Hybrid Co-Evolutionary Motion Planning via Visibility-Based Repair

NASA Technical Reports Server (NTRS)

Dozier, Gerry; McCullough, Shaun; Brown, Edward, Jr.; Homaifar, Abdollah; Bikdash, Mar-wan

1997-01-01

This paper introduces a hybrid co-evolutionary system for global motion planning within unstructured environments. This system combines the concept of co-evolutionary search along with a concept that we refer to as the visibility-based repair to form a hybrid which quickly transforms infeasible motions into feasible ones. Also, this system makes use of a novel representation scheme for the obstacles within an environment. Our hybrid evolutionary system differs from other evolutionary motion planners in that (1) more emphasis is placed on repairing infeasible motions to develop feasible motions rather than using simulated evolution exclusively as a means of discovering feasible motions, (2) a continuous map of the environment is used rather than a discretized map, and (3) it develops global motion plans for multiple mobile destinations by co-evolving populations of sub-global motion plans. In this paper, we demonstrate the effectiveness of this system by using it to solve two challenging motion planning problems where multiple targets try to move away from a point robot.

Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes".

PubMed

Araripe, Luciana O; Montenegro, Horácio; Lemos, Bernardo; Hartl, Daniel L

2010-12-14

Hybrid male sterility (HMS) is a usual outcome of hybridization between closely related animal species. It arises because interactions between alleles that are functional within one species may be disrupted in hybrids. The identification of genes leading to hybrid sterility is of great interest for understanding the evolutionary process of speciation. In the current work we used marked P-element insertions as dominant markers to efficiently locate one genetic factor causing a severe reduction in fertility in hybrid males of Drosophila simulans and D. mauritiana. Our mapping effort identified a region of 9 kb on chromosome 3, containing three complete and one partial coding sequences. Within this region, two annotated genes are suggested as candidates for the HMS factor, based on the comparative molecular characterization and public-source information. Gene Taf1 is partially contained in the region, but yet shows high polymorphism with four fixed non-synonymous substitutions between the two species. Its molecular functions involve sequence-specific DNA binding and transcription factor activity. Gene agt is a small, intronless gene, whose molecular function is annotated as methylated-DNA-protein-cysteine S-methyltransferase activity. High polymorphism and one fixed non-synonymous substitution suggest this is a fast evolving gene. The gene trees of both genes perfectly separate D. simulans and D. mauritiana into monophyletic groups. Analysis of gene expression using microarray revealed trends that were similar to those previously found in comparisons between whole-genome hybrids and parental species. The identification following confirmation of the HMS candidate gene will add another case study leading to understanding the evolutionary process of hybrid incompatibility.

Regulatory divergence of X-linked genes and hybrid male sterility in mice.

PubMed

Oka, Ayako; Shiroishi, Toshihiko

2014-01-01

Postzygotic reproductive isolation is the reduction of fertility or viability in hybrids between genetically diverged populations. One example of reproductive isolation, hybrid male sterility, may be caused by genetic incompatibility between diverged genetic factors in two distinct populations. Genetic factors involved in hybrid male sterility are disproportionately located on the X chromosome. Recent studies showing the evolutionary divergence in gene regulatory networks or epigenetic effects suggest that the genetic incompatibilities occur at much broader levels than had previously been thought (e.g., incompatibility of protein-protein interactions). The latest studies suggest that evolutionary divergence of transcriptional regulation causes genetic incompatibilities in hybrid animals, and that such incompatibilities preferentially involve X-linked genes. In this review, we focus on recent progress in understanding hybrid sterility in mice, including our studies, and we discuss the evolutionary significance of regulatory divergence for speciation.

Evolutionary Dynamic Multiobjective Optimization Via Kalman Filter Prediction.

PubMed

Muruganantham, Arrchana; Tan, Kay Chen; Vadakkepat, Prahlad

2016-12-01

Evolutionary algorithms are effective in solving static multiobjective optimization problems resulting in the emergence of a number of state-of-the-art multiobjective evolutionary algorithms (MOEAs). Nevertheless, the interest in applying them to solve dynamic multiobjective optimization problems has only been tepid. Benchmark problems, appropriate performance metrics, as well as efficient algorithms are required to further the research in this field. One or more objectives may change with time in dynamic optimization problems. The optimization algorithm must be able to track the moving optima efficiently. A prediction model can learn the patterns from past experience and predict future changes. In this paper, a new dynamic MOEA using Kalman filter (KF) predictions in decision space is proposed to solve the aforementioned problems. The predictions help to guide the search toward the changed optima, thereby accelerating convergence. A scoring scheme is devised to hybridize the KF prediction with a random reinitialization method. Experimental results and performance comparisons with other state-of-the-art algorithms demonstrate that the proposed algorithm is capable of significantly improving the dynamic optimization performance.

Improved Evolutionary Hybrids for Flexible Ligand Docking in Autodock

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

Belew, R.K.; Hart, W.E.; Morris, G.M.

1999-01-27

In this paper we evaluate the design of the hybrid evolutionary algorithms (EAs) that are currently used to perform flexible ligand binding in the Autodock docking software. Hybrid EAs incorporate specialized operators that exploit domain-specific features to accelerate an EA's search. We consider hybrid EAs that use an integrated local search operator to reline individuals within each iteration of the search. We evaluate several factors that impact the efficacy of a hybrid EA, and we propose new hybrid EAs that provide more robust convergence to low-energy docking configurations than the methods currently available in Autodock.

A master-slave parallel hybrid multi-objective evolutionary algorithm for groundwater remediation design under general hydrogeological conditions

NASA Astrophysics Data System (ADS)

Wu, J.; Yang, Y.; Luo, Q.; Wu, J.

2012-12-01

This study presents a new hybrid multi-objective evolutionary algorithm, the niched Pareto tabu search combined with a genetic algorithm (NPTSGA), whereby the global search ability of niched Pareto tabu search (NPTS) is improved by the diversification of candidate solutions arose from the evolving nondominated sorting genetic algorithm II (NSGA-II) population. Also, the NPTSGA coupled with the commonly used groundwater flow and transport codes, MODFLOW and MT3DMS, is developed for multi-objective optimal design of groundwater remediation systems. The proposed methodology is then applied to a large-scale field groundwater remediation system for cleanup of large trichloroethylene (TCE) plume at the Massachusetts Military Reservation (MMR) in Cape Cod, Massachusetts. Furthermore, a master-slave (MS) parallelization scheme based on the Message Passing Interface (MPI) is incorporated into the NPTSGA to implement objective function evaluations in distributed processor environment, which can greatly improve the efficiency of the NPTSGA in finding Pareto-optimal solutions to the real-world application. This study shows that the MS parallel NPTSGA in comparison with the original NPTS and NSGA-II can balance the tradeoff between diversity and optimality of solutions during the search process and is an efficient and effective tool for optimizing the multi-objective design of groundwater remediation systems under complicated hydrogeologic conditions.

Mapping of within-species segregation distortion in Drosophila persimilis and hybrid sterility between D. persimilis and D. pseudoobscura.

PubMed

McDermott, S R; Noor, M A F

2012-10-01

In contrast to the prevailing dogma in the 1990s, recent studies have suggested that an evolutionary history of segregation distortion within species may contribute to sterility in species hybrids. However, this recent work identified segregation distortion exclusively in species hybrids that may never have had an evolutionary history of segregation distortion in either parent species. We expand on previous work using a strain of Drosophila persimilis exhibiting segregation distortion within species to generate QTL maps for segregation distortion and hybrid sterility in crosses between D. persimilis and D. pseudoobscura. The maps localize regions along the XR contributing to both phenotypes, and they indicate one region of overlap between the two maps. This overlap could provide preliminary evidence for an association between segregation distortion within species and hybrid sterility, but the localizations are currently too broad to have confidence in this conclusion. This work is a first step towards possibly supporting a genetic conflict model of speciation in this system. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

A single gene causes both male sterility and segregation distortion in Drosophila hybrids.

PubMed

Phadnis, Nitin; Orr, H Allen

2009-01-16

A central goal of evolutionary biology is to identify the genes and evolutionary forces that cause speciation, the emergence of reproductive isolation between populations. Despite the identification of several genes that cause hybrid sterility or inviability-many of which have evolved rapidly under positive Darwinian selection-little is known about the ecological or genomic forces that drive the evolution of postzygotic isolation. Here, we show that the same gene, Overdrive, causes both male sterility and segregation distortion in F1 hybrids between the Bogota and U.S. subspecies of Drosophila pseudoobscura. This segregation distorter gene is essential for hybrid sterility, a strong reproductive barrier between these young taxa. Our results suggest that genetic conflict may be an important evolutionary force in speciation.

Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy

PubMed Central

Zozomová-Lihová, Judita; Krak, Karol; Mandáková, Terezie; Shimizu, Kentaro K.; Španiel, Stanislav; Vít, Petr; Lysak, Martin A.

2014-01-01

Background and Aims Recently formed allopolyploid species represent excellent subjects for exploring early stages of polyploid evolution. The hexaploid Cardamine schulzii was regarded as one of the few nascent allopolyploid species formed within the past ∼150 years that presumably arose by autopolyploidization of a triploid hybrid, C. × insueta; however, the most recent investigations have shown that it is a trigenomic hybrid. The aims of this study were to explore the efficiency of progenitor-specific microsatellite markers in detecting the hybrid origins and genome composition of these two allopolyploids, to estimate the frequency of polyploid formation events, and to outline their evolutionary potential for long-term persistence and speciation. Methods Flow-cytometric ploidy-level screening and genotyping by progenitor-specific microsatellite markers (20 microsatellite loci) were carried out on samples focused on hybridizing populations at Urnerboden, Switzerland, but also including comparative material of the parental species from other sites in the Alps and more distant areas. Key Results It was confirmed that hybridization between the diploids C. amara and C. rivularis auct. gave rise to triploid C. × insueta, and it is inferred that this has occurred repeatedly. Evidence is provided that C. schulzii comprises three parental genomes and supports its origin from hybridization events between C. × insueta and the locally co-occurring hypotetraploid C. pratensis, leading to two cytotypes of C. schulzii: hypopentaploid and hypohexaploid. Each cytotype of C. schulzii is genetically uniform, suggesting their single origins. Conclusions Persistence of C. schulzii has presumably been achieved only by perennial growth and clonal reproduction. This contrasts with C. × insueta, in which multiple origins and occasional sexual reproduction have generated sufficient genetic variation for long-term survival and evolutionary success. This study illustrates a complex case of recurrent hybridization and polyploidization events, and highlights the role of triploids that promoted the origin of trigenomic hybrids. PMID:24577071

A single gene causes both male sterility and segregation distortion in Drosophila hybrids*

PubMed Central

Phadnis, Nitin; Orr, H. Allen

2008-01-01

A central goal of evolutionary biology is to identify the genes and evolutionary forces that cause speciation, the emergence of reproductive isolation between populations. Despite the identification of several genes that cause hybrid sterility or inviability— many of which have evolved rapidly under positive Darwinian selection— little is known about the ecological or genomic forces that drive the evolution of postzygotic isolation. Here we show that the same gene, Overdrive, causes both male sterility and segregation distortion in F1 hybrids between the Bogota and USA subspecies of Drosophila pseudoobscura. This segregation distorter gene is essential for hybrid sterility, a strong reproductive barrier between these young taxa. Our results suggest that genetic conflict may be an important evolutionary force in speciation. PMID:19074311

Differential evolution-simulated annealing for multiple sequence alignment

NASA Astrophysics Data System (ADS)

Addawe, R. C.; Addawe, J. M.; Sueño, M. R. K.; Magadia, J. C.

2017-10-01

Multiple sequence alignments (MSA) are used in the analysis of molecular evolution and sequence structure relationships. In this paper, a hybrid algorithm, Differential Evolution - Simulated Annealing (DESA) is applied in optimizing multiple sequence alignments (MSAs) based on structural information, non-gaps percentage and totally conserved columns. DESA is a robust algorithm characterized by self-organization, mutation, crossover, and SA-like selection scheme of the strategy parameters. Here, the MSA problem is treated as a multi-objective optimization problem of the hybrid evolutionary algorithm, DESA. Thus, we name the algorithm as DESA-MSA. Simulated sequences and alignments were generated to evaluate the accuracy and efficiency of DESA-MSA using different indel sizes, sequence lengths, deletion rates and insertion rates. The proposed hybrid algorithm obtained acceptable solutions particularly for the MSA problem evaluated based on the three objectives.

Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.

PubMed

Cui, Rongfeng; Schumer, Molly; Kruesi, Karla; Walter, Ronald; Andolfatto, Peter; Rosenthal, Gil G

2013-08-01

Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high-confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long-standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Hybrid female mate choice as a species isolating mechanism: environment matters.

PubMed

Schmidt, E M; Pfennig, K S

2016-04-01

A fundamental goal of biology is to understand how new species arise and are maintained. Female mate choice is potentially critical to the speciation process: mate choice can prevent hybridization and thereby generate reproductive isolation between potentially interbreeding groups. Yet, in systems where hybridization occurs, mate choice by hybrid females might also play a key role in reproductive isolation by affecting hybrid fitness and contributing to patterns of gene flow between species. We evaluated whether hybrid mate choice behaviour could serve as such an isolating mechanism using spadefoot toad hybrids of Spea multiplicata and Spea bombifrons. We assessed the mate preferences of female hybrid spadefoot toads for sterile hybrid males vs. pure-species males in two alternative habitat types in which spadefoots breed: deep or shallow water. We found that, in deep water, hybrid females preferred the calls of sterile hybrid males to those of S. multiplicata males. Thus, maladaptive hybrid mate preferences could serve as an isolating mechanism. However, in shallow water, the preference for hybrid male calls was not expressed. Moreover, hybrid females did not prefer hybrid calls to those of S. bombifrons in either environment. Because hybrid female mate choice was context-dependent, its efficacy as a reproductive isolating mechanism will depend on both the environment in which females choose their mates as well as the relative frequencies of males in a given population. Thus, reproductive isolation between species, as well as habitat specific patterns of gene flow between species, might depend critically on the nature of hybrid mate preferences and the way in which they vary across environments. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Hybrid glowworm swarm optimization for task scheduling in the cloud environment

NASA Astrophysics Data System (ADS)

Zhou, Jing; Dong, Shoubin

2018-06-01

In recent years many heuristic algorithms have been proposed to solve task scheduling problems in the cloud environment owing to their optimization capability. This article proposes a hybrid glowworm swarm optimization (HGSO) based on glowworm swarm optimization (GSO), which uses a technique of evolutionary computation, a strategy of quantum behaviour based on the principle of neighbourhood, offspring production and random walk, to achieve more efficient scheduling with reasonable scheduling costs. The proposed HGSO reduces the redundant computation and the dependence on the initialization of GSO, accelerates the convergence and more easily escapes from local optima. The conducted experiments and statistical analysis showed that in most cases the proposed HGSO algorithm outperformed previous heuristic algorithms to deal with independent tasks.

Analysis and optimization of hybrid electric vehicle thermal management systems

NASA Astrophysics Data System (ADS)

Hamut, H. S.; Dincer, I.; Naterer, G. F.

2014-02-01

In this study, the thermal management system of a hybrid electric vehicle is optimized using single and multi-objective evolutionary algorithms in order to maximize the exergy efficiency and minimize the cost and environmental impact of the system. The objective functions are defined and decision variables, along with their respective system constraints, are selected for the analysis. In the multi-objective optimization, a Pareto frontier is obtained and a single desirable optimal solution is selected based on LINMAP decision-making process. The corresponding solutions are compared against the exergetic, exergoeconomic and exergoenvironmental single objective optimization results. The results show that the exergy efficiency, total cost rate and environmental impact rate for the baseline system are determined to be 0.29, ¢28 h-1 and 77.3 mPts h-1 respectively. Moreover, based on the exergoeconomic optimization, 14% higher exergy efficiency and 5% lower cost can be achieved, compared to baseline parameters at an expense of a 14% increase in the environmental impact. Based on the exergoenvironmental optimization, a 13% higher exergy efficiency and 5% lower environmental impact can be achieved at the expense of a 27% increase in the total cost.

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling.

PubMed

Gerard, David; Gibbs, H Lisle; Kubatko, Laura

2011-10-06

A well-known characteristic of multi-locus data is that each locus has its own phylogenetic history which may differ substantially from the overall phylogenetic history of the species. Although the possibility that this arises through incomplete lineage sorting is often incorporated in models for the species-level phylogeny, it is much less common for hybridization to also be formally included in such models. We have modified the evolutionary model of Meng and Kubatko (2009) to incorporate intraspecific sampling of multiple individuals for estimation of speciation times and times of hybridization events for testing for hybridization in the presence of incomplete lineage sorting. We have also utilized a more efficient algorithm for obtaining our estimates. Using simulations, we demonstrate that our approach performs well under conditions motivated by an empirical data set for Sistrurus rattlesnakes where putative hybridization has occurred. We further demonstrate that the method is able to accurately detect the signature of hybridization in the data, while this signal may be obscured when other species-tree inference methods that ignore hybridization are used. Our approach is shown to be powerful in detecting hybridization when it is present. When applied to the Sistrurus data, we find no evidence of hybridization; instead, it appears that putative hybrid snakes in Missouri are most likely pure S. catenatus tergeminus in origin, which has significant conservation implications.

A hybrid multi-objective evolutionary algorithm for wind-turbine blade optimization

NASA Astrophysics Data System (ADS)

Sessarego, M.; Dixon, K. R.; Rival, D. E.; Wood, D. H.

2015-08-01

A concurrent-hybrid non-dominated sorting genetic algorithm (hybrid NSGA-II) has been developed and applied to the simultaneous optimization of the annual energy production, flapwise root-bending moment and mass of the NREL 5 MW wind-turbine blade. By hybridizing a multi-objective evolutionary algorithm (MOEA) with gradient-based local search, it is believed that the optimal set of blade designs could be achieved in lower computational cost than for a conventional MOEA. To measure the convergence between the hybrid and non-hybrid NSGA-II on a wind-turbine blade optimization problem, a computationally intensive case was performed using the non-hybrid NSGA-II. From this particular case, a three-dimensional surface representing the optimal trade-off between the annual energy production, flapwise root-bending moment and blade mass was achieved. The inclusion of local gradients in the blade optimization, however, shows no improvement in the convergence for this three-objective problem.

Transgressive Hybrids as Hopeful Monsters.

PubMed

Dittrich-Reed, Dylan R; Fitzpatrick, Benjamin M

2013-06-01

The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt's infamous "hopeful monster". Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, "monstrous" phenotypes beyond the range of parental populations. Transgressive phenotypes can be products of epistatic interactions or additive effects of multiple recombined loci. We compare several epistatic and additive models of transgressive segregation in hybrids and find that they are special cases of a general, classic quantitative genetic model. The Dobzhansky-Muller model predicts "hopeless" monsters, sterile and inviable transgressive phenotypes. The Bateson model predicts "hopeful" monsters with fitness greater than either parental population. The complementation model predicts both. Transgressive segregation after hybridization can rapidly produce novel phenotypes by recombining multiple loci simultaneously. Admixed populations will also produce many similar recombinant phenotypes at the same time, increasing the probability that recombinant "hopeful monsters" will establish true-breeding evolutionary lineages. Recombination is not the only (or even most common) process generating evolutionary novelty, but might be the most credible mechanism for sudden appearance of new forms.

A Novel Handwritten Letter Recognizer Using Enhanced Evolutionary Neural Network

NASA Astrophysics Data System (ADS)

Mahmoudi, Fariborz; Mirzashaeri, Mohsen; Shahamatnia, Ehsan; Faridnia, Saed

This paper introduces a novel design for handwritten letter recognition by employing a hybrid back-propagation neural network with an enhanced evolutionary algorithm. Feeding the neural network consists of a new approach which is invariant to translation, rotation, and scaling of input letters. Evolutionary algorithm is used for the global search of the search space and the back-propagation algorithm is used for the local search. The results have been computed by implementing this approach for recognizing 26 English capital letters in the handwritings of different people. The computational results show that the neural network reaches very satisfying results with relatively scarce input data and a promising performance improvement in convergence of the hybrid evolutionary back-propagation algorithms is exhibited.

Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

PubMed

Pitiot, Alain; Toga, Arthur W; Thompson, Paul M

2002-08-01

This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of algorithmic efficiency.

Pollinator-mediated selection on floral morphology: evidence for transgressive evolution in a derived hybrid lineage.

PubMed

Anton, K A; Ward, J R; Cruzan, M B

2013-03-01

Hybridization between closely related lineages is a mechanism that might promote substantive changes in phenotypic traits of descendants, resulting in transgressive evolution. Interbreeding between divergent but morphologically similar lineages can produce exceptional phenotypes, but the potential for transgressive variation to facilitate long-term trait changes in derived hybrid lineages has received little attention. We compare pollinator-mediated selection on transgressive floral traits in both early-generation and derived hybrid lineages of the Piriqueta cistoides ssp. caroliniana complex. The bowl-shaped flowers of morphotypes in this complex have similar gross morphologies and attract a common suite of small insect pollinators. However, they are defined by significant differences in characters that generate pollinator interest and visitation, including floral area and petal separation. In common garden experiments, patterns of pollen deposition in early-generation recombinant hybrids indicate that Piriqueta's pollinators favour flowers with greater area and reduced petal separation. Changes in floral morphology in derived hybrid lineages are consistent with predictions from selection gradients, but the magnitude of change is limited relative to the range of transgressive variation. These results suggest that hybridization provides variation for evolution of divergent floral traits. However, the potential for extreme transgressive variants to contribute to phenotypic shifts may be limited due to reduced heritability, evolutionary constraints or fitness trade-offs. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Genetic and morphological structure of a spruce hybrid (Picea sitchensis x P. glauca) zone along a climatic gradient.

PubMed

Hamilton, Jill A; Aitken, Sally N

2013-08-01

Historic colonization and contemporary evolutionary processes contribute to patterns of genetic variation and differentiation among populations. However, separating the respective influences of these processes remains a challenge, particularly for natural hybrid zones, where standing genetic variation may result from evolutionary processes both preceding and following contact, influencing the evolutionary trajectory of hybrid populations. Where adaptation to novel environments may be facilitated by interspecific hybridization, teasing apart these processes will have practical implications for forest management in changing environments. We evaluated the neutral genetic architecture of the Picea sitchensis (Sitka spruce) × P. glauca (white spruce) hybrid zone along the Nass and Skeena river valleys in northwestern British Columbia using chloroplast, mitochondrial, and nuclear microsatellite markers, in combination with cone morphological traits. Sitka spruce mitotype "capture", evidenced by this species dominating the maternal lineage, is consistent with earlier colonization of the region by Sitka spruce. This "capture" differs from the spatial distribution of chloroplast haplotypes, indicating pollen dispersal and its contribution to geographic structure. Genetic ancestry, based on nuclear markers, was strongly influenced by climate and geography. Highly parallel results for replicate transects along environmental gradients provide support for the bounded hybrid superiority model of hybrid zone maintenance. • This broad-scale analysis of neutral genetic structure indicates the importance of historic and contemporary gene flow, environmental selection, and their interaction in shaping neutral genetic variation within this hybrid zone, informative to seed transfer development and reforestation for future climates.

Hybridization could be a common phenomenon within the highly diverse lizard genus Liolaemus.

PubMed

Olave, Melisa; Avila, Luciano J; Sites, Jack W; Morando, Mariana

2018-03-26

Hybridization is likely to occur more often between closely related taxa that have had insufficient time to diverge to the point of reproductive incompatibility; hybridization between deeply divergent lineages is rare. In squamate reptiles, hybridization has been proposed as a possible explanation for the extensive paraphyly observed in mitochondrial gene trees in several species complexes of the South American lizard genus Liolaemus. One of the best-documented cases is within the L. boulengeri and L. rothi complexes, which diverged ~5.5 million years ago. Here, we describe a comprehensive study for approaching the hybridization hypothesis between these lizard species complexes. We explored the level of gene tree discordance using the novel 'extra lineage contribution' statistics (XLC, presented in this study) that quantifies the level of gene tree discordance contribution per individual within a species. We included molecular data (12 nuclear and two mitochondrial genes) from 127 individuals, and results of a coalescent model-based analysis show that the most likely explanation for the gene tree-species tree discordance is interspecific hybridization. Our best-supported hypothesis suggests current and past hybridization between L. rothi (rothi complex) and L. tehuelche (boulengeri complex), and independently between L. rothi and L. boulengeri and L. telsen (boulengeri complex). The hybrid descendants are characterized by intermediate phenotypes between the parental species, but are more similar to L. rothi in body size. We discuss the possible role of hybridization in Liolaemus evolution. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Genetic architecture of hybrid male sterility in Drosophila: analysis of intraspecies variation for interspecies isolation.

PubMed

Reed, Laura K; LaFlamme, Brooke A; Markow, Therese A

2008-08-27

The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Isofemale strains of D. mojavensis vary significantly in their production of sterile F(1) sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F(1) hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F(1) is complex, involving multiple QTL, epistasis, and cytoplasmic effects. The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation.

Hybridization between invasive Spartina Densiflora (Poaceae) and native S. Foliosa in San Francisco Bay, California, USA

EPA Science Inventory

Rapid evolution in contemporary time can result when related species, brought together through human-aided introduction, hybridize. The evolutionary consequences of post introduction hybridization range from allopolyploid speciation to extinction of species through genetic amalg...

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling.

PubMed

Kane, Patrick; Zollman, Kevin J S

2015-01-01

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the "hybrid equilibrium," to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith's Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory.

Hybrid soft computing systems for electromyographic signals analysis: a review.

PubMed

Xie, Hong-Bo; Guo, Tianruo; Bai, Siwei; Dokos, Socrates

2014-02-03

Electromyographic (EMG) is a bio-signal collected on human skeletal muscle. Analysis of EMG signals has been widely used to detect human movement intent, control various human-machine interfaces, diagnose neuromuscular diseases, and model neuromusculoskeletal system. With the advances of artificial intelligence and soft computing, many sophisticated techniques have been proposed for such purpose. Hybrid soft computing system (HSCS), the integration of these different techniques, aims to further improve the effectiveness, efficiency, and accuracy of EMG analysis. This paper reviews and compares key combinations of neural network, support vector machine, fuzzy logic, evolutionary computing, and swarm intelligence for EMG analysis. Our suggestions on the possible future development of HSCS in EMG analysis are also given in terms of basic soft computing techniques, further combination of these techniques, and their other applications in EMG analysis.

Hybrid soft computing systems for electromyographic signals analysis: a review

PubMed Central

2014-01-01

Electromyographic (EMG) is a bio-signal collected on human skeletal muscle. Analysis of EMG signals has been widely used to detect human movement intent, control various human-machine interfaces, diagnose neuromuscular diseases, and model neuromusculoskeletal system. With the advances of artificial intelligence and soft computing, many sophisticated techniques have been proposed for such purpose. Hybrid soft computing system (HSCS), the integration of these different techniques, aims to further improve the effectiveness, efficiency, and accuracy of EMG analysis. This paper reviews and compares key combinations of neural network, support vector machine, fuzzy logic, evolutionary computing, and swarm intelligence for EMG analysis. Our suggestions on the possible future development of HSCS in EMG analysis are also given in terms of basic soft computing techniques, further combination of these techniques, and their other applications in EMG analysis. PMID:24490979

Hybrid Motion Planning with Multiple Destinations

NASA Technical Reports Server (NTRS)

Clouse, Jeffery

1998-01-01

In our initial proposal, we laid plans for developing a hybrid motion planning system that combines the concepts of visibility-based motion planning, artificial potential field based motion planning, evolutionary constrained optimization, and reinforcement learning. Our goal was, and still is, to produce a hybrid motion planning system that outperforms the best traditional motion planning systems on problems with dynamic environments. The proposed hybrid system will be in two parts the first is a global motion planning system and the second is a local motion planning system. The global system will take global information about the environment, such as the placement of the obstacles and goals, and produce feasible paths through those obstacles. We envision a system that combines the evolutionary-based optimization and visibility-based motion planning to achieve this end.

Stream noise, hybridization, and uncoupled evolution of call traits in two lineages of poison frogs: Oophaga histrionica and Oophaga lehmanni.

PubMed

Vargas-Salinas, Fernando; Amézquita, Adolfo

2013-01-01

According to the acoustic adaptation hypothesis, communication signals are evolutionary shaped in a way that minimizes its degradation and maximizes its contrast against the background noise. To compare the importance for call divergence of acoustic adaptation and hybridization, an evolutionary force allegedly promoting phenotypic variation, we compared the mate recognition signal of two species of poison frogs (Oophaga histrionica and O. lehmanni) at five localities: two (one per species) alongside noisy streams, two away from streams, and one interspecific hybrid. We recorded the calls of 47 males and characterized the microgeographic variation in their spectral and temporal features, measuring ambient noise level, body size, and body temperature as covariates. As predicted, frogs living in noisy habitats uttered high frequency calls and, in one species, were much smaller in size. These results support a previously unconsidered role of noise on streams as a selective force promoting an increase in call frequency and pleiotropic effects in body size. Regarding hybrid frogs, their calls overlapped in the signal space with the calls of one of the parental lineages. Our data support acoustic adaptation following two evolutionary routes but do not support the presumed role of hybridization in promoting phenotypic diversity.

