterized primarily through differences in male courtship song. We find that Laupala has the highest rate of speciation so far recorded in arthropods, supporting the idea that divergence in courtship or sexual behaviour drives rapid speciation in animals.

  12. 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.

  13. Arsenic speciation in edible mushrooms.

    PubMed

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

    2014-12-16

    The fruiting bodies, or mushrooms, of terrestrial fungi have been found to contain a high proportion of the nontoxic arsenic compound arsenobetaine (AB), but data gaps include a limited phylogenetic diversity of the fungi for which arsenic speciation is available, a focus on mushrooms with higher total arsenic concentrations, and the unknown formation and role of AB in mushrooms. To address these, the mushrooms of 46 different fungus species (73 samples) over a diverse range of phylogenetic groups were collected from Canadian grocery stores and background and arsenic-contaminated areas. Total arsenic was determined using ICP-MS, and arsenic speciation was determined using HPLC-ICP-MS and complementary X-ray absorption spectroscopy (XAS). The major arsenic compounds in mushrooms were found to be similar among phylogenetic groups, and AB was found to be the major compound in the Lycoperdaceae and Agaricaceae families but generally absent in log-growing mushrooms, suggesting the microbial community may influence arsenic speciation in mushrooms. The high proportion of AB in mushrooms with puffball or gilled morphologies may suggest that AB acts as an osmolyte in certain mushrooms to help maintain fruiting body structure. The presence of an As(III)-sulfur compound, for the first time in mushrooms, was identified in the XAS analysis. Except for Agaricus sp. (with predominantly AB), inorganic arsenic predominated in most of the store-bought mushrooms (albeit with low total arsenic concentrations). Should inorganic arsenic predominate in these mushrooms from contaminated areas, the risk to consumers under these circumstances should be considered.

  14. 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.

  15. 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

  16. 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 ...

  17. Speciation genetics: current status and evolving approaches.

    PubMed

    Wolf, Jochen B W; Lindell, Johan; Backström, Niclas

    2010-06-12

    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.

  18. Advances in Ecological Speciation: an integrative approach.

    PubMed

    Faria, Rui; Renaut, Sebastien; Galindo, Juan; Pinho, Catarina; Melo-Ferreira, José; Melo, Martim; Jones, Felicity; Salzburger, Walter; Schluter, Dolph; Butlin, Roger

    2014-02-01

    The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunity to study the mechanisms involved in ecological speciation. Genome scans provide significant insights but have some important limitations; efforts are needed to integrate them with other approaches to make full use of the sequencing data deluge. An international conference 'Advances in Ecological Speciation' organized by the University of Porto (Portugal) aimed to review current progress in ecological speciation. Using some of the examples presented at the conference, we highlight the benefits of integrating ecological and genomic data and discuss different mechanisms of parallel evolution. Finally, future avenues of research are suggested to advance our knowledge concerning the role of natural selection in the establishment of reproductive isolation during ecological speciation.

  19. 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.

  20. Rates of speciation in the fossil record.

    PubMed Central

    Sepkoski, J J

    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. PMID:11541734

  1. Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains.

    PubMed

    Knowles, L L

    2001-02-01

    Grasshoppers in the genus Melanoplus have undergone a radiation in the 'sky islands' of western North America, with many species originating during the Pleistocene. Despite their recent origins, phylogenetic analyses indicate that all the species exhibit monophyletic or paraphyletic gene trees. The objectives of this study were to determine whether the monophyletic genealogies are the result of a bottleneck at speciation and to investigate the extent to which the different phylogenetic states of eight species (i.e. monophyletic versus paraphyletic gene trees) can be ascribed to the effects of speciation. A coalescent simulation was used to test for a bottleneck at speciation in each species. The effective population sizes and demographic histories of species were compared across taxa to evaluate the possibility that the paraphyly versus monophyly of the species reflects differential rates of lineage loss rather than speciation mode. While coalescent analyses indicate that the monophyly of Melanoplus species might not be indicative of bottlenecks at speciation, the results suggest that the paraphyletic gene trees may reflect the demography of speciation, involving localized divergences in the ancestral species. With respect to different models of Pleistocene divergence, the data do not support a model of founder-effect speciation but are compatible with divergence in allopatric refugia. PMID:11217904

  2. Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains.

    PubMed Central

    Knowles, L. L.

    2001-01-01

    Grasshoppers in the genus Melanoplus have undergone a radiation in the 'sky islands' of western North America, with many species originating during the Pleistocene. Despite their recent origins, phylogenetic analyses indicate that all the species exhibit monophyletic or paraphyletic gene trees. The objectives of this study were to determine whether the monophyletic genealogies are the result of a bottleneck at speciation and to investigate the extent to which the different phylogenetic states of eight species (i.e. monophyletic versus paraphyletic gene trees) can be ascribed to the effects of speciation. A coalescent simulation was used to test for a bottleneck at speciation in each species. The effective population sizes and demographic histories of species were compared across taxa to evaluate the possibility that the paraphyly versus monophyly of the species reflects differential rates of lineage loss rather than speciation mode. While coalescent analyses indicate that the monophyly of Melanoplus species might not be indicative of bottlenecks at speciation, the results suggest that the paraphyletic gene trees may reflect the demography of speciation, involving localized divergences in the ancestral species. With respect to different models of Pleistocene divergence, the data do not support a model of founder-effect speciation but are compatible with divergence in allopatric refugia. PMID:11217904

  3. 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

  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.

  5. 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...

  6. 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

  7. Environmental harshness, latitude and incipient speciation.

    PubMed

    Weir, Jason T

    2014-02-01

    Are rates of evolution and speciation fastest where diversity is greatest - the tropics? A commonly accepted theory links the latitudinal diversity gradient to a speciation pump model whereby the tropics produce species at a faster rate than extra-tropical regions. In this issue of Molecular Ecology, Botero et al. () test the speciation pump model using subspecies richness patterns for more than 9000 species of birds and mammals as a proxy for incipient speciation opportunity. Rather than using latitudinal centroids, the authors investigate the role of various environmental correlates of latitude as drivers of subspecies richness. Their key finding points to environmental harshness as a positive predictor of subspecies richness. The authors link high subspecies richness in environmental harsh areas to increased opportunities for geographic range fragmentation and/or faster rates of trait evolution as drivers of incipient speciation. Because environmental harshness generally increases with latitude, these results suggest that opportunity for incipient speciation is lowest where species richness is highest. The authors interpret this finding as incompatible with the view of the tropics as a cradle of diversity. Their results are consistent with a growing body of evidence that reproductive isolation and speciation occur fastest at high latitudes. PMID:26010836

  8. 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

  9. Drift promotes speciation by sexual selection.

    PubMed

    Uyeda, Josef C; Arnold, Stevan J; Hohenlohe, Paul A; Mead, Louise S

    2009-03-01

    Quantitative genetic models of sexual selection have generally failed to provide a direct connection to speciation and to explore the consequences of finite population size. The connection to speciation has been indirect because the models have treated only the evolution of male and female traits and have stopped short of modeling the evolution of sexual isolation. In this article we extend Lande's (1981) model of sexual selection to quantify predictions about the evolution of sexual isolation and speciation. Our results, based on computer simulations, support and extend Lande's claim that drift along a line of equilibria can rapidly lead to sexual isolation and speciation. Furthermore, we show that rapid speciation can occur by drift in populations of appreciable size (N(e) >or= 1000). These results are in sharp contrast to the opinion of many researchers and textbook writers who have argued that drift does not play an important role in speciation. We argue that drift may be a powerful amplifier of speciation under a wide variety of modeling assumptions, even when selection acts directly on female mating preferences.

  10. 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

  11. 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

  12. 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

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

    PubMed

    Kashiwagi, Tom; Marshall, Andrea D; Bennett, Michael B; Ovenden, Jennifer R

    2012-07-01

    Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondrial CO1 (574 bp) and ND5 genes (1188 bp). The assay with CO1 sequences, widely used in DNA barcoding, failed to distinguish the two species. The two species were clearly distinguishable, however, with no shared RAG1 or ND5 haplotypes. The species were reciprocally monophyletic for RAG1, but paraphyletic for ND5 sequences. Qualitative evidence and statistical inferences using the 'Isolation-with-Migration models' indicated that these results were better explained with post-divergence gene flow in the recent past rather than incomplete lineage sorting with zero gene flow since speciation. An estimate of divergence time was less than 0.5 Ma with an upper confidence limit of within 1 Ma. Recent speciation of highly mobile species in the marine environment is of great interest, as it suggests that speciation may have occurred in the absence of long-term physical barriers to gene flow. We propose that the ecologically driven forces such as habitat choice played a significant role in speciation in manta rays.

  14. Primate extinction risk and historical patterns of speciation and extinction in relation to body mass.

    PubMed

    Matthews, Luke J; Arnold, Christian; Machanda, Zarin; Nunn, Charles L

    2011-04-22

    Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximum-likelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass.

  15. Primate extinction risk and historical patterns of speciation and extinction in relation to body mass.

    PubMed

    Matthews, Luke J; Arnold, Christian; Machanda, Zarin; Nunn, Charles L

    2011-04-22

    Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximum-likelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass. PMID:20943699

  16. Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation.

    PubMed

    Martin, Christopher H; Cutler, Joseph S; Friel, John P; Dening Touokong, Cyrille; Coop, Graham; Wainwright, Peter C

    2015-06-01

    One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.

  17. Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation.

    PubMed

    Martin, Christopher H; Cutler, Joseph S; Friel, John P; Dening Touokong, Cyrille; Coop, Graham; Wainwright, Peter C

    2015-06-01

    One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature. PMID:25929355

  18. 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.

  19. 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...

  20. 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,…

  1. 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.

  2. Speciation dynamics during the global radiation of extant bats.

    PubMed

    Shi, Jeff J; Rabosky, Daniel L

    2015-06-01

    Species richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference, we assemble a time-calibrated, species-level phylogeny using a supermatrix of mitochondrial and nuclear sequence data. We analyze the phylogeny using a Bayesian method for modeling complex evolutionary dynamics. Surprisingly, we find that variation in family richness can largely be explained without invoking heterogeneous diversification dynamics. We document only a single well-supported shift in diversification dynamics across bats, occurring at the base of the subfamily Stenodermatinae. Bat diversity is phylogenetically imbalanced, but-contrary to previous hypotheses-this pattern is unexplained by any simple patterns of diversification rate heterogeneity. This discordance may indicate that diversification dynamics are more complex than can be captured using the statistical tools available for modeling data at this scale. We infer that bats as a whole are almost entirely united into one macroevolutionary cohort, with decelerating speciation through time. There is also a significant relationship between clade age and richness, suggesting that global bat diversity may still be expanding.

  3. 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.

  4. Mistaking geography for biology: inferring processes from species distributions.

    PubMed

    Warren, Dan L; Cardillo, Marcel; Rosauer, Dan F; Bolnick, Daniel I

    2014-10-01

    Over the past few decades, there has been a rapid proliferation of statistical methods that infer evolutionary and ecological processes from data on species distributions. These methods have led to considerable new insights, but they often fail to account for the effects of historical biogeography on present-day species distributions. Because the geography of speciation can lead to patterns of spatial and temporal autocorrelation in the distributions of species within a clade, this can result in misleading inferences about the importance of deterministic processes in generating spatial patterns of biodiversity. In this opinion article, we discuss ways in which patterns of species distributions driven by historical biogeography are often interpreted as evidence of particular evolutionary or ecological processes. We focus on three areas that are especially prone to such misinterpretations: community phylogenetics, environmental niche modelling, and analyses of beta diversity (compositional turnover of biodiversity).

  5. Ecological speciation in marine v. freshwater fishes.

    PubMed

    Puebla, O

    2009-10-01

    Absolute barriers to dispersal are not common in marine systems, and the prevalence of planktonic larvae in marine taxa provides potential for gene flow across large geographic distances. These observations raise the fundamental question in marine evolutionary biology as to whether geographic and oceanographic barriers alone can account for the high levels of species diversity observed in marine environments such as coral reefs, or whether marine speciation also operates in the presence of gene flow between diverging populations. In this respect, the ecological hypothesis of speciation, in which reproductive isolation results from divergent or disruptive natural selection, is of particular interest because it may operate in the presence of gene flow. Although important insights into the process of ecological speciation in aquatic environments have been provided by the study of freshwater fishes, comparatively little is known about the possibility of ecological speciation in marine teleosts. In this study, the evidence consistent with different aspects of the ecological hypothesis of speciation is evaluated in marine fishes. Molecular approaches have played a critical role in the development of speciation hypotheses in marine fishes, with a role of ecology suggested by the occurrence of sister clades separated by ecological factors, rapid cladogenesis or the persistence of genetically and ecologically differentiated species in the presence of gene flow. Yet, ecological speciation research in marine fishes is still largely at an exploratory stage. Cases where the major ingredients of ecological speciation, namely a source of natural divergent or disruptive selection, a mechanism of reproductive isolation and a link between the two have been explicitly documented are few. Even in these cases, specific predictions of the ecological hypothesis of speciation remain largely untested. Recent developments in the study of freshwater fishes illustrate the potential for

  6. 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

  7. A personal particle speciation sampler.

    PubMed

    Hering, Susanne; Kreisberg, Nathan; John, Walter

    2003-02-01

    Fuller understanding of personal exposures to particulate matter with aerodynamic diameters below 2.5 microm (PM2.5*) requires a personal sampler suitable for assaying not only PM2.5 mass but also its major chemical constituents: elemental carbon, organic carbon, sulfates, and nitrates. The goal to measure these constituents simultaneously imposes several constraints on personal sampler design. The aim of this project was to develop a sampler within these constraints that would be suitable for personal monitoring over 8 hours. In addition, with the intent to improve the precision of mass measurements, we investigated offline use of beta attenuation. The personal particle speciation sampler (PPSS) includes an inlet to remove particles larger than 2.5 microm, 2 sampling channels, and a pump with flow control. One channel serves for measuring particle mass and inorganic ions; the other, for measuring organic carbon and elemental carbon. Denuders can be placed in either channel or both channels. A backup filter can be placed on the denuded channel to collect volatilized particulate nitrate. Two prototype PPSS units were built and tested. The results of both laboratory testing of key PPSS components and a limited field study of the prototype in comparison to an AIHL (Air and Industrial Hygiene Laboratory) cyclone-based sampler are reported. PMID:12670062

  8. 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

  9. 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

  10. Accelerated speciation in colour-polymorphic birds.

    PubMed

    Hugall, Andrew F; Stuart-Fox, Devi

    2012-05-09

    Colour polymorphism exemplifies extreme morphological diversity within populations. It is taxonomically widespread but generally rare. Theory suggests that where colour polymorphism does occur, processes generating and maintaining it can promote speciation but the generality of this claim is unclear. Here we confirm, using species-level molecular phylogenies for five families of non-passerine birds, that colour polymorphism is associated with accelerated speciation rates in the three groups in which polymorphism is most prevalent. In all five groups, colour polymorphism is lost at a significantly greater rate than it is gained. Thus, the general rarity and phylogenetic dispersion of colour polymorphism is accounted for by a combination of higher speciation rate and higher transition rate from polymorphism to monomorphism, consistent with theoretical models where speciation is driven by fixation of one or more morphs. This is corroborated by evidence from a species-level molecular phylogeny of passerines, incorporating 4,128 (66.5%) extant species, that polymorphic species tend to be younger than monomorphic species. Our results provide empirical support for the general proposition, dating from classical evolutionary theory, that colour polymorphism can increase speciation rates.

  11. 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

  12. 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.

  13. Speciation along a depth gradient in a marine adaptive radiation

    PubMed Central

    Ingram, Travis

    2011-01-01

    Oceans are home to much of the world's biodiversity, but we know little about the processes driving speciation in marine ecosystems with few geographical barriers to gene flow. Ecological speciation resulting from divergent natural selection between ecological niches can occur in the face of gene flow. Sister species in the young and ecologically diverse rockfish genus Sebastes coexist in the northeast Pacific, implying that speciation may not require geographical isolation. Here, I use a novel phylogenetic comparative analysis to show that rockfish speciation is instead associated with divergence in habitat depth and depth-associated morphology, consistent with models of parapatric speciation. Using the same analysis, I find no support for alternative hypotheses that speciation involves divergence in diet or life history, or that speciation involves geographic isolation by latitude. These findings support the hypothesis that rockfishes undergo ecological speciation on an environmental gradient. PMID:20810434

  14. Trace metal speciation in natural waters: Computational vs. analytical

    USGS Publications Warehouse

    Kirk, Nordstrom D.

