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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-11-01

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

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

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

PubMed

Andújar, Carmelo; Pérez-González, Sergio; Arribas, Paula; Zaballos, Juan P; Vogler, Alfried P; Ribera, Ignacio

2017-11-01

Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species' habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below-ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement inside the soil. We studied a species-rich endogean ground beetle lineage, Typhlocharina, including three genera and more than 60 species, as a model for the evolutionary biology of dispersal and speciation in the deep soil. A time-calibrated molecular phylogeny generated from >400 individuals was used to delimit candidate species, to study the accumulation of lineages through space and time by species-area-age relationships and to determine the geographical structure of the diversification using the relationship between phylogenetic and geographic distances across the phylogeny. Our results indicated a small spatial scale of speciation in Typhlocharina and low dispersal capacity combined with sporadic long distance, presumably passive dispersal events that fuelled the speciation process. Analysis of lineage growth within Typhlocharina revealed a richness plateau correlated with the range of distribution of lineages, suggesting a long-term species richness equilibrium mediated by density dependence through limits of habitat availability. The interplay of area- and age-dependent processes ruling the lineage diversification in Typhlocharina may serve as a general model for the evolution of high species diversity in endogean mesofauna. © 2017 John Wiley & Sons Ltd.

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

PubMed

Sillanpää, M; Orama, M; Rämö, J; Oikari, A

2001-02-21

The speciations of EDTA and DTPA in process, waste and river waters are modelled and simulated, specifically to the mode of occurrence in the pulp and paper mill effluents and subsequently in receiving waters. Due to relatively short residence times in bleaching process and waste water treatment and slow exchange kinetics, it is expected that the thermodynamic equilibrium is not necessarily reached. Therefore, the initial speciation plays a key role. As such, the simulations have been extended to the process waters of the pulp and paper industry taking into account estimated average conditions. The results reveal that the main species are; Mn and Ca complexes of EDTA and DTPA in pulp mill process waters; Fe(III) and Mn complexes of EDTA and DTPA in waste waters; Fe(III) and Zn complexes of EDTA and DTPA in receiving waters. It is also shown how the increasing concentration of complexing agents effects the speciation. Alkaline earth metal chelation plays a significant role in the speciation of EDTA and DTPA when there is a noticeable molar excess of complexing agents compared with transition metals.

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

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

PubMed

Potter, Sally; Bragg, Jason G; Blom, Mozes P K; Deakin, Janine E; Kirkpatrick, Mark; Eldridge, Mark D B; Moritz, Craig

2017-01-01

The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale . We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.

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. © 2015 John Wiley & Sons Ltd.

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

PubMed

Burbrink, Frank T; Yao, Helen; Ingrasci, Matthew; Bryson, Robert W; Guiher, Timothy J; Ruane, Sara

2011-09-01

Studies of speciation and taxon delimitation are usually decoupled. Combining these methods provides a stronger theoretical ground for recognizing new taxa and understanding processes of speciation. Using coalescent methods, we examine speciation, post-speciation population demographics, and taxon delimitation in the Arizona Mountain Kingsnake (Lampropeltis pyromelana), a species restricted to high elevations in southwestern United States and northern Mexico (SW). These methods provide a solid foundation for understanding how biogeographic barriers operate at the regional scale in the SW. Bayesian species delimitation methods, using three loci from samples of L. pyromelana taken throughout their range, show strong support for the existence of two species that are separated by low elevation habitats found between the Colorado Plateau/ Mogollon Rim and the Sierra Madre Occidental. Our results suggest an allopatric mode of speciation given the near absence of gene flow over time, which resulted in two lineages of unequal population sizes. Speciation likely occurred prior to the Pleistocene, during the aridification of the SW and/or the uplift of the Colorado Plateau, and while these species occupy similar high-elevation niches, they are isolated by xeric conditions found in the intervening low deserts. Furthermore, post-speciation demographics suggest that populations of both lineages were not negatively impacted by climate change throughout the Pleistocene. Finally, our results suggest that at least for this group, where divergence is old and gene flow is low, Bayesian species delimitation performs well. Copyright © 2011 Elsevier Inc. All rights reserved.

The inference from a single case: moral versus scientific inferences in implementing new biotechnologies.

PubMed

Hofmann, B

2008-06-01

Are there similarities between scientific and moral inference? This is the key question in this article. It takes as its point of departure an instance of one person's story in the media changing both Norwegian public opinion and a brand-new Norwegian law prohibiting the use of saviour siblings. The case appears to falsify existing norms and to establish new ones. The analysis of this case reveals similarities in the modes of inference in science and morals, inasmuch as (a) a single case functions as a counter-example to an existing rule; (b) there is a common presupposition of stability, similarity and order, which makes it possible to reason from a few cases to a general rule; and (c) this makes it possible to hold things together and retain order. In science, these modes of inference are referred to as falsification, induction and consistency. In morals, they have a variety of other names. Hence, even without abandoning the fact-value divide, there appear to be similarities between inference in science and inference in morals, which may encourage communication across the boundaries between "the two cultures" and which are relevant to medical humanities.

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

PubMed

Pigot, Alex L; Phillimore, Albert B; Owens, Ian P F; Orme, C David L

2010-12-01

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of

Speciation and Neutral Molecular Evolution in One-Dimensional Closed Population

NASA Astrophysics Data System (ADS)

Semovski, Sergei V.; Bukin, Yuri S.; Sherbakov, Dmitry Yu.

Models are presented suitable for a description of speciation processes arising due to reproductive isolation depending on genetic distance. The main attention is paid to the model of a one-dimensional closed population, which describes the evolution of littoral benthic organisms. In order to correspond the modeling results to the results obtained in the course of experimental phylogenetic studies, all individual-based models described here involve neutrally evolving and maternally inherited DNA sequence. Sub-samples of the resulting sequences were used for a posteriori phylogenetic inferences which then were compared to the "true" evolutionary histories.

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

EPA Pesticide Factsheets

This training provides general concepts on chemical speciation, the SPECIATE database and browser, and how to use the Speciation Tool to create model ready speciation inputs for a photochemical air quality model.

Visualizing speciation in artificial cichlid fish.

PubMed

Clement, Ross

2006-01-01

The Cichlid Speciation Project (CSP) is an ALife simulation system for investigating open problems in the speciation of African cichlid fish. The CSP can be used to perform a wide range of experiments that show that speciation is a natural consequence of certain biological systems. A visualization system capable of extracting the history of speciation from low-level trace data and creating a phylogenetic tree has been implemented. Unlike previous approaches, this visualization system presents a concrete trace of speciation, rather than a summary of low-level information from which the viewer can make subjective decisions on how speciation progressed. The phylogenetic trees are a more objective visualization of speciation, and enable automated collection and summarization of the results of experiments. The visualization system is used to create a phylogenetic tree from an experiment that models sympatric speciation.

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

PubMed

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

2012-07-01

Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondrial CO1 (574 bp) and ND5 genes (1188 bp). The assay with CO1 sequences, widely used in DNA barcoding, failed to distinguish the two species. The two species were clearly distinguishable, however, with no shared RAG1 or ND5 haplotypes. The species were reciprocally monophyletic for RAG1, but paraphyletic for ND5 sequences. Qualitative evidence and statistical inferences using the 'Isolation-with-Migration models' indicated that these results were better explained with post-divergence gene flow in the recent past rather than incomplete lineage sorting with zero gene flow since speciation. An estimate of divergence time was less than 0.5 Ma with an upper confidence limit of within 1 Ma. Recent speciation of highly mobile species in the marine environment is of great interest, as it suggests that speciation may have occurred in the absence of long-term physical barriers to gene flow. We propose that the ecologically driven forces such as habitat choice played a significant role in speciation in manta rays. Copyright © 2012 Elsevier Inc. All rights reserved.

Speciation of Iberian diving beetles in Pleistocene refugia (Coleoptera, Dytiscidae).

PubMed

Ribera, Ignacio; Vogler, Alfried P

2004-01-01

The Mediterranean basin is an area of high diversity and endemicity, but the age and origin of its fauna are still largely unknown. Here we use species-level phylogenies based on approximately 1300 base pairs of the genes 16S rRNA and cytochrome oxidase I to establish the relationships of 27 of the 34 endemic Iberian species of diving beetles in the family Dytiscidae, and to investigate their level of divergence. Using a molecular clock approach, 18-19 of these species were estimated to be of Pleistocene origin, with four to six of them from the Late Pleistocene ( approximately 100 000 years). A second, lower speciation frequency peak was assigned to Late Miocene or Early Pliocene. Analysis of the distributional ranges showed that endemic species placed in the tip nodes of the trees are significantly more likely to be allopatric with their sisters than endemic species at lower node levels. Allopatric sister species are also significantly younger than sympatric clades, in agreement with an allopatric mode of speciation and limited subsequent range movement. These results strongly suggest that for some taxa Iberian populations were isolated during the Pleistocene long enough to speciate, and apparently did not expand their ranges to recolonize areas north of the Pyrenees. This is in contradiction to observations from fossil beetles in areas further north, which document large range movements associated with the Pleistocene glacial cycles hypothesized to suppress population isolation and allopatric speciation.

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

PubMed

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

2013-01-01

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

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...

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

PubMed Central

Feder, Jeffrey L.; Xie, Xianfa; Rull, Juan; Velez, Sebastian; Forbes, Andrew; Leung, Brian; Dambroski, Hattie; Filchak, Kenneth E.; Aluja, Martin

2005-01-01

The Rhagoletis pomonella sibling species complex is a model for sympatric speciation by means of host plant shifting. However, genetic variation aiding the sympatric radiation of the group in the United States may have geographic roots. Inversions on chromosomes 1-3 affecting diapause traits adapting flies to differences in host fruiting phenology appear to exist in the United States because of a series of secondary introgression events from Mexico. Here, we investigate whether these inverted regions of the genome may have subsequently evolved to become more recalcitrant to introgression relative to collinear regions, consistent with new models for chromosomal speciation. As predicted by the models, gene trees for six nuclear loci mapping to chromosomes other than 1-3 tended to have shallower node depths separating Mexican and U.S. haplotypes relative to an outgroup sequence than nine genes residing on chromosomes 1-3. We discuss the implications of secondary contact and differential introgression with respect to sympatric host race formation and speciation in Rhagoletis, reconciling some of the seemingly dichotomous views of Mayr, Dobzhansky, and Bush concerning modes of divergence. PMID:15851672

Neural correlates of species-typical illogical cognitive bias in human inference.

PubMed

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

2010-09-01

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, although it may be true, it is not necessarily true. Given pairs of conditional relations, such as AB and BC, humans reflexively perform two additional modes of inference: transitivity, whereby one (validly) infers AC; and equivalence, whereby one (invalidly) infers CA. In sharp contrast, nonhuman animals can handle transitivity but can rarely be made to acquire symmetry or equivalence. In the present study, human subjects performed logical and illogical inferences about the relations between abstract, visually presented figures while their brain activation was monitored with fMRI. The prefrontal, medial frontal, and intraparietal cortices were activated during all modes of inference. Additional activation in the precuneus and posterior parietal cortex was observed during transitivity and equivalence, which may reflect the need to retrieve the intermediate stimulus (B) from memory. Surprisingly, the patterns of brain activation in illogical and logical inference were very similar. We conclude that the observed inference-related fronto-parietal network is adapted for processing categorical, but not logical, structures of association among stimuli. Humans might prefer categorization over the memorization of logical structures in order to minimize the cognitive working memory load when processing large volumes of information.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-02-01

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

Inference and Biogeochemical Response of Vertical Velocities inside a Mode Water Eddy

NASA Astrophysics Data System (ADS)

Barceló-Llull, B.; Pallas Sanz, E.; Sangrà, P.

2016-02-01

With the aim to study the modulation of the biogeochemical fluxes by the ageostrophic secondary circulation in anticyclonic mesoscale eddies, a typical eddy of the Canary Eddy Corridor was interdisciplinary surveyed on September 2014 in the framework of the PUMP project. The eddy was elliptical shaped, 4 month old, 110 km diameter and 400 m depth. It was an intrathermocline type often also referred as mode water eddy type. We inferred the mesoscale vertical velocity field resolving a generalized omega equation from the 3D density and ADCP velocity fields of a five-day sampled CTD-SeaSoar regular grid centred on the eddy. The grid transects where 10 nautical miles apart. Although complex, in average, the inferred omega velocity field (hereafter w) shows a dipolar structure with downwelling velocities upstream of the propagation path (west) and upwelling velocities downstream. The w at the eddy center was zero and maximum values were located at the periphery attaining ca. 6 m day-1. Coinciding with the occurrence of the vertical velocities cells a noticeable enhancement of phytoplankton biomass was observed at the eddy periphery respect to the far field. A corresponding upward diapycnal flux of nutrients was also observed at the periphery. As minimum velocities where reached at the eddy center, lineal Ekman pumping mechanism was discarded. Minimum values of phytoplankton biomass where also observed at the eddy center. The possible mechanisms for such dipolar w cell are still being investigated, but an analysis of the generalized omega equation forcing terms suggest that it may be a combination of horizontal deformation and advection of vorticity by the ageostrophic current (related to nonlinear Ekman pumping). As expected for Trades, the wind was rather constant and uniform with a speed of ca. 5 m s-1. Diagnosed nonlinear Ekman pumping leaded also to a dipolar cell that mirrors the omega w dipolar cell.

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...

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

PubMed

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

2014-08-05

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

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

PubMed

Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min

2014-10-01

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus. © 2014 John Wiley & Sons Ltd.

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...

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. Copyright © 2014 Elsevier Inc. All rights reserved.

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

Speciation genes in plants

PubMed Central

Rieseberg, Loren H.; Blackman, Benjamin K.

2010-01-01

Background Analyses of speciation genes – genes that contribute to the cessation of gene flow between populations – can offer clues regarding the ecological settings, evolutionary forces and molecular mechanisms that drive the divergence of populations and species. This review discusses the identities and attributes of genes that contribute to reproductive isolation (RI) in plants, compares them with animal speciation genes and investigates what these genes can tell us about speciation. Scope Forty-one candidate speciation genes were identified in the plant literature. Of these, seven contributed to pre-pollination RI, one to post-pollination, prezygotic RI, eight to hybrid inviability, and 25 to hybrid sterility. Genes, gene families and genetic pathways that were frequently found to underlie the evolution of RI in different plant groups include the anthocyanin pathway and its regulators (pollinator isolation), S RNase-SI genes (unilateral incompatibility), disease resistance genes (hybrid necrosis), chimeric mitochondrial genes (cytoplasmic male sterility), and pentatricopeptide repeat family genes (cytoplasmic male sterility). Conclusions The most surprising conclusion from this review is that identities of genes underlying both prezygotic and postzygotic RI are often predictable in a broad sense from the phenotype of the reproductive barrier. Regulatory changes (both cis and trans) dominate the evolution of pre-pollination RI in plants, whereas a mix of regulatory mutations and changes in protein-coding genes underlie intrinsic postzygotic barriers. Also, loss-of-function mutations and copy number variation frequently contribute to RI. Although direct evidence of positive selection on speciation genes is surprisingly scarce in plants, analyses of gene family evolution, along with theoretical considerations, imply an important role for diversifying selection and genetic conflict in the evolution of RI. Unlike in animals, however, most candidate speciation

Extraordinarily rapid speciation in a marine fish

PubMed Central

Momigliano, Paolo; Jokinen, Henri; Fraimout, Antoine; Florin, Ann-Britt; Norkko, Alf; Merilä, Juha

2017-01-01

Divergent selection may initiate ecological speciation extremely rapidly. How often and at what pace ecological speciation proceeds to yield strong reproductive isolation is more uncertain. Here, we document a case of extraordinarily rapid speciation associated with ecological selection in the postglacial Baltic Sea. European flounders (Platichthys flesus) in the Baltic exhibit two contrasting reproductive behaviors: pelagic and demersal spawning. Demersal spawning enables flounders to thrive in the low salinity of the Northern Baltic, where eggs cannot achieve neutral buoyancy. We show that demersal and pelagic flounders are a species pair arising from a recent event of speciation. Despite having a parapatric distribution with extensive overlap, the two species are reciprocally monophyletic and show strongly bimodal genotypic clustering and no evidence of contemporary migration, suggesting strong reproductive isolation. Divergence across the genome is weak but shows strong signatures of selection, a pattern suggestive of a recent ecological speciation event. We propose that spawning behavior in Baltic flounders is the trait under ecologically based selection causing reproductive isolation, directly implicating a process of ecological speciation. We evaluated different possible evolutionary scenarios under the approximate Bayesian computation framework and estimate that the speciation process started in allopatry ∼2,400 generations ago, following the colonization of the Baltic by the demersal lineage. This is faster than most known cases of ecological speciation and represents the most rapid event of speciation ever reported for any marine vertebrate. PMID:28533412

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

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

Trace metal speciation in natural waters: Computational vs. analytical

USGS Publications Warehouse

Nordstrom, D. Kirk

1996-01-01

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

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...

Evolution of habitat preference and nutrition mode in a cosmopolitan fungal genus with evidence of interkingdom host jumps and major shifts in ecology.

PubMed

Chaverri, Priscila; Samuels, Gary J

2013-10-01

Host jumps by microbial symbionts are often associated with bursts of species diversification driven by the exploitation of new adaptive zones. The objective of this study was to infer the evolution of habitat preference (decaying plants, soil, living fungi, and living plants), and nutrition mode (saprotrophy and mycoparasitism) in the fungal genus Trichoderma to elucidate possible interkingdom host jumps and shifts in ecology. Host and ecological role shifts were inferred by phylogenetic analyses and ancestral character reconstructions. The results support several interkingdom host jumps and also show that the preference for a particular habitat was gained or lost multiple times. Diversification analysis revealed that mycoparasitism is associated with accelerated speciation rates, which then suggests that this trait may be linked to the high number of species in Trichoderma. In this study it was also possible to infer the cryptic roles that endophytes or soil inhabitants play in their hosts by evaluating their closest relatives and determining their most recent ancestors. Findings from this study may have implications for understanding certain evolutionary processes such as species radiations in some hyperdiverse groups of fungi, and for more applied fields such as the discovery and development of novel biological control strategies. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

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). Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Testing the role of climate in speciation: new methods and applications to squamate reptiles (lizards and snakes).

PubMed

Jezkova, Tereza; Wiens, John J

2018-05-19

Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large-scale phylogeny to identify 242 sister-species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n=49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61-76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

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

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,…

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

PubMed

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

2015-09-01

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 modelling assumptions, compares results across different predetermined 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 postprocessing of results of model-based population structure analyses. For analysing 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. © 2015 John Wiley & Sons Ltd.

US EPA's SPECIATE 4.4 Database: Development and Uses

EPA Science Inventory

SPECIATE is the U.S. Environmental Protection Agency’s (EPA) repository of volatile organic gas and particulate matter (PM) speciation profiles of air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, volatile o...

EPA’s SPECIATE 4.4 Database:Development and Uses

EPA Science Inventory

SPECIATE is the U.S. Environmental Protection Agency's (EPA)repository of volatile organic gas and particulate matter (PM) speciation profiles for air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, VOC, total...

EPA’s SPECIATE 4.4 Database: Development and Uses

EPA Science Inventory

SPECIATE is the U.S. Environmental Protection Agency's (EPA)repository of volatile organic gas and particulate matter (PM) speciation profiles for air pollution sources. EPA released SPECIATE 4.4 in early 2014 and, in total, the SPECIATE 4.4 database includes 5,728 PM, VOC, total...

Inferring the demographic history of European Ficedula flycatcher populations

PubMed Central

2013-01-01

Background Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations. Conclusions Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account. PMID:23282063

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

PubMed

Wang, Ning; Liang, Bin; Wang, Jichao; Yeh, Chia-Fen; Liu, Yang; Liu, Yanlin; Liang, Wei; Yao, Cheng-Te; Li, Shou-Hsien

2016-09-01

Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process. Copyright © 2016 Elsevier Inc. All rights reserved.

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

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...

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.

Measurement Error Calibration in Mixed-Mode Sample Surveys

ERIC Educational Resources Information Center

Buelens, Bart; van den Brakel, Jan A.

2015-01-01

Mixed-mode surveys are known to be susceptible to mode-dependent selection and measurement effects, collectively referred to as mode effects. The use of different data collection modes within the same survey may reduce selectivity of the overall response but is characterized by measurement errors differing across modes. Inference in sample surveys…

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

PubMed Central

Blakemore, James D.; Hull, Jonathan F.

2012-01-01

The speciation behavior of a water-soluble manganese(III) tetrasulfonated phthalocyanine complex was investigated with UV-visible and electron paramagnetic resonance (EPR) spectroscopies, as well as cyclic voltammetry. Parallel-mode EPR (in dimethylformamide:pyridine solvent mix) reveals a six-line hyperfine signal, centered at a g-value of 8.8, for the manganese(III) monomer, characteristic of the d4 S=2 system. The color of an aqueous solution containing the complex is dependent upon the pH of the solution; the phthalocyanine complex can exist as a water-bound monomer, a hydroxide-bound monomer, or an oxo-bridged dimer. Addition of coordinating bases such as borate or pyridine changes the speciation behavior by coordinating the manganese center. From the UV-visible spectra, complete speciation diagrams are plotted by global analysis of the pH-dependent UV-visible spectra, and a complete set of pKa values is obtained by fitting the data to a standard pKa model. Electrochemical studies reveal a pH-independent quasi-reversible oxidation event for the monomeric species, which likely involves oxidation of the organic ligand to the radical cation species. Adsorption of the phthalocyanine complex on the carbon working electrode was sometimes observed. The pKa values and electrochemistry data are discussed in the context of the development of mononuclear water-oxidation catalysts. PMID:22585306

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

Chemical Speciation and Metallomics.

PubMed

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

2018-01-01

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

Speciation in Drosophila: from phenotypes to molecules.

PubMed

Orr, H Allen; Masly, J P; Phadnis, Nitin

2007-01-01

Study of the genetics of speciation--and especially of the genetics of intrinsic postzygotic isolation-has enjoyed remarkable progress over the last 2 decades. Indeed progress has been so rapid that one might be tempted to ask if the genetics of postzygotic isolation is now wrapped up. Here we argue that the genetics of speciation is far from complete. In particular, we review 2 topics where recent work has revealed major surprises: 1) the role of meiotic drive in hybrid sterility and 2) the role of gene transposition in speciation. These surprises, and others like them, suggest that evolutionary biologists may understand less about the genetic basis of speciation than seemed likely a few years ago.

The importance of trace element speciation in biomedical science.

PubMed

Templeton, Douglas M

2003-04-01

According to IUPAC terminology, trace element speciation reflects differences in chemical composition at multiple levels from nuclear and electronic structure to macromolecular complexation. In the medical sciences, all levels of composition are important in various circumstances, and each can affect the bioavailability, distribution, physiological function, toxicity, diagnostic utility, and therapeutic potential of an element. Here we discuss, with specific examples, three biological principles in the intimate relation between speciation and biological behavior: i) the kinetics of interconversion of species determines distribution within the organism, ii) speciation governs transport across various biological barriers, and iii) speciation can limit potentially undesirable interactions between physiologically essential elements. We will also describe differences in the speciation of iron in states of iron overload, to illustrate how speciation analysis can provide insight into cellular processes in human disease.

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

PubMed

Matzke, Nicholas J

2014-11-01

Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC + J, which adds founder-event speciation, the importance of which is governed by a new free parameter, [Formula: see text]. The identifiability of DEC and DEC + J is tested on data sets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC + J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes + J. DEC and DEC + J are compared on 13 empirical data sets drawn from studies of island clades. Likelihood-ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC + J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC + J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods. © The Author(s) 2014. Published by Oxford

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).

Sympatric speciation by sexual selection alone is unlikely.

PubMed

Arnegard, Matthew E; Kondrashov, Alexey S

2004-02-01

According to Darwin, sympatric speciation is driven by disruptive, frequency-dependent natural selection caused by competition for diverse resources. Recently, several authors have argued that disruptive sexual selection can also cause sympatric speciation. Here, we use hypergeometric phenotypic and individual-based genotypic models to explore sympatric speciation by sexual selection under a broad range of conditions. If variabilities of preference and display traits are each caused by more than one or two polymorphic loci, sympatric speciation requires rather strong sexual selection when females exert preferences for extreme male phenotypes. Under this kind of mate choice, speciation can occur only if initial distributions of preference and display are close to symmetric. Otherwise, the population rapidly loses variability. Thus, unless allele replacements at very few loci are enough for reproductive isolation, female preferences for extreme male displays are unlikely to drive sympatric speciation. By contrast, similarity-based female preferences that do not cause sexual selection are less destabilizing to the maintenance of genetic variability and may result in sympatric speciation across a broader range of initial conditions. Certain groups of African cichlids have served as the exclusive motivation for the hypothesis of sympatric speciation by sexual selection. Mate choice in these fishes appears to be driven by female preferences for extreme male phenotypes rather than similarity-based preferences, and the evolution of premating reproductive isolation commonly involves at least several genes. Therefore, differences in female preferences and male display in cichlids and other species of sympatric origin are more likely to have evolved as isolating mechanisms under disruptive natural selection.

Speciation by Symbiosis: the Microbiome and Behavior.

PubMed

Shropshire, J Dylan; Bordenstein, Seth R

2016-03-31

Species are fundamental units of comparison in biology. The newly discovered importance and ubiquity of host-associated microorganisms are now stimulating work on the roles that microbes can play in animal speciation. We previously synthesized the literature and advanced concepts of speciation by symbiosis with notable attention to hybrid sterility and lethality. Here, we review recent studies and relevant data on microbes as players in host behavior and behavioral isolation, emphasizing the patterns seen in these analyses and highlighting areas worthy of additional exploration. We conclude that the role of microbial symbionts in behavior and speciation is gaining exciting traction and that the holobiont and hologenome concepts afford an evolving intellectual framework to promote research and intellectual exchange between disciplines such as behavior, microbiology, genetics, symbiosis, and speciation. Given the increasing centrality of microbiology in macroscopic life, microbial symbiosis is arguably the most neglected aspect of animal and plant speciation, and studying it should yield a better understanding of the origin of species. Copyright © 2016 Shropshire and Bordenstein.

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.

Chromosomes, conflict, and epigenetics: chromosomal speciation revisited.

PubMed

Brown, Judith D; O'Neill, Rachel J

2010-01-01

Since Darwin first noted that the process of speciation was indeed the "mystery of mysteries," scientists have tried to develop testable models for the development of reproductive incompatibilities-the first step in the formation of a new species. Early theorists proposed that chromosome rearrangements were implicated in the process of reproductive isolation; however, the chromosomal speciation model has recently been questioned. In addition, recent data from hybrid model systems indicates that simple epistatic interactions, the Dobzhansky-Muller incompatibilities, are more complex. In fact, incompatibilities are quite broad, including interactions among heterochromatin, small RNAs, and distinct, epigenetically defined genomic regions such as the centromere. In this review, we will examine both classical and current models of chromosomal speciation and describe the "evolving" theory of genetic conflict, epigenetics, and chromosomal speciation.

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…

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

PubMed

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

2005-05-03

Molecular studies of speciation in birds over the last three decades have been dominated by a focus on the geography, ecology, and timing of speciation, a tradition traceable to Mayr's Systematics and the Origin of Species. However, in the recent years, interest in the behavioral and molecular mechanisms of speciation in birds has increased, building in part on the older traditions and observations from domesticated species. The result is that many of the same mechanisms proffered for model lineages such as Drosophila--mechanisms such as genetic incompatibilities, reinforcement, and sexual selection--are now being seriously entertained for birds, albeit with much lower resolution. The recent completion of a draft sequence of the chicken genome, and an abundance of single-nucleotide polymorphisms on the autosomes and sex chromosomes, will dramatically accelerate research on the molecular mechanisms of avian speciation over the next few years. The challenge for ornithologists is now to inform well studied examples of speciation in nature with increased molecular resolution-to clone speciation genes if they exist--and thereby evaluate the relative roles of extrinsic, intrinsic, deterministic, and stochastic causes for avian diversification.

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

PubMed

Loera, Israel; Sosa, Victoria; Ickert-Bond, Stefanie M

2012-11-01

A lineage of 12 arid land shrubby species in the gymnosperm genus Ephedra (Gnetales) from North America is used to evaluate the influence of climate on speciation. With a long evolutionary history, and a well documented fossil record this lineage is an ideal model for understanding the process of speciation under a niche conservatism scenario. Using seven DNA molecular markers, Bayesian inference is carried out to uncover sister species and to estimate time of divergence of the lineages. Ecological niche models are generated for four parapatric and sympatric sister species and two analyses of niche evolution are performed, one based on ecological niche models and another using raw data and multivariate analysis. As previous analyses suggest, the diversification of North America Ephedra species may be the result of a recent secondary radiation. Both parapatric and sympatric species diverged mostly in a scenario of climatic niche conservatism. However, we also found strong evidence for niche divergence for one of the sister species pairs (E. californica-E. trifurca). Moreover, the multivariate analysis found environmental differences for some variables between sister species. The estimated divergence time of three pairs of sister species distributed in southwestern North America (E. cutleri-E. aspera, E. californica-E. trifurca and E. torreyana-E. viridis) is inferred to have occurred in the Late Miocene to Pliocene and for the sister species pair E. antisyphilitica-E. coryi distributed in the southern United States and northeastern Mexico, it was inferred from the Pliocene to Pleistocene. The orogenetic and climatic changes documented for these regions related to expansion of arid lands, may have contributed to the diversification in North American Ephedra, rather than adaptations to new climatic conditions. Copyright © 2012 Elsevier Inc. All rights reserved.

Refining the conditions for sympatric ecological speciation.

PubMed

Débarre, F

2012-12-01

Can speciation occur in a single population when different types of resources are available, in the absence of any geographical isolation, or any spatial or temporal variation in selection? The controversial topics of sympatric speciation and ecological speciation have already stimulated many theoretical studies, most of them agreeing on the fact that mechanisms generating disruptive selection, some level of assortment, and enough heterogeneity in the available resources, are critical for sympatric speciation to occur. Few studies, however, have combined the three factors and investigated their interactions. In this article, I analytically derive conditions for sympatric speciation in a general model where the distribution of resources can be uni- or bimodal, and where a parameter controls the range of resources that an individual can exploit. This approach bridges the gap between models of a unimodal continuum of resources and Levene-type models with discrete resources. I then test these conditions against simulation results from a recently published article (Thibert-Plante & Hendry, 2011, J. Evol. Biol. 24: 2186-2196) and confirm that sympatric ecological speciation is favoured when (i) selection is disruptive (i.e. individuals with an intermediate trait are at a local fitness minimum), (ii) resources are differentiated enough and (iii) mating is assortative. I also discuss the role of mating preference functions and the need (or lack thereof) for bimodality in resource distributions for diversification. © 2012 The Author. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

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

Monte Carlo simulations of parapatric speciation

NASA Astrophysics Data System (ADS)

Schwämmle, V.; Sousa, A. O.; de Oliveira, S. M.

2006-06-01

Parapatric speciation is studied using an individual-based model with sexual reproduction. We combine the theory of mutation accumulation for biological ageing with an environmental selection pressure that varies according to the individuals geographical positions and phenotypic traits. Fluctuations and genetic diversity of large populations are crucial ingredients to model the features of evolutionary branching and are intrinsic properties of the model. Its implementation on a spatial lattice gives interesting insights into the population dynamics of speciation on a geographical landscape and the disruptive selection that leads to the divergence of phenotypes. Our results suggest that assortative mating is not an obligatory ingredient to obtain speciation in large populations at low gene flow.

Anagenesis, Cladogenesis, and Speciation on Islands.

PubMed

Emerson, Brent C; Patiño, Jairo

2018-05-03

Anagenesis and cladogenesis are fundamental evolutionary concepts, but are increasingly being adopted as speciation models in the field of island biogeography. Here, we review the origin of the terms 'anagenetic' and 'cladogenetic' speciation, critique their utility, and finally suggest alternative terminology that better describes the geographical relationships of insular sister species. Copyright © 2018 Elsevier Ltd. All rights reserved.

Organotin speciation in environmental matrices by automated on-line hydride generation-programmed temperature vaporization-capillary gas chromatography-mass spectrometry detection.

PubMed

Serra, H; Nogueira, J M F

2005-11-11

In the present contribution, a new automated on-line hydride generation methodology was developed for dibutyltin and tributyltin speciation at the trace level, using a programmable temperature-vaporizing inlet followed by capillary gas chromatography coupled to mass spectrometry in the selected ion-monitoring mode acquisition (PTV-GC/MS(SIM)). The methodology involves a sequence defined by two running methods, the first one configured for hydride generation with sodium tetrahydroborate as derivatising agent and the second configured for speciation purposes, using a conventional autosampler and data acquisition controlled by the instrument's software. From the method-development experiments, it had been established that injector configuration has a great effect on the speciation of the actual methodology, particularly, the initial inlet temperature (-20 degrees C; He: 150 ml/min), injection volume (2 microl) and solvent characteristics using the solvent venting mode. Under optimized conditions, a remarkable instrumental performance including very good precision (RSD < 4%), excellent linear dynamic range (up to 50 microg/ml) and limits of detection of 0.12 microg/ml and 9 ng/ml, were obtained for dibutyltin and tributyltin, respectively. The feasibility of the present methodology was validated through assays upon in-house spiked water (2 ng/ml) and a certified reference sediment matrix (Community Bureau of Reference, CRM 462, Nr. 330 dibutyltin: 68+/-12 ng/g; tributyltin: 54+/-15 ng/g on dry mass basis), using liquid-liquid extraction (LLE) and solid-phase extraction (SPE) sample enrichment and multiple injections (2 x 5 microl) for sensitivity enhancement. The methodology evidenced high reproducibility, is easy to work-up, sensitive and showed to be a suitable alternative to replace the currently dedicated analytical systems for organotin speciation in environmental matrices at the trace level.

Ecology, sexual selection and speciation.

PubMed

Maan, Martine E; Seehausen, Ole

2011-06-01

The spectacular diversity in sexually selected traits among animal taxa has inspired the hypothesis that divergent sexual selection can drive speciation. Unfortunately, speciation biologists often consider sexual selection in isolation from natural selection, even though sexually selected traits evolve in an ecological context: both preferences and traits are often subject to natural selection. Conversely, while behavioural ecologists may address ecological effects on sexual communication, they rarely measure the consequences for population divergence. Herein, we review the empirical literature addressing the mechanisms by which natural selection and sexual selection can interact during speciation. We find that convincing evidence for any of these scenarios is thin. However, the available data strongly support various diversifying effects that emerge from interactions between sexual selection and environmental heterogeneity. We suggest that evaluating the evolutionary consequences of these effects requires a better integration of behavioural, ecological and evolutionary research. © 2011 Blackwell Publishing Ltd/CNRS.

AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.

PubMed

Schaefer, Nathan K; Shapiro, Beth; Green, Richard E

2017-04-04

Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA. We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage. AD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool.

How humans drive speciation as well as extinction

PubMed Central

Maron, M.

2016-01-01

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity. PMID:27358365

How humans drive speciation as well as extinction.

PubMed

Bull, J W; Maron, M

2016-06-29

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation-and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon 'no net loss' conservation literature-considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity. © 2016 The Author(s).

Speciation in fungal and oomycete plant pathogens

USDA-ARS?s Scientific Manuscript database

The process of speciation by definition involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed ...

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

PubMed

Pinho, Catarina; Faria, Rui

2016-04-01

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

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].

Considerations in As analysis and speciation

USGS Publications Warehouse

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

1998-01-01

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

Correcting for sequencing error in maximum likelihood phylogeny inference.

PubMed

Kuhner, Mary K; McGill, James

2014-11-04

Accurate phylogenies are critical to taxonomy as well as studies of speciation processes and other evolutionary patterns. Accurate branch lengths in phylogenies are critical for dating and rate measurements. Such accuracy may be jeopardized by unacknowledged sequencing error. We use simulated data to test a correction for DNA sequencing error in maximum likelihood phylogeny inference. Over a wide range of data polymorphism and true error rate, we found that correcting for sequencing error improves recovery of the branch lengths, even if the assumed error rate is up to twice the true error rate. Low error rates have little effect on recovery of the topology. When error is high, correction improves topological inference; however, when error is extremely high, using an assumed error rate greater than the true error rate leads to poor recovery of both topology and branch lengths. The error correction approach tested here was proposed in 2004 but has not been widely used, perhaps because researchers do not want to commit to an estimate of the error rate. This study shows that correction with an approximate error rate is generally preferable to ignoring the issue. Copyright © 2014 Kuhner and McGill.

The reality and importance of founder speciation in evolution.

PubMed

Templeton, Alan R

2008-05-01

A founder event occurs when a new population is established from a small number of individuals drawn from a large ancestral population. Mayr proposed that genetic drift in an isolated founder population could alter the selective forces in an epistatic system, an observation supported by recent studies. Carson argued that a period of relaxed selection could occur when a founder population is in an open ecological niche, allowing rapid population growth after the founder event. Selectable genetic variation can actually increase during this founder-flush phase due to recombination, enhanced survival of advantageous mutations, and the conversion of non-additive genetic variance into additive variance in an epistatic system, another empirically confirmed prediction. Templeton combined the theories of Mayr and Carson with population genetic models to predict the conditions under which founder events can contribute to speciation, and these predictions are strongly confirmed by the empirical literature. Much of the criticism of founder speciation is based upon equating founder speciation to an adaptive peak shift opposed by selection. However, Mayr, Carson and Templeton all modeled a positive interaction of selection and drift, and Templeton showed that founder speciation is incompatible with peak-shift conditions. Although rare, founder speciation can have a disproportionate importance in adaptive innovation and radiation, and examples are given to show that "rare" does not mean "unimportant" in evolution. Founder speciation also interacts with other speciation mechanisms such that a speciation event is not a one-dimensional process due to either selection alone or drift alone. (c) 2008 Wiley Periodicals, Inc.

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...

Ephemeral ecological speciation and the latitudinal biodiversity gradient.

PubMed

Cutter, Asher D; Gray, Jeremy C

2016-10-01

The richness of biodiversity in the tropics compared to high-latitude parts of the world forms one of the most globally conspicuous patterns in biology, and yet few hypotheses aim to explain this phenomenon in terms of explicit microevolutionary mechanisms of speciation and extinction. We link population genetic processes of selection and adaptation to speciation and extinction by way of their interaction with environmental factors to drive global scale macroecological patterns. High-latitude regions are both cradle and grave with respect to species diversification. In particular, we point to a conceptual equivalence of "environmental harshness" and "hard selection" as eco-evolutionary drivers of local adaptation and ecological speciation. By describing how ecological speciation likely occurs more readily at high latitudes, with such nascent species especially prone to extinction by fusion, we derive the ephemeral ecological speciation hypothesis as an integrative mechanistic explanation for latitudinal gradients in species turnover and the net accumulation of biodiversity. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

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

PubMed Central

Harrison, Alexis; Mahler, D. Luke; Castañeda, María del Rosario; Glor, Richard E.; Herrel, Anthony; Stuart, Yoel E.; Losos, Jonathan B.

2016-01-01

Phenotypic traits may be linked to speciation in two distinct ways: character values may influence the rate of speciation or diversification in the trait may be associated with speciation events. Traits involved in signal transmission, such as the dewlap of Anolis lizards, are often involved in the speciation process. The dewlap is an important visual signal with roles in species recognition and sexual selection, and dewlaps vary among species in relative size as well as colour and pattern. We compile a dataset of relative dewlap size digitized from photographs of 184 anole species from across the genus' geographical range. We use phylogenetic comparative methods to test two hypotheses: that larger dewlaps are associated with higher speciation rates, and that relative dewlap area diversifies according to a speciational model of evolution. We find no evidence of trait-dependent speciation, indicating that larger signals do not enhance any role the dewlap has in promoting speciation. Instead, we find a signal of mixed speciational and gradual trait evolution, with a particularly strong signal of speciational change in the dewlaps of mainland lineages. This indicates that dewlap size diversifies in association with the speciation process, suggesting that divergent selection may play a role in the macroevolution of this signalling trait. PMID:28003450

Ecological Impacts of Reverse Speciation in Threespine Stickleback.

PubMed

Rudman, Seth M; Schluter, Dolph

2016-02-22

Young species are highly prone to extinction via increased gene flow after human-caused environmental changes. This mechanism of biodiversity loss, often termed reverse speciation or introgressive extinction, is of exceptional interest because the parent species are typically highly differentiated ecologically. Reverse speciation events are potentially powerful case studies for the role of evolution in driving ecological changes, as the phenotypic shifts associated with introgressive extinction can be large and they occur over particularly short timescales. Furthermore, reverse speciation can lead to novel phenotypes, which may in turn produce novel ecological effects. Here we investigate the ecological shift associated with reverse speciation in threespine stickleback fish using a field study and a replicated experiment. We find that an instance of introgressive extinction had cascading ecological consequences that altered the abundance of both aquatic prey and the pupating aquatic insects that emerged into the terrestrial ecosystem. The community and ecosystem impacts of reverse speciation were novel, and yet they were also predictable based on ecological and morphological considerations. The study suggests that knowledge about the community ecology and changes in functional morphology of a dominant species may lead to some predictive power for the ecological effects of evolutionary change. Moreover, the rapid nature and resultant ecological impacts associated with reverse speciation demonstrates the interplay between biodiversity, evolutionary change, and ecosystem function. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantum state and mode profile tomography by the overlap

NASA Astrophysics Data System (ADS)

Tiedau, J.; Shchesnovich, V. S.; Mogilevtsev, D.; Ansari, V.; Harder, G.; Bartley, T. J.; Korolkova, N.; Silberhorn, Ch

2018-03-01

Any measurement scheme involving interference of quantum states of the electromagnetic field necessarily mixes information about the spatiotemporal structure of these fields and quantum states in the recorded data. We show that in this case, a trade-off is possible between extracting information about the quantum states and the structure of the underlying fields, with the modal overlap being either a goal or a convenient tool of the reconstruction. We show that varying quantum states in a controlled way allows one to infer temporal profiles of modes. Vice versa, for the known quantum state of the probe and controlled variable overlap, one can infer the quantum state of the signal. We demonstrate this trade-off by performing an experiment using the simplest on-off detection in an unbalanced weak homodyning scheme. For the single-mode case, we demonstrate experimentally inference of the overlap and a few-photon signal state. Moreover, we show theoretically that the same single-detector scheme is sufficient even for arbitrary multi-mode fields.

Long-Term Evolution of the Luteoviridae: Time Scale and Mode of Virus Speciation▿ †

PubMed Central

Pagán, Israel; Holmes, Edward C.

2010-01-01

Despite their importance as agents of emerging disease, the time scale and evolutionary processes that shape the appearance of new viral species are largely unknown. To address these issues, we analyzed intra- and interspecific evolutionary processes in the Luteoviridae family of plant RNA viruses. Using the coat protein gene of 12 members of the family, we determined their phylogenetic relationships, rates of nucleotide substitution, times to common ancestry, and patterns of speciation. An associated multigene analysis enabled us to infer the nature of selection pressures and the genomic distribution of recombination events. Although rates of evolutionary change and selection pressures varied among genes and species and were lower in some overlapping gene regions, all fell within the range of those seen in animal RNA viruses. Recombination breakpoints were commonly observed at gene boundaries but less so within genes. Our molecular clock analysis suggested that the origin of the currently circulating Luteoviridae species occurred within the last 4 millennia, with intraspecific genetic diversity arising within the last few hundred years. Speciation within the Luteoviridae may therefore be associated with the expansion of agricultural systems. Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature. PMID:20375155

Speciation gradients and the distribution of biodiversity.