Hybrid Artificial Root Foraging Optimizer Based Multilevel Threshold for Image Segmentation

PubMed Central

Liu, Yang; Liu, Junfei

2016-01-01

This paper proposes a new plant-inspired optimization algorithm for multilevel threshold image segmentation, namely, hybrid artificial root foraging optimizer (HARFO), which essentially mimics the iterative root foraging behaviors. In this algorithm the new growth operators of branching, regrowing, and shrinkage are initially designed to optimize continuous space search by combining root-to-root communication and coevolution mechanism. With the auxin-regulated scheme, various root growth operators are guided systematically. With root-to-root communication, individuals exchange information in different efficient topologies, which essentially improve the exploration ability. With coevolution mechanism, the hierarchical spatial population driven by evolutionary pressure of multiple subpopulations is structured, which ensure that the diversity of root population is well maintained. The comparative results on a suit of benchmarks show the superiority of the proposed algorithm. Finally, the proposed HARFO algorithm is applied to handle the complex image segmentation problem based on multilevel threshold. Computational results of this approach on a set of tested images show the outperformance of the proposed algorithm in terms of optimization accuracy computation efficiency. PMID:27725826

Hybrid Artificial Root Foraging Optimizer Based Multilevel Threshold for Image Segmentation.

PubMed

Liu, Yang; Liu, Junfei; Tian, Liwei; Ma, Lianbo

2016-01-01

This paper proposes a new plant-inspired optimization algorithm for multilevel threshold image segmentation, namely, hybrid artificial root foraging optimizer (HARFO), which essentially mimics the iterative root foraging behaviors. In this algorithm the new growth operators of branching, regrowing, and shrinkage are initially designed to optimize continuous space search by combining root-to-root communication and coevolution mechanism. With the auxin-regulated scheme, various root growth operators are guided systematically. With root-to-root communication, individuals exchange information in different efficient topologies, which essentially improve the exploration ability. With coevolution mechanism, the hierarchical spatial population driven by evolutionary pressure of multiple subpopulations is structured, which ensure that the diversity of root population is well maintained. The comparative results on a suit of benchmarks show the superiority of the proposed algorithm. Finally, the proposed HARFO algorithm is applied to handle the complex image segmentation problem based on multilevel threshold. Computational results of this approach on a set of tested images show the outperformance of the proposed algorithm in terms of optimization accuracy computation efficiency.

Evidence of Natural Selection Acting on a Polymorphic Hybrid Incompatibility Locus in Mimulus

PubMed Central

Sweigart, Andrea L.; Flagel, Lex E.

2015-01-01

As a common cause of reproductive isolation in diverse taxa, hybrid incompatibilities are fundamentally important to speciation. A key question is which evolutionary forces drive the initial substitutions within species that lead to hybrid dysfunction. Previously, we discovered a simple genetic incompatibility that causes nearly complete male sterility and partial female sterility in hybrids between the two closely related yellow monkeyflower species Mimulus guttatus and M. nasutus. In this report, we fine map the two major incompatibility loci—hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2)—to small nuclear genomic regions (each <70 kb) that include strong candidate genes. With this improved genetic resolution, we also investigate the evolutionary dynamics of hms1 in a natural population of M. guttatus known to be polymorphic at this locus. Using classical genetic crosses and population genomics, we show that a 320-kb region containing the hms1 incompatibility allele has risen to intermediate frequency in this population by strong natural selection. This finding provides direct evidence that natural selection within plant species can lead to hybrid dysfunction between species. PMID:25428983

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes.

PubMed

DiBattista, Joseph D; Whitney, Jonathan; Craig, Matthew T; Hobbs, Jean-Paul A; Rocha, Luiz A; Feldheim, Kevin A; Berumen, Michael L; Bowen, Brian W

2016-08-01

Closely related species can provide valuable insights into evolutionary processes through comparison of their ecology, geographic distribution and the history recorded in their genomes. In the Indo-Pacific, many reef fishes are divided into sister species that come into secondary contact at biogeographic borders, most prominently where Indian Ocean and Pacific Ocean faunas meet. It is unclear whether hybridization in this contact zone represents incomplete speciation, secondary contact, an evolutionary dead-end (for hybrids) or some combination of the above. To address these issues, we conducted comprehensive surveys of two widely-distributed surgeonfish species, Acanthurus leucosternon (N=141) and A. nigricans (N=412), with mtDNA cytochrome b sequences and ten microsatellite loci. These surgeonfishes are found primarily in the Indian and Pacific Oceans, respectively, but overlap at the Christmas and Cocos-Keeling Islands hybrid zone in the eastern Indian Ocean. We also sampled the two other Pacific members of this species complex, A. achilles (N=54) and A. japonicus (N=49), which are known to hybridize with A. nigricans where their ranges overlap. Our results indicate separation between the four species that range from the recent Pleistocene to late Pliocene (235,000-2.25million years ago). The Pacific A. achilles is the most divergent (and possibly ancestral) species with mtDNA dcorr≈0.04, whereas the other two Pacific species (A. japonicus and A. nigricans) are distinguishable only at a population or subspecies level (ΦST=0.6533, P<0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had concordance between mtDNA lineage and species identification based on external morphology, indicating that species integrity may not be eroding. The A. nigricans complex demonstrates a range of outcomes from incomplete speciation to secondary contact to decreasing hybridization with increasing evolutionary depth. Copyright © 2016 Elsevier Inc. All rights reserved.

A diversity study of Saccharomycopsis fibuligera in rice wine starter nuruk, reveals the evolutionary process associated with its interspecies hybrid.

PubMed

Farh, Mohamed El-Agamy; Cho, Yunjoo; Lim, Jae Yun; Seo, Jeong-Ah

2017-05-01

The amylolytic yeast Saccharomycopsis fibuligera is the predominant yeast in the starter product, nuruk, which is utilized for rice wine production in South Korea. Latest molecular studies explore a recently developed interspecific hybridization among stains of S. fibuligera with a unique genetic feature. However, the origin of the natural hybridization occurrence is still unclear. Thus, to respectively distinguish parental and hybrid strains, specific primer sets were applied on 141 yeast strains isolated from different nuruk samples fermented in different provinces. Sixty-seven strains were defined accordingly as parental species with genome A while 8 strains were defined as hybrid strains. Unexpectedly, another parental species with genome B could not be found among the strain pools yet. Furthermore, it was observed that hybrid strains are phenotypically different from A genome strains; asci containing tetrad ascospores were observed in A genome strains more frequent than in hybrid strains. Nevertheless, hybrid strains were slightly more thermotolerant than A genome strains. Interestingly, all hybrid strains were located only in Jeju province. Based on these sets of data, we speculated that the unique climate of Jeju province might play an evolutionary role in the interspecific hybridization between A genome strains, as well as the unculturable allopatric B genome strains.

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling

PubMed Central

Kane, Patrick; Zollman, Kevin J. S.

2015-01-01

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the “hybrid equilibrium,” to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith’s Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory. PMID:26348617

Genetic Architecture of Hybrid Male Sterility in Drosophila: Analysis of Intraspecies Variation for Interspecies Isolation

PubMed Central

Reed, Laura K.; LaFlamme, Brooke A.; Markow, Therese A.

2008-01-01

Background The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Methodology/Principal Findings Isofemale strains of D. mojavensis vary significantly in their production of sterile F1 sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F1 hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F1 is complex, involving multiple QTL, epistasis, and cytoplasmic effects. Conclusions/Significance The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation. PMID:18728782

Mapping of within-species segregation distortion in D. persimilis and hybrid sterility between D. persimilis and D. pseudoobscura

PubMed Central

McDermott, Shannon R.; Noor, Mohamed A. F.

2012-01-01

In contrast to the prevailing dogma in the 1990s, recent studies have suggested that an evolutionary history of segregation distortion within species may contribute to sterility in species hybrids. However, this recent work identified segregation distortion exclusively in species hybrids which may never have had an evolutionary history of segregation distortion in either parent species. We expand on previous work by using a strain of Drosophila persimilis exhibiting segregation distortion within species to generate QTL maps for segregation distortion and hybrid sterility in crosses between D. persimilis and D. pseudoobscura. The maps localize regions along the XR contributing to both phenotypes, and they indicate one region of overlap between the two maps. This overlap could provide preliminary evidence for an association between segregation distortion within species and hybrid sterility, but the localizations are currently too broad to have confidence in this conclusion. This work is a first step towards possibly supporting a genetic conflict model of speciation in this system. PMID:22966762

Design Optimization of a Centrifugal Fan with Splitter Blades

NASA Astrophysics Data System (ADS)

Heo, Man-Woong; Kim, Jin-Hyuk; Kim, Kwang-Yong

2015-05-01

Multi-objective optimization of a centrifugal fan with additionally installed splitter blades was performed to simultaneously maximize the efficiency and pressure rise using three-dimensional Reynolds-averaged Navier-Stokes equations and hybrid multi-objective evolutionary algorithm. Two design variables defining the location of splitter, and the height ratio between inlet and outlet of impeller were selected for the optimization. In addition, the aerodynamic characteristics of the centrifugal fan were investigated with the variation of design variables in the design space. Latin hypercube sampling was used to select the training points, and response surface approximation models were constructed as surrogate models of the objective functions. With the optimization, both the efficiency and pressure rise of the centrifugal fan with splitter blades were improved considerably compared to the reference model.

Bands selection and classification of hyperspectral images based on hybrid kernels SVM by evolutionary algorithm

NASA Astrophysics Data System (ADS)

Hu, Yan-Yan; Li, Dong-Sheng

2016-01-01

The hyperspectral images(HSI) consist of many closely spaced bands carrying the most object information. While due to its high dimensionality and high volume nature, it is hard to get satisfactory classification performance. In order to reduce HSI data dimensionality preparation for high classification accuracy, it is proposed to combine a band selection method of artificial immune systems (AIS) with a hybrid kernels support vector machine (SVM-HK) algorithm. In fact, after comparing different kernels for hyperspectral analysis, the approach mixed radial basis function kernel (RBF-K) with sigmoid kernel (Sig-K) and applied the optimized hybrid kernels in SVM classifiers. Then the SVM-HK algorithm used to induce the bands selection of an improved version of AIS. The AIS was composed of clonal selection and elite antibody mutation, including evaluation process with optional index factor (OIF). Experimental classification performance was on a San Diego Naval Base acquired by AVIRIS, the HRS dataset shows that the method is able to efficiently achieve bands redundancy removal while outperforming the traditional SVM classifier.

Aerodynamic Shape Optimization Using Hybridized Differential Evolution

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2003-01-01

An aerodynamic shape optimization method that uses an evolutionary algorithm known at Differential Evolution (DE) in conjunction with various hybridization strategies is described. DE is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Various hybridization strategies for DE are explored, including the use of neural networks as well as traditional local search methods. A Navier-Stokes solver is used to evaluate the various intermediate designs and provide inputs to the hybrid DE optimizer. The method is implemented on distributed parallel computers so that new designs can be obtained within reasonable turnaround times. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. (The final paper will include at least one other aerodynamic design application). The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated.

Evidence of natural selection acting on a polymorphic hybrid incompatibility locus in Mimulus.

PubMed

Sweigart, Andrea L; Flagel, Lex E

2015-02-01

As a common cause of reproductive isolation in diverse taxa, hybrid incompatibilities are fundamentally important to speciation. A key question is which evolutionary forces drive the initial substitutions within species that lead to hybrid dysfunction. Previously, we discovered a simple genetic incompatibility that causes nearly complete male sterility and partial female sterility in hybrids between the two closely related yellow monkeyflower species Mimulus guttatus and M. nasutus. In this report, we fine map the two major incompatibility loci-hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2)-to small nuclear genomic regions (each <70 kb) that include strong candidate genes. With this improved genetic resolution, we also investigate the evolutionary dynamics of hms1 in a natural population of M. guttatus known to be polymorphic at this locus. Using classical genetic crosses and population genomics, we show that a 320-kb region containing the hms1 incompatibility allele has risen to intermediate frequency in this population by strong natural selection. This finding provides direct evidence that natural selection within plant species can lead to hybrid dysfunction between species. Copyright © 2015 by the Genetics Society of America.

Prevalence of cryptic species in morphologically uniform taxa - fast speciation and evolutionary radiation in Asian toads.

PubMed

Liu, Zuyao; Chen, Guoling; Zhu, Tianqi; Zeng, Zhaochi; Lyu, Zhitong; Wang, Jian; Messenger, Kevin; Greenberg, Anthony J; Guo, Zixiao; Yang, Ziheng; Shi, Suhua; Wang, Yingyong

2018-06-16

Diversity and distributions of cryptic species have long been a vexing issue. Identification of species boundaries is made difficult by the lack of obvious morphological differences. Here, we investigate the cryptic diversity and evolutionary history of an underappreciated group of Asian frog species (Megophrys) to explore the pattern and dynamic of amphibian cryptic species. We sequenced four mitochondrial genes and five nuclear genes and delineated species using multiple approaches, combining DNA and mating-call data. A Bayesian species tree was generated to estimate divergence times and to reconstruct ancestral ranges. Macroevolutionary analyses and hybridization tests were conducted to explore the evolutionary dynamics of this cryptic group. Our phylogenies support the current subgenera. We revealed 43 cryptic species, 158% higher than previously thought. The species-delimitation results were further confirmed by mating-call data and morphological divergence. We found that these Asian frogss entered China from the Sunda Shelf 48 Mya, followed by an ancient radiation event during middle Miocene. We confirmed the efficiency of the multispecies coalescent model for delimitation of species with low morphological diversity. Species diversity of Megophrys is severely underappreciated, and species distributions have been misestimated as a result. Copyright © 2018. Published by Elsevier Inc.

Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms

PubMed Central

James, Karen E.; Schneider, Harald; Ansell, Stephen W.; Evers, Margaret; Robba, Lavinia; Uszynski, Grzegorz; Pedersen, Niklas; Newton, Angela E.; Russell, Stephen J.; Vogel, Johannes C.; Kilian, Andrzej

2008-01-01

Background High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms. Methodology/Principal Findings This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples. Conclusions/Significance These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography. PMID:18301759

Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams

Treesearch

Kevin S. McKelvey; Michael K. Young; Taylor M. Wilcox; Daniel M. Bingham; Kristine L. Pilgrim; Michael K. Schwartz

2016-01-01

Introgressive hybridization between native and introduced species is a growing conservation concern. For native cutthroat trout and introduced rainbow trout in western North America, this process is thought to lead to the formation of hybrid swarms and the loss of monophyletic evolutionary lineages. Previous studies of this phenomenon, however, indicated that...

Nuclear and plastid markers reveal the persistence of genetic identity: a new perspective on the evolutionary history of Petunia exserta.

PubMed

Segatto, Ana Lúcia Anversa; Cazé, Ana Luíza Ramos; Turchetto, Caroline; Klahre, Ulrich; Kuhlemeier, Cris; Bonatto, Sandro Luis; Freitas, Loreta Brandão

2014-01-01

Recently divergent species that can hybridize are ideal models for investigating the genetic exchanges that can occur while preserving the species boundaries. Petunia exserta is an endemic species from a very limited and specific area that grows exclusively in rocky shelters. These shaded spots are an inhospitable habitat for all other Petunia species, including the closely related and widely distributed species P. axillaris. Individuals with intermediate morphologic characteristics have been found near the rocky shelters and were believed to be putative hybrids between P. exserta and P. axillaris, suggesting a situation where Petunia exserta is losing its genetic identity. In the current study, we analyzed the plastid intergenic spacers trnS/trnG and trnH/psbA and six nuclear CAPS markers in a large sampling design of both species to understand the evolutionary process occurring in this biological system. Bayesian clustering methods, cpDNA haplotype networks, genetic diversity statistics, and coalescence-based analyses support a scenario where hybridization occurs while two genetic clusters corresponding to two species are maintained. Our results reinforce the importance of coupling differentially inherited markers with an extensive geographic sample to assess the evolutionary dynamics of recently diverged species that can hybridize. Copyright © 2013 Elsevier Inc. All rights reserved.

Hybrid Microgrid Configuration Optimization with Evolutionary Algorithms

NASA Astrophysics Data System (ADS)

Lopez, Nicolas

This dissertation explores the Renewable Energy Integration Problem, and proposes a Genetic Algorithm embedded with a Monte Carlo simulation to solve large instances of the problem that are impractical to solve via full enumeration. The Renewable Energy Integration Problem is defined as finding the optimum set of components to supply the electric demand to a hybrid microgrid. The components considered are solar panels, wind turbines, diesel generators, electric batteries, connections to the power grid and converters, which can be inverters and/or rectifiers. The methodology developed is explained as well as the combinatorial formulation. In addition, 2 case studies of a single objective optimization version of the problem are presented, in order to minimize cost and to minimize global warming potential (GWP) followed by a multi-objective implementation of the offered methodology, by utilizing a non-sorting Genetic Algorithm embedded with a monte Carlo Simulation. The method is validated by solving a small instance of the problem with known solution via a full enumeration algorithm developed by NREL in their software HOMER. The dissertation concludes that the evolutionary algorithms embedded with Monte Carlo simulation namely modified Genetic Algorithms are an efficient form of solving the problem, by finding approximate solutions in the case of single objective optimization, and by approximating the true Pareto front in the case of multiple objective optimization of the Renewable Energy Integration Problem.

Invasions and extinctions through the looking glass of evolutionary ecology

PubMed Central

2017-01-01

Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift. Endangered species are less likely to benefit from admixture, which offsets mutation load but also reduces fitness when populations are locally adapted. Invading species generally experience more benign environments with fewer natural enemies, which increases fitness directly and also indirectly by masking inbreeding depression. Adaptive phenotypic plasticity can maintain fitness in novel environments but is more likely to evolve in invasive species encountering variable habitats and to be compromised by demographic factors in endangered species. Placed in an eco-evolutionary context, these differences affect the breadth of the ecological niche, which arises as an emergent property of antagonistic selection and genetic constraints. Comparative studies of invasions and extinctions that apply an eco-evolutionary perspective could provide new insights into the environmental and genetic basis of ecological success in novel environments and improve efforts to preserve global biodiversity. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’. PMID:27920376

Concordant morphological and molecular clines in a contact zone of the Common and Spined toad (Bufo bufo and B. spinosus) in the northwest of France.

PubMed

Arntzen, Jan W; Trujillo, Tania; Butôt, Roland; Vrieling, Klaas; Schaap, Onno; Gutiérrez-Rodríguez, Jorge; Martínez-Solano, Iñigo

2016-01-01

Hybrid zones are regions where individuals of two species meet and produce hybrid progeny, and are often regarded as natural laboratories to understand the process of species formation. Two microevolutionary processes can take place in hybrid zones, with opposing effects on population differentiation. Hybridization tends to produce genetic homogenization, reducing species differences, whereas the presence of mechanisms of reproductive isolation result in barriers to gene flow, maintaining or increasing differences between taxa. Here we study a contact zone between two hybridizing toad species, Bufo bufo and B. spinosus , through a combination of molecular (12 polymorphic microsatellites, four nuclear and two mitochondrial SNP markers) and morphological data in a transect in the northwest of France. The results show largely concordant clines across markers, defining a narrow hybrid zone of ca. 30 km wide. Most hybrids in the centre of the contact zone are classified as F 2 or backcrossed individuals, with no individuals assigned to the F 1 hybrid class. We discuss the implications of these results for our understanding of the evolutionary history of these species. We anticipate that the toad contact zone here described will become an important asset in the study of hybrid zone dynamics and evolutionary biology because of its easy access and the abundance of the species involved.

iACP-GAEnsC: Evolutionary genetic algorithm based ensemble classification of anticancer peptides by utilizing hybrid feature space.

PubMed

Akbar, Shahid; Hayat, Maqsood; Iqbal, Muhammad; Jan, Mian Ahmad

2017-06-01

Cancer is a fatal disease, responsible for one-quarter of all deaths in developed countries. Traditional anticancer therapies such as, chemotherapy and radiation, are highly expensive, susceptible to errors and ineffective techniques. These conventional techniques induce severe side-effects on human cells. Due to perilous impact of cancer, the development of an accurate and highly efficient intelligent computational model is desirable for identification of anticancer peptides. In this paper, evolutionary intelligent genetic algorithm-based ensemble model, 'iACP-GAEnsC', is proposed for the identification of anticancer peptides. In this model, the protein sequences are formulated, using three different discrete feature representation methods, i.e., amphiphilic Pseudo amino acid composition, g-Gap dipeptide composition, and Reduce amino acid alphabet composition. The performance of the extracted feature spaces are investigated separately and then merged to exhibit the significance of hybridization. In addition, the predicted results of individual classifiers are combined together, using optimized genetic algorithm and simple majority technique in order to enhance the true classification rate. It is observed that genetic algorithm-based ensemble classification outperforms than individual classifiers as well as simple majority voting base ensemble. The performance of genetic algorithm-based ensemble classification is highly reported on hybrid feature space, with an accuracy of 96.45%. In comparison to the existing techniques, 'iACP-GAEnsC' model has achieved remarkable improvement in terms of various performance metrics. Based on the simulation results, it is observed that 'iACP-GAEnsC' model might be a leading tool in the field of drug design and proteomics for researchers. Copyright © 2017 Elsevier B.V. All rights reserved.

Hybrid Disease Diagnosis Using Multiobjective Optimization with Evolutionary Parameter Optimization

PubMed Central

Nalluri, MadhuSudana Rao; K., Kannan; M., Manisha

2017-01-01

With the widespread adoption of e-Healthcare and telemedicine applications, accurate, intelligent disease diagnosis systems have been profoundly coveted. In recent years, numerous individual machine learning-based classifiers have been proposed and tested, and the fact that a single classifier cannot effectively classify and diagnose all diseases has been almost accorded with. This has seen a number of recent research attempts to arrive at a consensus using ensemble classification techniques. In this paper, a hybrid system is proposed to diagnose ailments using optimizing individual classifier parameters for two classifier techniques, namely, support vector machine (SVM) and multilayer perceptron (MLP) technique. We employ three recent evolutionary algorithms to optimize the parameters of the classifiers above, leading to six alternative hybrid disease diagnosis systems, also referred to as hybrid intelligent systems (HISs). Multiple objectives, namely, prediction accuracy, sensitivity, and specificity, have been considered to assess the efficacy of the proposed hybrid systems with existing ones. The proposed model is evaluated on 11 benchmark datasets, and the obtained results demonstrate that our proposed hybrid diagnosis systems perform better in terms of disease prediction accuracy, sensitivity, and specificity. Pertinent statistical tests were carried out to substantiate the efficacy of the obtained results. PMID:29065626

Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

PubMed

Zhang, Linbin; Sun, Tianai; Woldesellassie, Fitsum; Xiao, Hailian; Tao, Yun

2015-03-01

Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s) that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

Sex Ratio Meiotic Drive as a Plausible Evolutionary Mechanism for Hybrid Male Sterility

PubMed Central

Zhang, Linbin; Xiao, Hailian; Tao, Yun

2015-01-01

Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s) that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome – two patterns widely observed across animals. PMID:25822261

Homoploid hybrid speciation in a rare endemic Castilleja from Idaho (Castilleja christii, Orobanchaceae).

PubMed

Clay, Danielle L; Novak, Stephen J; Serpe, Marcelo D; Tank, David C; Smith, James F

2012-12-01

Hybridization is an important evolutionary force in the history of angiosperms; however, there are few examples of stabilized species derived through homoploid hybrid speciation. Homoploid hybrid species are generally detected via the presence of genetic additivity of parental markers, novel ecological and spatial distinctions, and novel morphological traits, all of which may aid in the successful establishment of hybrid species from parental types. Speciation and diversification within the genus Castilleja (Orobanchaceae) has been attributed to high levels of hybridization and polyploidy, though currently there are no examples of homoploid hybrid speciation within the genus. We employed multiple lines of evidence to examine a putative hybrid origin in C. christii, a rare endemic, known only from 80 hectares at the summit of Mt. Harrison (Cassia Co., Idaho). • We used granule-bound starch synthase II (waxy) sequences and 26 morphological characters to address hybridization between C. christii and widespread congeners C. miniata and/or C. linariifolia in an area of sympatry. Chromosomes of C. christii were also counted for the first time. • All 230 direct-sequenced C. christii individuals had the additive genomes of both C. miniata and C. linariifolia. Castilleja christii shares traits with both parents but also has floral characters that are unique and transgressive. Cytological counts indicated that all three taxa are diploid. • We conclude that C. christii is a stabilized homoploid hybrid derivative of C. linariifolia and C. miniata and is likely following an independent evolutionary trajectory from its progenitors.

Misregulation of spermatogenesis genes in Drosophila hybrids is lineage-specific and driven by the combined effects of sterility and fast male regulatory divergence.

PubMed

Gomes, S; Civetta, A

2014-09-01

Hybrid male sterility is a common outcome of crosses between different species. Gene expression studies have found that a number of spermatogenesis genes are differentially expressed in sterile hybrid males, compared with parental species. Late-stage sperm development genes are particularly likely to be misexpressed, with fewer early-stage genes affected. Thus, a link has been posited between misexpression and sterility. A more recent alternative explanation for hybrid gene misexpression has been that it is independent of sterility and driven by divergent evolution of male-specific regulatory elements between species (faster male hypothesis). The faster male hypothesis predicts that misregulation of spermatogenesis genes should be independent of sterility and approximately the same in both hybrids, whereas sterility should only affect gene expression in sterile hybrids. To test the faster male hypothesis vs. the effect of sterility on gene misexpression, we analyse spermatogenesis gene expression in different species pairs of the Drosophila phylogeny, where hybrid male sterility occurs in only one direction of the interspecies cross (i.e. unidirectional sterility). We find significant differences among genes in misexpression with effects that are lineage-specific and caused by sterility or fast male regulatory divergence. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Tangled trios? Characterizing a hybrid zone in Castilleja (Orobanchaceae)

Treesearch

Erika l. Hersch-Green; Richard Cronn

2009-01-01

Hybridization and polyploidization are exceedingly important processes because both influence the ecological envelope and evolutionary trajectory of land plants. These processes are frequently invoked for Castilleja (Indian paintbrushes) as contributors to morphological and genetic novelty and as complicating factors in species delimitations. Here...

Hybridisation among groupers (genus Cephalopholis) at the eastern Indian Ocean suture zone: taxonomic and evolutionary implications

NASA Astrophysics Data System (ADS)

Payet, Samuel D.; Hobbs, Jean-Paul A.; DiBattista, Joseph D.; Newman, Stephen J.; Sinclair-Taylor, Tane; Berumen, Michael L.; McIlwain, Jennifer L.

2016-12-01

Hybridisation is a significant evolutionary process that until recently was considered rare in the marine environment. A suture zone in the eastern Indian Ocean is home to numerous hybridising sister species, providing an ideal opportunity to determine how hybridisation affects speciation and biodiversity in coral reef fishes. At this location, hybridisation between two grouper (Epinephelidae) species: Cephalopholis urodeta (Pacific Ocean) and C. nigripinnis (Indian Ocean) was investigated to determine the genetic basis of hybridisation and to compare the ecology and life history of hybrids and their parent species. This approach aimed to provide insights into the taxonomic and evolutionary consequences of hybridisation. Despite clear phenotypic differences, multiple molecular markers revealed hybrids, and their parent species were genetically homogenous within and (thousands of kilometres) outside of the hybrid zone. Hybrids were at least as fit as their parent species (in terms of growth, reproduction, and abundance) and were observed in a broad range of intermediate phenotypes. The two species appear to be interbreeding at Christmas Island due to inherent biological and ecological compatibilities, and the lack of genetic structure may be explained by three potential scenarios: (1) hybridisation and introgression; (2) discordance between morphology and genetics; and (3) incomplete lineage sorting. Further molecular analyses are necessary to discriminate these scenarios. Regardless of which applies, C. urodeta and C. nigripinnis are unlikely to evolve in reproductive isolation as they cohabit where they are common (Christmas Island) and will source congeneric mates where they are rare (Cocos Keeling Islands). Our results add to the growing body of evidence that hybridisation among coral reef fishes is a dynamic evolutionary factor.

Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico

PubMed Central

Ávila-Flores, Israel Jaime; Hernández-Díaz, José Ciro; González-Elizondo, Maria Socorro; Prieto-Ruíz, José Ángel; Wehenkel, Christian

2016-01-01

Hybridization is an important evolutionary force, because interspecific gene transfer can introduce more new genetic material than is directly generated by mutations. Pinus engelmannii Carr. is one of the nine most common pine species in the pine-oak forest ecoregion in the state of Durango, Mexico. This species is widely harvested for lumber and is also used in reforestation programmes. Interspecific hybrids between P.engelmannii and Pinus arizonica Engelm. have been detected by morphological analysis. The presence of hybrids in P. engelmannii seed stands may affect seed quality and reforestation success. Therefore, the goals of this research were to identify introgressive hybridization between P. engelmannii and other pine species in eight seed stands of this species in Durango, Mexico, and to examine how hybrid proportion is related to mean genetic dissimilarity between trees in these stands, using Amplified Fragment Length Polymorphism (AFLP) markers and morphological traits. Differences in the average current annual increment of putative hybrids and pure trees were also tested for statistical significance. Morphological and genetic analyses of 280 adult trees were carried out. Putative hybrids were found in all the seed stands studied. The hybrids did not differ from the pure trees in vigour or robustness. All stands with putative P. engelmannii hybrids detected by both AFLPs and morphological traits showed the highest average values of the Tanimoto distance, which indicates: i) more heterogeneous genetic material, ii) higher genetic variation and therefore iii) the higher evolutionary potential of these stands, and iv) that the morphological differentiation (hybrid/not hybrid) is strongly associated with the Tanimoto distance per stand. We conclude that natural pairwise hybrids are very common in the studied stands. Both morphological and molecular approaches are necessary to confirm the genetic identity of forest reproductive material. PMID:27064490

Hybridization between Yellowstone cutthroat trout and rainbow trout alters the expression of muscle growth-related genes and their relationships with growth patterns

USGS Publications Warehouse

Ostberg, Carl O.; Chase, Dorothy M.; Hauser, Lorenz

2015-01-01

Hybridization creates novel gene combinations that may generate important evolutionary novelty, but may also reduce existing adaptation by interrupting inherent biological processes, such as genotype-environment interactions. Hybridization often causes substantial change in patterns of gene expression, which, in turn, may cause phenotypic change. Rainbow trout (Oncorhynchus mykiss) and cutthroat trout (O. clarkii) produce viable hybrids in the wild, and introgressive hybridization with introduced rainbow trout is a major conservation concern for native cutthroat trout. The two species differ in body shape, which is likely an evolutionary adaptation to their native environments, and their hybrids tend to show intermediate morphology. The characterization of gene expression patterns may provide insights on the genetic basis of hybrid and parental morphologies, as well as on the ecological performance of hybrids in the wild. Here, we evaluated the expression of eight growth-related genes (MSTN-1a, MSTN-1b, MyoD1a, MyoD1b, MRF-4, IGF-1, IGF-2, and CAST-L) and the relationship of these genes with growth traits (length, weight, and condition factor) in six line crosses: both parental species, both reciprocal F1 hybrids, and both first-generation backcrosses (F1 x rainbow trout and F1 x cutthroat trout). Four of these genes were differentially expressed among rainbow, cutthroat, and their hybrids. Transcript abundance was significantly correlated with growth traits across the parent species, but not across hybrids. Our findings suggest that rainbow and cutthroat trout exhibit differences in muscle growth regulation, that transcriptional networks may be modified by hybridization, and that hybridization disrupts intrinsic relationships between gene expression and growth patterns that may be functionally important for phenotypic adaptations.

Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico.

PubMed

Ávila-Flores, Israel Jaime; Hernández-Díaz, José Ciro; González-Elizondo, Maria Socorro; Prieto-Ruíz, José Ángel; Wehenkel, Christian

2016-01-01

Hybridization is an important evolutionary force, because interspecific gene transfer can introduce more new genetic material than is directly generated by mutations. Pinus engelmannii Carr. is one of the nine most common pine species in the pine-oak forest ecoregion in the state of Durango, Mexico. This species is widely harvested for lumber and is also used in reforestation programmes. Interspecific hybrids between P.engelmannii and Pinus arizonica Engelm. have been detected by morphological analysis. The presence of hybrids in P. engelmannii seed stands may affect seed quality and reforestation success. Therefore, the goals of this research were to identify introgressive hybridization between P. engelmannii and other pine species in eight seed stands of this species in Durango, Mexico, and to examine how hybrid proportion is related to mean genetic dissimilarity between trees in these stands, using Amplified Fragment Length Polymorphism (AFLP) markers and morphological traits. Differences in the average current annual increment of putative hybrids and pure trees were also tested for statistical significance. Morphological and genetic analyses of 280 adult trees were carried out. Putative hybrids were found in all the seed stands studied. The hybrids did not differ from the pure trees in vigour or robustness. All stands with putative P. engelmannii hybrids detected by both AFLPs and morphological traits showed the highest average values of the Tanimoto distance, which indicates: i) more heterogeneous genetic material, ii) higher genetic variation and therefore iii) the higher evolutionary potential of these stands, and iv) that the morphological differentiation (hybrid/not hybrid) is strongly associated with the Tanimoto distance per stand. We conclude that natural pairwise hybrids are very common in the studied stands. Both morphological and molecular approaches are necessary to confirm the genetic identity of forest reproductive material.

Jumping genes: Genomic ballast or powerhouse of biological diversification.

PubMed

Choudhury, Rimjhim Roy; Parisod, Christian

2017-09-01

Studying hybridization has the potential to elucidate challenging questions in evolutionary biology such as the nature of adaptive genetic variation and reproductive isolation. A growing body of work highlights that the merging of divergent genomes goes beyond the reshuffling of standing variation from related species and promotes mutations (Abbott et al., ). However, to what extent such genome instability generates evolutionary significant variation remains largely elusive. In this issue of Molecular Ecology, Dennenmoser et al. () report considerable dynamics of transposable elements (TEs) in a recent invasive fish species of hybrid origin (Cottus; Figure ). It adds to the recent examples from plants to support TE-specific genome variation following hybridization. Insights from early, as well as established, hybrids are largely coherent with increased TE activity, and this fish system thus represents an inspiring opportunity to further address the possible association between genome dynamics and "rapid evolution of hybrid species." This work based on genome (re)sequencing contrasts with prior transcriptomics or PCR-based studies of TEs and illustrates how unprecedented amount of information promises a better understanding of the multiple patterns of variation across eukaryotic genomes; provided that we get the better of methodological advances. As discussed here, unbiased assessment of TE variation from genome surveys indeed remains a challenge precluding firm conclusions to be reached about the evolutionary significance of TEs. Despite methodological and conceptual developments that appear necessary to unambiguously uncover the unexplored iceberg below the known tip, the role of coding genes vs. TEs in promoting adaptation and speciation might be clarified in a not so remote future. © 2017 John Wiley & Sons Ltd.

Speciation via autoimmunity: a dangerous mix.

PubMed

Phadnis, Nitin; Malik, Harmit S

2014-12-04

In this issue of Cell, Chae et al. find that genomic "hot spots" encoding NLR plant immune receptor genes are recurrently responsible for hybrid necrosis, highlighting the role of host-pathogen evolutionary arms races in driving the evolution of hybrid incompatibilities. Copyright © 2014 Elsevier Inc. All rights reserved.

Evolutionary algorithm based heuristic scheme for nonlinear heat transfer equations.

PubMed

Ullah, Azmat; Malik, Suheel Abdullah; Alimgeer, Khurram Saleem

2018-01-01

In this paper, a hybrid heuristic scheme based on two different basis functions i.e. Log Sigmoid and Bernstein Polynomial with unknown parameters is used for solving the nonlinear heat transfer equations efficiently. The proposed technique transforms the given nonlinear ordinary differential equation into an equivalent global error minimization problem. Trial solution for the given nonlinear differential equation is formulated using a fitness function with unknown parameters. The proposed hybrid scheme of Genetic Algorithm (GA) with Interior Point Algorithm (IPA) is opted to solve the minimization problem and to achieve the optimal values of unknown parameters. The effectiveness of the proposed scheme is validated by solving nonlinear heat transfer equations. The results obtained by the proposed scheme are compared and found in sharp agreement with both the exact solution and solution obtained by Haar Wavelet-Quasilinearization technique which witnesses the effectiveness and viability of the suggested scheme. Moreover, the statistical analysis is also conducted for investigating the stability and reliability of the presented scheme.

Hybrid intelligent methodology to design translation invariant morphological operators for Brazilian stock market prediction.

PubMed

Araújo, Ricardo de A

2010-12-01

This paper presents a hybrid intelligent methodology to design increasing translation invariant morphological operators applied to Brazilian stock market prediction (overcoming the random walk dilemma). The proposed Translation Invariant Morphological Robust Automatic phase-Adjustment (TIMRAA) method consists of a hybrid intelligent model composed of a Modular Morphological Neural Network (MMNN) with a Quantum-Inspired Evolutionary Algorithm (QIEA), which searches for the best time lags to reconstruct the phase space of the time series generator phenomenon and determines the initial (sub-optimal) parameters of the MMNN. Each individual of the QIEA population is further trained by the Back Propagation (BP) algorithm to improve the MMNN parameters supplied by the QIEA. Also, for each prediction model generated, it uses a behavioral statistical test and a phase fix procedure to adjust time phase distortions observed in stock market time series. Furthermore, an experimental analysis is conducted with the proposed method through four Brazilian stock market time series, and the achieved results are discussed and compared to results found with random walk models and the previously introduced Time-delay Added Evolutionary Forecasting (TAEF) and Morphological-Rank-Linear Time-lag Added Evolutionary Forecasting (MRLTAEF) methods. Copyright © 2010 Elsevier Ltd. All rights reserved.

Reinforcement and a cline in mating behaviour evolve in response to secondary contact and hybridization in shield-back katydids (Orthoptera: Tettigoniidae).

PubMed

Cole, J A

2016-09-01

In a dispersal-limited species that has evolved reproductive character displacement at a contact zone, a cline in mating behaviour may result if gene flow diffuses alleles out of the contact zone into allopatric populations. Prior work has found such a clinal pattern in the shield-back katydid Aglaothorax morsei, in which the male calling songs in a sympatric population have a displaced, short interpulse interval that increases in length with increasing distance from the contact zone. In this study, molecular phylogenetic and female preference data show that (1) sympatric populations result from secondary contact, (2) hybridization in sympatry has resulted in unidirectional mitochondrial introgression and (3) female preferences are consistent with reproductive character displacement and could generate a cline in mating behaviour. These data together suggest a history of reinforcement, generally considered rare in acoustically communicating insects; thus, Aglaothorax represents an important example of a rarely documented evolutionary process. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

An Evolutionary Algorithm for Fast Intensity Based Image Matching Between Optical and SAR Satellite Imagery

NASA Astrophysics Data System (ADS)

Fischer, Peter; Schuegraf, Philipp; Merkle, Nina; Storch, Tobias

2018-04-01

This paper presents a hybrid evolutionary algorithm for fast intensity based matching between satellite imagery from SAR and very high-resolution (VHR) optical sensor systems. The precise and accurate co-registration of image time series and images of different sensors is a key task in multi-sensor image processing scenarios. The necessary preprocessing step of image matching and tie-point detection is divided into a search problem and a similarity measurement. Within this paper we evaluate the use of an evolutionary search strategy for establishing the spatial correspondence between satellite imagery of optical and radar sensors. The aim of the proposed algorithm is to decrease the computational costs during the search process by formulating the search as an optimization problem. Based upon the canonical evolutionary algorithm, the proposed algorithm is adapted for SAR/optical imagery intensity based matching. Extensions are drawn using techniques like hybridization (e.g. local search) and others to lower the number of objective function calls and refine the result. The algorithm significantely decreases the computational costs whilst finding the optimal solution in a reliable way.

Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout

USGS Publications Warehouse

Muhlfeld, Clint C.; Kovach, Ryan P.; Al-Chokhachy, Robert K.; Amish, Stephen J.; Kershner, Jeffrey L.; Leary, Robb F.; Lowe, Winsor H.; Luikart, Gordon; Matson, Phil; Schmetterling, David A.; Shepard, Bradley B.; Westley, Peter A. H.; Whited, Diane; Whiteley, Andrew R.; Allendorf, Fred W.

2017-01-01

Hybridization between invasive and native species, a significant threat to worldwide biodiversity, is predicted to increase due to climate-induced expansions of invasive species. Long-term research and monitoring are crucial for understanding the ecological and evolutionary processes that modulate the effects of invasive species. Using a large, multi-decade genetics dataset (N = 582 sites, 12,878 individuals) with high-resolution climate predictions and extensive stocking records, we evaluate the spatiotemporal dynamics of hybridization between native cutthroat trout and invasive rainbow trout, the world’s most widely introduced invasive fish, across the northern Rocky Mountains of the United States. Historical effects of stocking and contemporary patterns of climatic variation were strongly related to the spread of hybridization across space and time. The probability of occurrence, extent of, and temporal changes in hybridization increased at sites in close proximity to historical stocking locations with greater rainbow trout propagule pressure, warmer water temperatures, and lower spring precipitation. Although locations with warmer water temperatures were more prone to hybridization, cold sites were not protected from invasion; 58% of hybridized sites had cold mean summer water temperatures (<11°C). Despite cessation of stocking over 40 years ago, hybridization increased over time at half (50%) of the locations with long-term data, the vast majority of which (74%) were initially non-hybridized, emphasizing the chronic, negative impacts of human-mediated hybridization. These results show that effects of climate change on biodiversity must be analyzed in the context of historical human impacts that set ecological and evolutionary trajectories.

Widespread Over-Expression of the X Chromosome in Sterile F1 Hybrid Mice

PubMed Central

Good, Jeffrey M.; Giger, Thomas; Dean, Matthew D.; Nachman, Michael W.

2010-01-01

The X chromosome often plays a central role in hybrid male sterility between species, but it is unclear if this reflects underlying regulatory incompatibilities. Here we combine phenotypic data with genome-wide expression data to directly associate aberrant expression patterns with hybrid male sterility between two species of mice. We used a reciprocal cross in which F1 males are sterile in one direction and fertile in the other direction, allowing us to associate expression differences with sterility rather than with other hybrid phenotypes. We found evidence of extensive over-expression of the X chromosome during spermatogenesis in sterile but not in fertile F1 hybrid males. Over-expression was most pronounced in genes that are normally expressed after meiosis, consistent with an X chromosome-wide disruption of expression during the later stages of spermatogenesis. This pattern was not a simple consequence of faster evolutionary divergence on the X chromosome, because X-linked expression was highly conserved between the two species. Thus, transcriptional regulation of the X chromosome during spermatogenesis appears particularly sensitive to evolutionary divergence between species. Overall, these data provide evidence for an underlying regulatory basis to reproductive isolation in house mice and underscore the importance of transcriptional regulation of the X chromosome to the evolution of hybrid male sterility. PMID:20941395

Widespread over-expression of the X chromosome in sterile F₁hybrid mice.

PubMed

Good, Jeffrey M; Giger, Thomas; Dean, Matthew D; Nachman, Michael W

2010-09-30

The X chromosome often plays a central role in hybrid male sterility between species, but it is unclear if this reflects underlying regulatory incompatibilities. Here we combine phenotypic data with genome-wide expression data to directly associate aberrant expression patterns with hybrid male sterility between two species of mice. We used a reciprocal cross in which F₁ males are sterile in one direction and fertile in the other direction, allowing us to associate expression differences with sterility rather than with other hybrid phenotypes. We found evidence of extensive over-expression of the X chromosome during spermatogenesis in sterile but not in fertile F₁ hybrid males. Over-expression was most pronounced in genes that are normally expressed after meiosis, consistent with an X chromosome-wide disruption of expression during the later stages of spermatogenesis. This pattern was not a simple consequence of faster evolutionary divergence on the X chromosome, because X-linked expression was highly conserved between the two species. Thus, transcriptional regulation of the X chromosome during spermatogenesis appears particularly sensitive to evolutionary divergence between species. Overall, these data provide evidence for an underlying regulatory basis to reproductive isolation in house mice and underscore the importance of transcriptional regulation of the X chromosome to the evolution of hybrid male sterility.

Comparative genetics of hybrid incompatibility: sterility in two Solanum species crosses.

PubMed

Moyle, Leonie C; Nakazato, Takuya

2008-07-01

The genetic basis of hybrid sterility can provide insight into the genetic and evolutionary origins of species barriers. We examine the genetics of hybrid incompatibility between two diploid plant species in the plant clade Solanum sect. Lycopersicon. Using a set of near-isogenic lines (NILs) representing the wild species Solanum pennellii (formerly Lycopersicon pennellii) in the genetic background of the cultivated tomato S. lycopersicum (formerly L. esculentum), we found that hybrid pollen and seed infertility are each based on a modest number of loci, male (pollen) and other (seed) incompatibility factors are roughly comparable in number, and seed-infertility QTL act additively or recessively. These findings are remarkably consistent with our previous analysis in a different species pair, S. lycopersicum x S. habrochaites. Data from both studies contrast strongly with data from Drosophila. Finally, QTL for pollen and seed sterility from the two Solanum studies were chromosomally colocalized, indicating a shared evolutionary history for these QTL, a nonrandom genomic distribution of loci causing sterility, and/or a proclivity of certain genes to be involved in hybrid sterility. We show that comparative mapping data can delimit the probable timing of evolution of detected QTL and discern which sterility loci likely evolved earliest among species.

Evolutionary domestication in Drosophila subobscura.

PubMed

Simões, P; Rose, M R; Duarte, A; Gonçalves, R; Matos, M

2007-03-01

The domestication of plants and animals is historically one of the most important topics in evolutionary biology. The evolutionary genetic changes arising from human cultivation are complex because of the effects of such varied processes as continuing natural selection, artificial selection, deliberate inbreeding, genetic drift and hybridization of different lineages. Despite the interest of domestication as an evolutionary process, few studies of multicellular sexual species have approached this topic using well-replicated experiments. Here we present a comprehensive study in which replicated evolutionary trajectories from several Drosophila subobscura populations provide a detailed view of the evolutionary dynamics of domestication in an outbreeding animal species. Our results show a clear evolutionary response in fecundity traits, but no clear pattern for adult starvation resistance and juvenile traits such as development time and viability. These results supply new perspectives on the confounding of adaptation with other evolutionary mechanisms in the process of domestication.

Risk and efficacy of human-enabled interspecific hybridization for climate-change adaptation: Response to Hamilton and Miller (2016)

USGS Publications Warehouse

Kovach, Ryan P.; Luikart, Gordon; Lowe, Winsor H.; Boyer, Matthew C.; Muhlfeld, Clint C.

2016-01-01

Hamilton and Miller (2016) provide an interesting and provocative discussion of how hybridization and introgression can promote evolutionary potential in the face of climate change. They argue that hybridization—mating between individuals from genetically distinct populations—can alleviate inbreeding depression and promote adaptive introgression and evolutionary rescue. We agree that deliberate intraspecific hybridization (mating between individuals of the same species) is an underused management tool for increasing fitness in inbred populations (i.e., genetic rescue; Frankham 2015; Whiteley et al. 2015). The potential risks and benefits of assisted gene flow have been discussed in the literature, and an emerging consensus suggests that mating between populations isolated for approximately 50–100 generations can benefit fitness, often with a minor risk of outbreeding depression (Frankham et al. 2011; Aitken & Whitlock 2013; Allendorf et al. 2013).

Overcoming obstacles to interspecies hybridization of ash

Treesearch

Jennifer L. Koch; David W. Carey; Mary E. Mason; M. Nurul Islam-Faridi

2010-01-01

Tree species that share a long co-evolutionary history with insects and pathogens are likely to have developed mechanisms of resistance that allow them to coexist. When insects and pathogens are introduced to different parts of the world, high levels of susceptibility can be observed, presumably in part due to the lack of co-evolutionary history between the insect (or...

Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout.

PubMed

Muhlfeld, Clint C; Kovach, Ryan P; Al-Chokhachy, Robert; Amish, Stephen J; Kershner, Jeffrey L; Leary, Robb F; Lowe, Winsor H; Luikart, Gordon; Matson, Phil; Schmetterling, David A; Shepard, Bradley B; Westley, Peter A H; Whited, Diane; Whiteley, Andrew; Allendorf, Fred W

2017-11-01

Hybridization between invasive and native species, a significant threat to worldwide biodiversity, is predicted to increase due to climate-induced expansions of invasive species. Long-term research and monitoring are crucial for understanding the ecological and evolutionary processes that modulate the effects of invasive species. Using a large, multidecade genetics dataset (N = 582 sites, 12,878 individuals) with high-resolution climate predictions and extensive stocking records, we evaluate the spatiotemporal dynamics of hybridization between native cutthroat trout and invasive rainbow trout, the world's most widely introduced invasive fish, across the Northern Rocky Mountains of the United States. Historical effects of stocking and contemporary patterns of climatic variation were strongly related to the spread of hybridization across space and time. The probability of occurrence, extent of, and temporal changes in hybridization increased at sites in close proximity to historical stocking locations with greater rainbow trout propagule pressure, warmer water temperatures, and lower spring precipitation. Although locations with warmer water temperatures were more prone to hybridization, cold sites were not protected from invasion; 58% of hybridized sites had cold mean summer water temperatures (<11°C). Despite cessation of stocking over 40 years ago, hybridization increased over time at half (50%) of the locations with long-term data, the vast majority of which (74%) were initially nonhybridized, emphasizing the chronic, negative impacts of human-mediated hybridization. These results show that effects of climate change on biodiversity must be analyzed in the context of historical human impacts that set ecological and evolutionary trajectories. © 2017 John Wiley & Sons Ltd.

Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions

USDA-ARS?s Scientific Manuscript database

Hybridization is known to occur between cultivated and wild populations of numerous plant species. This represents a major mechanism by which a wild population’s genetic structure and evolutionary dynamics could be altered. Studying crop-derived alleles in wild populations is also relevant to assess...

The evolutionary turnover of recombination hot spots contributes to speciation in mice.

PubMed

Smagulova, Fatima; Brick, Kevin; Pu, Yongmei; Camerini-Otero, R Daniel; Petukhova, Galina V

2016-02-01

Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. In most mammals, the DNA double-strand breaks (DSBs) that initiate meiotic recombination are directed to a subset of genomic loci (hot spots) by sequence-specific binding of the PRDM9 protein. Rapid evolution of the DNA-binding specificity of PRDM9 and gradual erosion of PRDM9-binding sites by gene conversion will alter the recombination landscape over time. To better understand the evolutionary turnover of recombination hot spots and its consequences, we mapped DSB hot spots in four major subspecies of Mus musculus with different Prdm9 alleles and in their F1 hybrids. We found that hot spot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hot spots that become active in the hybrids. As crossovers are disfavored at such hot spots, we propose that sequence divergence generated by hot spot turnover may create an impediment for recombination in hybrids, potentially leading to reduced fertility and, eventually, speciation. Published by Cold Spring Harbor Laboratory Press.

The evolutionary turnover of recombination hot spots contributes to speciation in mice

PubMed Central

Smagulova, Fatima; Brick, Kevin; Pu, Yongmei; Camerini-Otero, R. Daniel; Petukhova, Galina V.

2016-01-01

Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. In most mammals, the DNA double-strand breaks (DSBs) that initiate meiotic recombination are directed to a subset of genomic loci (hot spots) by sequence-specific binding of the PRDM9 protein. Rapid evolution of the DNA-binding specificity of PRDM9 and gradual erosion of PRDM9-binding sites by gene conversion will alter the recombination landscape over time. To better understand the evolutionary turnover of recombination hot spots and its consequences, we mapped DSB hot spots in four major subspecies of Mus musculus with different Prdm9 alleles and in their F1 hybrids. We found that hot spot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hot spots that become active in the hybrids. As crossovers are disfavored at such hot spots, we propose that sequence divergence generated by hot spot turnover may create an impediment for recombination in hybrids, potentially leading to reduced fertility and, eventually, speciation. PMID:26833728

Allopolyploidy in bryophytes: Multiple origins of Plagiomnium medium

PubMed Central

Wyatt, Robert; Odrzykoski, Ireneusz J.; Stoneburner, Ann; Bass, Henry W.; Galau, Glenn A.

1988-01-01

Bryophytes are thought to be unique among land plants in lacking the important evolutionary process of allopolyploidy, which involves interspecific hybridization and chromosome doubling. Electrophoretic data show, however, that the polyploid moss Plagiomnium medium is an allopolyploid derivative of Plagiomnium ellipticum and Plagiomnium insigne, that P. medium has originated more than once from these progenitors, and that cross-fertilization results in interlocus genetic recombination. Evidence from restriction fragment length polymorphisms in chloroplast DNA implicates P. insigne as the female parent in interspecific hybridizations with P. ellipticum. Contrary to prevailing views, it appears that those evolutionary processes responsible for genetic differentiation and speciation in other land plants occur in the bryophytes as well. Images PMID:16593968

Chimeric Protein Complexes in Hybrid Species Generate Novel Phenotypes

PubMed Central

Piatkowska, Elzbieta M.; Naseeb, Samina; Knight, David; Delneri, Daniela

2013-01-01

Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently deemed to be responsible for the phenotypic properties seen in hybrids. However, since the majority of the biological functions in a cell are carried out by protein complexes, inter-specific protein assemblies therefore represent another important source of natural variation upon which evolutionary forces can act. Here we studied the composition of six protein complexes in two different Saccharomyces “sensu stricto” hybrids, to understand whether chimeric interactions can be freely formed in the cell in spite of species-specific co-evolutionary forces, and whether the different types of complexes cause a change in hybrid fitness. The protein assemblies were isolated from the hybrids via affinity chromatography and identified via mass spectrometry. We found evidence of spontaneous chimericity for four of the six protein assemblies tested and we showed that different types of complexes can cause a variety of phenotypes in selected environments. In the case of TRP2/TRP3 complex, the effect of such chimeric formation resulted in the fitness advantage of the hybrid in an environment lacking tryptophan, while only one type of parental combination of the MBF complex allowed the hybrid to grow under respiratory conditions. These phenotypes were dependent on both genetic and environmental backgrounds. This study provides empirical evidence that chimeric protein complexes can freely assemble in cells and reveals a new mechanism to generate phenotypic novelty and plasticity in hybrids to complement the genomic innovation resulting from gene duplication. The ability to exchange orthologous members has also important implications for the adaptation and subsequent genome evolution of the hybrids in terms of pattern of gene loss. PMID:24137105

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

PubMed Central

Wen, Dingqiao; Yu, Yun; Hahn, Matthew W.; Nakhleh, Luay

2016-01-01

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

Evolutionary search for new high-k dielectric materials: methodology and applications to hafnia-based oxides.

PubMed

Zeng, Qingfeng; Oganov, Artem R; Lyakhov, Andriy O; Xie, Congwei; Zhang, Xiaodong; Zhang, Jin; Zhu, Qiang; Wei, Bingqing; Grigorenko, Ilya; Zhang, Litong; Cheng, Laifei

2014-02-01

High-k dielectric materials are important as gate oxides in microelectronics and as potential dielectrics for capacitors. In order to enable computational discovery of novel high-k dielectric materials, we propose a fitness model (energy storage density) that includes the dielectric constant, bandgap, and intrinsic breakdown field. This model, used as a fitness function in conjunction with first-principles calculations and the global optimization evolutionary algorithm USPEX, efficiently leads to practically important results. We found a number of high-fitness structures of SiO2 and HfO2, some of which correspond to known phases and some of which are new. The results allow us to propose characteristics (genes) common to high-fitness structures--these are the coordination polyhedra and their degree of distortion. Our variable-composition searches in the HfO2-SiO2 system uncovered several high-fitness states. This hybrid algorithm opens up a new avenue for discovering novel high-k dielectrics with both fixed and variable compositions, and will speed up the process of materials discovery.

Hybridization in a warmer world

PubMed Central

Chunco, Amanda J

2014-01-01

Climate change is profoundly affecting the evolutionary trajectory of individual species and ecological communities, in part through the creation of novel species assemblages. How climate change will influence competitive interactions has been an active area of research. Far less attention, however, has been given to altered reproductive interactions. Yet, reproductive interactions between formerly isolated species are inevitable as populations shift geographically and temporally as a result of climate change, potentially resulting in introgression, speciation, or even extinction. The susceptibility of hybridization rates to anthropogenic disturbance was first recognized in the 1930s. To date, work on anthropogenically mediated hybridization has focused primarily on either physical habitat disturbance or species invasion. Here, I review recent literature on hybridization to identify how ecological responses to climate change will increase the likelihood of hybridization via the dissolution of species barriers maintained by habitat, time, or behavior. Using this literature, I identify several cases where novel hybrid zones have recently formed, likely as a result of changing climate. Future research should focus on identifying areas and taxonomic groups where reproductive species interactions are most likely to be influenced by climate change. Furthermore, a better understanding of the evolutionary consequences of climate-mediated secondary contact is urgently needed. Paradoxically, hybridization is both a major conservation concern and an important source of novel genetic and phenotypic variation. Hybridization may therefore both contribute to increasing rates of extinction and stimulate the creation of novel phenotypes that will speed adaptation to novel climates. Predicting which result will occur following secondary contact will be an important contribution to conservation for many species. PMID:24963394

Inbreeding and outbreeding depression in Stylidium hispidum: implications for mixing seed sources for ecological restoration

PubMed Central

Hufford, Kristina M; Krauss, Siegfried L; Veneklaas, Erik J

2012-01-01

The benefits of composite rather than local seed provenances for ecological restoration have recently been argued, largely on the basis of maximizing evolutionary potential. However, these arguments have downplayed the potentially negative consequences of outbreeding depression once mixed provenances interbreed. In this study, we compared intraspecific F1 hybrid performance and molecular marker differentiation among four populations of Stylidium hispidum, a species endemic to Southwestern Australia. Multivariate ordination of 134 AFLP markers analyzed genetic structure and detected two clusters of paired sites that diverged significantly for marker variation along a latitudinal boundary. To test for outbreeding depression and to determine the consequences of molecular population divergence for hybrid fitness, we conducted controlled pollinations and studied germination and survival for three cross categories (within-population crosses, short- and long-distance F1 hybrids) for paired sites distributed within and between the two genetically differentiated regions. We found evidence of outbreeding depression in long-distance hybrids (111–124 km), and inbreeding depression among progeny of within-population crosses, relative to short-distance (3–10 km) hybrids, suggesting an intermediate optimal outcrossing distance in this species. These results are discussed in light of the evolutionary consequences of mixing seed sources for biodiversity restoration. PMID:23139884

Cytonuclear genetic architecture in mosquitofish populations and the possible roles of introgressive hybridization

USGS Publications Warehouse

Scribner, Kim T.; Avise, John C.