    1996-01-01

    Improvements in the field sampling, preservation, and determination of trace metals in natural waters have made many analyses more reliable and less affected by contamination. The speciation of trace metals, however, remains controversial. Chemical model speciation calculations do not necessarily agree with voltammetric, ion exchange, potentiometric, or other analytical speciation techniques. When metal-organic complexes are important, model calculations are not usually helpful and on-site analytical separations are essential. Many analytical speciation techniques have serious interferences and only work well for a limited subset of water types and compositions. A combined approach to the evaluation of speciation could greatly reduce these uncertainties. The approach proposed would be to (1) compare and contrast different analytical techniques with each other and with computed speciation, (2) compare computed trace metal speciation with reliable measurements of solubility, potentiometry, and mean activity coefficients, and (3) compare different model calculations with each other for the same set of water analyses, especially where supplementary data on speciation already exist. A comparison and critique of analytical with chemical model speciation for a range of water samples would delineate the useful range and limitations of these different approaches to speciation. Both model calculations and analytical determinations have useful and different constraints on the range of possible speciation such that they can provide much better insight into speciation when used together. Major discrepancies in the thermodynamic databases of speciation models can be evaluated with the aid of analytical speciation, and when the thermodynamic models are highly consistent and reliable, the sources of error in the analytical speciation can be evaluated. Major thermodynamic discrepancies also can be evaluated by simulating solubility and activity coefficient data and testing various

  15. Evidence for ecology's role in speciation.

    PubMed

    McKinnon, Jeffrey S; Mori, Seiichi; Blackman, Benjamin K; David, Lior; Kingsley, David M; Jamieson, Leia; Chou, Jennifer; Schluter, Dolph

    2004-05-20

    A principal challenge in testing the role of natural selection in speciation is to connect the build-up of reproductive isolation between populations to divergence of ecologically important traits. Demonstrations of 'parallel speciation', or assortative mating by selective environment, link ecology and isolation, but the phenotypic traits mediating isolation have not been confirmed. Here we show that the parallel build-up of mating incompatibilities between stickleback populations can be largely accounted for by assortative mating based on one trait, body size, which evolves predictably according to environment. In addition to documenting the influence of body size on reproductive isolation for stickleback populations spread across the Northern Hemisphere, we have confirmed its importance through a new experimental manipulation. Together, these results suggest that speciation may arise largely as a by-product of ecological differences and divergent selection on a small number of phenotypic traits. PMID:15152252

  16. [XANES study of lead speciation in duckweed].

    PubMed

    Chu, Bin-Bin; Luo, Li-Qiang; Xu, Tao; Yuan, Jing; Sun, Jian-Ling; Zeng, Yuan; Ma, Yan-Hong; Yi, Shan

    2012-07-01

    Qixiashan lead-zinc mine of Nanjing was one of the largest lead zinc deposits in East China Its exploitation has been over 50 years, and the environmental pollution has also been increasing. The lead concentration in the local environment was high, but lead migration and toxic mechanism has not been clear. Therefore, biogeochemistry research of the lead zinc mine was carried out. Using ICP-MS and Pb-L III edge XANES, lead concentration and speciation were analyzed respectively, and duckweed which can tolerate and enriched heavy metals was found in the pollution area. The results showed that the lead concentration of duckweed was 39.4 mg x kg(-1). XANES analysis and linear combination fit indicated that lead stearate and lead sulfide accounted for 65% and 36.9% respectively in the lead speciation of duckweed, suggesting that the main lead speciation of duckweed was sulfur-containing lead-organic acid.

  17. Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco).

    PubMed

    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

  18. [Speciation of metals in occupational medicine].

    PubMed

    Apostoli, P

    1998-01-01

    The identification and quantification of elements as such (that make up the historical analytical method used in toxicological studies) are necessary but not sufficient, in all cases, to understand and evaluate the mechanism of interaction between elements and biological targets. In fact, in order to approximate the factors that control the concentrations of elements in environmental or biological media, we need to know the occurrence of species of the elements themselves. This is element speciation, i.e. the capability of separating, identifying and determining the species in which an element is present and/or transformed. There are few, although increasing in latter years, examples of element speciation able to confirm the importance of this research approach in toxicological studies. Some basic information from these studies have found specific application in selecting the most appropriate indicators and the most representative matrices for biological monitoring. Furthermore, element speciation provides additional and often essential information in evaluating metal toxicity. The toxicity of the three oxidation states of Mercury differ considerably. For arsenic, a decreasing order of toxicity arsenite > arsenate > monomethylarsonic (MMA) > dimethylarsenite (DMA) has been proposed. However, the use of speciation in investigating toxicokinetic aspects appears to be difficult to apply to many other metals, mainly due to the lack of information about the existence and significance of species whose determination would be worthwhile and to the lack of analytical methods enabling us to measure species in biological media. Nonetheless, the horizon for speciation is more extensive and less linear than expected since about 15 elements, 20 oxidation states, and 25 organic compounds have been just involved in speciation. Problems might arise for biological monitoring practices, and the following topics should be considered: (i) identification of species and determination of

  19. 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...

  20. 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...

  1. 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.

  2. Phenotypic plasticity's impacts on diversification and speciation.

    PubMed

    Pfennig, David W; Wund, Matthew A; Snell-Rood, Emilie C; Cruickshank, Tami; Schlichting, Carl D; Moczek, Armin P

    2010-08-01

    Phenotypic plasticity (the ability of a single genotype to produce multiple phenotypes in response to variation in the environment) is commonplace. Yet its evolutionary significance remains controversial, especially in regard to whether and how it impacts diversification and speciation. Here, we review recent theory on how plasticity promotes: (i) the origin of novel phenotypes, (ii) divergence among populations and species, (iii) the formation of new species and (iv) adaptive radiation. We also discuss the latest empirical support for each of these evolutionary pathways to diversification and identify potentially profitable areas for future research. Generally, phenotypic plasticity can play a largely underappreciated role in driving diversification and speciation.

  3. 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.

  4. 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

  5. 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.…

  6. Multimodel inference and adaptive management

    USGS Publications Warehouse

    Rehme, S.E.; Powell, L.A.; Allen, C.R.

    2011-01-01

    Ecology is an inherently complex science coping with correlated variables, nonlinear interactions and multiple scales of pattern and process, making it difficult for experiments to result in clear, strong inference. Natural resource managers, policy makers, and stakeholders rely on science to provide timely and accurate management recommendations. However, the time necessary to untangle the complexities of interactions within ecosystems is often far greater than the time available to make management decisions. One method of coping with this problem is multimodel inference. Multimodel inference assesses uncertainty by calculating likelihoods among multiple competing hypotheses, but multimodel inference results are often equivocal. Despite this, there may be pressure for ecologists to provide management recommendations regardless of the strength of their study’s inference. We reviewed papers in the Journal of Wildlife Management (JWM) and the journal Conservation Biology (CB) to quantify the prevalence of multimodel inference approaches, the resulting inference (weak versus strong), and how authors dealt with the uncertainty. Thirty-eight percent and 14%, respectively, of articles in the JWM and CB used multimodel inference approaches. Strong inference was rarely observed, with only 7% of JWM and 20% of CB articles resulting in strong inference. We found the majority of weak inference papers in both journals (59%) gave specific management recommendations. Model selection uncertainty was ignored in most recommendations for management. We suggest that adaptive management is an ideal method to resolve uncertainty when research results in weak inference.

  7. 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

  8. 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

  9. Does Speciation between Arabidopsis halleri and Arabidopsis lyrata Coincide with Major Changes in a Molecular Target of Adaptation?

    PubMed Central

    Roux, Camille; Castric, Vincent; Pauwels, Maxime; Wright, Stephen I.; Saumitou-Laprade, Pierre; Vekemans, Xavier

    2011-01-01

    Ever since Darwin proposed natural selection as the driving force for the origin of species, the role of adaptive processes in speciation has remained controversial. In particular, a largely unsolved issue is whether key divergent ecological adaptations are associated with speciation events or evolve secondarily within sister species after the split. The plant Arabidopsis halleri is one of the few species able to colonize soils highly enriched in zinc and cadmium. Recent advances in the molecular genetics of adaptation show that the physiology of this derived ecological trait involves copy number expansions of the AhHMA4 gene, for which orthologs are found in single copy in the closely related A. lyrata and the outgroup A. thaliana. To gain insight into the speciation process, we ask whether adaptive molecular changes at this candidate gene were contemporary with important stages of the speciation process. We first inferred the scenario and timescale of speciation by comparing patterns of variation across the genomic backgrounds of A. halleri and A. lyrata. Then, we estimated the timing of the first duplication of AhHMA4 in A. halleri. Our analysis suggests that the historical split between the two species closely coincides with major changes in this molecular target of adaptation in the A. halleri lineage. These results clearly indicate that these changes evolved in A. halleri well before industrial activities fostered the spread of Zn- and Cd-polluted areas, and suggest that adaptive processes related to heavy-metal homeostasis played a major role in the speciation process. PMID:22069475

  10. 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.

  11. 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.

  12. Graphical inference for Infovis.

    PubMed

    Wickham, Hadley; Cook, Dianne; Hofmann, Heike; Buja, Andreas

    2010-01-01

    How do we know if what we see is really there? When visualizing data, how do we avoid falling into the trap of apophenia where we see patterns in random noise? Traditionally, infovis has been concerned with discovering new relationships, and statistics with preventing spurious relationships from being reported. We pull these opposing poles closer with two new techniques for rigorous statistical inference of visual discoveries. The "Rorschach" helps the analyst calibrate their understanding of uncertainty and "line-up" provides a protocol for assessing the significance of visual discoveries, protecting against the discovery of spurious structure.

  13. 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

  14. 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...

  15. Ecological speciation in tropical reef fishes.

    PubMed

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

    2005-03-22

    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.

  16. 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.

  17. 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 ...

  18. Actinide speciation in relation to biological processes.

    PubMed

    Ansoborlo, Eric; Prat, Odette; Moisy, Philippe; Den Auwer, Christophe; Guilbaud, Philippe; Carriere, M; Gouget, Barbara; Duffield, John; Doizi, Denis; Vercouter, Thomas; Moulin, Christophe; Moulin, Valérie

    2006-11-01

    In case of accidental release of radionuclides into the environment, actinides represent a severe health risk to human beings following internal contamination (inhalation, ingestion or wound). For a better understanding of the actinide behaviour in man (in term of metabolism, retention, excretion) and in specific biological systems (organs, cells or biochemical pathways), it is of prime importance to have a good knowledge of the relevant actinide solution chemistry and biochemistry, in particular of the thermodynamic constants needed for computing actinide speciation. To a large extent, speciation governs bioavailability and toxicity of elements and has a significant impact on the mechanisms by which toxics accumulate in cell compartments and organs and by which elements are transferred and transported from cell to cell. From another viewpoint, speciation is the prerequisite for the design and success of potential decorporation therapies. The purpose of this review is to present the state of the art of actinide knowledge within biological media. It is also to discuss how actinide speciation can be determined or predicted and to highlight the areas where information is lacking with the aim to encourage new research efforts.

  19. 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...

  20. 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...

  1. 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.

  2. 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

  3. 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

  4. Inferring horizontal gene transfer.

    PubMed

    Ravenhall, Matt; Škunca, Nives; Lassalle, Florent; Dessimoz, Christophe

    2015-05-01

    Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events. PMID:26020646

  5. 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.

  6. 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.

  7. Inferring Horizontal Gene Transfer

    PubMed Central

    Lassalle, Florent; Dessimoz, Christophe

    2015-01-01

    Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages [1]. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events. PMID:26020646

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification.

    PubMed

    Goldberg, Emma E; Lancaster, Lesley T; Ree, Richard H

    2011-07-01

    Geographic characters--traits describing the spatial distribution of a species-may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of ranges and the growth of phylogenetic trees. Here, we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model in which these processes are interdependent. We demonstrate the method with simulation tests that accurately recover parameters relating to the mode of speciation and source-sink dynamics. We then apply it to the evolution of habitat occupancy in Californian plant communities, where we find higher rates of speciation in chaparral than in forests and evidence for expanding habitat tolerances.

  14. 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.

  15. 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.

  16. Robustness to divergence time underestimation when inferring species trees from estimated gene trees.

    PubMed

    DeGiorgio, Michael; Degnan, James H

    2014-01-01

    To infer species trees from gene trees estimated from phylogenomic data sets, tractable methods are needed that can handle dozens to hundreds of loci. We examine several computationally efficient approaches-MP-EST, STAR, STEAC, STELLS, and STEM-for inferring species trees from gene trees estimated using maximum likelihood (ML) and Bayesian approaches. Among the methods examined, we found that topology-based methods often performed better using ML gene trees and methods employing coalescent times typically performed better using Bayesian gene trees, with MP-EST, STAR, STEAC, and STELLS outperforming STEM under most conditions. We examine why the STEM tree (also called GLASS or Maximum Tree) is less accurate on estimated gene trees by comparing estimated and true coalescence times, performing species tree inference using simulations, and analyzing a great ape data set keeping track of false positive and false negative rates for inferred clades. We find that although true coalescence times are more ancient than speciation times under the multispecies coalescent model, estimated coalescence times are often more recent than speciation times. This underestimation can lead to increased bias and lack of resolution with increased sampling (either alleles or loci) when gene trees are estimated with ML. The problem appears to be less severe using Bayesian gene-tree estimates.

  17. Bayes factors and multimodel inference

    USGS Publications Warehouse

    Link, W.A.; Barker, R.J.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael 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.

  18. 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.

  19. 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

  20. 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.

  1. The quest for the solar g modes

    NASA Astrophysics Data System (ADS)

    Appourchaux, T.; Belkacem, K.; Broomhall, A.-M.; Chaplin, W. J.; Gough, D. O.; Houdek, G.; Provost, J.; Baudin, F.; Boumier, P.; Elsworth, Y.; García, R. A.; Andersen, B. N.; Finsterle, W.; Fröhlich, C.; Gabriel, A.; Grec, G.; Jiménez, A.; Kosovichev, A.; Sekii, T.; Toutain, T.; Turck-Chièze, S.

    2010-02-01

    Solar gravity modes (or g modes)—oscillations of the solar interior on which buoyancy acts as the restoring force—have the potential to provide unprecedented inference on the structure and dynamics of the solar core, inference that is not possible with the well-observed acoustic modes (or p modes). The relative high amplitude of the g-mode eigenfunctions in the core and the evanesence of the modes in the convection zone make the modes particularly sensitive to the physical and dynamical conditions in the core. Owing to the existence of the convection zone, the g modes have very low amplitudes at photospheric levels, which makes the modes extremely hard to detect. In this article, we review the current state of play regarding attempts to detect g modes. We review the theory of g modes, including theoretical estimation of the g-mode frequencies, amplitudes and damping rates. Then we go on to discuss the techniques that have been used to try to detect g modes. We review results in the literature, and finish by looking to the future, and the potential advances that can be made—from both data and data-analysis perspectives—to give unambiguous detections of individual g modes. The review ends by concluding that, at the time of writing, there is indeed a consensus amongst the authors that there is currently no undisputed detection of solar g modes.

  2. 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.

  3. The Genetics of Speciation by Reinforcement

    PubMed Central

    2004-01-01

    Reinforcement occurs when natural selection strengthens behavioral discrimination to prevent costly interspecies matings, such as when matings produce sterile hybrids. This evolutionary process can complete speciation, thereby providing a direct link between Darwin's theory of natural selection and the origin of new species. Here, by examining a case of speciation by reinforcement in Drosophila, we present the first high-resolution genetic study of variation within species for female mating discrimination that is enhanced by natural selection. We show that reinforced mating discrimination is inherited as a dominant trait, exhibits variability within species, and may be influenced by a known set of candidate genes involved in olfaction. Our results show that the genetics of reinforced mating discrimination is different from the genetics of mating discrimination between species, suggesting that overall mating discrimination might be a composite phenomenon, which in Drosophila could involve both auditory and olfactory cues. Examining the genetics of reinforcement provides a unique opportunity for both understanding the origin of new species in the face of gene flow and identifying the genetic basis of adaptive female species preferences, two major gaps in our understanding of speciation. PMID:15550988

  4. First passage time to allopatric speciation

    PubMed Central

    Yamaguchi, Ryo; Iwasa, Yoh

    2013-01-01

    Allopatric speciation is a mechanism to evolve reproductive isolation; it is caused by the accumulation of genetic differences between populations while they are geographically isolated. Here, we studied a simple stochastic model for the time until speciation caused by geographical isolation in fragmented populations that experience recurrent but infrequent migration between subpopulations. We assumed that mating incompatibility is controlled by a number of loci that behave as neutral characters in the accumulation of novel mutations within each population. Genetic distance between populations was defined as the number of incompatibility-controlling loci that differ between them. Genetic distance increases through the separate accumulation of mutations in different populations, but decreases after a successful migration event followed by genetic mixing between migrants and residents. We calculated the time to allopatric speciation, which occurs when the genetic distance exceeds a specified threshold. If the number of invasive individuals relative to the resident population is not very large, diffusion approximation provides an accurate prediction. There is an intermediate optimal rate of migration that maximizes the rate of species creation by recurrent invasion and diversification. We also examined cases that involved more than two populations. PMID:24516714

  5. The genetics of speciation by reinforcement.

    PubMed

    Ortiz-Barrientos, Daniel; Counterman, Brian A; Noor, Mohamed A F

    2004-12-01

    Reinforcement occurs when natural selection strengthens behavioral discrimination to prevent costly interspecies matings, such as when matings produce sterile hybrids. This evolutionary process can complete speciation, thereby providing a direct link between Darwin's theory of natural selection and the origin of new species. Here, by examining a case of speciation by reinforcement in Drosophila,we present the first high-resolution genetic study of variation within species for female mating discrimination that is enhanced by natural selection. We show that reinforced mating discrimination is inherited as a dominant trait, exhibits variability within species, and may be influenced by a known set of candidate genes involved in olfaction. Our results show that the genetics of reinforced mating discrimination is different from the genetics of mating discrimination between species, suggesting that overall mating discrimination might be a composite phenomenon, which in Drosophila could involve both auditory and olfactory cues. Examining the genetics of reinforcement provides a unique opportunity for both understanding the origin of new species in the face of gene flow and identifying the genetic basis of adaptive female species preferences, two major gaps in our understanding of speciation.