PubMed

Schluter, Dolph; Pennell, Matthew W

2017-05-31

Global patterns of biodiversity are influenced by spatial and environmental variations in the rate at which new species form. We relate variations in speciation rates to six key patterns of biodiversity worldwide, including the species-area relationship, latitudinal gradients in species and genetic diversity, and between-habitat differences in species richness. Although they sometimes mirror biodiversity patterns, recent rates of speciation, at the tip of the tree of life, are often highest where species richness is low. Speciation gradients therefore shape, but are also shaped by, biodiversity gradients and are often more useful for predicting future patterns of biodiversity than for interpreting the past.

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

PubMed Central

Hobolth, Asger; Dutheil, Julien Y.; Hawks, John; Schierup, Mikkel H.; Mailund, Thomas

2011-01-01

We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent hidden Markov model (HMM) framework. We find ILS present in ∼1% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. The existence of ILS is validated with simulations, site pattern analysis, and analysis of rare genomic events. The existence of ILS allows us to disentangle the time of isolation of humans and orangutans (the speciation time) from the genetic divergence time, and we find speciation to be as recent as 9–13 million years ago (Mya; contingent on the calibration point). The analyses provide further support for a recent speciation of human and chimpanzee at ∼4 Mya and a diverse ancestor of human and chimpanzee with an effective population size of about 50,000 individuals. Posterior decoding infers ILS for each nucleotide in the genome, and we use this to deduce patterns of selection in the ancestral species. We demonstrate the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS was found to be reduced in exons and gene-dense regions when we control for confounding factors such as GC content and recombination rate. Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny. PMID:21270173

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.

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

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...

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

Co-speciation in bedbug Wolbachia parallel the pattern in nematode hosts.

PubMed

Balvín, Ondřej; Roth, Steffen; Talbot, Benoit; Reinhardt, Klaus

2018-06-11

Wolbachia bacteria, vertically transmitted intracellular endosymbionts, are associated with two major host taxa in which they show strikingly different symbiotic modes. In some taxa of filarial nematodes, where Wolbachia are strictly obligately beneficial to the host, they show complete within- and among-species prevalence as well as co-phylogeny with their hosts. In arthropods, Wolbachia usually are parasitic; if beneficial effects occurs, they can be facultative or obligate, related to host reproduction. In arthropods, the prevalence of Wolbachia varies within and among taxa, and no co-speciation events are known. However, one arthropod species, the common bedbug Cimex lectularius was recently found to be dependent on the provision of biotin and riboflavin by Wolbachia, representing a unique case of Wolbachia providing nutritional and obligate benefits to an arthropod host, perhaps even in a mutualistic manner. Using the presence of presumably functional biotin gene copies, our study demonstrates that the obligate relationship is maintained at least in 10 out of 15 species of the genera Cimex and Paracimex. The remaining five species harboured Wolbachia as well, demonstrating the first known case of 100% prevalence of Wolbachia among higher arthropod taxa. Moreover, we show the predicted co-cladogenesis between Wolbachia and their bedbug hosts, also as the first described case of Wolbachia co-speciation in arthropods.

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...

Molybdenum speciation and burial pathway in weakly sulfidic environments: Insights from XAFS

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

Wagner, Meghan; Chappaz, Anthony; Lyons, Timothy W.

Sedimentary molybdenum (Mo) accumulation is a robust proxy for sulfidic conditions in both modern and ancient aquatic systems and has been used to infer changing marine redox chemistry throughout Earth’s history. Accurate interpretation of any proxy requires a comprehensive understanding of its biogeochemical cycling, but knowledge gaps remain concerning the geochemical mechanism(s) leading to Mo burial in anoxic sediments. Better characterization of Mo speciation should provide mechanistic insight into sedimentary Mo accumulation, and therefore in this study we investigate Mo speciation from both modern (Castle Lake, USA) and ancient (Doushantuo Formation, China) environments using X-ray Absorption Near Edge Structure (XANES)more » spectroscopy. By utilizing a series of laboratory-synthesized oxythiomolybdate complexes—many containing organic ligands—we expand the number of available standards to encompass a greater range of known Mo chemistry and test the linkage between Mo and total organic carbon (TOC). In weakly euxinic systems ([H 2S (aq)] < 11 µM), or where sulfide is restricted to pore waters, natural samples are best represented by a linear combination of MoO 3, MoO xS 4-x 2- (intermediate thiomolybdates), and [MoO x(cat) 4-x] 2- (cat = catechol, x = 2 or 3). These results suggest a revised model for how Mo accumulates in weakly sulfidic sediments, including a previously unrecognized role for organic matter in early sequestration of Mo and a de-emphasized importance for MoS 4 2- (tetrathiomolybdate).« less

Molybdenum speciation and burial pathway in weakly sulfidic environments: Insights from XAFS

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

Wagner, Meghan; Chappaz, Anthony; Lyons, Timothy W.

Sedimentary molybdenum (Mo) accumulation is a robust proxy for sulfidic conditions in both modern and ancient aquatic systems and has been used to infer changing marine redox chemistry throughout Earth’s history. Accurate interpretation of any proxy requires a comprehensive understanding of its biogeochemical cycling, but knowledge gaps remain concerning the geochemical mechanism(s) leading to Mo burial in anoxic sediments. Better characterization of Mo speciation should provide mechanistic insight into sedimentary Mo accumulation, and therefore in this study we investigate Mo speciation from both modern (Castle Lake, USA) and ancient (Doushantuo Formation, China) environments using X-ray Absorption Near Edge Structure (XANES)more » spectroscopy. By utilizing a series of laboratory-synthesized oxythiomolybdate complexes—many containing organic ligands—we expand the number of available standards to encompass a greater range of known Mo chemistry and test the linkage between Mo and total organic carbon (TOC). In weakly euxinic systems ([H2S(aq)] < 11 µM), or where sulfide is restricted to pore waters, natural samples are best represented by a linear combination of MoO3, MoOxS4-x2- (intermediate thiomolybdates), and [MoOx(cat)4-x]2- (cat = catechol, x = 2 or 3). These results suggest a revised model for how Mo accumulates in weakly sulfidic sediments, including a previously unrecognized role for organic matter in early sequestration of Mo and a de-emphasized importance for MoS42- (tetrathiomolybdate).« less

Molybdenum speciation and burial pathway in weakly sulfidic environments: Insights from XAFS

NASA Astrophysics Data System (ADS)

Wagner, Meghan; Chappaz, Anthony; Lyons, Timothy W.

2017-06-01

Sedimentary molybdenum (Mo) accumulation is a robust proxy for sulfidic conditions in both modern and ancient aquatic systems and has been used to infer changing marine redox chemistry throughout Earth's history. Accurate interpretation of any proxy requires a comprehensive understanding of its biogeochemical cycling, but knowledge gaps remain concerning the geochemical mechanism(s) leading to Mo burial in anoxic sediments. Better characterization of Mo speciation should provide mechanistic insight into sedimentary Mo accumulation, and therefore in this study we investigate Mo speciation from both modern (Castle Lake, USA) and ancient (Doushantuo Formation, China) environments using X-ray Absorption Near Edge Structure (XANES) spectroscopy. By utilizing a series of laboratory-synthesized oxythiomolybdate complexes-many containing organic ligands-we expand the number of available standards to encompass a greater range of known Mo chemistry and test the linkage between Mo and total organic carbon (TOC). In weakly euxinic systems ([H2S(aq)] < 11 μM), or where sulfide is restricted to pore waters, natural samples are best represented by a linear combination of MoO3, MoOxS4-x2- (intermediate thiomolybdates), and [MoOx(cat)4-x]2- (cat = catechol, x = 2 or 3). These results suggest a revised model for how Mo accumulates in weakly sulfidic sediments, including a previously unrecognized role for organic matter in early sequestration of Mo and a de-emphasized importance for MoS42- (tetrathiomolybdate).

[Geographical variation in the species Montivagum dihumerale and speciation in chigger mites (Acari: Trombiculidae)].

PubMed

Stekol'nikov, A A

2006-01-01

Intraspecific morphological variation of the chigger mite species Montivagum dihumerale (Traub et Nadchatram, 1967) is studied. Eco-geographic rules of the variation are revealed. General size of mites is found to be increased along with the rise of the high-mountain character of the landscape in the collection localities. The numbers of idiosomal setae are varied independently from the size parameters and geographically close populations are proved to be the most similar by these characters. At the same time, numbers of the setae of different types play the leading role in the discrimination of closely related Montivagum species, while the eco-geographical rules have not been found in this genus at the level of interspecific differences. As a result, the hypothesis is set up, that a significant degree of isolation of local populations separated from each other by high mountain ranges of the Central Asia is the main factor of speciation in the genus Montivagum. Regional character of this speciation mode is confirmed by the comparison with other chigger mites taxa.

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.

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.'

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

PubMed

Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

2015-09-24

A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

Chemical Speciation - General Information

EPA Pesticide Factsheets

This page includes general information about the Chemical Speciation Network that is not covered on the main page. Commonly visited documents, including calendars, site lists, and historical files for the program are listed here

Arsenic Speciation of Terrestrial Invertebrates

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

Moriarty, M.M.; Koch, I.; Gordon, R.A.

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 absorptionmore » 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.« less

The role of ecological divergence in speciation between intertidal and subtidal Scoloplos armiger (Polychaeta, Orbiniidae)

NASA Astrophysics Data System (ADS)

Kruse, Inken; Strasser, Matthias; Thiermann, Frank

2004-02-01

The concept of ecological speciation implies that habitat differences may split a species by strong selection and rapid adaptation even under sympatric conditions. Studies on the polychaete Scoloplos armiger in the Wadden Sea (North Sea) indicate sibling species existing in sympatry: the intertidal 'Type I' with holobenthic development out of egg cocoons and the subtidal 'Type S' producing pelagic larvae. In the current study, Types I and S are compared in habitat-related traits of reproductive timing and physiological response to hypoxia and sulphide. Spawnings of Type I and Type S recorded over six years overlap in spring and both appear to be triggered by a rise in seawater temperature above 5 °C. Type S exhibits an additional autumn spawning (at seawater temperatures around 10 °C) which was previously unknown and is absent in Type I. The overall abundance of pelagic larvae in the Wadden Sea is higher in spring than in autumn. Tolerance of both sulphide and hypoxia was lower in Type S than in Type I. This correlates with a 5 to 10-fold lower sulphide concentration in the subtidal compared to the intertidal habitat. Physiological tolerance and divergence in developmental mode appear as traits which may have led to reproductive isolation between Type I and Type S. Their role in allopatric and sympatric speciation scenarios in S. armiger is discussed. Since the pelagic dispersal mode has been neglected so far, a reassessment of population dynamics models for S. armiger is suggested.

Sympatric speciation as a consequence of male pregnancy in seahorses

PubMed Central

Jones, Adam G.; Moore, Glenn I.; Kvarnemo, Charlotta; Walker, DeEtte; Avise, John C.

2003-01-01

The phenomenon of male pregnancy in the family Syngnathidae (seahorses, pipefishes, and sea dragons) undeniably has sculpted the course of behavioral evolution in these fishes. Here we explore another potentially important but previously unrecognized consequence of male pregnancy: a predisposition for sympatric speciation. We present microsatellite data on genetic parentage that show that seahorses mate size-assortatively in nature. We then develop a quantitative genetic model based on these empirical findings to demonstrate that sympatric speciation indeed can occur under this mating regime in response to weak disruptive selection on body size. We also evaluate phylogenetic evidence bearing on sympatric speciation by asking whether tiny seahorse species are sister taxa to large sympatric relatives. Overall, our results indicate that sympatric speciation is a plausible mechanism for the diversification of seahorses, and that assortative mating (in this case as a result of male parental care) may warrant broader attention in the speciation process for some other taxonomic groups as well. PMID:12732712

Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation.

PubMed

Corl, Ammon; Davis, Alison R; Kuchta, Shawn R; Sinervo, Barry

2010-03-02

Polymorphism may play an important role in speciation because new species could originate from the distinctive morphs observed in polymorphic populations. However, much remains to be understood about the process by which morphs found new species. To detail the steps of this mode of speciation, we studied the geographic variation and evolutionary history of a throat color polymorphism that distinguishes the "rock-paper-scissors" mating strategies of the side-blotched lizard, Uta stansburiana. We found that the polymorphism is geographically widespread and has been maintained for millions of years. However, there are many populations with reduced numbers of throat color morphs. Phylogenetic reconstruction showed that the polymorphism is ancestral, but it has been independently lost eight times, often giving rise to morphologically distinct subspecies/species. Changes to the polymorphism likely involved selection because the allele for one particular male strategy, the "sneaker" morph, has been lost in all cases. Polymorphism loss was associated with accelerated evolution of male size, female size, and sexual dimorphism, which suggests that polymorphism loss can promote rapid divergence among populations and aid species formation.

New analytic results for speciation times in neutral models.

PubMed

Gernhard, Tanja

2008-05-01

In this paper, we investigate the standard Yule model, and a recently studied model of speciation and extinction, the "critical branching process." We develop an analytic way-as opposed to the common simulation approach-for calculating the speciation times in a reconstructed phylogenetic tree. Simple expressions for the density and the moments of the speciation times are obtained. Methods for dating a speciation event become valuable, if for the reconstructed phylogenetic trees, no time scale is available. A missing time scale could be due to supertree methods, morphological data, or molecular data which violates the molecular clock. Our analytic approach is, in particular, useful for the model with extinction, since simulations of birth-death processes which are conditioned on obtaining n extant species today are quite delicate. Further, simulations are very time consuming for big n under both models.

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

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.

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.

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

NASA Astrophysics Data System (ADS)

Pérez-Corona, Teresa; Madrid-Albarrán, Yolanda; Cámara, Carmen; Beceiro, Elisa

1998-02-01

The use of living organisms for metal preconcentration and speciation is discussed. Among substrates, Saccharomyces cerevisiae baker's yeast has been successfully used for the speciation of mercury [Hg(II) and CH 3Hg +], selenium [Se(IV) and Se(VI)] and antimony [Sb(III) and Sb(V)]. To illustrate the capabilities of these organisms, the analytical performance of baker's yeast immobilized on silica gel for on-line preconcentration and speciation of Hg(II) and methylmercury is reported. The immobilized cells were packed in a PTFE microcolumn, through which mixtures of organic and inorganic mercury solutions were passed. Retention of inorganic and organic mercury solutions took place simultaneously, with the former retained in the silica and the latter on the yeast. The efficiency uptake for both species was higher than 95% over a wide pH range. The speciation was carried out by selective and sequential elution with 0.02 mol L -1 HCl for methylmercury and 0.8 mol L -1 CN - for Hg(II). This method allows both preconcentration and speciation of mercury. The preconcentration factors were around 15 and 100 for methylmercury and mercury(II), respectively. The method has been successfully applied to spiked sea water samples.

Characterization of Technetium Speciation in Cast Stone

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

Um, Wooyong; Jung, Hun Bok; Wang, Guohui

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 frommore » 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.« less

Modal Decomposition of TTV: Inferring Planet Masses and Eccentricities

NASA Astrophysics Data System (ADS)

Linial, Itai; Gilbaum, Shmuel; Sari, Re’em

2018-06-01

Transit timing variations (TTVs) are a powerful tool for characterizing the properties of transiting exoplanets. However, inferring planet properties from the observed timing variations is a challenging task, which is usually addressed by extensive numerical searches. We propose a new, computationally inexpensive method for inverting TTV signals in a planetary system of two transiting planets. To the lowest order in planetary masses and eccentricities, TTVs can be expressed as a linear combination of three functions, which we call the TTV modes. These functions depend only on the planets’ linear ephemerides, and can be either constructed analytically, or by performing three orbital integrations of the three-body system. Given a TTV signal, the underlying physical parameters are found by decomposing the data as a sum of the TTV modes. We demonstrate the use of this method by inferring the mass and eccentricity of six Kepler planets that were previously characterized in other studies. Finally we discuss the implications and future prospects of our new method.

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.

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 ...

Anaerobic Digestion Alters Copper and Zinc Speciation.

PubMed

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

2017-09-19

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

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...

Cloud iron speciation: Experimental simulations

NASA Astrophysics Data System (ADS)

Sofikitis, A. M.; Colin, J. L.; Desboeufs, K. V.; Losno, R.

2003-04-01

The aim of our contribution is to identify major processes controlling iron speciation in the atmospheric aqueous phase. Fe is known to participate in a variety of redox reactions in cloud chemistry, as well as controlling free radical production in the troposphere. Iron cycling is slower than cycles with other catalytic transition metals (Cu, Mn). The residence time of each iron species is around ten minutes, this allows analytical separation and determination of each iron redox species and therefore its ratio. As the only source of trace metals in aqueous atmospheric phase is due to the solubilization of aerosols, we present here dissolution rate measurements obtained by laboratory experiments with an open flow reactor. This reactor enables us to reproduce the dissolution of a particle in aqueous atmospheric water. The dissolution rate and the speciation of iron are dependent on the mineralogy of the solid phase. Our experiments included Goethite, hematite and vermiculite, which are typical mineral constituents of dust particles. Comparisons were made with natural loess which is a blend of various crystalline and amorphous phases. We will present results of crustal origin particles dissolution experiments where kinetic parameters are determined, including iron speciation. Major functions of variation are pH and photochemistry in the aqueous weathering solution.

Selenium analysis in waters. Part 2: Speciation methods.

PubMed

LeBlanc, Kelly L; Kumkrong, Paramee; Mercier, Patrick H J; Mester, Zoltán

2018-06-21

In aquatic ecosystems, there is often no correlation between the total concentration of selenium present in the water column and the toxic effects observed in that environment. This is due, in part, to the variation in the bioavailability of different selenium species to organisms at the base of the aquatic food chain. The first part of this review (Kumkrong et al., 2018) discusses regulatory framework and standard methodologies for selenium analysis in waters. In this second article, we are reviewing the state of speciation analysis and importance of speciation data for decision makers in industry and regulators. We look in detail at fractionation methods for speciation, including the popular selective sequential hydride generation. We examine advantages and limitations of these methods, in terms of achievable detection limits and interferences from other matrix species, as well as the potential to over- or under-estimate operationally-defined fractions based on the various conversion steps involved in fractionation processes. Additionally, we discuss methods of discrete speciation (through separation methods), their importance in analyzing individual selenium species, difficulties associated with their implementation, as well as ways to overcome these difficulties. We also provide a brief overview of biological treatment methods for the remediation of selenium-contaminated waters. We discuss the importance of selenium speciation in the application of these methods and their potential to actually increase the bioavailability of selenium despite decreasing its total waterborne concentration. Copyright © 2018. Published by Elsevier B.V.

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. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

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

PubMed

Holman, Eric W

2017-11-01

It is known that phylogenetic trees are more imbalanced than expected from a birth-death model with constant rates of speciation and extinction, and also that imbalance can be better fit by allowing the rate of speciation to decrease as the age of the parent species increases. If imbalance is measured in more detail, at nodes within trees as a function of the number of species descended from the nodes, age-dependent models predict levels of imbalance comparable to real trees for small numbers of descendent species, but predicted imbalance approaches an asymptote not found in real trees as the number of descendent species becomes large. Age-dependence must therefore be complemented by another process such as inheritance of different rates along different lineages, which is known to predict insufficient imbalance at nodes with few descendent species, but can predict increasing imbalance with increasing numbers of descendent species. [Crump-Mode-Jagers process; diversification; macroevolution; taxon sampling; tree of life.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

[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.

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

PubMed Central

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

2012-01-01

The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record. PMID:23043116

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.

Perturbative momentum transport in MAST L-mode plasmas

DOE PAGES

Guttenfelder, W.; Field, A. R.; Lupelli, I.; ...

2017-03-28

Non-axisymmetric magnetic fields are used to perturbatively probe momentum transport physics in MAST L-mode plasmas. The low beta L-mode target was chosen to complement previous experiments conducted in high beta NSTX H-mode plasmas (beta N = 3.5-4.6) where an inward momentum pinch was measured. In those cases quasi-linear gyrokinetic simulations of unstable ballooning micro-instabilities predict weak or outward momentum convection, in contrast to the measurements. The weak pinch was predicted to be due to both electromagnetic effects at high beta and low aspect ratio minimizing the symmetry-breaking of the instabilities responsible for momentum transport. In an attempt to lessen thesemore » electromagnetic effects at low aspect ratio, perturbative experiments were run in MAST L-mode discharges at lower beta (beta N = 2). The perturbative transport analysis used the time-dependent response following the termination of applied 3D fields that briefly brake the plasma rotation ( similar to the NSTX H-mode experiments). Assuming time-invariant diffusive (chi(phi))and convective (V-phi) transport coefficients, an inward pinch is inferred with magnitudes, (RV phi/chi(phi)) = (-1)-(-9), similar to those found in NSTX H-modes and in conventional tokamaks. However, if experimental uncertainties due to non-stationary conditions during and after the applied 3D field are considered, a weak pinch or even outward convection is inferred, ( RV phi/chi(phi)) = (-1)-(+5). Linear gyrokinetic simulations indicate that for these lower beta L-modes, the predicted momentum pinch is predicted to be relatively small, ( RV phi/chi(phi))(sim) approximate to -1. While this falls within the experimentally inferred range, the uncertainties are practically too large to quantitatively validate the predictions. Challenges and implications for this particular experimental technique are discussed, as well as additional possible physical mechanisms that may be important in understanding momentum

Perturbative momentum transport in MAST L-mode plasmas

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

Guttenfelder, W.; Field, A. R.; Lupelli, I.

Non-axisymmetric magnetic fields are used to perturbatively probe momentum transport physics in MAST L-mode plasmas. The low beta L-mode target was chosen to complement previous experiments conducted in high beta NSTX H-mode plasmas (beta N = 3.5-4.6) where an inward momentum pinch was measured. In those cases quasi-linear gyrokinetic simulations of unstable ballooning micro-instabilities predict weak or outward momentum convection, in contrast to the measurements. The weak pinch was predicted to be due to both electromagnetic effects at high beta and low aspect ratio minimizing the symmetry-breaking of the instabilities responsible for momentum transport. In an attempt to lessen thesemore » electromagnetic effects at low aspect ratio, perturbative experiments were run in MAST L-mode discharges at lower beta (beta N = 2). The perturbative transport analysis used the time-dependent response following the termination of applied 3D fields that briefly brake the plasma rotation ( similar to the NSTX H-mode experiments). Assuming time-invariant diffusive (chi(phi))and convective (V-phi) transport coefficients, an inward pinch is inferred with magnitudes, (RV phi/chi(phi)) = (-1)-(-9), similar to those found in NSTX H-modes and in conventional tokamaks. However, if experimental uncertainties due to non-stationary conditions during and after the applied 3D field are considered, a weak pinch or even outward convection is inferred, ( RV phi/chi(phi)) = (-1)-(+5). Linear gyrokinetic simulations indicate that for these lower beta L-modes, the predicted momentum pinch is predicted to be relatively small, ( RV phi/chi(phi))(sim) approximate to -1. While this falls within the experimentally inferred range, the uncertainties are practically too large to quantitatively validate the predictions. Challenges and implications for this particular experimental technique are discussed, as well as additional possible physical mechanisms that may be important in understanding momentum

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.

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.

Arsenic speciation and sorption in natural environments

USGS Publications Warehouse

Campbell, Kate M.; Nordstrom, D. Kirk

2014-01-01

Aqueous arsenic speciation, or the chemical forms in which arsenic exists in water, is a challenging, interesting, and complicated aspect of environmental arsenic geochemistry. Arsenic has the ability to form a wide range of chemical bonds with carbon, oxygen, hydrogen, and sulfur, resulting in a large variety of compounds that exhibit a host of chemical and biochemical properties. Besides the intriguing chemical diversity, arsenic also has the rare capacity to capture our imaginations in a way that few elements can duplicate: it invokes images of foul play that range from sinister to comedic (e.g., “inheritance powder” and arsenic-spiked elderberry wine). However, the emergence of serious large-scale human health problems from chronic arsenic exposure in drinking water has placed a high priority on understanding environmental arsenic mobility, toxicity, and bioavailability, and chemical speciation is key to these important questions. Ultimately, the purpose of arsenic speciation research is to predict future occurrences, mitigate contamination, and provide successful management of water resources.

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.

Pleistocene phylogeographic effects on avian populations and the speciation process.

PubMed Central

Avise, J C; Walker, D

1998-01-01

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

Ruminant-specific multiple duplication events of PRDM9 before speciation

USDA-ARS?s Scientific Manuscript database

Understanding the genetic and evolutionary mechanisms of speciation genes in sexually reproducing organisms would provide important insights into mammalian reproduction and fitness. PRDM9, a widely known speciation gene, has recently gained attention for its important role in meiotic recombination a...

Speciation of heavy metals in landfill leachate: a review.

PubMed

Baun, Dorthe L; Christensen, Thomas H

2004-02-01

The literature was reviewed with respect to metal speciation methods in aquatic samples specifically emphasizing speciation of heavy metals in landfill leachate. Speciation here refers to physical fractionation (particulate, colloidal, dissolved), chemical fractionation (organic complexes, inorganic complexes, free metal ions), as well as computer-based thermodynamic models. Relatively few landfill leachate samples have been speciated in detail (less than 30) representing only a few landfills (less than 15). This suggests that our knowledge about metal species in landfill leachate still is indicative. In spite of the limited database and the different definitions of the dissolved fraction (< 0.45 microm or < 0.001 microm) the studies consistently show that colloids as well as organic and inorganic complexes are important for all heavy metals in landfill leachate. The free metal ion constitutes less than 30%, typically less than 10%, of the total metal concentration. This has significant implications for sampling, since no standardized procedures exist, and for assessing the content of metals in leachate in the context of its treatment, toxicity and migration in aquifers.

Tempo and mode of genomic mutations unveil human evolutionary history.

PubMed

Hara, Yuichiro

2015-01-01

Mutations that have occurred in human genomes provide insight into various aspects of evolutionary history such as speciation events and degrees of natural selection. Comparing genome sequences between human and great apes or among humans is a feasible approach for inferring human evolutionary history. Recent advances in high-throughput or so-called 'next-generation' DNA sequencing technologies have enabled the sequencing of thousands of individual human genomes, as well as a variety of reference genomes of hominids, many of which are publicly available. These sequence data can help to unveil the detailed demographic history of the lineage leading to humans as well as the explosion of modern human population size in the last several thousand years. In addition, high-throughput sequencing illustrates the tempo and mode of de novo mutations, which are producing human genetic variation at this moment. Pedigree-based human genome sequencing has shown that mutation rates vary significantly across the human genome. These studies have also provided an improved timescale of human evolution, because the mutation rate estimated from pedigree analysis is half that estimated from traditional analyses based on molecular phylogeny. Because of the dramatic reduction in sequencing cost, sequencing on-demand samples designed for specific studies is now also becoming popular. To produce data of sufficient quality to meet the requirements of the study, it is necessary to set an explicit sequencing plan that includes the choice of sample collection methods, sequencing platforms, and number of sequence reads.

Great Salt Lake Composition and Rare Earth Speciation Analysis

DOE Data Explorer

Jiao, Yongqin; Lammers, Laura; Brewer, Aaron

2017-04-19

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

The development of exhaust speciation profiles for commercial jet engines.

DOT National Transportation Integrated Search

2007-10-01

This study reports the emissions of CO, CO2, NOx, Particulate Matter (PM) mass, : speciated PM and speciated hydrocarbons at six thrust settings: 4%, 7%, 30%, 40%, 65% : and 85%, measured from both engines on four parked 737 aircraft at the Oakland :...

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

PubMed Central

Van der Niet, Timotheüs; Peakall, Rod; Johnson, Steven D.

2014-01-01

Background The hypothesis that pollinators have been important drivers of angiosperm diversity dates back to Darwin, and remains an important research topic today. Mounting evidence indicates that pollinators have the potential to drive diversification at several different stages of the evolutionary process. Microevolutionary studies have provided evidence for pollinator-mediated floral adaptation, while macroevolutionary evidence supports a general pattern of pollinator-driven diversification of angiosperms. However, the overarching issue of whether, and how, shifts in pollination system drive plant speciation represents a critical gap in knowledge. Bridging this gap is crucial to fully understand whether pollinator-driven microevolution accounts for the observed macroevolutionary patterns. Testable predictions about pollinator-driven speciation can be derived from the theory of ecological speciation, according to which adaptation (microevolution) and speciation (macroevolution) are directly linked. This theory is a particularly suitable framework for evaluating evidence for the processes underlying shifts in pollination systems and their potential consequences for the evolution of reproductive isolation and speciation. Scope This Viewpoint paper focuses on evidence for the four components of ecological speciation in the context of plant-pollinator interactions, namely (1) the role of pollinators as selective agents, (2) floral trait divergence, including the evolution of ‘pollination ecotypes‘, (3) the geographical context of selection on floral traits, and (4) the role of pollinators in the evolution of reproductive isolation. This Viewpoint also serves as the introduction to a Special Issue on Pollinator-Driven Speciation in Plants. The 13 papers in this Special Issue range from microevolutionary studies of ecotypes to macroevolutionary studies of historical ecological shifts, and span a wide range of geographical areas and plant families. These studies

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

PubMed Central

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

2014-01-01

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

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. Copyright © 2016 Elsevier B.V. All rights reserved.

Biology and toxicology of tellurium explored by speciation analysis.

PubMed

Ogra, Yasumitsu

2017-05-24

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

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).

What initiates speciation in passion-vine butterflies?

PubMed Central

McMillan, W. Owen; Jiggins, Chris D.; Mallet, James

1997-01-01

Studies of the continuum between geographic races and species provide the clearest insights into the causes of speciation. Here we report on mate choice and hybrid viability experiments in a pair of warningly colored butterflies, Heliconius erato and Heliconius himera, that maintain their genetic integrity in the face of hybridization. Hybrid sterility and inviability have been unimportant in the early stages of speciation of these two Heliconius. We find no evidence of reduced fecundity, egg hatch, or larval survival nor increases in developmental time in three generations of hybrid crosses. Instead, speciation in this pair appears to have been catalyzed by the association of strong mating preferences with divergence in warning coloration and ecology. In mate choice experiments, matings between the two species are a tenth as likely as matings within species. F1 hybrids of both sexes mate frequently with both pure forms. However, male F1 progeny from crosses between H. himera mothers and H. erato fathers have somewhat reduced mating success. The strong barrier to gene flow provided by divergence in mate preference is probably enhanced by frequency-dependent predation against hybrids similar to the type known to occur across interracial hybrid zones of H. erato. In addition, the transition between this pair falls at the boundary between wet and dry forest, and rare hybrids may also be selected against because they are poorly adapted to either biotope. These results add to a growing body of evidence that challenge the importance of genomic incompatibilities in the earliest stages of speciation. PMID:9238028

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...

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.

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

Bromine speciation in hydrous haplogranitic melts up to 7 GPa

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

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...

A reconstruction of sexual modes throughout animal evolution.

PubMed

Sasson, Daniel A; Ryan, Joseph F

2017-12-06

Although most extant animals have separate sexes, simultaneous hermaphrodites can be found in lineages throughout the animal kingdom. However, the sexual modes of key ancestral nodes including the last common ancestor (LCA) of all animals remain unclear. Without these data, it is difficult to infer the reproductive-state transitions that occurred early in animal evolution, and thus a broad understanding of the evolution of animal reproduction remains elusive. In this study, we use a composite phylogeny from four previously published studies, two alternative topologies (ctenophores or sponges as sister to the rest of animals), and multiple phylogenetic approaches to conduct the most extensive analysis to date of the evolution of animal sexual modes. Our analyses clarify the sexual mode of many ancestral animal nodes and allow for sound inferences of modal transitions that have occurred in animal history. Our results also indicate that the transition from separate sexes to hermaphroditism has been more common in animal history than the reverse. These results provide the most complete view of the evolution of animal sexual modes to date and provide a framework for future inquiries into the correlation of these transitions with genes, behaviors, and physiology. These results also suggest that mutations promoting hermaphroditism have historically been more likely to invade gonochoristic populations than vice versa.

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.

Ancient tetraploidy and slow molecular evolution in Scaphiophryne: ecological correlates of speciation mode in Malagasy relict amphibians.

PubMed

Vences, Miguel; Aprea, Gennaro; Capriglione, Teresa; Andreone, Franco; Odierna, Gaetano

2002-01-01

Karyotypes of three microhylid frog species of the Malagasy relict genus Scaphiophryne were studied: Scaphiophryne gottlebei, S. madagascariensis and S. spinosa. The latter two showed a plesiomorphic ranoid karyotype of 2n = 26. In contrast, tetraploidy was demonstrated in S. gottlebei, which constitutes an exceptional state among Malagasy amphibians. A combination of different banding techniques and of rDNA-FISH provided evidence for allopolyploidy in the species and for a completed subsequent functional and structural diploidization. Phylogenetic analysis of mitochondrial 16S rDNA sequences revealed a significant deceleration of nucleotide substitution rates in Scaphiophryne. The tetraploidy of S. gottlebei probably occurred early in their radiation. Ecological and behavioural patterns of Scaphiophryne probably favoured intraspecific gene flow and hybridization events, thereby leading to slow molecular substitution rates and to allopolyploid chromosome speciation in S. gottlebei.

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.

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

Transformation of heavy metal speciation during sludge drying: mechanistic insights

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

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

2014-01-30

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

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

PubMed

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

2014-01-30

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

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

PubMed

Tran, Lucy A P

2016-04-01

Biotic and abiotic factors often are treated as mutually exclusive drivers of diversification processes. In this framework, ecological specialists are expected to have higher speciation rates than generalists if abiotic factors are the primary controls on species diversity but lower rates if biotic interactions are more important. Speciation rate is therefore predicted to positively correlate with ecological specialization in the purely abiotic model but negatively correlate in the biotic model. In this study, I show that the positive relationship between ecological specialization and speciation expected from the purely abiotic model is recovered only when a species-specific trait, digestive strategy, is modeled in the terrestrial, herbivorous mammals (Mammalia). This result suggests a more nuanced model in which the response of specialized lineages to abiotic factors is dependent on a biological trait. I also demonstrate that the effect of digestive strategy on the ecological specialization-speciation rate relationship is not due to a difference in either the degree of ecological specialization or the speciation rate between foregut- and hindgut-fermenting mammals. Together, these findings suggest that a biological trait, alongside historical abiotic events, played an important role in shaping mammal speciation at long temporal and large geographic scales.

Geologic drivers of late ordovician faunal change in laurentia: investigating links between tectonics, speciation, and biotic invasions.

PubMed

Wright, David F; Stigall, Alycia L

2013-01-01

Geologic process, including tectonics and global climate change, profoundly impact the evolution of life because they have the propensity to facilitate episodes of biogeographic differentiation and influence patterns of speciation. We investigate causal links between a dramatic faunal turnover and two dominant geologic processes operating within Laurentia during the Late Ordovician: the Taconian Orogeny and GICE related global cooling. We utilize a novel approach for elucidating the relationship between biotic and geologic changes using a time-stratigraphic, species-level evolutionary framework for articulated brachiopods from North America. Phylogenetic biogeographic analyses indicate a fundamental shift in speciation mode-from a vicariance to dispersal dominated macroevolutionary regime-across the boundary between the Sandbian to Katian Stages. This boundary also corresponds to the onset of renewed intensification of tectonic activity and mountain building, the development of an upwelling zone that introduced cool, nutrient-rich waters into the epieric seas of eastern Laurentia, and the GICE isotopic excursion. The synchronicity of these dramatic geologic, oceanographic, and macroevolutionary changes supports the influence of geologic events on biological evolution. Together, the renewed tectonic activity and oceanographic changes facilitated fundamental changes in habitat structure in eastern North America that reduced opportunities for isolation and vicariance. They also facilitated regional biotic dispersal of taxa that led to the subsequent establishment of extrabasinal (=invasive) species and may have led to a suppression of speciation within Laurentian faunas. Phylogenetic biogeographic analysis further indicates that the Richmondian Invasion was a multidirectional regional invasion event that involved taxa immigrating into the Cincinnati region from basins located near the continental margins and within the continental interior.

Soil properties controlling Zn speciation and fractionation in contaminated soils

NASA Astrophysics Data System (ADS)

Jacquat, Olivier; Voegelin, Andreas; Kretzschmar, Ruben

2009-09-01

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

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. Copyright © 2016 Elsevier Inc. All rights reserved.

Mercury speciation with fluorescent gold nanocluster as a probe.

PubMed

Yang, Jian-Yu; Yang, Ting; Wang, Xiao-Yan; Chen, Ming-Li; Yu, Yong-Liang; Wang, Jian-Hua

2018-05-11

Fluorescent nanoparticles are widely used for sensing biologically significant species. However, it is rarely reported for the discrimination or speciation of metal species. In this work, we report for the first time the speciation of mercury (Hg 2+ ) and methylmercury (CH 3 Hg + ) by taking advantage of the fluorescence feature of folic acid-capped gold nanoclusters (FA-AuNCs). FA-Au NCs exhibit an average size of 2.08±0.15 nm and a maximum emission at λ ex /λ em = 280/440 nm with a quantum yield of 27.3%. It is interesting that Hg 2+ causes a significant quench on the fluorescence of FA-Au NCs, whereas CH 3 Hg + leads to a remarkable fluorescence enhancement. Based on this discriminative fluorescent response between Hg 2+ and CH 3 Hg + , a novel nanosensor for the speciation of CH 3 Hg + and Hg 2+ was developed, providing limits of detection (LOD) of 28 nM for Hg 2+ and 25 nM for CH 3 Hg + within 100-1000 nM. This sensing system is highly selective to mercury. Its practical applications were further demonstrated by the analysis of CH 3 Hg + and the speciation of mercury (CH 3 Hg + and Hg 2+ ) in environmental water and fish samples.

Mitochondrial Recombination and Introgression during Speciation by Hybridization.

PubMed

Leducq, Jean-Baptiste; Henault, Mathieu; Charron, Guillaume; Nielly-Thibault, Lou; Terrat, Yves; Fiumera, Heather L; Shapiro, B Jesse; Landry, Christian R

2017-08-01

Genome recombination is a major source of genotypic diversity and contributes to adaptation and speciation following interspecies hybridization. The contribution of recombination in these processes has been thought to be largely limited to the nuclear genome because organelles are mostly uniparentally inherited in animals and plants, which prevents recombination. Unicellular eukaryotes such as budding yeasts do, however, transmit mitochondria biparentally, suggesting that during hybridization, both parents could provide alleles that contribute to mitochondrial functions such as respiration and metabolism in hybrid populations or hybrid species. We examined the dynamics of mitochondrial genome transmission and evolution during speciation by hybridization in the natural budding yeast Saccharomyces paradoxus. Using population-scale mitochondrial genome sequencing in two endemic North American incipient species SpB and SpC and their hybrid species SpC*, we found that both parental species contributed to the hybrid mitochondrial genome through recombination. We support our findings by showing that mitochondrial recombination between parental types is frequent in experimental crosses that recreate the early step of this speciation event. In these artificial hybrids, we observed that mitochondrial genome recombination enhances phenotypic variation among diploid hybrids, suggesting that it could play a role in the phenotypic differentiation of hybrid species. Like the nuclear genome, the mitochondrial genome can, therefore, also play a role in hybrid speciation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed Central

Beheregaray, Luciano B.; Cooke, Georgina M.; Chao, Ning L.; Landguth, Erin L.

2015-01-01

Evolution creates and sustains biodiversity via adaptive changes in ecologically relevant traits. Ecologically mediated selection contributes to genetic divergence both in the presence or absence of geographic isolation between populations, and is considered an important driver of speciation. Indeed, the genetics of ecological speciation is becoming increasingly studied across a variety of taxa and environments. In this paper we review the literature of ecological speciation in the tropics. We report on low research productivity in tropical ecosystems and discuss reasons accounting for the rarity of studies. We argue for research programs that simultaneously address biogeographical and taxonomic questions in the tropics, while effectively assessing relationships between reproductive isolation and ecological divergence. To contribute toward this goal, we propose a new framework for ecological speciation that integrates information from phylogenetics, phylogeography, population genomics, and simulations in evolutionary landscape genetics (ELG). We introduce components of the framework, describe ELG simulations (a largely unexplored approach in ecological speciation), and discuss design and experimental feasibility within the context of tropical research. We then use published genetic datasets from populations of five codistributed Amazonian fish species to assess the performance of the framework in studies of tropical speciation. We suggest that these approaches can assist in distinguishing the relative contribution of natural selection from biogeographic history in the origin of biodiversity, even in complex ecosystems such as Amazonia. We also discuss on how to assess ecological speciation using ELG simulations that include selection. These integrative frameworks have considerable potential to enhance conservation management in biodiversity rich ecosystems and to complement historical biogeographic and evolutionary studies of tropical biotas. PMID:25653668

Speciation of arsenic in biological samples.

PubMed

Mandal, Badal Kumar; Ogra, Yasumitsu; Anzai, Kazunori; Suzuki, Kazuo T

2004-08-01

Speciation of arsenicals in biological samples is an essential tool to gain insight into its distribution in tissues and its species-specific toxicity to target organs. Biological samples (urine, hair, fingernail) examined in the present study were collected from 41 people of West Bengal, India, who were drinking arsenic (As)-contaminated water, whereas 25 blood and urine samples were collected from a population who stopped drinking As contaminated water 2 years before the blood collection. Speciation of arsenicals in urine, water-methanol extract of freeze-dried red blood cells (RBCs), trichloroacetic acid treated plasma, and water extract of hair and fingernail was carried out by high-performance liquid chromatography (HPLC)-inductively coupled argon plasma mass spectrometry (ICP MS). Urine contained arsenobetaine (AsB, 1.0%), arsenite (iAs(III), 11.3), arsenate (iAs(V), 10.1), monomethylarsonous acid (MMA(III), 6.6), monomethylarsonic acid (MMA(V), 10.5), dimethylarsinous acid (DMA(III), 13.0), and dimethylarsinic acid (DMA(V), 47.5); fingernail contained iAs(III) (62.4%), iAs(V) (20.2), MMA(V) (5.7), DMA(III) (8.9), and DMA(V) (2.8); hair contained iAs(III) (58.9%), iAs(V) (34.8), MMA(V) (2.9), and DMA(V) (3.4); RBCs contained AsB (22.5%) and DMA(V) (77.5); and blood plasma contained AsB (16.7%), iAs(III) (21.1), MMA(V) (27.1), and DMA(V) (35.1). MMA(III), DMA(III), and iAs(V) were not found in any plasma and RBCs samples, but urine contained all of them. Arsenic in urine, fingernails, and hair are positively correlated with water As, suggesting that any of these measurements could be considered as a biomarker to As exposure. Status of urine and exogenous contamination of hair urgently need speciation of As in these samples, but speciation of As in nail is related to its total As (tAs) concentration. Therefore, total As concentrations of nails could be considered as biomarker to As exposure in the endemic areas.

A PERSONAL PARTICLE SPECIATION SAMPLER

EPA Science Inventory

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

Genie: An Inference Engine with Applications to Vulnerability Analysis.