1993-01-01

Spatial genetic structure in populations of mosquitofish (Gambusia) sampled throughout the south-eastern United States was characterized using mitochondrial (mt) DNA and allozyme markers. Both sets of data revealed a pronounced genetic discontinuity (along a broad path extending from south-eastern Mississippi to north-eastern Georgia) that corresponds to a recently recognized distinction between the nominal forms G. affinis to the west and G. holbrookito the east. However, several populations from the general contact region exhibited unusual allelic associations in high frequency, suggestive of evolutionary processes within a zone of introgressive hybridization. These involve: (i) cytonuclear profiles representing combinations of nuclear and mitochondrial genotypes that tended to be more nearly species-specific and concordant elsewhere; and (ii) significant nuclear gametic disequilibria, perhaps attributable to positive assortative mating and/or differential fitnesses of homospecific vs. recombinant genotypes. However, outside this suspected hybrid region, ‘heterospecific’ genetic markers also appeared in low frequency, thus complicating interpretations. These discordant alleles on a broader geographic scale may reflect: (a) the retention of polymorphisms from an ancestral gene pool; (b) occasional evolutionary convergence (especially with respect to electrophoretic mobility of allozyme alleles); (c) the ‘footprints’ of a moving hybrid zone; or (d) differential introgressive penetrance across the current hybrid region.

How evolutionary crystal structure prediction works--and why.

PubMed

Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario

2011-03-15

Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an overall shape and explore their intrinsic dimensionalities. Because of the inverse relationships between order and energy and between the dimensionality and diversity of an ensemble of crystal structures, the chances that a random search will find the ground state decrease exponentially with increasing system size. A well-designed evolutionary algorithm allows for much greater computational efficiency. We illustrate the power of evolutionary CSP through applications that examine matter at high pressure, where new, unexpected phenomena take place. Evolutionary CSP has allowed researchers to make unexpected discoveries such as a transparent phase of sodium, a partially ionic form of boron, complex superconducting forms of calcium, a novel superhard allotrope of carbon, polymeric modifications of nitrogen, and a new class of compounds, perhydrides. These methods have also led to the discovery of novel hydride superconductors including the "impossible" LiH(n) (n=2, 6, 8) compounds, and CaLi(2). We discuss extensions of the method to molecular crystals, systems of variable composition, and the targeted optimization of specific physical properties. © 2011 American Chemical Society

The pachytene checkpoint and its relationship to evolutionary patterns of polyploidization and hybrid sterility.

PubMed

Li, X C; Barringer, B C; Barbash, D A

2009-01-01

Sterility is a commonly observed phenotype in interspecific hybrids. Sterility may result from chromosomal or genic incompatibilities, and much progress has been made toward understanding the genetic basis of hybrid sterility in various taxa. The underlying mechanisms causing hybrid sterility, however, are less well known. The pachytene checkpoint is a meiotic surveillance system that many organisms use to detect aberrant meiotic products, in order to prevent the production of defective gametes. We suggest that activation of the pachytene checkpoint may be an important mechanism contributing to two types of hybrid sterility. First, the pachytene checkpoint may form the mechanistic basis of some gene-based hybrid sterility phenotypes. Second, the pachytene checkpoint may be an important mechanism that mediates chromosomal-based hybrid sterility phenotypes involving gametes with non-haploid (either non-reduced or aneuploid) chromosome sets. Studies in several species suggest that the strength of the pachytene checkpoint is sexually dimorphic, observations that warrant future investigation into whether such variation may contribute to differences in patterns of sterility between male and female interspecific hybrids. In addition, plants seem to lack the pachytene checkpoint, which correlates with increased production of unreduced gametes and a higher incidence of polyploid species in plants versus animals. Although the pachytene checkpoint occurs in many animals and in fungi, at least some of the genes that execute the pachytene checkpoint are different among organisms. This finding suggests that the penetrance of the pachytene checkpoint, and even its presence or absence can evolve rapidly. The surprising degree of evolutionary flexibility in this meiotic surveillance system may contribute to the observed variation in patterns of hybrid sterility and in rates of polyploidization.

New yeasts-new brews: modern approaches to brewing yeast design and development.

PubMed

Gibson, B; Geertman, J-M A; Hittinger, C T; Krogerus, K; Libkind, D; Louis, E J; Magalhães, F; Sampaio, J P

2017-06-01

The brewing industry is experiencing a period of change and experimentation largely driven by customer demand for product diversity. This has coincided with a greater appreciation of the role of yeast in determining the character of beer and the widespread availability of powerful tools for yeast research. Genome analysis in particular has helped clarify the processes leading to domestication of brewing yeast and has identified domestication signatures that may be exploited for further yeast development. The functional properties of non-conventional yeast (both Saccharomyces and non-Saccharomyces) are being assessed with a view to creating beers with new flavours as well as producing flavoursome non-alcoholic beers. The discovery of the psychrotolerant S. eubayanus has stimulated research on de novo S. cerevisiae × S. eubayanus hybrids for low-temperature lager brewing and has led to renewed interest in the functional importance of hybrid organisms and the mechanisms that determine hybrid genome function and stability. The greater diversity of yeast that can be applied in brewing, along with an improved understanding of yeasts' evolutionary history and biology, is expected to have a significant and direct impact on the brewing industry, with potential for improved brewing efficiency, product diversity and, above all, customer satisfaction. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation.

PubMed

Marino, I A M; Benazzo, A; Agostini, C; Mezzavilla, M; Hoban, S M; Patarnello, T; Zane, L; Bertorelle, G

2013-10-01

Determining the timing, extent and underlying causes of interspecific gene exchange during or following speciation is central to understanding species' evolution. Antarctic notothenioid fish, thanks to the acquisition of antifreeze glycoproteins during Oligocene transition to polar conditions, experienced a spectacular radiation to >100 species during Late Miocene cooling events. The impact of recent glacial cycles on this group is poorly known, but alternating warming and cooling periods may have affected species' distributions, promoted ecological divergence into recurrently opening niches and/or possibly brought allopatric species into contact. Using microsatellite markers and statistical methods including Approximate Bayesian Computation, we investigated genetic differentiation, hybridization and the possible influence of the last glaciation/deglaciation events in three icefish species of the genus Chionodraco. Our results provide strong evidence of contemporary and past introgression by showing that: (i) a substantial fraction of contemporary individuals in each species has mixed ancestry, (ii) evolutionary scenarios excluding hybridization or including it only in ancient times have small or zero posterior probabilities, (iii) the data support a scenario of interspecific gene flow associated with the two most recent interglacial periods. Glacial cycles might therefore have had a profound impact on the genetic composition of Antarctic fauna, as newly available shelf areas during the warmer intervals might have favoured secondary contacts and hybridization between diversified groups. If our findings are confirmed in other notothenioids, they offer new perspectives for understanding evolutionary dynamics of Antarctic fish and suggest a need for new predictions on the effects of global warming in this group. © 2013 John Wiley & Sons Ltd.

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.

Hybrid Genetic Agorithms and Line Search Method for Industrial Production Planning with Non-Linear Fitness Function

NASA Astrophysics Data System (ADS)

Vasant, Pandian; Barsoum, Nader

2008-10-01

Many engineering, science, information technology and management optimization problems can be considered as non linear programming real world problems where the all or some of the parameters and variables involved are uncertain in nature. These can only be quantified using intelligent computational techniques such as evolutionary computation and fuzzy logic. The main objective of this research paper is to solve non linear fuzzy optimization problem where the technological coefficient in the constraints involved are fuzzy numbers which was represented by logistic membership functions by using hybrid evolutionary optimization approach. To explore the applicability of the present study a numerical example is considered to determine the production planning for the decision variables and profit of the company.

EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments.

PubMed

Milewski, Marek C; Kamel, Karol; Kurzynska-Kokorniak, Anna; Chmielewski, Marcin K; Figlerowicz, Marek

2017-10-01

Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. The software applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions. To provide optimal solutions, the evolutionary algorithm sorts oligonucleotides into sets, preserves preselected parts of the oligonucleotides, and shapes their remaining parts. In addition, the oligonucleotide sets can be designed and grouped based on their melting temperatures. For the user's convenience, EvOligo is provided with a user-friendly graphical interface. EvOligo was used to design individual oligonucleotides, oligonucleotide pairs, and groups of oligonucleotide pairs that are characterized by the following parameters: (1) weaker cross-interactions between the non-complementary oligonucleotides and (2) more uniform ranges of the oligonucleotide pair melting temperatures than other available software products. In addition, in contrast to other grouping algorithms, EvOligo offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user.

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.

Multi-objective AGV scheduling in an FMS using a hybrid of genetic algorithm and particle swarm optimization.

PubMed

Mousavi, Maryam; Yap, Hwa Jen; Musa, Siti Nurmaya; Tahriri, Farzad; Md Dawal, Siti Zawiah

2017-01-01

Flexible manufacturing system (FMS) enhances the firm's flexibility and responsiveness to the ever-changing customer demand by providing a fast product diversification capability. Performance of an FMS is highly dependent upon the accuracy of scheduling policy for the components of the system, such as automated guided vehicles (AGVs). An AGV as a mobile robot provides remarkable industrial capabilities for material and goods transportation within a manufacturing facility or a warehouse. Allocating AGVs to tasks, while considering the cost and time of operations, defines the AGV scheduling process. Multi-objective scheduling of AGVs, unlike single objective practices, is a complex and combinatorial process. In the main draw of the research, a mathematical model was developed and integrated with evolutionary algorithms (genetic algorithm (GA), particle swarm optimization (PSO), and hybrid GA-PSO) to optimize the task scheduling of AGVs with the objectives of minimizing makespan and number of AGVs while considering the AGVs' battery charge. Assessment of the numerical examples' scheduling before and after the optimization proved the applicability of all the three algorithms in decreasing the makespan and AGV numbers. The hybrid GA-PSO produced the optimum result and outperformed the other two algorithms, in which the mean of AGVs operation efficiency was found to be 69.4, 74, and 79.8 percent in PSO, GA, and hybrid GA-PSO, respectively. Evaluation and validation of the model was performed by simulation via Flexsim software.

Multi-objective AGV scheduling in an FMS using a hybrid of genetic algorithm and particle swarm optimization

PubMed Central

Yap, Hwa Jen; Musa, Siti Nurmaya; Tahriri, Farzad; Md Dawal, Siti Zawiah

2017-01-01

Flexible manufacturing system (FMS) enhances the firm’s flexibility and responsiveness to the ever-changing customer demand by providing a fast product diversification capability. Performance of an FMS is highly dependent upon the accuracy of scheduling policy for the components of the system, such as automated guided vehicles (AGVs). An AGV as a mobile robot provides remarkable industrial capabilities for material and goods transportation within a manufacturing facility or a warehouse. Allocating AGVs to tasks, while considering the cost and time of operations, defines the AGV scheduling process. Multi-objective scheduling of AGVs, unlike single objective practices, is a complex and combinatorial process. In the main draw of the research, a mathematical model was developed and integrated with evolutionary algorithms (genetic algorithm (GA), particle swarm optimization (PSO), and hybrid GA-PSO) to optimize the task scheduling of AGVs with the objectives of minimizing makespan and number of AGVs while considering the AGVs’ battery charge. Assessment of the numerical examples’ scheduling before and after the optimization proved the applicability of all the three algorithms in decreasing the makespan and AGV numbers. The hybrid GA-PSO produced the optimum result and outperformed the other two algorithms, in which the mean of AGVs operation efficiency was found to be 69.4, 74, and 79.8 percent in PSO, GA, and hybrid GA-PSO, respectively. Evaluation and validation of the model was performed by simulation via Flexsim software. PMID:28263994

Hybridization and differential introgression associated with environmental shifts in a mistletoe species complex.

PubMed

Baena-Díaz, Fernanda; Ramírez-Barahona, Santiago; Ornelas, Juan Francisco

2018-04-03

Host specialization after host shifting is traditionally viewed as the pathway to speciation in parasitic plants. However, geographical and environmental changes can also influence parasite speciation, through hybridization processes. Here we investigated the impact of past climatic fluctuations, environment, and host shifts on the genetic structure and patterns of hybridization and gene flow between Psittacanthus calyculatus and P. schiedeanus, a Mesoamerican species complex. Using microsatellites (408 individuals), we document moderate genetic diversity but high genetic differentiation between widespread parental clusters, calyculatus in dry pine-oak forests and schiedeanus in cloud forests. Bayesian analyses identified a third cluster, with admixture between parental clusters in areas of xeric and tropical dry forests and high levels of migration rates following secondary contact. Coincidently host associations in these areas differ from those in areas of parental species, suggesting that past hybridization played a role in environmental and host shifts. Overall, the observed genetic and geographic patterns suggest that these Psittacanthus populations could have entered a distinct evolutionary pathway. The results provide evidence for highlights on the importance of the Pleistocene climate changes, habitat differences, and potential host shifts in the evolutionary history of Neotropical mistletoes.

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

PubMed Central

Yu, Yun; Degnan, James H.; Nakhleh, Luay

2012-01-01

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. PMID:22536161

Nonrandom patterns of genetic admixture expose the complex historical hybrid origin of unisexual leaf beetle species in the genus Calligrapha.

PubMed

Montelongo, Tinguaro; Gómez-Zurita, Jesús

2015-01-01

Many unisexual animal lineages supposedly arose from hybridization. However, support for their putative hybrid origins mostly comes from indirect methodologies, which are rarely confirmatory. Here we provide compelling data indicating that tetraploid unisexual Calligrapha are true genetic mosaics obtained via analysis of mitochondrial DNA (mtDNA) and allelic variation and coalescence times for three single-copy nuclear genes (CPS, HARS, and Wg) in five of six unisexual Calligrapha and a representative sample of bisexual species. Nuclear allelic diversity in unisexuals consistently segregates in the gene pools of at least two but up to three divergent bisexual species, interpreted as putative parentals of interspecific hybridization crosses. Interestingly, their mtDNA diversity derives from an additional yet undiscovered older evolutionary lineage that is possibly the same for all independently originated unisexual species. One possibly extinct species transferred its mtDNA to several evolutionary lineages in a wave of hybridization events during the Pliocene, whereby descendant species retained a polymorphic mtDNA constitution. Recent hybridizations, in the Pleistocene and always involving females with the old introgressed mtDNA, seemingly occurred in the lineages leading to unisexual species, decoupling mtDNA introgression (and inferences derived from these data, such as timing and parentage) from subsequent acquisition of the new reproductive mode. These results illuminate an unexpected complexity in possible routes to animal unisexuality, with implications for the interpretation of ancient unisexuality. If the origin of unisexuality requires a mechanism where (1) hybridization is a necessary but insufficient condition and (2) multiple bouts of hybridization involving more than two divergent lineages are required, then the origins of several classical unisexual systems may have to be reassessed.

Efficient feature selection using a hybrid algorithm for the task of epileptic seizure detection

NASA Astrophysics Data System (ADS)

Lai, Kee Huong; Zainuddin, Zarita; Ong, Pauline

2014-07-01

Feature selection is a very important aspect in the field of machine learning. It entails the search of an optimal subset from a very large data set with high dimensional feature space. Apart from eliminating redundant features and reducing computational cost, a good selection of feature also leads to higher prediction and classification accuracy. In this paper, an efficient feature selection technique is introduced in the task of epileptic seizure detection. The raw data are electroencephalography (EEG) signals. Using discrete wavelet transform, the biomedical signals were decomposed into several sets of wavelet coefficients. To reduce the dimension of these wavelet coefficients, a feature selection method that combines the strength of both filter and wrapper methods is proposed. Principal component analysis (PCA) is used as part of the filter method. As for wrapper method, the evolutionary harmony search (HS) algorithm is employed. This metaheuristic method aims at finding the best discriminating set of features from the original data. The obtained features were then used as input for an automated classifier, namely wavelet neural networks (WNNs). The WNNs model was trained to perform a binary classification task, that is, to determine whether a given EEG signal was normal or epileptic. For comparison purposes, different sets of features were also used as input. Simulation results showed that the WNNs that used the features chosen by the hybrid algorithm achieved the highest overall classification accuracy.

Effects of Hybridization and Evolutionary Constraints on Secondary Metabolites: The Genetic Architecture of Phenylpropanoids in European Populus Species

PubMed Central

Caseys, Celine; Stritt, Christoph; Glauser, Gaetan; Blanchard, Thierry; Lexer, Christian

2015-01-01

The mechanisms responsible for the origin, maintenance and evolution of plant secondary metabolite diversity remain largely unknown. Decades of phenotypic studies suggest hybridization as a key player in generating chemical diversity in plants. Knowledge of the genetic architecture and selective constraints of phytochemical traits is key to understanding the effects of hybridization on plant chemical diversity and ecological interactions. Using the European Populus species P. alba (White poplar) and P. tremula (European aspen) and their hybrids as a model, we examined levels of inter- and intraspecific variation, heritabilities, phenotypic correlations, and the genetic architecture of 38 compounds of the phenylpropanoid pathway measured by liquid chromatography and mass spectrometry (UHPLC-MS). We detected 41 quantitative trait loci (QTL) for chlorogenic acids, salicinoids and flavonoids by genetic mapping in natural hybrid crosses. We show that these three branches of the phenylpropanoid pathway exhibit different geographic patterns of variation, heritabilities, and genetic architectures, and that they are affected differently by hybridization and evolutionary constraints. Flavonoid abundances present high species specificity, clear geographic structure, and strong genetic determination, contrary to salicinoids and chlorogenic acids. Salicinoids, which represent important defence compounds in Salicaceae, exhibited pronounced genetic correlations on the QTL map. Our results suggest that interspecific phytochemical differentiation is concentrated in downstream sections of the phenylpropanoid pathway. In particular, our data point to glycosyltransferase enzymes as likely targets of rapid evolution and interspecific differentiation in the ‘model forest tree’ Populus. PMID:26010156

Effects of hybridization and evolutionary constraints on secondary metabolites: the genetic architecture of phenylpropanoids in European populus species.

PubMed

Caseys, Celine; Stritt, Christoph; Glauser, Gaetan; Blanchard, Thierry; Lexer, Christian

2015-01-01

The mechanisms responsible for the origin, maintenance and evolution of plant secondary metabolite diversity remain largely unknown. Decades of phenotypic studies suggest hybridization as a key player in generating chemical diversity in plants. Knowledge of the genetic architecture and selective constraints of phytochemical traits is key to understanding the effects of hybridization on plant chemical diversity and ecological interactions. Using the European Populus species P. alba (White poplar) and P. tremula (European aspen) and their hybrids as a model, we examined levels of inter- and intraspecific variation, heritabilities, phenotypic correlations, and the genetic architecture of 38 compounds of the phenylpropanoid pathway measured by liquid chromatography and mass spectrometry (UHPLC-MS). We detected 41 quantitative trait loci (QTL) for chlorogenic acids, salicinoids and flavonoids by genetic mapping in natural hybrid crosses. We show that these three branches of the phenylpropanoid pathway exhibit different geographic patterns of variation, heritabilities, and genetic architectures, and that they are affected differently by hybridization and evolutionary constraints. Flavonoid abundances present high species specificity, clear geographic structure, and strong genetic determination, contrary to salicinoids and chlorogenic acids. Salicinoids, which represent important defence compounds in Salicaceae, exhibited pronounced genetic correlations on the QTL map. Our results suggest that interspecific phytochemical differentiation is concentrated in downstream sections of the phenylpropanoid pathway. In particular, our data point to glycosyltransferase enzymes as likely targets of rapid evolution and interspecific differentiation in the 'model forest tree' Populus.

Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers in Arabidopsis thaliana

PubMed Central

Simon, Matthieu; Durand, Stéphanie; Pluta, Natacha; Gobron, Nicolas; Botran, Lucy; Ricou, Anthony; Camilleri, Christine; Budar, Françoise

2016-01-01

Species differentiation and the underlying genetics of reproductive isolation are central topics in evolutionary biology. Hybrid sterility is one kind of reproductive barrier that can lead to differentiation between species. Here, we analyze the complex genetic basis of the intraspecific hybrid male sterility that occurs in the offspring of two distant natural strains of Arabidopsis thaliana, Shahdara and Mr-0, with Shahdara as the female parent. Using both classical and quantitative genetic approaches as well as cytological observation of pollen viability, we demonstrate that this particular hybrid sterility results from two causes of pollen mortality. First, the Shahdara cytoplasm induces gametophytic cytoplasmic male sterility (CMS) controlled by several nuclear loci. Second, several segregation distorters leading to allele-specific pollen abortion (pollen killers) operate in hybrids with either cytoplasm. The complete sterility of the hybrid with the Shahdara cytoplasm results from the genetic linkage of the two causes of pollen mortality, i.e., CMS nuclear determinants and pollen killers. Furthermore, natural variation at these loci in A. thaliana is associated with different male-sterility phenotypes in intraspecific hybrids. Our results suggest that the genomic conflicts that underlie segregation distorters and CMS can concurrently lead to reproductive barriers between distant strains within a species. This study provides a new framework for identifying molecular mechanisms and the evolutionary history of loci that contribute to reproductive isolation, and possibly to speciation. It also suggests that two types of genomic conflicts, CMS and segregation distorters, may coevolve in natural populations. PMID:27182945

Multi-Objective and Multidisciplinary Design Optimisation (MDO) of UAV Systems using Hierarchical Asynchronous Parallel Evolutionary Algorithms

DTIC Science & Technology

2007-09-17

been proposed; these include a combination of variable fidelity models, parallelisation strategies and hybridisation techniques (Coello, Veldhuizen et...Coello et al (Coello, Veldhuizen et al. 2002). 4.4.2 HIERARCHICAL POPULATION TOPOLOGY A hierarchical population topology, when integrated into...to hybrid parallel Multi-Objective Evolutionary Algorithms (pMOEA) (Cantu-Paz 2000; Veldhuizen , Zydallis et al. 2003); it uses a master slave

Inferring explicit weighted consensus networks to represent alternative evolutionary histories

PubMed Central

2013-01-01

Background The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species evolutionary history by causing discordance among phylogenies inferred from different genes. Methods To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny. Results We provide a way of building a weighted phylogenetic network for each of the following reticulation mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species. Conclusions Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks. PMID:24359207

A hybrid genetic algorithm-queuing multi-compartment model for optimizing inpatient bed occupancy and associated costs.

PubMed

Belciug, Smaranda; Gorunescu, Florin

2016-03-01

Explore how efficient intelligent decision support systems, both easily understandable and straightforwardly implemented, can help modern hospital managers to optimize both bed occupancy and utilization costs. This paper proposes a hybrid genetic algorithm-queuing multi-compartment model for the patient flow in hospitals. A finite capacity queuing model with phase-type service distribution is combined with a compartmental model, and an associated cost model is set up. An evolutionary-based approach is used for enhancing the ability to optimize both bed management and associated costs. In addition, a "What-if analysis" shows how changing the model parameters could improve performance while controlling costs. The study uses bed-occupancy data collected at the Department of Geriatric Medicine - St. George's Hospital, London, period 1969-1984, and January 2000. The hybrid model revealed that a bed-occupancy exceeding 91%, implying a patient rejection rate around 1.1%, can be carried out with 159 beds plus 8 unstaffed beds. The same holding and penalty costs, but significantly different bed allocations (156 vs. 184 staffed beds, and 8 vs. 9 unstaffed beds, respectively) will result in significantly different costs (£755 vs. £1172). Moreover, once the arrival rate exceeds 7 patient/day, the costs associated to the finite capacity system become significantly smaller than those associated to an Erlang B queuing model (£134 vs. £947). Encoding the whole information provided by both the queuing system and the cost model through chromosomes, the genetic algorithm represents an efficient tool in optimizing the bed allocation and associated costs. The methodology can be extended to different medical departments with minor modifications in structure and parameterization. Copyright © 2016 Elsevier B.V. All rights reserved.

Neo-sex chromosome inheritance across species in Silene hybrids.

PubMed

Weingartner, L A; Delph, L F

2014-07-01

Neo-sex chromosomes, which form through the major restructuring of ancestral sex chromosome systems, have evolved in various taxa. Such restructuring often consists of the fusion of an autosome to an existing sex chromosome, resulting in novel sex chromosome formations (e.g. X1X2Y or XY1Y2.). Comparative studies are often made between restructured sex chromosome systems of closely related species, and here we evaluate the consequences of variable sex chromosome systems to hybrids. If neo-sex chromosomes are improperly inherited across species, this could lead to aberrant development and reproductive isolation. In this study, we examine the fate of neo-sex chromosomes in hybrids of the flowering plants Silene diclinis and Silene latifolia. Silene diclinis has a neo-sex chromosome system (XY1Y2) that is thought to have evolved from an ancestral XY system that is still present in S. latifolia. These species do not hybridize naturally, and improper sex chromosome inheritance could contribute to reproductive isolation. We investigated whether this major restructuring of sex chromosomes prevents their proper inheritance in a variety of hybrid crosses, including some F2 - and later-generation hybrids, with sex chromosome-linked, species-specific, polymorphic markers and chromosome squashes. We discovered that despite the differences in sex chromosomes that exist between these two species, proper segregation had occurred in hybrids that made it to flowering, including later-generation hybrids, indicating that neo-sex chromosome formation alone does not result in complete reproductive isolation between these two species. Additionally, hybrids with aberrant sex expression (e.g. neuter, hermaphrodite) also inherited the restructured sex chromosomes properly, highlighting that issues with sexual development in hybrids can be caused by intrinsic genetic incompatibility rather than improper sex chromosome inheritance. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Adaptive Peircean decision aid project summary assessments.

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

Senglaub, Michael E.

2007-01-01

This efforts objective was to identify and hybridize a suite of technologies enabling the development of predictive decision aids for use principally in combat environments but also in any complex information terrain. The technologies required included formal concept analysis for knowledge representation and information operations, Peircean reasoning to support hypothesis generation, Mill's's canons to begin defining information operators that support the first two technologies and co-evolutionary game theory to provide the environment/domain to assess predictions from the reasoning engines. The intended application domain is the IED problem because of its inherent evolutionary nature. While a fully functioning integrated algorithm wasmore » not achieved the hybridization and demonstration of the technologies was accomplished and demonstration of utility provided for a number of ancillary queries.« less

Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia.

PubMed

Hoang, Phuong T N; Schubert, Ingo

2017-12-01

The monophyletic duckweeds comprising five genera within the monocot order Alismatales are neotenic, free-floating, aquatic organisms with fast vegetative propagation. Some species are considered for efficient biomass production, for life stock feeding, and for (simultaneous) wastewater phytoremediation. The ancestral genus Spirodela consists of only two species, Spirodela polyrhiza and Spirodela intermedia, both with a similar small genome (~160 Mbp/1C). Reference genome drafts and a physical map of 96 BACs on the 20 chromosome pairs of S. polyrhiza strain 7498 are available and provide useful tools for further evolutionary studies within and between duckweed genera. Here we applied sequential comparative multicolor fluorescence in situ hybridization (mcFISH) to address homeologous chromosomes in S. intermedia (2n = 36), to detect chromosome rearrangements between both species and to elucidate the mechanisms which may have led to the chromosome number alteration after their evolutionary separation. Ten chromosome pairs proved to be conserved between S. polyrhiza and S. intermedia, the remaining ones experienced, depending on the assumed direction of evolution, translocations, inversion, and fissions, respectively. These results represent a first step to unravel karyotype evolution among duckweeds and are anchor points for future genome assembly of S. intermedia.

A Philosophical Perspective on Evolutionary Systems Biology

PubMed Central

Soyer, Orkun S.; Siegal, Mark L.

2015-01-01

Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB’s progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology. PMID:26085823

New lager yeast strains generated by interspecific hybridization.

PubMed

Krogerus, Kristoffer; Magalhães, Frederico; Vidgren, Virve; Gibson, Brian

2015-05-01

The interspecific hybrid Saccharomyces pastorianus is the most commonly used yeast in brewery fermentations worldwide. Here, we generated de novo lager yeast hybrids by mating a domesticated and strongly flocculent Saccharomyces cerevisiae ale strain with the Saccharomyces eubayanus type strain. The hybrids were characterized with respect to the parent strains in a wort fermentation performed at temperatures typical for lager brewing (12 °C). The resulting beers were analysed for sugar and aroma compounds, while the yeasts were tested for their flocculation ability and α-glucoside transport capability. These hybrids inherited beneficial properties from both parent strains (cryotolerance, maltotriose utilization and strong flocculation) and showed apparent hybrid vigour, fermenting faster and producing beer with higher alcohol content (5.6 vs 4.5 % ABV) than the parents. Results suggest that interspecific hybridization is suitable for production of novel non-GM lager yeast strains with unique properties and will help in elucidating the evolutionary history of industrial lager yeast.

ANDROGENETICS AND TRIPLOIDS FROM AN INTERACTING PARTHENOGENETIC HYBRID AND ITS ANCESTORS IN STICK INSECTS.