  6. Determination of metal speciation by reverse titrations.

    PubMed

    Nuester, Jochen; van den Berg, Constant M G

    2005-01-01

    A new method is proposed to determine metal speciation by varying the concentration of a competing ligand at a constant metal concentration, with detection by cathodic stripping voltammetry. The free metal ion concentration is gradually lowered from its natural level while the method probes progressively deeper into the already complexed metal fraction: it is therefore a reverse titration rather than the forward titration which is used for conventional complexing ligand titrations. The sensitivity is greatest at the lowest free metal ion concentration, where it matters most, and the method can be carried out in a single sample aliquot in the voltammetric cell. The method is applied here to copper speciation, but in principle, it can also be used for other metals. Modeling shows that this method has good sensitivity at ligand concentrations near the metal concentration (lower as well as greater). Comparative measurements of copper speciation using reverse and forward titrations of representative water samples of oceanic and coastal origin show good agreement. The data showed that these samples did not contain low levels of strong ligands in addition to the ligands detected by the forward titrations.

  7. 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

  8. 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.

  9. Soil Properties Controlling Zn Speciation and Fractionation in Contaminated Soils

    SciTech Connect

    Jacquat, O.; Voegelin, A; Kretzschmar, R

    2009-01-01

    We determined the speciation of Zn in 49 field soils differing widely in pH (4.1-7.7) and total Zn content (251-30,090 mg/kg) by using extended X-ray absorption fine structure (EXAFS) spectroscopy. All soils had been contaminated since several decades by inputs of aqueous Zn with runoff-water from galvanized power line towers. Pedogenic Zn species identified by EXAFS spectroscopy included Zn in hydroxy-interlayered minerals (Zn-HIM), Zn-rich phyllosilicates, Zn-layered double hydroxide (Zn-LDH), hydrozincite, and octahedrally and tetrahedrally coordinated sorbed or complexed Zn. Zn-HIM was only observed in (mostly acidic) soils containing less than 2000 mg/kg of Zn, reflecting the high affinity but limited sorption capacity of HIM. Zn-bearing precipitates, such as Zn-LDH and Zn-rich trioctahedral phyllosilicates, became more dominant with increasing pH and increasing total Zn content relative to available adsorption sites. Zn-LDH was the most abundant Zn-precipitate and was detected in soils with pH > 5.2. Zn-rich phyllosilicates were detected even at lower soil pH, but were generally less abundant than Zn-LDH. Hydrozincite was only identified in two calcareous soils with extremely high Zn contents. In addition to Zn-LDH, large amounts of Zn in highly contaminated soils were mainly accumulated as sorbed/complexed Zn in tetrahedral coordination. Soils grouped according to their Zn speciation inferred from EXAFS spectroscopy mainly differed with respect to soil pH and total Zn content. Clear differences were observed with respect to Zn fractionation by sequential extraction: From Zn-HIM containing soils, most of the total Zn was recovered in the exchangeable and the most recalcitrant fractions. In contrast, from soils containing the highest percentage of Zn-precipitates, Zn was mainly extracted in intermediate extraction steps. The results of this study demonstrate that soil pH and Zn contamination level relative to available adsorption sites are the most important

  10. 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

  11. 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…

  12. Feature Inference Learning and Eyetracking

    ERIC Educational Resources Information Center

    Rehder, Bob; Colner, Robert M.; Hoffman, Aaron B.

    2009-01-01

    Besides traditional supervised classification learning, people can learn categories by inferring the missing features of category members. It has been proposed that feature inference learning promotes learning a category's internal structure (e.g., its typical features and interfeature correlations) whereas classification promotes the learning of…

  13. 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.…

  14. 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…

  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. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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].

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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...

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. Chapter A5. Section 6.4.A. Arsenic Speciation

    USGS Publications Warehouse

    Garbarino, John R.

    2005-01-01

    Two sample-processing methods (field speciation and laboratory speciation) used at the USGS National Water Quality Laboratory (NWQL) are specific to sample analysis by inductively coupled plasma-mass spectrometry (ICP-MS) for determining the concentration of inorganic and organic arsenic species in a water sample. The field-speciation method requires NWQL Schedule 1729. The laboratory-speciation method requires use either of NWQL Schedule 1730, 1731, or 1732, as appropriate for study objectives. For either the field- or laboratory-speciation method, prior knowledge is needed of sample matrix-composition characteristics (that is, major-ion concentrations in filtered samples). Major-ion data are necessary to determine (1) the volume of ethylenediaminetetraacetic acid (EDTA) that will be required for sample preservation, and (2) if sample dilution is required.

  20. The reconstructed tree in the lineage-based model of protracted speciation.

    PubMed

    Lambert, Amaury; Morlon, Hélène; Etienne, Rampal S

    2015-01-01

    A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree produced by a given model of diversification. Etienne and Rosindell in Syst Biol 61(2):204-213, (2012) proposed a lineage-based model of diversification, called protracted speciation, where species remain incipient during a random duration before turning good species, and showed that this can explain the slowdown in lineage accumulation observed in real phylogenies. However, they were unable to provide a general likelihood formula. Here, we present a likelihood formula for protracted speciation models, where rates at which species turn good or become extinct can depend both on their age and on time. Our only restrictive assumption is that speciation rate does not depend on species status. Our likelihood formula utilizes a new technique, based on the contour of the phylogenetic tree and first developed by Lambert in Ann Probab 38(1):348-395, (2010). We consider the reconstructed trees spanned by all extant species, by all good extant species, or by all representative species, which are either good extant species or incipient species representative of some good extinct species. Specifically, we prove that each of these trees is a coalescent point process, that is, a planar, ultrametric tree where the coalescence times between two consecutive tips are independent, identically distributed random variables. We characterize the common distribution of these coalescence times in some, biologically meaningful, special cases for which the likelihood reduces to an elegant analytical formula or becomes numerically tractable. PMID:24615006

  1. Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies

    PubMed Central

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

    2015-01-01

    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

  2. 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

  3. Sexual signaling and speciation, a microevolutionary perspective.

    PubMed

    Boake, Christine R B

    2002-11-01

    Despite the growing evidence that sexual selection can drive speciation, the evolution of sexual signals in natural populations is far from being well-understood. Sexual signals evolve in response to a variety of factors. Some of the most important selective factors are conspecifics, transmission efficiency in a particular environment, detection by predators, and phylogenetic constraints. These factors have been addressed quite successfully in studies of single types of signals in both vertebrates and invertebrates. However, it is less clear how multimodal signals evolve because the factors listed above will act on every component of the signaling system, and the relative weights of each type of signal must be taken into account. Species of Drosophila are excellent for such analyses because they are amenable to both phenotypic experimentation and genetic manipulation. This paper presents an approach that involves two analyses: studies of which signals are sexually selected within a species, and parallel studies of the signals that are involved in behavioral isolation between closely related species. If the same signal characteristics are involved in both processes, they would provide support for the hypothesis that sexual selection can drive speciation. This approach is illustrated with studies of Hawaiian Drosophila and a review of signals that could be sexually selected in Drosophila melanogaster.

  4. Pleistocene speciation in the genus Populus (salicaceae).

    PubMed

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

    2012-05-01

    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.

  5. Gene regulation and speciation in house mice

    PubMed Central

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

    2016-01-01

    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 between Mus musculus musculus and M. m. domesticus was characterized by studying allele-specific expression in fertile hybrid males using mRNA-sequencing of whole testes. We found extensive regulatory divergence between M. m. musculus and M. m. domesticus, largely attributable to cis-regulatory changes. When both cis and trans changes 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

  6. Physicochemical speciation of molybdenum in rain water.

    PubMed

    Kawakubo, S; Hashi, S; Iwatsuki, M

    2001-07-01

    A combination of a sensitive catalytic determination method with filtration and ultrafiltration has been used for the physicochemical speciation of molybdenum in natural and synthetic rain water samples. The concentration (CL) of labile molybdenum was evaluated by a direct catalytic determination. The total concentration (CT ) of molybdenum was determined after the acid decomposition of the sample to calculate the non-labile concentration (CT-CL). From the speciation results, molybdenum species in the successive rainfall sample were found in a fraction with smaller molecular weights < 10(3) Da and characterized as labile forms, i.e. simple molybdate ions. Non-labile molybdenum existed in particulate matter (> or = 0.45 microm in particle size) and distributed predominantly in the initial rainfall sample. The coprecipitation with Fe(III) hydroxide contributed to the formation of the non-labile molybdenum. In the initial rainfall sample, a small part of molybdenum was labile in the particle fraction (> or = 0.45 microm). This type of molybdenum was associated with the formation of humic iron aggregates.

  7. Mercury speciation by CE: an update.

    PubMed

    Kubán, Petr; Pelcová, Pavlína; Margetínová, Jana; Kubán, Vlastimil

    2009-01-01

    This review provides an update on mercury speciation by CE. It includes a brief discussion on physicochemical properties, toxicity and transformation pathways of mercury species (i.e. methyl-, ethyl-, phenyl- and inorganic mercury) and outlines recent trends in Hg speciation by CE. CE is presented as a complementary technique to chromatographic separation techniques, especially in cases when speed, high efficiency and low sample volumes are required. The development of suitable sample preconcentration/isolation (sample stacking, ion exchange, liquid-liquid-liquid extraction, dual-cloud point extraction) to achieve low LODs for analysis of trace concentrations of mercury species in real samples is emphasized. Hyphenation of CE to element specific detectors (i.e. electrothermal atomic absorption spectrometry, atomic fluorescence spectrometry, inductively coupled plasma-optical emission spectrometry, inductively coupled plasma-mass spectrometry) is discussed as well as a potential of CE in interaction studies that may provide useful information on interaction of various Hg species with selected bio-macromolecules.

  8. 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

  9. Alternative adaptations, speciation, and phylogeny (A Review)

    PubMed Central

    West-Eberhard, Mary Jane

    1986-01-01

    Alternative adaptations—different adaptive phenotypes maintained in the same life stage and the same population but not necessarily simultaneously expressed in the same individual—represent contrasting character sets produced by the same genome, in effect allowing a single species to occupy more than one sympatric niche. Such alternatives are particularly likely to give rise to novel adaptations because of selection for extreme dissimilarity between them and because established traits buffer populations against extinction while independently expressed alternatives evolve in new directions. Particular alternatives can be suddenly fixed in populations with little or no genetic change, leading to a period of rapid evolution (especially, of morphology) exaggerating the characteristics of the newly fixed form. This burst of change would facilitate rapid speciation and could produce “punctuated” patterns of evolution. Evidence from a wide variety of organisms shows that alternative phenotypes are exceedingly common in nature and that they are probably important in speciation and macroevolution. Although many of these ideas and observations have been noted piecemeal by previous authors, bringing them together demonstrates the probable importance of alternative adaptations in the origin of major evolutionary novelties and calls for a revision of current and traditional ideas about the role of behavior and ontogeny in the genesis of organic diversity. PMID:16578790

  10. Climatic oscillations triggered post-Messinian speciation of Western Palearctic brown frogs (Amphibia, Ranidae).

    PubMed

    Veith, M; Kosuch, J; Vences, M

    2003-02-01

    Oscillating glacial cycles over the past 2.4 million years are proposed to have had a major impact on the diversity of contemporary species communities. We used mitochondrial and nuclear DNA sequence data to infer phylogenetic relationships within Western Palearctic brown frogs and to test the influence of Pliocene and Pleistocene climatic changes on their evolution. We sequenced 1976bp of the mitochondrial genes 16S rRNA and cytochrome b and of the nuclear rhodopsin gene for all current species and subspecies. Based on an established allozyme clock for Western Palearctic water frogs and substitution rate constancy among water frogs and brown frogs, we calibrated a molecular clock for 1425bp of the 16S and rhodopsin genes. We applied this clock to date speciation events among brown frogs. Western Palearctic brown frogs underwent a basal post-Messinian radiation about 4 million years ago (mya) into five major clades: three monotypic lineages (Rana dalmatina, Rana latastei, Rana graeca), an Anatolian lineage, and a lineage comprising Rana italica, Rana arvalis, and all Iberian taxa. Polytypic lineages radiated further in concordance with the onset of climatic oscillations ca. 3.2, 2.0, and 1.0-0.6 mya, respectively. The dated fossil record corroborates our paleobiogeographic scenario. We conclude that drastic climatic changes followed by successive temperature oscillations "trapped" most brown frog species in their southern European glacial refugia with enough time to speciate. Substantial dispersal was only possible during extensive interglacial periods of a constant subtropical climate.

  11. 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

  12. 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

  13. 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

  14. 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

    2015-08-26

    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.

  15. 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

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

    NASA Astrophysics Data System (ADS)

    Bray, Timothy C.; Bocak, Ladislav

    2016-09-01

    We demonstrate the controversial origin of a biological species within an area of a few kilometres in the absence of physical barriers. We employed nuclear rRNA/mitochondrial and genome-wide SNP approaches to infer relationships of four species of net-winged beetles characterised by female neoteny. Three species are distributed at low elevations and a single population colonised a 40 km2 highland plateau and established distinct biological species despite incomplete genetic isolation. The speciation process is extreme in the highly localised spatial scale, due to the low dispersal power of neotenics, and provides clear support for a microallopatric model based on ecological conditions. In contrast with neutral evolution in a homogenous environment, as demonstrated by the genetic divergence and morphological similarity of two widely distributed low-mountain species, the environmental characteristics of the high-mountain plateau led to the origin of a species adapted to the local mimetic pattern and characterised by morphologically distinct genitalia. We conclude that the low dispersal propensity promotes neutral genetic differentiation in the first stage, but environmental characteristics play an important role the final phase of the speciation process. The unexpected speciation at such an extreme geographic scale points to the in situ origin and uniqueness of the mountain fauna.

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

    PubMed Central

    Bray, Timothy C.; Bocak, Ladislav

    2016-01-01

    We demonstrate the controversial origin of a biological species within an area of a few kilometres in the absence of physical barriers. We employed nuclear rRNA/mitochondrial and genome-wide SNP approaches to infer relationships of four species of net-winged beetles characterised by female neoteny. Three species are distributed at low elevations and a single population colonised a 40 km2 highland plateau and established distinct biological species despite incomplete genetic isolation. The speciation process is extreme in the highly localised spatial scale, due to the low dispersal power of neotenics, and provides clear support for a microallopatric model based on ecological conditions. In contrast with neutral evolution in a homogenous environment, as demonstrated by the genetic divergence and morphological similarity of two widely distributed low-mountain species, the environmental characteristics of the high-mountain plateau led to the origin of a species adapted to the local mimetic pattern and characterised by morphologically distinct genitalia. We conclude that the low dispersal propensity promotes neutral genetic differentiation in the first stage, but environmental characteristics play an important role the final phase of the speciation process. The unexpected speciation at such an extreme geographic scale points to the in situ origin and uniqueness of the mountain fauna. PMID:27633844

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

    PubMed

    Bray, Timothy C; Bocak, Ladislav

    2016-01-01

    We demonstrate the controversial origin of a biological species within an area of a few kilometres in the absence of physical barriers. We employed nuclear rRNA/mitochondrial and genome-wide SNP approaches to infer relationships of four species of net-winged beetles characterised by female neoteny. Three species are distributed at low elevations and a single population colonised a 40 km(2) highland plateau and established distinct biological species despite incomplete genetic isolation. The speciation process is extreme in the highly localised spatial scale, due to the low dispersal power of neotenics, and provides clear support for a microallopatric model based on ecological conditions. In contrast with neutral evolution in a homogenous environment, as demonstrated by the genetic divergence and morphological similarity of two widely distributed low-mountain species, the environmental characteristics of the high-mountain plateau led to the origin of a species adapted to the local mimetic pattern and characterised by morphologically distinct genitalia. We conclude that the low dispersal propensity promotes neutral genetic differentiation in the first stage, but environmental characteristics play an important role the final phase of the speciation process. The unexpected speciation at such an extreme geographic scale points to the in situ origin and uniqueness of the mountain fauna. PMID:27633844

  19. 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...

  20. 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...

  1. 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...

  2. Children's Category-Based Inferences Affect Classification

    ERIC Educational Resources Information Center

    Ross, Brian H.; Gelman, Susan A.; Rosengren, Karl S.

    2005-01-01

    Children learn many new categories and make inferences about these categories. Much work has examined how children make inferences on the basis of category knowledge. However, inferences may also affect what is learned about a category. Four experiments examine whether category-based inferences during category learning influence category knowledge…

  3. 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

  4. 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

  5. Inferring Diversity: Life After Shannon

    NASA Astrophysics Data System (ADS)

    Giffin, Adom

    The diversity of a community that cannot be fully counted must be inferred. The two preeminent inference methods are the MaxEnt method, which uses information in the form of constraints and Bayes' rule which uses information in the form of data. It has been shown that these two methods are special cases of the method of Maximum (relative) Entropy (ME). We demonstrate how this method can be used as a measure of diversity that not only reproduces the features of Shannon's index but exceeds them by allowing more types of information to be included in the inference. A specific example is solved in detail. Additionally, the entropy that is found is the same form as the thermodynamic entropy.

  6. A Japanese view on speciation: "Sumiwake" explosive speciation of the cichlids in Lake Victoria.

    PubMed

    Kawamiya, Nobuo

    2003-01-01

    Imanishi's "mental" (cerebral) view of speciation is presented, in Mizuhata's revision. The key concept here is the "ethological partition" of the species. Members of each species=society (etho-species) share the same mental (brain) software, irrespective of their genetic structure. Cerebral animals perform active programmed selection, not to be confused with passive, non-programmed "natural selection" as in Neo-Darwinism. The program includes mating-choice of peculiar characters, distinct from the Neo-Darwinian sexual selection supposed due to the specific choosy genes. Speciation can occur, as a "partition of species=society", with bifurcation of mate-choosing program in the parent species. A main promoter for this bifurcation is species-specific "passion" for especially significant characters: long necks, ornamental antlers, ocelli feathers, bright nuptial colors etc. The cichlids in Lake Victoria achieved explosive speciation, while retaining their genetic homogeneity completely. Therefore it is illogical to attribute this divergence to extraordinary mutations in "action controlling genes". The origin of species=society (etho-species) can trace along to the Cambrian Period.