DTIC Science & Technology

1986-06-01

Stanford Artifcial intelligence Laboratory, 1976. 15 D. A. Waterman and F. Hayes-Roth, eds. Pattern-Directed Inference Systems. Academic Press, Inc...Continue an reverse aide It nlecessary mid Identify by block rnmbor) ; f Expert Systems Artificial Intelligence % Vulnerability Analysis Knowledge...deduction it is used wherever possible in data -driven mode (forward chaining). Production rules - JIM 0 g79OOFMV55@S I INCLASSTpnF SECURITY CLASSIFICATION OF

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

EPA Science Inventory

The US Environmental Protection Agency (EPA)’s SPECIATE database contains speciation profiles for both particulate matter (PM) and volatile organic compounds (VOCs) that are key inputs for creating speciated emission inventories for air quality modeling. The objective of th...

Responses of Mn2+ speciation in Deinococcus radiodurans and Escherichia coli to γ-radiation by advanced paramagnetic resonance methods

PubMed Central

Sharma, Ajay; Gaidamakova, Elena K.; Matrosova, Vera Y.; Bennett, Brian; Daly, Michael J.; Hoffman, Brian M.

2013-01-01

The remarkable ability of bacterium Deinococcus radiodurans to survive extreme doses of γ-rays (12,000 Gy), 20 times greater than Escherichia coli, is undiminished by loss of Mn-dependent superoxide dismutase (SodA). D. radiodurans radiation resistance is attributed to the accumulation of low-molecular-weight (LMW) “antioxidant” Mn2+–metabolite complexes that protect essential enzymes from oxidative damage. However, in vivo information about such complexes within D. radiodurans cells is lacking, and the idea that they can supplant reactive-oxygen-species (ROS)–scavenging enzymes remains controversial. In this report, measurements by advanced paramagnetic resonance techniques [electron-spin-echo (ESE)-EPR/electron nuclear double resonance/ESE envelope modulation (ESEEM)] reveal differential details of the in vivo Mn2+ speciation in D. radiodurans and E. coli cells and their responses to 10 kGy γ-irradiation. The Mn2+ of D. radiodurans exists predominantly as LMW complexes with nitrogenous metabolites and orthophosphate, with negligible EPR signal from Mn2+ of SodA. Thus, the extreme radiation resistance of D. radiodurans cells cannot be attributed to SodA. Correspondingly, 10 kGy irradiation causes no change in D. radiodurans Mn2+ speciation, despite the paucity of holo-SodA. In contrast, the EPR signal of E. coli is dominated by signals from low-symmetry enzyme sites such as that of SodA, with a minority pool of LMW Mn2+ complexes that show negligible coordination by nitrogenous metabolites. Nonetheless, irradiation of E. coli majorly changes LMW Mn2+ speciation, with extensive binding of nitrogenous ligands created by irradiation. We infer that E. coli is highly susceptible to radiation-induced ROS because it lacks an adequate supply of LMW Mn antioxidants. PMID:23536297

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

PubMed Central

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

2015-01-01

The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades. PMID:26019156

Metal Ion Speciation and Dissolved Organic Matter Composition in Soil Solutions

NASA Astrophysics Data System (ADS)

Benedetti, M. F.; Ren, Z. L.; Bravin, M.; Tella, M.; Dai, J.

2014-12-01

Knowledge of the speciation of heavy metals and the role of dissolved organic matter (DOM) in soil solution is a key to understand metal mobility and ecotoxicity. In this study, soil column-Donnan membrane technique (SC-DMT) was used to measure metal speciation of Cd, Cu, Ni, Pb, and Zn in eighteen soil solutions, covering a wide range of metal sources and concentrations. DOM composition in these soil solutions was also determined. Our results show that in soil solution Pb and Cu are dominant in complex form, whereas Cd, Ni and Zn mainly exist as free ions; for the whole range of soil solutions, only 26.2% of DOM is reactive and consists mainly of fulvic acid (FA). The metal speciation measured by SC-DMT was compared to the predicted ones obtained via the NICA-Donnan model using the measured FA concentrations. The free ion concentrations predicted by speciation modelling were in good agreement with the measurements. Diffusive gradients in thin-films gels (DGT) were also performed to quantify the labile metal species in the fluxes from solid phase to solution in fourteen soils. The concentrations of metal species detected by DGT were compared with the free ion concentrations measured by DMT and the maximum concentrations calculated based on the predicted metal speciation in SC-DMT soil solutions. It is concluded that both inorganic species and a fraction of FA bound species account for the amount of labile metals measured by DGT, consistent with the dynamic features of this technique. The comparisons between measurements using analytical techniques and mechanistic model predictions provided mutual validation in their performance. Moreover, we show that to make accurate modelling of metal speciation in soil solutions, the knowledge of DOM composition is the crucial information, especially for Cu; like in previous studies the modelling of Pb speciation is not optimal and an updated of Pb generic binding parameters is required to reduce model prediction uncertainties.

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

NASA Astrophysics Data System (ADS)

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

2006-12-01

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

Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions

PubMed Central

Friston, Karl J.; Dolan, Raymond J.

2017-01-01

Normative models of human cognition often appeal to Bayesian filtering, which provides optimal online estimates of unknown or hidden states of the world, based on previous observations. However, in many cases it is necessary to optimise beliefs about sequences of states rather than just the current state. Importantly, Bayesian filtering and sequential inference strategies make different predictions about beliefs and subsequent choices, rendering them behaviourally dissociable. Taking data from a probabilistic reversal task we show that subjects’ choices provide strong evidence that they are representing short sequences of states. Between-subject measures of this implicit sequential inference strategy had a neurobiological underpinning and correlated with grey matter density in prefrontal and parietal cortex, as well as the hippocampus. Our findings provide, to our knowledge, the first evidence for sequential inference in human cognition, and by exploiting between-subject variation in this measure we provide pointers to its neuronal substrates. PMID:28486504

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

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2009-12-01

The composition and location of 15N atoms on N2O isotopomers and isotopologues during isotope speciation has been used to characterize soil biological N cycling and N2O surface emissions. Although there exist few experimental observations, no attempt has been made to model N2O isotopomer speciation. The mathematical treatment of biological kinetic reactions in isotopic applications normally makes use of first-order and quasi steady-state complexation assumptions without taking into account changes in enzyme concentration, reaction stoichiometry, and isotopologue and isotopomer speciation. When multiatomic isotopically-labeled reactants are used in a multi-molecurar reaction, these assumptions may fail since they always lead to a constant fractionation factor and cannot describe speciation of isotopologues and isotopomers. We have developed a mathematical framework that is capable of describing isotopologue and isotopmer speciation and fractionation under the assumption of non-steady complexation during biological kinetic reactions that overcome the limitations mentioned above. This framework was applied to a case study of non-steady (variable and inverse) isotopic effects observed during N2O production and consumption in soils. Our mathematical treatment has led to generalized kinetic equations which replicate experimental observations with high accuracy and help interpret non-steady isotopic effects and isotopologue and isotopomer speciation. The kinetic equations introduced and applied here have general validity in describing isotopic effects in any biochemical reactions by considering: changing enzyme concentrations, mass and isotope conservation, and reaction stoichiometry. The equations also describe speciation of any isotopologue and isotopomer product from any isotopologue and isotopmer reactant.

Sex chromosomes and speciation in birds and other ZW systems.

PubMed

Irwin, Darren E

2018-02-14

Theory and empirical patterns suggest a disproportionate role for sex chromosomes in evolution and speciation. Focusing on ZW sex determination (females ZW, males ZZ; the system in birds, many snakes, and lepidopterans), I review how evolutionary dynamics are expected to differ between the Z, W and the autosomes, discuss how these differences may lead to a greater role of the sex chromosomes in speciation and use data from birds to compare relative evolutionary rates of sex chromosomes and autosomes. Neutral mutations, partially or completely recessive beneficial mutations, and deleterious mutations under many conditions are expected to accumulate faster on the Z than on autosomes. Sexually antagonistic polymorphisms are expected to arise on the Z, raising the possibility of the spread of preference alleles. The faster accumulation of many types of mutations and the potential for complex evolutionary dynamics of sexually antagonistic traits and preferences contribute to a role for the Z chromosome in speciation. A quantitative comparison among a wide variety of bird species shows that the Z tends to have less within-population diversity and greater between-species differentiation than the autosomes, likely due to both adaptive evolution and a greater rate of fixation of deleterious alleles. The W chromosome also shows strong potential to be involved in speciation, in part because of its co-inheritance with the mitochondrial genome. While theory and empirical evidence suggest a disproportionate role for sex chromosomes in speciation, the importance of sex chromosomes is moderated by their small size compared to the whole genome. © 2018 John Wiley & Sons Ltd.

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

PubMed Central

Amaral, Ana R.; Lovewell, Gretchen; Coelho, Maria M.; Amato, George; Rosenbaum, Howard C.

2014-01-01

Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow. PMID:24421898

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

PubMed

Amaral, Ana R; Lovewell, Gretchen; Coelho, Maria M; Amato, George; Rosenbaum, Howard C

2014-01-01

Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow.

XANES Identification of Plutonium Speciation in RFETS Samples

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

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.

Data-driven Inference and Investigation of Thermosphere Dynamics and Variations

NASA Astrophysics Data System (ADS)

Mehta, P. M.; Linares, R.

2017-12-01

This paper presents a methodology for data-driven inference and investigation of thermosphere dynamics and variations. The approach uses data-driven modal analysis to extract the most energetic modes of variations for neutral thermospheric species using proper orthogonal decomposition, where the time-independent modes or basis represent the dynamics and the time-depedent coefficients or amplitudes represent the model parameters. The data-driven modal analysis approach combined with sparse, discrete observations is used to infer amplitues for the dynamic modes and to calibrate the energy content of the system. In this work, two different data-types, namely the number density measurements from TIMED/GUVI and the mass density measurements from CHAMP/GRACE are simultaneously ingested for an accurate and self-consistent specification of the thermosphere. The assimilation process is achieved with a non-linear least squares solver and allows estimation/tuning of the model parameters or amplitudes rather than the driver. In this work, we use the Naval Research Lab's MSIS model to derive the most energetic modes for six different species, He, O, N2, O2, H, and N. We examine the dominant drivers of variations for helium in MSIS and observe that seasonal latitudinal variation accounts for about 80% of the dynamic energy with a strong preference of helium for the winter hemisphere. We also observe enhanced helium presence near the poles at GRACE altitudes during periods of low solar activity (Feb 2007) as previously deduced. We will also examine the storm-time response of helium derived from observations. The results are expected to be useful in tuning/calibration of the physics-based models.

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

NASA Astrophysics Data System (ADS)

Chen, Xinming; Romaniello, Stephen J.; Anbar, Ariel D.

2017-10-01

Natural variations of 238U/235U in marine CaCO3 rocks are being explored as a novel paleoredox proxy to investigate oceanic anoxia events. Although it is generally assumed that U isotopes in CaCO3 directly record 238U/235U of seawater, recently published laboratory experiments demonstrate slight U isotope fractionation during U(VI) incorporation into abiotic calcium carbonates. This fractionation is hypothesized to depend on aqueous U(VI) speciation, which is controlled by pH, ionic strength, pCO2 and Mg2+ and Ca2+ concentrations. Secular variation in seawater chemistry could lead to changes in aqueous U(VI) speciation, and thus, may affect the extent of U isotope fractionation during U(VI) incorporation into CaCO3. In this study, we combine estimates of seawater composition over the Phanerozoic with a model of aqueous U speciation and isotope fractionation to explore variations in the expected offset between the U isotope composition of seawater and primary marine CaCO3 through time. We find that U isotope fractionation between U in primary marine CaCO3 and seawater could have varied between 0.11 and 0.23‰ over the Phanerozoic due to secular variations in seawater chemistry. Such variations would significantly impact estimates of the extent of marine anoxia derived from the U isotope record. For example, at the Permo-Triassic boundary, this effect might imply that the estimated extent of anoxia is ∼32% more extreme than previously inferred. One significant limitation of our model is that the existing experimental database covers only abiotic carbonate precipitation, and does not include a possible range of biological effects which might enhance or suppress the range of isotopic fractionation calculated here. As biotic carbonates dominate the marine carbonate record, more work is need to assess controls on U isotopic fractionation into biotic marine carbonates.

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

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

PubMed

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

1999-11-01

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

NICKEL SPECIATION OF RESIDUAL OIL ASH

EPA Science Inventory

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

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 ...

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

PubMed

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

2015-07-17

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-04-28

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

Speciation of Mg in biogenic calcium carbonates

NASA Astrophysics Data System (ADS)

Farges, F.; Meibom, A.; Flank, A.-M.; Lagarde, P.; Janousch, M.; Stolarski, J.

2009-11-01

A selection of marine biominerals, mostly aragonitic coral skeletons were probed at the Mg K-edge by XANES spectroscopy coupled to μXRF methods and compared to an extensive set of relevant model compounds (silicates, carbonates, oxides and organic). Extensive methodologies are required to better describe the speciation of Mg in those minerals. A combination of ab-initio XANES calculations for defective clusters around Mg in aragonite together with wavelets analyzes of the XANES region are required to robustly interpret the spectra. When using those methodologies, the speciation of Mg ranges from a magnesite-type environment in some scleractinian corals to an organic-type environment. In all environments, the Mg-domains probed appear to be less than 1 nm in size.

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

PubMed

Chi, Haifeng; Zhang, Youchi; Williams, Paul N; Lin, Shanna; Hou, Yanwei; Cai, Chao

2018-05-09

Shrimp, a popular and readily consumed seafood, contains high concentrations of arsenic. However, few studies have focused on whether arsenic in the shrimp could be transformed during the cooking process and gastrointestinal digestion. In this study, a combined in vitro model [Unified Bioaccessibility Research Group of Europe (BARGE) Method-Simulator of Human Intestinal Microbial Ecosystem (UBM-SHIME)] was used to investigate arsenic bioaccessibility and its speciation in raw and cooked shrimps. The results showed that the cooking practices had little effect on the arsenic content and speciation. Bioaccessibility of arsenic in raw shrimp was at a high level, averaging 76.9 ± 4.28 and 86.7 ± 3.74% in gastric and small intestinal phases, respectively. Arsenic speciation was stable in all of the shrimp digestions, with nontoxic arsenobetaine (AsB) being the dominated speciation. The cooking practice significantly increased the bioaccessibility of arsenate ( p < 0.05) in shrimp digests, indicating the increase of the potential health risks.

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

PubMed

Marcinkowska, Monika; Barałkiewicz, Danuta

2016-12-01

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

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

PubMed Central

Feder, Jeffrey L.; Nosil, Patrik; Flaxman, Samuel M.

2014-01-01

Many hypotheses have been put forth to explain the origin and spread of inversions, and their significance for speciation. Several recent genic models have proposed that inversions promote speciation with gene flow due to the adaptive significance of the genes contained within them and because of the effects inversions have on suppressing recombination. However, the consequences of inversions for the dynamics of genome wide divergence across the speciation continuum remain unclear, an issue we examine here. We review a framework for the genomics of speciation involving the congealing of the genome into alternate adaptive states representing species (“genome wide congealing”). We then place inversions in this context as examples of how genetic hitchhiking can potentially hasten genome wide congealing. Specifically, we use simulation models to (i) examine the conditions under which inversions may speed genome congealing and (ii) quantify predicted magnitudes of these effects. Effects of inversions on promoting speciation were most common and pronounced when inversions were initially fixed between populations before secondary contact and adaptation involved many genes with small fitness effects. Further work is required on the role of underdominance and epistasis between a few loci of major effect within inversions. The results highlight five important aspects of the roles of inversions in speciation: (i) the geographic context of the origins and spread of inversions, (ii) the conditions under which inversions can facilitate divergence, (iii) the magnitude of that facilitation, (iv) the extent to which the buildup of divergence is likely to be biased within vs. outside of inversions, and (v) the dynamics of the appearance and disappearance of exceptional divergence within inversions. We conclude by discussing the empirical challenges in showing that inversions play a central role in facilitating speciation with gene flow. PMID:25206365

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

A Drawing Task to Assess Emotion Inference in Language-Impaired Children.

PubMed

Vendeville, Nathalie; Blanc, Nathalie; Brechet, Claire

2015-10-01

Studies investigating the ability of children with language impairment (LI) to infer emotions rely on verbal responses (which can be challenging for these children) and/or the selection of a card representing an emotion (which limits the response range). In contrast, a drawing task might allow a broad spectrum of responses without involving language. This study used a drawing task to compare the ability to make emotional inferences in children with and without LI. Twenty-two children with LI and 22 typically developing children ages 6 to 10 years were assessed in school during 3 sessions. They were asked to listen to audio stories. At specific moments, the experimenter stopped the recording and asked children to complete the drawing of a face to depict the emotion felt by the story's character. Three adult study-blind judges were subsequently asked to evaluate the expressiveness of the drawings. Children with LI had more difficulty than typically developing children making emotional inferences. Children with LI also made more errors of different valence than their typically developing peers. Our findings confirm that children with LI show difficulty in producing emotional inferences, even when performing a drawing task--a relatively language-free response mode.

Two Androdioecious and One Dioecious New Species of Pristionchus (Nematoda: Diplogastridae): New Reference Points for the Evolution of Reproductive Mode

PubMed Central

Kanzaki, Natsumi; Ragsdale, Erik J.; Herrmann, Matthias; Susoy, Vladislav

2013-01-01

Rhabditid nematodes are one of a few animal taxa in which androdioecious reproduction, involving hermaphrodites and males, is found. In the genus Pristionchus, several cases of androdioecy are known, including the model species P. pacificus. A comprehensive understanding of the evolution of reproductive mode depends on dense taxon sampling and careful morphological and phylogenetic reconstruction. In this article, two new androdioecious species, P. boliviae n. sp. and P. mayeri n. sp., and one gonochoristic outgroup, P. atlanticus n. sp., are described on morphological, molecular, and biological evidence. Their phylogenetic relationships are inferred from 26 ribosomal protein genes and a partial SSU rRNA gene. Based on current representation, the new androdioecious species are sister taxa, indicating either speciation from an androdioecious ancestor or rapid convergent evolution in closely related species. Male sexual characters distinguish the new species, and new characters for six closely related Pristionchus species are presented. Male papillae are unusually variable in P. boliviae n. sp. and P. mayeri n. sp., consistent with the predictions of “selfing syndrome.” Description and phylogeny of new androdioecious species, supported by fuller outgroup representation, establish new reference points for mechanistic studies in the Pristionchus system by expanding its comparative context. PMID:24115783

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

PubMed Central

Williams, David R.

2004-01-01

Over the last half-century both the identification of the causes of diseases and the use of inorganic compounds to treat such conditions have been considerably enlightened through our emerging capabilities to identify the pivotal chemical species involved. The ‘duty of care’ placed upon scientists to protect the environment from manufactured chemicals and to limit their effects upon humans therefrom is best realised from a speciation knowledge database. This paper discusses categorising chemicals in terms of their persistence, bioaccumulation, and toxicities and uses speciation information to optimise desirable effects of chemicals in several applications such as the manufacture of pulp for paper and in the foliar nutrition of crops. Simultaneously, the chemical wasting side effects of industrial overdosing is easily avoided if speciation approaches are used. The move towards new environmentally friendly ligand agents is described and methods of finding substitute agents (often combinations of two or more chemicals) to replace nonbiodegradable EDTA. The geosphere migration of metals through the environment is discussed in terms of speciation. Future objectives discussed include improved means of communicating speciation-based recommendations to decision makers. PMID:18365083

SPECIATE Version 4.5 Database Development Documentation

EPA Science Inventory

This product updated SPECIATE 4.4 with new emission profiles to address high priority Agency data gaps and to included new, more accurate emission profiles generated by research underway within and outside the Agency.

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

EPA Science Inventory

Although gasoline direct injection (GDI) vehicles represent nearly half of the light-duty vehicle market share, few studies have reported speciated volatile organic compounds (VOCs) in GDI vehicle exhaust emissions. In this study, speciated VOC emissions were characterized from t...

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 ...

Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

PubMed

Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

2011-12-01

Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

PubMed Central

Hettling, Hannes; Condamine, Fabien L.; Vos, Karin; Nilsson, R. Henrik; Sanderson, Michael J.; Sauquet, Hervé; Scharn, Ruud; Silvestro, Daniele; Töpel, Mats; Bacon, Christine D.; Oxelman, Bengt; Vos, Rutger A.

2017-01-01

Abstract Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable. PMID:27616324

Anomalous double-mode RR Lyrae stars in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Soszyński, I.; Smolec, R.; Dziembowski, W. A.; Udalski, A.; Szymański, M. K.; Wyrzykowski, Ł.; Ulaczyk, K.; Poleski, R.; Pietrukowicz, P.; Kozłowski, S.; Skowron, D.; Skowron, J.; Mróz, P.; Pawlak, M.

2016-12-01

We report the discovery of a new subclass of double-mode RR Lyrae stars in the Large and Small Magellanic Clouds. The sample of 22 pulsating stars has been extracted from the latest edition of the Optical Gravitational Lensing Experiment collection of RR Lyrae variables in the Magellanic System. The stars pulsating simultaneously in the fundamental (F) and first-overtone (1O) modes have distinctly different properties than regular double-mode RR Lyrae variables (RRd stars). The P1O/PF period ratios of our anomalous RRd stars are within a range of 0.725-0.738, while `classical' double-mode RR Lyrae variables have period ratios in the range of 0.742-0.748. In contrast to the typical RRd stars, in the majority of the anomalous pulsators, the F-mode amplitudes are higher than the 1O-mode amplitudes. The light curves associated with the F-mode in the anomalous RRd stars show different morphology than the light curves of, both, regular RRd stars and single-mode RRab stars. Most of the anomalous double-mode stars show long-term modulations of the amplitudes (Blazhko-like effect). Translating the period ratios into the abundance parameter, Z, we find for our stars Z ∈ (0.002, 0.005) - an order of magnitude higher values than typical for RR Lyrae stars. The mass range of the RRd stars inferred from the WI versus PF diagram is (0.55-0.75) M⊙. These parameters cannot be accounted for with single star evolution assuming a Reimers-like mass-loss. Much greater mass-loss caused by interaction with other stars is postulated. We blame the peculiar pulsation properties of our stars to the parametric resonance instability of the 1O-mode to excitation of the F- and 2O-modes as with the inferred parameters of the stars 2ω1O ≈ ωF + ω2O.

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

PubMed

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

2011-05-01

unreported mode of adaptive speciation that helps to understand its rate of diversification. Copyright © 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

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

PubMed

Johnson, Ned K; Cicero, Carla

2004-05-01

The timing of origin of modern North American bird species in relation to Pleistocene glaciations has long been the topic of significant discussion and disagreement. Recently, Klicka and Zink (1997) and Avise and Walker (1998) enlivened this debate by using calibrated molecular distance values to estimate timing of speciations. Here we use new molecular studies to test their conclusions. Molecular distance values for 39 pairs of proven sister species, 27 of which are based on new data, alter the currently perceived pattern that avian species splits occurred mainly in the Pliocene and early-mid-Pleistocene. Mitochondrial DNA divergence values for this set of taxa showed a skewed distribution pointing toward relatively young speciation times, in contrast to the pattern presented by Klicka and Zink (1997) for 35 sister plus non-sister species pairs. Our pattern was not significantly different from that of Avise and Walker (1998) for "intraspecific phylogroups," some of which are species. We conclude that the entire Pleistocene, including the last two glacial cycles (<250,000 years ago), was important in speciations of modern North American birds. A substantial number of speciations were both initiated and completed in the last 250,000 years. Simultaneously, many taxa began to diverge in the Pleistocene but their speciations are not yet complete (per Avise and Walker 1998). The suggestion that durations of speciations average two million years is probably a substantial overestimate.

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

PubMed

Beaulieu, Jeremy M; O'Meara, Brian C

2016-07-01

The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved

Aerosol Chemical Speciation Monitor (ACSM) Instrument Handbook

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

Watson, Thomas B.

The Aerodyne Aerosol Chemical Speciation Monitor (ACSM) measures particle mass loading and chemical composition in real time for non-refractory sub-micron aerosol particles. The ACSM is designed for long-term unattended deployment and routine monitoring applications.

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

PubMed Central

Ovenden, J. R.; White, RWG.

1990-01-01

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

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

PubMed Central

Iwasa, Yoh

2017-01-01

We studied the time to speciation by geographical isolation for a species living on three islands connected by rare migration. We assumed that incompatibility was controlled by a number of quantitative loci and that individuals differing in loci by more than a threshold did not mix genetically with each other. For each locus, we defined the geographical configuration (GC), which specifies islands with common alleles, and traced the stochastic transitions between different GCs. From these results, we calculated the changes in genetic distances. As a single migration event provides an opportunity for transitions in multiple loci, the GCs of different loci are correlated, which can be evaluated by constructing the stochastic differential equations of the number of loci with different GCs. Our model showed that the low number of incompatibility loci facilitates parapatric speciation and that migrants arriving as a group shorten the waiting time to speciation compared with the same number of migrants arriving individually. We also discuss how speciation rate changes with geographical structure. PMID:28386439

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

PubMed Central

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

2016-01-01

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

Mode switching in volcanic seismicity: El Hierro 2011-2013

NASA Astrophysics Data System (ADS)

Roberts, Nick S.; Bell, Andrew F.; Main, Ian G.

2016-05-01

The Gutenberg-Richter b value is commonly used in volcanic eruption forecasting to infer material or mechanical properties from earthquake distributions. Such studies typically analyze discrete time windows or phases, but the choice of such windows is subjective and can introduce significant bias. Here we minimize this sample bias by iteratively sampling catalogs with randomly chosen windows and then stack the resulting probability density functions for the estimated b>˜ value to determine a net probability density function. We examine data from the El Hierro seismic catalog during a period of unrest in 2011-2013 and demonstrate clear multimodal behavior. Individual modes are relatively stable in time, but the most probable b>˜ value intermittently switches between modes, one of which is similar to that of tectonic seismicity. Multimodality is primarily associated with intermittent activation and cessation of activity in different parts of the volcanic system rather than with respect to any systematic inferred underlying process.

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

USGS Publications Warehouse

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

2000-01-01

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

Early events in speciation: Cryptic species of Drosophila aldrichi.

PubMed

Castro Vargas, Cynthia; Richmond, Maxi Polihronakis; Ramirez Loustalot Laclette, Mariana; Markow, Therese Ann

2017-06-01

Understanding the earliest events in speciation remains a major challenge in evolutionary biology. Thus identifying species whose populations are beginning to diverge can provide useful systems to study the process of speciation. Drosophila aldrichi , a cactophilic fruit fly species with a broad distribution in North America, has long been assumed to be a single species owing to its morphological uniformity. While previous reports either of genetic divergence or reproductive isolation among different D. aldrichi strains have hinted at the existence of cryptic species, the evolutionary relationships of this species across its range have not been thoroughly investigated. Here we show that D. aldrichi actually is paraphyletic with respect to its closest relative, Drosophila wheeleri , and that divergent D. aldrichi lineages show complete hybrid male sterility when crossed. Our data support the interpretation that there are at least two species of D. aldrichi, making these flies particularly attractive for studies of speciation in an ecological and geographical context.

Computer simulations of sympatric speciation in a simple food web

NASA Astrophysics Data System (ADS)

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

2005-07-01

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

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

PubMed

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

2016-07-19

Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Author(s).

Children's and adults' evaluation of the certainty of deductive inferences, inductive inferences, and guesses.

PubMed

Pillow, Bradford H

2002-01-01

Two experiments investigated kindergarten through fourth-grade children's and adults' (N = 128) ability to (1) evaluate the certainty of deductive inferences, inductive inferences, and guesses; and (2) explain the origins of inferential knowledge. When judging their own cognitive state, children in first grade and older rated deductive inferences as more certain than guesses; but when judging another person's knowledge, children did not distinguish valid inferences from invalid inferences and guesses until fourth grade. By third grade, children differentiated their own deductive inferences from inductive inferences and guesses, but only adults both differentiated deductive inferences from inductive inferences and differentiated inductive inferences from guesses. Children's recognition of their own inferences may contribute to the development of knowledge about cognitive processes, scientific reasoning, and a constructivist epistemology.

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

PubMed Central

Manoukis, Nicholas C.; Powell, Jeffrey R.; Touré, Mahamoudou B.; Sacko, Adama; Edillo, Frances E.; Coulibaly, Mamadou B.; Traoré, Sekou F.; Taylor, Charles E.; Besansky, Nora J.

2008-01-01

The role of chromosomal inversions in speciation has long been of interest to evolutionists. Recent quantitative modeling has stimulated reconsideration of previous conceptual models for chromosomal speciation. Anopheles gambiae, the most important vector of human malaria, carries abundant chromosomal inversion polymorphism nonrandomly associated with ecotypes that mate assortatively. Here, we consider the potential role of paracentric inversions in promoting speciation in A. gambiae via “ecotypification,” a term that refers to differentiation arising from local adaptation. In particular, we focus on the Bamako form, an ecotype characterized by low inversion polymorphism and fixation of an inversion, 2Rj, that is very rare or absent in all other forms of A. gambiae. The Bamako form has a restricted distribution by the upper Niger River and its tributaries that is associated with a distinctive type of larval habitat, laterite rock pools, hypothesized to be its optimal breeding site. We first present computer simulations to investigate whether the population dynamics of A. gambiae are consistent with chromosomal speciation by ecotypification. The models are parameterized using field observations on the various forms of A. gambiae that exist in Mali, West Africa. We then report on the distribution of larvae of this species collected from rock pools and more characteristic breeding sites nearby. Both the simulations and field observations support the thesis that speciation by ecotypification is occurring, or has occurred, prompting consideration of Bamako as an independent species. PMID:18287019

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

PubMed

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

2013-01-01

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

Iron solubility driven by speciation in dust sources to the ocean

USGS Publications Warehouse

Schroth, A.W.; Crusius, John; Sholkovitz, E.R.; Bostick, B.C.

2009-01-01

Although abundant in the Earths crust, iron is present at trace concentrations in sea water and is a limiting nutrient for phytoplankton in approximately 40% of the ocean. Current literature suggests that aerosols are the primary external source of iron to offshore waters, yet controls on iron aerosol solubility remain unclear. Here we demonstrate that iron speciation (oxidation state and bonding environment) drives iron solubility in arid region soils, glacial weathering products (flour) and oil combustion products (oil fly ash). Iron speciation varies by aerosol source, with soils in arid regions dominated by ferric (oxy)hydroxides, glacial flour by primary and secondary ferrous silicates and oil fly ash by ferric sulphate salts. Variation in iron speciation produces systematic differences in iron solubility: less than 1% of the iron in arid soils was soluble, compared with 2-3% in glacial products and 77-81% in oil combustion products, which is directly linked to fractions of more soluble phases. We conclude that spatial and temporal variations in aerosol iron speciation, driven by the distribution of deserts, glaciers and fossil-fuel combustion, could have a pronounced effect on aerosol iron solubility and therefore on biological productivity and the carbon cycle in the ocean. ?? 2009 Macmillan Publishers Limited.

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...

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.

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

PubMed

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

2007-09-01

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

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

NASA Astrophysics Data System (ADS)

von Schneidemesser, E.; Coates, J.; Denier van der Gon, H. A. C.; Visschedijk, A. J. H.; Butler, T. M.

2016-06-01

Non-methane volatile organic compounds (NMVOCs) are detrimental to human health owing to the toxicity of many of the NMVOC species, as well as their role in the formation of secondary air pollutants such as tropospheric ozone (O3) and secondary organic aerosol. The speciation and amount of NMVOCs emitted into the troposphere are represented in emission inventories (EIs) for input to chemical transport models that predict air pollutant levels. Much of the information in EIs pertaining to speciation of NMVOCs is likely outdated, but before taking on the task of providing an up-to-date and highly speciated EI, a better understanding of the sensitivity of models to the change in NMVOC input would be highly beneficial. According to the EIs, the solvent sector is the most important sector for NMVOC emissions. Here, the sensitivity of modelled tropospheric O3 to NMVOC emission inventory speciation was investigated by comparing the maximum potential difference in O3 produced using a variety of reported solvent sector EI speciations in an idealized study using a box model. The sensitivity was tested using three chemical mechanisms that describe O3 production chemistry, typically employed for different types of modelling scales - point (MCM v3.2), regional (RADM2), and global (MOZART-4). In the box model simulations, a maximum difference of 15 ppbv (ca. 22% of the mean O3 mixing ratio of 69 ppbv) between the different EI speciations of the solvent sector was calculated. In comparison, for the same EI speciation, but comparing the three different mechanisms, a maximum difference of 6.7 ppbv was observed. Relationships were found between the relative contribution of NMVOC compound classes (alkanes and oxygenated species) in the speciations to the amount of Ox produced in the box model. These results indicate that modelled tropospheric O3 is sensitive to the speciation of NMVOCs as specified by emission inventories, suggesting that detailed updates to the EI speciation

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

NASA Astrophysics Data System (ADS)

Menut, Laurent; Siour, Guillaume; Mailler, Sylvain; Couvidat, Florian; Bessagnet, Bertrand

2016-10-01

The aerosol speciation and size distribution is modeled during the summer 2013 and over a large area encompassing Africa, Mediterranean and western Europe. The modeled aerosol is compared to available measurements such as the AERONET aerosol optical depth (AOD) and aerosol size distribution (ASD) and the EMEP network for surface concentrations of particulate matter PM2.5, PM10 and inorganic species (nitrate, sulfate and ammonium). The main goal of this study is to quantify the model ability to realistically model the speciation and size distribution of the aerosol. Results first showed that the long-range transport pathways are well reproduced and mainly constituted by mineral dust: spatial correlation is ≈ 0.9 for AOD and Ångström exponent, when temporal correlations show that the day-to-day variability is more difficult to reproduce. Over Europe, PM2.5 and PM10 have a mean temporal correlation of ≈ 0.4 but the lowest spatial correlation ( ≈ 0.25 and 0.62, respectively), showing that the fine particles are not well localized or transported. Being short-lived species, the uncertainties on meteorology and emissions induce these lowest scores. However, time series of PM2.5 with the speciation show a good agreement between model and measurements and are useful for discriminating the aerosol composition. Using a classification from the south (Africa) to the north (northern Europe), it is shown that mineral dust relative mass contribution decreases from 50 to 10 % when nitrate increases from 0 to 20 % and all other species, sulfate, sea salt, ammonium, elemental carbon, primary organic matter, are constant. The secondary organic aerosol contribution is between 10 and 20 % with a maximum at the latitude of the Mediterranean Sea (Spanish stations). For inorganic species, it is shown that nitrate, sulfate and ammonium have a mean temporal correlation of 0.25, 0.37 and 0.17, respectively. The spatial correlation is better (0.25, 0.5 and 0.87), showing that the mean

Concentrations and speciation of arsenic along a groundwater flow-path in the Upper Floridan aquifer, Florida, USA

NASA Astrophysics Data System (ADS)

Haque, S. E.; Johannesson, K. H.

2006-05-01

Arsenic (As) concentrations and speciation were determined in groundwaters along a flow-path in the Upper Floridan aquifer (UFA) to investigate the biogeochemical “evolution“ of As in this relatively pristine aquifer. Dissolved inorganic As species were separated in the field using anion-exchange chromatography and subsequently analyzed by inductively coupled plasma mass spectrometry. Total As concentrations are higher in the recharge area groundwaters compared to down-gradient portions of UFA. Redox conditions vary from relatively oxic to anoxic along the flow-path. Mobilization of As species in UFA groundwaters is influenced by ferric iron reduction and subsequent dissolution, sulfate reduction, and probable pyrite precipitation that are inferred from the data to occur along distinct regions of the flow-path. In general, the distribution of As species are consistent with equilibrium thermodynamics, such that arsenate dominates in more oxidizing waters near the recharge area, and arsenite predominates in the progressively reducing groundwaters beyond the recharge area.

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...

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...

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

PubMed

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

2016-09-14

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

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

PubMed

Vilmin, Franck; Bazin, Philippe; Thibault-Starzyk, Frédéric; Travert, Arnaud

2015-09-03

Speciation, i.e. identification and quantification, of surface species on heterogeneous surfaces by infrared spectroscopy is important in many fields but remains a challenging task when facing strongly overlapped spectra of multiple adspecies. Here, we propose a new methodology, combining state of the art instrumental developments for quantitative infrared spectroscopy of adspecies and chemometrics tools, mainly a novel data processing algorithm, called SORB-MCR (SOft modeling by Recursive Based-Multivariate Curve Resolution) and multivariate calibration. After formal transposition of the general linear mixture model to adsorption spectral data, the main issues, i.e. validity of Beer-Lambert law and rank deficiency problems, are theoretically discussed. Then, the methodology is exposed through application to two case studies, each of them characterized by a specific type of rank deficiency: (i) speciation of physisorbed water species over a hydrated silica surface, and (ii) speciation (chemisorption and physisorption) of a silane probe molecule over a dehydrated silica surface. In both cases, we demonstrate the relevance of this approach which leads to a thorough surface speciation based on comprehensive and fully interpretable multivariate quantitative models. Limitations and drawbacks of the methodology are also underlined. Copyright © 2015 Elsevier B.V. All rights reserved.

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

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

PubMed

Steinfartz, Sebastian; Weitere, Markus; Tautz, Diethard

2007-11-01

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

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

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...

Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles.

PubMed

Title, Pascal O; Rabosky, Daniel L

2017-09-01

Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"-large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches-provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles-each consisting of more than 4000 species-yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field. [Australia; macroevolution; macrophylogeny; squamates; time calibration.]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Role of natural nanoparticles on the speciation of Ni in andosols of la Reunion

NASA Astrophysics Data System (ADS)

Levard, Clément; Doelsch, Emmanuel; Rose, Jérôme; Masion, Armand; Basile-Doelsch, Isabelle; Proux, Olivier; Hazemann, Jean-Louis; Borschneck, Daniel; Bottero, Jean-Yves

2009-08-01

Andosols on the island of Réunion have high nickel (Ni) concentrations due to the natural pedo-geochemical background. Enhanced knowledge of Ni speciation is necessary to predict the bioavailability and potential toxicity of this element. Ni speciation in these andosols, marked by the presence of high amounts of natural aluminosilicate nanoparticles, was investigated in two complementary systems: (i) In a soil sample—densimetric fractionation was first performed in order to separate the potential bearing phases, prior to Ni speciation characterization. (ii) In a synthetic sample—Ni reactivity with synthetic aluminosilicate nanoparticle analogs were studied. In both cases, Ni speciation was determined using X-ray absorption spectroscopy (XAS). The results revealed that Ni had the same local environment in both systems (natural and synthetic systems), and Ni was chemically linked to natural short-range ordered aluminosilicates or analogs. This complex represented about 75% of the total Ni in the studied soil.

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.

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

PubMed

Wilke, Claudia; Barkleit, Astrid; Stumpf, Thorsten; Ikeda-Ohno, Atsushi

2017-10-01

In case radioactive materials are released into the environment, their incorporation into our digestive system would be a significant concern. Trivalent f-elements, i.e., trivalent actinides and lanthanides, could potentially represent a serious health risk due to their chemo- and radiotoxicity, nevertheless the biochemical behavior of these elements are mostly unknown even to date. This study, therefore, focuses on the chemical speciation of trivalent f-elements in the human gastrointestinal tract. To simulate the digestive system artificial digestive juices (saliva, gastric juice, pancreatic juice and bile fluid) were prepared. The chemical speciation of lanthanides (as Eu(III)) and actinides (as Cm(III)) was determined experimentally by time-resolved laser-induced fluorescence spectroscopy (TRLFS) and the results were compared with thermodynamic modeling. The results indicate a dominant inorganic species with phosphate/carbonate in the mouth, while the aquo ion is predominantly formed with a minor contribution of the enzyme pepsin in the stomach. In the intestinal tract the most significant species are with the protein mucin. We demonstrated the first experimental results on the chemical speciation of trivalent f-elements in the digestive media by TRLFS. The results highlight a significant gap in chemical speciation between experiments and thermodynamic modeling due to the limited availability of thermodynamic stability constants particularly for organic species. Chemical speciation strongly influences the in vivo behavior of metal ions. Therefore, the results of this speciation study will help to enhance the assessment of health risks and to improve decorporation strategies after ingestion of these (radio-)toxic heavy metal ions. Copyright © 2017 Elsevier Inc. All rights reserved.

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

PubMed

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

2001-08-01

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

Detection of multiple damages employing best achievable eigenvectors under Bayesian inference

NASA Astrophysics Data System (ADS)

Prajapat, Kanta; Ray-Chaudhuri, Samit

2018-05-01

A novel approach is presented in this work to localize simultaneously multiple damaged elements in a structure along with the estimation of damage severity for each of the damaged elements. For detection of damaged elements, a best achievable eigenvector based formulation has been derived. To deal with noisy data, Bayesian inference is employed in the formulation wherein the likelihood of the Bayesian algorithm is formed on the basis of errors between the best achievable eigenvectors and the measured modes. In this approach, the most probable damage locations are evaluated under Bayesian inference by generating combinations of various possible damaged elements. Once damage locations are identified, damage severities are estimated using a Bayesian inference Markov chain Monte Carlo simulation. The efficiency of the proposed approach has been demonstrated by carrying out a numerical study involving a 12-story shear building. It has been found from this study that damage scenarios involving as low as 10% loss of stiffness in multiple elements are accurately determined (localized and severities quantified) even when 2% noise contaminated modal data are utilized. Further, this study introduces a term parameter impact (evaluated based on sensitivity of modal parameters towards structural parameters) to decide the suitability of selecting a particular mode, if some idea about the damaged elements are available. It has been demonstrated here that the accuracy and efficiency of the Bayesian quantification algorithm increases if damage localization is carried out a-priori. An experimental study involving a laboratory scale shear building and different stiffness modification scenarios shows that the proposed approach is efficient enough to localize the stories with stiffness modification.

Latitude, elevational climatic zonation and speciation in New World vertebrates

PubMed Central

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

2012-01-01

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

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

PubMed Central

Suvarapu, Lakshmi Narayana; Baek, Sung-Ok

2015-01-01

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

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

Treesearch

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

2017-01-01

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

Inference or Observation?

ERIC Educational Resources Information Center

Finson, Kevin D.

2010-01-01

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

Chromium fractionation and speciation in natural waters.

PubMed

Pereira, Catarinie Diniz; Techy, João Gabriel; Ganzarolli, Edgard Moreira; Quináia, Sueli Pércio

2012-05-01

It is common for leather industries to dump chromium-contaminated effluent into rivers and other bodies of water. Thus, it is crucial to know the impacts caused by this practice to the environment. A study on chromium partitioning and speciation, with determination at trace levels, was carried out in a potentially contaminated creek. Chromium fractionation and speciation was performed using a flow-injection preconcentration system and detection by flame atomic absorption spectrometry. High levels of this element were found in the particulate material (449-9320 mg kg(-1)), which indicates its compatibility with this fraction. The concentration of Cr(iii) in the water samples collected ranged from 5.2-105.2 μg L(-1). Cr(vi) was always below of the DL (0.3 μg L(-1)). Chromium accumulation observed in the sediment (873-1691 mg kg(-1)) may confirm contamination due to the long term release of contaminated effluents in the creek.