PubMed

Tinti, Fausto; Scali, Valerio

1996-06-01

Populations of unisexual organisms are often assumed to be genetically invariant (clones) and destined to a short existence on an evolutionary timescale. Unisexual organisms are most often obligate parthenogens and, by definition, ought to be completely isolated reproductively from related bisexual organisms. The assumption of complete reproductive isolation between amphimictic ancestors and thelytokous hybrids is common to most hypotheses on the evolution of sex and its adaptive significance. Stick insects of the genus Bacillus however provide evidence for reproductive interactions between allodiploid parthenogens and their ancestors, because pure species progeny (androgenetics) and triploid descendants are produced. These findings demonstrate that, through androgenesis, offspring of parthenogenetic hybrid females can contribute specimens of both sexes to the fathering species when fertilized by syntopic ancestral males and the parthenogenetic egg of strictly clonal females, when fertilized, allows a third genome to be added to the allodiploid chromosome set. These triploid genomes promote further genetic diversification and evolution of the unisexual populations through the formation of new clones by recombination during the changed maturation mode of allotriploid eggs. All this argues for much more complex breeding systems and evolutionary pathways than are usually assumed for hybrid unisexual organisms. © 1996 The Society for the Study of Evolution.

Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers in Arabidopsis thaliana.

PubMed

Simon, Matthieu; Durand, Stéphanie; Pluta, Natacha; Gobron, Nicolas; Botran, Lucy; Ricou, Anthony; Camilleri, Christine; Budar, Françoise

2016-07-01

Species differentiation and the underlying genetics of reproductive isolation are central topics in evolutionary biology. Hybrid sterility is one kind of reproductive barrier that can lead to differentiation between species. Here, we analyze the complex genetic basis of the intraspecific hybrid male sterility that occurs in the offspring of two distant natural strains of Arabidopsis thaliana, Shahdara and Mr-0, with Shahdara as the female parent. Using both classical and quantitative genetic approaches as well as cytological observation of pollen viability, we demonstrate that this particular hybrid sterility results from two causes of pollen mortality. First, the Shahdara cytoplasm induces gametophytic cytoplasmic male sterility (CMS) controlled by several nuclear loci. Second, several segregation distorters leading to allele-specific pollen abortion (pollen killers) operate in hybrids with either cytoplasm. The complete sterility of the hybrid with the Shahdara cytoplasm results from the genetic linkage of the two causes of pollen mortality, i.e., CMS nuclear determinants and pollen killers. Furthermore, natural variation at these loci in A. thaliana is associated with different male-sterility phenotypes in intraspecific hybrids. Our results suggest that the genomic conflicts that underlie segregation distorters and CMS can concurrently lead to reproductive barriers between distant strains within a species. This study provides a new framework for identifying molecular mechanisms and the evolutionary history of loci that contribute to reproductive isolation, and possibly to speciation. It also suggests that two types of genomic conflicts, CMS and segregation distorters, may coevolve in natural populations. Copyright © 2016 by the Genetics Society of America.

Improving HybrID: How to best combine indirect and direct encoding in evolutionary algorithms.

PubMed

Helms, Lucas; Clune, Jeff

2017-01-01

Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot exploit regularity. An algorithm called HybrID combines the best of both: it first evolves with indirect encoding to exploit problem regularity, then switches to direct encoding to handle problem irregularity. While HybrID has been shown to outperform both indirect and direct encoding, its initial implementation required the manual specification of when to switch from indirect to direct encoding. In this paper, we test two new methods to improve HybrID by eliminating the need to manually specify this parameter. Auto-Switch-HybrID automatically switches from indirect to direct encoding when fitness stagnates. Offset-HybrID simultaneously evolves an indirect encoding with directly encoded offsets, eliminating the need to switch. We compare the original HybrID to these alternatives on three different problems with adjustable regularity. The results show that both Auto-Switch-HybrID and Offset-HybrID outperform the original HybrID on different types of problems, and thus offer more tools for researchers to solve challenging problems. The Offset-HybrID algorithm is particularly interesting because it suggests a path forward for automatically and simultaneously combining the best traits of indirect and direct encoding.

Bursts of transposable elements as an evolutionary driving force.

PubMed

Belyayev, A

2014-12-01

A burst of transposable elements (TEs) is a massive outbreak that may cause radical genomic rebuilding. This phenomenon has been reported in connection with the formation of taxonomic groups and species and has therefore been associated with major evolutionary events in the past. Over the past few years, several research groups have discovered recent stress-induced bursts of different TEs. The events for which bursts of TEs have been recorded include domestication, polyploidy, changes in mating systems, interspecific and intergeneric hybridization and abiotic stress. Cases involving abiotic stress, particularly bursts of TEs in natural populations driven by environmental change, are of special interest because this phenomenon may underlie micro- and macro-evolutionary events and ultimately support the maintenance and generation of biological diversity. This study reviews the known cases of bursts of TEs and their possible consequences, with particular emphasis on the speciation process. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Early events in speciation: Polymorphism for hybrid male sterility in Drosophila

PubMed Central

Reed, Laura K.; Markow, Therese A.

2004-01-01

Capturing the process of speciation early enough to determine the initial genetic causes of reproductive isolation remains a major challenge in evolutionary biology. We have found, to our knowledge, the first example of substantial intraspecific polymorphism for genetic factors contributing to hybrid male sterility. Specifically, we show that the occurrence of hybrid male sterility in crosses between Drosophila mojavensis and its sister species, Drosophila arizonae, is controlled by factors present at different frequencies in different populations of D. mojavensis. In addition, we show that hybrid male sterility is a complex phenotype; some hybrid males with motile sperm still cannot sire offspring. Because male sterility factors in hybrids between these species are not yet fixed within D. mojavensis, this system provides an invaluable opportunity to characterize the genetics of reproductive isolation at an early stage. PMID:15184657

Early events in speciation: polymorphism for hybrid male sterility in Drosophila.

PubMed

Reed, Laura K; Markow, Therese A

2004-06-15

Capturing the process of speciation early enough to determine the initial genetic causes of reproductive isolation remains a major challenge in evolutionary biology. We have found, to our knowledge, the first example of substantial intraspecific polymorphism for genetic factors contributing to hybrid male sterility. Specifically, we show that the occurrence of hybrid male sterility in crosses between Drosophila mojavensis and its sister species, Drosophila arizonae, is controlled by factors present at different frequencies in different populations of D. mojavensis. In addition, we show that hybrid male sterility is a complex phenotype; some hybrid males with motile sperm still cannot sire offspring. Because male sterility factors in hybrids between these species are not yet fixed within D. mojavensis, this system provides an invaluable opportunity to characterize the genetics of reproductive isolation at an early stage.

Is the Red Wolf a Listable Unit Under the US Endangered Species Act?

PubMed

Waples, Robin S; Kays, Roland; Fredrickson, Richard J; Pacifici, Krishna; Mills, L Scott

2018-06-08

Defining units that can be afforded legal protection is a crucial, albeit challenging, step in conservation planning. As we illustrate with a case study of the red wolf (Canis rufus) from the southeastern United States, this step is especially complex when the evolutionary history of the focal taxon is uncertain. The US Endangered Species Act (ESA) allows listing of species, subspecies, or Distinct Population Segments (DPSs) of vertebrates. Red wolves were listed as an endangered species in 1973, and their status remains precarious. However, some recent genetic studies suggest that red wolves are part of a small wolf species (C. lycaon) specialized for heavily forested habitats of eastern North America, whereas other authors suggest that red wolves arose, perhaps within the last ~400 years, through hybridization between gray wolves (C. lupus) and coyotes (C. latrans). Using published genetic, morphological, behavioral, and ecological data, we evaluated whether each evolutionary hypothesis would lead to a listable unit for red wolves. Although the potential hybrid origin of red wolves, combined with abundant evidence for recent hybridization with coyotes, raises questions about status as a separate species or subspecies, we conclude that under any proposed evolutionary scenario red wolves meet both criteria to be considered a DPS: they are discrete compared with other conspecific populations, and they are Significant to the taxon to which they belong. As population-level units can qualify for legal protection under endangered-species legislation in many countries throughout the world, this general approach could potentially be applied more broadly.

"Bringing Taxonomy to the Service of Genetics": Edgar Anderson and Introgressive Hybridization.

PubMed

Kleinman, Kim

2016-12-01

In introgressive hybridization (the repeated backcrossing of hybrids with parental populations), Edgar Anderson found a source for variation upon which natural selection could work. In his 1953 review article "Introgressive Hybridization," he asserted that he was "bringing taxonomy to the service of genetics" whereas distinguished colleagues such as Theodosius Dobzhansky and Ernst Mayr did the precise opposite. His work as a geneticist particularly focused on linkage and recombination and was enriched by collaborations with Missouri Botanical Garden colleagues interested in taxonomy as well as with cytologists C.D. Darlington and Karl Sax. As the culmination of a biosystemtatic research program, Anderson's views challenged the mainstream of the Evolutionary Synthesis.

Phylogenetic comparative methods on phylogenetic networks with reticulations.

PubMed

Bastide, Paul; Solís-Lemus, Claudia; Kriebel, Ricardo; Sparks, K William; Ané, Cécile

2018-04-25

The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

GALAXY: A new hybrid MOEA for the optimal design of Water Distribution Systems

NASA Astrophysics Data System (ADS)

Wang, Q.; Savić, D. A.; Kapelan, Z.

2017-03-01

A new hybrid optimizer, called genetically adaptive leaping algorithm for approximation and diversity (GALAXY), is proposed for dealing with the discrete, combinatorial, multiobjective design of Water Distribution Systems (WDSs), which is NP-hard and computationally intensive. The merit of GALAXY is its ability to alleviate to a great extent the parameterization issue and the high computational overhead. It follows the generational framework of Multiobjective Evolutionary Algorithms (MOEAs) and includes six search operators and several important strategies. These operators are selected based on their leaping ability in the objective space from the global and local search perspectives. These strategies steer the optimization and balance the exploration and exploitation aspects simultaneously. A highlighted feature of GALAXY lies in the fact that it eliminates majority of parameters, thus being robust and easy-to-use. The comparative studies between GALAXY and three representative MOEAs on five benchmark WDS design problems confirm its competitiveness. GALAXY can identify better converged and distributed boundary solutions efficiently and consistently, indicating a much more balanced capability between the global and local search. Moreover, its advantages over other MOEAs become more substantial as the complexity of the design problem increases.

Mobile DNA and evolution in the 21st century

PubMed Central

2010-01-01

Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW) memory system rather than an organism blueprint. Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings (WGDs). The natural genetic engineering functions that mediate genome restructuring are activated by multiple stimuli, in particular by events similar to those found in the DNA record: microbial infection and interspecific hybridization leading to the formation of allotetraploids. These molecular genetic discoveries, plus a consideration of how mobile DNA rearrangements increase the efficiency of generating functional genomic novelties, make it possible to formulate a 21st century view of interactive evolutionary processes. This view integrates contemporary knowledge of the molecular basis of genetic change, major genome events in evolution, and stimuli that activate DNA restructuring with classical cytogenetic understanding about the role of hybridization in species diversification. PMID:20226073

Hybrid incompatibility arises in a sequence-based bioenergetic model of transcription factor binding.

PubMed

Tulchinsky, Alexander Y; Johnson, Norman A; Watt, Ward B; Porter, Adam H

2014-11-01

Postzygotic isolation between incipient species results from the accumulation of incompatibilities that arise as a consequence of genetic divergence. When phenotypes are determined by regulatory interactions, hybrid incompatibility can evolve even as a consequence of parallel adaptation in parental populations because interacting genes can produce the same phenotype through incompatible allelic combinations. We explore the evolutionary conditions that promote and constrain hybrid incompatibility in regulatory networks using a bioenergetic model (combining thermodynamics and kinetics) of transcriptional regulation, considering the bioenergetic basis of molecular interactions between transcription factors (TFs) and their binding sites. The bioenergetic parameters consider the free energy of formation of the bond between the TF and its binding site and the availability of TFs in the intracellular environment. Together these determine fractional occupancy of the TF on the promoter site, the degree of subsequent gene expression and in diploids, and the degree of dominance among allelic interactions. This results in a sigmoid genotype-phenotype map and fitness landscape, with the details of the shape determining the degree of bioenergetic evolutionary constraint on hybrid incompatibility. Using individual-based simulations, we subjected two allopatric populations to parallel directional or stabilizing selection. Misregulation of hybrid gene expression occurred under either type of selection, although it evolved faster under directional selection. Under directional selection, the extent of hybrid incompatibility increased with the slope of the genotype-phenotype map near the derived parental expression level. Under stabilizing selection, hybrid incompatibility arose from compensatory mutations and was greater when the bioenergetic properties of the interaction caused the space of nearly neutral genotypes around the stable expression level to be wide. F2's showed higher hybrid incompatibility than F1's to the extent that the bioenergetic properties favored dominant regulatory interactions. The present model is a mechanistically explicit case of the Bateson-Dobzhansky-Muller model, connecting environmental selective pressure to hybrid incompatibility through the molecular mechanism of regulatory divergence. The bioenergetic parameters that determine expression represent measurable properties of transcriptional regulation, providing a predictive framework for empirical studies of how phenotypic evolution results in epistatic incompatibility at the molecular level in hybrids. Copyright © 2014 by the Genetics Society of America.

Improving HybrID: How to best combine indirect and direct encoding in evolutionary algorithms

PubMed Central

Helms, Lucas; Clune, Jeff

2017-01-01

Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot exploit regularity. An algorithm called HybrID combines the best of both: it first evolves with indirect encoding to exploit problem regularity, then switches to direct encoding to handle problem irregularity. While HybrID has been shown to outperform both indirect and direct encoding, its initial implementation required the manual specification of when to switch from indirect to direct encoding. In this paper, we test two new methods to improve HybrID by eliminating the need to manually specify this parameter. Auto-Switch-HybrID automatically switches from indirect to direct encoding when fitness stagnates. Offset-HybrID simultaneously evolves an indirect encoding with directly encoded offsets, eliminating the need to switch. We compare the original HybrID to these alternatives on three different problems with adjustable regularity. The results show that both Auto-Switch-HybrID and Offset-HybrID outperform the original HybrID on different types of problems, and thus offer more tools for researchers to solve challenging problems. The Offset-HybrID algorithm is particularly interesting because it suggests a path forward for automatically and simultaneously combining the best traits of indirect and direct encoding. PMID:28334002

Segregation of male-sterility alleles across a species boundary.

PubMed

Weller, S G; Sakai, A K; Culley, T M; Duong, L; Danielson, R E

2014-02-01

Hybrid zones may serve as bridges permitting gene flow between species, including alleles influencing the evolution of breeding systems. Using greenhouse crosses, we assessed the likelihood that a hybrid zone could serve as a conduit for transfer of nuclear male-sterility alleles between a gynodioecious species and a hermaphroditic species with very rare females in some populations. Segregation patterns in progeny of crosses between rare females of hermaphroditic Schiedea menziesii and hermaphroditic plants of gynodioecious Schiedea salicaria heterozygous at the male-sterility locus, and between female S. salicaria and hermaphroditic plants from the hybrid zone, were used to determine whether male-sterility was controlled at the same locus in the parental species and the hybrid zone. Segregations of females and hermaphrodites in approximately equal ratios from many of the crosses indicate that the same nuclear male-sterility allele occurs in the parent species and the hybrid zone. These rare male-sterility alleles in S. menziesii may result from gene flow from S. salicaria through the hybrid zone, presumably facilitated by wind pollination in S. salicaria. Alternatively, rare male-sterility alleles might result from a reversal from gynodioecy to hermaphroditism in S. menziesii, or possibly de novo evolution of male sterility. Phylogenetic analysis indicates that some species of Schiedea have probably evolved separate sexes independently, but not in the lineage containing S. salicaria and S. menziesii. High levels of selfing and expression of strong inbreeding depression in S. menziesii, which together should favour females in populations, argue against a reversal from gynodioecy to hermaphroditism in S. menziesii. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Hybrid zone formation and contrasting outcomes of secondary contact over transects in common toads.

PubMed

Arntzen, Jan W; de Vries, Wouter; Canestrelli, Daniele; Martínez-Solano, Iñigo

2017-10-01

Much progress in speciation research stems from documenting patterns of morphological and genetic variation in hybrid zones. Contrasting patterns of marker introgression in different sections of the contact can provide valuable insights on the relative importance of various evolutionary mechanisms maintaining species differences in the face of hybridization and gene flow and on hybrid zone temporal and spatial dynamics. We studied species interactions in the common toads Bufo bufo and B. spinosus in France and northwestern Italy using morphological and molecular data from the mitochondrial and nuclear genomes in an extensive survey, including two independent transects west and east of the Alps. At both, we found sharp, coincident and concordant nuclear genetic transitions. However, morphological clines were wider or absent and mtDNA introgression was asymmetric. We discuss alternative, nonexclusive hypotheses about evolutionary processes generating these patterns, including drift, selection, long-distance dispersal and spatial shifts in hybrid zone location and structure. The distribution of intraspecific mtDNA lineages supports a scenario in which B. bufo held a local refugium during the last glacial maximum. Present-day genetic profiles are best explained by an advance of B. spinosus from a nearby Iberian refugium, largely superseding the local B. bufo population, followed by an advance of B. bufo from the Balkans, with prongs north and south of the Alps, driving B. spinosus southwards. A pendulum moving hybrid zone, first northwards and then southwards, explains the wide areas of introgression at either side of the current position of the contact zones. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Hybridization among distantly related species: Examples from the polyploid genus Curcuma (Zingiberaceae).

PubMed

Záveská, Eliška; Fér, Tomáš; Šída, Otakar; Marhold, Karol; Leong-Škorničková, Jana

2016-07-01

Discerning relationships among species evolved by reticulate and/or polyploid evolution is not an easy task, although it is widely discussed. The economically important genus Curcuma (ca. 120 spp.; Zingiberaceae), broadly distributed in tropical SE Asia, is a particularly interesting example of a group of palaeopolyploid origin whose evolution is driven mainly by hybridization and polyploidization. Although a phylogeny and a new infrageneric classification of Curcuma, based on commonly used molecular markers (ITS and cpDNA), have recently been proposed, significant evolutionary questions remain unresolved. We applied a multilocus approach and a combination of modern analytical methods to this genus to distinguish causes of gene tree incongruence and to identify hybrids and their parental species. Five independent regions of nuclear DNA (DCS, GAPDH, GLOBOSA3, LEAFY, ITS) and four non-coding cpDNA regions (trnL-trnF, trnT-trnL, psbA-trnH and matK), analysed as a single locus, were employed to construct a species tree and hybrid species trees using (*)BEAST and STEM-hy. Detection of hybridogenous species in the dataset was also conducted using the posterior predictive checking approach as implemented in JML. The resulting species tree outlines the relationships among major evolutionary lineages within Curcuma, which were previously unresolved or which conflicted depending upon whether they were based on ITS or cpDNA markers. Moreover, by using the additional markers in tests of plausible topologies of hybrid species trees for C. vamana, C. candida, C. roscoeana and C. myanmarensis suggested by previous molecular and morphological evidence, we found strong evidence that all the species except C. candida are of subgeneric hybrid origin. Copyright © 2016 Elsevier Inc. All rights reserved.

Whole-mount in situ hybridization in the rotifer Brachionus plicatilis representing a basal branch of lophotrochozoans.

PubMed

Boell, Louis A; Bucher, Gregor

2008-08-01

In order to broaden the comparative scope of evolutionary developmental biology and to refine our picture of animal macroevolution, it is necessary to establish new model organisms, especially from previously underrepresented groups, like the Lophotrochozoa. We have established the culture and protocols for molecular developmental biology in the rotifer species Brachionus plicatilis Müller (Rotifera, Monogononta). Rotifers are nonsegmented animals with enigmatic basal position within the lophotrochozoans and marked by several evolutionary novelties like the wheel organ (corona), the median eye, and the nonpaired posterior foot. The expression of Bp-Pax-6 is shown using whole-mount in situ hybridization. The inexpensive easy culture and experimental tractability of Brachionus as well as the range of interesting questions to which it holds the key make it a promising addition to the "zoo" of evo-devo model organisms.

Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species

PubMed Central

Baack, Eric J.; Whitney, Kenneth D.; Rieseberg, Loren H.

2008-01-01

Summary Hybridization and polyploidy can induce rapid genomic changes, including the gain or loss of DNA, but the magnitude and timing of such changes are not well understood. The homoploid hybrid system in Helianthus (three hybrid-derived species and their two parents) provides an opportunity to examine the link between hybridization and genome size changes in a replicated fashion. Flow cytometry was used to estimate the nuclear DNA content in multiple populations of three homoploid hybrid Helianthus species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus), the parental species (Helianthus annuus and Helianthus petiolaris), synthetic hybrids, and natural hybrid-zone populations. Results confirm that hybrid-derived species have 50% more nuclear DNA than the parental species. Despite multiple origins, hybrid species were largely consistent in their DNA content across populations, although H. deserticola showed significant interpopulation differences. First- and sixth-generation synthetic hybrids and hybrid-zone plants did not show an increase from parental DNA content. First-generation hybrids differed in DNA content according to the maternal parent. In summary, hybridization by itself does not lead to increased nuclear DNA content in Helianthus, and the evolutionary forces responsible for the repeated increases in DNA content seen in the hybrid-derived species remain mysterious. PMID:15998412

Hybridization and extinction.

PubMed

Todesco, Marco; Pascual, Mariana A; Owens, Gregory L; Ostevik, Katherine L; Moyers, Brook T; Hübner, Sariel; Heredia, Sylvia M; Hahn, Min A; Caseys, Celine; Bock, Dan G; Rieseberg, Loren H

2016-08-01

Hybridization may drive rare taxa to extinction through genetic swamping, where the rare form is replaced by hybrids, or by demographic swamping, where population growth rates are reduced due to the wasteful production of maladaptive hybrids. Conversely, hybridization may rescue the viability of small, inbred populations. Understanding the factors that contribute to destructive versus constructive outcomes of hybridization is key to managing conservation concerns. Here, we survey the literature for studies of hybridization and extinction to identify the ecological, evolutionary, and genetic factors that critically affect extinction risk through hybridization. We find that while extinction risk is highly situation dependent, genetic swamping is much more frequent than demographic swamping. In addition, human involvement is associated with increased risk and high reproductive isolation with reduced risk. Although climate change is predicted to increase the risk of hybridization-induced extinction, we find little empirical support for this prediction. Similarly, theoretical and experimental studies imply that genetic rescue through hybridization may be equally or more probable than demographic swamping, but our literature survey failed to support this claim. We conclude that halting the introduction of hybridization-prone exotics and restoring mature and diverse habitats that are resistant to hybrid establishment should be management priorities.

Efficient Organic/Inorganic Hybrid Solar Cell Integrating Polymer Nanowires and Inorganic Nanotetrapods.

PubMed

Xu, Weizhe; Tan, Furui; Liu, Xiansheng; Zhang, Weifeng; Qu, Shengchun; Wang, Zhijie; Wang, Zhanguo

2017-12-01

Constructing a highly efficient bulk-heterojunction is of critical importance to the hybrid organic/inorganic solar cells. Here in this work, we introduce a novel hybrid architecture containing P3HT nanowire and CdSe nanotetrapod as bicontinuous charge channels for holes and electrons, respectively. Compared to the traditionally applied P3HT molecules, the well crystallized P3HT nanowires qualify an enhanced light absorption at the long wavelength as well as strengthened charge carrier transport in the hybrid active layer. Accordingly, based on efficient dissociation of photogenerated excitons, the interpercolation of these two nano-building blocks allows a photovoltaic conversion efficiency of 1.7% in the hybrid solar cell, up to 42% enhancement compared to the reference solar cell with traditional P3HT molecules as electron donor. Our work provides a promising hybrid structure for efficient organic/inorganic bulk-heterojunction solar cells.

Evolution of postmating reproductive isolation: measuring the fitness effects of chromosomal regions containing hybrid male sterility factors.

PubMed

Johnson, N A; Wu, C I

1993-08-01

At least six regions of the X chromosome can cause male sterility when introgressed from Drosophila mauritiana into Drosophila simulans. In this article, we present the results of the other fitness effects caused by two X-linked regions that contain hybrid male sterility factors. In both regions, females that are heterozygous for an introgression with such a sterility factor produce substantially-fewer offspring than females heterozygous for an introgression that lacks the sterility factor. Thus, the hybrid male sterility factors, or other genes nearby, have substantial effects on female productivity. In contrast, hybrid male sterility factors have little or no effect on the relative viabilities of either sex. The evolutionary implications of these findings are discussed.

Comprehensive phylogenetic analysis of all species of swordtails and platies (Pisces: Genus Xiphophorus) uncovers a hybrid origin of a swordtail fish, Xiphophorus monticolus, and demonstrates that the sexually selected sword originated in the ancestral lineage of the genus, but was lost again secondarily.

PubMed

Kang, Ji Hyoun; Schartl, Manfred; Walter, Ronald B; Meyer, Axel

2013-01-29

Males in some species of the genus Xiphophorus, small freshwater fishes from Meso-America, have an extended caudal fin, or sword - hence their common name "swordtails". Longer swords are preferred by females from both sworded and - surprisingly also, non-sworded (platyfish) species that belong to the same genus. Swordtails have been studied widely as models in research on sexual selection. Specifically, the pre-existing bias hypothesis was interpreted to best explain the observed bias of females in presumed ancestral lineages of swordless species that show a preference for assumed derived males with swords over their conspecific swordless males. However, many of the phylogenetic relationships within this genus still remained unresolved. Here we construct a comprehensive molecular phylogeny of all 26 known Xiphophorus species, including the four recently described species (X. kallmani, X. mayae, X. mixei and X. monticolus). We use two mitochondrial and six new nuclear markers in an effort to increase the understanding of the evolutionary relationships among the species in this genus. Based on the phylogeny, the evolutionary history and character state evolution of the sword was reconstructed and found to have originated in the common ancestral lineage of the genus Xiphophorus and that it was lost again secondarily. We estimated the evolutionary relationships among all known species of the genus Xiphophorus based on the largest set of DNA markers so far. The phylogeny indicates that one of the newly described swordtail species, Xiphophorus monticolus, is likely to have arisen through hybridization since it is placed with the southern platyfish in the mitochondrial phylogeny, but with the southern swordtails in the nuclear phylogeny. Such discordance between these two types of markers is a strong indication for a hybrid origin. Additionally, by using a maximum likelihood approach the possession of the sexually selected sword trait is shown to be the most likely ancestral state for the genus Xiphophorus. Further, we provide a well supported estimation of the phylogenetic relationships between the previously unresolved northern swordtail groups. This comprehensive molecular phylogeny of the entire genus Xiphophorus provides evidence that a second swordtail species, X. monticolus, arose through hybridization. Previously, we demonstrated that X. clemenciae, another southern swordtail species, arose via hybridization. These findings highlight the potential key role of hybridization in the evolution of this genus and suggest the need for further investigations into how hybridization contributes to speciation more generally.

The genetic basis for fruit odor discrimination in Rhagoletis flies and its significance for sympatric host shifts.

PubMed

Dambroski, Hattie R; Linn, Charles; Berlocher, Stewart H; Forbes, Andrew A; Roelofs, Wendell; Feder, Jeffrey L

2005-09-01

Rhagoletis pomonella (Diptera: Tephritidae) use volatile compounds emitted from the surface of ripening fruit as important chemosensory cues for recognizing and distinguishing among alternative host plants. Host choice is of evolutionary significance in Rhagoletis because these flies mate on or near the fruit of their respective host plants. Differences in host choice based on fruit odor discrimination therefore result in differential mate choice and prezygotic reproductive isolation, facilitating sympatric speciation in the absence of geographic isolation. We test for a genetic basis for host fruit odor discrimination through an analysis of F2 and backcross hybrids constructed between apple-, hawthorn-, and flowering dogwood-infesting Rhagoletis flies. We recovered a significant proportion (30-65%) of parental apple, hawthorn, and dogwood fly response phenotypes in F2 hybrids, despite the general failure of F1 hybrids to reach odor source spheres. Segregation patterns in F2 and backcross hybrids suggest that only a modest number of allelic differences at a few loci may underlie host fruit odor discrimination. In addition, a strong bias was observed for F2 and backcross flies to orient to the natal fruit blend of their maternal grandmother, implying the existence of cytonuclear gene interactions. We explore the implications of our findings for the evolutionary dynamics of sympatric host race formation and speciation.

Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing.

PubMed

Kamneva, Olga K; Syring, John; Liston, Aaron; Rosenberg, Noah A

2017-08-04

Hybridization is observed in many eukaryotic lineages and can lead to the formation of polyploid species. The study of hybridization and polyploidization faces challenges both in data generation and in accounting for population-level phenomena such as coalescence processes in phylogenetic analysis. Genus Fragaria is one example of a set of plant taxa in which a range of ploidy levels is observed across species, but phylogenetic origins are unknown. Here, using 20 diploid and polyploid Fragaria species, we combine approaches from NGS data analysis and phylogenetics to infer evolutionary origins of polyploid strawberries, taking into account coalescence processes. We generate haplotype sequences for 257 low-copy nuclear markers assembled from Illumina target capture sequence data. We then identify putative hybridization events by analyzing gene tree topologies, and further test predicted hybridizations in a coalescence framework. This approach confirms the allopolyploid ancestry of F. chiloensis and F. virginiana, and provides new allopolyploid ancestry hypotheses for F. iturupensis, F. moschata, and F. orientalis. Evidence of gene flow between diploids F. bucharica and F. vesca is also detected, suggesting that it might be appropriate to consider these groups as conspecifics. This study is one of the first in which target capture sequencing followed by computational deconvolution of individual haplotypes is used for tracing origins of polyploid taxa. The study also provides new perspectives on the evolutionary history of Fragaria.