  7. Perception, illusions and Bayesian inference.

    PubMed

    Nour, Matthew M; Nour, Joseph M

    2015-01-01

    Descriptive psychopathology makes a distinction between veridical perception and illusory perception. In both cases a perception is tied to a sensory stimulus, but in illusions the perception is of a false object. This article re-examines this distinction in light of new work in theoretical and computational neurobiology, which views all perception as a form of Bayesian statistical inference that combines sensory signals with prior expectations. Bayesian perceptual inference can solve the 'inverse optics' problem of veridical perception and provides a biologically plausible account of a number of illusory phenomena, suggesting that veridical and illusory perceptions are generated by precisely the same inferential mechanisms.

  8. 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.

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

    PubMed

    Pastene, Luis A; Goto, Mutsuo; Kanda, Naohisa; Zerbini, Alexandre N; Kerem, Dan; Watanabe, Kazuo; Bessho, Yoshitaka; Hasegawa, Masami; Nielsen, Rasmus; Larsen, Finn; Palsbøll, Per J

    2007-04-01

    How do populations of highly mobile species inhabiting open environments become reproductively isolated and evolve into new species? We test the hypothesis that elevated ocean-surface temperatures can facilitate allopatry among pelagic populations and thus promote speciation. Oceanographic modelling has shown that increasing surface temperatures cause localization and reduction of upwelling, leading to fragmentation of feeding areas critical to pelagic species. We test our hypothesis by genetic analyses of populations of two closely related baleen whales, the Antarctic minke whale (Balaenoptera bonaerensis) and common minke whale (Balaenoptera acutorostrata) whose current distributions and migration patterns extent are largely determined by areas of consistent upwelling with high primary production. Phylogeographic and population genetic analyses of mitochondrial DNA control-region nucleotide sequences collected from 467 whales sampled in four different ocean basins were employed to infer the evolutionary relationship among populations of B. acutorostrata by rooting an intraspecific phylogeny with a population of B. bonaerensis. Our findings suggest that the two species diverged in the Southern Hemisphere less than 5 million years ago (Ma). This estimate places the speciation event during a period of extended global warming in the Pliocene. We propose that elevated ocean temperatures in the period facilitated allopatric speciation by disrupting the continuous belt of upwelling maintained by the Antarctic Circumpolar Current. Our analyses revealed that the current populations of B. acutorostrata likely diverged after the Pliocene some 1.5 Ma when global temperatures had decreased and presumably coinciding with the re-establishment of the polar-equatorial temperature gradient that ultimately drives upwelling. In most population samples, we detected genetic signatures of exponential population expansions, consistent with the notion of increasing carrying capacity

  10. 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).

  11. Initial steps of speciation by geographic isolation and host switch in salmonid pathogen Gyrodactylus salaris (Monogenea: Gyrodactylidae).

    PubMed

    Meinilä, Maria; Kuusela, Jussi; Zietara, Marek S; Lumme, Jaakko

    2004-03-29

    To test the hypothesis that host-switching can be an important step in the speciation of gyrodactylid monogenean flatworms, we inferred the phylogeny within a cluster of parasites morphologically close to Gyrodactylus salaris Malmberg 1957, collected from Atlantic, Baltic and White Sea salmon (Salmo salar), farmed rainbow trout (Oncorhynchus mykiss), and grayling (Thymallus thymallus) from Northern Europe. The internal transcribed spacer region of the nuclear ribosomal gene was sequenced for taxonomic identification. Parasites on grayling from the White Sea Basin differed from the others by one nucleotide (0.08%), the remainder were identical to the sequence published earlier from Norway (G. salaris on salmon), England (Gyrodactylus thymalli on grayling), and the Czech Republic (unidentified salaris/thymalli on trout). For increased resolution, 813 nucleotides of the mitochondrial COI gene of 88 parasites were sequenced and compared with 76 published sequences using phylogenetic analysis. For all tree building algorithms (NJ, MP), the parasites formed a star-like phylogeny of six definite sister clades, indicating nearly simultaneous radiation. Average K2P distances between clades were 1.8-2.6%, and internal mean distances 0.2-1.1%. The genetic distance to the nearest known relative, Gyrodactylus lavareti Malmberg, was 24%. A variable salmon-specific mitochondrial Clade I was observed both in the Baltic Basin and in pathogenic populations introduced to the Atlantic and White Sea coasts. An invariable Clade II was common in rainbow trout farms in Sweden, Denmark and Finland; the same haplotype was also infecting salmon in a landlocked population in Russian Karelia, and in Oslo fjord and Sognefjord in Norway. Four geographically vicariant sister clades were observed on graylings: Clade III in the Baltic Sea Basin; Clade IV in Karelian rivers draining to the White Sea; Clade V in Norwegian river draining to Swedish lake Vänern; and Clade VI in rivers draining to Oslo

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Horizontal gene transfer, dispersal and haloarchaeal speciation.

    PubMed

    Papke, R Thane; Corral, Paulina; Ram-Mohan, Nikhil; Haba, Rafael R de la; 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

  18. 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.

  19. 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

  20. 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

  1. Arsenic distribution and speciation in Daphnia pulex.

    PubMed

    Caumette, Guilhem; Koch, Iris; Moriarty, Maeve; Reimer, Kenneth J

    2012-08-15

    Rat Lake, Yellowknife, Northwest Territories, is situated on arsenic-rich tailings from a historical gold mine. The abundant zooplankton species Daphnia pulex in this lake was used to study the impact of arsenic at the base of the freshwater food web; the speciation and distribution of arsenic in D. pulex and its food sources; and the origin of formation of organoarsenicals in freshwater systems. The arsenic concentration in lake water was measured as 0.25 mg L(-1), while the zooplankton organisms contained up to 35 mg kg(-1) d.w. arsenic. Plankton samples were analyzed for arsenic speciation, by using X-ray Absorption Near Edge Structure (XANES) on the whole, dried samples and High Performance Liquid Chromatography coupled to Inductively Coupled Plasma Mass Spectrometry (HPLC-ICP-MS) on water extracts. XANES data suggest that D. pulex mainly contain inorganic arsenicals with 56% of arsenic with +5 oxidation state and 10% of arsenic with +3 oxidation state, but also 34% of organoarsenic compounds that were identified with HPLC-ICP-MS as monomethylarsonate (MMA), dimethylarsinate (DMA), and arsenosugars. The most abundant of the organoarsenicals was the glycerol sugar (Sugar 1). X-ray Fluorescence (XRF) mapping of D. pulex for arsenic distribution showed that arsenic was mainly distributed in the gut of the animal, where its concentration was ten times higher than in the surrounding tissues. Moreover, the analysis of residues from extractions targeting water-soluble and lipid-soluble arsenicals suggested that part of the measured arsenic signal comes from ingested sediments, phytoplankton, or other food sources. These food sources contain inorganic arsenic only, with As(V)-O in phytoplankton and As(III)-S in sediments, suggesting the possibility that the organoarsenicals compounds detected in the tissues of the organism are created by the Daphnia. PMID:22750169

  2. Mimicry: developmental genes that contribute to speciation.

    PubMed

    Naisbit, Russell E; Jiggins, Chris D; Mallet, James

    2003-01-01

    Despite renewed interest in the role of natural selection as a catalyst for the origin of species, the developmental and genetic basis of speciation remains poorly understood. Here we describe the genetics of Müllerian mimicry in Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae), sister species that recently diverged to mimic other Heliconius. This mimetic shift was a key step in their speciation, leading to pre- and postmating isolation. We identify 10 autosomal loci, half of which have major effects. At least eight appear to be homologous with genes known to control pattern differences within each species. Dominance has evolved under the influence of identifiable "modifier" loci rather than being a fixed characteristic of each locus. Epistasis is found at many levels: phenotypic interaction between specific pairs of genes, developmental canalization due to polygenic modifiers so that patterns are less sharply defined in hybrids, and overall fitness through ecological selection against nonmimetic hybrid genotypes. Most of the loci are clustered into two genomic regions or "supergenes," suggesting color pattern evolution is constrained by preexisting linked elements that may have arisen via tandem duplication rather than having been assembled by natural selection. Linkage, modifiers, and epistasis affect the strength of mimicry as a barrier to gene flow between these naturally hybridizing species and may permit introgression in genomic regions unlinked to those under disruptive selection. Müllerian mimics in Heliconius use different genetic architectures to achieve the same mimetic patterns, implying few developmental constraints. Therefore, although developmental and genomic constraints undoubtedly influence the evolutionary process, their effects are probably not strong in comparison with natural selection.

  3. 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…

  4. 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…

  5. 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,…

  6. 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)…

  7. Dynamic speciation analysis and bioavailability of metals in aquatic systems.

    PubMed

    van Leeuwen, Herman P; Town, Raewyn M; Buffle, Jacques; Cleven, Rob F M J; Davison, William; Puy, Jaume; van Riemsdijk, Willem H; Sigg, Laura

    2005-11-15

    Dynamic metal speciation analysis in aquatic ecosystems is emerging as a powerful basis for development of predictions of bioavailability and reliable risk assessment strategies. A given speciation sensor is characterized by an effective time scale or kinetic window that defines the measurable metal species via their labilities. Here we review the current state of the art for the theory and application of dynamic speciation sensors. We show that a common dynamic interpretation framework, based on rigorous flux expressions incorporating the relevant diffusion and reaction steps, is applicable for a suite of sensors that span a range of time scales. Interpolation from a kinetic spectrum of speciation data is proposed as a practical strategy for addressing questions of bioavailability. Case studies illustrate the practical significance of knowledge on the dynamic features of metal complex species in relation to biouptake, and highlight the limitations of equilibrium-based models. PMID:16323747

  8. 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) ...

  9. 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.

  10. 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.

  11. 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

  12. XAS Studies of Se Speciation in Selenite-Fed Rats

    PubMed Central

    Weekley, Claire M.; Aitken, Jade B.; Witting, Paul K.; Harris, Hugh H.

    2014-01-01

    The biological activity of selenium is dependent on its chemical form. Therefore, knowledge of Se chemistry in vivo is required for efficacious use of selenium compounds in disease prevention and treatment. Using X-ray absorption spectroscopy, Se speciation in the kidney, liver, heart, spleen, testis and red blood cells of rats fed control (~0.3 ppm Se) or selenite-supplemented (1 ppm or 5 ppm Se) diets for 3 or 6 weeks, was investigated. X-ray absorption spectroscopy revealed the presence of Se–Se and Se–C species in the kidney and liver, and Se–S species in the kidney, but not the liver. X-ray absorption near edge structure (XANES) spectra showed that there was variation in speciation in the liver and kidneys, but Se speciation was much more uniform in the remaining organs. Using principal component analysis (PCA) to interpret the Se K-edge X-ray absorption spectra, we were able to directly compare the speciation of Se in two different models of selenite metabolism – human lung cancer cells and rat tissues. The effects of Se dose, tissue type and duration of diet on selenium speciation in rat tissues were investigated, and a relationship between the duration of the diet (3 weeks versus 6 weeks) and selenium speciation was observed. PMID:25363824

  13. Geographical range and speciation in fossil and living molluscs.

    PubMed Central

    Jablonski, David; Roy, Kaustuv

    2003-01-01

    The notion of a positive relation between geographical range and speciation rate or speciation probability may go back to Darwin, but a negative relation between these parameters is equally plausible. Here, we test these alternatives in fossil and living molluscan taxa. Late Cretaceous gastropod genera exhibit a strong negative relation between the geographical ranges of constituent species and speciation rate per species per million years; this result is robust to sampling biases against small-bodied taxa and is not attributable to phylogenetic effects. They also exhibit weak inverse or non-significant relations between geographical range and (i) the total number of species produced over the 18 million year timeframe, and (ii) the number of species in a single timeplane. Sister-group comparisons using extant molluscan species also show a non-significant relation between median geographical range and species richness of genera. These results support the view that the factors promoting broad geographical ranges also tend to damp speciation rates. They also demonstrate that a strong inverse relation between per-species speciation rate and geographical range need not be reflected in analyses conducted within a single timeplane, underscoring the inadequacy of treating net speciation as a proxy for raw per-taxon rates. PMID:12639320

  14. 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

  15. 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

  16. 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 variation

  17. Plasma Modes

    NASA Astrophysics Data System (ADS)

    Dubin, D. H. E.

    This chapter explores several aspects of the linear electrostatic normal modes of oscillation for a single-species non-neutral plasma in a Penning trap. Linearized fluid equations of motion are developed, assuming the plasma is cold but collisionless, which allow derivation of the cold plasma dielectric tensor and the electrostatic wave equation. Upper hybrid and magnetized plasma waves in an infinite uniform plasma are described. The effect of the plasma surface in a bounded plasma system is considered, and the properties of surface plasma waves are characterized. The normal modes of a cylindrical plasma column are discussed, and finally, modes of spheroidal plasmas, and finite temperature effects on the modes, are briefly described.

  18. 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.

  19. 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

  20. Sulfur speciation in natural hydrothermal waters, Iceland

    NASA Astrophysics Data System (ADS)

    Kaasalainen, Hanna; Stefánsson, Andri

    2011-05-01

    The speciation of aqueous dissolved sulfur was determined in hydrothermal waters in Iceland. The waters sampled included hot springs, acid-sulfate pools and mud pots, sub-boiling well discharges and two-phase wells. The water temperatures ranged from 4 to 210 °C, the pH T was between 2.20 and 9.30 at the discharge temperature and the SO 4 and Cl concentrations were 0.020-52.7 and <0.01-10.0 mmol kg -1, respectively. The analyses were carried out on-site within ˜10 min of sampling using ion chromatography (IC) for sulfate (SO 42-), thiosulfate (S 2O 32-) and polythionates (S xO 62-) and titration and/or colorimetry for total dissolved sulfide (S 2-). Sulfite (SO 32-) could also be determined in a few cases using IC. Alternatively, for few samples in remote locations the sulfur oxyanions were stabilized on a resin on site following elution and analysis by IC in the laboratory. Dissolved sulfate and with few exceptions also S 2- were detected in all samples with concentrations of 0.02-52.7 mmol kg -1 and <1-4100 μmol kg -1, respectively. Thiosulfate was detected in 49 samples of the 73 analyzed with concentrations in the range of <1-394 μmol kg -1 (S-equivalents). Sulfite was detected in few samples with concentrations in the range of <1-3 μmol kg -1. Thiosulfate and SO 32- were not detected in <100 °C well waters and S 2O 32- was observed only at low concentrations (<1-8 μmol kg -1) in ˜200 °C well waters. In alkaline and neutral pH hot springs, S 2O 32- was present in significant concentrations sometimes corresponding to up to 23% of total dissolved sulfur (S TOT). In steam-heated acid-sulfate waters, S 2O 32- was not a significant sulfur species. The results demonstrate that S 2O 32- and SO 32- do not occur in the deeper parts of <150 °C hydrothermal systems and only in trace concentrations in ˜200-300 °C systems. Upon ascent to the surface and mixing with oxygenated ground and surface waters and/or dissolution of atmospheric O 2, S 2- is degassed and

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Cortical circuits for perceptual inference.

    PubMed

    Friston, Karl; Kiebel, Stefan

    2009-10-01

    This paper assumes that cortical circuits have evolved to enable inference about the causes of sensory input received by the brain. This provides a principled specification of what neural circuits have to achieve. Here, we attempt to address how the brain makes inferences by casting inference as an optimisation problem. We look at how the ensuing recognition dynamics could be supported by directed connections and message-passing among neuronal populations, given our knowledge of intrinsic and extrinsic neuronal connections. We assume that the brain models the world as a dynamic system, which imposes causal structure on the sensorium. Perception is equated with the optimisation or inversion of this internal model, to explain sensory input. Given a model of how sensory data are generated, we use a generic variational approach to model inversion to furnish equations that prescribe recognition; i.e., the dynamics of neuronal activity that represents the causes of sensory input. Here, we focus on a model whose hierarchical and dynamical structure enables simulated brains to recognise and predict sequences of sensory states. We first review these models and their inversion under a variational free-energy formulation. We then show that the brain has the necessary infrastructure to implement this inversion and present stimulations using synthetic birds that generate and recognise birdsongs.

  7. Cortical circuits for perceptual inference.

    PubMed

    Friston, Karl; Kiebel, Stefan

    2009-10-01

    This paper assumes that cortical circuits have evolved to enable inference about the causes of sensory input received by the brain. This provides a principled specification of what neural circuits have to achieve. Here, we attempt to address how the brain makes inferences by casting inference as an optimisation problem. We look at how the ensuing recognition dynamics could be supported by directed connections and message-passing among neuronal populations, given our knowledge of intrinsic and extrinsic neuronal connections. We assume that the brain models the world as a dynamic system, which imposes causal structure on the sensorium. Perception is equated with the optimisation or inversion of this internal model, to explain sensory input. Given a model of how sensory data are generated, we use a generic variational approach to model inversion to furnish equations that prescribe recognition; i.e., the dynamics of neuronal activity that represents the causes of sensory input. Here, we focus on a model whose hierarchical and dynamical structure enables simulated brains to recognise and predict sequences of sensory states. We first review these models and their inversion under a variational free-energy formulation. We then show that the brain has the necessary infrastructure to implement this inversion and present stimulations using synthetic birds that generate and recognise birdsongs. PMID:19635656

  8. 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.