[The progress in speciation analysis of trace elements by atomic spectrometry].

PubMed

Wang, Zeng-Huan; Wang, Xu-Nuo; Ke, Chang-Liang; Lin, Qin

2013-12-01

The main purpose of the present work is to review the different non-chromatographic methods for the speciation analysis of trace elements in geological, environmental, biological and medical areas. In this paper, the sample processing methods in speciation analysis were summarized, and the main strategies for non-chromatographic technique were evaluated. The basic principles of the liquid extractions proposed in the published literatures recently and their advantages and disadvantages were discussed, such as conventional solvent extraction, cloud point extraction, single droplet microextraction, and dispersive liquid-liquid microextraction. Solid phase extraction, as a non-chromatographic technique for speciation analysis, can be used in batch or in flow detection, and especially suitable for the online connection to atomic spectrometric detector. The developments and applications of sorbent materials filled in the columns of solid phase extraction were reviewed. The sorbents include chelating resins, nanometer materials, molecular and ion imprinted materials, and bio-sorbents. Other techniques, e. g. hydride generation technique and coprecipitation, were also reviewed together with their main applications.

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

Speciation and distribution of arsenic and localization of nutrients in rice grains

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

Lombi, E.; Scheckel, K.G.; Pallon, J.

2012-09-05

Arsenic (As) contamination of rice grains and the generally low concentration of micronutrients in rice have been recognized as a major concern for human health. Here, we investigated the speciation and localization of As and the distribution of (micro)nutrients in rice grains because these are key factors controlling bioavailability of nutrients and contaminants. Bulk total and speciation analyses using high-pressure liquid chromatography (HPLC)-inductively coupled plasma mass spectrometry (ICP-MS) and X-ray absorption near-edge spectroscopy (XANES) was complemented by spatially resolved microspectroscopic techniques ({mu}-XANES, {mu}-X-ray fluorescence ({mu}-XRF) and particle induced X-ray emission (PIXE)) to investigate both speciation and distribution of As andmore » localization of nutrients in situ. The distribution of As and micronutrients varied between the various parts of the grains (husk, bran and endosperm) and was characterized by element-specific distribution patterns. The speciation of As in bran and endosperm was dominated by As(III)-thiol complexes. The results indicate that the translocation from the maternal to filial tissues may be a bottleneck for As accumulation in the grain. Strong similarities between the distribution of iron (Fe), manganese (Mn) and phosphorus (P) and between zinc (Zn) and sulphur (S) may be indicative of complexation mechanisms in rice grains.« less

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

PubMed Central

Beltman, J.B; Metz, J.A.J

2005-01-01

A problem in understanding sympatric speciation is establishing how reproductive isolation can arise when there is disruptive selection on an ecological trait. One of the solutions that has been proposed is that a habitat preference evolves, and that mates are chosen within the preferred habitat. We present a model where the habitat preference can evolve either by means of a genetic mechanism or by means of learning. Employing an adaptive-dynamical analysis, we show that evolution proceeds either to a single population of specialists with a genetic preference for their optimal habitat, or to a population of generalists without a habitat preference. The generalist population subsequently experiences disruptive selection. Learning promotes speciation because it increases the intensity of disruptive selection. An individual-based version of the model shows that, when loci are completely unlinked and learning confers little cost, the presence of disruptive selection most probably leads to speciation via the simultaneous evolution of a learned habitat preference. For high costs of learning, speciation is most likely to occur via the evolution of a genetic habitat preference. However, the latter only happens when the effect of mutations is large, or when there is linkage between genes coding for the different traits. PMID:16011920

Entropic Inference

NASA Astrophysics Data System (ADS)

Caticha, Ariel

2011-03-01

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

The Dimensionality of Inference Making: Are Local and Global Inferences Distinguishable?

ERIC Educational Resources Information Center

Muijselaar, Marloes M. L.

2018-01-01

We investigated the dimensionality of inference making in samples of 4- to 9-year-olds (Ns = 416-783) to determine if local and global coherence inferences could be distinguished. In addition, we examined the validity of our experimenter-developed inference measure by comparing with three additional measures of listening comprehension. Multitrait,…

Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia.

PubMed

Pettengill, James B; Moeller, David A

2012-09-01

The origins of hybrid zones between parapatric taxa have been of particular interest for understanding the evolution of reproductive isolation and the geographic context of species divergence. One challenge has been to distinguish between allopatric divergence (followed by secondary contact) versus primary intergradation (parapatric speciation) as alternative divergence histories. Here, we use complementary phylogeographic and population genetic analyses to investigate the recent divergence of two subspecies of Clarkia xantiana and the formation of a hybrid zone within the narrow region of sympatry. We tested alternative phylogeographic models of divergence using approximate Bayesian computation (ABC) and found strong support for a secondary contact model and little support for a model allowing for gene flow throughout the divergence process (i.e. primary intergradation). Two independent methods for inferring the ancestral geography of each subspecies, one based on probabilistic character state reconstructions and the other on palaeo-distribution modelling, also support a model of divergence in allopatry and range expansion leading to secondary contact. The membership of individuals to genetic clusters suggests geographic substructure within each taxon where allopatric and sympatric samples are primarily found in separate clusters. We also observed coincidence and concordance of genetic clines across three types of molecular markers, which suggests that there is a strong barrier to gene flow. Taken together, our results provide evidence for allopatric divergence followed by range expansion leading to secondary contact. The location of refugial populations and the directionality of range expansion are consistent with expectations based on climate change since the last glacial maximum. Our approach also illustrates the utility of combining phylogeographic hypothesis testing with species distribution modelling and fine-scale population genetic analyses for inferring

Postcopulatory sexual selection generates speciation phenotypes in Drosophila.

PubMed

Manier, Mollie K; Lüpold, Stefan; Belote, John M; Starmer, William T; Berben, Kirstin S; Ala-Honkola, Outi; Collins, William F; Pitnick, Scott

2013-10-07

Identifying traits that reproductively isolate species, and the selective forces underlying their divergence, is a central goal of evolutionary biology and speciation research. There is growing recognition that postcopulatory sexual selection, which can drive rapid diversification of interacting ejaculate and female reproductive tract traits that mediate sperm competition, may be an engine of speciation. Conspecific sperm precedence (CSP) is a taxonomically widespread form of reproductive isolation, but the selective causes and divergent traits responsible for CSP are poorly understood. To test the hypothesis that postcopulatory sexual selection can generate reproductive isolation, we expressed GFP or RFP in sperm heads of recently diverged sister species, Drosophila simulans and D. mauritiana, to enable detailed resolution of species-specific sperm precedence mechanisms. Between-species divergence in sperm competition traits and mechanisms prompted six a priori predictions regarding mechanisms of CSP and degree of cross asymmetry in reproductive isolation. We resolved four distinct mechanisms of CSP that were highly consistent with predictions. These comprise interactions between multiple sex-specific traits, including two independent mechanisms by which females exert sophisticated control over sperm fate to favor the conspecific male. Our results confirm that reproductive isolation can quickly arise from diversifying (allopatric) postcopulatory sexual selection. This experimental approach to "speciation phenotypes" illustrates how knowledge of sperm precedence mechanisms can be used to predict the mechanisms and extent of reproductive isolation between populations and species. Copyright © 2013 Elsevier Ltd. All rights reserved.

Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria).

PubMed

Bapst, D W; Wright, A M; Matzke, N J; Lloyd, G T

2016-07-01

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences. © 2016 The Author(s).

[Primary speciation analysis of iron in edible flowers].

PubMed

Peng, Shan-shan; Huang, Guo-qing

2003-02-01

In this paper seven primary speciations of iron in three edible flowers, i.e. chrysanthemum, cottonrose hibiscus and honeysucker have been studied by atomic absorption spectrometry. Speciation parameters of iron such as extractive rate, residue rate, immerse-residue ratio in the samples were calculated. It was found that the first extractive rates of Fe were higher than the second ones in all three edible flowers, and the immerse-residue ratios of Fe were similar to the extractive rates. But the extraction of iron in all three edible flowers were no more than fifty percent. It is showed that the iron isn't easy to extract by water in the three edible flowers. The recovery was in the range of 96.5%-103.2% and RSD was in the range of 1.2%-3.1%. The results were satisfactory.

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

PubMed

de Aguiar, Marcus A M; Bar-Yam, Yaneer

2011-09-01

In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.

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

PubMed Central

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

2015-01-01

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

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

NASA Astrophysics Data System (ADS)

de Aguiar, Marcus A. M.; Bar-Yam, Yaneer

2011-03-01

In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.

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...

Self-enforcing Private Inference Control

NASA Astrophysics Data System (ADS)

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

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

Dynamic Behavior of Spicules Inferred from Perpendicular Velocity Components

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

Sharma, Rahul; Verth, Gary; Erdélyi, Robertus

2017-05-10

Understanding the dynamic behavior of spicules, e.g., in terms of magnetohydrodynamic (MHD) wave mode(s), is key to unveiling their role in energy and mass transfer from the photosphere to corona. The transverse, torsional, and field-aligned motions of spicules have previously been observed in imaging spectroscopy and analyzed separately for embedded wave-mode identification. Similarities in the Doppler signatures of spicular structures for both kink and torsional Alfvén wave modes have led to the misinterpretation of the dominant wave mode in these structures and is a subject of debate. Here, we aim to combine line- of-sight (LOS) and plane-of-sky (POS) velocity componentsmore » using the high spatial/temporal resolution H α imaging-spectroscopy data from the CRisp Imaging SpectroPolarimeter based at the Swedish Solar Telescope to achieve better insight into the underlying nature of these motions as a whole. The resultant three-dimensional velocity vectors and the other derived quantities (e.g., magnetic pressure perturbations) are used to identify the MHD wave mode(s) responsible for the observed spicule motion. We find a number of independent examples where the bulk transverse motion of the spicule is dominant either in the POS or along the LOS. It is shown that the counterstreaming action of the displaced external plasma due to spicular bulk transverse motion has a similar Doppler profile to that of the m = 0 torsional Alfvén wave when this motion is predominantly perpendicular to the LOS. Furthermore, the inferred magnetic pressure perturbations support the kink wave interpretation of observed spicular bulk transverse motion rather than any purely incompressible MHD wave mode, e.g., the m = 0 torsional Alfvén wave.« less

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

PubMed Central

Stieritz, Donald D.; Law, Edward J.; Holder, Ian Alan

1973-01-01

Methods of speciating Candida isolates from clinical specimens are described and the necessity of speciation is emphasized. Differences in susceptibility of C. albicans and C. tropicalis to amphotericin B were observed and the implications of this in relation to treatment with amphotericin B and the development of resistance are discussed. PMID:4578160

A role for a neo-sex chromosome in stickleback speciation

PubMed Central

Kitano, Jun; Ross, Joseph A.; Mori, Seiichi; Kume, Manabu; Jones, Felicity C.; Chan, Yingguang F.; Absher, Devin M.; Grimwood, Jane; Schmutz, Jeremy; Myers, Richard M.; Kingsley, David M.; Peichel, Catherine L.

2009-01-01

Sexual antagonism, or conflict between the sexes, has been proposed as a driving force in both sex chromosome turnover and speciation. Although closely related species often have different sex chromosome systems, it is unknown whether sex chromosome turnover contributes to the evolution of reproductive isolation between species. In this study, we show that a newly evolved sex chromosome harbours genes that contribute to speciation in threespine stickleback fish (Gasterosteus aculeatus). We first identified a neo-sex chromosome system found only in one member of a sympatric species pair in Japan. We then performed genetic linkage mapping of male-specific traits important for reproductive isolation between the Japanese species pair. The neo-X chromosome harbours loci for male courtship display traits that contribute to behavioural isolation, while the ancestral X chromosome contains loci for both behavioural isolation and hybrid male sterility. Our work not only provides strong evidence for a large-X effect on reproductive isolation in a vertebrate system, but also provides direct evidence that a young neo-X chromosome contributes to reproductive isolation between closely related species. Our data suggest that sex chromosome turnover might play a greater role in speciation than previously appreciated. PMID:19783981

A role for a neo-sex chromosome in stickleback speciation.

PubMed

Kitano, Jun; Ross, Joseph A; Mori, Seiichi; Kume, Manabu; Jones, Felicity C; Chan, Yingguang F; Absher, Devin M; Grimwood, Jane; Schmutz, Jeremy; Myers, Richard M; Kingsley, David M; Peichel, Catherine L

2009-10-22

Sexual antagonism, or conflict between the sexes, has been proposed as a driving force in both sex-chromosome turnover and speciation. Although closely related species often have different sex-chromosome systems, it is unknown whether sex-chromosome turnover contributes to the evolution of reproductive isolation between species. Here we show that a newly evolved sex chromosome contains genes that contribute to speciation in threespine stickleback fish (Gasterosteus aculeatus). We first identified a neo-sex chromosome system found only in one member of a sympatric species pair in Japan. We then performed genetic linkage mapping of male-specific traits important for reproductive isolation between the Japanese species pair. The neo-X chromosome contains loci for male courtship display traits that contribute to behavioural isolation, whereas the ancestral X chromosome contains loci for both behavioural isolation and hybrid male sterility. Our work not only provides strong evidence for a large X-effect on reproductive isolation in a vertebrate system, but also provides direct evidence that a young neo-X chromosome contributes to reproductive isolation between closely related species. Our data indicate that sex-chromosome turnover might have a greater role in speciation than was previously appreciated.

More than one kind of inference: re-examining what's learned in feature inference and classification.

PubMed

Sweller, Naomi; Hayes, Brett K

2010-08-01

Three studies examined how task demands that impact on attention to typical or atypical category features shape the category representations formed through classification learning and inference learning. During training categories were learned via exemplar classification or by inferring missing exemplar features. In the latter condition inferences were made about missing typical features alone (typical feature inference) or about both missing typical and atypical features (mixed feature inference). Classification and mixed feature inference led to the incorporation of typical and atypical features into category representations, with both kinds of features influencing inferences about familiar (Experiments 1 and 2) and novel (Experiment 3) test items. Those in the typical inference condition focused primarily on typical features. Together with formal modelling, these results challenge previous accounts that have characterized inference learning as producing a focus on typical category features. The results show that two different kinds of inference learning are possible and that these are subserved by different kinds of category representations.

Perceptual inference.

PubMed

Aggelopoulos, Nikolaos C

2015-08-01

Perceptual inference refers to the ability to infer sensory stimuli from predictions that result from internal neural representations built through prior experience. Methods of Bayesian statistical inference and decision theory model cognition adequately by using error sensing either in guiding action or in "generative" models that predict the sensory information. In this framework, perception can be seen as a process qualitatively distinct from sensation, a process of information evaluation using previously acquired and stored representations (memories) that is guided by sensory feedback. The stored representations can be utilised as internal models of sensory stimuli enabling long term associations, for example in operant conditioning. Evidence for perceptual inference is contributed by such phenomena as the cortical co-localisation of object perception with object memory, the response invariance in the responses of some neurons to variations in the stimulus, as well as from situations in which perception can be dissociated from sensation. In the context of perceptual inference, sensory areas of the cerebral cortex that have been facilitated by a priming signal may be regarded as comparators in a closed feedback loop, similar to the better known motor reflexes in the sensorimotor system. The adult cerebral cortex can be regarded as similar to a servomechanism, in using sensory feedback to correct internal models, producing predictions of the outside world on the basis of past experience. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterizing Zinc Speciation in Soils from a Smelter-Affected Boreal Forest Ecosystem.

PubMed

Hamilton, Jordan G; Farrell, Richard E; Chen, Ning; Feng, Renfei; Reid, Joel; Peak, Derek

2016-03-01

HudBay Minerals, Inc., has mined and/or processed Zn and Cu ore in Flin Flon, MB, Canada, since the 1930s. The boreal forest ecosystem and soil surrounding these facilities have been severely impacted by mixed metal contamination and HSO deposition. Zinc is one of the most prevalent smelter-derived contaminants and has been identified as a key factor that may be limiting revegetation. Metal toxicity is related to both total concentrations and speciation; therefore, X-ray absorption spectroscopy and X-ray fluorescence mapping were used to characterize Zn speciation in soils throughout the most heavily contaminated areas of the landscape. Zinc speciation was linked to two distinct soil types. Group I soils consist of exposed soils in weathered positions of bedrock outcrops with Zn present primarily as franklinite, a (ZnFeO) spinel mineral. Group II soils are stabilized by an invasive metal-tolerant grass species, with Zn found as a mixture of octahedral (Fe oxides) and tetrahedral Mn oxides) adsorption complexes with a franklinite component. Soil erosion influences Zn speciation through the redistribution of Zn and soil particulates from Group I landscape positions to Group II soils. Despite Group II soils having the highest concentrations of CaCl-extractable Zn, they support metal-tolerant plant growth. The metal-tolerant plants are probably preferentially colonizing these areas due to better soil and nutrient conditions as a result of soil deposition from upslope Group I areas. Zinc concentration and speciation appears to not influence the colonization by metal-tolerant grasses, but the overall soil properties and erosion effects prevent the revegetation by native boreal forest species. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Aqueous and solid phase speciation of arsenic in a Bengali aquifer using IC-ICP-MS and EXAFS

NASA Astrophysics Data System (ADS)

Gault, A. G.; Davidson, L. E.; Lythgoe, P. R.; Charnock, J. M.; Chatterjee, D.; Abou-Shakra, F. R.; Walker, H. J.; Polya, D. A.

2003-04-01

Contamination of groundwater and drinking water supplies with arsenic has been reported in many parts of the world and constitutes a serious public health threat. Nowhere is this more apparent than in West Bengal and Bangladesh where arsenic concentrations exceed both World Health Organisation (WHO) and national limits in drinking water supplies leading to what has been described as the worst mass poisoning of a human population in history. Knowledge of both aqueous and solid phase speciation of arsenic in such hazardous arsenic-rich groundwaters is crucial to understanding the processes controlling arsenic release. We report here preliminary work involving the determination of dissolved arsenic speciation in West Bengali groundwaters and extended X-ray absorption fine structure (EXAFS) analysis of the associated sediment. Groundwater samples collected from Nadia district, West Bengal were analysed for arsenic speciation by ion chromatography-inductively coupled plasma-mass spectrometry (IC-ICP-MS) within 14 days of collection. Total arsenic concentrations exceeding 850 ug/L were determined; inorganic arsenic constituted the bulk of the dissolved arsenic burden with As(III) as the dominant form. Minor amounts of methylated arsenicals were also detected, however, their concentration did not exceed 5 ug/L. The local coordination environment of arsenic in sediment associated with such groundwaters was probed using K-edge As EXAFS. This revealed that arsenic exists predominantly in its oxidised form, As(V), most likely adsorbed as bidentate arsenate tetrahedra on metal (Fe and/or Al) oxide/hydroxide surfaces, although incorporation of arsenic into a metal oxide structure cannot be unequivocally ruled out. Arsenic was found to occur in several different coordination environments and this, together with the low concentration (< 5 ug/g) of arsenic in the sediment, prevented the unambiguous assignment of the second coordination sphere. The analysis of the trends of key

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 ...

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...

Arsenic Speciation and Cadmium Determination in Tobacco Leaves, Ash and Smoke.

PubMed

Iwai, Takahiro; Chiba, Koichi; Narukawa, Tomohiro

2016-01-01

The concentrations of arsenic (As) and cadmium (Cd) in the tobacco leaves, ash and smoke of 10 kinds of cigarettes collected from different countries worldwide were determined by ICP-MS after microwave-assisted digestion. Total As and Cd concentrations in the tobacco leaves ranged from 0.20 to 0.63 and 1.8 to 9.9 mg kg(-1), respectively. By the speciation analysis of As in tobacco leaves and ash by HPLC-ICP-MS following acid extraction, arsenite [As(III)] and arsenate [As(V)] were determined and trace amounts of monomethylarsonic acid (MMAA), dimethylarsinic acid (DMAA), trimethylarsine oxide (TMAO), tetramethylarsonium (TeMA) and some unidentified As species were also found. Arsenic speciation for smoke absorbed in an aqueous solution was carried out. The sum of the As species in tobacco leaves, ash and smoke was in good agreement with the result of total As determination in each sample, and the recoveries of speciation were 100 ± 10%. The distributions and the behaviors of As species were clarified.

The Role of Transposable Elements in Speciation

PubMed Central

Serrato-Capuchina, Antonio; Matute, Daniel R.

2018-01-01

Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species. PMID:29762547

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

PubMed

Roux, Camille; Fraïsse, Christelle; Romiguier, Jonathan; Anciaux, Yoann; Galtier, Nicolas; Bierne, Nicolas

2016-12-01

Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids-the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.

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

Speciation in the Derrida-Higgs model with finite genomes and spatial populations

NASA Astrophysics Data System (ADS)

de Aguiar, Marcus A. M.

2017-02-01

The speciation model proposed by Derrida and Higgs demonstrated that a sexually reproducing population can split into different species in the absence of natural selection or any type of geographic isolation, provided that mating is assortative and the number of genes involved in the process is infinite. Here we revisit this model and simulate it for finite genomes, focusing on the question of how many genes it actually takes to trigger neutral sympatric speciation. We find that, for typical parameters used in the original model, it takes the order of 105 genes. We compare the results with a similar spatially explicit model where about 100 genes suffice for speciation. We show that when the number of genes is small the species that emerge are strongly segregated in space. For a larger number of genes, on the other hand, the spatial structure of the population is less important and the species distribution overlap considerably.

Polymorphic butterfly reveals the missing link in ecological speciation.

PubMed

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

2009-11-06

Ecological speciation occurs when ecologically based, divergent selection causes the evolution of reproductive isolation. There are many empirical examples of this process; however, there exists a poorly characterized stage during which the traits that distinguish species ecologically and reproductively segregate in a single population. By 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 the butterflies 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 of the missing link between an interbreeding population and isolated species.

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Bioconcentration and arsenic speciation analysis in ragworm, Hediste diversicolor (Muller 1776).

PubMed

Gaion, Andrea; Scuderi, Alice; Pellegrini, David; Sartori, Davide

2013-01-01

This study focused on bioconcentrations of arsenic in Hediste diversicolor (Müller 1776) after exposure to three different molecule solutions: arsenate, dimethyl-arsinate and arsenobetaine. Speciation analysis was carried out after exposing the organisms to these solutions in order to investigate their arsenic biotransformation capacity. Arsenic reached to the maximum level in these tissues after 15 days' exposure to a solution of 100 μg L(-1) of arsenobetaine, although a significant increase was obtained in worms exposed to arsenate. Speciation analysis shows that trimethyl-arsine oxide is the slowest detoxification phase recorded in experiment.

Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus).

PubMed

Moody, Michael L; Rieseberg, Loren H

2012-07-01

The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.

Lead Speciation in Microorganisms.

PubMed

Stewart, Theodora J

2017-04-10

The biogeochemical cycles of lead (Pb) have been largely affected by anthropogenic activities as a result of its high natural abundance and use over the centuries [1]. At sites more strongly impacted by urbanization [2] and mining [3], Pb is found at high nano to low micromolar concentrations in surface waters, and can be significantly higher in soil and sediment [4]. Microorganisms are found everywhere and their responses to Pb exposure can range from resistant to highly sensitive [5, 6]. These varying levels of toxicity can be attributed to the cellular handling of Pb, making it important to understand the role of intracellular Pb speciation for more accurate toxicity predictions.

Evaluation of comprehensive two-dimensional gas chromatography with flame photometric detection: potential application for sulfur speciation in shale oil.

PubMed

Mitrevski, Blagoj; Amer, Mohammad W; Chaffee, Alan L; Marriott, Philip J

2013-11-25

Flame photometric detection in the sulfur channel has been evaluated for sulfur speciation and quantification in comprehensive two-dimensional gas chromatography [GC × GC-FPD(S)] for S-compound speciation in shale extracts. Signal non-linearity and potential quenching effects were reportedly major limitations of this detector for analysis of sulfur in complex matrices. However, reliable linear relationships with correlation coefficient >0.99 can be obtained if the sum of the square root of each modulation slice in GC × GC is plotted vs. sulfur concentration. Furthermore, the quenching effects are reduced due to essentially complete separation of S-containing components from the hydrocarbon matrix. An increase of S/N of up to 150 times has been recorded for benzothiophene and dibenzothiophene in GC × GC-FPD when compared to GC-FPD due to the modulation process. As a consequence, 10 times lower detection limits were observed in the former mode. The applicability of the method was demonstrated using shale oil sample extracts. Three sulfur classes were completely separated and the target class (thiophenes) was successfully quantified after the rest of the sample was diverted to the second detector by using a heart-cut strategy. Based on the proposed method, 70% of the sulfur in the shale oil was assigned to the thiophenes, 24% to benzothiophenes, and 5% to dibenzothiophene compounds. Copyright © 2013 Elsevier B.V. All rights reserved.

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

USGS Publications Warehouse

Yeung, Carol K.L.; Tsai, Pi-Wen; Chesser, R. Terry; Lin, Rong-Chien; Yao, Cheng-Te; Tian, Xiu-Hua; Li, Shou-Hsien

2011-01-01

Although founder effect speciation has been a popular theoretical model for the speciation of geographically isolated taxa, its empirical importance has remained difficult to evaluate due to the intractability of past demography, which in a founder effect speciation scenario would involve a speciational bottleneck in the emergent species and the complete cessation of gene flow following divergence. Using regression-weighted approximate Bayesian computation, we tested the validity of these two fundamental conditions of founder effect speciation in a pair of sister species with disjunct distributions: the royal spoonbill Platalea regia in Australasia and the black-faced spoonbill Pl. minor in eastern Asia. When compared with genetic polymorphism observed at 20 nuclear loci in the two species, simulations showed that the founder effect speciation model had an extremely low posterior probability (1.55 × 10-8) of producing the extant genetic pattern. In contrast, speciation models that allowed for postdivergence gene flow were much more probable (posterior probabilities were 0.37 and 0.50 for the bottleneck with gene flow and the gene flow models, respectively) and postdivergence gene flow persisted for a considerable period of time (more than 80% of the divergence history in both models) following initial divergence (median = 197,000 generations, 95% credible interval [CI]: 50,000-478,000, for the bottleneck with gene flow model; and 186,000 generations, 95% CI: 45,000-477,000, for the gene flow model). Furthermore, the estimated population size reduction in Pl. regia to 7,000 individuals (median, 95% CI: 487-12,000, according to the bottleneck with gene flow model) was unlikely to have been severe enough to be considered a bottleneck. Therefore, these results do not support founder effect speciation in Pl. regia but indicate instead that the divergence between Pl. regia and Pl. minor was probably driven by selection despite continuous gene flow. In this light, we

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...

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

Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats?

PubMed

Kautt, Andreas F; Machado-Schiaffino, Gonzalo; Torres-Dowdall, Julian; Meyer, Axel

2016-08-01

Understanding how speciation can occur without geographic isolation remains a central objective in evolutionary biology. Generally, some form of disruptive selection and assortative mating are necessary for sympatric speciation to occur. Disruptive selection can arise from intraspecific competition for resources. If this competition leads to the differential use of habitats and variation in relevant traits is genetically determined, then assortative mating can be an automatic consequence (i.e., habitat isolation). In this study, we caught Midas cichlid fish from the limnetic (middle of the lake) and benthic (shore) habitats of Crater Lake Asososca Managua to test whether some of the necessary conditions for sympatric speciation due to intraspecific competition and habitat isolation are given. Lake As. Managua is very small (<900 m in diameter), extremely young (maximally 1245 years of age), and completely isolated. It is inhabited by, probably, only a single endemic species of Midas cichlids, Amphilophus tolteca. We found that fish from the limnetic habitat were more elongated than fish collected from the benthic habitat, as would be predicted from ecomorphological considerations. Stable isotope analyses confirmed that the former also exhibit a more limnetic lifestyle than the latter. Furthermore, split-brood design experiments in the laboratory suggest that phenotypic plasticity is unlikely to explain much of the observed differences in body elongation that we observed in the field. Yet, neutral markers (microsatellites) did not reveal any genetic clustering in the population. Interestingly, demographic inferences based on RAD-seq data suggest that the apparent lack of genetic differentiation at neutral markers could simply be due to a lack of time, as intraspecific competition may only have begun a few hundred generations ago.

Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons

PubMed Central

Verneau, Olivier; Catzeflis, François; Furano, Anthony V.

1998-01-01

Phylogenies based on the inheritance of shared derived characters will be ambiguous when the shared characters are not the result of common ancestry. Such characters are called homoplasies. Phylogenetic analysis also can be problematic if the characters have not changed sufficiently, as might be the case for rapid or recent speciations. The latter are of particular interest because evolutionary processes may be more accessible the more recent the speciation. The repeated DNA subfamilies generated by the mammalian L1 (LINE-1) retrotransposon are apparently homoplasy-free phylogenetic characters. L1 retrotransposons are transmitted only by inheritance and rapidly generate novel variants that produce distinct subfamilies of mostly defective copies, which then “age” as they diverge. Here we show that the L1 character can both resolve and date recent speciation events within the large group of very closely related rats known as Rattus sensu stricto. This lineage arose 5–6 million years ago (Mya) and subsequently underwent two episodes of speciation: an intense one, ≈2.7 Mya, produced at least five lineages in <0.3 My; a second began ≈1.2 Mya and may still be continuing. PMID:9736728

Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons.

PubMed

Verneau, O; Catzeflis, F; Furano, A V

1998-09-15

Phylogenies based on the inheritance of shared derived characters will be ambiguous when the shared characters are not the result of common ancestry. Such characters are called homoplasies. Phylogenetic analysis also can be problematic if the characters have not changed sufficiently, as might be the case for rapid or recent speciations. The latter are of particular interest because evolutionary processes may be more accessible the more recent the speciation. The repeated DNA subfamilies generated by the mammalian L1 (LINE-1) retrotransposon are apparently homoplasy-free phylogenetic characters. L1 retrotransposons are transmitted only by inheritance and rapidly generate novel variants that produce distinct subfamilies of mostly defective copies, which then "age" as they diverge. Here we show that the L1 character can both resolve and date recent speciation events within the large group of very closely related rats known as Rattus sensu stricto. This lineage arose 5-6 million years ago (Mya) and subsequently underwent two episodes of speciation: an intense one, approximately 2.7 Mya, produced at least five lineages in <0.3 My; a second began approximately 1.2 Mya and may still be continuing.

Phylogenetic congruence of parasitic smut fungi (Anthracoidea, Anthracoideaceae) and their host plants (Carex, Cyperaceae): Cospeciation or host-shift speciation?

PubMed

Escudero, Marcial

2015-07-01

• Fahrenholz's rule states that common ancestors of extant parasites were parasites of the common ancestors of extant hosts. Consequently, parasite phylogeny should mirror host phylogeny. The smut fungi genus Anthracoidea (Anthracoideaceae) is mainly hosted by species of the genus Carex (Cyperaceae). Whether smut fungi phylogeny mirrors sedge phylogeny is still under debate.• The nuclear large subunit DNA region (LSU; 57 accessions) from 31 Anthracoidea species and the ITS, ETS, and trnL-F spacer-trnL intron complex from 41 Carex species were used to infer the phylogenetic history of parasites and their hosts using a maximum likelihood approach. Event-based and distance-based cophylogenetic methods were used to test the hypothesis of whether the phylogeny of smut fungi from the genus Anthracoidea matches the phylogeny of the sedge Carex species they host.• Cophylogenetic reconstructions taking into account phylogenetic uncertainties based on event-based analyses demonstrated that the Anthracoidea phylogeny has significant topological congruence with the phylogeny of their Carex hosts. A distance-based test was also significant; therefore, the phylogenies of Anthracoide and Carex are partially congruent.• The phylogenetic congruence of Anthracoidea and Carex is partially based on smut fungi species being preferentially hosted by closely related sedges (host conservatism). In addition, many different events rather than only codivergence events are inferred. All of this evidence suggests that host-shift speciation rather than cospeciation seems to explain the cophylogenetic patterns of Anthracoidea and Carex. © 2015 Botanical Society of America, Inc.

Concurrent speciation in the eastern woodland salamanders (Genus Plethodon):DNA sequences of the complete albumin nuclear and partialmitochondrial 12s genes

USGS Publications Warehouse

Highton, Richard; Hastings, Amy Picard; Palmer, Catherine; Watts, Richard; Hass, Carla A.; Culver, Melanie; Arnold, Stevan

2012-01-01

Salamanders of the North American plethodontid genus Plethodon are important model organisms in a variety of studies that depend on a phylogenetic framework (e.g., chemical communication, ecological competition, life histories, hybridization, and speciation), and consequently their systematics has been intensively investigated over several decades. Nevertheless, we lack a synthesis of relationships among the species. In the analyses reported here we use new DNA sequence data from the complete nuclear albumin gene (1818 bp) and the 12s mitochondrial gene (355 bp), as well as published data for four other genes (Wiens et al., 2006), up to a total of 6989 bp, to infer relationships. We relate these results to past systematic work based on morphology, allozymes, and DNA sequences. Although basal relationships show a strong consensus across studies, many terminal relationships remain in flux despite substantial sequencing and other molecular and morphological studies. This systematic instability appears to be a consequence of contemporaneous bursts of speciation in the late Miocene and Pliocene, yielding many closely related extant species in each of the four eastern species groups. Therefore we conclude that many relationships are likely to remain poorly resolved in the face of additional sequencing efforts. On the other hand, the current classification of the 45 eastern species into four species groups is supported. The Plethodon cinereus group (10 species) is the sister group to the clade comprising the other three groups, but these latter groups (Plethodon glutinosus [28 species], Plethodon welleri [5 species], and Plethodon wehrlei [2 species]) probably diverged from each other at approximately the same time.

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

PubMed Central

McCann, Jamie; Stuessy, Tod F.; Villaseñor, Jose L.; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction. PMID:27611687

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae).

PubMed

McCann, Jamie; Schneeweiss, Gerald M; Stuessy, Tod F; Villaseñor, Jose L; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.

SPECIATED VOC EMISSIONS FROM MODERN GDI LIGHT DUTY VEHICLES

EPA Science Inventory

Chassis dynamometer emissions testing was conducted to characterize speciated volatile organic compounds (VOCs), including mobile source air toxics (MSATs) and ozone precursors, in exhaust emissions from three modern gasoline direct injection (GDI) light-duty vehicles. Each GDI v...

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

USGS Publications Warehouse

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

2014-01-01

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

Characterization and speciation of mercury-bearing mine wastes using X-ray absorption spectroscopy

USGS Publications Warehouse

Kim, C.S.; Brown, Gordon E.; Rytuba, J.J.

2000-01-01

Mining of mercury deposits located in the California Coast Range has resulted in the release of mercury to the local environment and water supplies. The solubility, transport, and potential bioavailability of mercury are controlled by its chemical speciation, which can be directly determined for samples with total mercury concentrations greater than 100 mg kg-1 (ppm) using X-ray absorption spectroscopy (XAS). This technique has the additional benefits of being non-destructive to the sample, element-specific, relatively sensitive at low concentrations, and requiring minimal sample preparation. In this study, Hg L(III)-edge extended X-ray absorption fine structure (EXAFS) spectra were collected for several mercury mine tailings (calcines) in the California Coast Range. Total mercury concentrations of samples analyzed ranged from 230 to 1060 ppm. Speciation data (mercury phases present and relative abundances) were obtained by comparing the spectra from heterogeneous, roasted (calcined) mine tailings samples with a spectral database of mercury minerals and sorbed mercury complexes. Speciation analyses were also conducted on known mixtures of pure mercury minerals in order to assess the quantitative accuracy of the technique. While some calcine samples were found to consist exclusively of mercuric sulfide, others contain additional, more soluble mercury phases, indicating a greater potential for the release of mercury into solution. Also, a correlation was observed between samples from hot-spring mercury deposits, in which chloride levels are elevated, and the presence of mercury-chloride species as detected by the speciation analysis. The speciation results demonstrate the ability of XAS to identify multiple mercury phases in a heterogeneous sample, with a quantitative accuracy of ??25% for the mercury-containing phases considered. Use of this technique, in conjunction with standard microanalytical techniques such as X-ray diffraction and electron probe microanalysis

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

PubMed

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

2006-07-01

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

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

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

Robinson, Troy A

2011-08-01

This dissertation explores lanthanide speciation in liquid solution systems related to separation schemes involving the acidic ligands: bis(2-ethylhexyl) phosphoric acid (HDEHP), lactate, and 8-hydroxyquinoline. Equilibrium speciation of neodymium (Nd 3+), sodium (Na+), HDEHP, water, and lactate in the TALSPEAK liquid-liquid extraction system was explored under varied Nd 3+ loading of HDEHP in the organic phase and through extraction from aqueous HCl and lactate media. System speciation was probed through vapor pressure osmometry, visible and Fourier Transform Infrared (FTIR) spectroscopy, 22Na and 13C labeled lactate radiotracer distribution measurements, Karl Fischer titrations, and equilibrium pH measurements. Distribution of Nd 3+, Na +,more » lactate, and equilibrium pH were modeled using the SXLSQI software to obtain logKNd and logKNa extraction constants under selected conditions. Results showed that high Nd 3+ loading of the HDEHP led to Nd 3+ speciation that departs from the ion exchange mechanism and includes formation of highly aggregated, polynuclear [NdLactate(DEHP) 2] x; (with x > 1). By substituting lanthanum (La 3+) for Nd 3+ in this system, NMR scoping experiments using 23Na, 31P nuclei and 13C labeled lactate were performed. Results indicated that this technique is sensitive to changes in system speciation, and that further experiments are warranted. In a homogeneous system representing the TALSPEAK aqueous phase, Lactate protonation behavior at various temperatures was characterized using a combination of potentiometric titration and modeling with the Hyperquad computer program. The temperature dependent deprotonation behavior of lactate showed little change with temperature at 2.0 M NaCl ionic strength. Cloud point extraction is a non-traditional separation technique that starts with a homogeneous phase that becomes heterogeneous by the micellization of surfactants through the increase of temperature. To better understand the behavior of

The luminosity of the double-mode Cepheid Y Carinae

NASA Technical Reports Server (NTRS)

Evans, Nancy R.

1992-01-01

IUE spectra of the double-mode Cepheid Y Carinae have been used to determine the spectral type of the binary companion. From the companion spectral type (B9.O V), the absolute magnitude of the Cepheid is found to be -2.94 mag, with an estimated uncertainty of +/-0.3. This luminosity is in good agreement with that from the period-luminosity-color relation of Feast and Walker for the fundamental mode. This agreement, together with the large magnitude difference between the B9.0 V star and the Cepheid, confirm that the Cepheid is a normal classical Cepheid with a mass much larger than that inferred from the ratio of the two periods (beat mass). The two double-mode Cepheids with independently determined luminosities (Y Car and V 367 Sct) both fall on the blue edge of the instability strip.

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...

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

PubMed

Zuo, Xiaojun; Fu, Dafang; Li, He

2012-11-01

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

Learning to speciate: The biased learning of mate preferences promotes adaptive radiation

PubMed Central

Gilman, R. Tucker; Kozak, Genevieve M.

2015-01-01

Bursts of rapid repeated speciation called adaptive radiations have generated much of Earth's biodiversity and fascinated biologists since Darwin, but we still do not know why some lineages radiate and others do not. Understanding what causes assortative mating to evolve rapidly and repeatedly in the same lineage is key to understanding adaptive radiation. Many species that have undergone adaptive radiations exhibit mate preference learning, where individuals acquire mate preferences by observing the phenotypes of other members of their populations. Mate preference learning can be biased if individuals also learn phenotypes to avoid in mates, and shift their preferences away from these avoided phenotypes. We used individual‐based computational simulations to study whether biased and unbiased mate preference learning promotes ecological speciation and adaptive radiation. We found that ecological speciation can be rapid and repeated when mate preferences are biased, but is inhibited when mate preferences are learned without bias. Our results suggest that biased mate preference learning may play an important role in generating animal biodiversity through adaptive radiation. PMID:26459795

Thermodynamic behavior of a phase transition in a model for sympatric speciation

NASA Astrophysics Data System (ADS)

Luz-Burgoa, K.; Moss de Oliveira, S.; Schwämmle, Veit; Sá Martins, J. S.

2006-08-01

We investigate the macroscopic effects of the ingredients that drive the origin of species through sympatric speciation. In our model, sympatric speciation is obtained as we tune up the strength of competition between individuals with different phenotypes. As a function of this control parameter, we can characterize, through the behavior of a macroscopic order parameter, a phase transition from a nonspeciation to a speciation state of the system. The behavior of the first derivative of the order parameter with respect to the control parameter is consistent with a phase transition and exhibits a sharp peak at the transition point. For different resources distribution, the transition point is shifted, an effect similar to pressure in a PVT system. The inverse of the parameter related to a sexual selection strength behaves like an external field in the system and, as thus, is also a control parameter. The macroscopic effects of the biological parameters used in our model are a reminiscent of the behavior of thermodynamic quantities in a phase transition of an equilibrium physical system.

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

EPA Science Inventory

The US Environmental Protection Agency (EPA)’s SPECIATE database contains speciation profiles for both particulate matter (PM) and volatile organic compounds (VOCs) that are key inputs for creating speciated emission inventories for air quality modeling. The objective of th...

High-frequency coherent edge fluctuations in a high-pedestal-pressure quiescent H-mode plasma.

PubMed

Yan, Z; McKee, G R; Groebner, R J; Snyder, P B; Osborne, T H; Burrell, K H

2011-07-29

A set of high frequency coherent (HFC) modes (f=80-250 kHz) is observed with beam emission spectroscopy measurements of density fluctuations in the pedestal of a strongly shaped quiescent H-mode plasma on DIII-D, with characteristics predicted for kinetic ballooning modes (KBM): propagation in the ion-diamagnetic drift direction; a frequency near 0.2-0.3 times the ion-diamagnetic frequency; inferred toroidal mode numbers of n∼10-25; poloidal wave numbers of k(θ)∼0.17-0.4 cm(-1); and high measured decorrelation rates (τ(c)(-1)∼ω(s)∼0.5×10(6) s(-1)). Their appearance correlates with saturation of the pedestal pressure. © 2011 American Physical Society

Arsenic speciation in rice and risk assessment of inorganic arsenic in Taiwan population.

PubMed

Chen, Hsiu-Ling; Lee, Ching-Chang; Huang, Winn-Jung; Huang, Han-Ting; Wu, Yi-Chen; Hsu, Ya-Chen; Kao, Yi-Ting

2016-03-01

This study assessed the total arsenic content and arsenic speciation in rice to determine the health risks associated with rice consumption in various age-gender subgroups in Taiwan. The average total arsenic levels in white rice and brown rice were 116.6 ± 39.2 and 215.5 ± 63.5 ng/g weight (n = 51 and 13), respectively. The cumulative cancer risk among males was 10.4/100,000. The highest fraction of inorganic/total arsenic content in white rice ranged from 76.9 to 88.2 % and from 81.0 to 96.5 % in brown rice. The current study found different arsenic speciation of rice in southern Taiwan, where the famous blackfoot disease has been reported compared with arsenic speciation from other Taiwan areas. Therefore, rice and other grains should be further monitored in southern Taiwan to evaluate whether arsenic contamination is well controlled in this area.

Capillary electrophoresis application in metal speciation and complexation characterization

USDA-ARS?s Scientific Manuscript database

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...