Hybrid PET/MR imaging: physics and technical considerations.

PubMed

Shah, Shetal N; Huang, Steve S

2015-08-01

In just over a decade, hybrid imaging with FDG PET/CT has become a standard bearer in the management of cancer patients. An exquisitely sensitive whole-body imaging modality, it combines the ability to detect subtle biologic changes with FDG PET and the anatomic information offered by CT scans. With advances in MR technology and advent of novel targeted PET radiotracers, hybrid PET/MRI is an evolutionary technique that is poised to revolutionize hybrid imaging. It offers unparalleled spatial resolution and functional multi-parametric data combined with biologic information in the non-invasive detection and characterization of diseases, without the deleterious effects of ionizing radiation. This article reviews the basic principles of FDG PET and MR imaging, discusses the salient technical developments of hybrid PET/MR systems, and provides an introduction to FDG PET/MR image acquisition.

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.

Restriction endonuclease analysis of chloroplast DNA in interspecies somatic Hybrids of Petunia.

PubMed

Kumar, A; Cocking, E C; Bovenberg, W A; Kool, A J

1982-12-01

Restriction endonuclease cleavage pattern analysis of chloroplast DNA (cpDNA) of three different interspecific somatic hybrid plants revealed that the cytoplasms of the hybrids contained only cpDNA of P. parodii. The somatic hybrid plants analysed were those between P. parodii (wild type) + P. hybrida (wild type); P. parodii (wild type)+P. inflata (cytoplasmic albino mutant); P. parodii (wild type) + P. parviflora (nuclear albino mutant). The presence of only P. parodii chloroplasts in the somatic hybrid of P. parodii + P. inflata is possibly due to the stringent selection used for somatic hybrid production. However, in the case of the two other somatic hybrids P. parodii + P. hybrida and P. parodii + P. parviflora it was not possible to determine whether the presence of only P. parodii chloroplasts in these somatic hybrid plants was due to the nature of the selection schemes used or simply occurred by chance. The relevance of such somatic hybrid material for the study of genomic-cytoplasmic interaction is discussed, as well as the use of restriction endonuclease fragment patterns for the analysis of taxonomic and evolutionary inter-relationships in the genus Petunia.

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

Tumuluru, Jaya Shankar; McCulloch, Richard Chet James

In this work a new hybrid genetic algorithm was developed which combines a rudimentary adaptive steepest ascent hill climbing algorithm with a sophisticated evolutionary algorithm in order to optimize complex multivariate design problems. By combining a highly stochastic algorithm (evolutionary) with a simple deterministic optimization algorithm (adaptive steepest ascent) computational resources are conserved and the solution converges rapidly when compared to either algorithm alone. In genetic algorithms natural selection is mimicked by random events such as breeding and mutation. In the adaptive steepest ascent algorithm each variable is perturbed by a small amount and the variable that caused the mostmore » improvement is incremented by a small step. If the direction of most benefit is exactly opposite of the previous direction with the most benefit then the step size is reduced by a factor of 2, thus the step size adapts to the terrain. A graphical user interface was created in MATLAB to provide an interface between the hybrid genetic algorithm and the user. Additional features such as bounding the solution space and weighting the objective functions individually are also built into the interface. The algorithm developed was tested to optimize the functions developed for a wood pelleting process. Using process variables (such as feedstock moisture content, die speed, and preheating temperature) pellet properties were appropriately optimized. Specifically, variables were found which maximized unit density, bulk density, tapped density, and durability while minimizing pellet moisture content and specific energy consumption. The time and computational resources required for the optimization were dramatically decreased using the hybrid genetic algorithm when compared to MATLAB's native evolutionary optimization tool.« less

Hybridization Associated with Cycles of Ecological Succession in a Passerine Bird.

PubMed

Duckworth, Renée A; Semenov, Georgy A

2017-10-01

Identifying the diversity of contexts that can lead to hybridization is important for understanding its prevalence and dynamics in natural populations. Despite the potential of ecological succession to dramatically alter species co-occurrence and abundances, it is unknown whether it directly promotes hybridization and, if so, has long-lasting consequences. Here, we summarize 30 years of survey data across 10 populations to show that in western and mountain bluebirds, heterospecific pairing occurs during repeatable and transient colonization events at the early stages of species turnover. Despite mixed pairing occurring only during early succession, genetic data showed presence of hybrids at both early and late successional stages. Moreover, hybrids showed novel patterns of variation in morphology and behavior, emphasizing that even ephemeral contexts for hybridization can have important evolutionary consequences. Our results suggest that because ecological succession often brings together closely related competitors in disparate numbers but lasts for only a brief period of time, it may be a widespread but underappreciated context for hybridization.

Identification of transformer fault based on dissolved gas analysis using hybrid support vector machine-modified evolutionary particle swarm optimisation

PubMed Central

2018-01-01

Early detection of power transformer fault is important because it can reduce the maintenance cost of the transformer and it can ensure continuous electricity supply in power systems. Dissolved Gas Analysis (DGA) technique is commonly used to identify oil-filled power transformer fault type but utilisation of artificial intelligence method with optimisation methods has shown convincing results. In this work, a hybrid support vector machine (SVM) with modified evolutionary particle swarm optimisation (EPSO) algorithm was proposed to determine the transformer fault type. The superiority of the modified PSO technique with SVM was evaluated by comparing the results with the actual fault diagnosis, unoptimised SVM and previous reported works. Data reduction was also applied using stepwise regression prior to the training process of SVM to reduce the training time. It was found that the proposed hybrid SVM-Modified EPSO (MEPSO)-Time Varying Acceleration Coefficient (TVAC) technique results in the highest correct identification percentage of faults in a power transformer compared to other PSO algorithms. Thus, the proposed technique can be one of the potential solutions to identify the transformer fault type based on DGA data on site. PMID:29370230

Identification of transformer fault based on dissolved gas analysis using hybrid support vector machine-modified evolutionary particle swarm optimisation.

PubMed

Illias, Hazlee Azil; Zhao Liang, Wee

2018-01-01

Early detection of power transformer fault is important because it can reduce the maintenance cost of the transformer and it can ensure continuous electricity supply in power systems. Dissolved Gas Analysis (DGA) technique is commonly used to identify oil-filled power transformer fault type but utilisation of artificial intelligence method with optimisation methods has shown convincing results. In this work, a hybrid support vector machine (SVM) with modified evolutionary particle swarm optimisation (EPSO) algorithm was proposed to determine the transformer fault type. The superiority of the modified PSO technique with SVM was evaluated by comparing the results with the actual fault diagnosis, unoptimised SVM and previous reported works. Data reduction was also applied using stepwise regression prior to the training process of SVM to reduce the training time. It was found that the proposed hybrid SVM-Modified EPSO (MEPSO)-Time Varying Acceleration Coefficient (TVAC) technique results in the highest correct identification percentage of faults in a power transformer compared to other PSO algorithms. Thus, the proposed technique can be one of the potential solutions to identify the transformer fault type based on DGA data on site.

Bringing Together Evolution on Serpentine and Polyploidy: Spatiotemporal History of the Diploid-Tetraploid Complex of Knautia arvensis (Dipsacaceae)

PubMed Central

Kolář, Filip; Fér, Tomáš; Štech, Milan; Trávníček, Pavel; Dušková, Eva; Schönswetter, Peter; Suda, Jan

2012-01-01

Polyploidization is one of the leading forces in the evolution of land plants, providing opportunities for instant speciation and rapid gain of evolutionary novelties. Highly selective conditions of serpentine environments act as an important evolutionary trigger that can be involved in various speciation processes. Whereas the significance of both edaphic speciation on serpentine and polyploidy is widely acknowledged in plant evolution, the links between polyploid evolution and serpentine differentiation have not yet been examined. To fill this gap, we investigated the evolutionary history of the perennial herb Knautia arvensis (Dipsacaceae), a diploid-tetraploid complex that exhibits an intriguing pattern of eco-geographic differentiation. Using plastid DNA sequencing and AFLP genotyping of 336 previously cytotyped individuals from 40 populations from central Europe, we unravelled the patterns of genetic variation among the cytotypes and the edaphic types. Diploids showed the highest levels of genetic differentiation, likely as a result of long term persistence of several lineages in ecologically distinct refugia and/or independent immigration. Recurrent polyploidization, recorded in one serpentine island, seems to have opened new possibilities for the local serpentine genotype. Unlike diploids, the serpentine tetraploids were able to escape from the serpentine refugium and spread further; this was also attributable to hybridization with the neighbouring non-serpentine tetraploid lineages. The spatiotemporal history of K. arvensis allows tracing the interplay of polyploid evolution and ecological divergence on serpentine, resulting in a complex evolutionary pattern. Isolated serpentine outcrops can act as evolutionary capacitors, preserving distinct karyological and genetic diversity. The serpentine lineages, however, may not represent evolutionary ‘dead-ends’ but rather dynamic systems with a potential to further influence the surrounding populations, e.g., via independent polyplodization and hybridization. The complex eco-geographical pattern together with the incidence of both primary and secondary diploid-tetraploid contact zones makes K. arvensis a unique system for addressing general questions of polyploid research. PMID:22792207

The Rate of Evolution of Postmating-Prezygotic Reproductive Isolation in Drosophila

PubMed Central

Turissini, David A; McGirr, Joseph A; Patel, Sonali S; David, Jean R; Matute, Daniel R

2018-01-01

Abstract Reproductive isolation is an intrinsic aspect of species formation. For that reason, the identification of the precise isolating traits, and the rates at which they evolve, is crucial to understanding how species originate and persist. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has studied the rates of evolution of postmating-prezygotic (PMPZ) barriers. We measured the magnitude of two barriers to gene flow that act after mating occurs but before fertilization. We also measured the magnitude of a premating barrier (female mating rate in nonchoice experiments) and two postzygotic barriers (hybrid inviability and hybrid sterility) for all pairwise crosses of all nine known extant species within the melanogaster subgroup. Our results indicate that PMPZ isolation evolves faster than hybrid inviability but slower than premating isolation. Next, we partition postzygotic isolation into different components and find that, as expected, hybrid sterility evolves faster than hybrid inviability. These results lend support for the hypothesis that, in Drosophila, reproductive isolation mechanisms (RIMs) that act early in reproduction (or in development) tend to evolve faster than those that act later in the reproductive cycle. Finally, we tested whether there was evidence for reinforcing selection at any RIM. We found no evidence for generalized evolution of reproductive isolation via reinforcement which indicates that there is no pervasive evidence of this evolutionary process. Our results indicate that PMPZ RIMs might have important evolutionary consequences in initiating speciation and in the persistence of new species. PMID:29048573

Genome-wide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons

PubMed Central

Wall, Jeffrey D; Schlebusch, Stephen A; Alberts, Susan C; Cox, Laura A; Snyder-Mackler, Noah; Nevonen, Kimberly; Carbone, Lucia; Tung, Jenny

2017-01-01

Naturally occurring admixture has now been documented in every major primate lineage, suggesting its key role in primate evolutionary history. Active primate hybrid zones can provide valuable insight into this process. Here, we investigate the history of admixture in one of the best-studied natural primate hybrid zones, between yellow baboons (Papio cynocephalus) and anubis baboons (Papio anubis) in the Amboseli ecosystem of Kenya. We generated a new genome assembly for yellow baboon and low coverage genome-wide resequencing data from yellow baboons, anubis baboons, and known hybrids (n=44). Using a novel composite likelihood method for estimating local ancestry from low coverage data, we found high levels of genetic diversity and genetic differentiation between the parent taxa, and excellent agreement between genome-scale ancestry estimates and a priori pedigree, life history, and morphology-based estimates (r2=0.899). However, even putatively unadmixed Amboseli yellow individuals carried a substantial proportion of anubis ancestry, presumably due to historical admixture. Further, the distribution of shared versus fixed differences between a putatively unadmixed Amboseli yellow baboon and an unadmixed anubis baboon, both sequenced at high coverage, are inconsistent with simple isolation-migration or equilibrium migration models. Our findings suggest a complex process of intermittent contact that has occurred multiple times in baboon evolutionary history, despite no obvious fitness costs to hybrids or major geographic or behavioral barriers. In combination with the extensive phenotypic data available for baboon hybrids, our results provide valuable context for understanding the history of admixture in primates, including in our own lineage. PMID:27145036

Interploidy hybridization in sympatric zones: the formation of Epidendrum fulgens × E. puniceoluteum hybrids (Epidendroideae, Orchidaceae)

PubMed Central

Moraes, Ana P; Chinaglia, Mariana; Palma-Silva, Clarisse; Pinheiro, Fábio

2013-01-01

Interspecific hybridization is a primary cause of extensive morphological and chromosomal variation and plays an important role in plant species diversification. However, the role of interploidal hybridization in the formation of hybrid swarms is less clear. Epidendrum encompasses wide variation in chromosome number and lacks strong premating barriers, making the genus a good model for clarifying the role of chromosomes in postzygotic barriers in interploidal hybrids. In this sense, hybrids from the interploidal sympatric zone between E. fulgens (2n = 2x = 24) and E. puniceoluteum (2n = 4x = 56) were analyzed using cytogenetic techniques to elucidate the formation and establishment of interploidal hybrids. Hybrids were not a uniform group: two chromosome numbers were observed, with the variation being a consequence of severe hybrid meiotic abnormalities and backcrossing with E. puniceoluteum. The hybrids were triploids (2n = 3x = 38 and 40) and despite the occurrence of enormous meiotic problems associated with triploidy, the hybrids were able to backcross, producing successful hybrid individuals with broad ecological distributions. In spite of the nonpolyploidization of the hybrid, its formation is a long-term evolutionary process rather than a product of a recent disturbance, and considering other sympatric zones in Epidendrum, these events could be recurrent. PMID:24198942

In Vitro Evolution and Affinity-Maturation with Coliphage Qβ Display

PubMed Central

Skamel, Claudia; Aller, Stephen G.; Bopda Waffo, Alain

2014-01-01

The Escherichia coli bacteriophage, Qβ (Coliphage Qβ), offers a favorable alternative to M13 for in vitro evolution of displayed peptides and proteins due to high mutagenesis rates in Qβ RNA replication that better simulate the affinity maturation processes of the immune response. We describe a benchtop in vitro evolution system using Qβ display of the VP1 G-H loop peptide of foot-and-mouth disease virus (FMDV). DNA encoding the G-H loop was fused to the A1 minor coat protein of Qβ resulting in a replication-competent hybrid phage that efficiently displayed the FMDV peptide. The surface-localized FMDV VP1 G-H loop cross-reacted with the anti-FMDV monoclonal antibody (mAb) SD6 and was found to decorate the corners of the Qβ icosahedral shell by electron microscopy. Evolution of Qβ-displayed peptides, starting from fully degenerate coding sequences corresponding to the immunodominant region of VP1, allowed rapid in vitro affinity maturation to SD6 mAb. Qβ selected under evolutionary pressure revealed a non-canonical, but essential epitope for mAb SD6 recognition consisting of an Arg-Gly tandem pair. Finally, the selected hybrid phages induced polyclonal antibodies in guinea pigs with good affinity to both FMDV and hybrid Qβ-G-H loop, validating the requirement of the tandem pair epitope. Qβ-display emerges as a novel framework for rapid in vitro evolution with affinity-maturation to molecular targets. PMID:25393763

A hybrid zone revisited: molecular and morphological analysis of the maintenance, movement, and evolution of a Great Plains avian (Cardinalidae: Pheucticus) hybrid zone

PubMed Central

METTLER, R. D.; SPELLMAN, G. M.

2014-01-01

Black-headed Grosbeaks (Pheucticus melanocephalus) and Rose-breasted Grosbeaks (Pheucticus ludovicianus) are passerine bird species known to hybridize in the Great Plains of North America. Both extrinsic (environmental) and intrinsic factors (pre- and postzygotic reproductive isolation) have been credited for the generation and maintenance of the grosbeak hybrid zone, but little is known about the genetic characteristics of this hybrid zone. To investigate the stability and extent of the grosbeak hybrid zone, we constructed clines from both molecular sequence data (mtDNA, 3 autosomal intron loci, and 1 Z-linked locus) and morphological data (morphometric analyses and hybrid index scores) to determined zone center and width. Hybrid zone center and width were also determined for samples collected across the zone 40 years ago from morphological data. The present and past clines were compared and provided support for stability in hybrid zone location and width, and the evolutionary implications of this are discussed. Three models of hybrid zone maintenance were investigated to consider the influence of intrinsic and extrinsic factors on this zone. Our results suggest low hybrid frequencies, a stable zone location and narrow width, and reduced hybrid fitness over the past 40 years best categorize the grosbeak hybrid zone as a tension zone. PMID:19619198

Fabrication of Sb₂S₃ Hybrid Solar Cells Based on Embedded Photoelectrodes of Ag Nanowires-Au Nanoparticles Composite.

PubMed

Kim, Kang-Pil; Hwang, Dae-Kue; Woo, Sung-Ho; Kim, Dae-Hwan

2018-09-01

The Ag nanowire (NW) + Au nanoparticle (NP)-embedded TiO2 photoelectrodes were adopted for conventional planar TiO2-based Sb2S3 hybrid solar cells to improve the cell efficiency. Compared to conventional planar TiO2-based Sb2S3 hybrid solar cells, the Ag NW + Au NP/TiO2-based Sb2S3 hybrid solar cells exhibited an improvement of approximately 40% in the cell efficiency due to the significant increase in both Jsc and Voc. These enhanced Jsc and Voc were attributed to the increased surface area, charge-collection efficiency, and light absorption by embedding the Ag NWs + Au NPs composite. The Ag NW + Au NP/TiO2-based Sb2S3 hybrid solar cells showed the highest efficiency of 2.17%, demonstrating that the Ag NW + Au NP-embedded TiO2 photoelectrode was a suitable photoelectrode structure to improve the power conversion efficiency in the Sb2S3 hybrid solar cells.

Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians.

PubMed

Chamala, Srikar; Beckstead, Wesley A; Rowe, Mark J; McClellan, David A

2007-01-01

We investigated whether the effect of evolutionary selection on three recent Single Nucleotide Polymorphisms (SNPs) in the mitochondrial sub-haplogroups of Pima Indians is consistent with their effects on metabolic efficiency. The mitochondrial SNPs impact metabolic rate and respiratory quotient, and may be adaptations to caloric restriction in a desert habitat. Using TreeSAAP software, we examined evolutionary selection in 107 mammalian species at these SNPs, characterising the biochemical shifts produced by the amino acid substitutions. Our results suggest that two SNPs were affected by selection during mammalian evolution in a manner consistent with their effects on metabolic efficiency in Pima Indians.

Molecular evidence for asymmetric hybridization in three closely related sympatric species

PubMed Central

Zhang, Ning-Ning; Yu, Jiao-Jun; Wang, Yue-Hua; Gong, Xun

2018-01-01

Abstract Natural hybridization is common in plants and results in different evolutionary consequences to hybridizing species. Pre- and post-zygotic reproductive isolating barriers can impede hybridization between closely related species to maintain their species integrity. In Northwest Yunnan, three Ligularia species (Ligularia cyathiceps, L. duciformis and L. yunnanensis) and four types of morphologically intermediate individuals were discovered growing together in an area subject to human disturbance. In this study, we used three low-copy nuclear loci to test the natural hybridization hypothesis and the hybridization direction was ascertained by three chloroplast DNA fragments. The results indicated there were two hybridization groups at the study site, L. cyathiceps × L. duciformis and L. duciformis × L. yunnanensis, and two types of morphologically intermediate individuals were produced by L. cyathiceps and L. duciformis, and another two types were produced by L. duciformis and L. yunnanensis, while no hybrids between L. cyathiceps and L. yunnanensis were observed. Both hybridizing groups showed bidirectional but asymmetric hybridization and the factors influencing the symmetry are discussed. Most hybrids produced by the two hybridization groups seemed to be F1 generation. Hybrids with different morphologies within the same hybridization group showed similar genetic components. The results suggest that although human disturbance may promote natural hybridization among the three Ligularia species bringing them together, hybrids are limited to F1s and therefore species boundaries might be maintained. PMID:29492242

Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series

NASA Astrophysics Data System (ADS)

McKinney, B. A.; Crowe, J. E., Jr.; Voss, H. U.; Crooke, P. S.; Barney, N.; Moore, J. H.

2006-02-01

We introduce a grammar-based hybrid approach to reverse engineering nonlinear ordinary differential equation models from observed time series. This hybrid approach combines a genetic algorithm to search the space of model architectures with a Kalman filter to estimate the model parameters. Domain-specific knowledge is used in a context-free grammar to restrict the search space for the functional form of the target model. We find that the hybrid approach outperforms a pure evolutionary algorithm method, and we observe features in the evolution of the dynamical models that correspond with the emergence of favorable model components. We apply the hybrid method to both artificially generated time series and experimentally observed protein levels from subjects who received the smallpox vaccine. From the observed data, we infer a cytokine protein interaction network for an individual’s response to the smallpox vaccine.

High nutrient-use efficiency during early seedling growth in diverse Grevillea species (Proteaceae)

PubMed Central

He, Tianhua; Fowler, William M.; Causley, Casey L.

2015-01-01

Several hypotheses have been proposed to explain the rich floristic diversity in regions characterised by nutrient-impoverished soils; however, none of these hypotheses have been able to explain the rapid diversification over a relatively short evolutionary time period of Grevillea, an Australian plant genus with 452 recognised species/subspecies and only 11 million years of evolutionary history. Here, we hypothesise that the apparent evolutionary success of Grevillea might have been triggered by the highly efficient use of key nutrients. The nutrient content in the seeds and nutrient-use efficiency during early seedling growth of 12 species of Grevillea were compared with those of 24 species of Hakea, a closely related genus. Compared with Hakea, the Grevillea species achieved similar growth rates (root and shoot length) during the early stages of seedling growth but contained only approximately half of the seed nutrient content. We conclude that the high nutrient-use efficiency observed in Grevillea might have provided a selective advantage in nutrient-poor ecosystems during evolution and that this property likely contributed to the evolutionary success in Grevillea. PMID:26607493

Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast

PubMed Central

Brickwedde, Anja; van den Broek, Marcel; Geertman, Jan-Maarten A.; Magalhães, Frederico; Kuijpers, Niels G. A.; Gibson, Brian; Pronk, Jack T.; Daran, Jean-Marc G.

2017-01-01

The lager brewing yeast Saccharomyces pastorianus, an interspecies hybrid of S. eubayanus and S. cerevisiae, ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion (“attenuation”) of maltotriose by industrial S. pastorianus strains is a key requirement for process intensification. This study explores a new evolutionary engineering strategy for improving maltotriose fermentation kinetics. Prolonged carbon-limited, anaerobic chemostat cultivation of the reference strain S. pastorianus CBS1483 on a maltotriose-enriched sugar mixture was used to select for spontaneous mutants with improved affinity for maltotriose. Evolved populations exhibited an up to 5-fold lower residual maltotriose concentration and a higher ethanol concentration than the parental strain. Uptake studies with 14C-labeled sugars revealed an up to 4.75-fold higher transport capacity for maltotriose in evolved strains. In laboratory batch cultures on wort, evolved strains showed improved attenuation and higher ethanol concentrations. These improvements were also observed in pilot fermentations at 1,000-L scale with high-gravity wort. Although the evolved strain exhibited multiple chromosomal copy number changes, analysis of beer made from pilot fermentations showed no negative effects on flavor compound profiles. These results demonstrate the potential of evolutionary engineering for strain improvement of hybrid, alloploid brewing strains. PMID:28943864

Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast.

PubMed

Brickwedde, Anja; van den Broek, Marcel; Geertman, Jan-Maarten A; Magalhães, Frederico; Kuijpers, Niels G A; Gibson, Brian; Pronk, Jack T; Daran, Jean-Marc G

2017-01-01

The lager brewing yeast Saccharomyces pastorianus , an interspecies hybrid of S. eubayanus and S. cerevisiae , ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion ("attenuation") of maltotriose by industrial S. pastorianus strains is a key requirement for process intensification. This study explores a new evolutionary engineering strategy for improving maltotriose fermentation kinetics. Prolonged carbon-limited, anaerobic chemostat cultivation of the reference strain S. pastorianus CBS1483 on a maltotriose-enriched sugar mixture was used to select for spontaneous mutants with improved affinity for maltotriose. Evolved populations exhibited an up to 5-fold lower residual maltotriose concentration and a higher ethanol concentration than the parental strain. Uptake studies with 14 C-labeled sugars revealed an up to 4.75-fold higher transport capacity for maltotriose in evolved strains. In laboratory batch cultures on wort, evolved strains showed improved attenuation and higher ethanol concentrations. These improvements were also observed in pilot fermentations at 1,000-L scale with high-gravity wort. Although the evolved strain exhibited multiple chromosomal copy number changes, analysis of beer made from pilot fermentations showed no negative effects on flavor compound profiles. These results demonstrate the potential of evolutionary engineering for strain improvement of hybrid, alloploid brewing strains.

Genetic networks and soft computing.

PubMed

Mitra, Sushmita; Das, Ranajit; Hayashi, Yoichi

2011-01-01

The analysis of gene regulatory networks provides enormous information on various fundamental cellular processes involving growth, development, hormone secretion, and cellular communication. Their extraction from available gene expression profiles is a challenging problem. Such reverse engineering of genetic networks offers insight into cellular activity toward prediction of adverse effects of new drugs or possible identification of new drug targets. Tasks such as classification, clustering, and feature selection enable efficient mining of knowledge about gene interactions in the form of networks. It is known that biological data is prone to different kinds of noise and ambiguity. Soft computing tools, such as fuzzy sets, evolutionary strategies, and neurocomputing, have been found to be helpful in providing low-cost, acceptable solutions in the presence of various types of uncertainties. In this paper, we survey the role of these soft methodologies and their hybridizations, for the purpose of generating genetic networks.

A hybrid, auto-adaptive and rule-based multi-agent approach using evolutionary algorithms for improved searching

NASA Astrophysics Data System (ADS)

Izquierdo, Joaquín; Montalvo, Idel; Campbell, Enrique; Pérez-García, Rafael

2016-08-01

Selecting the most appropriate heuristic for solving a specific problem is not easy, for many reasons. This article focuses on one of these reasons: traditionally, the solution search process has operated in a given manner regardless of the specific problem being solved, and the process has been the same regardless of the size, complexity and domain of the problem. To cope with this situation, search processes should mould the search into areas of the search space that are meaningful for the problem. This article builds on previous work in the development of a multi-agent paradigm using techniques derived from knowledge discovery (data-mining techniques) on databases of so-far visited solutions. The aim is to improve the search mechanisms, increase computational efficiency and use rules to enrich the formulation of optimization problems, while reducing the search space and catering to realistic problems.

Genetic interactions underlying hybrid male sterility in the Drosophila bipectinata species complex.

PubMed

Mishra, Paras Kumar; Singh, Bashisth Narayan

2006-06-01

Understanding genetic mechanisms underlying hybrid male sterility is one of the most challenging problems in evolutionary biology especially speciation. By using the interspecific hybridization method roles of Y chromosome, Major Hybrid Sterility (MHS) genes and cytoplasm in sterility of hybrid males have been investigated in a promising group, the Drosophila bipectinata species complex that consists of four closely related species: D. pseudoananassae, D. bipectinata, D. parabipectinata and D. malerkotliana. The interspecific introgression analyses show that neither cytoplasm nor MHS genes are involved but X-Y interactions may be playing major role in hybrid male sterility between D. pseudoananassae and the other three species. The results of interspecific introgression analyses also show considerable decrease in the number of males in the backcross offspring and all males have atrophied testes. There is a significant positive correlation between sex - ratio distortion and severity of sterility in backcross males. These findings provide evidence that D. pseudoananassae is remotely related with other three species of the D. bipectinata species complex.

Hybrid Pareto artificial bee colony algorithm for multi-objective single machine group scheduling problem with sequence-dependent setup times and learning effects.

PubMed

Yue, Lei; Guan, Zailin; Saif, Ullah; Zhang, Fei; Wang, Hao

2016-01-01

Group scheduling is significant for efficient and cost effective production system. However, there exist setup times between the groups, which require to decrease it by sequencing groups in an efficient way. Current research is focused on a sequence dependent group scheduling problem with an aim to minimize the makespan in addition to minimize the total weighted tardiness simultaneously. In most of the production scheduling problems, the processing time of jobs is assumed as fixed. However, the actual processing time of jobs may be reduced due to "learning effect". The integration of sequence dependent group scheduling problem with learning effects has been rarely considered in literature. Therefore, current research considers a single machine group scheduling problem with sequence dependent setup times and learning effects simultaneously. A novel hybrid Pareto artificial bee colony algorithm (HPABC) with some steps of genetic algorithm is proposed for current problem to get Pareto solutions. Furthermore, five different sizes of test problems (small, small medium, medium, large medium, large) are tested using proposed HPABC. Taguchi method is used to tune the effective parameters of the proposed HPABC for each problem category. The performance of HPABC is compared with three famous multi objective optimization algorithms, improved strength Pareto evolutionary algorithm (SPEA2), non-dominated sorting genetic algorithm II (NSGAII) and particle swarm optimization algorithm (PSO). Results indicate that HPABC outperforms SPEA2, NSGAII and PSO and gives better Pareto optimal solutions in terms of diversity and quality for almost all the instances of the different sizes of problems.