  9. 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

  10. 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

  11. Gene transfer in bacteria: speciation without species?

    PubMed

    Lawrence, Jeffrey G

    2002-06-01

    Although Bacteria and Archaea reproduce by binary fission, exchange of genes among lineages has shaped the diversity of their populations and the diversification of their lineages. Gene exchange can occur by two distinct routes, each differentially impacting the recipient genome. First, homologous recombination mediates the exchange of DNA between closely related individuals (those whose sequences are sufficient similarly to allow efficient integration). As a result, homologous recombination mediates the dispersal of advantageous alleles that may rise to high frequency among genetically related individuals via periodic selection events. Second, lateral gene transfer can introduce novel DNA into a genome from completely unrelated lineages via illegitimate recombination. Gene exchange by this route serves to distribute genes throughout distantly related clades and therefore may confer complex abilities--not otherwise found among closely related lineages--onto the recipient organisms. These two mechanisms of gene exchange play complementary roles in the diversification of microbial populations into independent, ecologically distinct lineages. Although the delineation of microbial "species" then becomes difficult--if not impossible--to achieve, a cogent process of speciation can be predicted.

  12. Organotin speciation in Bizerte lagoon (Tunisia).

    PubMed

    Mzoughi, N; Lespes, G; Bravo, M; Dachraoui, M; Potin-Gautier, M

    2005-10-15

    For the first time, organotins have been assessed in samples collected from Bizerte lagoon, in Tunisia, during two seasons (summer and winter). The organotin distribution was studied in marine sediments and mussels tissues of this lagoon. Butyl-, phenyl- and octyltins were determined using a rapid speciation analytical method based on one-step ethylation/extraction with sodium tetraethylborate in aqueous phase. Simultaneously to the ethylation, the extraction was performed by either liquid/liquid extraction (LLE) or head-space solid phase microextraction (HS-SPME). Gas chromatography with pulsed flame photometric detection (GC-PFPD) was used to perform quantitative determination. The technique has been validated using biological and sediment reference materials. The different samples from Bizerte lagoon were found to be moderately contaminated, especially by butyltins. This pollution was attributed to industrial activities, which are very important in this area. Organotins appeared accumulated in both sediments and mussels, while significant degradations of triorganotins to monosubstituted ones was observed in water. PMID:16198682

  13. 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

  14. 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).

  15. Incipient speciation by sexual isolation in Drosophila: concurrent evolution at multiple loci.

    PubMed

    Ting, C T; Takahashi, A; Wu, C I

    2001-06-01

    Drosophila melanogaster from Zimbabwe and nearby regions shows strong but asymmetric sexual isolation from its cosmopolitan counterparts. By creating stable chromosome-substitution lines, earlier studies were able to show that the two major autosomes have very large effects on both male mating success and female mating preference. In this study, we genetically dissect this sexual isolation by recombination analysis between a whole-chromosome substitution line (which carries a Zimbabwe-derived third chromosome) and a strain with seven visible markers on that chromosome. Four loci are responsible for male mating success and three others are found to control female mating preference. Because male and female traits are not closely linked, their strong association among isofemale lines is most likely a reflection of sexual selection in nature. The results suggest that a large number of behavioral loci may evolve concurrently in the incipient stage of speciation before other aspects of reproductive isolation (such as hybrid sterility) have become evident. The results shed light on the population genetic processes underlying the formation of nascent species, as well as modes of speciation.

  16. [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

  17. Historical biogeography and speciation in the neotropical highlands: molecular phylogenetics of the jay genus Cyanolyca.

    PubMed

    Bonaccorso, Elisa

    2009-03-01

    Phylogenetic relationships were studied in the genus Cyanolyca, an assemblage of jays distributed from Mexico south to Bolivia. Given its fragmented distribution along the humid forests of the Neotropics, the genus Cyanolyca is a model group for exploring hypotheses on biogeography and speciation. Phylogenetic analyses were based on two mitochondrial and three nuclear loci; taxon sampling includes all species in the genus and most subspecies. Maximum parsimony, maximum likelihood, and Bayesian analyses produced trees that were congruent and highly robust at both terminal and deep nodes of the phylogeny. Cyanolyca comprises two major clades: one contains the Mesoamerican "dwarf" jays, and the other consists of two main groups--C. cucullata+C. pulchra and the "core" South American species. Prior hypotheses of relationships were explored statistically using Maximum Likelihood and Bayesian approaches. Dispersal-Vicariance analysis revealed the importance of the Northern Andes as a major center for biological diversification, and the effects of dispersal across the Panamanian Land Bridge in the composition of South American and Mesoamerican avifaunas. Phylogenetic patterns are highly congruent with an allopatric mode of speciation. Implications of these results are discussed in the context of the biogeography of Neotropical montane forests.

  18. [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.

  19. 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

  20. 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.

  1. 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.

  2. Category Representation for Classification and Feature Inference

    ERIC Educational Resources Information Center

    Johansen, Mark K.; Kruschke, John K.

    2005-01-01

    This research's purpose was to contrast the representations resulting from learning of the same categories by either classifying instances or inferring instance features. Prior inference learning research, particularly T. Yamauchi and A. B. Markman (1998), has suggested that feature inference learning fosters prototype representation, whereas…

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. Method for the speciation of aluminum in acidic streams

    SciTech Connect

    Miller, J.R.

    1985-01-01

    One of the impacts of acid rain falling on acid soils is the generation of high aluminum concentrations in the upper reaches of pristine mountain streams. The combination of high aluminum concentrations and lowered pH during times times of high flow is speculated by many fisheries biologists to be responsible for the decline of fish populations in these streams. In addition, this increased concern over the aquatic toxicity of aluminum has stimulated interest in the speciation of aluminum in the natural environmental. The toxicity of a metal depends greatly on its species or chemical state. The purpose of this research was to develop a practical method for speciating aluminum in those pristine streams impacted by acid rain. Aluminum has a complex chemistry involving interaction with both inorganic and organic constituents. Laboratory experiments using a chelating resin, Chelex-100, with synthetic solutions were used as the basis for speciating aluminum. The speciation procedure was applied to unfiltered samples collected from Linn Run Creek, a mildly acidic mountain stream in southwestern Pennsylvania. The results show that in upstream samples, where pH was low, rapidly exchangeable aluminum species dominated, while in the downstream samples, where pH was higher, the moderately fast exchangeable, slowly exchangeable, and inert aluminum species dominated. The laboratory experiments suggest the decline of the rapidly exchangeable fraction to be due to complexation of aluminum with humic substances. In addition, particulate aluminum was determined determined during all speciation assays.

  8. Elemental speciation analysis, from environmental to biochemical challenge

    NASA Astrophysics Data System (ADS)

    Jitaru, P.; Barbante, C.

    2006-12-01

    Information regarding the distribution of metallic/metalloid chemical species in biological compartments is required for understanding their biochemical impact on living organisms. To obtain such information implies the use of a dedicated measurement approach, namely speciation analysis. The current trend in (elemental) speciation analysis regards bioinorganic applications. New analytical methodologies are therefore necessary for identification, detection and characterization of metal(loids) complexed or incorporated into biomolecules. The established element-speciation approaches developed for the determination of low molecular mass metal(loid) species (e.g. organometallic compounds) in environmental, food, toxicological and health sciences are presently being adapted for the determination of high molecular mass metal-species, generally related to biological processes. This is one of the newest approaches in terms of element speciation and is called metallomics; this concept refers to the totality of metal species in a cell and covers the inorganic element content and the ensemble of its complexes with biomolecules, particularly proteins, participating in the organisms' response to beneficial or harmful conditions. Compared to conventional elemental speciation analysis, the approach applied to bioinorganic analysis is challenging, particularly given the difficulties in identification/characterization of the organic (e.g. protein) content of such species. In addition, quantification is not feasible with the conventional approaches, which led to the exploitation of the unique feature of (post-column) online isotope dilution-mass spectrometry for species quantification in metallomics.

  9. 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.

  10. Mode coupling in solar spicule oscillations

    NASA Astrophysics Data System (ADS)

    Fazel, Zahra

    2016-01-01

    In a real medium which has oscillations, the perturbations can cause an energy transfer between different modes. A perturbation, which is interpreted as an interaction between the modes, is inferred to be mode coupling. The mode coupling process in an inhomogeneous medium such as solar spicules may lead to the coupling of kink waves to local Alfvén waves. This coupling occurs in practically any conditions when there is smooth variation in density in the radial direction. This process is seen as the decay of transverse kink waves in the medium. To study the damping of kink waves due to mode coupling, a 2.5-dimensional numerical simulation of the initial wave is considered in spicules. The initial perturbation is assumed to be in a plane perpendicular to the spicule axis. The considered kink wave is a standing wave which shows an exponential damping in the inhomogeneous layer after the mode coupling occurs.

  11. 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.

  12. 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

  13. Universum Inference and Corpus Homogeneity

    NASA Astrophysics Data System (ADS)

    Vogel, Carl; Lynch, Gerard; Janssen, Jerom

    Universum Inference is re-interpreted for assessment of corpus homogeneity in computational stylometry. Recent stylometric research quantifies strength of characterization within dramatic works by assessing the homogeneity of corpora associated with dramatic personas. A methodological advance is suggested to mitigate the potential for the assessment of homogeneity to be achieved by chance. Baseline comparison analysis is constructed for contributions to debates by nonfictional participants: the corpus analyzed consists of transcripts of US Presidential and Vice-Presidential debates from the 2000 election cycle. The corpus is also analyzed in translation to Italian, Spanish and Portuguese. Adding randomized categories makes assessments of homogeneity more conservative.

  14. 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.

  15. 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.

  16. A speciation gene for left-right reversal in snails results in anti-predator adaptation.

    PubMed

    Hoso, Masaki; Kameda, Yuichi; Wu, Shu-Ping; Asami, Takahiro; Kato, Makoto; Hori, Michio

    2010-01-01

    How speciation genes can spread in a population is poorly understood. In land snails, a single gene for left-right reversal could be responsible for instant speciation, because dextral and sinistral snails have difficulty in mating. However, the traditional two-locus speciation model predicts that a mating disadvantage for the reversal should counteract this speciation. In this study, we show that specialized snake predation of the dextral majority drives prey speciation by reversal. Our experiments demonstrate that sinistral Satsuma snails (Stylommatophora: Camaenidae) survive predation by Pareas iwasakii (Colubroidea: Pareatidae). Worldwide biogeography reveals that stylommatophoran snail speciation by reversal has been accelerated in the range of pareatid snakes, especially in snails that gain stronger anti-snake defense and reproductive isolation from dextrals by sinistrality. Molecular phylogeny of Satsuma snails further provides intriguing evidence of repetitive speciation under snake predation. Our study demonstrates that a speciation gene can be fixed in populations by positive pleiotropic effects on survival.

  17. 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.

  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. Computer simulations of sympatric speciation in a simple food web.

    PubMed

    Luz-Burgoa, K; Dell, Tony; de Oliveira, S Moss

    2005-07-01

    Galapagos finches, have motivated much theoretical research aimed at understanding the processes associated with the formation of the species. Inspired by them, in this paper we investigate the process of sympatric speciation in a simple food web model. For that we modify the individual-based Penna model that has been widely used to study aging as well as other evolutionary processes. Initially, our web consists of a primary food source and a single herbivore species that feeds on this resource. Subsequently we introduce a predator that feeds on the herbivore. In both instances we manipulate directly a basal resource distribution and monitor the changes in the populations. Sympatric speciation is obtained for the top species in both cases, and our results suggest that the speciation velocity depends on how far up, in the food chain, the focus population is feeding. Simulations are done with three different sexual imprinting-like mechanisms, in order to discuss adaptation by natural selection.

  20. 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.

  1. SYMBOLIC INFERENCE OF XENOBIOTIC METABOLISM

    PubMed Central

    MCSHAN, D.C.; UPDADHAYAYA, M.; SHAH, I.

    2009-01-01

    We present a new symbolic computational approach to elucidate the biochemical networks of living systems de novo and we apply it to an important biomedical problem: xenobiotic metabolism. A crucial issue in analyzing and modeling a living organism is understanding its biochemical network beyond what is already known. Our objective is to use the available metabolic information in a representational framework that enables the inference of novel biochemical knowledge and whose results can be validated experimentally. We describe a symbolic computational approach consisting of two parts. First, biotransformation rules are inferred from the molecular graphs of compounds in enzyme-catalyzed reactions. Second, these rules are recursively applied to different compounds to generate novel metabolic networks, containing new biotransformations and new metabolites. Using data for 456 generic reactions and 825 generic compounds from KEGG we were able to extract 110 biotransformation rules, which generalize a subset of known biocatalytic functions. We tested our approach by applying these rules to ethanol, a common substance of abuse and to furfuryl alcohol, a xenobiotic organic solvent, which is absent in metabolic databases. In both cases our predictions on the fate of ethanol and furfuryl alcohol are consistent with the literature on the metabolism of these compounds. PMID:14992532

  2. Bayesian inference for OPC modeling

    NASA Astrophysics Data System (ADS)

    Burbine, Andrew; Sturtevant, John; Fryer, David; Smith, Bruce W.

    2016-03-01

    The use of optical proximity correction (OPC) demands increasingly accurate models of the photolithographic process. Model building and inference techniques in the data science community have seen great strides in the past two decades which make better use of available information. This paper aims to demonstrate the predictive power of Bayesian inference as a method for parameter selection in lithographic models by quantifying the uncertainty associated with model inputs and wafer data. Specifically, the method combines the model builder's prior information about each modelling assumption with the maximization of each observation's likelihood as a Student's t-distributed random variable. Through the use of a Markov chain Monte Carlo (MCMC) algorithm, a model's parameter space is explored to find the most credible parameter values. During parameter exploration, the parameters' posterior distributions are generated by applying Bayes' rule, using a likelihood function and the a priori knowledge supplied. The MCMC algorithm used, an affine invariant ensemble sampler (AIES), is implemented by initializing many walkers which semiindependently explore the space. The convergence of these walkers to global maxima of the likelihood volume determine the parameter values' highest density intervals (HDI) to reveal champion models. We show that this method of parameter selection provides insights into the data that traditional methods do not and outline continued experiments to vet the method.

  3. Dopamine, affordance and active inference.

    PubMed

    Friston, Karl J; Shiner, Tamara; FitzGerald, Thomas; Galea, Joseph M; Adams, Rick; Brown, Harriet; Dolan, Raymond J; Moran, Rosalyn; Stephan, Klaas Enno; Bestmann, Sven

    2012-01-01

    The role of dopamine in behaviour and decision-making is often cast in terms of reinforcement learning and optimal decision theory. Here, we present an alternative view that frames the physiology of dopamine in terms of Bayes-optimal behaviour. In this account, dopamine controls the precision or salience of (external or internal) cues that engender action. In other words, dopamine balances bottom-up sensory information and top-down prior beliefs when making hierarchical inferences (predictions) about cues that have affordance. In this paper, we focus on the consequences of changing tonic levels of dopamine firing using simulations of cued sequential movements. Crucially, the predictions driving movements are based upon a hierarchical generative model that infers the context in which movements are made. This means that we can confuse agents by changing the context (order) in which cues are presented. These simulations provide a (Bayes-optimal) model of contextual uncertainty and set switching that can be quantified in terms of behavioural and electrophysiological responses. Furthermore, one can simulate dopaminergic lesions (by changing the precision of prediction errors) to produce pathological behaviours that are reminiscent of those seen in neurological disorders such as Parkinson's disease. We use these simulations to demonstrate how a single functional role for dopamine at the synaptic level can manifest in different ways at the behavioural level.

  4. Trandimensional Inference in the Geosciences

    NASA Astrophysics Data System (ADS)

    Bodin, Thomas

    2016-04-01

    An inverse problem is the task often occurring in many branches of Earth sciences, where the values of some model parameters describing the Earth must be obtained given noisy observations made at the surface. In all applications of inversion, assumptions are made about the nature of the model parametrisation and data noise characteristics, and results can significantly depend on those assumptions. These quantities are often manually `tuned' by means of subjective trial-and-error procedures, and this prevents to accurately quantify uncertainties in the solution. A Bayesian approach allows these assumptions to be relaxed by incorporating relevant parameters as unknowns in the inference problem. Rather than being forced to make decisions on parametrisation, 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. Probabilistic sampling techniques such as transdimensional Markov chain Monte Carlo, allow sampling over complex posterior probability density functions, thus providing information on constraint, trade-offs and uncertainty in the unknowns. This presentation will present a review of transdimensional inference, and its application to different problems, ranging from Geochemistry to Solid Earth Geophysics.

  5. 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.

  6. Inference is bliss: using evolutionary relationship to guide categorical inferences.

    PubMed

    Novick, Laura R; Catley, Kefyn M; Funk, Daniel J

    2011-01-01

    Three experiments, adopting an evolutionary biology perspective, investigated subjects' inferences about living things. Subjects were told that different enzymes help regulate cell function in two taxa and asked which enzyme a third taxon most likely uses. Experiment 1 and its follow-up, with college students, used triads involving amphibians, reptiles, and mammals (reptiles and mammals are most closely related evolutionarily) and plants, fungi, and animals (fungi are more closely related to animals than to plants). Experiment 2, with 10th graders, also included triads involving mammals, birds, and snakes/crocodilians (birds and snakes/crocodilians are most closely related). Some subjects received cladograms (hierarchical diagrams) depicting the evolutionary relationships among the taxa. The effect of providing cladograms depended on students' background in biology. The results illuminate students' misconceptions concerning common taxa and constraints on their willingness to override faulty knowledge when given appropriate evolutionary evidence. Implications for introducing tree thinking into biology curricula are discussed. PMID:21463358

  7. 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...

  8. 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 ...

  9. 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

  10. 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.