Periphyton and abiotic factors influencing arsenic speciation in aquatic environments: Periphyton alters arsenic speciation

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

Lopez, Adeline R.; Silva, Silmara Costa; Webb, Samuel M.

Benthic periphytic biofilms are important food sources at the base of aquatic ecosystems. These biofilms also sit at the interface of oxic waters and hypoxic sediments, and can be influenced by or influence trace element speciation. In the present study, we compared arsenic (As) enrichment in periphyton exposed to arsenate (As[V]) or arsenite (As[III]) (20 μg/L, static renewal, 7 d), and we found similar accumulation patterns of total As (101 ± 27 and 88 ± 22mgkg -1 dry wt, respectively). Periphyton As was 6281- and 6684-fold higher than their aqueous exposures and occurred primarily as As(V). When these biofilms weremore » fed to larval mayflies, similar total As tissue concentrations (13.9 and 14.6mgkg -1 dry wt, respectively) were observed, revealing significant biodilution (~10% of their dietary concentrations). Finally, we investigated the influence of aeration and periphyton presence on As speciation in solutions and solid phases treated with As(III). Predominantly As(III) solutions were slowly oxidized over a 7-d time period, in the absence of periphyton, and aeration did not strongly affect oxidation rates. However, in the presence of periphyton, solution and solid-phase analyses (by microscale x-ray absorption spectroscopy) showed rapid As(III) oxidation to As(V) and an increasing proportion of organo-As forming over time. Thus periphyton plays several roles in As environmental behavior: 1) decreasing total dissolved As concentrations via abiotic and biotic accumulation, 2) rapidly oxidizing As(III) to As(V), 3) effluxing organo-As forms into solution, and 4) limiting trophic transfer to aquatic grazers.« less

Periphyton and abiotic factors influencing arsenic speciation in aquatic environments: Periphyton alters arsenic speciation

DOE PAGES

Lopez, Adeline R.; Silva, Silmara Costa; Webb, Samuel M.; ...

2017-11-02

Benthic periphytic biofilms are important food sources at the base of aquatic ecosystems. These biofilms also sit at the interface of oxic waters and hypoxic sediments, and can be influenced by or influence trace element speciation. In the present study, we compared arsenic (As) enrichment in periphyton exposed to arsenate (As[V]) or arsenite (As[III]) (20 μg/L, static renewal, 7 d), and we found similar accumulation patterns of total As (101 ± 27 and 88 ± 22mgkg -1 dry wt, respectively). Periphyton As was 6281- and 6684-fold higher than their aqueous exposures and occurred primarily as As(V). When these biofilms weremore » fed to larval mayflies, similar total As tissue concentrations (13.9 and 14.6mgkg -1 dry wt, respectively) were observed, revealing significant biodilution (~10% of their dietary concentrations). Finally, we investigated the influence of aeration and periphyton presence on As speciation in solutions and solid phases treated with As(III). Predominantly As(III) solutions were slowly oxidized over a 7-d time period, in the absence of periphyton, and aeration did not strongly affect oxidation rates. However, in the presence of periphyton, solution and solid-phase analyses (by microscale x-ray absorption spectroscopy) showed rapid As(III) oxidation to As(V) and an increasing proportion of organo-As forming over time. Thus periphyton plays several roles in As environmental behavior: 1) decreasing total dissolved As concentrations via abiotic and biotic accumulation, 2) rapidly oxidizing As(III) to As(V), 3) effluxing organo-As forms into solution, and 4) limiting trophic transfer to aquatic grazers.« less

SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT

PubMed Central

Baker, Robert J.; Bradley, Robert D.

2009-01-01

We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson–Dobzhansky–Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these “morphologically cryptic genetic species” are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species

Stan: Statistical inference

NASA Astrophysics Data System (ADS)

Stan Development Team

2018-01-01

Stan facilitates statistical inference at the frontiers of applied statistics and provides both a modeling language for specifying complex statistical models and a library of statistical algorithms for computing inferences with those models. These components are exposed through interfaces in environments such as R, Python, and the command line.

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

PubMed Central

Weekley, Claire M.; Aitken, Jade B.; Finney, Lydia; Vogt, Stefan; Witting, Paul K.; Harris, Hugh H.

2013-01-01

Determining the speciation of selenium in vivo is crucial to understanding the biological activity of this essential element, which is a popular dietary supplement due to its anti-cancer properties. Hyphenated techniques that combine separation and detection methods are traditionally and effectively used in selenium speciation analysis, but require extensive sample preparation that may affect speciation. Synchrotron-based X-ray absorption and fluorescence techniques offer an alternative approach to selenium speciation analysis that requires minimal sample preparation. We present a brief summary of some key HPLC-ICP-MS and ESI-MS/MS studies of the speciation of selenium in cells and rat tissues. We review the results of a top-down approach to selenium speciation in human lung cancer cells that aims to link the speciation and distribution of selenium to its biological activity using a combination of X-ray absorption spectroscopy (XAS) and X-ray fluorescence microscopy (XFM). The results of this approach highlight the distinct fates of selenomethionine, methylselenocysteine and selenite in terms of their speciation and distribution within cells: organic selenium metabolites were widely distributed throughout the cells, whereas inorganic selenium metabolites were compartmentalized and associated with copper. New data from the XFM mapping of electrophoretically-separated cell lysates show the distribution of selenium in the proteins of selenomethionine-treated cells. Future applications of this top-down approach are discussed. PMID:23698165

Influence of super-horizon modes on correlation functions during inflation

NASA Astrophysics Data System (ADS)

Deutsch, Anne-Sylvie

2018-05-01

Coupling between sub- and super-Hubble modes can affect the locally observed statistics of our universe. In the context of Quasi-Single Field Inflation, we can compute correlation functions and derive the influence of those unobservable modes on observed correlation functions as well as on the inferred cosmological parameters. We study how different classes of diagrams affect the bispectrum in the squeezed limit; in particular, while contact-like diagrams leave the scaling between the long and short modes unchanged, exchange-like diagrams do modify the shape of the bispectrum. We show that the mass of the hidden sector field can hence be biased by an unavoidable cosmic variance that can reach a 1-σ uncertainty of Script O(10%) for a weakly non-Gaussian universe. Finally, we go beyond the bispectrum and show how couplings between unobservable and observable modes can affect generic correlation functions with arbitrary order non-derivative self-interactions.

Speciation evolution of zinc and copper during pyrolysis and hydrothermal carbonization treatments of sewage sludges

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

Huang, Rixiang; Zhang, Bei; Saad, Emily M.

Thermal and hydrothermal treatments are promising techniques for sewage sludge management that can potentially facilitate safe waste disposal, energy recovery, and nutrient recovery/recycling. Content and speciation of heavy metals in the treatment products affect the potential environmental risks upon sludge disposal and/or application of the treatment products. Therefore, it is important to study the speciation transformation of heavy metals and the effects of treatment conditions. By combining synchrotron X-ray spectroscopy/microscopy analysis and sequential chemical extraction, this study systematically characterized the speciation of Zn and Cu in municipal sewage sludges and their chars derived from pyrolysis (a representative thermal treatment technique)more » and hydrothermal carbonization (HTC; a representative hydrothermal treatment technique). Spectroscopy analysis revealed enhanced sulfidation of Zn and Cu by anaerobic digestion and HTC treatments, as compared to desulfidation by pyrolysis. Overall, changes in the chemical speciation and matrix properties led to reduced mobility of Zn and Cu in the treatment products. These results provide insights into the reaction mechanisms during pyrolysis and HTC treatments of sludges and can help evaluate the environmental/health risks associated with the metals in the treatment products.« less

Speciation of mercury compounds by differential atomization - atomic absorption spectroscopy

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

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

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 formmore » 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.« less

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow.

PubMed

Ravinet, M; Faria, R; Butlin, R K; Galindo, J; Bierne, N; Rafajlović, M; Noor, M A F; Mehlig, B; Westram, A M

2017-08-01

Speciation, the evolution of reproductive isolation among populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting gene flow locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in factors such as background selection and selective sweeps, recombination and mutation rate variation, and heterogeneous gene density. Extracting the effects of gene flow, divergent selection and reproductive isolation from such modifying factors presents a major challenge to speciation genomics. We argue one of the principal aims of the field is to identify the barrier loci involved in limiting gene flow. We first summarize the expected signatures of selection at barrier loci, at the genomic regions linked to them and across the entire genome. We then discuss the modifying factors that complicate the interpretation of the observed genomic landscape. Finally, we end with a road map for future speciation research: a proposal for how to account for these modifying factors and to progress towards understanding the nature of barrier loci. Despite the difficulties of interpreting empirical data, we argue that the availability of promising technical and analytical methods will shed further light on the important roles that gene flow and divergent selection have in shaping the genomic landscape of speciation. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

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

PubMed

Ticknor, Jonathan L; Hsu-Kim, Heileen; Deshusses, Marc A

2014-01-15

Mercury emissions from coal combustion have become a global concern as growing energy demands have increased the consumption of coal. The effective implementation of treatment technologies requires knowledge of mercury speciation in the flue gas, namely concentrations of elemental, oxidized and particulate mercury at the exit of the boiler. A model that can accurately predict mercury species in flue gas would be very useful in that context. Here, a Bayesian regularized artificial neural network (BRANN) that uses five coal properties and combustion temperature was developed to predict mercury speciation in flue gases before treatment technology implementation. The results of the model show that up to 97 percent of the variation in mercury species concentration is captured through the use of BRANNs. The BRANN model was used to conduct a parametric sensitivity which revealed that the coal chlorine content and coal calorific value were the most sensitive parameters, followed by the combustion temperature. The coal sulfur content was the least important parameter. The results demonstrate the applicability of BRANNs for predicting mercury concentration and speciation in combustion flue gas and provide a more efficient and effective technique when compared to other advanced non-mechanistic modeling strategies. Copyright © 2013 Elsevier B.V. All rights reserved.

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

PubMed

Reeve, James; Ortiz-Barrientos, Daniel; Engelstädter, Jan

2016-10-26

Recombination can impede ecological speciation with gene flow by mixing locally adapted genotypes with maladapted migrant genotypes from a divergent population. In such a scenario, suppression of recombination can be selectively favoured. However, in finite populations evolving under the influence of random genetic drift, recombination can also facilitate adaptation by reducing Hill-Robertson interference between loci under selection. In this case, increased recombination rates can be favoured. Although these two major effects on recombination have been studied individually, their joint effect on ecological speciation with gene flow remains unexplored. Using a mathematical model, we investigated the evolution of recombination rates in two finite populations that exchange migrants while adapting to contrasting environments. Our results indicate a two-step dynamic where increased recombination is first favoured (in response to the Hill-Robertson effect), and then disfavoured, as the cost of recombining locally with maladapted migrant genotypes increases over time (the maladaptive gene flow effect). In larger populations, a stronger initial benefit for recombination was observed, whereas high migration rates intensify the long-term cost of recombination. These dynamics may have important implications for our understanding of the conditions that facilitate incipient speciation with gene flow and the evolution of recombination in finite populations. © 2016 The Author(s).

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

PubMed

Dang, Duc Huy; Evans, R Douglas

2018-03-01

High resolution electrospray ionization mass spectrometry (ESI-HRMS) was used to study the speciation of molybdate in interaction with halides (Cl, F, Br). Desolvation during electrospray ionization induced alteration of aqueous species but method optimization successfully suppressed artefact compounds. At low Mo concentrations, chloro(oxo)molybdate and fluoro(oxo)molybdate species were found and in natural samples, MoO 3 Cl was detected for the first time, to the best of our knowledge. Apparent equilibrium constants for Cl substitution on molybdate were calculated for a range of pH values from 4.5 to 8.5. A minor alteration in speciation during the gas phase (conversion of doubly charged MoO 4 2- to HMoO 4 - ) did not allow investigation of the molybdate acid-base properties; however this could be determined by speciation modeling. This study provides further evidence that ESI-HRMS is a fast and suitable tool to Deceasedassess the speciation of inorganic compounds such as Mo. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

Bhavsar, Satyendra P; Diamond, Miriam L; Gandhi, Nilima; Nilsen, Joel

2004-10-01

A coupled metal transport and speciation/complexation model (TRANSPEC) has been developed to estimate the speciation and fate of multiple interconverting species in surface aquatic systems. Dynamic-TRANSPEC loosely, sequentially couples the speciation/complexation and fate modules that, for the unsteady state formulation, run alternatively at every time step. The speciation module first estimates species abundance using, in this version, MINEQL+ considering time-dependent changes in water and pore-water chemistry. The fate module is based on the quantitative water air sediment interaction (QWASI) model and fugacity/aquivalence formulation, with the option of using a pseudo-steady state solution to account for past discharges. Similarly to the QWASI model for organic contaminants, TRANSPEC assumes the instantaneous equilibrium distribution of metal species among dissolved, colloidal, and particulate phases based on ambient chemistry parameters that can be collected through conventional field methods. The model is illustrated with its application to Ross Lake (Manitoba, Canada) that has elevated Zn concentrations due to discharges over 70 years from a mining operation. Using measurements from field studies, the model reproduces year-round variations in Zn water concentrations. A 10-year projection for current conditions suggests decreasing Zn remobilization and export from the lake. Decreasing Zn loadings increases sediment-to-water transport but decreases water concentrations, and vice versa. Species distribution is affected by pH such that a decrease in pH increases metal export from the lake and vice versa.

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

NASA Astrophysics Data System (ADS)

Szpunar, Joanna; McSheehy, Shona; Połeć, Kasia; Vacchina, Véronique; Mounicou, Sandra; Rodriguez, Isaac; Łobiński, Ryszard

2000-07-01

Recent advances in the coupling of gas chromatography (GC) and high performance liquid chromatography (HPLC) with inductively coupled plasma mass spectrometry (ICP MS) and their role in trace element speciation analysis of environmental materials are presented. The discussion is illustrated with three research examples concerning the following topics: (i) development and coupling of multicapillary microcolumn GC with ICP MS for speciation of organotin in sediment and biological tissue samples; (ii) speciation of arsenic in marine algae by size-exclusion-anion-exchange HPLC-ICP MS; and (iii) speciation of cadmium in plant cell cultures by size-exclusion HPLC-ICP MS. Particular attention is paid to the problem of signal identification in ICP MS chromatograms; the potential of electrospray MS/MS for this purpose is highlighted.

MULTINEST: an efficient and robust Bayesian inference tool for cosmology and particle physics

NASA Astrophysics Data System (ADS)

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

2009-10-01

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, which itself significantly outperformed existing Markov chain Monte Carlo techniques in a wide range of astrophysical inference problems. The accuracy and economy of the MULTINEST algorithm are demonstrated by application to two toy problems and to a cosmological inference problem focusing on the extension of the vanilla Λ cold dark matter model to include spatial curvature and a varying equation of state for dark energy. The MULTINEST software, which is fully parallelized using MPI and includes an interface to COSMOMC, is available at http://www.mrao.cam.ac.uk/software/multinest/. It will also be released as part of the SUPERBAYES package, for the analysis of supersymmetric theories of particle physics, at http://www.superbayes.org.

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

PubMed Central

Jabłońska-Czapla, Magdalena

2015-01-01

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

Is awareness necessary for true inference?

PubMed

Leo, Peter D; Greene, Anthony J

2008-09-01

In transitive inference, participants learn a set of context-dependent discriminations that can be organized into a hierarchy that supports inference. Several studies show that inference occurs with or without task awareness. However, some studies assert that without awareness, performance is attributable to pseudoinference. By this account, inference-like performance is achieved by differential stimulus weighting according to the stimuli's proximity to the end items of the hierarchy. We implement an inference task that cannot be based on differential stimulus weighting. The design itself rules out pseudoinference strategies. Success on the task without evidence of deliberative strategies would therefore suggest that true inference can be achieved implicitly. We found that accurate performance on the inference task was not dependent on explicit awareness. The finding is consistent with a growing body of evidence that indicates that forms of learning and memory supporting inference and flexibility do not necessarily depend on task awareness.

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

PubMed Central

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

1975-01-01

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

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

2013-09-07

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.

Speciation of Soil Phosphorus Assessed by XANES Spectroscopy at Different Spatial Scales

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

Hesterberg, Dean; McNulty, Ian; Thieme, Juergen

Precise management of soil phosphorus (P) to meet competing demands of agriculture and environmental protection can benefit from more comprehensive characterization of P speciation in soils. Our objectives were to provide spatial context for spectroscopic analyses of soil P speciation in relation to molecular-scale species and landscape-scale management of P, and to compare soil P-species diversity from spectroscopic measurements at submicron and millimeter scales. The spatial range of ~26 orders of magnitude between atomic and field scales presents a challenge to upscaling and downscaling information from spectroscopic analyses of soils. Scanning fluorescence X-ray microscopy images of a 50-mm ´ 45-mmmore » area of an organic soil sample showed heterogeneous distributions of P, Al, and Si. Microscale X-ray absorption near edge structure (μ-XANES) spectra collected at the P K-edge from 12 spots on the soil sample exhibited diverse features that indicated variations in highly localized P speciation. Linear combination fitting analysis of the μ-XANES spectra included various proportions of three standards that appeared in fits for most spots and five standards that appeared in fits for one spot each. The fit to a bulk-soil spectrum was dominated by two of the common standards in the μ-XANES fits, and a fit to the sum of m-XANES spectra included four of the standards. Lastly, these results illustrate a gain in P species sensitivity from spatially resolved XANES analysis. Integrating spectroscopic analyses from multiple scales determines soil P species diversity and will ultimately help connect speciation to the chemical reactivity and mobility of P in soils.« less

Speciation of Soil Phosphorus Assessed by XANES Spectroscopy at Different Spatial Scales

DOE PAGES

Hesterberg, Dean; McNulty, Ian; Thieme, Juergen

2017-07-27

Precise management of soil phosphorus (P) to meet competing demands of agriculture and environmental protection can benefit from more comprehensive characterization of P speciation in soils. Our objectives were to provide spatial context for spectroscopic analyses of soil P speciation in relation to molecular-scale species and landscape-scale management of P, and to compare soil P-species diversity from spectroscopic measurements at submicron and millimeter scales. The spatial range of ~26 orders of magnitude between atomic and field scales presents a challenge to upscaling and downscaling information from spectroscopic analyses of soils. Scanning fluorescence X-ray microscopy images of a 50-mm ´ 45-mmmore » area of an organic soil sample showed heterogeneous distributions of P, Al, and Si. Microscale X-ray absorption near edge structure (μ-XANES) spectra collected at the P K-edge from 12 spots on the soil sample exhibited diverse features that indicated variations in highly localized P speciation. Linear combination fitting analysis of the μ-XANES spectra included various proportions of three standards that appeared in fits for most spots and five standards that appeared in fits for one spot each. The fit to a bulk-soil spectrum was dominated by two of the common standards in the μ-XANES fits, and a fit to the sum of m-XANES spectra included four of the standards. Lastly, these results illustrate a gain in P species sensitivity from spatially resolved XANES analysis. Integrating spectroscopic analyses from multiple scales determines soil P species diversity and will ultimately help connect speciation to the chemical reactivity and mobility of P in soils.« less

Lead Speciation and In Vitro Bioaccessibility of Compost-Amended Urban Garden Soils

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

Attanayake, Chammi P.; Hettiarachchi, Ganga M.; Ma, Qing

In situ soil amendments can modify the Pb bioavailability by changing soil Pb speciation. Urban soils from three vegetable gardens containing different total Pb concentrations were used. The study evaluated how compost amendment and aging of soil-compost mixture in situ affected the following: (i) soil Pb speciation in the field and (ii) change of soil Pb speciation during an in vitro bioaccessibility extraction mimicking gastric phase dissolution at pH 2.5. X-ray absorption fine structure spectroscopy was used to determine Pb speciation in amended and nonamended soils and residues left after in vitro bioaccessibility extraction of those soils. Compost amendment andmore » aging of compost in the field had a negligible effect on Pb bioaccessibility in the soils. Major Pb species in the soils were Pb sorbed to Fe oxy(hydr)oxide (Pb-Fh) and to soil organic C (Pb-Org). The fraction of Pb-Org was increased as soil-compost mixture aged in the field. During the in vitro extraction, the fraction of Pb-Fh was decreased, the fraction of Pb-Org was increased, and hydroxypyromorphite was formed in both amended and nonamended soils. Freshly incorporated compost enhanced the dissolution of Pb-Fh during the extraction. As soil-compost mixture aged in the field, the dissolution of Pb-Fh was low, demonstrating more stability of the Pb-Fh during the extraction. Compost amendment showed potential to contribute to reduced bioaccessibility of Pb as compost aged in the soil by increasing Pb-Org fraction in the field and stability of Pb-Fh during the in vitro bioaccessibility extraction.« less

Selenium speciation in acidic environmental samples: application to acid rain-soil interaction at Mount Etna volcano.

PubMed

Floor, Geerke H; Iglesías, Mònica; Román-Ross, Gabriela; Corvini, Philippe F X; Lenz, Markus

2011-09-01

Speciation plays a crucial role in elemental mobility. However, trace level selenium (Se) speciation analyses in aqueous samples from acidic environments are hampered due to adsorption of the analytes (i.e. selenate, selenite) on precipitates. Such solid phases can form during pH adaptation up till now necessary for chromatographic separation. Thermodynamic calculations in this study predicted that a pH<4 is needed to prevent precipitation of Al and Fe phases. Therefore, a speciation method with a low pH eluent that matches the natural sample pH of acid rain-soil interaction samples from Etna volcano was developed. With a mobile phase containing 20mM ammonium citrate at pH 3, selenate and selenite could be separated in different acidic media (spiked water, rain, soil leachates) in <10 min with a LOQ of 0.2 μg L(-1) using (78)Se for detection. Applying this speciation analysis to study acid rain-soil interaction using synthetic rain based on H(2)SO(4) and soil samples collected at the flanks of Etna volcano demonstrated the dominance of selenate over selenite in leachates from samples collected close to the volcanic craters. This suggests that competitive behavior with sulfate present in acid rain might be a key factor in Se mobilization. The developed speciation method can significantly contribute to understand Se cycling in acidic, Al/Fe rich environments. Copyright © 2011 Elsevier Ltd. All rights reserved.

Judd-Ofelt Parameters via Bayesian Inference

NASA Astrophysics Data System (ADS)

Silva, Valdeir A.; Silva, José W.; de Morais, Paulo C.; Dantas, Noelio O.

2018-04-01

Bayesian inference was used as a new approach to calculate of rare earth (RE) ion spectroscopic parameters within the Judd-Ofelt theory using the Li2O-B2O3-Al2O3 glass system doped with Nd2O3 and TiO2. This system was synthesized by the fusion method, and the physical properties of the as-synthesized material were investigated. Optical absorption, photoluminescence, micro-Raman, mass density, refractive index, and radiative lifetime calcuations were performed. We investigated the effects of crystal field changes on Nd3+-ions caused due to co-doping with increasing TiO2 content. We observed that co-doping with TiO2 altered the radiative transition rates A( J, J '), favored symmetry enhancement around the Nd3+-ions, and promoted the onset of vibrational modes, contributed to the attenuation of O-H bonds, and substantially increased the spectroscopic quality, χ.

Macro- and microscale investigation of selenium speciation in Blackfoot river, Idaho sediments.

PubMed

Oram, Libbie L; Strawn, Daniel G; Marcus, Matthew A; Fakra, Sirine C; Möller, Gregory

2008-09-15

The transport and bioavailability of selenium in the environment is controlled by its chemical speciation. However, knowledge of the biogeochemistry and speciation of Se in streambed sediment is limited. We investigated the speciation of Se in sediment cores from the Blackfoot River (BFR), Idaho using sequential extractions and synchrotron-based micro-X-ray fluorescence (micro-SXRF). We collected micro-SXRF oxidation state maps of Se in sediments, which had not been done on natural sediment samples. Selective extractions showed that most Se in the sediments is present as either (1) nonextractable Se or (2) base extractable Se. Results from micro-SXRF showed three defined species of Se were present in all four samples: Se(-II,O), Se(IV), and Se(VI). Se(-II,O) was the predominant species in samples from one location, and Se(IV) was the predominant species in samples from a second location. Results from both techniques were consistent, and suggested that the predominant species were Se(-II) species associated with recalcitrant organic matter, and Se(IV) species tightly bound to organic materials. This information can be used to predict the biogeochemical cycling and bioavailability of Se in streambed sediment environments.

Relative Bioavailability and Bioaccessability and Speciation of ...

EPA Pesticide Factsheets

Background: Assessment of soil arsenic (As) bioavailability may profoundly affect the extent of remediation required at contaminated sites by improving human exposure estimates. Because small adjustments in soil As bioavailability estimates can significantly alter risk assessments and remediation goals, convenient, rapid, reliable, and inexpensive tools are needed to determine soil As bioavailability. Objectives: We evaluated inexpensive methods for assessing As bioavailability in soil as a means to improve human exposure estimates and potentially reduce remediation costs. Methods: Nine soils from residential sites affected by mining or smelting activity and two National Institute of Standards and Technology standard reference materials were evaluated for As bioavailability, bioaccessibility, and speciation. Arsenic bioavailability was determined using an in vivo mouse model, and As bioaccessibility was determined using the Solubility/Bioavailability Research Consortium in vitro assay. Arsenic speciation in soil and selected soil physicochemical properties were also evaluated to determine whether these parameters could be used as predictors of As bio¬availability and bioaccessibility. Results: In the mouse assay, we compared bioavailabilities of As in soils with that for sodium arsenate. Relative bioavailabilities (RBAs) of soil As ranged from 11% to 53% (mean, 33%). In vitro soil As bioaccessibility values were strongly correlated with soil As RBAs (R

Speciation of animal fat: Needs and challenges.

PubMed

Hsieh, Yun-Hwa Peggy; Ofori, Jack Appiah

2017-05-24

The use of pork fat is a concern for Muslims and Jews, who for religious reasons avoid consuming anything that is pig-derived. The use of bovine materials, including beef fat, is prohibited in Hinduism and may also pose a risk of carrying the infectious agent for bovine spongiform encephalopathy. Vegetable oils are sometimes adulterated with animal fat or pork fat with beef fat for economic gain. The development of methods to determine the species origin of fat has therefore become a priority due to the complex and global nature of the food trade, which creates opportunities for the fraudulent use of these animal fats as food ingredients. However, determining the species origin of fats in processed foods or composite blends is an arduous task as the adulterant has a composition that is very similar to that of the original fat or oil. This review examines some of the methods that have been developed for fat speciation, including both fat-based and DNA-based methods, their shortcomings, and the need for additional alternatives. Protein-based methods, specifically immunoassays targeting residual proteins in adipose tissue, that are being explored by researchers as a new tool for fat speciation will also be discussed.

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…

Differential rotation in main-sequence solar-like stars: Qualitative inference from asteroseismic data

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

Lund, Mikkel N.; Christensen-Dalsgaard, Jørgen; Miesch, Mark S., E-mail: mikkelnl@phys.au.dk

2014-08-01

Understanding differential rotation of Sun-like stars is of great importance for insight into the angular momentum transport in these stars. One means of gaining such information is that of asteroseismology. By a forward modeling approach we analyze in a qualitative manner the impact of different differential rotation profiles on the splittings of p-mode oscillation frequencies. The optimum modes for inference on differential rotation are identified along with the best value of the stellar inclination angle. We find that in general it is not likely that asteroseismology can be used to make an unambiguous distinction between a rotation profile such asmore » a conical Sun-like profile and a cylindrical profile. In addition, it seems unlikely that asteroseismology of Sun-like stars will result in inferences on the radial profile of the differential rotation, such as can be done for red giants. At best, one could possibly obtain the sign of the radial differential rotation gradient. Measurements of the extent of the latitudinal differential from frequency splitting are, however, more promising. One very interesting aspect that could likely be tested from frequency splittings is whether the differential rotation is solar-like or anti-solar-like in nature, in the sense that a solar-like profile has an equator rotating faster than the poles.« less

Observation, Inference, and Imagination: Elements of Edgar Allan Poe's Philosophy of Science

NASA Astrophysics Data System (ADS)

Gelfert, Axel

2014-03-01

Edgar Allan Poe's standing as a literary figure, who drew on (and sometimes dabbled in) the scientific debates of his time, makes him an intriguing character for any exploration of the historical interrelationship between science, literature and philosophy. His sprawling `prose-poem' Eureka (1848), in particular, has sometimes been scrutinized for anticipations of later scientific developments. By contrast, the present paper argues that it should be understood as a contribution to the raging debates about scientific methodology at the time. This methodological interest, which is echoed in Poe's `tales of ratiocination', gives rise to a proposed new mode of—broadly abductive—inference, which Poe attributes to the hybrid figure of the `poet-mathematician'. Without creative imagination and intuition, Science would necessarily remain incomplete, even by its own standards. This concern with imaginative (abductive) inference ties in nicely with his coherentism, which grants pride of place to the twin virtues of Simplicity and Consistency, which must constrain imagination lest it degenerate into mere fancy.

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

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

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

1993-11-01

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

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

DOE PAGES

Kaufeld, Kimberly Ann; Fuentes, Montse; Reich, Brian J.; ...

2017-09-11

Evidence suggests that exposure to elevated concentrations of air pollution during pregnancy is associated with increased risks of birth defects and other adverse birth outcomes. While current regulations put limits on total PM2.5 concentrations, there are many speciated pollutants within this size class that likely have distinct effects on perinatal health. However, due to correlations between these speciated pollutants, it can be difficult to decipher their effects in a model for birth outcomes. To combat this difficulty, we develop a multivariate spatio-temporal Bayesian model for speciated particulate matter using dynamic spatial factors. These spatial factors can then be interpolated tomore » the pregnant women’s homes to be used to model birth defects. The birth defect model allows the impact of pollutants to vary across different weeks of the pregnancy in order to identify susceptible periods. Here, the proposed methodology is illustrated using pollutant monitoring data from the Environmental Protection Agency and birth records from the National Birth Defect Prevention Study.« less

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

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

Kaufeld, Kimberly Ann; Fuentes, Montse; Reich, Brian J.

Evidence suggests that exposure to elevated concentrations of air pollution during pregnancy is associated with increased risks of birth defects and other adverse birth outcomes. While current regulations put limits on total PM2.5 concentrations, there are many speciated pollutants within this size class that likely have distinct effects on perinatal health. However, due to correlations between these speciated pollutants, it can be difficult to decipher their effects in a model for birth outcomes. To combat this difficulty, we develop a multivariate spatio-temporal Bayesian model for speciated particulate matter using dynamic spatial factors. These spatial factors can then be interpolated tomore » the pregnant women’s homes to be used to model birth defects. The birth defect model allows the impact of pollutants to vary across different weeks of the pregnancy in order to identify susceptible periods. Here, the proposed methodology is illustrated using pollutant monitoring data from the Environmental Protection Agency and birth records from the National Birth Defect Prevention Study.« less

Speciation network in Laurasiatheria: retrophylogenomic signals

PubMed Central

Doronina, Liliya; Churakov, Gennady; Kuritzin, Andrej; Shi, Jingjing; Baertsch, Robert; Clawson, Hiram; Schmitz, Jürgen

2017-01-01

Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods—too short to fix polymorphic alleles—is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla–Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories. PMID:28298429

Is there a hierarchy of social inferences? The likelihood and speed of inferring intentionality, mind, and personality.

PubMed

Malle, Bertram F; Holbrook, Jess

2012-04-01

People interpret behavior by making inferences about agents' intentionality, mind, and personality. Past research studied such inferences 1 at a time; in real life, people make these inferences simultaneously. The present studies therefore examined whether 4 major inferences (intentionality, desire, belief, and personality), elicited simultaneously in response to an observed behavior, might be ordered in a hierarchy of likelihood and speed. To achieve generalizability, the studies included a wide range of stimulus behaviors, presented them verbally and as dynamic videos, and assessed inferences both in a retrieval paradigm (measuring the likelihood and speed of accessing inferences immediately after they were made) and in an online processing paradigm (measuring the speed of forming inferences during behavior observation). Five studies provide evidence for a hierarchy of social inferences-from intentionality and desire to belief to personality-that is stable across verbal and visual presentations and that parallels the order found in developmental and primate research. (c) 2012 APA, all rights reserved.

Family level phylogenies reveal modes of macroevolution in RNA viruses.

PubMed

Kitchen, Andrew; Shackelton, Laura A; Holmes, Edward C

2011-01-04

Despite advances in understanding the patterns and processes of microevolution in RNA viruses, little is known about the determinants of viral diversification at the macroevolutionary scale. In particular, the processes by which viral lineages assigned as different "species" are generated remain largely uncharacterized. To address this issue, we use a robust phylogenetic approach to analyze patterns of lineage diversification in five representative families of RNA viruses. We ask whether the process of lineage diversification primarily occurs when viruses infect new host species, either through cross-species transmission or codivergence, and which are defined here as analogous to allopatric speciation in animals, or by acquiring new niches within the same host species, analogous to sympatric speciation. By mapping probable primary host species onto family level viral phylogenies, we reveal a strong clustering among viral lineages that infect groups of closely related host species. Although this is consistent with lineage diversification within individual hosts, we argue that this pattern more likely represents strong biases in our knowledge of viral biodiversity, because we also find that better-sampled human viruses rarely cluster together. Hence, although closely related viruses tend to infect related host species, it is unlikely that they often infect the same host species, such that evolutionary constraints hinder lineage diversification within individual host species. We conclude that the colonization of new but related host species may represent the principle mode of macroevolution in RNA viruses.

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

PubMed

Florio, A M; Ingram, C M; Rakotondravony, H A; Louis, E E; Raxworthy, C J

2012-07-01

Species delimitation within recently evolved groups can be challenging because species may be difficult to distinguish morphologically. Following the General Lineage Concept, we apply a multiple evidence approach to assess species limits within the carpet chameleon Furcifer lateralis, which is endemic to Madagascar and exported in large numbers for the pet trade. Cryptic speciation within F. lateralis was considered likely because this species (1) has a vast distribution, (2) occupies exceptionally diverse habitats and (3) exhibits subtle regional differences in morphology. Phylogenetic trees reconstructed using nuclear and mitochondrial genes recovered three well-supported clades corresponding with geography. Morphological results based on canonical variates analysis show that these clades exhibit subtle differences in head casque morphology. Ecological niche modelling results found that these phylogenetic groups also occupy unique environmental space and exhibit patterns of regional endemism typical of other endemic reptiles. Combined, our findings provide diverse yet consistent evidence for the existence of three species. Consequently, we elevate the subspecies F. lateralis major to species rank and name a new species distributed in northern and western Madagascar. Initial ecological divergence, associated with speciation of F. lateralis in humid eastern habitat, fits the Ecographic Constraint model for species diversification in Madagascar. By contrast, the second speciation event provides some support for the Riverine Barrier model, with the Mangoky River possibly causing initial isolation between species. These findings thus support two contrasting models of speciation within closely related species and demonstrate the utility of applying a combined-evidence approach for detecting cryptic speciation. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

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. © 2015 John Wiley & Sons Ltd.

Application Of Synchrotron Techniques To Investigate In-Situ Arsenic Speciation

EPA Science Inventory

The speciation, or chemical form of elements governs their fate, toxicity, mobility, and bioavailability in contaminated soils, sediments and water as well as food chain transfer mechanisms. To assess these chemical properties and to accurately gauge contaminant impact on human h...

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) ...

Selenium Speciation and Management in Wet FGD Systems

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

Searcy, K; Richardson, M; Blythe, G

2012-02-29

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

Speciation of Mercury in Selected Areas of the Petroleum Value Chain.

PubMed

Avellan, Astrid; Stegemeier, John P; Gai, Ke; Dale, James; Hsu-Kim, Heileen; Levard, Clément; O'Rear, Dennis; Hoelen, Thomas P; Lowry, Gregory V

2018-02-06

Petroleum, natural gas, and natural gas condensate can contain low levels of mercury (Hg). The speciation of Hg can affect its behavior during processing, transport, and storage so efficient and safe management of Hg requires an understanding of its chemical form in oil, gas and byproducts. Here, X-ray absorption spectroscopy was used to determine the Hg speciation in samples of solid residues collected throughout the petroleum value chain including stabilized crude oil residues, sediments from separation tanks and condensate glycol dehydrators, distillation column pipe scale, and biosludge from wastewater treatment. In all samples except glycol dehydrators, metacinnabar (β-HgS) was the primary form of Hg. Electron microscopy on particles from a crude sediment showed nanosized (<100 nm) particles forming larger aggregates, and confirmed the colocalization of Hg and sulfur. In sediments from glycol dehydrators, organic Hg(SR) 2 accounted for ∼60% of the Hg, with ∼20% present as β-HgS and/or Hg(SR) 4 species. β-HgS was the predominant Hg species in refinery biosludge and pipe scale samples. However, the balance of Hg species present in these samples depended on the nature of the crude oil being processed, i.e. sweet (low sulfur crudes) vs sour (higher sulfur crudes). This information on Hg speciation in the petroleum value chain will inform development of better engineering controls and management practices for Hg.

Network inference using informative priors.

PubMed

Mukherjee, Sach; Speed, Terence P

2008-09-23

Recent years have seen much interest in the study of systems characterized by multiple interacting components. A class of statistical models called graphical models, in which graphs are used to represent probabilistic relationships between variables, provides a framework for formal inference regarding such systems. In many settings, the object of inference is the network structure itself. This problem of "network inference" is well known to be a challenging one. However, in scientific settings there is very often existing information regarding network connectivity. A natural idea then is to take account of such information during inference. This article addresses the question of incorporating prior information into network inference. We focus on directed models called Bayesian networks, and use Markov chain Monte Carlo to draw samples from posterior distributions over network structures. We introduce prior distributions on graphs capable of capturing information regarding network features including edges, classes of edges, degree distributions, and sparsity. We illustrate our approach in the context of systems biology, applying our methods to network inference in cancer signaling.

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

PubMed Central

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

2014-01-01

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

Research on chromium and arsenic speciation in atmospheric particulate matter: short review

NASA Astrophysics Data System (ADS)

Nocoń, Katarzyna; Rogula-Kozłowska, Wioletta; Widziewicz, Kamila

2018-01-01

Atmospheric particulate matter (PM) plays an important role in the distribution of elements in the environment. The PM-bound elements penetrates into the other elements of the environment, in two basic forms - those dissolved in the atmospheric precipitation and those permanently bound to PM particles. Those forms differs greatly in their mobility, thus posing a potential threat to living organisms. They can also be an immediate threat, while being inhaled. Chromium (Cr) and arsenic (As) belong to the group of elements whose certain chemical states exhibit toxic properties, that is Cr(VI) and As(III). Thus, recognition of the actual threat posed by Cr and As in the environment, including those present in PM, is possible only through the in depth speciation analysis. Research on the Cr and As speciation in PM, more than the analogous studies of their presence in other compartments of the environment, have been undertaken quite rarely. Hence the knowledge on the speciation of PM-bound As and Cr is still limited. The state of knowledge in the field of PM-bound Cr and As is presented in the paper. The issues related to the characterization and occurrence of Cr and As species in PM, the share of Cr and As species mass in different PM size fractions, and in PM of different origin is also summarized. The analytical techniques used in the speciation analysis of PM-bound Cr and As are also discussed. In the existing literature there is no data on the physical characteristics of Cr and As (bound to a different PM size fractions), and thus it still lack of data needed for a comprehensive assessment of the actual environmental and health threat posed by airborne Cr and As.

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.

Visualization of the Mode Shapes of Pressure Oscillation in a Cylindrical Cavity

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

He, Xin; Qi, Yunliang; Wang, Zhi

Our work describes a novel experimental method to visualize the mode shapes of pressure oscillation in a cylindrical cavity. Acoustic resonance in a cavity is a grand old problem that has been under investigation (using both analytical and numerical methods) for more than a century. In this article, a novel method based on high speed imaging of combustion chemiluminescence was presented to visualize the mode shapes of pressure oscillation in a cylindrical cavity. By generating high-temperature combustion gases and strong pressure waves simultaneously in a cylindrical cavity, the pressure oscillation can be inferred due to the chemiluminescence emissions of themore » combustion products. We can then visualized the mode shapes by reconstructing the images based on the amplitudes of the luminosity spectrum at the corresponding resonant frequencies. Up to 11 resonant mode shapes were clearly visualized, each matching very well with the analytical solutions.« less

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.

Optimisation of the storage of natural freshwaters before organotin speciation.

PubMed

Bancon-Montigny, C; Lespes, G; Potin-Gautier, M

2001-01-01

The speciation of organotin compounds is essential due to the species-dependent toxicity, especially in natural waters. Precautions have to be taken during sampling and storage of waters in order to prevent degradations and losses. Experimental design methodology has been used to study the conditions of stability of organotins after water sampling in rivers. The modelling of results allows the determination of optimal conditions of preservation. After acidification at pH = 4 with nitric acid, the storage in polyethylene containers at 4 degrees C in the dark is suitable to preserve the most degradable trisubstituted (butyl- and phenyl-) species over 1 month. These conditions of sampling and storage are applied to two different freshwaters. The rate of species decomposition appears to be only dependent on the water nature, whatever the organotin concentrations in the sample. Speciation could be so preserved between 1 and 3 months.

A speciation solver for cement paste modeling and the semismooth Newton method

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

Georget, Fabien, E-mail: fabieng@princeton.edu; Prévost, Jean H., E-mail: prevost@princeton.edu; Vanderbei, Robert J., E-mail: rvdb@princeton.edu

2015-02-15

The mineral assemblage of a cement paste may vary considerably with its environment. In addition, the water content of a cement paste is relatively low and the ionic strength of the interstitial solution is often high. These conditions are extreme conditions with respect to the common assumptions made in speciation problem. Furthermore the common trial and error algorithm to find the phase assemblage does not provide any guarantee of convergence. We propose a speciation solver based on a semismooth Newton method adapted to the thermodynamic modeling of cement paste. The strong theoretical properties associated with these methods offer practical advantages.more » Results of numerical experiments indicate that the algorithm is reliable, robust, and efficient.« less

Peripatric speciation in an endemic Macaronesian plant after recent divergence from a widespread relative.