  11. 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

  12. What is Local Mode (LM)? Global Mode (GM)? Calibration Mode?

    Atmospheric Science Data Center

    2014-12-08

    ... measurement in Global Mode (GM), Local Mode (LM), and Calibration. Global Mode is the normal acquisition with pole to pole coverage ... targets approximately 300 km in length Calibration Implemented bi-monthly Spectralon solar ...

  13. 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.

  14. Parametric inference in the large data limit using maximally informative models.

    PubMed

    Kinney, Justin B; Atwal, Gurinder S

    2014-04-01

    Motivated by data-rich experiments in transcriptional regulation and sensory neuroscience, we consider the following general problem in statistical inference: when exposed to a high-dimensional signal S, a system of interest computes a representation R of that signal, which is then observed through a noisy measurement M. From a large number of signals and measurements, we wish to infer the "filter" that maps S to R. However, the standard method for solving such problems, likelihood-based inference, requires perfect a priori knowledge of the "noise function" mapping R to M. In practice such noise functions are usually known only approximately, if at all, and using an incorrect noise function will typically bias the inferred filter. Here we show that in the large data limit, this need for a precharacterized noise function can be circumvented by searching for filters that instead maximize the mutual information I[M; R] between observed measurements and predicted representations. Moreover, if the correct filter lies within the space of filters being explored, maximizing mutual information becomes equivalent to simultaneously maximizing every dependence measure that satisfies the data processing inequality. It is important to note that maximizing mutual information will typically leave a small number of directions in parameter space unconstrained. We term these directions diffeomorphic modes and present an equation that allows these modes to be derived systematically. The presence of diffeomorphic modes reflects a fundamental and nontrivial substructure within parameter space, one that is obscured by standard likelihood-based inference.

  15. 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.

  16. Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

    PubMed Central

    Shin, Junha; Lee, Insuk

    2015-01-01

    Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life—Archaea, Bacteria, and Eukaryota—suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co

  17. 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.

  18. 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

  19. Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events.

    PubMed

    Wang, Xiyin; Wang, Jingpeng; Jin, Dianchuan; Guo, Hui; Lee, Tae-Ho; Liu, Tao; Paterson, Andrew H

    2015-06-01

    Multiple comparisons among genomes can clarify their evolution, speciation, and functional innovations. To date, the genome sequences of eight grasses representing the most economically important Poaceae (grass) clades have been published, and their genomic-level comparison is an essential foundation for evolutionary, functional, and translational research. Using a formal and conservative approach, we aligned these genomes. Direct comparison of paralogous gene pairs all duplicated simultaneously reveal striking variation in evolutionary rates among whole genomes, with nucleotide substitution slowest in rice and up to 48% faster in other grasses, adding a new dimension to the value of rice as a grass model. We reconstructed ancestral genome contents for major evolutionary nodes, potentially contributing to understanding the divergence and speciation of grasses. Recent fossil evidence suggests revisions of the estimated dates of key evolutionary events, implying that the pan-grass polyploidization occurred ∼96 million years ago and could not be related to the Cretaceous-Tertiary mass extinction as previously inferred. Adjusted dating to reflect both updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome divergence and maize-sorghum divergence were virtually simultaneous, a coincidence that would be explained if polyploidization directly contributed to speciation. This work lays a solid foundation for Poaceae translational genomics.

  20. 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

  1. 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

  2. An expert system shell for inferring vegetation characteristics: Implementation of additional techniques (task E)

    NASA Technical Reports Server (NTRS)

    Harrison, P. Ann

    1992-01-01

    The NASA VEGetation Workbench (VEG) is a knowledge based system that infers vegetation characteristics from reflectance data. The VEG subgoal PROPORTION.GROUND.COVER has been completed and a number of additional techniques that infer the proportion ground cover of a sample have been implemented. Some techniques operate on sample data at a single wavelength. The techniques previously incorporated in VEG for other subgoals operated on data at a single wavelength so implementing the additional single wavelength techniques required no changes to the structure of VEG. Two techniques which use data at multiple wavelengths to infer proportion ground cover were also implemented. This work involved modifying the structure of VEG so that multiple wavelength techniques could be incorporated. All the new techniques were tested using both the VEG 'Research Mode' and the 'Automatic Mode.'

  3. 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

  4. Generic Comparison of Protein Inference Engines*

    PubMed Central

    Claassen, Manfred; Reiter, Lukas; Hengartner, Michael O.; Buhmann, Joachim M.; Aebersold, Ruedi

    2012-01-01

    Protein identifications, instead of peptide-spectrum matches, constitute the biologically relevant result of shotgun proteomics studies. How to appropriately infer and report protein identifications has triggered a still ongoing debate. This debate has so far suffered from the lack of appropriate performance measures that allow us to objectively assess protein inference approaches. This study describes an intuitive, generic and yet formal performance measure and demonstrates how it enables experimentalists to select an optimal protein inference strategy for a given collection of fragment ion spectra. We applied the performance measure to systematically explore the benefit of excluding possibly unreliable protein identifications, such as single-hit wonders. Therefore, we defined a family of protein inference engines by extending a simple inference engine by thousands of pruning variants, each excluding a different specified set of possibly unreliable identifications. We benchmarked these protein inference engines on several data sets representing different proteomes and mass spectrometry platforms. Optimally performing inference engines retained all high confidence spectral evidence, without posterior exclusion of any type of protein identifications. Despite the diversity of studied data sets consistently supporting this rule, other data sets might behave differently. In order to ensure maximal reliable proteome coverage for data sets arising in other studies we advocate abstaining from rigid protein inference rules, such as exclusion of single-hit wonders, and instead consider several protein inference approaches and assess these with respect to the presented performance measure in the specific application context. PMID:22057310

  5. Rotation of the Solar Core Inferred from GONG Data

    NASA Astrophysics Data System (ADS)

    Rabello-Soares, M. C.; Appourchaux, T.; Christensen-Dalsgaard, J.

    We present inferences of the solar core rotation derived from GONG frequency splittings. The GONG data for the low-degree modes (l <= 6) are for the one year period Aug. 1995-1996; these splittings were determined using a new method of fitting heliosismic spectra (Rabello-Soares & Appourchaux 1998). These are combined with GONG data for higher degree modes, as obtained by the GONG team (Hill et al. 1996). We have employed a new two-dimensional implementation of the optimally localized averages (OLA) inversion method (Chaplin et al. 1998). As in one dimension, the OLA produces better-localized averaging kernels than do least-squares techniques. This is particularly beneficial in the deep interior, where it is in any case difficult to obtain localized information.

  6. 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.

  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. 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

  9. Possible method of aluminium speciation in forest soils.

    PubMed

    Drabek, Ondrej; Boruvka, Lubos; Mladkova, Lenka; Kocarek, Martin

    2003-09-15

    Labile Al forms and species can be a threat in acid soils due to their potential toxicity to plants. However, there is no universally accepted extraction method. Several extraction reagents for Al release from soil have been tested. KCl (0.5 or 1 M) is recommended for extraction of exchangeable Al, while 0.5 or 0.3 M CuCl(2) is suggested for extraction of 'weakly organically bound Al'. Both 0.1 and 0.05 M Na(4)P(2)O(7) are shown to be suitable for the extraction of 'total organically bound Al'. These extractions are relatively simple, robust, and applicable to different soils and soil horizons. In the second part of the paper, detailed speciation of exchangeable soil Al by means of an HPLC instrument equipped with an ion column (IC) is presented. An experimental set-up is described and tested on a set of samples. Interpretation of the speciation results is proposed, based on the separation of Al ions and Al complexes according to their charge. Speciation is shown to be dependent mainly on soil pH and organic matter quality. A general scheme of Al fractionation and speciation in soil is proposed. PMID:14507455

  10. 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...

  11. 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...

  12. 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 ...

  13. 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.

  14. 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...

  15. 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...

  16. 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.

  17. 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...

  18. The secondary contact phase of allopatric speciation in Darwin's finches

    PubMed Central

    Grant, Peter R.; Grant, B. Rosemary

    2009-01-01

    Speciation, the process by which two species form from one, involves the development of reproductive isolation of two divergent lineages. Here, we report the establishment and persistence of a reproductively isolated population of Darwin's finches on the small Galápagos Island of Daphne Major in the secondary contact phase of speciation. In 1981, an immigrant medium ground finch (Geospiza fortis) arrived on the island. It was unusually large, especially in beak width, sang an unusual song, and carried some Geospiza scandens alleles. We followed the fate of this individual and its descendants for seven generations over a period of 28 years. In the fourth generation, after a severe drought, the lineage was reduced to a single brother and sister, who bred with each other. From then on this lineage, inheriting unusual song, morphology, and a uniquely homozygous marker allele, was reproductively isolated, because their own descendants bred with each other and with no other member of the resident G. fortis population. These observations agree with some expectations of an ecological theory of speciation in that a barrier to interbreeding arises as a correlated effect of adaptive divergence in morphology. However, the important, culturally transmitted, song component of the barrier appears to have arisen by chance through an initial imperfect copying of local song by the immigrant. The study reveals additional stochastic elements of speciation, in which divergence is initiated in allopatry; immigration to a new area of a single male hybrid and initial breeding with a rare hybrid female. PMID:19918081

  19. 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.

  20. 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

  1. 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

  2. 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...

  3. 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…

  4. 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.

  5. 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.

  6. Evidence for cryptic speciation in Carchesium polypinum Linnaeus, 1758 (Ciliophora: Peritrichia) inferred from mitochondrial, nuclear, and morphological markers.

    PubMed

    Gentekaki, Eleni; Lynn, Denis H

    2010-01-01

    Protist diversity is currently a much debated issue in eukaryotic microbiology. Recent evidence suggests that morphological and genetic diversity might be decoupled in some groups of protists, including ciliates, and that these organisms might be much more diverse than their morphology implies. We sought to assess the genetic and morphological diversity of Carchesium polypinum, a widely distributed peritrich ciliate. The mitochondrial marker cytochrome c oxidase subunit I and the nuclear small subunit ribosomal RNA were used to examine genetic diversity. For the morphological assessment, live microscopy and Protargol staining were used. The mitochondrial marker revealed six robust, deeply diverging, and strongly supported clades, while the nuclear gene was congruent for three of these clades. There were no major differences among individuals from the different clades in any of the morphological features examined. Thus, the underlying genetic diversity in C. polypinum is greater than what its morphology suggests, indicating that morphology and genetics are not congruent in this organism. Furthermore, because the clades identified by the mitochondrial marker are so genetically diverse and are confirmed by a conserved nuclear marker in at least three cases, we propose that C. polypinum be designated as a "cryptic species complex." Our results provide another example where species diversity can be underestimated in microbial eukaryotes when using only morphological criteria to estimate species richness.

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

    PubMed Central

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

    2006-01-01

    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. Preliminary Assessment of Potential for Metal-Ligand Speciation in Aqueous Solution via the Liquid Sampling-Atmospheric Pressure Glow Discharge (LS-APGD) Ionization Source: Uranyl Acetate.

    PubMed

    Zhang, Lynn X; Manard, Benjamin T; Powell, Brian A; Marcus, R Kenneth

    2015-07-21

    The determination of metals, including the generation of metal-ligand speciation information, is essential across a myriad of biochemical, environmental, and industrial systems. Metal speciation is generally affected by the combination of some form of chromatographic separation (reflective of the metal-ligand chemistry) with element-specific detection for the quantification of the metal composing the chromatographic eluent. Thus, the identity of the metal-ligand is assigned by inference. Presented here, the liquid sampling-atmospheric pressure glow discharge (LS-APGD) is assessed as an ionization source for metal speciation, with the uranyl ion-acetate system used as a test system. Molecular mass spectra can be obtained from the same source by simple modification of the sustaining electrolyte solution. Specifically, chemical information pertaining to the degree of acetate complexation of uranyl ion (UO2(2+)) is assessed as a function of pH in the spectral abundance of three metallic species: inorganic (nonligated) uranyl, UO2Ac(H2O)n(MeOH)m(+), and UO2Ac2(H2O)n(MeOH)(m)H(+) (n = 1, 2, 3, ...; m = 1, 2, 3, ...). The product mass spectra are different from what are obtained from electrospray ionization sources that have been applied to this system. The resulting relationships between the speciation and pH values have been compared to calculated concentrations of the corresponding uranyl species: UO2(2+), UO2Ac(+), UO2Ac2. The capacity for the LS-APGD to affect both atomic mass spectra and structurally significant spectra for organometallic complexes is a unique and potentially powerful combination.

  9. Redox speciation and biogeochemical gradients: Assessing spatial niches and monitoring dynamics in natural systems with voltammetric microelectrodes

    NASA Astrophysics Data System (ADS)

    Druschel, G. K.; Lorenson, G. W.; Eastmann, D. A.; Macalady, J. L.

    2005-12-01

    Biogeochemical gradients may be described by the spatial distribution of redox species distributed in water, where overlap of electron donors and acceptors out of equilibrium defines available sources of potential energy and essentially determines possible microbial metabolisms. Observed changes in redox speciation along a gradient associated with microbial biofilms may additionally provide some environmental basis for assessing physiology of sampled microorganisms. Voltammetric microelectrodes have been used in a variety of environments to describe the links between ecology and geochemistry (Luther et al., 2001). Recent work in Yellowstone National Park hydrothermal waters, the Frassassi caves in central Italy (a sulfidic cave system), and Green Lake in New York (a meromictic lake) have expanded our abilities to use microelectrodes for assessing As(III) concentrations and uncovering more details of sulfur speciation in a wide range of natural waters. We are using these data to design redox-specific culture media, make inferences about microbial physiology, constrain biogeochemical gradients over very fine scales, and observe dynamics in biogeochemical systems. Describing microbial communities and the geochemical environments that surround them at appropriate scales is of importance to begin assessing the links between microbial activity and geochemical cycling. Diversity in an environment may be better assessed if we first know how many different geochemical environments there are in that environment and if the microbial ecology in those environments is essentially independent from environments neighboring it. Because microelectrodes measure multiple redox species simultaneously and do so in matter of seconds, they are also useful in monitoring the dynamics of a biogeochemical system, which will be of use in studying the response of communities to perturbation. We will present results showing the characterization of lateral and vertical gradients over different

  10. 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.

  11. 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).

  12. 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

  13. 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…

  14. 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…

  15. 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.

  16. Genetic Network Inference Using Hierarchical Structure

    PubMed Central

    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

  17. 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…

  18. 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.

  19. 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

  20. 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

  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.

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

    PubMed

    Slowey, Aaron J; Rytuba, James J; Brown, Gordon E

    2005-03-15

    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 microg/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.

  3. 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.

  4. The inference of gene trees with species trees.

    PubMed

    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.

  5. 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

  6. Tempo and mode in plant breeding system evolution.

    PubMed

    Goldberg, Emma E; Igić, Boris

    2012-12-01

    Classic questions about trait evolution-including the directionality of character change and its interactions with lineage diversification-intersect in the study of plant breeding systems. Transitions from self-incompatibility to self-compatibility are frequent, and they may proceed within a species ("anagenetic" mode of breeding system change) or in conjunction with speciation events ("cladogenetic" mode of change). We apply a recently developed phylogenetic model to the nightshade family Solanaceae, quantifying the relative contributions of these two modes of evolution along with the tempo of breeding system change, speciation, and extinction. We find that self-incompatibility, a genetic mechanism that prevents self-fertilization, is lost largely by the cladogenetic mode. Self-compatible species are thus more likely to arise from the isolation of a newly self-compatible population than from species-wide fixation of self-compatible mutants. Shared polymorphism at the locus that governs self-incompatibility shows it to be ancestral and not regained within this family. We demonstrate that failing to account for cladogenetic character change misleads phylogenetic tests of evolutionary irreversibility, both for breeding system in Solanaceae and on simulated trees.

  7. 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.

  8. 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.

  9. On Bayesian Inductive Inference & Predictive Estimation

    NASA Technical Reports Server (NTRS)

    Cheeseman, Peter; Stutz, John; Smelyanskiy, Vadim

    2004-01-01

    We investigate Bayesian inference and the Principle of Maximum Entropy (PME) as methods for doing inference under uncertainty. This investigation is primarily through concrete examples that have been previously investigated in the literature. We find that it is possible to do Bayesian inference and PME inference using the same information, despite claims to the contrary, but that the results are not directly comparable. This is because Bayesian inference yields a probability density function (pdf) over the unknown model parameters, whereas PME yields point estimates. If mean estimates are extracted from the Bayesian pdfs, the resulting parameter estimates can differ radically from the PME values and also from the Maximum Likelihood values. We conclude that these differences are due to the Bayesian inference not assuming anything beyond the given prior probabilities and the data, whereas PME implicitly assumes that the given constraints are the only constraints that are operating. Since this assumption can be wrong, PME values may have to be revised when subsequent data shows evidence for more constraints. The entropy concentration previously "proved" by E. T. Jaynes is shown to be in error. Further, we show that PME is a generalized form of independence assumption, and so can be a very powerful method of inference when the variables being investigated are largely independent of each other.

  10. 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.

  11. 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).

  12. 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.

  13. 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.

  14. Polymorphic butterfly reveals the missing link in ecological speciation

    PubMed Central

    Chamberlain, Nicola L.; Hill, Ryan I.; Kapan, Durrell D.; Gilbert, Lawrence E.; Kronforst, Marcus R.