PubMed

Valtueña, Francisco J; Rodríguez-Riaño, Tomás; López, Josefa; Mayo, Carlos; Ortega-Olivencia, Ana

2017-01-01

The Macaronesian Scrophularia lowei is hypothesized to have arisen from the widespread S. arguta on the basis of several phylogenetic studies of the genus, but sampling has been limited. Although these two annual species are morphologically distinct, the origin of S. lowei is unclear because genetic studies focused on this Macaronesian species are lacking. We studied 5 S. lowei and 25 S. arguta populations to determine the relationship of both species and to infer the geographical origin of S. lowei. The timing of S. lowei divergence and differentiation was inferred by dating analysis of the ITS region. A phylogenetic analysis of two nuclear (ITS and ETS) and two chloroplast (psbJ-petA and psbA-trnH) DNA regions was performed to study the relationship between the two species, and genetic differentiation was analysed by AMOVA. Haplotype network construction and Bayesian phylogeographic analysis were conducted using chloroplast DNA regions and a spatial clustering analysis was carried out on a combined dataset of all studied regions. Our results indicate that both species constitute a well-supported clade that diverged in the Miocene and differentiated in the Late Miocene-Pleistocene. Although S. lowei constitutes a well-supported clade according to nDNA, cpDNA revealed a close relationship between S. lowei and western Canarian S. arguta, a finding supported by the spatial clustering analysis. Both species have strong population structure, with most genetic variability explained by inter-population differences. Our study therefore supports a recent peripatric speciation of S. lowei-a taxon that differs morphologically and genetically at the nDNA level from its closest relative, S. arguta, but not according to cpDNA, from the closest Macaronesian populations of that species. In addition, a recent dispersal of S. arguta to Madeira from Canary Islands or Selvagens Islands and a rapid morphological differentiation after the colonization to generate S. lowei is the most

Peripatric speciation in an endemic Macaronesian plant after recent divergence from a widespread relative

PubMed Central

Rodríguez-Riaño, Tomás; López, Josefa; Mayo, Carlos; Ortega-Olivencia, Ana

2017-01-01

The Macaronesian Scrophularia lowei is hypothesized to have arisen from the widespread S. arguta on the basis of several phylogenetic studies of the genus, but sampling has been limited. Although these two annual species are morphologically distinct, the origin of S. lowei is unclear because genetic studies focused on this Macaronesian species are lacking. We studied 5 S. lowei and 25 S. arguta populations to determine the relationship of both species and to infer the geographical origin of S. lowei. The timing of S. lowei divergence and differentiation was inferred by dating analysis of the ITS region. A phylogenetic analysis of two nuclear (ITS and ETS) and two chloroplast (psbJ–petA and psbA–trnH) DNA regions was performed to study the relationship between the two species, and genetic differentiation was analysed by AMOVA. Haplotype network construction and Bayesian phylogeographic analysis were conducted using chloroplast DNA regions and a spatial clustering analysis was carried out on a combined dataset of all studied regions. Our results indicate that both species constitute a well-supported clade that diverged in the Miocene and differentiated in the Late Miocene-Pleistocene. Although S. lowei constitutes a well-supported clade according to nDNA, cpDNA revealed a close relationship between S. lowei and western Canarian S. arguta, a finding supported by the spatial clustering analysis. Both species have strong population structure, with most genetic variability explained by inter-population differences. Our study therefore supports a recent peripatric speciation of S. lowei—a taxon that differs morphologically and genetically at the nDNA level from its closest relative, S. arguta, but not according to cpDNA, from the closest Macaronesian populations of that species. In addition, a recent dispersal of S. arguta to Madeira from Canary Islands or Selvagens Islands and a rapid morphological differentiation after the colonization to generate S. lowei is the

[Speciation and Risk Characteristics of Heavy Metals in the Sediments of the Yangtze Estuary].

PubMed

Yin, Su; Feng, Cheng-hong; Li, Yang-yang; Yin, Li-feng; Shen, Zhen-yao

2016-03-15

Based on the investigation on the distribution of total contents and speciation of 8 heavy metals (As, Cd, Cr, Cu, Hg, Ni, Pb, Zn) in the surface sediments at 14 typical sites of the Yangtze Estuary during three hydrological seasons ( wet, normal, and dry seasons) , this study applied equilibrium partitioning approach to build the sediment quality guidelines (SQGs) of the Yangtze Estuary, and assessed ecological risks of the heavy metals. The relationship between ecological risk and speciation of heavy metals was also revealed. The results showed that, except for Cd, the residual fraction was the main speciation of heavy metals, especially for As, Cr and Hg, their residual fraction proportions were all over 90%. The sediment quality guidelines of the Yangtze Estuary for As, Cd, Cr, Cu, Hg, Ni, Pb, Zn were 43.29, 0.672, 79.65, 19.08, 0.569, 339.09, 30.87, 411.36 µg · g⁻¹, respectively. Cu had the highest ecological risk to aquatic organisms. The upstream of Yangtze Estuary was mainly affected by Yangtze River runoff, where the risks were relatively high in wet season and relatively low in normal and dry seasons. However, the downstream of the estuary was mainly affected by municipal sewage of cities like Shanghai, where the risks were relatively high, especially in normal and dry seasons. There were three different relationships between the ecological risks and speciation of the eight heavy metals.

Evaluation of speciated VOC emission factors for Air Force hush houses

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

Sullivan, P.D.; Stevens, D.K.

1997-12-31

Data published in: ``Engine and Hush House Emissions from a TF30-P109 Jet Engine Tested at Cannon Air Force Base, NM`` by Radian Corporation and ``Aircraft Emissions. Characterization: TF41-A2, TF30-P103 , and TF30-P109 Engines`` by Battelle are reviewed and compared. Specifically CO, NO{sub x}, and VOC emission factors using EPA Method 19 are addressed, with comparisons between JP-4 and JP-8 jet fuels. CO and NO{sub x} emissions for JP-4 and JP-8 jet fuels were found to be essentially the same. VOC emission data exhibited high variability. Problems inherent in speciated VOC emission testing are discussed. A limiting of speciated VOC emissionmore » testing, with emission factor estimation based on fuel content is proposed.« less

Application of Hyphenated Techniques in Speciation Analysis of Arsenic, Antimony, and Thallium

PubMed Central

Michalski, Rajmund; Szopa, Sebastian; Jabłońska, Magdalena; Łyko, Aleksandra

2012-01-01

Due to the fact that metals and metalloids have a strong impact on the environment, the methods of their determination and speciation have received special attention in recent years. Arsenic, antimony, and thallium are important examples of such toxic elements. Their speciation is especially important in the environmental and biomedical fields because of their toxicity, bioavailability, and reactivity. Recently, speciation analytics has been playing a unique role in the studies of biogeochemical cycles of chemical compounds, determination of toxicity and ecotoxicity of selected elements, quality control of food products, control of medicines and pharmaceutical products, technological process control, research on the impact of technological installation on the environment, examination of occupational exposure, and clinical analysis. Conventional methods are usually labor intensive, time consuming, and susceptible to interferences. The hyphenated techniques, in which separation method is coupled with multidimensional detectors, have become useful alternatives. The main advantages of those techniques consist in extremely low detection and quantification limits, insignificant interference, influence as well as high precision and repeatability of the determinations. In view of their importance, the present work overviews and discusses different hyphenated techniques used for arsenic, antimony, and thallium species analysis, in different clinical, environmental and food matrices. PMID:22654649

Moving Speciation Genetics Forward: Modern Techniques Build on Foundational Studies in Drosophila.

PubMed

Castillo, Dean M; Barbash, Daniel A

2017-11-01

The question of how new species evolve has been examined at every level, from macroevolutionary patterns of diversification to molecular population genetic analyses of specific genomic regions between species pairs. Drosophila has been at the center of many of these research efforts. Though our understanding of the speciation process has grown considerably over the past few decades, very few genes have been identified that contribute to barriers to reproduction. The development of advanced molecular genetic and genomic methods provides promising avenues for the rapid discovery of more genes that contribute to speciation, particularly those involving prezygotic isolation. The continued expansion of tools and resources, especially for species other than Drosophila melanogaster , will be most effective when coupled with comparative approaches that reveal the genetic basis of reproductive isolation across a range of divergence times. Future research programs in Drosophila have high potential to answer long-standing questions in speciation. These include identifying the selective forces that contribute to divergence between populations and the genetic basis of traits that cause reproductive isolation. The latter can be expanded upon to understand how the genetic basis of reproductive isolation changes over time and whether certain pathways and genes are more commonly involved. Copyright © 2017 by the Genetics Society of America.

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

USGS Publications Warehouse

Cronin, T. M.

1987-01-01

Three types of geographic isolation - land barriers, deep water barriers, and climatic barriers - resulted in three distinct evolutionary responses in Neogene and Quaternary species of the epineritic ostracode genus Puriana. Through systematic, paleobiogeographic, and morphologic study of several hundred fossil and Recent populations from the eastern Pacific, western Atlantic, Gulf of Mexico, and the Caribbean, the phylogeny of the genus and the geography of speciation events were determined. Isolation of large populations by the Isthumus of Panama during the Pliocene did not lead to lineage splitting in species known to have existed before the Isthmus formed. Conversely, the establishment of small isolated populations on Caribbean islands by passive dispersal mechanisms frequently led to the evolution of new species or subspecies. Climatic changes along the southeastern United States during the Pliocene also catalyzed possible parapatric speciation as populations that immigrated to the northeastern periphery of the genus' range split to form new species. The results provide evidence that evolutionary models describing the influence of abiotic events on patterns of evolution and speciation can be tested using properly selected tectonic and climatic events and fossil groups amenable to species-level analysis. Two new species, P. bajaensis and P. paikensis, are described. -Author

Sulfur Speciation in Biochars by Very High Resolution Benchtop Kα X-ray Emission Spectroscopy.

PubMed

Holden, William M; Seidler, Gerald T; Cheah, Singfoong

2018-05-30

The analytical chemistry of sulfur-containing materials poses substantial technical challenges, especially due to the limitations of 33 S NMR and the time-intensive preparations required for wet-chemistry analyses. A number of prior studies have found that synchrotron-based X-ray absorption near edge structure (XANES) measurements can give detailed speciation of sulfur chemistry in such cases. However, due to the obvious access limitations, synchrotron XANES of sulfur cannot be part of routine analytical practice across the chemical sciences community. Here, in a study of the sulfur chemistry in biochars, we compare and contrast the chemical inferences available from synchrotron XANES with that given by benchtop, extremely high resolution wavelength-dispersive X-ray fluorescence (WD-XRF) spectroscopy, also often called X-ray emission spectroscopy (XES). While the XANES spectra have higher total information content, often giving differentiation between different moieties having the same oxidation state, the lower sensitivity of the S Kα XES to coordination and local structure provides pragmatic benefit for the more limited goal of quantifying the S oxidation state distribution. Within that constrained metric, we find good agreement between the two methods. As the sulfur concentrations were as low as 150 ppm, these measurements provide proof-of-principle for characterization of the sulfur chemistry of biochars and potential applications to other areas such as soils, batteries, catalysts, and fossil fuels and their combustion products.

Population genetics of mouse lemur vomeronasal receptors: current versus past selection and demographic inference.

PubMed

Hohenbrink, Philipp; Mundy, Nicholas I; Radespiel, Ute

2017-01-21

A major effort is underway to use population genetic approaches to identify loci involved in adaptation. One issue that has so far received limited attention is whether loci that show a phylogenetic signal of positive selection in the past also show evidence of ongoing positive selection at the population level. We address this issue using vomeronasal receptors (VRs), a diverse gene family in mammals involved in intraspecific communication and predator detection. In mouse lemurs, we previously demonstrated that both subfamilies of VRs (V1Rs and V2Rs) show a strong signal of directional selection in interspecific analyses. We predicted that ongoing sexual selection and/or co-evolution with predators may lead to current directional or balancing selection on VRs. Here, we re-sequence 17 VRs and perform a suite of selection and demographic analyses in sympatric populations of two species of mouse lemurs (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. M. ravelobensis had consistently higher genetic diversity at VRs than M. murinus. In general, we find little evidence for positive selection, with most loci evolving under purifying selection and one locus even showing evidence of functional loss in M. ravelobensis. However, a few loci in M. ravelobensis show potential evidence of positive selection. Using mismatch distributions and expansion models, we infer a more recent colonisation of the habitat by M. murinus than by M. ravelobensis, which most likely speciated in this region earlier on. These findings suggest that the analysis of VR variation is useful in inferring demographic and phylogeographic history of mouse lemurs. In conclusion, this study reveals a substantial heterogeneity over time in selection on VR loci, suggesting that VR evolution is episodic.

FUNDAMENTALS OF MERCURY SPECIATION AND CONTROL IN COAL-FIRED BOILERS

EPA Science Inventory

The report describes the progress of an experimental investigation of the speciation of mercury in simulated coal combustion flue gasses. The effects of flue gas parameters and coal fly ash on the oxidation of elemental mercury (Hgo) in the presence of hydrogen chloride (HCl) in ...

A Comparison of Solar p-Mode Parameters from MDI and Gong: Mode Frequencies and Structure Inversions

NASA Technical Reports Server (NTRS)

Basu, S.; Christensen-Dalsgaard, J.; Howe, R.; Schou, J.; Thompson, M. J.; Hill, F.; Komm, R.

2003-01-01

Helioseismic analysis of solar global oscillations allows investigation of the internal structure of the Sun. One important test of the reliability of the inferences from helioseismology is that the results from independent sets of contemporaneous data are consistent with one another. Here we compare mode frequencies from the Global Oscillation Network Group and Michelson Doppler Imager on board SOHO and resulting inversion results on the Sun's internal structure. The average relative differences between the data sets are typically less than 1 x 10(exp -5) substantially smaller than the formal errors in the differences; however, in some cases the frequency differences show a systematic behavior that might nonetheless influence the inversion results. We find that the differences in frequencies are not a result of instrumental effects but are almost entirely related to the data pipeline software. Inversion of the frequencies shows that their differences do not result in any significant effects on the resulting inferences on solar structure. We have also experimented with fitting asymmetric profiles to the oscillation power spectra and find that, compared with the symmetric fits, this causes no significant change in the inversion results.

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

PubMed Central

2009-01-01

Background The full power of modern genetics has been applied to the study of speciation in only a small handful of genetic model species - all of which speciated allopatrically. Here we report the first large expressed sequence tag (EST) study of a candidate for ecological sympatric speciation, the apple maggot Rhagoletis pomonella, using massively parallel pyrosequencing on the Roche 454-FLX platform. To maximize transcript diversity we created and sequenced separate libraries from larvae, pupae, adult heads, and headless adult bodies. Results We obtained 239,531 sequences which assembled into 24,373 contigs. A total of 6810 unique protein coding genes were identified among the contigs and long singletons, corresponding to 48% of all known Drosophila melanogaster protein-coding genes. Their distribution across GO classes suggests that we have obtained a representative sample of the transcriptome. Among these sequences are many candidates for potential R. pomonella "speciation genes" (or "barrier genes") such as those controlling chemosensory and life-history timing processes. Furthermore, we identified important marker loci including more than 40,000 single nucleotide polymorphisms (SNPs) and over 100 microsatellites. An initial search for SNPs at which the apple and hawthorn host races differ suggested at least 75 loci warranting further work. We also determined that developmental expression differences remained even after normalization; transcripts expected to show different expression levels between larvae and pupae in D. melanogaster also did so in R. pomonella. Preliminary comparative analysis of transcript presences and absences revealed evidence of gene loss in Drosophila and gain in the higher dipteran clade Schizophora. Conclusions These data provide a much needed resource for exploring mechanisms of divergence in this important model for sympatric ecological speciation. Our description of ESTs from a substantial portion of the R. pomonella transcriptome

Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation.

PubMed

Cánovas, Fernando G; Mota, Catarina F; Serrão, Ester A; Pearson, Gareth A

2011-12-21

Understanding the processes driving speciation in marine ecosystems remained a challenge until recently, due to the unclear nature of dispersal boundaries. However, recent evidence for marine adaptive radiations and ecological speciation, as well as previously undetected patterns of cryptic speciation is overturning this view. Here, we use multi-gene phylogenetics to infer the family-level evolutionary history of Fucaceae (intertidal brown algae of the northern Pacific and Atlantic) in order to investigate recent and unique patterns of radiative speciation in the genus Fucus in the Atlantic, in contrast with the mainly monospecific extant genera. We developed a set of markers from 13 protein coding genes based on polymorphic cDNA from EST libraries, which provided novel resolution allowing estimation of ancestral character states and a detailed reconstruction of the recent radiative history. Phylogenetic reconstructions yielded similar topologies and revealed four independent trans-Arctic colonization events by Fucaceae lineages, two of which also involved transitions from hermaphroditism to dioecy associated with Atlantic invasions. More recently, reversion of dioecious ancestral lineages towards hermaphroditism has occurred in the genus Fucus, particularly coinciding with colonization of more extreme habitats. Novel lineages in the genus Fucus were also revealed in association with southern habitats. These most recent speciation events occurred during the Pleistocene glaciations and coincided with a shift towards selfing mating systems, generally southward shifts in distribution, and invasion of novel habitats. Diversification of the family occurred in the Late-Mid Miocene, with at least four independent trans-Artic lineage crossings coincident with two reproductive mode transitions. The genus Fucus arose in the Pliocene but radiated within a relatively short time frame about 2.5 million years ago. Current species distributions of Fucus suggest that climatic

Variations on Bayesian Prediction and Inference

DTIC Science & Technology

2016-05-09

inference 2.2.1 Background There are a number of statistical inference problems that are not generally formulated via a full probability model...problem of inference about an unknown parameter, the Bayesian approach requires a full probability 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...the problem of inference about an unknown parameter, the Bayesian approach requires a full probability model/likelihood which can be an obstacle

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

PubMed

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

2015-02-01

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

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

PubMed

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

2017-06-01

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

Speciation network in Laurasiatheria: retrophylogenomic signals.

PubMed

Doronina, Liliya; Churakov, Gennady; Kuritzin, Andrej; Shi, Jingjing; Baertsch, Robert; Clawson, Hiram; Schmitz, Jürgen

2017-06-01

Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods-too short to fix polymorphic alleles-is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla-Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories. © 2017 Doronina et al.; Published by Cold Spring Harbor Laboratory Press.

A feature-based inference model of numerical estimation: the split-seed effect.

PubMed

Murray, Kyle B; Brown, Norman R

2009-07-01

Prior research has identified two modes of quantitative estimation: numerical retrieval and ordinal conversion. In this paper we introduce a third mode, which operates by a feature-based inference process. In contrast to prior research, the results of three experiments demonstrate that people estimate automobile prices by combining metric information associated with two critical features: product class and brand status. In addition, Experiments 2 and 3 demonstrated that when participants are seeded with the actual current base price of one of the to-be-estimated vehicles, they respond by revising the general metric and splitting the information carried by the seed between the two critical features. As a result, the degree of post-seeding revision is directly related to the number of these features that the seed and the transfer items have in common. The paper concludes with a general discussion of the practical and theoretical implications of our findings.

Generic comparison of protein inference engines.

PubMed

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

2012-04-01

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.

Inferring network structure in non-normal and mixed discrete-continuous genomic data

PubMed Central

Bhadra, Anindya; Rao, Arvind; Baladandayuthapani, Veerabhadran

2017-01-01

Inferring dependence structure through undirected graphs is crucial for uncovering the major modes of multivariate interaction among high-dimensional genomic markers that are potentially associated with cancer. Traditionally, conditional independence has been studied using sparse Gaussian graphical models for continuous data and sparse Ising models for discrete data. However, there are two clear situations when these approaches are inadequate. The first occurs when the data are continuous but display non-normal marginal behavior such as heavy tails or skewness, rendering an assumption of normality inappropriate. The second occurs when a part of the data is ordinal or discrete (e.g., presence or absence of a mutation) and the other part is continuous (e.g., expression levels of genes or proteins). In this case, the existing Bayesian approaches typically employ a latent variable framework for the discrete part that precludes inferring conditional independence among the data that are actually observed. The current article overcomes these two challenges in a unified framework using Gaussian scale mixtures. Our framework is able to handle continuous data that are not normal and data that are of mixed continuous and discrete nature, while still being able to infer a sparse conditional sign independence structure among the observed data. Extensive performance comparison in simulations with alternative techniques and an analysis of a real cancer genomics data set demonstrate the effectiveness of the proposed approach. PMID:28437848

Something's Fishy in Paxton Lake: A Case on Speciation in Sticklebacks.

ERIC Educational Resources Information Center

Sharp, Joan

2002-01-01

Introduces a case study on speciation and evolutionary mechanisms. Teaches science process skills as well as natural selection, biological species concepts, basic genetic terminology, and classification. Includes teaching notes and classroom management strategies. (Contains 14 references.) (YDS)

Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): an inference from nuclear protein-coding genes.

PubMed

Knapp, Jenny; Nakao, Minoru; Yanagida, Tetsuya; Okamoto, Munehiro; Saarma, Urmas; Lavikainen, Antti; Ito, Akira

2011-12-01

The family Taeniidae of tapeworms is composed of two genera, Echinococcus and Taenia, which obligately parasitize mammals including humans. Inferring phylogeny via molecular markers is the only way to trace back their evolutionary histories. However, molecular dating approaches are lacking so far. Here we established new markers from nuclear protein-coding genes for RNA polymerase II second largest subunit (rpb2), phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold). Bayesian inference and maximum likelihood analyses of the concatenated gene sequences allowed us to reconstruct phylogenetic trees for taeniid parasites. The tree topologies clearly demonstrated that Taenia is paraphyletic and that the clade of Echinococcus oligarthrus and Echinococcusvogeli is sister to all other members of Echinococcus. Both species are endemic in Central and South America, and their definitive hosts originated from carnivores that immigrated from North America after the formation of the Panamanian land bridge about 3 million years ago (Ma). A time-calibrated phylogeny was estimated by a Bayesian relaxed-clock method based on the assumption that the most recent common ancestor of E. oligarthrus and E. vogeli existed during the late Pliocene (3.0 Ma). The results suggest that a clade of Taenia including human-pathogenic species diversified primarily in the late Miocene (11.2 Ma), whereas Echinococcus started to diversify later, in the end of the Miocene (5.8 Ma). Close genetic relationships among the members of Echinococcus imply that the genus is a young group in which speciation and global radiation occurred rapidly. Copyright © 2011 Elsevier Inc. All rights reserved.

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...

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

PubMed

Lande, R; Seehausen, O; van Alphen, J J

2001-01-01

Mechanisms of speciation in cichlid fish were investigated by analyzing population genetic models of sexual selection on sex-determining genes associated with color polymorphisms. The models are based on a combination of laboratory experiments and field observations on the ecology, male and female mating behavior, and inheritance of sex-determination and color polymorphisms. The models explain why sex-reversal genes that change males into females tend to be X-linked and associated with novel colors, using the hypothesis of restricted recombination on the sex chromosomes, as suggested by previous theory on the evolution of recombination. The models reveal multiple pathways for rapid sympatric speciation through the origin of novel color morphs with strong assortative mating that incorporate both sex-reversal and suppressor genes. Despite the lack of geographic isolation or ecological differentiation, the new species coexists with the ancestral species either temporarily or indefinitely. These results may help to explain different patterns and rates of speciation among groups of cichlids, in particular the explosive diversification of rock-dwelling haplochromine cichlids.

A new approach to chemically-speciated submicron aerosol fluxes over tropical and temperate forests.

NASA Astrophysics Data System (ADS)

Farmer, D. K.; Kimmel, J. R.; Nemitz, E.; Phillips, G.; Docherty, K.; Chen, Q.; Martin, S.; Cubison, M.; Jimenez, J.

2008-12-01

Aerosols play an important role in the planet's radiation balance; however, their sources and sinks remain highly uncertain. In particular, due to instrumental limitations, there are few measurements of particle fluxes over the Earth's surface. Particles are expected to deposit over forests, leading not only to an aerosol sink, but also to an ecosystem source of nutrients and acids. However, forests emit volatile organic compounds (VOCs) that are known to produce secondary organic aerosol, thus also acting as aerosol sources. We have developed a new approach to measure biosphere-atmosphere exchange of chemically-speciated aerosol using a High Resolution-Time of Flight-Aerosol Mass Spectrometer (HR-ToF-AMS; DeCarlo et al., Anal. Chem., 2006) in a new Eddy Covariance Flux mode (10 Hz). This approach allows us to directly measure fluxes of non-refractory organic, sulphate, nitrate and ammonium in submicron particles. Measurements have been carried out over two forests: a temperate ponderosa pine plantation at Blodgett Forest (BEARPEX-I campaign, 2007) and a tropical rain forest in the Brazilian Amazon during the wet season (AMAZE campaign, 2008). Data collected at these sites allows us to demonstrate that the flux mode of the HR-ToF-AMS meets the rigorous instrumental requirements of the eddy covariance approach and that fluxes of different chemical species can be quantified. Aerosol fluxes under clean and anthropogenically-impacted conditions are compared. These measurements allow us to better constrain dry deposition over forested environments and to understand the potential of flux measurements to constrain the biogenic SOA budget.

Children's and Adults' Evaluation of Their Own Inductive Inferences, Deductive Inferences, and Guesses

ERIC Educational Resources Information Center

Pillow, Bradford H.; Pearson, RaeAnne M.

2009-01-01

Adults' and kindergarten through fourth-grade children's evaluations and explanations of inductive inferences, deductive inferences, and guesses were assessed. Beginning in kindergarten, participants rated deductions as more certain than weak inductions or guesses. Beginning in third grade, deductions were rated as more certain than strong…

Speciation reversal and biodiversity dynamics with hybridization in changing environments.

PubMed

Seehausen, Ole; Takimoto, Gaku; Roy, Denis; Jokela, Jukka

2008-01-01

A considerable fraction of the world's biodiversity is of recent evolutionary origin and has evolved as a by-product of, and is maintained by, divergent adaptation in heterogeneous environments. Conservationists have paid attention to genetic homogenization caused by human-induced translocations (e.g. biological invasions and stocking), and to the importance of environmental heterogeneity for the ecological coexistence of species. However, far less attention has been paid to the consequences of loss of environmental heterogeneity to the genetic coexistence of sympatric species. Our review of empirical observations and our theoretical considerations on the causes and consequences of interspecific hybridization suggest that a loss of environmental heterogeneity causes a loss of biodiversity through increased genetic admixture, effectively reversing speciation. Loss of heterogeneity relaxes divergent selection and removes ecological barriers to gene flow between divergently adapted species, promoting interspecific introgressive hybridization. Since heterogeneity of natural environments is rapidly deteriorating in most biomes, the evolutionary ecology of speciation reversal ought to be fully integrated into conservation biology.

Quantifying variation in speciation and extinction rates with clade data.

PubMed

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

2013-12-01

High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Arsenic speciation for the phytoremediation by the Chinese brake fern, Pteris vittata.

PubMed

Shoji, R; Yajima, R; Yano, Y

2008-01-01

Arsenic (As) speciation for the phytoremediation by the Chinese brake fern was studied. In particular, the mechanism of how plants induce compounds containing thiol (SH) and proteins by As exposure in terms of the relationship between As and phosphate uptaken into plant cells was examined. Pteris vittata callus could efficiently reduce As(V) to As(III) by the rapid introduction of reductase and synthesize thiols leading to phytochelatins production. Furthermore, Pteris vittata could control phosphate concentration in the cells corresponding to the concentration of arsenite and arsenate. To our best knowledge, this is the first report to show the mechanisms of such high As tolerance of Pteris vittata using their callus in terms of in vitro approach for the analysis of As speciation and metabolism route.

Speciation, Divergence, and the Origin of Gryllus rubens: Behavior, Morphology, and Molecules

PubMed Central

Gray, David A.

2011-01-01

The last 25 years or so has seen a huge resurgence of interest in speciation research. This has coincided with the development and widespread use of new tools in molecular genetics, especially DNA sequencing, to inform ecological and evolutionary questions. Here I review about a decade of work on the sister species of field crickets Gryllus texensis and G. rubens. This work has included analysis of morphology, behavior, and the mitochondrial DNA molecule. The molecular work in particular has dramatically re-shaped my interpretation of the speciational history of these taxa, suggesting that rather than ‘sister’ species we should consider these taxa as ‘mother-daughter’ species with G. rubens derived from within a subset of ancestral G. texensis. PMID:26467622

Copper speciation in variably toxic sediments at the Ely Copper Mine, Vermont, United States

USGS Publications Warehouse

Kimball, Bryn E.; Foster, Andrea L.; Seal, Robert R.; Piatak, Nadine M.; Webb, Samuel M.; Hammarstrom, Jane M.

2016-01-01

At the Ely Copper Mine Superfund site, Cu concentrations exceed background values in both streamwater (160–1200 times) and sediments (15–79 times). Previously, these sediment samples were incubated with laboratory test organisms, and they exhibited variable toxicity for different stream sites. In this study we combined bulk- and microscale techniques to determine Cu speciation and distribution in these contaminated sediments on the basis of evidence from previous work that Cu was the most important stressor in this environment and that variable observed toxicity could have resulted from differences in Cu speciation. Copper speciation results were similar at microscopic and bulk scales. The major Cu species in the more toxic samples were sorbed or coprecipitated with secondary Mn (birnessite) and Fe minerals (jarosite and goethite), which together accounted for nearly 80% of the total Cu. The major Cu species in the less toxic samples were Cu sulfides (chalcopyrite and a covellite-like phase), making up about 80–95% of the total Cu, with minor amounts of Cu associated with jarosite or goethite. These Cu speciation results are consistent with the toxicity results, considering that Cu sorbed or coprecipitated with secondary phases at near-neutral pH is relatively less stable than Cu bound to sulfide at lower pH. The more toxic stream sediment sites were those that contained fewer detrital sulfides and were upstream of the major mine waste pile, suggesting that removal and consolidation of sulfide-bearing waste piles on site may not eliminate all sources of bioaccessible Cu.

SPECIATION OF ARSENIC IN SULFIDIC SOLUTIONS USING X-RAY ABSORPTION SPECTROSCOPY

EPA Science Inventory

The fate of arsenic in the environment is fundamentally linked to its speciation. Arsenic in aerobic environments is predominantly arsenate, however under reducing conditions arsenite species dominate. In sulfidic environments, thioarsenic species are known to exist and play key...

Potential application of SERS for arsenic speciation in biological matrices.

PubMed

Yang, Mingwei; Matulis, Shannon; Boise, Lawrence H; McGoron, Anthony J; Cai, Yong

2017-08-01

Speciation of arsenic is usually carried out using chromatography-based methods coupled with spectroscopic determination; however, the inevitable procedures involving sample preparation and separation could potentially alter the integrity of the arsenic metabolites present in biological samples. Surface-enhanced Raman spectroscopy (SERS) could be a promising alternative for providing a reliable arsenic analysis under the influence of a cellular matrix. A method for arsenic speciation using SERS in cellular matrix was developed in this study and four arsenicals were selected, including arsenite (As III ), arsenate (As V ), monomethylarsonic acid (MMA V ) and dimethylarsinic acid (DMA V ). Silver nanoparticles in the form of colliodal suspension with different surface charges, i.e., coated with citrate (AgNPs-Citrate) and spermine (AgNPs-Spermine) were employed as SERS substrates. Adsorption of arsenicals on nanoparticles in colloidal suspensions and the cellular matrix and the pH, size, and zeta potential of the colloidal suspensions were investigated for a better understanding of the SERS signal response of arsenicals in the colloidal suspensions or under the influence of cellular matrix. Arsenicals showed substantially different SERS responses in the two colloidal suspensions, mainly because of the distinct difference in the interaction between the arsenicals and the nanoparticles. Arsenic speciation in cell lysate could be successfully carried out in AgNPs-Spermine suspension, while AgNPs-Citrate could not yield significant SERS signals under the experimental conditions. This study proved that AgNPs-Spermine colloidal suspension could be a promising SERS substrate for studying arsenic metabolism in a biological matrix, reducing the bias caused by traditional techniques that involve sample extraction and pretreatment.

Beryllium chemical speciation in elemental human biological fluids.

PubMed

Sutton, Mark; Burastero, Stephen R

2003-09-01

The understanding of beryllium chemistry in human body fluids is important for understanding the prevention and treatment of chronic beryllium disease. Thermodynamic modeling has traditionally been used to study environmental contaminant migration and rarely in the examination of metal (particularly beryllium) toxicology. In this work, a chemical thermodynamic speciation code (MINTEQA2) has been used to model and understand the chemistry of beryllium in simulated human biological fluids such as intracellular, interstitial, and plasma fluids, a number of airway surface fluids for patients with lung conditions, saliva, sweat, urine, bile, gastric juice, and pancreatic fluid. The results show that predicted beryllium solubility and speciation vary markedly between each simulated biological fluid. Formation of beryllium hydroxide and/or phosphate was observed in most of the modeled fluids, and results support the postulation that beryllium absorption in the gastrointestinal tract may be limited by the formation of beryllium phosphate solids. It is also postulated that beryllium is potentially 13% less soluble in the airway surface fluid of a patient with asthma when compared to a "normal" case. The results of this work, supported by experimental validation, can aid in the understanding of beryllium toxicology. Our results can potentially be applied to assessing the feasibility of biological monitoring or chelation treatment of beryllium body burden.

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

PubMed

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

2001-03-01

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

Geological and anthropogenic factors influencing mercury speciation in mine wastes: An EXAFS spectroscopy study

USGS Publications Warehouse

Kim, C.S.; Rytuba, J.J.; Brown, Gordon E.

2004-01-01

The speciation of Hg is a critical determinant of its mobility, reactivity, and potential bioavailability in mine-impacted regions. Furthermore, Hg speciation in these complex natural systems is influenced by a number of physical, geological, and anthropogenic variables. In order to investigate the degree to which several of these variables may affect Hg speciation, extended X-ray absorption fine structure (EXAFS) spectroscopy was used to determine the Hg phases and relative proportions of these phases present in Hg-bearing wastes from selected mine-impacted regions in California and Nevada. The geological origin of Hg ore has a significant effect on Hg speciation in mine wastes. Specifically, samples collected from hot-spring Hg deposits were found to contain soluble Hg-chloride phases, while such phases were largely absent in samples from silica-carbonate Hg deposits; in both deposit types, however, Hg-sulfides in the form of cinnabar (HgS, hex.) and metacinnabar (HgS, cub.) dominate. Calcined wastes in which Hg ore was crushed and roasted in excess of 600??C, contain high proportions of metacinnabar while the main Hg-containing phase in unroasted waste rock samples from the same mines is cinnabar. The calcining process is thought to promote the reconstructive phase transformation of cinnabar to metacinnabar, which typically occurs at 345??C. The total Hg concentration in calcines is strongly correlated with particle size, with increases of nearly an order of magnitude in total Hg concentration between the 500-2000 ??m and <45 ??m size fractions (e.g., from 97-810 mg/kg Hg in calcines from the Sulphur Bank Mine, CA). The proportion of Hg-sulfides present also increased by 8-18% as particle size decreased over the same size range. This finding suggests that insoluble yet soft Hg-sulfides are subject to preferential mechanical weathering and become enriched in the fine-grained fraction, while soluble Hg phases are leached out more readily as particle size decreases

THE ONTARIO HYDRO METHOD FOR SPECIATED MERCURY MEASUREMENTS: ISSUES AND CONSIDERATIONS

EPA Science Inventory

The Ontario Hydro (OH) method has been developed for the measurement of total and speciated mercury emissions from coal-fired combustion sources. The OH method was initially developed to support EPA's information collection request to characterize and inventory mercury emissions ...

Speciated VOC Emissions from an Outdoor Residential Pellet burning Hydronic Heater

EPA Science Inventory

Outdoor hydronic heaters used for residential heating emit air pollutants such as particulate matter and volatile organic compounds (VOCs), which can lead to deleterious impacts on local air quality and human health. Detailed speciated emissions measurements are required to accur...

Spontaneous Trait Inferences on Social Media.

PubMed

Levordashka, Ana; Utz, Sonja

2017-01-01

The present research investigates whether spontaneous trait inferences occur under conditions characteristic of social media and networking sites: nonextreme, ostensibly self-generated content, simultaneous presentation of multiple cues, and self-paced browsing. We used an established measure of trait inferences (false recognition paradigm) and a direct assessment of impressions. Without being asked to do so, participants spontaneously formed impressions of people whose status updates they saw. Our results suggest that trait inferences occurred from nonextreme self-generated content, which is commonly found in social media updates (Experiment 1) and when nine status updates from different people were presented in parallel (Experiment 2). Although inferences did occur during free browsing, the results suggest that participants did not necessarily associate the traits with the corresponding status update authors (Experiment 3). Overall, the findings suggest that spontaneous trait inferences occur on social media. We discuss implications for online communication and research on spontaneous trait inferences.

Using SINEs to probe ancient explosive speciation: "hidden" radiation of African cichlids?

PubMed

Terai, Yohey; Takahashi, Kazuhiko; Nishida, Mutsumi; Sato, Tetsu; Okada, Norihiro

2003-06-01

Cichlid fishes of the east African Great Lakes represent a paradigm of adaptive radiation. We conducted a phylogenetic analysis of cichlids including pan-African and west African species by using insertion patterns of short interspersed elements (SINEs) at orthologous loci. The monophyly of the east African cichlids was consistently supported by seven independent insertions of SINE sequences that are uniquely shared by these species. In addition, data from four other loci indicated that the genera Tilapia (pan-African) and Steatocranus (west African) are the closest relatives to east African cichlids. However, relationships among Tilapia, Steatocranus, and the east African clade were ambiguous because of incongruencies among topologies suggested by insertion patterns of SINEs at six other loci. One plausible explanation for this phenomenon is incomplete lineage sorting of alleles containing or missing a SINE insertion at these loci during ancestral speciation. Such incomplete sorting may have taken place earlier than 14 MYA, followed by random and stochastic fixation of the alleles in subsequent lineages. These observations prompted us to consider the possibility that cichlid speciation occurred at an accelerated rate during this period when the African Great Lakes did not exist. The SINE method could be useful for detecting ancient exclusive speciation events that tend to remain hidden during conventional sequence analyses because of accumulated point mutations.

AQUATIC PLANT SPECIATION AFFECTED BY DIVERSIFYING SELECTION OF ORGANELLE DNA REGIONS(1).

PubMed

Kato, Syou; Misawa, Kazuharu; Takahashi, Fumio; Sakayama, Hidetoshi; Sano, Satomi; Kosuge, Keiko; Kasai, Fumie; Watanabe, Makoto M; Tanaka, Jiro; Nozaki, Hisayoshi

2011-10-01

Many of the genes that control photosynthesis are carried in the chloroplast. These genes differ among species. However, evidence has yet to be reported revealing the involvement of organelle genes in the initial stages of plant speciation. To elucidate the molecular basis of aquatic plant speciation, we focused on the unique plant species Chara braunii C. C. Gmel. that inhabits both shallow and deep freshwater habitats and exhibits habitat-based dimorphism of chloroplast DNA (cpDNA). Here, we examined the "shallow" and "deep" subpopulations of C. braunii using two nuclear DNA (nDNA) markers and cpDNA. Genetic differentiation between the two subpopulations was measured in both nDNA and cpDNA regions, although phylogenetic analyses suggested nuclear gene flow between subpopulations. Neutrality tests based on Tajima's D demonstrated diversifying selection acting on organelle DNA regions. Furthermore, both "shallow" and "deep" haplotypes of cpDNA detected in cultures originating from bottom soils of three deep environments suggested that migration of oospores (dormant zygotes) between the two habitats occurs irrespective of the complete habitat-based dimorphism of cpDNA from field-collected vegetative thalli. Therefore, the two subpopulations are highly selected by their different aquatic habitats and show prezygotic isolation, which represents an initial process of speciation affected by ecologically based divergent selection of organelle genes. © 2011 Phycological Society of America.

Biotic immigration events, speciation, and the accumulation of biodiversity in the fossil record

NASA Astrophysics Data System (ADS)

Stigall, Alycia L.; Bauer, Jennifer E.; Lam, Adriane R.; Wright, David F.

2017-01-01

Biotic Immigration Events (BIMEs) record the large-scale dispersal of taxa from one biogeographic area to another and have significantly impacted biodiversity throughout geologic time. BIMEs associated with biodiversity increases have been linked to ecologic and evolutionary processes including niche partitioning, species packing, and higher speciation rates. Yet substantial biodiversity decline has also been documented following BIMEs due to elevated extinction and/or reduced speciation rates. In this review, we develop a conceptual model for biodiversity accumulation that links BIMEs and geographic isolation with local (α) diversity, regional (β) diversity, and global (γ) diversity metrics. Within the model, BIME intervals are characterized by colonization of existing species within new geographic regions and a lack of successful speciation events. Thus, there is no change in γ-diversity, and α-diversity increases at the cost of β-diversity. An interval of regional isolation follows in which lineage splitting results in successful speciation events and diversity increases across all three metrics. Alternation of these two regimes can result in substantial biodiversity accumulation. We tested this conceptual model using a series of case studies from the paleontological record. We primarily focus on two intervals during the Middle through Late Ordovician Period (470-458 Ma): the globally pervasive BIMEs during the Great Ordovician Biodiversification Event (GOBE) and a regional BIME, the Richmondian Invasion. We further test the conceptual model by examining the Great Devonian Interchange, Neogene mollusk migrations and diversification, and the Great American Biotic Interchange. Paleontological data accord well with model predictions. Constraining the mechanisms of biodiversity accumulation provides context for conservation biology. Because α-, β-, and γ-diversity are semi-independent, different techniques should be considered for sustaining various

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

PubMed

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

2006-01-01

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

Cadmium accumulation is enhanced by ammonium compared to nitrate in two hyperaccumulators, without affecting speciation

PubMed Central

Cheng, Miaomiao; Wang, Peng; Kopittke, Peter M.; Wang, Anan; Sale, Peter W.G.

2016-01-01

Nitrogen fertilization could improve the efficiency of Cd phytoextraction in contaminated soil and thus shorten the remediation time. However, limited information is available on the effect of N form on Cd phytoextraction and associated mechanisms in plants. This study examined the effect of N form on Cd accumulation, translocation, and speciation in Carpobrotus rossii and Solanum nigrum. Plants were grown in nutrient solution with 5–15 μM Cd in the presence of 1000 µM NH4 + or NO3 −. Plant growth and Cd uptake were measured, and Cd speciation was analyzed using synchrotron-based X-ray absorption spectroscopy. Shoot Cd accumulation was 30% greater with NH4 + than NO3 − supply. Carpobrotus rossii accumulated three times more Cd than S. nigrum. However, Cd speciation in the plants was not influenced by N form, but it did vary with species and tissues. In C. rossii, up to 91% of Cd was bound to S-containing ligands in all tissues except the xylem sap where 87–95% were Cd-OH complexes. Furthermore, the proportion of Cd-S in shoots was substantially lower in S. nigrum (44–69%) than in C. rossii (60–91%). It is concluded that the application of NH4 + (instead of NO3 −) increased shoot Cd accumulation by increasing uptake and translocation, rather than changing Cd speciation, and is potentially an effective approach for increasing Cd phytoextraction. PMID:27385767

How does male–male competition generate negative frequency-dependent selection and disruptive selection during speciation?

PubMed Central

Border, Shana E

2018-01-01

Abstract Natural selection has been shown to drive population differentiation and speciation. The role of sexual selection in this process is controversial; however, most of the work has centered on mate choice while the role of male–male competition in speciation is relatively understudied. Here, we outline how male–male competition can be a source of diversifying selection on male competitive phenotypes, and how this can contribute to the evolution of reproductive isolation. We highlight how negative frequency-dependent selection (advantage of rare phenotype arising from stronger male–male competition between similar male phenotypes compared with dissimilar male phenotypes) and disruptive selection (advantage of extreme phenotypes) drives the evolution of diversity in competitive traits such as weapon size, nuptial coloration, or aggressiveness. We underscore that male–male competition interacts with other life-history functions and that variable male competitive phenotypes may represent alternative adaptive options. In addition to competition for mates, aggressive interference competition for ecological resources can exert selection on competitor signals. We call for a better integration of male–male competition with ecological interference competition since both can influence the process of speciation via comparable but distinct mechanisms. Altogether, we present a more comprehensive framework for studying the role of male–male competition in speciation, and emphasize the need for better integration of insights gained from other fields studying the evolutionary, behavioral, and physiological consequences of agonistic interactions. PMID:29492042

Speciation of sulfur in biochar produced from pyrolysis and gasification of oak and corn stover.

PubMed

Cheah, Singfoong; Malone, Shealyn C; Feik, Calvin J

2014-01-01

The effects of feedstock type and biomass conversion conditions on the speciation of sulfur in biochars are not well-known. In this study, the sulfur content and speciation in biochars generated from pyrolysis and gasification of oak and corn stover were determined. We found the primary determinant of the total sulfur content of biomass to be the feedstock from which the biochar is generated, with oak and corn stover biochars containing 160 and 600-800 ppm sulfur, respectively. In contrast, for sulfur speciation, we found the primary determinant to be the temperature combined with the thermochemical conversion method. The speciation of sulfur in biochars was determined using X-ray absorption near-edge structure (XANES), ASTM method D2492, and scanning electron microscopy-energy-dispersive spectroscopy (SEM-EDS). Biochars produced under pyrolysis conditions at 500-600 °C contain sulfate, organosulfur, and sulfide. In some cases, the sulfate contents are up to 77-100%. Biochars produced in gasification conditions at 850 °C contain 73-100% organosulfur. The increase of the organosulfur content as the temperature of biochar production increases suggests a similar sulfur transformation mechanism as that in coal, where inorganic sulfur reacts with hydrocarbon and/or H2 to form organosulfur when the coal is heated. EDS mapping of a biochar produced from corn stover pyrolysis shows individual sulfur-containing mineral particles in addition to the sulfur that is distributed throughout the organic matrix.

Speciation of Sulfur in Biochar Produced from Pyrolysis and Gasification of Oak and Corn Stover

PubMed Central

2015-01-01

The effects of feedstock type and biomass conversion conditions on the speciation of sulfur in biochars are not well-known. In this study, the sulfur content and speciation in biochars generated from pyrolysis and gasification of oak and corn stover were determined. We found the primary determinant of the total sulfur content of biomass to be the feedstock from which the biochar is generated, with oak and corn stover biochars containing 160 and 600–800 ppm sulfur, respectively. In contrast, for sulfur speciation, we found the primary determinant to be the temperature combined with the thermochemical conversion method. The speciation of sulfur in biochars was determined using X-ray absorption near-edge structure (XANES), ASTM method D2492, and scanning electron microscopy–energy-dispersive spectroscopy (SEM–EDS). Biochars produced under pyrolysis conditions at 500–600 °C contain sulfate, organosulfur, and sulfide. In some cases, the sulfate contents are up to 77–100%. Biochars produced in gasification conditions at 850 °C contain 73–100% organosulfur. The increase of the organosulfur content as the temperature of biochar production increases suggests a similar sulfur transformation mechanism as that in coal, where inorganic sulfur reacts with hydrocarbon and/or H2 to form organosulfur when the coal is heated. EDS mapping of a biochar produced from corn stover pyrolysis shows individual sulfur-containing mineral particles in addition to the sulfur that is distributed throughout the organic matrix. PMID:25003702

Network inference using informative priors

PubMed Central

Mukherjee, Sach; Speed, Terence P.

2008-01-01

Recent years have seen much interest in the study of systems characterized by multiple interacting components. A class of statistical models called graphical models, in which graphs are used to represent probabilistic relationships between variables, provides a framework for formal inference regarding such systems. In many settings, the object of inference is the network structure itself. This problem of “network inference” is well known to be a challenging one. However, in scientific settings there is very often existing information regarding network connectivity. A natural idea then is to take account of such information during inference. This article addresses the question of incorporating prior information into network inference. We focus on directed models called Bayesian networks, and use Markov chain Monte Carlo to draw samples from posterior distributions over network structures. We introduce prior distributions on graphs capable of capturing information regarding network features including edges, classes of edges, degree distributions, and sparsity. We illustrate our approach in the context of systems biology, applying our methods to network inference in cancer signaling. PMID:18799736

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

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. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Influence of uranyl speciation and iron oxides on uranium biogeochemical redox reactions

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

Stewart, B.D.; Amos, R.T.; Nico, P.S.

2010-03-15

Uranium is a pollutant of concern to both human and ecosystem health. Uranium's redox state often dictates its partitioning between the aqueous- and solid-phases, and thus controls its dissolved concentration and, coupled with groundwater flow, its migration within the environment. In anaerobic environments, the more oxidized and mobile form of uranium (UO{sub 2}{sup 2+} and associated species) may be reduced, directly or indirectly, by microorganisms to U(IV) with subsequent precipitation of UO{sub 2}. However, various factors within soils and sediments may limit biological reduction of U(VI), inclusive of alterations in U(VI) speciation and competitive electron acceptors. Here we elucidate themore » impact of U(VI) speciation on the extent and rate of reduction with specific emphasis on speciation changes induced by dissolved Ca, and we examine the impact of Fe(III) (hydr)oxides (ferrihydrite, goethite and hematite) varying in free energies of formation on U reduction. The amount of uranium removed from solution during 100 h of incubation with S. putrefaciens was 77% with no Ca or ferrihydrite present but only 24% (with ferrihydrite) and 14% (no ferrihydrite) were removed for systems with 0.8 mM Ca. Imparting an important criterion on uranium reduction, goethite and hematite decrease the dissolved concentration of calcium through adsorption and thus tend to diminish the effect of calcium on uranium reduction. Dissimilatory reduction of Fe(III) and U(VI) can proceed through different enzyme pathways, even within a single organism, thus providing a potential second means by which Fe(III) bearing minerals may impact U(VI) reduction. We quantify rate coefficients for simultaneous dissimilatory reduction of Fe(III) and U(VI) in systems varying in Ca concentration (0 to 0.8 mM), and using a mathematical construct implemented with the reactive transport code MIN3P, we reveal the predominant influence of uranyl speciation, specifically the formation of uranyl

Standing Kink modes in three-dimensional coronal loops

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

Pascoe, D. J.; De Moortel, I., E-mail: dpascoe@mcs.st-andrews.ac.uk

2014-04-01

So far, the straight flux tube model proposed by Edwin and Roberts is the most commonly used tool in practical coronal seismology, in particular, to infer values of the (coronal) magnetic field from observed, standing kink mode oscillations. In this paper, we compare the period predicted by this basic model with three-dimensional (3D) numerical simulations of standing kink mode oscillations, as the period is a crucial parameter in the seismological inversion to determine the magnetic field. We perform numerical simulations of standing kink modes in both straight and curved 3D coronal loops and consider excitation by internal and external drivers.more » The period of oscillation for the displacement of dense coronal loops is determined by the loop length and the kink speed, in agreement with the estimate based on analytical theory for straight flux tubes. For curved coronal loops embedded in a magnetic arcade and excited by an external driver, a secondary mode with a period determined by the loop length and external Alfvén speed is also present. When a low number of oscillations is considered, these two periods can result in a single, non-resolved (broad) peak in the power spectrum, particularly for low values of the density contrast for which the two periods will be relatively similar. In that case (and for this particular geometry), the presence of this additional mode would lead to ambiguous seismological estimates of the magnetic field strength.« less

SPECIATED VOC EMISSIONS FROM MODERN GDI LIGHT ...

EPA Pesticide Factsheets

Chassis dynamometer emissions testing was conducted to characterize speciated volatile organic compounds (VOCs), including mobile source air toxics (MSATs) and ozone precursors, in exhaust emissions from three modern gasoline direct injection (GDI) light-duty vehicles. Each GDI vehicle tested in this study utilized slightly different fuel injection technology: Vehicle 1 used a 2.4 liter, naturally aspirated, wall-guided GDI; Vehicle 2 used a 1.8 liter, turbocharged GDI engine; Vehicle 3 used a 1.5 liter, turbocharged, spray-guided GDI engine. Vehicle testing was conducted in a temperature controlled chassis dynamometer test cell at 22 °C over the EPA Federal Test Procedure (FTP) and a portion of the Supplemental FTP (SFTP). The FTP was conducted as a three phase cycle with a cold start, hot transient, and warm start phase (also known as the FTP-75 driving cycle). The SFTP consisted of the US06 driving cycle (conducted without the vehicle’s air conditioning on), which provides a more aggressive driving pattern than the FTP. The vehicles operated on 10 percent ethanol blended gasoline (E10). VOC emissions from diluted vehicle exhaust were sampled over each FTP phase and over the Supplemental FTP with SUMMA canisters for EPA Method TO-15 analysis and with DNPH cartridges for carbonyl analysis by EPA Method TO-11A. This presentation will report the impact of driving cycle and GDI technology on speciated MSAT emissions. MSAT emission rates will be compared

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.

Social Dynamics Modeling and Inference

DTIC Science & Technology

2018-03-29

AFRL-AFOSR-JP-TR-2018-0027 Social Dynamics Modeling and Inference Kwang-Cheng Chen NATIONAL TAIWAN UNIVERSITY Final Report 03/29/2018 DISTRIBUTION A...DATES COVERED (From - To)      14 May 2014 to 13 May 2017 4.  TITLE AND SUBTITLE Social Dynamics Modeling and Inference 5a.  CONTRACT NUMBER 5b.  GRANT...behavior in human society, to set up the foundation of future possible inference and even control of social collective behavior. Two primary

The role of familiarity in binary choice inferences.

PubMed

Honda, Hidehito; Abe, Keiga; Matsuka, Toshihiko; Yamagishi, Kimihiko

2011-07-01

In research on the recognition heuristic (Goldstein & Gigerenzer, Psychological Review, 109, 75-90, 2002), knowledge of recognized objects has been categorized as "recognized" or "unrecognized" without regard to the degree of familiarity of the recognized object. In the present article, we propose a new inference model--familiarity-based inference. We hypothesize that when subjective knowledge levels (familiarity) of recognized objects differ, the degree of familiarity of recognized objects will influence inferences. Specifically, people are predicted to infer that the more familiar object in a pair of two objects has a higher criterion value on the to-be-judged dimension. In two experiments, using a binary choice task, we examined inferences about populations in a pair of two cities. Results support predictions of familiarity-based inference. Participants inferred that the more familiar city in a pair was more populous. Statistical modeling showed that individual differences in familiarity-based inference lie in the sensitivity to differences in familiarity. In addition, we found that familiarity-based inference can be generally regarded as an ecologically rational inference. Furthermore, when cue knowledge about the inference criterion was available, participants made inferences based on the cue knowledge about population instead of familiarity. Implications of the role of familiarity in psychological processes are discussed.

Spatio-temporal Distribution and Chemical Speciation of Iron and Manganese in Sediments from Lake Aha, China

NASA Astrophysics Data System (ADS)

Liu, Feng; Hu, Jiwei; Qin, Fanxin; Jiang, Cuihong; Huang, Xianfei; Deng, Jiajun; Li, Cunxiong

2010-11-01

This paper reports an investigation on pollution and potential risk on elements of iron (Fe) and manganese (Mn) in sediments from Lake Aha, which is a drinking-water source for Guiyang City, the capital of Guizhou Province in southwestern China. In the present research, chemical speciation of Fe and Mn in sediments from the lake was studied based on the sequential extraction procedure developed by Tessier et al.. The results obtained from the study are as follows. The average values of total Fe were 47617 mg/kg and 70325 mg/kg in sediments from the lake in summer and winter respectively, and its speciation consisted mainly of residual and Fe-Mn oxides fractions. The amounts of total Fe and the distribution of its speciation in the sediments should be affected by effluents from a large quantity of deserted coal mines in the lake basin in summer and winter. The average values of total Mn were 7996 mg/kg and 1753 mg/kg in summer and winter respectively, and its speciation is primarily comprised of carbonate and Fe-Mn oxides fractions. The amounts of total Mn and its distribution in different fractions in the sediments were believed to be primarily influenced by effluents from those deserted coal mines in summer and by the condition of redox interface in winter.

Composition of COH fluids at 1 GPa: an experimental study on speciation and solubility

NASA Astrophysics Data System (ADS)

Tiraboschi, Carla; Tumiati, Simone; Recchia, Sandro; Ulmer, Peter; Pettke, Thomas; Fumagalli, Patrizia; Poli, Stefano

2014-05-01

COH fluids play a fundamental role in many geological processes, controlling the location of melting in subduction zones and promoting mass transfer from the subducting litosphere to the overlying mantle wedge. The properties of COH fluids are strictly dependent on the composition of the fluid in subduction systems, i.e., the speciation of the volatile components of the fluid itself and the presence of solutes deriving from the dissolution of rock-forming minerals. In the scientific literature, the speciation of COH fluids has been generally determined through thermodynamic calculations using equations of state of simple H2O-non-polar gas systems (e.g., H2O-CO2-CH4), equations that do not consider the complexity related to dissolution processes, which are substantially unexplored in COH fluids and limited so far to aqueous fluids (Newton & Manning, 2002). The aim of this work is to investigate experimentally the speciation and the dissolution of mantle minerals in carbon-saturated COH fluids at buffered fO2 conditions. Our experimental approach relies on two different techniques: 1) analysis by means of quadrupole mass spectrometer (QMS) of the fluids from pierced run capsules to retrieve speciation of volatile components and 2) analysis of frozen COH fluid with laser-ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS) to measure the amount of solutes. Experiments were conducted at pressure of 1 GPa and temperatures from 800 to 900° C using a rocking piston cylinder apparatus. Mantle minerals in equilibrium with COH fluid are represented by synthetic forsterite. fO2 conditions were controlled using the double capsule technique and NNO buffer (ΔFMQ=-0.61 at 800° C; ΔFMQ =-0.98 at 900° C). For the speciation experiments, oxalic acid dihydrate and graphite have been used to generate carbon-saturated COH fluid. The speciation was determined by analyzing the quenched COH fluid, retrieved by piercing the capsule in a gas-tight vessel at T =80° C and

Uranium speciation in biofilms studied by laser fluorescence techniques.

PubMed

Arnold, Thuro; Grossmann, Kay; Baumann, Nils

2010-03-01

Biofilms may immobilize toxic heavy metals in the environment and thereby influence their migration behaviour. The mechanisms of these processes are currently not understood, because the complexity of such biofilms creates many discrete geochemical microenvironments which may differ from the surrounding bulk solution in their bacterial diversity, their prevailing geochemical properties, e.g. pH and dissolved oxygen concentration, the presence of organic molecules, e.g. metabolites, and many more, all of which may affect metal speciation. To obtain such information, which is necessary for performance assessment studies or the development of new cost-effective strategies for cleaning waste waters, it is very important to develop new non-invasive methods applicable to study the interactions of metals within biofilm systems. Laser fluorescence techniques have some superior features, above all very high sensitivity for fluorescent heavy metals. An approach combining confocal laser scanning microscopy and laser-induced fluorescence spectroscopy for study of the interactions of biofilms with uranium is presented. It was found that coupling these techniques furnishes a promising tool for in-situ non-invasive study of fluorescent heavy metals within biofilm systems. Information on uranium speciation and uranium redox states can be obtained.

A coevolutionary arms race causes ecological speciation in crossbills.

PubMed

Smith, Julie W; Benkman, Craig W

2007-04-01

We examined three ecological factors potentially causing premating reproductive isolation to determine whether divergent selection as a result of coevolution between South Hills crossbills (Loxia curvirostra complex) and Rocky Mountain lodgepole pine (Pinus contorta latifolia) promotes ecological speciation. One factor was habitat isolation arising because of enhanced seed defenses of lodgepole pine in the South Hills. This caused the crossbill call types (morphologically and vocally differentiated forms) adapted to alternative resources to be rare. Another occurred when crossbills of other call types moved into the South Hills late in the breeding season and feeding conditions were deteriorating so that relatively few non-South Hills crossbills bred ("immigrant infecundity"). Finally, among those crossbills that bred, pairing was strongly assortative by call type (behavioral isolation). Total reproductive isolation between South Hills crossbills and the two other crossbills most common in the South Hills (call types 2 and 5) summed to .9975 and .9998, respectively, on a scale of 0 (no reproductive isolation) to 1 (complete reproductive isolation). These extremely high levels of reproductive isolation indicate that the divergent selection resulting from the coevolutionary arms race between crossbills and lodgepole pine is causing the South Hills crossbill to speciate.

Radiating on oceanic islands: patterns and processes of speciation in the land snail genus Theba (Risso 1826).

PubMed

Greve, Carola; Gimnich, France; Hutterer, Rainer; Misof, Bernhard; Haase, Martin

2012-01-01

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors.

Radiating on Oceanic Islands: Patterns and Processes of Speciation in the Land Snail Genus Theba (Risso 1826)

PubMed Central

Greve, Carola; Gimnich, France; Hutterer, Rainer; Misof, Bernhard; Haase, Martin

2012-01-01

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors. PMID:22493687

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

PubMed

Schneider, Arnaud R; Ponthieu, Marie; Cancès, Benjamin; Conreux, Alexandra; Morvan, Xavier; Gommeaux, Maxime; Marin, Béatrice; Benedetti, Marc F

2016-06-01

Trace element (TE) speciation modelling in soil solution is controlled by the assumptions made about the soil solution composition. To evaluate this influence, different assumptions using Visual MINTEQ were tested and compared to measurements of free TE concentrations. The soil column Donnan membrane technique (SC-DMT) was used to estimate the free TE (Cd, Cu, Ni, Pb and Zn) concentrations in six acidic soil solutions. A batch technique using DAX-8 resin was used to fractionate the dissolved organic matter (DOM) into four fractions: humic acids (HA), fulvic acids (FA), hydrophilic acids (Hy) and hydrophobic neutral organic matter (HON). To model TE speciation, particular attention was focused on the hydrous manganese oxides (HMO) and the Hy fraction, ligands not considered in most of the TE speciation modelling studies in soil solution. In this work, the model predictions of free ion activities agree with the experimental results. The knowledge of the FA fraction seems to be very useful, especially in the case of high DOM content, for more accurately representing experimental data. Finally, the role of the manganese oxides and of the Hy fraction on TE speciation was identified and, depending on the physicochemical conditions of the soil solution, should be considered in future studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Migration and speciation of heavy metal in salinized mine tailings affected by iron mining.

PubMed

Zhang, Xu; Yang, Huanhuan; Cui, Zhaojie

2017-10-01

The negative effects of heavy metals have aroused much attention due to their high toxicity to human beings. Migration and transformation trend of heavy metals have a close relationship with soil safety. Researching on migration and transformation of heavy metals in tailings can provide a reliable basis for pollution management and ecosystem restoration. Heavy metal speciation plays an important role in risk assessment. We chose Anshan tailings for our study, including field investigations and laboratory research. Four typical heavy metal elements of mine tailings {Fe (373.89 g/kg), Mn (2,303.80 mg/kg), Pb (40.99 mg/kg) and Cr (199.92 mg/kg)} were studied via Tessier test in vertical and horizontal direction. The main speciation of heavy metals in Anshan tailings was the residual. However, heavy metals have a strong ability for migration and transformation in vertical and horizontal directions. Its tendency to change from stable to unstable speciation results in increasing bioavailability and potential bioavailability. Fe, Mn, Pb and Cr showed different ability in the migration and transformation process (Mn > Pb > Fe > Cr) depending on the characteristics of heavy metals and physicochemical properties of the environment.

Presumable incipient hybrid speciation of door snails in previously glaciated areas in the Caucasus.

PubMed

Koch, Eva L; Neiber, Marco T; Walther, Frank; Hausdorf, Bernhard

2016-04-01

Homoploid hybrid speciation, speciation by hybridization without a change in chromosome number, may be the result of an encounter of closely related species in a habitat that is different from that usually occupied by these species. In the northwestern Caucasus the land snail species Micropontica caucasica and M. circassica form two distinct entities with little admixture at low and intermediate altitudes. However, at higher altitudes in the Lagonaki plateau, which were repeatedly glaciated, Micropontica populations with intermediate characters occur. Admixture analyses based on AFLP data demonstrated that the populations from the Lagonaki plateau are homoploid hybrids that now form a cluster separate from the parental species. The Lagonaki populations are characterized by a mtDNA haplotype clade that has been found in the parental species only once. The fixation of this haplotype clade in most hybrid populations suggests that these haplotypes are better adapted to the cooler conditions in high altitude habitats and have replaced the haplotypes of the parental species in a selective sweep. The fixation of a presumably adaptive mitochondrial haplotype clade in the Lagonaki populations is an important step towards speciation under the differential fitness species concept. Copyright © 2015 Elsevier Inc. All rights reserved.

Zonal Flow Velocimetry in Spherical Couette Flow using Acoustic Modes

NASA Astrophysics Data System (ADS)

Adams, Matthew M.; Mautino, Anthony R.; Stone, Douglas R.; Triana, Santiago A.; Lekic, Vedran; Lathrop, Daniel P.

2015-11-01

We present studies of spherical Couette flows using the technique of acoustic mode Doppler velocimetry. This technique uses rotational splittings of acoustic modes to infer the azimuthal velocity profile of a rotating flow, and is of special interest in experiments where direct flow visualization is impractical. The primary experimental system consists of a 60 cm diameter outer spherical shell concentric with a 20 cm diameter sphere, with air or nitrogen gas serving as the working fluid. The geometry of the system approximates that of the Earth's core, making these studies geophysically relevant. A turbulent shear flow is established in the system by rotating the inner sphere and outer shell at different rates. Acoustic modes of the fluid volume are excited using a speaker and measured via microphones, allowingdetermination of rotational splittings. Preliminary results comparing observed splittings with those predicted by theory are presented. While the majority of these studies were performed in the 60 cm diameter device using nitrogen gas, some work has also been done looking at acoustic modes in the 3 m diameter liquid sodium spherical Couette experiment. Prospects for measuring zonal velocity profiles in a wide variety of experiments are discussed.

Three-dimensional modeling of the neutron spectrum to infer plasma conditions in cryogenic inertial confinement fusion implosions

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

Weilacher, F.; Radha, P. B.; Forrest, C.

Neutron-based diagnostics are typically used to infer compressed core conditions such as areal density and ion temperature in deuterium–tritium (D–T) inertial confinement fusion (ICF) implosions. Asymmetries in the observed neutron-related quantities are important to understanding failure modes in these implosions. Neutrons from fusion reactions and their subsequent interactions including elastic scattering and neutron-induced deuteron breakup reactions are tracked to create spectra. Here, it is shown that background subtraction is important for inferring areal density from backscattered neutrons and is less important for the forward-scattered neutrons. A three-dimensional hydrodynamic simulation of a cryogenic implosion on the OMEGA Laser System [T. R.more » Boehly et al., Opt. Commun. 133, 495 (1997)] using the hydrodynamic code HYDRA [M. M. Marinak et al., Phys. Plasmas 8, 2275 (2001)] is post-processed using the tracking code IRIS3D. It is shown that different parts of the neutron spectrum from the view can be mapped into different regions of the implosion, enabling an inference of an areal-density map. It is also shown that the average areal-density and an areal-density map of the compressed target can be reconstructed with a finite number of detectors placed around the target chamber. Ion temperatures are inferred from the width of the D–D and D–T fusion neutron spectra. Backgrounds can significantly alter the inferred ion temperatures from the D–D reaction, whereas they insignificantly influence the inferred D–T ion temperatures for the areal densities typical of OMEGA implosions. Asymmetries resulting in fluid flow in the core are shown to influence the absolute inferred ion temperatures from both reactions, although relative inferred values continue to reflect the underlying asymmetry pattern. The work presented here is part of the wide range of the first set of studies performed with IRIS3D. Finally, this code will continue to be used for

Three-dimensional modeling of the neutron spectrum to infer plasma conditions in cryogenic inertial confinement fusion implosions

DOE PAGES

Weilacher, F.; Radha, P. B.; Forrest, C.

2018-04-26

Neutron-based diagnostics are typically used to infer compressed core conditions such as areal density and ion temperature in deuterium–tritium (D–T) inertial confinement fusion (ICF) implosions. Asymmetries in the observed neutron-related quantities are important to understanding failure modes in these implosions. Neutrons from fusion reactions and their subsequent interactions including elastic scattering and neutron-induced deuteron breakup reactions are tracked to create spectra. Here, it is shown that background subtraction is important for inferring areal density from backscattered neutrons and is less important for the forward-scattered neutrons. A three-dimensional hydrodynamic simulation of a cryogenic implosion on the OMEGA Laser System [T. R.more » Boehly et al., Opt. Commun. 133, 495 (1997)] using the hydrodynamic code HYDRA [M. M. Marinak et al., Phys. Plasmas 8, 2275 (2001)] is post-processed using the tracking code IRIS3D. It is shown that different parts of the neutron spectrum from the view can be mapped into different regions of the implosion, enabling an inference of an areal-density map. It is also shown that the average areal-density and an areal-density map of the compressed target can be reconstructed with a finite number of detectors placed around the target chamber. Ion temperatures are inferred from the width of the D–D and D–T fusion neutron spectra. Backgrounds can significantly alter the inferred ion temperatures from the D–D reaction, whereas they insignificantly influence the inferred D–T ion temperatures for the areal densities typical of OMEGA implosions. Asymmetries resulting in fluid flow in the core are shown to influence the absolute inferred ion temperatures from both reactions, although relative inferred values continue to reflect the underlying asymmetry pattern. The work presented here is part of the wide range of the first set of studies performed with IRIS3D. Finally, this code will continue to be used for

Three-dimensional modeling of the neutron spectrum to infer plasma conditions in cryogenic inertial confinement fusion implosions

NASA Astrophysics Data System (ADS)

Weilacher, F.; Radha, P. B.; Forrest, C.

2018-04-01

Neutron-based diagnostics are typically used to infer compressed core conditions such as areal density and ion temperature in deuterium-tritium (D-T) inertial confinement fusion (ICF) implosions. Asymmetries in the observed neutron-related quantities are important to understanding failure modes in these implosions. Neutrons from fusion reactions and their subsequent interactions including elastic scattering and neutron-induced deuteron breakup reactions are tracked to create spectra. It is shown that background subtraction is important for inferring areal density from backscattered neutrons and is less important for the forward-scattered neutrons. A three-dimensional hydrodynamic simulation of a cryogenic implosion on the OMEGA Laser System [Boehly et al., Opt. Commun. 133, 495 (1997)] using the hydrodynamic code HYDRA [Marinak et al., Phys. Plasmas 8, 2275 (2001)] is post-processed using the tracking code IRIS3D. It is shown that different parts of the neutron spectrum from the view can be mapped into different regions of the implosion, enabling an inference of an areal-density map. It is also shown that the average areal-density and an areal-density map of the compressed target can be reconstructed with a finite number of detectors placed around the target chamber. Ion temperatures are inferred from the width of the D-D and D-T fusion neutron spectra. Backgrounds can significantly alter the inferred ion temperatures from the D-D reaction, whereas they insignificantly influence the inferred D-T ion temperatures for the areal densities typical of OMEGA implosions. Asymmetries resulting in fluid flow in the core are shown to influence the absolute inferred ion temperatures from both reactions, although relative inferred values continue to reflect the underlying asymmetry pattern. The work presented here is part of the wide range of the first set of studies performed with IRIS3D. This code will continue to be used for post-processing detailed hydrodynamic simulations

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

PubMed

Stankowski, Sean

2013-05-01

Speciation is the process by which reproductive isolation evolves between populations. Two general models of speciation have been proposed: ecological speciation, where reproductive barriers evolve due to ecologically based divergent selection, and mutation-order speciation, where populations fix different mutations as they adapt to similar selection pressures. I evaluate these alternative models and determine the progress of speciation in a diverse group of land snails, genus Rhagada, inhabiting Rosemary Island. A recently derived keeled-flat morphotype occupies two isolated rocky hills, while globose-shelled snails inhabit the surrounding plains. The study of one hill reveals that they are separated by a narrow hybrid zone. As predicted by ecological speciation theory, there are local and landscape level associations between shell shape and habitat, and the morphological transition coincides with a narrow ecotone between the two distinct environments. Microsatellite DNA revealed a cline of hybrid index scores much wider than the morphological cline, further supporting the ecological maintenance of the morphotypes. The hybrid zone does not run through an area of low population density, as is expected for mutation-order hybrid zones, and there is a unimodal distribution of phenotypes at the centre, suggesting that there is little or no prezygotic isolation. Instead, these data suggest that the ecotypes are maintained by ecologically dependent postzygotic isolation (i.e. ecological selection against hybrids). Mitochondrial and Microsatellite DNA indicate that the keeled-flat form evolved recently, and without major historical disruptions to gene flow. The data also suggest that the two keeled-flat populations, inhabiting similar rocky hills, have evolved in parallel. These snails provide a complex example of ecological speciation in its early stages. © 2013 Blackwell Publishing Ltd.

EVALUATION OF THE EFFECT OF SCR ON MERCURY SPECIATION AND EMISSIONS

EPA Science Inventory

The paper presents the results of an investigation on the impact that selective catalytic reduction (SCR) has on both the total emissions and the speciation of mercury (Hg). SCR systems can be used as multipollutant technologies if they enhance Hg conversion/capture. Previous pil...

VARIATION OF ELEMENT SPECIATION IN COAL COMBUSTION AEROSOLS WITH PARTICLE SIZE

EPA Science Inventory

The speciation of sulfur, iron and key trace elements (Cr, As, Se, Zn) in combustion ash aerosols has been examined as a function of size from experimental combustion units burning Utah and Illinois bituminous coals. Although predominantly present as sulfate, sulfur was also pre...

ASSESSING SPECIATION AND RELEASE OF HEAVY METALS FROM COAL COMBUSTION PRODUCTS

EPA Science Inventory

In this study, the speciation of heavy metals such as arsenic, selenium, lead, zinc and mercury in coal combustion products (CCPs) was evaluated using sequential extraction procedures. Coal fly ash, bottom ash and flue gas desulphurization (FGD) sludge samples were used in the ex...

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…

Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

PubMed

Pyron, R Alexander; Costa, Gabriel C; Patten, Michael A; Burbrink, Frank T

2015-11-01

Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species. © 2014 Cambridge Philosophical Society.

Inferring network structure in non-normal and mixed discrete-continuous genomic data.

PubMed

Bhadra, Anindya; Rao, Arvind; Baladandayuthapani, Veerabhadran

2018-03-01

Inferring dependence structure through undirected graphs is crucial for uncovering the major modes of multivariate interaction among high-dimensional genomic markers that are potentially associated with cancer. Traditionally, conditional independence has been studied using sparse Gaussian graphical models for continuous data and sparse Ising models for discrete data. However, there are two clear situations when these approaches are inadequate. The first occurs when the data are continuous but display non-normal marginal behavior such as heavy tails or skewness, rendering an assumption of normality inappropriate. The second occurs when a part of the data is ordinal or discrete (e.g., presence or absence of a mutation) and the other part is continuous (e.g., expression levels of genes or proteins). In this case, the existing Bayesian approaches typically employ a latent variable framework for the discrete part that precludes inferring conditional independence among the data that are actually observed. The current article overcomes these two challenges in a unified framework using Gaussian scale mixtures. Our framework is able to handle continuous data that are not normal and data that are of mixed continuous and discrete nature, while still being able to infer a sparse conditional sign independence structure among the observed data. Extensive performance comparison in simulations with alternative techniques and an analysis of a real cancer genomics data set demonstrate the effectiveness of the proposed approach. © 2017, The International Biometric Society.

Numerical analysis of two-fluid tearing mode instability in a finite aspect ratio cylinder

NASA Astrophysics Data System (ADS)

Ito, Atsushi; Ramos, Jesús J.

2018-01-01

The two-fluid resistive tearing mode instability in a periodic plasma cylinder of finite aspect ratio is investigated numerically for parameters such that the cylindrical aspect ratio and two-fluid effects are of order unity, hence the real and imaginary parts of the mode eigenfunctions and growth rate are comparable. Considering a force-free equilibrium, numerical solutions of the complete eigenmode equations for general aspect ratios and ion skin depths are compared and found to be in very good agreement with the corresponding analytic solutions derived by means of the boundary layer theory [A. Ito and J. J. Ramos, Phys. Plasmas 24, 072102 (2017)]. Scaling laws for the growth rate and the real frequency of the mode are derived from the analytic dispersion relation by using Taylor expansions and Padé approximations. The cylindrical finite aspect ratio effect is inferred from the scaling law for the real frequency of the mode.

Miscibility and Speciation in the Water/carbon Dioxide System

NASA Astrophysics Data System (ADS)

Abramson, E.; Bollengier, O.; Brown, J. M.

2017-12-01

We have been exploring fluid-fluid solubilities and speciation in mixed systems of CO2-H2O. Fluid-fluid immiscibility extends to the highest pressures and temperatures yet explored (7 GPa, 700K). In this region, commonly used COH fluid models agree neither with the data nor among themselves. The range of immiscibility is extended by addition of NaCl, but miscibility limits determined in preliminary experiments are not as expected from extrapolation of lower pressure (<0.2 GPa) results. For majority-water systems (XCO2<0.5) an abrupt increase of solubility with pressure is linked to an observed change in speciation as CO2(aq) reacts with water. The identity of the newly formed species is, as of the writing of this abstract, unknown, but presumed to be either H2CO3 or HCO3-. A reasonable match between the observed equilibria and an application of HKF theory suggests that the new species is, indeed, HCO3-, but with a Raman frequency shifted from that found in the dilute aqueous solution. Application of HKF theory to the CO2(f)-CO2(aq) equilibrium suffers from an incompatibility of the usual formulation of the theory with known molar volumes of CO2(f) at higher pressures. On the basis of these studies we conclude that models of CO2-H2O fluids must take into account major changes in speciation, and that simple equations-of-state, of a few fitted parameters, will not afford an adequate description of such fluids. "First principles" models, tested against real data, seem more likely to yield the desired results. This statement extends as well to the calculation of the dielectric constants of these mixed fluids, the basis of ionic solution chemistry. Further, semi-empirical formulations of solution thermodynamics, which function well at pressures of kbars, ought to be re-worked for use over larger pressure ranges.

Speciation within Columnea section Angustiflora (Gesneriaceae): islands, pollinators and climate.

PubMed

Schulte, Lacie J; Clark, John L; Novak, Stephen J; Jeffries, Shandra K; Smith, James F

2015-03-01

Despite many advances in evolutionary biology, understanding the proximate mechanisms that lead to speciation for many taxonomic groups remains elusive. Phylogenetic analyses provide a means to generate well-supported estimates of species relationships. Understanding how genetic isolation (restricted gene flow) occurred in the past requires not only a well-supported molecular phylogenetic analysis, but also an understanding of when character states that define species may have changed. In this study, phylogenetic trees resolve species level relationships for fourteen of the fifteen species within Columnea section Angustiflorae (Gesneriaceae). The distributions of sister species pairs are compared and ancestral character states are reconstructed using Bayesian stochastic mapping. Climate variables were also assessed and shifts in ancestral climate conditions were mapped using SEEVA. The relationships between morphological character states and climate variables were assessed with correlation analyses. These results indicate that species in section Angustiflorae have likely diverged as a result of allopatric, parapatric, and sympatric speciation, with both biotic and abiotic forces driving morphological and phenological divergence. Copyright © 2015 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Morgan, G. B., VI; Chou, I.-Ming; Pasteris, J. D.

1992-01-01

Fluid speciations and their related reaction pathways were studied in C-O-H-system fluids produced by the thermal dissociation of oxalic acid dihydrate (OAD: H 2C 2O 4 · 2H 2O) sealed in silica glass capsules. Experiments were conducted in the temperature range 230-750°C, with bulk fluid densities in the range 0.01-0.53 g/cm 3. Pressure was controlled by temperature and density in the isochoric systems. The quenched products of dissociation experiments were an aqueous liquid and one (supercritical fluid) or, rarely, two (vapor plus liquid) carbonic phase (s). In-situ Raman microanalyses were performed on the quenched carbonic phases at room temperature, at which fluid pressures ranged from about 50 to 340 bars. Bulk fluid speciations were reconstructed from the Raman analyses via mass balance constraints, and appear to monitor the true fluid speciations at run conditions. In experiments from the lowtemperature range (230-350°C), fluid speciations record the dissociation of OAD according to the reaction OAD = CO2 + CO + 3 H2O. A process of the form CO + H2O = CO2 + H2 is driven to the right with increasing temperature. The hydrogen gas produced tends to escape from the sample systems via diffusion into/through the silica glass capsules, shifting bulk compositions toward equimolar binary H 2O-CO 2 mixtures. The speciations of fluids in experiments with minimal hydrogen loss show poor agreement with speciations calculated for equilibrium fluids by the corresponding-states model of SAXENA and FEI (1988). Such disagreement suggests that the formations of CH 4 and graphite are metastably inhibited in the current experiments, which correlates with their absence or trivial abundances in experimental products. Moreover, calculations in which the stabilities of methane and graphite are suppressed suggest that such metastable equilibrium is approached only in experiments at temperatures greater than about 600-650°C. These results have applications to fluid processes in

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

USGS Publications Warehouse

Morgan, G.B.; Chou, I.-Ming; Pasteris, J.D.

1992-01-01

Fluid speciations and their related reaction pathways were studied in C-O-H-system fluids produced by the thermal dissociation of oxalic acid dihydrate (OAD: H2C2O4 ?? 2H2O) sealed in silica glass capsules. Experiments were conducted in the temperature range 230-750??C, with bulk fluid densities in the range 0.01-0.53 g/cm3. Pressure was controlled by temperature and density in the isochoric systems. The quenched products of dissociation experiments were an aqueous liquid and one (supercritical fluid) or, rarely, two (vapor plus liquid) carbonic phase (s). In-situ Raman microanalyses were performed on the quenched carbonic phases at room temperature, at which fluid pressures ranged from about 50 to 340 bars. Bulk fluid speciations were reconstructed from the Raman analyses via mass balance constraints, and appear to monitor the true fluid speciations at run conditions. In experiments from the lowtemperature range (230-350??C), fluid speciations record the dissociation of OAD according to the reaction OAD = CO2 + CO + 3H2O. A process of the form CO + H2O = CO2 + H2 is driven to the right with increasing temperature. The hydrogen gas produced tends to escape from the sample systems via diffusion into/through the silica glass capsules, shifting bulk compositions toward equimolar binary H2O-CO2 mixtures. The speciations of fluids in experiments with minimal hydrogen loss show poor agreement with speciations calculated for equilibrium fluids by the corresponding-states model of Saxena and Fei (1988). Such disagreement suggests that the formations of CH4 and graphite are metastably inhibited in the current experiments, which correlates with their absence or trivial abundances in experimental products. Moreover, calculations in which the stabilities of methane and graphite are suppressed suggest that such metastable equilibrium is approached only in experiments at temperatures greater than about 600-650??C. These results have applications to fluid processes in geological

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

EPA Science Inventory

Updated methane, non-methane organic gas, and volatile organic compound calculations based on speciation data. Updated speciation and toxic emission rates for new model year 2010 and later heavy-duty diesel engines. Updated particulate matter emission rates for 2004 and later mod...

Sulfur Speciation in Biochars by Very High Resolution Benchtop Ka X-Ray Emission Spectroscopy

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

Cheah, Singfoong; Holden, William M.; Seidler, Gerald T.

The analytical chemistry of sulfur-containing materials poses substantial technical challenges, especially due to the limitations of 33S NMR and the time-intensive preparations required for wet-chemistry analyses. A number of prior studies have found that synchrotron-based X-ray absorption near edge structure (XANES) measurements can give detailed speciation of sulfur chemistry in such cases. However, due to the obvious access limitations, synchrotron XANES of sulfur cannot be part of routine analytical practice across the chemical sciences community. Here, in a study of the sulfur chemistry in biochars, we compare and contrast the chemical inferences available from synchrotron XANES with that given bymore » benchtop, extremely high resolution wavelength-dispersive X-ray fluorescence (WD-XRF) spectroscopy, also often called X-ray emission spectroscopy (XES). While the XANES spectra have higher total information content, often giving differentiation between different moieties having the same oxidation state, the lower sensitivity of the S Ka XES to coordination and local structure provides pragmatic benefit for the more limited goal of quantifying the S oxidation state distribution. Within that constrained metric, we find good agreement between the two methods. As the sulfur concentrations were as low as 150 ppm, these measurements provide proof-of-principle for characterization of the sulfur chemistry of biochars and potential applications to other areas such as soils, batteries, catalysts, and fossil fuels and their combustion products.« less

Mode analysis for energetics of a moving charge in Lorentz- and C P T -violating electrodynamics

NASA Astrophysics Data System (ADS)

DeCosta, Richard; Altschul, Brett

2018-03-01

In isotropic but Lorentz- and C P T -violating electrodynamics, it is known that a charge in uniform motion does not lose any energy to Cerenkov radiation. This presents a puzzle, since the radiation appears to be kinematically allowed for many modes. Studying the Fourier transforms of the most important terms in the modified magnetic field and Poynting vector, we confirm the vanishing of the radiation rate. Moreover, we show that the Fourier transform of the field changes sign between small and large wave numbers. This enables modes with very long wavelengths to carry negative energies, which cancel out the positive energies carried away by modes with shorter wavelengths. This cancelation had previously been inferred but never explicitly demonstrated.

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

NASA Astrophysics Data System (ADS)

Chorover, J.; Kong, S.; Root, R. A.; Thomas, A.

2015-12-01

Bioaccessibility of contaminant metals in geomedia is often measured on the basis of kinetic release to solution during in vitro reaction with biofluid simulants. We postulate that development of a predictive-mechanistic understanding of bioaccessibility requires knowledge of metal(loid) molecular speciation upon sample introduction, as well as its change over the course of the in vitro reaction. Our results - including data from batch, column, mesocosm and field studies pertaining to arsenic, lead, and zinc contaminated materials - indicate the strong influence of organic matter and associated biological activity on metal(loid) speciation in mine tailings and related model systems. Furthermore, presence/absence of organic matter during bioassays affects the kinetics of metal(loid) release into biofluid simulants through multiple mechanisms.

Silver speciation and release in commercial antimicrobial textiles as influenced by washing.

PubMed

Lombi, Enzo; Donner, Erica; Scheckel, Kirk G; Sekine, Ryo; Lorenz, Christiane; Von Goetz, Natalie; Nowack, Bernd

2014-09-01

The use of nanoscale Ag in textiles is one the most often mentioned uses of nano-Ag. It has previously been shown that significant amounts of the Ag in the textiles are released upon washing. However, the form of Ag present in the textiles remains largely unknown as product labelling is insufficient. The aim of this study was therefore to investigate the solid phase speciation of Ag in original and washed silver textiles using XANES. The original Ag speciation in the textiles was found to vary greatly between different materials with Ag(0), AgCl, Ag2S, Ag-phosphate, ionic Ag and other species identified. Furthermore, within the same textile a number of different species were found to coexist. This is likely due to a combination of factors such as the synthesis processes at industrial scale and the possible reaction of Ag with atmospheric gases. Washing with two different detergents resulted in marked changes in Ag-speciation. For some textiles the two detergents induced similar transformation, in other textiles they resulted in very different Ag species. This study demonstrates that in functional Ag textiles a variety of different Ag species coexist before and after washing. These results have important implications for the risk assessment of Ag textiles because they show that the metallic Ag is only one of the many silver species that need to be considered. Copyright © 2014 Elsevier Ltd. All rights reserved.

Speciation and leaching of trace metal contaminants from e-waste contaminated soils.