    2010-01-01

    Ecological speciation occurs when ecologically-based divergent selection causes the evolution of reproductive isolation. While there are many empirical examples of this process, there exists a poorly characterized stage during which the traits that distinguish species ecologically and reproductively segregate in a single population. Using a combination of genetic mapping, mate choice experiments, field observations, and population genetics, we studied a butterfly population with a mimetic wing color polymorphism and found that they exhibited partial color-based assortative mate preference. These traits represent the divergent, ecologically-based signal and preference components of sexual isolation that usually distinguish incipient and sibling species. The association between behavior and recognition trait in a single population may enhance the probability of speciation and provides an example for the missing link between an interbreeding population and isolated species. PMID:19892982

  15. Metal accumulation by stream bryophytes, related to chemical speciation.

    PubMed

    Tipping, E; Vincent, C D; Lawlor, A J; Lofts, S

    2008-12-01

    Metal accumulation by aquatic bryophytes was investigated using data for headwater streams of differing chemistry. The Windermere Humic Aqueous Model (WHAM) was applied to calculate chemical speciation, including competitive proton and metal interactions with external binding sites on the plants. The speciation modelling approach gives smaller deviations between observed and predicted bryophyte contents of Cu, Zn, Cd and Pb than regressions based on total filtered metal concentrations. If all four metals, and Ni, are considered together, the WHAM predictions are superior at the 1% level. Optimised constants for bryophyte binding by the trace metals are similar to those for humic substances and simple carboxylate ligands. Bryophyte contents of Na, Mg and Ca are approximately explained by binding at external sites, while most of the K is intracellular. Oxide phases account for some of the Al, and most of the Mn, Fe and Co.

  16. 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

  17. Sexual selection accelerates signal evolution during speciation in birds.

    PubMed

    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

    2013-09-01

    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.

  18. Quantifying variation in speciation and extinction rates with clade data.

    PubMed

    Paradis, Emmanuel; Tedesco, Pablo A; Hugueny, Bernard

    2013-12-01

    High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented.

  19. 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.

  20. Ultrasensitive DNAzyme beacon for lanthanides and metal speciation.

    PubMed

    Huang, Po-Jung Jimmy; Lin, Jenny; Cao, Jing; Vazin, Mahsa; Liu, Juewen

    2014-02-01

    Metal-ion detection and speciation analysis is crucial for environmental monitoring. Despite the importance of lanthanides, few sensors are available for their detection. DNAzymes have been previously used to detect divalent metals, while no analytical work was carried out for trivalent and tetravalent ions. Herein, in vitro selection was performed using a Ce(4+) salt as the target metal, and a new DNAzyme (named Ce13) with a bulged hairpin structure was isolated and characterized. Interestingly, Ce13 has almost no activity with Ce(4+) but is highly active with all trivalent lanthanides and Y(3+), serving as a general probe for rare earth metals (omitting Sc). A DNAzyme beacon was engineered detecting down to 1.7 nM Ce(3+) (240 parts per trillion), and other lanthanides showed similar sensitivity. The feasibility of metal speciation analysis was demonstrated by measuring the reduction of Ce(4+) to Ce(3+).

  1. 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.

  2. Hybrid zones and the speciation continuum in Heliconius butterflies.

    PubMed

    Mallet, James; Dasmahapatra, Kanchon K

    2012-12-01

    Tropical butterflies in the genus Heliconius have long been models in the study of the stages of speciation. Heliconius are unpalatable to predators, and many species are notable for multiple geographic populations with striking warning colour pattern differences associated with Müllerian mimicry. A speciation continuum is evident in Heliconius hybrid zones. Examples range from hybrid zones across which (a) there is little genetic differentiation other than at mimicry loci, but where hybrids are common, (b) to 'bimodal' hybrid zones with strong genetic divergence and few hybrids, (c) through to 'good' sympatric species, with hybridization extremely rare or absent. Now, in this issue of Molecular Ecology, Arias et al. (2012) have found an intermediate case in Colombian Heliconius cydno showing evidence for assortative mating and molecular differences, but where hybrids are abundant.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. Hybrid speciation in angiosperms: parental divergence drives ploidy

    PubMed Central

    Paun, Ovidiu; Forest, Félix; Fay, Michael F.; Chase, Mark W.

    2010-01-01

    Summary Hybridization and polyploidy are now hypothesized to have regularly stimulated speciation in angiosperms, but individual or combined involvement of these two processes seems to involve significant differences in pathways of formation, establishment and evolutionary consequences of resulting lineages. We evaluate here the classical cytological hypothesis that ploidy in hybrid speciation is governed by the extent of chromosomal rearrangements among parental species. Within a phylogenetic framework, we calculate genetic divergence indices for 50 parental species pairs and use these indices as surrogates for the overall degree of genomic divergence (i.e. as proxy for assessments of dissimilarity of the parental chromosomes). The results confirm that genomic differentiation between progenitor taxa influences the likelihood of diploid (homoploid) versus polyploid hybrid speciation because genetic divergence between parents of polyploids is found to be significantly greater than in the case of homoploid hybrid species. We argue that this asymmetric relationship may be reinforced immediately after hybrid formation, during stabilization and establishment. Underlying mechanisms potentially producing this pattern are discussed. PMID:19220761

  8. 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

  9. Factors effecting aluminum speciation in drinking water by laboratory research.

    PubMed

    Wang, Wendong; Yang, Hongwei; Wang, Xiaochang; Jiang, Jing; Zhu, Wanpeng

    2010-01-01

    Effects of aluminum on water distribution system and human health mainly attribute to its speciation in drinking water. Laboratory experiments were performed to investigate factors that may influence aluminum speciation in water supply system. The concentration of soluble aluminum and its transformation among other aluminum species were mainly controlled by kinetics processes of related reactions. Total aluminum concentration had a notable effect on the concentrations of mononuclear and soluble aluminum in the first 4 day; then its effect became weak. At pH above 7.50, both fluoride and orthophosphate had little effect on aluminum speciation; while, when the solution pH was below 7.50, the concentrations of mononuclear and soluble aluminum were proportional to the concentration of fluoride and inversely proportional to the concentration of orthophosphate. Both mononuclear and polynuclear silicic acids could complex with mononuclear aluminum by forming soluble aluminosilicates. In addition, the adding sequence of orthophosphate and aluminum into drinking water would also affect the distribution of aluminum species in the first 4 day. In order to minimize aluminum bioavailability in drinking water, it was suggested that orthophosphate should be added prior to coagulant process, and that the concentrations of fluoride and silicic acids should be controlled below 2.0 and 25 mg/L, respectively, prior to the treatment. The solution pH in coagulation and filtration processes should be controlled in the range of 6.50-7.50.

  10. 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

  11. 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

  12. Tree of life reveals clock-like speciation and diversification.

    PubMed

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

    2015-04-01

    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.

  13. 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.

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

    PubMed

    Khaokaew, Saengdao; Landrot, Gautier; Chaney, Rufus L; Pandya, Kaumudi; Sparks, Donald L

    2012-04-01

    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 cocontaminated alkaline and acidified paddy soils, under various flooding periods and draining conditions, by employing synchrotron-based techniques and a stirred-flow kinetic method. Results showed almost no change in Zn speciation and release kinetics in the two soils, although the soils were subjected to different flooding periods and draining conditions. The mineral phases in which Zn is immobilized in the soil samples were constrained by linear least squares fitting (LLSF) analyses of bulk X-ray absorption fine structure (XAFS) spectra. Only two main phases were identified by LLSF, i.e., Zn-layered double hydroxides (Zn/Mg-hydrotalcite-like, and ZnAl-LDH) and Zn-phyllosilicates (Zn-kerolite). Under all soil pHs, flooding, and draining conditions, less than 22% of Zn was desorbed from the soil after a two-hour desorption experiment. The information on Zn chemistry obtained in this study will be useful in finding the best strategy to control Cd and Zn bioavailability in the Cd-Zn cocontaminated paddy soils. PMID:22423594

  15. Role of sexual selection in speciation in Drosophila.

    PubMed

    Singh, Akanksha; Singh, Bashisth N

    2014-02-01

    The power of sexual selection to drive changes in the mate recognition system through divergence in sexually selected traits gives it the potential to be a potent force in speciation. To know how sexual selection can bring such type of divergence in the genus Drosophila, comparative studies based on intra- and inter-sexual selection are documented in this review. The studies provide evidence that both mate choice and male-male competition can cause selection of trait and preference which thereby leads to divergence among species. In the case of intrasexual selection, various kinds of signals play significant role in affecting the species mate recognition system and hence causing divergence between the species. However, intrasexual selection can bring the intraspecific divergence at the level of pre- and post-copulatory stage. This has been better explained through Hawaiian Drosophila which has been suggested a wonderful model system in explaining the events of speciation via sexual selection. This is due to their elaborate mating displays and some kind of ethological isolation persisting among them. Similarly, the genetic basis of sexually selected variations can provide yet another path in understanding the speciation genetics via sexual selection more closely.

  16. Speciation Progress: A Case Study on the Bushcricket Poecilimon veluchianus

    PubMed Central

    Eweleit, Lucienne; Reinhold, Klaus; Sauer, Jan

    2015-01-01

    Different mechanisms such as selection or genetic drift permitted e.g. by geographical isolation can lead to differentiation of populations and could cause subsequent speciation. The two subspecies of Poecilimon veluchianus, a bushcricket endemic to central Greece, show a parapatric distribution and are partially reproductively isolated. Therefore, P. veluchianus is suitable to investigate an ongoing speciation process. We based our analysis on sequences of the internal transcribed spacer (ITS) and the mitochondrial control region (CR). The population genetic analysis based on the nuclear marker ITS revealed a barrier to gene flow within the range of Poecilimon veluchianus, which corresponds well to the described subspecies. In contrast to the results based on the nuclear ITS marker, the mitochondrial CR marker does not clearly support the separation into two subspecies with restricted gene flow and a clear contact zone. Furthermore, we could identify isolation by distance (IBD) as one important mechanism responsible for the observed genetic structure (based on the ITS marker). The population genetic analysis based on the nuclear marker ITS also suggests the existence of hybrids in the wild. Furthermore, the simultaneous lack of strong prezygotic barriers and the presence of postzygotic mating barriers, observed in previous laboratory experiments, suggest that a secondary contact after an allopatric phase is more likely than parapatric speciation. PMID:26436732

  17. 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.

  18. 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.

  19. 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

  20. 48 CFR 1631.205-81 - Inferred reasonableness.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 6 2011-10-01 2011-10-01 false Inferred reasonableness... PRINCIPLES AND PROCEDURES Contracts With Commercial Organizations 1631.205-81 Inferred reasonableness. If the... the subcontract's costs shall be inferred....

  1. 48 CFR 1631.205-81 - Inferred reasonableness.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Inferred reasonableness... PRINCIPLES AND PROCEDURES Contracts With Commercial Organizations 1631.205-81 Inferred reasonableness. If the... the subcontract's costs shall be inferred....

  2. 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.

  3. Metacognitive inferences from other people's memory performance.

    PubMed

    Smith, Robert W; Schwarz, Norbert

    2016-09-01

    Three studies show that people draw metacognitive inferences about events from how well others remember the event. Given that memory fades over time, detailed accounts of distant events suggest that the event must have been particularly memorable, for example, because it was extreme. Accordingly, participants inferred that a physical assault (Study 1) or a poor restaurant experience (Studies 2-3) were more extreme when they were well remembered one year rather than one week later. These inferences influence behavioral intentions. For example, participants recommended a more severe punishment for a well-remembered distant rather than recent assault (Study 1). These metacognitive inferences are eliminated when people attribute the reporter's good memory to an irrelevant cause (e.g., photographic memory), thus undermining the informational value of memory performance (Study 3). These studies illuminate how people use lay theories of memory to learn from others' memory performance about characteristics of the world. (PsycINFO Database Record

  4. Metacognitive inferences from other people's memory performance.

    PubMed

    Smith, Robert W; Schwarz, Norbert

    2016-09-01

    Three studies show that people draw metacognitive inferences about events from how well others remember the event. Given that memory fades over time, detailed accounts of distant events suggest that the event must have been particularly memorable, for example, because it was extreme. Accordingly, participants inferred that a physical assault (Study 1) or a poor restaurant experience (Studies 2-3) were more extreme when they were well remembered one year rather than one week later. These inferences influence behavioral intentions. For example, participants recommended a more severe punishment for a well-remembered distant rather than recent assault (Study 1). These metacognitive inferences are eliminated when people attribute the reporter's good memory to an irrelevant cause (e.g., photographic memory), thus undermining the informational value of memory performance (Study 3). These studies illuminate how people use lay theories of memory to learn from others' memory performance about characteristics of the world. (PsycINFO Database Record PMID:27414693

  5. 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)

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

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

    PubMed

    Kisel, Yael; Barraclough, Timothy G

    2010-03-01

    Area is generally assumed to affect speciation rates, but work on the spatial context of speciation has focused mostly on patterns of range overlap between emerging species rather than on questions of geographical scale. A variety of geographical theories of speciation predict that the probability of speciation occurring within a given region should (1) increase with the size of the region and (2) increase as the spatial extent of intraspecific gene flow becomes smaller. Using a survey of speciation events on isolated oceanic islands for a broad range of taxa, we find evidence for both predictions. The probability of in situ speciation scales with island area in bats, carnivorous mammals, birds, flowering plants, lizards, butterflies and moths, and snails. Ferns are an exception to these findings, but they exhibit high frequencies of polyploid and hybrid speciation, which are expected to be scale independent. Furthermore, the minimum island size for speciation correlates across groups with the strength of intraspecific gene flow, as is estimated from a meta-analysis of published population genetic studies. These results indicate a general geographical model of speciation rates that are dependent on both area and gene flow. The spatial scale of population divergence is an important but neglected determinant of broad-scale diversity patterns. PMID:20100106

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

    PubMed

    Kisel, Yael; Barraclough, Timothy G

    2010-03-01

    Area is generally assumed to affect speciation rates, but work on the spatial context of speciation has focused mostly on patterns of range overlap between emerging species rather than on questions of geographical scale. A variety of geographical theories of speciation predict that the probability of speciation occurring within a given region should (1) increase with the size of the region and (2) increase as the spatial extent of intraspecific gene flow becomes smaller. Using a survey of speciation events on isolated oceanic islands for a broad range of taxa, we find evidence for both predictions. The probability of in situ speciation scales with island area in bats, carnivorous mammals, birds, flowering plants, lizards, butterflies and moths, and snails. Ferns are an exception to these findings, but they exhibit high frequencies of polyploid and hybrid speciation, which are expected to be scale independent. Furthermore, the minimum island size for speciation correlates across groups with the strength of intraspecific gene flow, as is estimated from a meta-analysis of published population genetic studies. These results indicate a general geographical model of speciation rates that are dependent on both area and gene flow. The spatial scale of population divergence is an important but neglected determinant of broad-scale diversity patterns.

  13. 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.

  14. 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.

  15. 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.

    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.

  16. The spatio-temporal colonization and diversification across the Indo-Pacific by a 'great speciator' (Aves, Erythropitta erythrogaster).

    PubMed

    Irestedt, Martin; Fabre, Pierre-Henri; Batalha-Filho, Henrique; Jønsson, Knud A; Roselaar, Cees S; Sangster, George; Ericson, Per G P

    2013-05-22

    The Indo-Pacific region has arguably been the most important area for the formulation of theories about biogeography and speciation, but modern studies of the tempo, mode and magnitude of diversification across this region are scarce. We study the biogeographic history and characterize levels of diversification in the wide-ranging passerine bird Erythropitta erythrogaster using molecular, phylogeographic and population genetics methods, as well as morphometric and plumage analyses. Our results suggest that E. erythrogaster colonized the Indo-Pacific during the Pleistocene in an eastward direction following a stepping stone pathway, and that sea-level fluctuations during the Pleistocene may have promoted gene flow only locally. A molecular species delimitation test suggests that several allopatric island populations of E. erythrogaster may be regarded as species. Most of these putative new species are further characterized by diagnostic differences in plumage. Our study reconfirms the E. erythrogaster complex as a 'great speciator': it represents a complex of up to 17 allopatrically distributed, reciprocally monophyletic and/or morphologically diagnosable species that originated during the Pleistocene. Our results support the view that observed latitudinal gradients of genetic divergence among avian sister species may have been affected by incomplete knowledge of taxonomic limits in tropical bird species. PMID:23554394

  17. 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.

  18. 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

  19. 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

  20. 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

  1. An application of Bayesian inference for solar-like pulsators

    NASA Astrophysics Data System (ADS)

    Benomar, O.

    2008-12-01

    As the amount of data collected by space-borne asteroseismic instruments (such as CoRoT and Kepler) increases drastically, it will be useful to have automated processes to extract a maximum of information from these data. The use of a Bayesian approach could be very help- ful for this goal. Only a few attempts have been made in this way (e.g. Brewer et al. 2007). We propose to use Markov Chain Monte Carlo simulations (MCMC) with Metropolis-Hasting (MH) based algorithms to infer the main stellar oscillation parameters from the power spec- trum, in the case of solar-like pulsators. Given a number of modes to be fitted, the algorithm is able to give the best set of parameters (frequency, linewidth, amplitude, rotational split- ting) corresponding to a chosen input model. We illustrate this algorithm with one of the first CoRoT targets: HD 49933.

  2. Integrating fossils with molecular phylogenies improves inference of trait evolution.

    PubMed

    Slater, Graham J; Harmon, Luke J; Alfaro, Michael E

    2012-12-01

    Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and process contained in the fossil record. In this article, we show through simulation that incorporation of fossil information dramatically improves our ability to distinguish among models of quantitative trait evolution using comparative data. We further suggest a novel Bayesian approach that allows fossil information to be integrated even when explicit phylogenetic hypotheses are lacking for extinct representatives of extant clades. By applying this approach to a comparative dataset comprising body sizes for caniform carnivorans, we show that incorporation of fossil information not only improves ancestral state estimates relative to those derived from extant taxa alone, but also results in preference of a model of evolution with trend toward large body size over alternative models such as Brownian motion or Ornstein-Uhlenbeck processes. Our approach highlights the importance of considering fossil information when making macroevolutionary inference, and provides a way to integrate the kind of sparse fossil information that is available to most evolutionary biologists.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. Maximum likelihood inference of reticulate evolutionary histories.

    PubMed

    Yu, Yun; Dong, Jianrong; Liu, Kevin J; Nakhleh, Luay

    2014-11-18

    Hybridization plays an important role in the evolution of certain groups of organisms, adaptation to their environments, and diversification of their genomes. The evolutionary histories of such groups are reticulate, and methods for reconstructing them are still in their infancy and have limited applicability. We present a maximum likelihood method for inferring reticulate evolutionary histories while accounting simultaneously for incomplete lineage sorting. Additionally, we propose methods for assessing confidence in the amount of reticulation and the topology of the inferred evolutionary history. Our method obtains accurate estimates of reticulate evolutionary histories on simulated datasets. Furthermore, our method provides support for a hypothesis of a reticulate evolutionary history inferred from a set of house mouse (Mus musculus) genomes. As evidence of hybridization in eukaryotic groups accumulates, it is essential to have methods that infer reticulate evolutionary histories. The work we present here allows for such inference and provides a significant step toward putting phylogenetic networks on par with phylogenetic trees as a model of capturing evolutionary relationships. PMID:25368173

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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…

  1. 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.

  2. Evidence for parallel ecological speciation in scincid lizards of the Eumeces skiltonianus species group (Squamata: Scincidae).

    PubMed

    Richmond, Jonathan Q; Reeder, Tod W

    2002-07-01

    We identify instances of parallel morphological evolution in North American scincid lizards of the Eumeces skiltonianus species group and provide evidence that this system is consistent with a model of ecological speciation. The group consists of three putative species divided among two morphotypes, the small-bodied and striped E. skiltonianus and E. lagunensis versus the large-bodied and typically uniform-colored E. gilberti. Members of the group pass through markedly similar phenotypic stages during early development, but differ with respect to where terminal morphology occurs along the developmental sequence. The morphotypes also differ in habitat preference, with the large-bodied gilberti form generally inhabiting lower elevations and drier environments than the smaller, striped morphs. We inferred the phylogenetic relationships of 53 skiltonianus group populations using mtDNA sequence data from the ND4 protein-coding gene and three flanking tRNAs (900 bp total). Sampling encompassed nearly the entire geographic range of the group, and all currently recognized species and subspecies were included. Our results provide strong evidence for parallel origins of three clades characterized by the gilberti morphotype, two of which are nested within the more geographically widespread E. skiltonianus. Eumeces lagunensis was also nested among populations of E. skiltonianus. Comparative analyses using independent contrasts show that evolutionary changes in body size are correlated with differences in adult color pattern. The independently derived association of gilberti morphology with warm, arid environments suggests that phenotypic divergence is the result of adaptation to contrasting selection regimes. We provide evidence that body size was likely the target of natural selection, and that divergences in color pattern and mate recognition are probable secondary consequences of evolving large body size.

  3. Coupling iodine speciation to primary, regenerated or ``new'' production: a re-evaluation

    NASA Astrophysics Data System (ADS)

    Wong, George T. F.

    2001-06-01

    In two recent studies (Tian et al., Deep-Sea Res. I 43 (1996) 723-738; Campos et al., Deep-Sea Res. II 43 (1996) 455-466), in order to explain the observed temporal variations in the distributions of the dissolved iodine species at the time-series stations in the Mediterranean Sea, the North Atlantic and the North Pacific, diverse assumptions were invoked on the relationships between changes in the speciation of dissolved iodine in the surface oceans and biological production such that the surface enrichment of I - was linked to both regenerated production and primary production while the surface depletion of [IO 3-+I -] was linked to "new" production. However, while some of the major conclusions in these studies are critically dependent on these assumptions, the validity of the assumptions has yet to be verified with experimental evidence. On the other hand, while there are still significant unknowns in the understanding of the cycling among dissolved iodine species in the surface oceans, presently available data from laboratory cultures and field observations are consistent with an alternative conceptual model in which IO 3- and NO 3- are taken up at some ratio to each other during NO 3- uptake and almost all of the IO 3- taken up is exuded as I -. Thus, the depletion of IO 3- and the enrichment of I - in the surface water are linked to NO 3- uptake. This alternative model is also consistent with the data sets presented by Tian et al. (1996) and Campos et al. (1996). By linking the surface depletion of IO 3- to NO 3- uptake, significantly different biogeochemical behavior of the marine dissolved iodine system may be inferred. The extent to which I - may be oxidized to IO 3- within the euphotic zone during the residence time of the water in the surface ocean is still an open question.

  4. 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

  5. Speciation and stasis in marine Ostracoda: Climatic modulation of evolution

    USGS Publications Warehouse

    Cronin, T. M.

    1985-01-01

    Morphologic and paleozoogeographic analysis of Cenozoic marine Ostracoda from the Atlantic, Caribbean, and Pacific indicates that climatic change modulates evolution by disrupting long-term stasis and catalyzing speciation during sustained, unidirectional climatic transitions and, conversely, by maintaining morphologic stasis during rapid, high-frequency climatic osculations. In the middle Pliocene, 4 to 3 million years ago, at least six new species of Puriana suddenly appeared as the Isthmus of Panama closed, changing oceanographic circulation and global climate. Since then morphologic stasis has characterized ancestral and descendant species during many glacial-interglacial cycles. The frequency and duration of climatic events have more impact on ostracode evolution than the magnitude of climatic changes.

  6. 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.

  7. 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 ...

  8. 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...

  9. 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...

  10. 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...

  11. 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

  12. 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...

  13. 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…

  14. 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.

  15. A Learning Algorithm for Multimodal Grammar Inference.

    PubMed

    D'Ulizia, A; Ferri, F; Grifoni, P

    2011-12-01

    The high costs of development and maintenance of multimodal grammars in integrating and understanding input in multimodal interfaces lead to the investigation of novel algorithmic solutions in automating grammar generation and in updating processes. Many algorithms for context-free grammar inference have been developed in the natural language processing literature. An extension of these algorithms toward the inference of multimodal grammars is necessary for multimodal input processing. In this paper, we propose a novel grammar inference mechanism that allows us to learn a multimodal grammar from its positive samples of multimodal sentences. The algorithm first generates the multimodal grammar that is able to parse the positive samples of sentences and, afterward, makes use of two learning operators and the minimum description length metrics in improving the grammar description and in avoiding the over-generalization problem. The experimental results highlight the acceptable performances of the algorithm proposed in this paper since it has a very high probability of parsing valid sentences.

  16. 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

  17. Explanatory Preferences Shape Learning and Inference.

    PubMed

    Lombrozo, Tania

    2016-10-01

    Explanations play an important role in learning and inference. People often learn by seeking explanations, and they assess the viability of hypotheses by considering how well they explain the data. An emerging body of work reveals that both children and adults have strong and systematic intuitions about what constitutes a good explanation, and that these explanatory preferences have a systematic impact on explanation-based processes. In particular, people favor explanations that are simple and broad, with the consequence that engaging in explanation can shape learning and inference by leading people to seek patterns and favor hypotheses that support broad and simple explanations. Given the prevalence of explanation in everyday cognition, understanding explanation is therefore crucial to understanding learning and inference. PMID:27567318

  18. Nonintentional analogical inference in text comprehension.

    PubMed

    Day, Samuel B; Gentner, Dedre

    2007-01-01

    We present findings suggesting that analogical inference processes can play a role in fluent comprehension and interpretation. Participants were found to use information from a prior relationally similar example in understanding the content of a later example, but they reported that they were not aware of having done so. These inference processes were sensitive to structural mappings between the two instances, ruling out explanations based solely on more general kinds of activation, such as priming. Reading speed measures were consistent with the possibility that these inferences had taken place during encoding of the target rather than during the later recognition test. These findings suggest that analogical mapping, though often viewed as an explicit deliberative process, can sometimes operate without intent or even awareness.

  19. Consumer psychology: categorization, inferences, affect, and persuasion.

    PubMed

    Loken, Barbara

    2006-01-01

    This chapter reviews research on consumer psychology with emphasis on the topics of categorization, inferences, affect, and persuasion. The chapter reviews theory-based empirical research during the period 1994-2004. Research on categorization includes empirical research on brand categories, goals as organizing frameworks and motivational bases for judgments, and self-based processing. Research on inferences includes numerous types of inferences that are cognitively and/or experienced based. Research on affect includes the effects of mood on processing and cognitive and noncognitive bases for attitudes and intentions. Research on persuasion focuses heavily on the moderating role of elaboration and dual-process models, and includes research on attitude strength responses, advertising responses, and negative versus positive evaluative dimensions.

  20. Influence of ligands on metal speciation, transport and toxicity in a tropical river during wet (monsoon) period.

    PubMed

    Gogoi, Anindita; Tushara Chaminda, G G; An, Alicia K J; Snow, Daniel D; Li, Yusong; Kumar, Manish

    2016-11-01

    Metal speciation and transport are seldom assessed in densely populated Tropical River. An evaluation of the phase distribution for Copper (Cu), Lead (Pb) and Zinc (Zn) along with chemical speciation, variance with different water quality parameters and toxicity were conducted in the Brahmaputra River of India from upstream to downstream during wet (monsoon) periods in July 2014. Results indicated that metal free ions and carbonates were dominant in the inorganic fractions whereas metal concentrations were negligible in the anionic inorganic fractions. Due to high sediment load in the river during monsoon, metals were substantially higher in the particulate fractions than in the aqueous phase. Partition coefficient for Cu (3.1-6.1), Pb (3.4-6.5) and Zn (3.5-6.9), demonstrated strong adsorption of the metals on suspended matter. Q-mode hierarchical cluster analysis (HCA) illustrated groupings mainly governed by quality parameters rather than by the river course. R-mode results imply selectivity of the affinities of metals for different ligands. Health risk index (HRI) values were less than 1 for dissolved metal for Cu, Pb and Zn while it was greater than 1 for total metal for Pb and Cu indicating potential human health risk. The study demonstrated that binding of metals with naturally occurring dissolved organic matter or suspended particulate matter affects metal bioavailability in river during wet periods when sediment load is particularly high. A combination of empirical, computational and statistical relationships between ionic species and fractions of metals provided greater certitude in identifying the resemblance among the different locations of the river. PMID:27544655

  1. Speciation of Water-Soluble Organic Carbons in Aerosols from two collecting methods: PILS and filters

    NASA Astrophysics Data System (ADS)

    Kim, J.; Yoon, H.; Ahn, Y.; Shin, J.; Lee, M.; Park, M.

    2013-12-01

    Total suspended particles aerosol sampling for collection of 24 h by high volume air sampler at Campus of Korea University in metropolitan city Seoul. To measure WSOC, an aliquot (2 cm2) of quartz fiber filter ( 20.3 × 25.4 cm) was extracted 5 mL Milli-Q water with hot water (80 °C) and room temperature water (25 °C) under ultrasonication (10 min, three times). Hot water extracted method was comparison with PILS samples. WSOC was quantified using a total organic carbon (TOC) analyzer. For speciation analysis of organic compounds, the extracts were concentrated to dryness using freeze dryer and then derivatized with MSTFA (N-Methyl-N-trimethy- silyltrifluoroacetamide+1% trimethylchlorosilane) and analyzed with GC-MS scan mode. In extracted with hot water, total carbon concentrations were higher than room temperature extracts. Organic compounds widely recognized to be generated from anthropogenic sources with a low solubility at ambient temperature organic were detected in both samples obtained from PILS and hot water extraction. It is demonstrating that difference between total carbon concentration and composition of sampling obtain from two different systems (i.e. PILS and filter) in analytical procedure of WSOCs. Acknowledgement This research was susported by Center for Women In Science, Engineering Technology(WISET) commissioned by the Ministry of Science, ICT & Future Planning and the National Research Foundation of korea. The authors also acknowledge the support made by a grant from the Korea Basic Science Institute.

  2. Ba and Ni speciation in a nodule of binary Mn oxide phase composition from Lake Baikal

    NASA Astrophysics Data System (ADS)

    Manceau, Alain; Kersten, Michael; Marcus, Matthew A.; Geoffroy, Nicolas; Granina, Liba

    2007-04-01

    The partitioning and incorporation mechanism of Ni and Ba in a ferromanganese nodule from Lake Baikal were characterized by X-ray microfluorescence, microdiffraction, and absorption spectroscopy. Fe is speciated as goethite, and Mn as romanechite (psilomelane) and 10 Å-vernadite (turbostratic buserite) with minor 7 Å-vernadite (turbostratic birnessite). Barium is associated with romanechite and Ni with vernadite in distinct and irregularly distributed layers, and each type of Mn oxide is separated from the other type by goethite. The binary Mn oxide banding pattern is interpreted by a two-mode accretionary model, in which the variation in Ba flux induced by hydrothermal water pulses determines whether a tectomanganate (romanechite) or phyllomanganate (vernadite) is formed during the ferromanganese nodule accretion. Consistent with the dependence of Ni sorption on pH and the circumneutral pH of the lake water, nickel is mainly substituted isomorphically for Mn in the manganese layer, and is not sorbed at vacant Mn layer sites in the interlayer.

  3. 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

  4. Declarative memory, awareness, and transitive inference.

    PubMed

    Smith, Christine; Squire, Larry R

    2005-11-01

    A characteristic usually attributed to declarative memory is that what is learned is accessible to awareness. Recently, the relationship between awareness and declarative (hippocampus-dependent) memory has been questioned on the basis of findings from transitive inference tasks. In transitive inference, participants are first trained on overlapping pairs of items (e.g., A+B-, B+C-, C+D-, and D+E-, where + and - indicate correct and incorrect choices). Later, participants who choose B over D when presented with the novel pair BD are said to demonstrate transitive inference. The ability to exhibit transitive inference is thought to depend on the fact that participants have represented the stimulus elements hierarchically (i.e., A>B>C>D>E). We found that performance on five-item and six-item transitive inference tasks was closely related to awareness of the hierarchical relationship among the elements of the training pairs. Participants who were aware of the hierarchy performed near 100% correct on all tests of transitivity, but participants who were unaware of the hierarchy performed poorly (e.g., on transitive pair BD in the five-item problem; on transitive pairs BD, BE, and CE in the six-item problem). When the five-item task was administered to memory-impaired patients with damage thought to be limited to the hippocampal region, the patients were impaired at learning the training pairs. All patients were unaware of the hierarchy and, like unaware controls, performed poorly on the BD pair. The findings indicate that awareness is critical for robust performance on tests of transitive inference and support the view that awareness of what is learned is a fundamental characteristic of declarative memory.

  5. 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.

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

    PubMed

    Rabosky, Daniel L; Title, Pascal O; Huang, Huateng

    2015-06-22

    The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades.

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

    PubMed

    Leducq, Jean-Baptiste; Nielly-Thibault, Lou; Charron, Guillaume; Eberlein, Chris; Verta, Jukka-Pekka; Samani, Pedram; Sylvester, Kayla; Hittinger, Chris Todd; Bell, Graham; Landry, Christian R

    2016-01-11

    Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfil all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the interpretation that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here, we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. List mode multichannel analyzer

    SciTech Connect

    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.

  15. 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.

  16. Dynamic of lead speciation in sewage sludge composting.

    PubMed

    Zheng, G D; Chen, T B; Gao, D; Luo, W

    2004-01-01

    A large-scale sewage sludge composting experiment was conducted to develop an understanding of changes that occur to Pb chemical speciation, distribution and bio-availability during the course of composting. The four-stage Tessier sequential extraction method was employed to investigate the dynamics of heavy metal Pb speciation (exchangeable, bound to carbonates, bound to Fe-Mn oxides, bound to organic matter and sulphides, residual) during the course of sewage sludge composting. The concentrations of the total Pb and the five Pb fractions concentrations were increased during the whole stage of compost. However, the percentages of Pb distribution with respect to total Pb were changed in the following manner: exchangeable, bound to Fe-Mn oxides and bound to carbonates Pb with respect to total Pb were increased, while the percentages of bound to organic matter and sulphides, and residual Pb with respect to total Pb were decreased during composting. The data showed that the quantity of Pb in the less toxic portion, such as consisting of organic matter and sulphides bound and residual Pb, was increased, and that the contamination and bio-availability of heavy metal Pb in sewage sludge was reduced during the composting process.

  17. Reinforcement can overcome gene flow during speciation in Drosophila.

    PubMed

    Matute, Daniel R

    2010-12-21

    Reinforcement, the strengthening of prezygotic reproductive isolation by natural selection in response to maladaptive hybridization [1-3], is one of the few processes in which natural selection directly favors the evolution of species as discrete groups (e.g., [4-7]). The evolution of reproductive barriers via reinforcement is expected to evolve in regions where the ranges of two species overlap and hybridize as an evolutionary solution to avoiding the costs of maladaptive hybridization [2,3,8]. The role of reinforcement in speciation has, however, been highly controversial because population-genetic theory suggests that the process is severely impeded by both hybridization [8-11] and migration of individuals from outside the contact zone [12,13]. To determine whether reinforcement could strengthen the reproductive barriers between two sister species of Drosophila in the face of these impediments, I initiated experimental populations of these two species that allowed different degrees of hybridization, as well as migration from outside populations. Surprisingly, even in the face of gene flow, reinforcement could promote the evolution of reproductive isolation within only five generations. As theory predicts, high levels of hybridization (and/or strong selection against hybrids) and migration impeded this evolution. These results suggest that reinforcement can help complete the process of speciation.

  18. 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.

  19. 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

  20. 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