PubMed

Cui, Jin-Li; Luo, Chun-Ling; Tang, Chloe Wing-Yee; Chan, Ting-Shan; Li, Xiang-Dong

2017-05-05

Primitive electrical and electronic waste (e-waste) recycling activities have caused serious environmental problems. However, little is known about the speciation and leaching behaviors of metal contaminants at e-waste contaminated sites. This study investigated trace metal speciation/mobilization from e-waste polluted soil through column leaching experiments involving irrigation with rainwater for almost 2.5 years. Over the experimental period, Cu and Zn levels in the porewater were 0.14±0.08mg/L, and 0.16±0.08mg/L, respectively, increasing to 0.33±0.16mg/L, and 0.69±0.28mg/L with plant growth. The amounts of Cu, Zn, and Pb released in surface soil (0-2cm) contributed 43.8%, 22.5%, and 13.8%, respectively, to the original levels. The released Cu and Zn were primarily caused by the mobilization of the carbonate species of metals, including Cu(OH) 2 , CuCO 3 , and Zn 5 (CO 3 ) 2 (OH) 6 , and amorphous Fe/Mn oxides associated fractions characterized by sequential extraction coupling with X-ray absorption spectroscopy. During the experiments, trace metals were not detected in the effluent, and the re-sequestration of trace metals was mainly attributed to the adsorption on the abundant Fe/Mn oxides in the sub-layer soil. This study quantitatively elucidated the molecular speciation of Cu and Zn in e-waste contaminated soil during the column leaching process. Copyright © 2017 Elsevier B.V. All rights reserved.

North Pacific Meridional Mode over the Common Era

NASA Astrophysics Data System (ADS)

Sanchez, S. C.; Charles, C. D.; Amaya, D. J.; Miller, A. J.

2016-12-01

The Pacific Meridional Mode (PMM) has been increasingly recognized as an influential mode of variability for channeling extratropical anomalies to the equatorial ocean-atmosphere system. The PMM has been identified as an important precursor for ENSO, a source of much decadal power in the tropical Pacific, and is potentially intensifying. It is still unknown why the Pacific Meridional Mode might be intensifying; most arguments center around the changing mean state associated with anthropogenic global warming. There are a number of processes by which the background state could influence the PMM: altering the location of trade winds, the characteristics of stochastic forcing, the sensitivity of latent heat flux to surface wind anomalies, the wind response to SST anomalies, or changing the Intertropical Convergence Zone (ITCZ) structure. Recent work has found that the PMM is particularly sensitive to ITCZ shifts in intensity and location (using a simple linear coupled model, [Martinez-Villalobos and Vimont 2016]). Over the last millennium the ITCZ has experienced epochs of notable latitudinal shifts to balance the cross equatorial energy transport. Here we investigate how the strength of the PMM may have varied with these shifts in the ITCZ over the Common Era using the CESM-Last Millennium Ensemble (LME). We assess the strength of the PMM pathway by the degree of air-sea coupling and the amplitude of tropical decadal variability. We expect the ITCZ location and the degree of air-sea coupling (WES feedback) to play a critical role in determining the effectiveness and intensity of the PMM pathway. We verify our inferences in the LME with coral paleoproxy records from the central tropical Pacific. Chiefly we target records from the Line Islands (spanning 1°N to 6°N) to infer variations in the location of the ITCZ and the amplitude of decadal variability. This work enables us to discuss the idea of an intensifying PMM in a more historical context.

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

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

PubMed

Rossetto, Maurizio; Allen, Chris B; Thurlby, Katie A G; Weston, Peter H; Milner, Melita L

2012-08-20

Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters

Forward and backward inference in spatial cognition.

PubMed

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

2013-01-01

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

Relationship between metal speciation in soil solution and metal adsorption at the root surface of ryegrass.

PubMed

Kalis, Erwin J J; Temminghoff, Erwin J M; Town, Raewyn M; Unsworth, Emily R; van Riemsdijk, Willem H

2008-01-01

The total metal content of the soil or total metal concentration in the soil solution is not always a good indicator for metal availability to plants. Therefore, several speciation techniques have been developed that measure a defined fraction of the total metal concentration in the soil solution. In this study the Donnan Membrane Technique (DMT) was used to measure free metal ion concentrations in CaCl(2) extractions (to mimic the soil solution, and to work under standardized conditions) of 10 different soils, whereas diffusive gradients in thin-films (DGT) and scanning chronopotentiometry (SCP) were used to measure the sum of free and labile metal concentrations in the CaCl(2) extracts. The DGT device was also exposed directly to the (wetted) soil (soil-DGT). The metal concentrations measured with the speciation techniques are related to the metal adsorption at the root surface of ryegrass (Lolium perenne L.), to be able to subsequently predict metal uptake. In most cases the metal adsorption related pH-dependently to the metal concentrations measured by DMT, SCP, and DGT in the CaCl(2) extract. However, the relationship between metal adsorption at the root surface and the metal concentrations measured by the soil-DGT was not-or only slightly-pH dependent. The correlations between metal adsorption at the root surface and metal speciation detected by different speciation techniques allow discussion about rate limiting steps in biouptake and the contribution of metal complexes to metal bioavailability.

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

PubMed

Kim, Sora; Kaila, Lauri; Lee, Seunghwan

2016-08-01

Phylogenetic relationships within family Oecophoridae have been poorly understood. Consequently the subfamily and genus level classifications with this family problematic. A comprehensive phylogenetic analysis of Oecophoridae, the concealer moths, was performed based on analysis of 4444 base pairs of mitochondrial COI, nuclear ribosomal RNA genes (18S and 28S) and nuclear protein coding genes (IDH, MDH, Rps5, EF1a and wingless) for 82 taxa. Data were analyzed using maximum likelihood (ML), parsimony (MP) and Bayesian (BP) phylogenetic frameworks. Phylogenetic analyses indicated that (i) genera Casmara, Tyrolimnas and Pseudodoxia did not belong to Oecophoridae, suggesting that Oecophoridae s. authors was not monophyletic; (ii) other oecophorids comprising two subfamilies, Pleurotinae and Oecophorinae, were nested within the same clade, and (iii) Martyringa, Acryptolechia and Periacmini were clustered with core Xyloryctidae. They appeared to be sister lineage with core Oecophoridae. BayesTraits were implemented to explore the ancestral character states to infer historical microhabitat patterns and sheltering strategy of larvae. Reconstruction of ancestral microhabitat of oecophorids indicated that oecophorids might have evolved from dried plant feeders and further convergently specialized. The ancestral larva sheltering strategy of oecophorids might have used a silk tube by making itself, shifting from mining leaves. Copyright © 2016 Elsevier Inc. All rights reserved.

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

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

PubMed

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

2015-04-01

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. 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. 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. 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 refugia and that range expansion from unstable areas

Where are the r-modes? Chandra Observations of Millisecond Pulsars

NASA Technical Reports Server (NTRS)

Mahmoodifar, Simin; Strohmayer, Tod E.

2017-01-01

We present the results of Chandra observations of two non-accreting millisecond pulsars, PSRs J1640+2224(J1640) and J1709+2313 (J1709), with low inferred magnetic fields and spin-down rates in order to constrain their surface temperatures, obtain limits on the amplitude of unstable r-modes in them, and make comparisons with similar limits obtained for a sample of accreting low-mass X-ray binary (LMXB) neutron stars. We detect both pulsars in the X-ray band for the first time. They are faint, with inferred soft X-ray fluxes(0.3-3 keV) of approx. 6 x 10(exp -15) and 3 x 10( exp -15) erg/sq cm for J1640 and J1709, respectively. Spectral analysis assuming hydrogen atmosphere emission gives global effective temperature upper limits (90% confidence) of 3.3-4.3 x 10(exp 5) K for J1640 and 3.6-4.7 x 10(exp 5) K for J1709, where the low end of the range corresponds to canonical neutron stars (M = 1.4 Stellar Mass), and the upper end corresponds to higher-mass stars (M = 2.21 Stellar Mass). Under the assumption that r-mode heating provides the thermal support, we obtain dimensionless r-mode amplitude upper limits of 3.2-4.8 x 10(exp -8) and 1.8-2.8 x 10(exp -7) for J1640 and J1709, respectively, where again the low end of the range corresponds to lower-mass, canonical neutron stars (M =1.4 Stellar Mass). These limits are about an order of magnitude lower than those we derived previously for a sample of LMXBs, except for the accreting millisecond X-ray pulsar SAX J1808.43658, which has a comparable amplitude limit to J1640 and J1709.

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…

Uranium speciation in acid waste-weathered sediments: The role of aging and phosphate amendments

DOE PAGES

Perdrial, Nicolas; Vázquez-Ortega, Angélica; Wang, Guohui; ...

2017-12-05

Uranium speciation and lability are strongly coupled to mineral transformations in silicate sediments, particularly for sediments subjected to weathering in acidic, high-level radioactive waste, as occurred at the Department of Energy's Hanford (WA) site. Here, uncontaminated Hanford sediments were reacted for 365 days with acidic (pH 3), uranium-bearing waste solutions, with and without phosphate in batch experiments, prior to detailed characterizations using electron microscopy, x-ray diffraction and x-ray absorption spectroscopy. In PO 4-reactant free systems, uranium speciation was controlled initially by precipitation of compreignacite [K 2(UO 2) 6O 4(OH) 6·8H 2O]- and becquerelite [Ca(UO 2) 6O 4(OH) 6·8H 2O]-like species.more » Subsequent further removal of uranium coincided with that of Si and accumulation of boltwoodite, [(K, Na)(UO 2) 2O 4(HSiO 4) 2•0.5(H 2O)]-like species of uranium at 180 and 365 days. When present, PO 4 exerted a direct and strong control over U speciation. Furthermore, the detection of meta-ankoleite, [K 2(UO 2) 2O 4(PO 4) 2·6H 2O] at all reaction times when U was present emphasizes the importance of dissolved phosphate as a control on U speciation. Here, meta-ankoleite appears well crystallized and when it occurs as the principal product of sediment weathering, its low solubility is expected to limit dissolved U(VI) concentrations in groundwater. Although boltwoodite solubility is also low, it is formed more slowly (and only when PO 4 is absent), after initial precipitation of more soluble, less crystalline uranyl hydroxides. In the context of Hanford crib waste our results suggest that with PO 4 present, nearly all uranium would have precipitated in the upper soil.« less

Uranium speciation in acid waste-weathered sediments: The role of aging and phosphate amendments

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

Perdrial, Nicolas; Vázquez-Ortega, Angélica; Wang, Guohui

Uranium speciation and lability are strongly coupled to mineral transformations in silicate sediments, particularly for sediments subjected to weathering in acidic, high-level radioactive waste, as occurred at the Department of Energy's Hanford (WA) site. In this study, uncontaminated Hanford sediments were reacted for 365 days with acidic (pH 3), uranium-bearing waste solutions, with and without phosphate in batch experiments, prior to detailed characterizations using electron microscopy, x-ray diffraction and x-ray absorption spectroscopy. In PO(4)(-)reactant free systems, uranium speciation was controlled initially by precipitation of compreignacite [K-2(UO2)(6)O-4(OH)(6)center dot 8H(2)O]-and becquerelite [Ca(UO2)(6)O-4(OH)(6)center dot 8H(2)O]-like species. Subsequent further removal of uranium coincided withmore » that of Si and accumulation of boltwoodite, [(K, Na)(UO2)(2)O-4(HSiO4)(2)center dot 0.5(H2O)]-like species of uranium at 180 and 365 days. When present, PO4 exerted a direct and strong control over U speciation. The detection of meta-ankoleite, [K-2(UO2)(2)O-4(PO4)(2)center dot 6H(2)O] at all reaction times when U was present emphasizes the importance of dissolved phosphate as a control on U speciation. Here, meta-ankoleite appears well crystallized and when it occurs as the principal product of sediment weathering, its low solubility is expected to limit dissolved U(VI) concentrations in groundwater. Although boltwoodite solubility is also low, it is formed more slowly (and only when PO4 is absent), after initial precipitation of more soluble, less crystalline uranyl hydroxides. In the context of Hanford crib waste our results suggest that with PO4 present, nearly all uranium would have precipitated in the upper soil.« less

Uranium speciation in acid waste-weathered sediments: The role of aging and phosphate amendments

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

Perdrial, Nicolas; Vázquez-Ortega, Angélica; Wang, Guohui

Uranium speciation and lability are strongly coupled to mineral transformations in silicate sediments, particularly for sediments subjected to weathering in acidic, high-level radioactive waste, as occurred at the Department of Energy's Hanford (WA) site. Here, uncontaminated Hanford sediments were reacted for 365 days with acidic (pH 3), uranium-bearing waste solutions, with and without phosphate in batch experiments, prior to detailed characterizations using electron microscopy, x-ray diffraction and x-ray absorption spectroscopy. In PO 4-reactant free systems, uranium speciation was controlled initially by precipitation of compreignacite [K 2(UO 2) 6O 4(OH) 6·8H 2O]- and becquerelite [Ca(UO 2) 6O 4(OH) 6·8H 2O]-like species.more » Subsequent further removal of uranium coincided with that of Si and accumulation of boltwoodite, [(K, Na)(UO 2) 2O 4(HSiO 4) 2•0.5(H 2O)]-like species of uranium at 180 and 365 days. When present, PO 4 exerted a direct and strong control over U speciation. Furthermore, the detection of meta-ankoleite, [K 2(UO 2) 2O 4(PO 4) 2·6H 2O] at all reaction times when U was present emphasizes the importance of dissolved phosphate as a control on U speciation. Here, meta-ankoleite appears well crystallized and when it occurs as the principal product of sediment weathering, its low solubility is expected to limit dissolved U(VI) concentrations in groundwater. Although boltwoodite solubility is also low, it is formed more slowly (and only when PO 4 is absent), after initial precipitation of more soluble, less crystalline uranyl hydroxides. In the context of Hanford crib waste our results suggest that with PO 4 present, nearly all uranium would have precipitated in the upper soil.« less

Plant speciation in continental island floras as exemplified by Nigella in the Aegean Archipelago.

PubMed

Comes, Hans Peter; Tribsch, Andreas; Bittkau, Christiane

2008-09-27

Continental shelf island systems, created by rising sea levels, provide a premier setting for studying the effects of geographical isolation on non-adaptive radiation and allopatric speciation brought about by genetic drift. The Aegean Archipelago forms a highly fragmented complex of mostly continental shelf islands that have become disconnected from each other and the mainland in relatively recent geological times (ca <5.2 Ma). These ecologically fairly homogenous islands thus provide a suitable biogeographic context for assessing the relative influences of past range fragmentation, colonization, gene flow and drift on taxon diversification. Indeed, recent molecular biogeographic studies on the Aegean Nigella arvensis complex, combining phylogenetic, phylogeographic and population level approaches, exemplify the importance of allopatry and genetic drift coupled with restricted gene flow in driving plant speciation in this continental archipelago at different temporal and spatial scales. While the recent (Late Pleistocene) radiation of Aegean Nigella, as well as possible instances of incipient speciation (in the Cyclades), is shown to be strongly conditioned by (palaeo)geographic factors (including changes in sea level), shifts in breeding system (selfing) and associated isolating mechanisms have also contributed to this radiation. By contrast, founder event speciation has probably played only a minor role, perhaps reflecting a migratory situation typical for continental archipelagos characterized by niche pre-emption because of a long established resident flora. Overall, surveys of neutral molecular markers in Aegean Nigella have so far revealed population genetic processes that conform remarkably well to predictions raised by genetic drift theory. The challenge is now to gain more direct insights into the relative importance of the role of genetic drift, as opposed to natural selection, in the phenotypic and reproductive divergence among these Aegean plant

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

PubMed

Roccaro, Paolo; Chang, Hyun-shik; Vagliasindi, Federico G A; Korshin, Gregory V

2013-10-15

This study examined effects of bromide on yields and speciation of dihaloacetonitrile (DHAN) species that included dichloro-, bromochloro- and dibromoacetonitriles generated in chlorinated water. Experimental data obtained using two water sources, varying concentrations and characters of Natural Organic Matter (NOM), bromide concentrations, reaction times, chlorine doses, temperatures and pHs were interpreted using a semi-phenomenological model that assumed the presence of three kinetically distinct sites in NOM (denoted as sites S1, S2 and S3) and the occurrence of sequential incorporation of bromine and chlorine into them. One site was found to react very fast with the chlorine and bromine but its contribution in the DHAN generation was very low. The site with the highest contribution to the yield of DHAN (>70%) has the lowest reaction rates. The model introduced dimensionless coefficients (denoted as φ1(DHAN), φ2(DHAN) and φ3(DHAN)) applicable to the initial DHAN generation sites and their monochlorinated and monobrominated products, respectively. These parameters were used to quantify the kinetic preference to bromine incorporation over that of chlorine. Values of these coefficients optimized for DHAN formation were indicative of the strongly preferential incorporation of bromine into the engaged NOM sites. The same set of φ(i)(DHAN) coefficients could be used to model the speciation of DHAN released from their kinetically different precursors. The dimensionless speciation coefficients φ(i)(DHAN) were determined to be site specific and dependent on the NOM content and character as well as pH. The presented model of DHAN formation and speciation can help quantify in more detail the generation of DHAN and provide more insight necessary for further assessment of their potential health effects. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inference.

PubMed

Halas, Dominik; Simons, Andrew M

2014-01-01

Mitochondrial and nuclear introgression among closely related taxa can greatly complicate the process of determining their phylogenetic relationships. In the Central Highlands of North America, many fish taxa have undergone introgression; in this study, we demonstrate the existence of an unusual introgression event in the Etheostoma zonale species group. We used one mitochondrial and seven nuclear loci to determine the relationships of the taxa within the E. zonale group, and their degree of differentiation. We found evidence of multiple divergent populations within each species; much of the divergence within species has taken place during the Pleistocene. We also found evidence of a previously unknown cryptic species in the Upper Tennessee River which diverged from the remainder of the group during the Pliocene, and has undergone mitochondrial and nuclear introgression with E. zonale, in an apparent process of speciation reversal. We examined the effects that using varying types of recombination tests to eliminate the signal of recombination from nuclear loci would have on the phylogenetic placement of this introgressed lineage in our species tree analyses. Copyright © 2013 Elsevier Inc. All rights reserved.

Inferring Microbial Fitness Landscapes

DTIC Science & Technology

2016-02-25

infer from data the determinants of microbial evolution with sufficient resolution that we can quantify 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...Distribution Unlimited UU UU UU UU 25-02-2016 1-Oct-2012 30-Sep-2015 Final Report: Inferring Microbial Fitness Landscapes The views, opinions and/or findings...Triangle Park, NC 27709-2211 evolution, fitness landscapes, epistasis, microbial populations REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT

Chemical speciation and enzymatic impact of silver in antimicrobial fabric buried in soil.

PubMed

Takeuchi, Satoshi; Hashimoto, Yohey; Yamaguchi, Noriko; Toyota, Koki

2016-11-05

This study investigated the impact of Ag in antibacterial fabric on soil enzymes in relation to solubility and speciation of Ag. Sections of Ag-containing sock fabric (1.0-1.5cm(2)) were incubated in soils with aerobic and anaerobic conditions and periodically determined activity of arylsulfatase, dehydrogenase and urease. Microscale distribution and speciation of Ag at the interface between socks and soil particles were investigated using micro-focused X-ray fluorescence (μ-XRF), and Ag speciation was determined using micro-focused X-ray absorption near edge structure (μ-XANES) spectroscopy. Results showed that the sock fabric consisted of elemental Ag and Ag2S. After 60-day exposure to soil, majority (50-90%) of Ag in sock did not undergo phase transformation and present as elemental Ag and Ag2S in aerobic and anaerobic conditions. A part of Ag in sock fabric was bound with soil colloids (<15%), depending on the distance from the edge of sock fabric. Soil enzyme activities were overall unaffected by Ag in sock textile after 60days of incubation, although a significant decrease in arylsulfatase activity was found only in the initial stage of soil incubation. Silver in the sock fabric is relatively stable and has little detrimental impacts on enzyme activity in ordinary soil conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

PRELIMINARY RESULTS FROM THE USEPA MERCURY SPECIATION NETWORK AND AIRCRAFT MEASUREMENT CAMPAIGNS

EPA Science Inventory

Since EPA measured high concentrations of reactive gaseous mercury (RGM) in emissions from municipal and hospital waste incinerators in 1995, we have been working to elucidate the role of RGM on atmospheric mercury deposition. EPA has recently established automated speciated me...

AN ASSESSMENT OF THERMODYNAMIC REACTION CONSTANTS FOR SIMULATING AQUEOUS ENVIRONMENTAL MONOMETHYLMERCURY SPECIATION

EPA Science Inventory

Monomethylmercury (CH3Hg+) is both the most ecologically significant and the least well characterized species of mercury in environmental settings. Our understanding of the environmental speciation behavior of this compound is limited both as the result of lesser available labor...

Microscale imaging and identification of Fe speciation and distribution during fluid-mineral reactions under highly reducing conditions.

PubMed

Mayhew, L E; Webb, S M; Templeton, A S

2011-05-15

The oxidation state, speciation, and distribution of Fe are critical determinants of Fe reactivity in natural and engineered environments. However, it is challenging to follow dynamic changes in Fe speciation in environmental systems during progressive fluid-mineral interactions. Two common geological and aquifer materials-basalt and Fe(III) oxides-were incubated with saline fluids at 55 °C under highly reducing conditions maintained by the presence of Fe(0). We tracked changes in Fe speciation after 48 h (incipient water-rock reaction) and 10 months (extensive water-rock interaction) using synchrotron-radiation μXRF maps collected at multiple energies (ME) within the Fe K-edge. Immediate PCA analysis of the ME maps was used to optimize μXANES analyses; in turn, refitting the ME maps with end-member XANES spectra enabled us to detect and spatially resolve the entire variety of Fe-phases present in the system. After 48 h, we successfully identified and mapped the major Fe-bearing components of our samples (Fe(III) oxides, basalt, and rare olivine), as well as small quantities of incipient brucite associated with olivine. After 10 months, the Fe(III)-oxides remained stable in the presence of Fe(0), whereas significant alteration of basalt to minnesotaite and chlinochlore had occurred, providing new insights into heterogeneous Fe speciation in complex geological media under highly reducing conditions.

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

PubMed

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

2018-05-01

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

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…

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…

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

PubMed

Ricklefs, Robert E; Bermingham, Eldredge

2004-08-01

Understanding patterns of diversity can be furthered by analysis of the dynamics of colonization, speciation, and extinction on islands using historical information provided by molecular phylogeography. The land birds of the Lesser Antilles are one of the most thoroughly described regional faunas in this context. In an analysis of colonization times, Ricklefs and Bermingham (2001) found that the cumulative distribution of lineages with respect to increasing time since colonization exhibits a striking change in slope at a genetic distance of about 2% mitochondrial DNA sequence divergence (about one million years). They further showed how this heterogeneity could be explained by either an abrupt increase in colonization rates or a mass extinction event. Cherry et al. (2002), referring to a model developed by Johnson et al. (2000), argued instead that the pattern resulted from a speciation threshold for reproductive isolation of island populations from their continental source populations. Prior to this threshold, genetic divergence is slowed by migration from the source, and species of varying age accumulate at a low genetic distance. After the threshold is reached, source and island populations diverge more rapidly, creating heterogeneity in the distribution of apparent ages of island taxa. We simulated of Johnson et al.'s speciation-threshold model, incorporating genetic divergence at rate k and fixation at rate M of genes that have migrated between the source and the island population. Fixation resets the divergence clock to zero. The speciation-threshold model fits the distribution of divergence times of Lesser Antillean birds well with biologically plausible parameter estimates. Application of the model to the Hawaiian avifauna, which does not exhibit marked heterogeneity of genetic divergence, and the West Indian herpetofauna, which does, required unreasonably high migration-fixation rates, several orders of magnitude greater than the colonization rate. However

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...

Solid-phase arsenic speciation in aquifer sediments: A micro-X-ray absorption spectroscopy approach for quantifying trace-level speciation

USGS Publications Warehouse

Nicholas, Sarah L.; Erickson, Melinda L.; Woodruff, Laurel G.; Knaeble, Alan R.; Marcus, Matthew A.; Lynch, Joshua K.; Toner, Brandy M.

2017-01-01

e of this research is to identify the solid-phase sources and geochemical mechanisms of release of As in aquifers of the Des Moines Lobe glacial advance. The overarching concept is that conditions present at the aquifer-aquitard interfaces promote a suite of geochemical reactions leading to mineral alteration and release of As to groundwater. A microprobe X-ray absorption spectroscopy (lXAS) approach is developed and applied to rotosonic drill core samples to identify the solid-phase speciation of As in aquifer, aquitard, and aquifer-aquitard interface sediments. This approach addresses the low solid-phase As concentrations, as well as the fine-scale physical and chemical heterogeneity of the sediments. The spectroscopy data are analyzed using novel cosine-distance and correlation-distance hierarchical clustering for Fe 1s and As 1s lXAS datasets. The solid-phase Fe and As speciation is then interpreted using sediment and well-water chemical data to propose solid-phase As reservoirs and release mechanisms. The results confirm that in two of the three locations studied, the glacial sediment forming the aquitard is the source of As to the aquifer sediments. The results are consistent with three different As release mechanisms: (1) desorption from Fe (oxyhydr)oxides, (2) reductive dissolution of Fe (oxyhydr)oxides, and (3) oxidative dissolution of Fe sulfides. The findings confirm that glacial sediments at the interface between aquifer and aquitard are geochemically active zones for As. The diversity of As release mechanisms is consistent with the geographic heterogeneity observed in the distribution of elevated-As wells.

Analyzing x-ray hotspot images with Ince-Gaussian modes

NASA Astrophysics Data System (ADS)

Kruse, Michael; Field, John; Nora, Ryan; Benedetti, Robin; Khan, Shahab; Ma, Tammy; Peterson, Luc; Spears, Brian

2017-10-01

X-ray images at the National Ignition Facility (NIF) provide important metrics regarding the shape of the hotspot along a given line-of-sight. The 17% contour from peak brightness is usually used to infer the size of the hotspot as well as determine shape perturbations quantified through the Legendre coefficients P2 and P4. Unfortunately features that lie inside the contour such as those that could arise from tent or fill-tube perturbations are not easily captured. An analysis that takes into account the two-dimensional nature of the x-ray image is desirable. Ince-Gaussian modes (for short: Ince) offer such an analysis and could provide a new way to encode and understand the images recorded at NIF. The Ince modes are the solutions to the paraxial wave equation expressed in elliptical coordinates and thus form an orthonormal basis. Due to their elliptical nature they are suitable for decomposing images that have a non-zero P2 or P4 coefficient. We show that the Ince modes can be used to uncover structure that is missed by the contour analysis and how the modes aid in compressing images produced in large ensemble calculations. Finally a comparison is made to the Zernike modes which form an orthonormal basis on a circular disk. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-734741.

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…

Forward and Backward Inference in Spatial Cognition

PubMed Central

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

2013-01-01

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

Fair Inference on Outcomes

PubMed Central

Nabi, Razieh; Shpitser, Ilya

2017-01-01

In this paper, we consider the problem of fair statistical inference involving outcome variables. Examples include classification and regression problems, and estimating treatment effects in randomized trials or observational data. The issue of fairness arises in such problems where some covariates or treatments are “sensitive,” in the sense of having potential of creating discrimination. In this paper, we argue that the presence of discrimination can be formalized in a sensible way as the presence of an effect of a sensitive covariate on the outcome along certain causal pathways, a view which generalizes (Pearl 2009). A fair outcome model can then be learned by solving a constrained optimization problem. We discuss a number of complications that arise in classical statistical inference due to this view and provide workarounds based on recent work in causal and semi-parametric inference.

Chemical speciation and bioavailability of rare earth elements (REEs) in the ecosystem: a review.

PubMed

Khan, Aysha Masood; Bakar, Nor Kartini Abu; Bakar, Ahmad Farid Abu; Ashraf, Muhammad Aqeel

2017-10-01

Rare earths (RE), chemically uniform group of elements due to similar physicochemical behavior, are termed as lanthanides. Natural occurrence depends on the geological circumstances and has been of long interest for geologist as tools for further scientific research into the region of ores, rocks, and oceanic water. The review paper mainly focuses to provide scientific literature about rare earth elements (REEs) with potential environmental and health effects in understanding the research. This is the initial review of RE speciation and bioavailability with current initiative toward development needs and research perceptive. In this paper, we have also discussed mineralogy, extraction, geochemistry, analytical methods of rare earth elements. In this study, REEs with their transformation and vertical distribution in different environments such as fresh and seawater, sediments, soil, weathering, transport, and solubility have been reported with most recent literature along key methods of findings. Speciation and bioavailability have been discussed in detail with special emphasis on soil, plant, and aquatic ecosystems and their impacts on the environment. This review shows that REE gained more importance in last few years due to their detrimental effects on living organisms, so their speciation, bioavailability, and composition are much more important to evaluate their health risks and are discussed thoroughly as well.

Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae.

PubMed

Reyes, Elisabeth; Morlon, Hélène; Sauquet, Hervé

2015-07-01

The Proteaceae is a large angiosperm family displaying the common pattern of uneven distribution of species among genera. Previous studies have shown that this disparity is a result of variation in diversification rates across lineages, but the reasons for this variation are still unclear. Here, we tested the impact of floral symmetry and occurrence in Mediterranean climate regions on speciation and extinction rates in the Proteaceae. A rate shift analysis was conducted on dated genus-level phylogenetic trees of the Proteaceae. Character-dependent analyses were used to test for differences in diversification rates between actinomorphic and zygomorphic lineages and between lineages located within or outside Mediterranean climate regions. The rate shift analysis identified 5-10 major diversification rate shifts in the Proteaceae tree. The character-dependent analyses showed that speciation rates, extinction rates and net diversification rates of the Proteaceae were significantly higher for lineages occurring in Mediterranean hotspots. Higher speciation and extinction rates were also detected for zygomorphic species, but net diversification rates appeared to be similar in actinomorphic and zygomorphic Proteaceae. Presence in Mediterranean hotspots favors Proteaceae diversification. In contrast with observations at the scale of angiosperms, floral symmetry is not a trait that strongly influences their evolutionary success. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Carbon speciation in ash, residual waste and contaminated soil by thermal and chemical analyses.

PubMed

Kumpiene, Jurate; Robinson, Ryan; Brännvall, Evelina; Nordmark, Désirée; Bjurström, Henrik; Andreas, Lale; Lagerkvist, Anders; Ecke, Holger

2011-01-01

Carbon in waste can occur as inorganic (IC), organic (OC) and elemental carbon (EC) each having distinct chemical properties and possible environmental effects. In this study, carbon speciation was performed using thermogravimetric analysis (TGA), chemical degradation tests and the standard total organic carbon (TOC) measurement procedures in three types of waste materials (bottom ash, residual waste and contaminated soil). Over 50% of the total carbon (TC) in all studied materials (72% in ash and residual waste, and 59% in soil) was biologically non-reactive or EC as determined by thermogravimetric analyses. The speciation of TOC by chemical degradation also showed a presence of a non-degradable C fraction in all materials (60% of TOC in ash, 30% in residual waste and 13% in soil), though in smaller amounts than those determined by TGA. In principle, chemical degradation method can give an indication of the presence of potentially inert C in various waste materials, while TGA is a more precise technique for C speciation, given that waste-specific method adjustments are made. The standard TOC measurement yields exaggerated estimates of organic carbon and may therefore overestimate the potential environmental impacts (e.g. landfill gas generation) of waste materials in a landfill environment. Copyright © 2010 Elsevier Ltd. All rights reserved.

Metal Speciation in Landfill Leachates with a Focus on the Influence of Organic Matter

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

F Claret; C Tournassat; C Crouzet

This study characterizes the heavy-metal content in leachates collected from eight landfills in France. In order to identify heavy metal occurrence in the different size fractions of leachates, a cascade filtration protocol was applied directly in the field, under a nitrogen gas atmosphere to avoid metal oxidation. The results of analyses performed on the leachates suggest that most of the metals are concentrated in the <30 kDa fraction, while lead, copper and cadmium show an association with larger particles. Initial speciation calculations, without considering metal association with organic matter, suggest that leachate concentrations in lead, copper, nickel and zinc aremore » super-saturated with respect to sulphur phases. Speciation calculations that account for metal complexation with organic matter, considered as fulvic acids based on C1(s) NEXAFS spectroscopy, show that this mechanism is not sufficient to explain such deviation from equilibrium conditions. It is therefore hypothesized that the deviation results also from the influence of biological activity on the kinetics of mineral phase precipitation and dissolution, thus providing a dynamic system. The results of chemical analyses of sampled fluids are compared with speciation calculations and some implications for the assessment of metal mobility and natural attenuation in a context of landfill risk assessment are discussed.« less

Surfing among species, populations and morphotypes: Inferring boundaries between two species of new world silversides (Atherinopsidae).

PubMed

González-Castro, Mariano; Rosso, Juan José; Mabragaña, Ezequiel; Díaz de Astarloa, Juan Martín

2016-01-01

Atherinopsidae are widespread freshwater and shallow marine fish with singular economic importance. Morphological, genetical and life cycles differences between marine and estuarine populations were already reported in this family, suggesting ongoing speciation. Also, coexistence and interbreeding between closely related species were documented. The aim of this study was to infer boundaries among: (A) Odontesthes bonariensis and O. argentinensis at species level, and intermediate morphs; (B) the population of O. argentinensis of Mar Chiquita Lagoon and its marine conspecifics. To achieve this, we integrated, meristic, Geometrics Morphometrics and DNA Barcode approaches. Four groups were discriminated and subsequently characterized according to their morphological traits, shape and meristic characters. No shared haplotypes between O. bonariensis and O. argentinensis were found. Significative-meristic and body shape differences between the Mar Chiquita and marine individuals of O. argentinensis were found, suggesting they behave as well differentiated populations, or even incipient ecological species. The fact that the Odontesthes morphotypes shared haplotypes with both, O. argentinensis and O. bonariensis, but also possess meristic and morphometric distinctive traits open new questions related to the origin of this morphogroup. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

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

PubMed

Sonntag, Darrell B; Baldauf, Richard W; Yanca, Catherine A; Fulper, Carl R

2014-05-01

Representative profiles for particulate matter particles less than or equal to 2.5 microm (PM2.5) are developed from the Kansas City Light-Duty Vehicle Emissions Study for use in the US. Environmental Protection Agency (EPA) vehicle emission model, the Motor Vehicle Emission Simulator (MOVES), and for inclusion in the EPA SPECIATE database for speciation profiles. The profiles are compatible with the inputs of current photochemical air quality models, including the Community Multiscale Air Quality Aerosol Module Version 6 (AE6). The composition of light-duty gasoline PM2.5 emissions differs significantly between cold start and hot stabilized running emissions, and between older and newer vehicles, reflecting both impacts of aging/deterioration and changes in vehicle technology. Fleet-average PM2.5 profiles are estimated for cold start and hot stabilized running emission processes. Fleet-average profiles are calculated to include emissions from deteriorated high-emitting vehicles that are expected to continue to contribute disproportionately to the fleet-wide PM2.5 emissions into the future. The profiles are calculated using a weighted average of the PM2.5 composition according to the contribution of PM2.5 emissions from each class of vehicles in the on-road gasoline fleet in the Kansas City Metropolitan Statistical Area. The paper introduces methods to exclude insignificant measurements, correct for organic carbon positive artifact, and control for contamination from the testing infrastructure in developing speciation profiles. The uncertainty of the PM2.5 species fraction in each profile is quantified using sampling survey analysis methods. The primary use of the profiles is to develop PM2.5 emissions inventories for the United States, but the profiles may also be used in source apportionment, atmospheric modeling, and exposure assessment, and as a basis for light-duty gasoline emission profiles for countries with limited data. PM2.5 speciation profiles were

Origin and speciation of Picea schrenkiana and Piceasmithiana in the Center Asian Highlands and Himalayas.

PubMed

Li, Lili; Sun, Yongshuai; Zou, Jiabin; Yue, Wei; Wang, Xi; Liu, Jianquan

Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of Picea schrenkiana and Picea smithiana using population genetic data from chloroplast (cp), mitochondrial (mt), and nuclear (nr) genomes. These two species occur in the Central Asian Highlands and Himalayas, respectively, where they are isolated from other Asian congeneric species by the Qinghai-Tibet Plateau (QTP) or adjacent deserts. Previous studies based on both morphological and molecular evidence suggest that they have contrasting phylogenetic relationships with Picea likiangensis or Picea wilsonii which are closely related and both located in the QTP. We examined genetic variation among 16 loci of three genomes from 30 populations of these four species. At both cpDNA loci and mtDNA loci, P. schrenkiana appeared to be closely related to P. likiangensis , although statistical support for this was weak. However, phylogenetic analyses and speciation tests based on the nuclear data from 11 loci provided evidence that P. schrenkiana and P. smithiana are sister species. These two species diverged around five million years ago (Mya) while the divergence between them and the P. likiangensis - P. wilsonii clade occurred about 18.4 Mya. We also detected gene flow accompanying these speciation events. Our results highlight the complex speciation histories of these alpine conifers due to interspecific gene flow and/or incomplete lineage sorting, and the importance of the early QTP uplifts in promoting the origin of these important conifer species in the Asian highlands.

Recent Advances in On-Line Methods Based on Extraction for Speciation Analysis of Chromium in Environmental Matrices.

PubMed

Trzonkowska, Laura; Leśniewska, Barbara; Godlewska-Żyłkiewicz, Beata

2016-07-03

The biological activity of Cr(III) and Cr(VI) species, their chemical behavior, and toxic effects are dissimilar. The speciation analysis of Cr(III) and Cr(VI) in environmental matrices is then of great importance and much research has been devoted to this area. This review presents recent developments in on-line speciation analysis of chromium in such samples. Flow systems have proved to be excellent tools for automation of sample pretreatment, separation/preconcentration of chromium species, and their detection by various instrumental techniques. Analytical strategies used in chromium speciation analysis discussed in this review are divided into categories based on selective extraction/separation of chromium species on solid sorbents and liquid-liquid extraction of chromium species. The most popular strategy is that based on solid-phase extraction. Therefore, this review shows the potential of novel materials designed and used for selective binding of chromium species. The progress in miniaturization of measurement systems is also presented.

Bio-metals imaging and speciation in cells using proton and synchrotron radiation X-ray microspectroscopy

PubMed Central

Ortega, Richard; Devès, Guillaume; Carmona, Asunción

2009-01-01

The direct detection of biologically relevant metals in single cells and of their speciation is a challenging task that requires sophisticated analytical developments. The aim of this article is to present the recent achievements in the field of cellular chemical element imaging, and direct speciation analysis, using proton and synchrotron radiation X-ray micro- and nano-analysis. The recent improvements in focusing optics for MeV-accelerated particles and keV X-rays allow application to chemical element analysis in subcellular compartments. The imaging and quantification of trace elements in single cells can be obtained using particle-induced X-ray emission (PIXE). The combination of PIXE with backscattering spectrometry and scanning transmission ion microscopy provides a high accuracy in elemental quantification of cellular organelles. On the other hand, synchrotron radiation X-ray fluorescence provides chemical element imaging with less than 100 nm spatial resolution. Moreover, synchrotron radiation offers the unique capability of spatially resolved chemical speciation using micro-X-ray absorption spectroscopy. The potential of these methods in biomedical investigations will be illustrated with examples of application in the fields of cellular toxicology, and pharmacology, bio-metals and metal-based nano-particles. PMID:19605403

[Speciation Characteristics and Bioavailability of Heavy Metals in Oasis Soil Under Pb, Zn Combined Stress].

PubMed

Jin, Cheng; Zhao, Zhuan-jun; Nan, Zhong-ren; Wang, Sheng-li; Wu, Wen-fei; Wang, Hou-cheng

2015-05-01

Pot experiments were conducted on cole (Brassica) grown in oasis soil under combined stress of lead and zinc, to study the effect of heavy metal combined pollution on cole growth as well as the speciation conversion rules and bioavailability. The result showed that the promoting effect on cole growth was shown in the low concentration treatments, especially on stem leaves. With addition of exotic heavy metals, the main speciations of Pb and Zn in the soil transformed from tight-bound to loose-bound forms as compared to the control, and the bioavailability of heavy metals was increased. And, the exchangeable Pb and the carbonate bound form of Zn were the major contributing speciations which were absorbed in different parts of cole. What's more, the capabilities of uptake and translocation of Pb and Zn by cole were stronger at lower stress levels, and the enrichment and migration coefficients decreased with the increasing content of bioavailable fraction of the corresponding element or the coexisting element. In all treatments, the Pb concentration in the stem leaves of cole exceeded the food safety threshold, therefore it is recommended to conduct detection of relevant indicators before planting foliage vegetables in this kind of soil.

Selective determination of heavy metals (Cd, Pb, Cr) speciation forms from hortic anthrosols

NASA Astrophysics Data System (ADS)

Bulgariu, Dumitru; Bulgariu, Laura; Filipov, Feodor; Astefanei, Dan; Stoleru, Vasile

2010-05-01

In soils from glass houses, the speciation and inter-phases distribution processes of heavy metals have a particular dynamic, different in comparison with those from non-protected soils. The predominant distribution forms of heavy metals in such soils types are: complexes with low mass organic molecules, organic-mineral complexes, complexes with inorganic ligands (hydroxide-complexes, carbonate-complexes, sulphate-complexes, etc.) and basic salts. All of these have high stabilities in conditions of soils from glass houses, and in consequence, the separation and determination of speciation forms (which is directly connected with biodisponibility of heavy metals) by usual methods id very difficult and has a high uncertain degree. In this study is presented an original method for the selective separation and differentiation of speciation forms of heavy metals from glass houses soils, which is based by the combination of solid-liquid sequential extraction (SPE) with the extraction in aqueous polymer-inorganic salt two-phase systems (ABS). The soil samples used for this study have been sampled from three different locations (glass houses from Iasi, Barlad and Bacau - Romania) where the vegetables cultivation have been performed by three different technologies. In this way was estimated the applicability and the analytical limits of method proposed by as, in function of the chemical-mineralogical and physical-chemical characteristics of soils. As heavy metals have been studied cadmium, lead and chromium, all being known for their high toxicity. The procedure used for the selective separation and differentiation of speciation forms of heavy metals from glass houses soils has two main steps: (i) non-destructive separation of chemical-mineralogical associations and aggregates from soils samples - for this the separation method with heavy liquids (bromophorme) and isodynamic magnetic method have been used; (ii) sequential extraction of heavy metals from soil fractions

Solid phase extraction for the speciation and preconcentration of inorganic selenium in water samples: a review.

PubMed

Herrero Latorre, C; Barciela García, J; García Martín, S; Peña Crecente, R M

2013-12-04

Selenium is an essential element for the normal cellular function of living organisms. However, selenium is toxic at concentrations of only three to five times higher than the essential concentration. The inorganic forms (mainly selenite and selenate) present in environmental water generally exhibit higher toxicity (up to 40 times) than organic forms. Therefore, the determination of low levels of different inorganic selenium species in water is an analytical challenge. Solid-phase extraction has been used as a separation and/or preconcentration technique prior to the determination of selenium species due to the need for accurate measurements for Se species in water at extremely low levels. The present paper provides a critical review of the published methods for inorganic selenium speciation in water samples using solid phase extraction as a preconcentration procedure. On the basis of more than 75 references, the different speciation strategies used for this task have been highlighted and classified. The solid-phase extraction sorbents and the performance and analytical characteristics of the developed methods for Se speciation are also discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-01-01

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