Phylogenomic evidence for a recent and rapid radiation of lizards in the Patagonian Liolaemus fitzingerii species group.

PubMed

Grummer, Jared A; Morando, Mariana M; Avila, Luciano J; Sites, Jack W; Leaché, Adam D

2018-08-01

Rapid evolutionary radiations are difficult to resolve because divergence events are nearly synchronous and gene flow among nascent species can be high, resulting in a phylogenetic "bush". Large datasets composed of sequence loci from across the genome can potentially help resolve some of these difficult phylogenetic problems. A suitable test case is the Liolaemus fitzingerii species group of lizards, which includes twelve species that are broadly distributed in Argentinean Patagonia. The species in the group have had a complex evolutionary history that has led to high morphological variation and unstable taxonomy. We generated a sequence capture dataset for 28 ingroup individuals of 580 nuclear loci, alongside a mitogenomic dataset, to infer phylogenetic relationships among species in this group. Relationships among species were generally weakly supported with the nuclear data, and along with an inferred age of ∼2.6 million years old, indicate either rapid evolution, hybridization, incomplete lineage sorting, non-informative data, or a combination thereof. We inferred a signal of mito-nuclear discordance, indicating potential hybridization between L. melanops and L. martorii, and phylogenetic network analyses provided support for 5 reticulation events among species. Phasing the nuclear loci did not provide additional insight into relationships or suspected patterns of hybridization. Only one clade, composed of L. camarones, L. fitzingerii, and L. xanthoviridis was recovered across all analyses. Genomic datasets provide molecular systematists with new opportunities to resolve difficult phylogenetic problems, yet the lack of phylogenetic resolution in Patagonian Liolaemus is biologically meaningful and indicative of a recent and rapid evolutionary radiation. The phylogenetic relationships of the Liolaemus fitzingerii group may be best modeled as a reticulated network instead of a bifurcating phylogeny. Copyright © 2018 Elsevier Inc. All rights reserved.

The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio (Asteraceae).

PubMed

Chapman, M A; Hiscock, S J; Filatov, D A

2016-01-01

Ecological speciation, driven by adaptation to contrasting environments, provides an attractive opportunity to study the formation of distinct species, and the role of selection and genomic divergence in this process. Here, we focus on a particularly clear-cut case of ecological speciation to reveal the genomic bases of reproductive isolation and morphological differences between closely related Senecio species, whose recent divergence within the last ~200,000 years was likely driven by the uplift of Mt. Etna (Sicily). These species form a hybrid zone, yet remain morphologically and ecologically distinct, despite active gene exchange. Here, we report a high-density genetic map of the Senecio genome and map hybrid breakdown to one large and several small quantitative trait loci (QTL). Loci under diversifying selection cluster in three 5 cM regions which are characterized by a significant increase in relative (F(ST)), but not absolute (d(XY)), interspecific differentiation. They also correspond to some of the regions of greatest marker density, possibly corresponding to 'cold-spots' of recombination, such as centromeres or chromosomal inversions. Morphological QTL for leaf and floral traits overlap these clusters. We also detected three genomic regions with significant transmission ratio distortion (TRD), possibly indicating accumulation of intrinsic genetic incompatibilities between these recently diverged species. One of the TRD regions overlapped with a cluster of high species differentiation, and another overlaps the large QTL for hybrid breakdown, indicating that divergence of these species may have occurred due to a complex interplay of ecological divergence and accumulation of intrinsic genetic incompatibilities. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Molecular marker suggests rapid changes of sex-determining mechanisms in Australian dragon lizards.

PubMed

Ezaz, Tariq; Quinn, Alexander E; Sarre, Stephen D; O'Meally, Denis; Georges, Arthur; Graves, Jennifer A Marshall

2009-01-01

Distribution of sex-determining mechanisms across Australian agamids shows no clear phylogenetic segregation, suggesting multiple transitions between temperature-dependent (TSD) and genotypic sex determination (GSD). These taxa thus present an excellent opportunity for studying the evolution of sex chromosomes, and evolutionary transitions between TSD and GSD. Here we report the hybridization of a 3 kb genomic sequence (PvZW3) that marks the Z and W microchromosomes of the Australian central bearded dragon (Pogona vitticeps) to chromosomes of 12 species of Australian agamids from eight genera using fluorescence in-situ hybridization (FISH). The probe hybridized to a single microchromosome pair in 11 of these species, but to the tip of the long arm of chromosome pair 2 in the twelfth (Physignathus lesueurii), indicating a micro-macro chromosome rearrangement. Three TSD species shared the marked microchromosome, implying that it is a conserved autosome in related species that determine sex by temperature. C-banding identified the marked microchromosome as the heterochromatic W chromosome in two of the three GSD species. However, in Ctenophorus fordi, the probe hybridized to a different microchromosome from that shown by C-banding to be the heterochromatic W, suggesting an independent origin for the ZW chromosome pair in that species. Given the haphazard distribution of GSD and TSD in this group and the existence of at least two sets of sex microchromosomes in GSD species, we conclude that sex-determining mechanisms in this family have evolved independently, multiple times in a short evolutionary period.

Discordant introgression in a rapidly expanding hybrid swarm

USGS Publications Warehouse

Ward, Jessica L.; Blum, Mike J.; Walters, David M.; Porter, Brady A.; Burkhead, Noel; Freeman, Byron

2012-01-01

The erosion of species boundaries can involve rapid evolutionary change. Consequently, many aspects of the process remain poorly understood, including the formation, expansion, and evolution of hybrid swarms. Biological invasions involving hybridization present exceptional opportunities to study the erosion of species boundaries because timelines of interactions and outcomes are frequently well known. Here, we examined clinal variation across codominant and maternally inherited genetic markers as well as phenotypic traits to characterize the expansion and evolution of a hybrid swarm between native Cyprinella venusta and invasive Cyprinella lutrensis minnows. Discordant introgression of phenotype, microsatellite multilocus genotype, and mtDNA haplotype indicates that the observable expansion of the C. venusta x C. lutrensis hybrid swarm is a false invasion front. Both parental and hybrid individuals closely resembling C. lutrensis are numerically dominant in the expansion wake, indicating that the non-native parental phenotype may be selectively favored. These findings show that cryptic introgression can extend beyond the phenotypic boundaries of hybrid swarms and that hybrid swarms likely expand more rapidly than can be documented from phenotypic variation alone. Similarly, dominance of a single parental phenotype following an introduction event may lead to instances of species erosion being mistaken for species displacement without hybridization.

Reconstruction of the evolutionary history of Saccharomyces cerevisiae x S. kudriavzevii hybrids based on multilocus sequence analysis.

PubMed

Peris, David; Lopes, Christian A; Arias, Armando; Barrio, Eladio

2012-01-01

In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S. cerevisiae x S. kudriavzevii hybrids isolated from both fermentative and non-fermentative environments. Different wine S. cerevisiae strains and European S. kudriavzevii strains were probably involved in the hybridization events according to gene sequence information, as well as from previous data on their genome composition and ploidy. Finally, we postulate that these hybrids may have originated after the introduction of vine growing and winemaking practices by the Romans to the present Northern vine-growing limits and spread during the expansion of improved viticulture and enology practices that occurred during the Late Middle Ages.

Hybrid cars now, fuel cell cars later.

PubMed

Demirdöven, Nurettin; Deutch, John

2004-08-13

We compare the energy efficiency of hybrid and fuel cell vehicles as well as conventional internal combustion engines. Our analysis indicates that fuel cell vehicles using hydrogen from fossil fuels offer no significant energy efficiency advantage over hybrid vehicles operating in an urban drive cycle. We conclude that priority should be placed on hybrid vehicles by industry and government.

Hybrid Cars Now, Fuel Cell Cars Later

NASA Astrophysics Data System (ADS)

Demirdöven, Nurettin; Deutch, John

2004-08-01

We compare the energy efficiency of hybrid and fuel cell vehicles as well as conventional internal combustion engines. Our analysis indicates that fuel cell vehicles using hydrogen from fossil fuels offer no significant energy efficiency advantage over hybrid vehicles operating in an urban drive cycle. We conclude that priority should be placed on hybrid vehicles by industry and government.

An evolving trio of hybrid stars: C111

NASA Technical Reports Server (NTRS)

Sonneborn, George (Technical Monitor); Dupree, Andrea K.

2005-01-01

Hybrid stars are a class of cool, luminous single stars originally identified based on the appearance of their ultraviolet IUE spectra. C IV emission is present (signifying temperatures of at least lo5 K), and asymmetric emission cores of Mg I1 are found, accompanied by absorption features at low and high velocities, indicating a massive stellar wind and circumstellar material. Many members of this class have been identified and X-rays have been detected from most hybrids. They represent the critical evolutionary state between coronal-like objects and the Alpha Ori-like objects and assume a pivotal role in the definition of coronal evolution, atmospheric heating processes, and mechanisms to drive winds of cool stars.

An Adaptive Evolutionary Algorithm for Traveling Salesman Problem with Precedence Constraints

PubMed Central

Sung, Jinmo; Jeong, Bongju

2014-01-01

Traveling sales man problem with precedence constraints is one of the most notorious problems in terms of the efficiency of its solution approach, even though it has very wide range of industrial applications. We propose a new evolutionary algorithm to efficiently obtain good solutions by improving the search process. Our genetic operators guarantee the feasibility of solutions over the generations of population, which significantly improves the computational efficiency even when it is combined with our flexible adaptive searching strategy. The efficiency of the algorithm is investigated by computational experiments. PMID:24701158

An adaptive evolutionary algorithm for traveling salesman problem with precedence constraints.

PubMed

Sung, Jinmo; Jeong, Bongju

2014-01-01

Traveling sales man problem with precedence constraints is one of the most notorious problems in terms of the efficiency of its solution approach, even though it has very wide range of industrial applications. We propose a new evolutionary algorithm to efficiently obtain good solutions by improving the search process. Our genetic operators guarantee the feasibility of solutions over the generations of population, which significantly improves the computational efficiency even when it is combined with our flexible adaptive searching strategy. The efficiency of the algorithm is investigated by computational experiments.

A narrow hybrid zone between two Cottus species in Wills Creek, Potomac drainage.

PubMed

Kinziger, A P; Raesly, R L

2001-01-01

We describe a narrow hybrid zone between the mottled sculpin (Cottus b. bairdi) and the Blue Ridge sculpin (C. caeruleomentum). Seven characters (dorsal fin rays, pectoral fin rays, caudal base band condition, male spawning coloration, and one frequency and two fixed allozyme differences) distinguish the two taxa in the hybrid zone. C. caeruleomentum and C. b. bairdi diverged in these characters in allopatry as indicated by their distribution on opposite sides of the Atlantic-Ohio divide. However, a stream capture placed these two taxa in secondary contact in Wills Creek, Potomac drainage (Atlantic slope). Allozyme data indicate the presence of post-F(1) hybrids in the zone of secondary contact. Changes in allozymes, morphology, and spawning coloration along a transect in Wills Creek reveal the hybrid zone is less than 20 river kilometers in length. Estimates of root mean square dispersal and gene flow tentatively suggest that selection is operating in the Wills Creek hybrid zone. C. b. bairdi and C. caeruleomentum are maintaining their identity in seven distinguishing characters on opposite ends of the hybrid zone revealing these two taxa are independent evolutionary lineages.

Subcellular Localization and Rolling Circle Replication of Peach Latent Mosaic Viroid: Hallmarks of Group A Viroids

PubMed Central

Bussière, F.; Lehoux, J.; Thompson, D. A.; Skrzeczkowski, L. J.; Perreault, J.-P.

1999-01-01

We characterized the peach latent mosaic viroid (PLMVd) replication intermediates that accumulate in infected peach leaves and determined the tissue and subcellular localization of the RNA species. Using in situ hybridization, we showed that PLMVd strands of both plus and minus polarities concentrate in the cells forming the palisade parenchyma. At the cellular level, PLMVd was found to accumulate predominantly in chloroplasts. Northern blot analyses demonstrated that PLMVd replicates via a symmetric mode involving the accumulation of both circular and linear monomeric strands of both polarities. No multimeric conformer was detected, indicating that both strands self-cleave efficiently via their hammerhead sequences. Dot blot hybridizations revealed that PLMVd strands of both polarities accumulate equally but that the relative concentrations vary by more than 50-fold between peach cultivars. Taken together these results establish two hallmarks for the classification of viroids. Group A viroids (e.g., PLMVd), which possess hammerhead structures, replicate in the chloroplasts via the symmetric mode. By contrast, group B viroids, which share a conserved central region, replicate in the nucleus via an asymmetric mechanism. This is an important difference between self-cleaving and non-self-cleaving viroids, and the implications for the evolutionary origin and replication are discussed. PMID:10400727

Efficient parameter estimation in longitudinal data analysis using a hybrid GEE method.

PubMed

Leung, Denis H Y; Wang, You-Gan; Zhu, Min

2009-07-01

The method of generalized estimating equations (GEEs) provides consistent estimates of the regression parameters in a marginal regression model for longitudinal data, even when the working correlation model is misspecified (Liang and Zeger, 1986). However, the efficiency of a GEE estimate can be seriously affected by the choice of the working correlation model. This study addresses this problem by proposing a hybrid method that combines multiple GEEs based on different working correlation models, using the empirical likelihood method (Qin and Lawless, 1994). Analyses show that this hybrid method is more efficient than a GEE using a misspecified working correlation model. Furthermore, if one of the working correlation structures correctly models the within-subject correlations, then this hybrid method provides the most efficient parameter estimates. In simulations, the hybrid method's finite-sample performance is superior to a GEE under any of the commonly used working correlation models and is almost fully efficient in all scenarios studied. The hybrid method is illustrated using data from a longitudinal study of the respiratory infection rates in 275 Indonesian children.

Comprehensive phylogenetic analysis of all species of swordtails and platies (Pisces: Genus Xiphophorus) uncovers a hybrid origin of a swordtail fish, Xiphophorus monticolus, and demonstrates that the sexually selected sword originated in the ancestral lineage of the genus, but was lost again secondarily

PubMed Central

2013-01-01

Background Males in some species of the genus Xiphophorus, small freshwater fishes from Meso-America, have an extended caudal fin, or sword – hence their common name “swordtails”. Longer swords are preferred by females from both sworded and – surprisingly also, non-sworded (platyfish) species that belong to the same genus. Swordtails have been studied widely as models in research on sexual selection. Specifically, the pre-existing bias hypothesis was interpreted to best explain the observed bias of females in presumed ancestral lineages of swordless species that show a preference for assumed derived males with swords over their conspecific swordless males. However, many of the phylogenetic relationships within this genus still remained unresolved. Here we construct a comprehensive molecular phylogeny of all 26 known Xiphophorus species, including the four recently described species (X. kallmani, X. mayae, X. mixei and X. monticolus). We use two mitochondrial and six new nuclear markers in an effort to increase the understanding of the evolutionary relationships among the species in this genus. Based on the phylogeny, the evolutionary history and character state evolution of the sword was reconstructed and found to have originated in the common ancestral lineage of the genus Xiphophorus and that it was lost again secondarily. Results We estimated the evolutionary relationships among all known species of the genus Xiphophorus based on the largest set of DNA markers so far. The phylogeny indicates that one of the newly described swordtail species, Xiphophorus monticolus, is likely to have arisen through hybridization since it is placed with the southern platyfish in the mitochondrial phylogeny, but with the southern swordtails in the nuclear phylogeny. Such discordance between these two types of markers is a strong indication for a hybrid origin. Additionally, by using a maximum likelihood approach the possession of the sexually selected sword trait is shown to be the most likely ancestral state for the genus Xiphophorus. Further, we provide a well supported estimation of the phylogenetic relationships between the previously unresolved northern swordtail groups. Conclusions This comprehensive molecular phylogeny of the entire genus Xiphophorus provides evidence that a second swordtail species, X. monticolus, arose through hybridization. Previously, we demonstrated that X. clemenciae, another southern swordtail species, arose via hybridization. These findings highlight the potential key role of hybridization in the evolution of this genus and suggest the need for further investigations into how hybridization contributes to speciation more generally. PMID:23360326

Whole-mount in situ hybridization in the Rotifer Brachionus plicatilis representing a basal branch of lophotrochozoans

PubMed Central

Boell, Louis A.

2008-01-01

In order to broaden the comparative scope of evolutionary developmental biology and to refine our picture of animal macroevolution, it is necessary to establish new model organisms, especially from previously underrepresented groups, like the Lophotrochozoa. We have established the culture and protocols for molecular developmental biology in the rotifer species Brachionus plicatilis Müller (Rotifera, Monogononta). Rotifers are nonsegmented animals with enigmatic basal position within the lophotrochozoans and marked by several evolutionary novelties like the wheel organ (corona), the median eye, and the nonpaired posterior foot. The expression of Bp-Pax-6 is shown using whole-mount in situ hybridization. The inexpensive easy culture and experimental tractability of Brachionus as well as the range of interesting questions to which it holds the key make it a promising addition to the “zoo” of evo-devo model organisms. Electronic supplementary material The online version of this article (doi:10.1007/s00427-008-0234-z) contains supplementary material, which is available to authorized users. PMID:18594859

A Hybrid Optimization Framework with POD-based Order Reduction and Design-Space Evolution Scheme

NASA Astrophysics Data System (ADS)

Ghoman, Satyajit S.

The main objective of this research is to develop an innovative multi-fidelity multi-disciplinary design, analysis and optimization suite that integrates certain solution generation codes and newly developed innovative tools to improve the overall optimization process. The research performed herein is divided into two parts: (1) the development of an MDAO framework by integration of variable fidelity physics-based computational codes, and (2) enhancements to such a framework by incorporating innovative features extending its robustness. The first part of this dissertation describes the development of a conceptual Multi-Fidelity Multi-Strategy and Multi-Disciplinary Design Optimization Environment (M3 DOE), in context of aircraft wing optimization. M 3 DOE provides the user a capability to optimize configurations with a choice of (i) the level of fidelity desired, (ii) the use of a single-step or multi-step optimization strategy, and (iii) combination of a series of structural and aerodynamic analyses. The modularity of M3 DOE allows it to be a part of other inclusive optimization frameworks. The M 3 DOE is demonstrated within the context of shape and sizing optimization of the wing of a Generic Business Jet aircraft. Two different optimization objectives, viz. dry weight minimization, and cruise range maximization are studied by conducting one low-fidelity and two high-fidelity optimization runs to demonstrate the application scope of M3 DOE. The second part of this dissertation describes the development of an innovative hybrid optimization framework that extends the robustness of M 3 DOE by employing a proper orthogonal decomposition-based design-space order reduction scheme combined with the evolutionary algorithm technique. The POD method of extracting dominant modes from an ensemble of candidate configurations is used for the design-space order reduction. The snapshot of candidate population is updated iteratively using evolutionary algorithm technique of fitness-driven retention. This strategy capitalizes on the advantages of evolutionary algorithm as well as POD-based reduced order modeling, while overcoming the shortcomings inherent with these techniques. When linked with M3 DOE, this strategy offers a computationally efficient methodology for problems with high level of complexity and a challenging design-space. This newly developed framework is demonstrated for its robustness on a nonconventional supersonic tailless air vehicle wing shape optimization problem.

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions.

PubMed

Zenni, Rafael Dudeque; Dickie, Ian A; Wingfield, Michael J; Hirsch, Heidi; Crous, Casparus J; Meyerson, Laura A; Burgess, Treena I; Zimmermann, Thalita G; Klock, Metha M; Siemann, Evan; Erfmeier, Alexandra; Aragon, Roxana; Montti, Lia; Le Roux, Johannes J

2016-12-30

Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics, and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand, and manage biological invasions. Published by Oxford University Press on behalf of the Annals of Botany Company.

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions

PubMed Central

Dickie, Ian A.; Wingfield, Michael J.; Hirsch, Heidi; Crous, Casparus J.; Meyerson, Laura A.; Burgess, Treena I.; Zimmermann, Thalita G.; Klock, Metha M.; Siemann, Evan; Erfmeier, Alexandra; Aragon, Roxana; Montti, Lia; Le Roux, Johannes J.

2017-01-01

Abstract Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand and manage biological invasions. PMID:28039118

Non-Evolutionary Algorithms for Scheduling Dependent Tasks in Distributed Heterogeneous Computing Environments

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

Wayne F. Boyer; Gurdeep S. Hura

2005-09-01

The Problem of obtaining an optimal matching and scheduling of interdependent tasks in distributed heterogeneous computing (DHC) environments is well known to be an NP-hard problem. In a DHC system, task execution time is dependent on the machine to which it is assigned and task precedence constraints are represented by a directed acyclic graph. Recent research in evolutionary techniques has shown that genetic algorithms usually obtain more efficient schedules that other known algorithms. We propose a non-evolutionary random scheduling (RS) algorithm for efficient matching and scheduling of inter-dependent tasks in a DHC system. RS is a succession of randomized taskmore » orderings and a heuristic mapping from task order to schedule. Randomized task ordering is effectively a topological sort where the outcome may be any possible task order for which the task precedent constraints are maintained. A detailed comparison to existing evolutionary techniques (GA and PSGA) shows the proposed algorithm is less complex than evolutionary techniques, computes schedules in less time, requires less memory and fewer tuning parameters. Simulation results show that the average schedules produced by RS are approximately as efficient as PSGA schedules for all cases studied and clearly more efficient than PSGA for certain cases. The standard formulation for the scheduling problem addressed in this paper is Rm|prec|Cmax.,« less

How just a few makes a lot: Speciation via reticulation and apomixis on example of European brambles (Rubus subgen. Rubus, Rosaceae).

PubMed

Sochor, Michal; Vašut, Radim J; Sharbel, Timothy F; Trávníček, Bohumil

2015-08-01

New species are generated by many means, among which hybridization plays an important role. Interspecific hybrids can form isolated evolutionary units, especially when mechanisms increasing viability and fertility, like polyploidy and apomixis, are involved. A good model system to study reticulate evolution in plants is Rubus subgen. Rubus (brambles, blackberries), which only in Europe includes 748 accepted species, out of which only four are sexual diploids and all others are polyploid apomicts. We employed two molecular markers (ITS and cpDNA) to shed light on the evolutionary history of European bramble flora and main processes generating such high species diversity. We distinguished just six ancestral diploids (including two extinct ones) for both markers, which gave rise to all European polyploid accessions, and revealed an extreme reticulation in bramble evolution. We furthermore detected hybridogenous origins and identified putative parents for several taxa (e.g. ser. Nessenses), while in other groups (e.g. ser. Discolores) we could also infer the direction of hybridization. By comparing different cp haplotypes having clear geographic patterns, we hypothesize that the origin of European brambles can be attributed to both Holocene species range expansion and Pleistocene climate fluctuations. Copyright © 2015 Elsevier Inc. All rights reserved.

Toward the evolutionary genomics of gametophytic divergence: patterns of transmission ratio distortion in monkeyflower (Mimulus) hybrids reveal a complex genetic basis for conspecific pollen precedence.

PubMed

Fishman, Lila; Aagaard, Jan; Tuthill, John C

2008-12-01

Conspecific pollen precedence (CPP) is a major component of reproductive isolation between many flowering plant taxa and may reveal mechanisms of gametophytic evolution within species, but little is known about the genetic basis and evolutionary history of CPP. We systematically investigated the genetic architecture of CPP using patterns of transmission ratio distortion (TRD) in F2 and backcross hybrids between closely related species of Mimulus (Phrymaceae) with divergent mating systems. We found that CPP in Mimulus hybrids was polygenic and was the majority source of interspecific TRD genome-wide, with at least eight genomic regions contributing to the transmission advantage of M. guttatus pollen grains on M. guttatus styles. In aggregate, these male-specific transmission ratio distorting loci (TRDLs) were more than sufficient to account for the 100% precedence of pure M. guttatus pollen over M. nasutus pollen in mixed pollinations of M. guttatus. All but one of these pollen TRDLs were style-dependent; that is, we observed pollen TRD in F(1) and/or M. guttatus styles, but not in M. nasutus styles. These findings suggest that species-specific differences in pollen tube performance accumulate gradually and may have been driven by coevolution between pollen and style in the predominantly outcrossing M. guttatus.

Morphological and molecular evidence reveals recent hybridization between gorilla taxa.

PubMed

Ackermann, Rebecca Rogers; Bishop, Jacqueline M

2010-01-01

Molecular studies have demonstrated a deep lineage split between the two gorilla species, as well as divisions within these taxa; estimates place this divergence in the mid-Pleistocene, with gene flow continuing until approximately 80,000 years ago. Here, we present analyses of skeletal data indicating the presence of substantial recent gene flow among gorillas at all taxonomic levels: between populations, subspecies, and species. Complementary analyses of DNA sequence variation suggest that low-level migration occurred primarily in a westerly-to-easterly direction. In western gorillas, the locations of hybrid phenotypes map closely to expectations based on population refugia and riverine barrier hypotheses, supporting the presence of significant vicariance-driven structuring and occasional admixture within this taxon. In eastern lowland gorillas, the high frequency of hybrid phenotypes is surprising, suggesting that this region represents a zone of introgression between eastern gorillas and migrants from the west, and underscoring the conservation priority of this critically endangered group. These results highlight the complex nature of evolutionary divergence in this genus, indicate that historical gene flow has played a major role in structuring gorilla diversity, and demonstrate that our understanding of the evolutionary processes responsible for shaping biodiversity can benefit immensely from consideration of morphological and molecular data in conjunction.

New paradigms in clonal evolution: punctuated equilibrium in cancer.

PubMed

Cross, William Ch; Graham, Trevor A; Wright, Nicholas A

2016-10-01

Evolutionary theories are themselves subject to evolution. Clonal evolution - the model that describes the initiation and progression of cancer - is entering a period of profound change, brought about largely by technological developments in genome analysis. A flurry of recent publications, using modern mathematical and bioinformatics techniques, have revealed both punctuated and neutral evolution phenomena that are poorly explained by the conventional graduated perspectives. In this review, we propose that a hybrid model, inspired by the evolutionary model of punctuated equilibrium, could better explain these recent observations. We also discuss the conceptual changes and clinical implications of variable evolutionary tempos. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Diversity and adaptive evolution of Saccharomyces wine yeast: a review

PubMed Central

Marsit, Souhir; Dequin, Sylvie

2015-01-01

Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. PMID:26205244

Dynamic nucleolar activity in wheat × Aegilops hybrids: evidence of C-genome dominance.

PubMed

Mirzaghaderi, Ghader; Abdolmalaki, Zinat; Zohouri, Mohsen; Moradi, Zeinab; Mason, Annaliese S

2017-08-01

NOR loci of C-subgenome are dominant in wheat × Aegilops interspecific hybrids, which may have evolutionary implications for wheat group genome dynamics and evolution. After interspecific hybridisation, some genes are often expressed from only one of the progenitor species, shaping subsequent allopolyploid genome evolution processes. A well-known example is nucleolar dominance, i.e. the formation of cell nucleoli from chromosomes of only one parental species. We studied nucleolar organizing regions (NORs) in diploid Aegilops markgrafii (syn: Ae. caudata; CC), Ae. umbellulata (UU), allotetraploids Aegilops cylindrica (C c C c D c D c ) and Ae. triuncialis (C t C t U t U t ), synthetic interspecific F 1 hybrids between these two allotetraploids and bread wheat (Triticum aestivum, AABBDD) and in F 3 generation hybrids with genome composition AABBDDC t C t U t U t using silver staining and fluorescence in situ hybridization (FISH). In Ae. markgrafii (CC), NORs of both 1C and 5C or only 5C chromosome pairs were active in different individual cells, while only NORs on 1U chromosomes were active in Ae. umbellulata (UU). Although all 35S rDNA loci of the C t subgenome (located on 1C t and 5C t ) were active in Ae. triuncialis, only one pair (occupying either 1C c or 5C c ) was active in Ae. cylindrica, depending on the genotype studied. These C-genome expression patterns were transmitted to the F 1 and F 3 generations. Wheat chromosome NOR activity was variable in Ae. triuncialis × T. aestivum F 1 seeds, but silenced by the F 3 generation. No effect of maternal or paternal cross direction was observed. These results indicate that C-subgenome NOR loci are dominant in wheat × Aegilops interspecific hybrids, which may have evolutionary implications for wheat group genome dynamics and allopolyploid evolution.

Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini)

PubMed Central

Wahlberg, Niklas; Weingartner, Elisabet; Warren, Andrew D; Nylin, Sören

2009-01-01

Background Major conflict between mitochondrial and nuclear genes in estimating species relationships is an increasingly common finding in animals. Usually this is attributed to incomplete lineage sorting, but recently the possibility has been raised that hybridization is important in generating such phylogenetic patterns. Just how widespread ancient and/or recent hybridization is in animals and how it affects estimates of species relationships is still not well-known. Results We investigate the species relationships and their evolutionary history over time in the genus Polygonia using DNA sequences from two mitochondrial gene regions (COI and ND1, total 1931 bp) and four nuclear gene regions (EF-1α, wingless, GAPDH and RpS5, total 2948 bp). We found clear, strongly supported conflict between mitochondrial and nuclear DNA sequences in estimating species relationships in the genus Polygonia. Nodes at which there was no conflict tended to have diverged at the same time when analyzed separately, while nodes at which conflict was present diverged at different times. We find that two species create most of the conflict, and attribute the conflict found in Polygonia satyrus to ancient hybridization and conflict found in Polygonia oreas to recent or ongoing hybridization. In both examples, the nuclear gene regions tended to give the phylogenetic relationships of the species supported by morphology and biology. Conclusion Studies inferring species-level relationships using molecular data should never be based on a single locus. Here we show that the phylogenetic hypothesis generated using mitochondrial DNA gives a very different interpretation of the evolutionary history of Polygonia species compared to that generated from nuclear DNA. We show that possible cases of hybridization in Polygonia are not limited to sister species, but may be inferred further back in time. Furthermore, we provide more evidence that Haldane's effect might not be as strong a process in preventing hybridization in butterflies as has been previously thought. PMID:19422691

Genetic characterization of hybridization and introgression between anadromous rainbow trout (oncorhynchus mykiss irideus) and coastal cutthroat trout (o. clarki clarki)

USGS Publications Warehouse

Young, W.P.; Ostberg, C.O.; Keim, P.; Thorgaard, G.H.

2001-01-01

Interspecific hybridization represents a dynamic evolutionary phenomenon and major conservation problem in salmonid fishes. In this study we used amplified fragment length polymorphisms (AFLP) and mitochondrial DNA (mtDNA) markers to describe the extent and characterize the pattern of hybridization and introgression between coastal rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Hybrid individuals were initially identified using principle coordinate analysis of 133 polymorphic AFLP markers. Subsequent analysis using 23 diagnostic AFLP markers revealed the presence of F1, rainbow trout backcross, cutthroat trout backcross and later-generation hybrids. mtDNA analysis demonstrated equal numbers of F1 hybrids with rainbow and cutthroat trout mtDNA indicating reciprocal mating of the parental types. In contrast, rainbow and cutthroat trout backcross hybrids always exhibited the mtDNA from the recurrent parent, indicating a male hybrid mating with a pure female. This study illustrates the usefulness of the AFLP technique for generating large numbers of species diagnostic markers. The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment-dependent reduction in hybrid fitness.

Hybridization rates between lettuce (Lactuca sativa) and its wild relative (L. serriola) under field conditions.

PubMed

D'Andrea, Luigi; Felber, François; Guadagnuolo, Roberto

2008-01-01

Hybridization and introgression between crops and wild relatives may have important evolutionary and ecological consequences such as gene swamping or increased invasiveness. In the present study, we investigated hybridization under field conditions between crop lettuce (Lactuca sativa) and its wild relative prickly lettuce (L. serriola), two cross-compatible, predominantly autogamous and insect pollinated species. In 2003 and 2004, we estimated the rates of hybridization between L. sativa and L. serriola in close-to-reality field experiments carried out in two locations of Northern Switzerland. Seeds set by the experimental wild plants were collected and sown (44 352 in 2003 and 252 345 in 2004). Progeny was screened morphologically for detecting natural hybrids. Prior to the experiment, specific RAPD markers were used to confirm that morphological characters were reliable for hybrid identification. Hybridization occurred up to the maximal distance tested (40 m), and hybridization rates varied between 0 to 26%, decreasing with distance. More than 80% of the wild plants produced at least one hybrid (incidence of hybridization, IH) at 0 m and 1 m. It equaled 4 to 5% at 40 m. In sympatric crop-wild populations, cross-pollination between cultivated lettuce and its wild relative has to be seen as the rule rather than the exception for short distances.

Development and characterization of microsatellite markers in Sarracenia L. (pitcher plant) species.

PubMed

Rogers, Willie L; Cruse-Sanders, Jennifer M; Determann, Ron; Malmberg, Russell L

2010-12-01

Sarracenia species (pitcher plants) are carnivorous plants which obtain a portion of their nutrients from insects captured in the pitchers. Sarracenia species naturally hybridize with each other, and hybrid swarms have been identified. A number of the taxa within the genus are considered endangered. In order to facilitate evolutionary, ecological and conservation genetic analyses within the genus, we developed 25 microsatellite loci which show variability either within species or between species. Three S. purpurea populations were examined with 10 primer sets which showed within population variability.

Development and characterization of microsatellite markers in Sarracenia L. (pitcher plant) species

PubMed Central

Rogers, Willie L.; Cruse-Sanders, Jennifer M.; Determann, Ron; Malmberg, Russell L.

2010-01-01

Sarracenia species (pitcher plants) are carnivorous plants which obtain a portion of their nutrients from insects captured in the pitchers. Sarracenia species naturally hybridize with each other, and hybrid swarms have been identified. A number of the taxa within the genus are considered endangered. In order to facilitate evolutionary, ecological and conservation genetic analyses within the genus, we developed 25 microsatellite loci which show variability either within species or between species. Three S. purpurea populations were examined with 10 primer sets which showed within population variability. PMID:21170168

Hybridization among the ancient mariners: characterization of marine turtle hybrids with molecular genetic assays.

PubMed

Karl, S A; Bowen, B W; Avise, J C

1995-01-01

Reports of hybridization between marine turtle species (family Cheloniidae) have been difficult to authenticate based solely on morphological evidence. Here we employ molecular genetic assays to document the sporadic, natural occurrence of viable interspecific hybrids between species representing four of the five genera of cheloniid sea turtles. Using multiple DNA markers from single-copy nuclear loci, eight suspected hybrids (based on morphology) were confirmed to be the products of matings involving the loggerhead turtle (Caretta caretta) x Kemp's ridley (Lepidochelys kempii) (N = 1 specimen), loggerhead turtle x hawksbill (Eretmochelys imbricata) (N = 2), loggerhead turtle x green turtle (Chelonia mydas) (N = 4), and green turtle x hawksbill (N = 1). Molecular markers from mitochondrial DNA permitted identification of the maternal parental species in each cross. The species involved in these hybridization events represent evolutionary lineages thought to have separated 10-75 million years ago (mya) and thus may be among the oldest vertebrate lineages capable of producing viable hybrids in nature. In some cases, human intervention with the life cycles of marine turtles (e.g., through habitat alteration, captive rearing, or attempts to establish new breeding sites) may have increased the opportunities for interspecific hybridization.

Species collapse via hybridization in Darwin's tree finches.

PubMed

Kleindorfer, Sonia; O'Connor, Jody A; Dudaniec, Rachael Y; Myers, Steven A; Robertson, Jeremy; Sulloway, Frank J

2014-03-01

Species hybridization can lead to fitness costs, species collapse, and novel evolutionary trajectories in changing environments. Hybridization is predicted to be more common when environmental conditions change rapidly. Here, we test patterns of hybridization in three sympatric tree finch species (small tree finch Camarhynchus parvulus, medium tree finch Camarhynchus pauper, and large tree finch: Camarhynchus psittacula) that are currently recognized on Floreana Island, Galápagos Archipelago. Genetic analysis of microsatellite data from contemporary samples showed two genetic populations and one hybrid cluster in both 2005 and 2010; hybrid individuals were derived from genetic population 1 (small morph) and genetic population 2 (large morph). Females of the large and rare species were more likely to pair with males of the small common species. Finch populations differed in morphology in 1852-1906 compared with 2005/2010. An unsupervised clustering method showed (a) support for three morphological clusters in the historical tree finch sample (1852-1906), which is consistent with current species recognition; (b) support for two or three morphological clusters in 2005 with some (19%) hybridization; and (c) support for just two morphological clusters in 2010 with frequent (41%) hybridization. We discuss these findings in relation to species demarcations of Camarhynchus tree finches on Floreana Island.

HELPR: Hybrid Evolutionary Learning for Pattern Recognition

DTIC Science & Technology

2005-12-01

to a new approach called memetic algorithms that combines machine learning systems with human expertise to create new tools that have the advantage...architecture could form the foundation for a memetic system capable of solving ATR problems faster and more accurately than possible using pure human expertise

Segregation distortion causes large-scale differences between male and female genomes in hybrid ants.

PubMed

Kulmuni, Jonna; Seifert, Bernhard; Pamilo, Pekka

2010-04-20

Hybridization in isolated populations can lead either to hybrid breakdown and extinction or in some cases to speciation. The basis of hybrid breakdown lies in genetic incompatibilities between diverged genomes. In social Hymenoptera, the consequences of hybridization can differ from those in other animals because of haplodiploidy and sociality. Selection pressures differ between sexes because males are haploid and females are diploid. Furthermore, sociality and group living may allow survival of hybrid genotypes. We show that hybridization in Formica ants has resulted in a stable situation in which the males form two highly divergent gene pools whereas all the females are hybrids. This causes an exceptional situation with large-scale differences between male and female genomes. The genotype differences indicate strong transmission ratio distortion depending on offspring sex, whereby the mother transmits some alleles exclusively to her daughters and other alleles exclusively to her sons. The genetic differences between the sexes and the apparent lack of multilocus hybrid genotypes in males can be explained by recessive incompatibilities which cause the elimination of hybrid males because of their haploid genome. Alternatively, differentiation between sexes could be created by prezygotic segregation into male-forming and female-forming gametes in diploid females. Differentiation between sexes is stable and maintained throughout generations. The present study shows a unique outcome of hybridization and demonstrates that hybridization has the potential of generating evolutionary novelties in animals.

Parallel evolution of image processing tools for multispectral imagery

NASA Astrophysics Data System (ADS)

Harvey, Neal R.; Brumby, Steven P.; Perkins, Simon J.; Porter, Reid B.; Theiler, James P.; Young, Aaron C.; Szymanski, John J.; Bloch, Jeffrey J.

2000-11-01

We describe the implementation and performance of a parallel, hybrid evolutionary-algorithm-based system, which optimizes image processing tools for feature-finding tasks in multi-spectral imagery (MSI) data sets. Our system uses an integrated spatio-spectral approach and is capable of combining suitably-registered data from different sensors. We investigate the speed-up obtained by parallelization of the evolutionary process via multiple processors (a workstation cluster) and develop a model for prediction of run-times for different numbers of processors. We demonstrate our system on Landsat Thematic Mapper MSI , covering the recent Cerro Grande fire at Los Alamos, NM, USA.

Improved Efficiency and Enhanced Color Quality of Light-Emitting Diodes with Quantum Dot and Organic Hybrid Tandem Structure.

PubMed

Zhang, Heng; Feng, Yuanxiang; Chen, Shuming

2016-10-03

Light-emitting diodes based on organic (OLEDs) and colloidal quantum dot (QLEDs) are widely considered as next-generation display technologies because of their attractive advantages such as self-emitting and flexible form factor. The OLEDs exhibit relatively high efficiency, but their color saturation is quite poor compared with that of QLEDs. In contrast, the QLEDs show very pure color emission, but their efficiency is lower than that of OLEDs currently. To combine the advantages and compensate for the weaknesses of each other, we propose a hybrid tandem structure which integrates both OLED and QLED in a single device architecture. With ZnMgO/Al/HATCN interconnecting layer, hybrid tandem LEDs are successfully fabricated. The demonstrated hybrid tandem devices feature high efficiency and high color saturation simultaneously; for example, the devices exhibit maximum current efficiency and external quantum efficiency of 96.28 cd/A and 25.90%, respectively. Meanwhile, the full width at half-maximum of the emission spectra is remarkably reduced from 68 to 44 nm. With the proposed hybrid tandem structure, the color gamut of the displays can be effectively increased from 81% to 100% NTSC. The results indicate that the advantages of different LED technologies can be combined in a hybrid tandem structure.

Domestication, Genomics and the Future for Banana

PubMed Central

Heslop-Harrison, J. S.; Schwarzacher, Trude

2007-01-01

Background Cultivated bananas and plantains are giant herbaceous plants within the genus Musa. They are both sterile and parthenocarpic so the fruit develops without seed. The cultivated hybrids and species are mostly triploid (2n = 3x = 33; a few are diploid or tetraploid), and most have been propagated from mutants found in the wild. With a production of 100 million tons annually, banana is a staple food across the Asian, African and American tropics, with the 15 % that is exported being important to many economies. Scope There are well over a thousand domesticated Musa cultivars and their genetic diversity is high, indicating multiple origins from different wild hybrids between two principle ancestral species. However, the difficulty of genetics and sterility of the crop has meant that the development of new varieties through hybridization, mutation or transformation was not very successful in the 20th century. Knowledge of structural and functional genomics and genes, reproductive physiology, cytogenetics, and comparative genomics with rice, Arabidopsis and other model species has increased our understanding of Musa and its diversity enormously. Conclusions There are major challenges to banana production from virulent diseases, abiotic stresses and new demands for sustainability, quality, transport and yield. Within the genepool of cultivars and wild species there are genetic resistances to many stresses. Genomic approaches are now rapidly advancing in Musa and have the prospect of helping enable banana to maintain and increase its importance as a staple food and cash crop through integration of genetical, evolutionary and structural data, allowing targeted breeding, transformation and efficient use of Musa biodiversity in the future. PMID:17766312

Multiple sequence alignment using multi-objective based bacterial foraging optimization algorithm.

PubMed

Rani, R Ranjani; Ramyachitra, D

2016-12-01

Multiple sequence alignment (MSA) is a widespread approach in computational biology and bioinformatics. MSA deals with how the sequences of nucleotides and amino acids are sequenced with possible alignment and minimum number of gaps between them, which directs to the functional, evolutionary and structural relationships among the sequences. Still the computation of MSA is a challenging task to provide an efficient accuracy and statistically significant results of alignments. In this work, the Bacterial Foraging Optimization Algorithm was employed to align the biological sequences which resulted in a non-dominated optimal solution. It employs Multi-objective, such as: Maximization of Similarity, Non-gap percentage, Conserved blocks and Minimization of gap penalty. BAliBASE 3.0 benchmark database was utilized to examine the proposed algorithm against other methods In this paper, two algorithms have been proposed: Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC) and Bacterial Foraging Optimization Algorithm. It was found that Hybrid Genetic Algorithm with Artificial Bee Colony performed better than the existing optimization algorithms. But still the conserved blocks were not obtained using GA-ABC. Then BFO was used for the alignment and the conserved blocks were obtained. The proposed Multi-Objective Bacterial Foraging Optimization Algorithm (MO-BFO) was compared with widely used MSA methods Clustal Omega, Kalign, MUSCLE, MAFFT, Genetic Algorithm (GA), Ant Colony Optimization (ACO), Artificial Bee Colony (ABC), Particle Swarm Optimization (PSO) and Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC). The final results show that the proposed MO-BFO algorithm yields better alignment than most widely used methods. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Hybrid ODE/SSA methods and the cell cycle model

NASA Astrophysics Data System (ADS)

Wang, S.; Chen, M.; Cao, Y.

2017-07-01

Stochastic effect in cellular systems has been an important topic in systems biology. Stochastic modeling and simulation methods are important tools to study stochastic effect. Given the low efficiency of stochastic simulation algorithms, the hybrid method, which combines an ordinary differential equation (ODE) system with a stochastic chemically reacting system, shows its unique advantages in the modeling and simulation of biochemical systems. The efficiency of hybrid method is usually limited by reactions in the stochastic subsystem, which are modeled and simulated using Gillespie's framework and frequently interrupt the integration of the ODE subsystem. In this paper we develop an efficient implementation approach for the hybrid method coupled with traditional ODE solvers. We also compare the efficiency of hybrid methods with three widely used ODE solvers RADAU5, DASSL, and DLSODAR. Numerical experiments with three biochemical models are presented. A detailed discussion is presented for the performances of three ODE solvers.

Designing from minimum to optimum functionality

NASA Astrophysics Data System (ADS)

Bannova, Olga; Bell, Larry

2011-04-01

This paper discusses a multifaceted strategy to link NASA Minimal Functionality Habitable Element (MFHE) requirements to a compatible growth plan; leading forward to evolutionary, deployable habitats including outpost development stages. The discussion begins by reviewing fundamental geometric features inherent in small scale, vertical and horizontal, pressurized module configuration options to characterize applicability to meet stringent MFHE constraints. A proposed scenario to incorporate a vertical core MFHE concept into an expanded architecture to provide continuity of structural form and a logical path from "minimum" to "optimum" design of a habitable module. The paper describes how habitation and logistics accommodations could be pre-integrated into a common Hab/Log Module that serves both habitation and logistics functions. This is offered as a means to reduce unnecessary redundant development costs and to avoid EVA-intensive on-site adaptation and retrofitting requirements for augmented crew capacity. An evolutionary version of the hard shell Hab/Log design would have an expandable middle section to afford larger living and working accommodations. In conclusion, the paper illustrates that a number of cargo missions referenced for NASA's 4.0.0 Lunar Campaign Scenario could be eliminated altogether to expedite progress and reduce budgets. The plan concludes with a vertical growth geometry that provides versatile and efficient site development opportunities using a combination of hard Hab/Log modules and a hybrid expandable "CLAM" (Crew Lunar Accommodations Module) element.

Radiation use efficiency, biomass production, and grain yield in two maize hybrids differing in drought tolerance

USDA-ARS?s Scientific Manuscript database

Drought tolerant (DT) maize (Zea mays L.) hybrids have potential to increase yield under drought conditions. However, little information is known about the physiological determinations of yield in DT hybrids. Our objective was to assess radiation use efficiency (RUE), biomass production, and yield ...

Sex chromosomes and speciation in Drosophila

PubMed Central

Presgraves, Daven C.

2010-01-01

Two empirical rules suggest that sex chromosomes play a special role in speciation. The first is Haldane's rule— the preferential sterility and inviability of species hybrids of the heterogametic (XY) sex. The second is the disproportionately large effect of the X chromosome in genetic analyses of hybrid sterility. Whereas the causes of Haldane's rule are well established, the causes of the ‘large X-effect’ have remained controversial. New genetic analyses in Drosophila confirm that the X is a hotspot for hybrid male sterility factors, providing a proximate explanation for the large X-effect. Several other new findings— on faster X evolution, X chromosome meiotic drive, and the regulation of the X chromosome in the male-germline— provide plausible evolutionary explanations for the large X-effect. PMID:18514967

Hybridization between multi-objective genetic algorithm and support vector machine for feature selection in walker-assisted gait.

PubMed

Martins, Maria; Costa, Lino; Frizera, Anselmo; Ceres, Ramón; Santos, Cristina

2014-03-01

Walker devices are often prescribed incorrectly to patients, leading to the increase of dissatisfaction and occurrence of several problems, such as, discomfort and pain. Thus, it is necessary to objectively evaluate the effects that assisted gait can have on the gait patterns of walker users, comparatively to a non-assisted gait. A gait analysis, focusing on spatiotemporal and kinematics parameters, will be issued for this purpose. However, gait analysis yields redundant information that often is difficult to interpret. This study addresses the problem of selecting the most relevant gait features required to differentiate between assisted and non-assisted gait. For that purpose, it is presented an efficient approach that combines evolutionary techniques, based on genetic algorithms, and support vector machine algorithms, to discriminate differences between assisted and non-assisted gait with a walker with forearm supports. For comparison purposes, other classification algorithms are verified. Results with healthy subjects show that the main differences are characterized by balance and joints excursion in the sagittal plane. These results, confirmed by clinical evidence, allow concluding that this technique is an efficient feature selection approach. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Hybrid haplotype vigor in Florida (USA) populations of the invasive exotic Brazilian peppertree, Schinus terebinthifolius

USDA-ARS?s Scientific Manuscript database

The process of invasive species establishment allows ecologists and evolutionary biologists to study these occurrences as human induced experiments in contemporary evolution. The success of invasive species exposes a genetic paradox. How can successful invaders overcome the hurdle of reduced genet...

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

USDA-ARS?s Scientific Manuscript database

Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring by crossing two inbred parents. We test these ideas using evolutionary measures of sequence conservati...

Mitochondrial Fitness, Gene Expression, and Hypoxic Stress in a Hybrid Population of the Killifish, Fundulus Heteroclitus

EPA Science Inventory

The physiological link between oxygen availability and mitochondrial function is well established. However, whether or not fitness variation is associated with mitochondrial genotypes in the field remains a contested topic in evolutionary biology. In this study we draw on a popul...

Avian predation pressure as a potential driver of periodical cicada cycle length

Treesearch

Walter E. Koenig; Andrew M. Liebhold

2013-01-01

The extraordinarily long life cycles, synchronous emergences at 13- or 17-year intervals, and complex geographic distribution of periodical cicadas (Magicicada spp.) in eastern North America are a long-standing evolutionary enigma. Although a variety of factors, including satiation of aboveground predators and avoidance of interbrood hybridization,...

A steep cline in Pinus muricata

Treesearch

Constance I. Millar

1983-01-01

Clines, including hybrid zones, have long been studied empirically and theoretically, especially for the opportunity they present to study evolutionary forces (Sumner, 1929; Haldane, 1948; Barber and Jackson, 195 7). Recent theoretical studies have emphasized that clines may be important in speciation (summarized in Endler, 1977). This emphasis has motivated...

Spatial targeting of agri-environmental policy using bilevel evolutionary optimization

USDA-ARS?s Scientific Manuscript database

In this study we describe the optimal designation of agri-environmental policy as a bilevel optimization problem and propose an integrated solution method using a hybrid genetic algorithm. The problem is characterized by a single leader, the agency, that establishes a policy with the goal of optimiz...

Mandible shape in hybrid mice.

PubMed

Renaud, Sabrina; Alibert, Paul; Auffray, Jean-Christophe

2009-09-01

Hybridisation between closely related species is frequently seen as retarding evolutionary divergence and can also promote it by creating novel phenotypes due to new genetic combinations and developmental interactions. We therefore investigated how hybridisation affects the shape of the mouse mandible, a well-known feature in evo-devo studies. Parental groups corresponded to two strains of the European mouse sub-species Mus musculus domesticus and Mus musculus musculus. Parents and hybrids were bred in controlled conditions. The mandibles of F(1) hybrids are mostly intermediate between parental phenotypes as expected for a complex multigenic character. Nevertheless, a transgressive effect as well as an increased phenotypic variance characterise the hybrids. This suggests that hybridisation between the two subspecies could lead to a higher phenotypic variance due to complex interactions among the parental genomes including non-additive genetic effects. The major direction of variance is conserved, however, among hybrids and parent groups. Hybridisation may thus play a role in the production of original transgressive phenotypes occurring following pre-existing patterns of variance.

Towards unbiased benchmarking of evolutionary and hybrid algorithms for real-valued optimisation

NASA Astrophysics Data System (ADS)

MacNish, Cara

2007-12-01

Randomised population-based algorithms, such as evolutionary, genetic and swarm-based algorithms, and their hybrids with traditional search techniques, have proven successful and robust on many difficult real-valued optimisation problems. This success, along with the readily applicable nature of these techniques, has led to an explosion in the number of algorithms and variants proposed. In order for the field to advance it is necessary to carry out effective comparative evaluations of these algorithms, and thereby better identify and understand those properties that lead to better performance. This paper discusses the difficulties of providing benchmarking of evolutionary and allied algorithms that is both meaningful and logistically viable. To be meaningful the benchmarking test must give a fair comparison that is free, as far as possible, from biases that favour one style of algorithm over another. To be logistically viable it must overcome the need for pairwise comparison between all the proposed algorithms. To address the first problem, we begin by attempting to identify the biases that are inherent in commonly used benchmarking functions. We then describe a suite of test problems, generated recursively as self-similar or fractal landscapes, designed to overcome these biases. For the second, we describe a server that uses web services to allow researchers to 'plug in' their algorithms, running on their local machines, to a central benchmarking repository.

Reconstruction of the Evolutionary History of Saccharomyces cerevisiae x S. kudriavzevii Hybrids Based on Multilocus Sequence Analysis

PubMed Central

Peris, David; Lopes, Christian A.; Arias, Armando; Barrio, Eladio

2012-01-01

In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S. cerevisiae x S. kudriavzevii hybrids isolated from both fermentative and non-fermentative environments. Different wine S. cerevisiae strains and European S. kudriavzevii strains were probably involved in the hybridization events according to gene sequence information, as well as from previous data on their genome composition and ploidy. Finally, we postulate that these hybrids may have originated after the introduction of vine growing and winemaking practices by the Romans to the present Northern vine-growing limits and spread during the expansion of improved viticulture and enology practices that occurred during the Late Middle Ages. PMID:23049811

The Genomic Signature of Crop-Wild Introgression in Maize

PubMed Central

Hufford, Matthew B.; Lubinksy, Pesach; Pyhäjärvi, Tanja; Devengenzo, Michael T.; Ellstrand, Norman C.; Ross-Ibarra, Jeffrey

2013-01-01

The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes appeared resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these genomic regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly inform our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies. PMID:23671421

Recurrent hybridization and recent origin obscure phylogenetic relationships within the ‘white-headed’ gull (Larus sp.) complex

USGS Publications Warehouse

Sonsthagen, Sarah A.; Wilson, Robert E.; Chesser, Terry; Pons, Jean-Marc; Crochet, Pierre-Andre; Driscoll, Amy; Dove, Carla

2016-01-01

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

Recent hybrid origin of three rare chinese turtles

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

Stuart, Bryan L.; Parham, James F.

Three rare geoemydid turtles described from Chinese tradespecimens in the early 1990s, Ocadia glyphistoma, O. philippeni, andSacalia pseudocellata, are suspected to be hybrids because they are knownonly from their original descriptions and because they have morphologiesintermediate between other, better-known species. We cloned the allelesof a bi-parentally inherited nuclear intron from samples of these threespecies. The two aligned parental alleles of O. glyphistoma, O.philippeni, and S. pseudocellata have 5-11.5 times more heterozygouspositions than do 13 other geoemydid species. Phylogenetic analysis showsthat the two alleles from each turtle are strongly paraphyletic, butcorrectly match sequences of other species that were hypothesized frommorphology tomore » be their parental species. We conclude that these rareturtles represent recent hybrids rather than valid species. Specifically,"O. glyphistoma" is a hybrid of Mauremys sinensis and M. cf. annamensis,"O. philippeni" is a hybrid of M. sinensis and Cuora trifasciata, and "S.pseudocellata" is a hybrid of C. trifasciata and S. quadriocellata.Conservation resources are better directed toward finding and protectingpopulations of other rare Southeast Asian turtles that do representdistinct evolutionary lineages.« less

Beam-column joint shear prediction using hybridized deep learning neural network with genetic algorithm

NASA Astrophysics Data System (ADS)

Mundher Yaseen, Zaher; Abdulmohsin Afan, Haitham; Tran, Minh-Tung

2018-04-01

Scientifically evidenced that beam-column joints are a critical point in the reinforced concrete (RC) structure under the fluctuation loads effects. In this novel hybrid data-intelligence model developed to predict the joint shear behavior of exterior beam-column structure frame. The hybrid data-intelligence model is called genetic algorithm integrated with deep learning neural network model (GA-DLNN). The genetic algorithm is used as prior modelling phase for the input approximation whereas the DLNN predictive model is used for the prediction phase. To demonstrate this structural problem, experimental data is collected from the literature that defined the dimensional and specimens’ properties. The attained findings evidenced the efficitveness of the hybrid GA-DLNN in modelling beam-column joint shear problem. In addition, the accurate prediction achived with less input variables owing to the feasibility of the evolutionary phase.

An evolutionary morphological approach for software development cost estimation.

PubMed

Araújo, Ricardo de A; Oliveira, Adriano L I; Soares, Sergio; Meira, Silvio

2012-08-01

In this work we present an evolutionary morphological approach to solve the software development cost estimation (SDCE) problem. The proposed approach consists of a hybrid artificial neuron based on framework of mathematical morphology (MM) with algebraic foundations in the complete lattice theory (CLT), referred to as dilation-erosion perceptron (DEP). Also, we present an evolutionary learning process, called DEP(MGA), using a modified genetic algorithm (MGA) to design the DEP model, because a drawback arises from the gradient estimation of morphological operators in the classical learning process of the DEP, since they are not differentiable in the usual way. Furthermore, an experimental analysis is conducted with the proposed model using five complex SDCE problems and three well-known performance metrics, demonstrating good performance of the DEP model to solve SDCE problems. Copyright © 2012 Elsevier Ltd. All rights reserved.

Repeated Reticulate Evolution in North American Papilio machaon Group Swallowtail Butterflies

PubMed Central

Dupuis, Julian R.; Sperling, Felix A. H.

2015-01-01

Hybridization between distinct populations or species is increasingly recognized as an important process for generating biodiversity. However, the interaction between hybridization and speciation is complex, and the diverse evolutionary outcomes of hybridization are difficult to differentiate. Here we characterize potential hybridization in a species group of swallowtail butterflies using microsatellites, DNA sequences, and morphology, and assess whether adaptive introgression or homoploid hybrid speciation was the primary process leading to each putative hybrid lineage. Four geographically separated hybrid populations were identified in the Papilio machaon species group. One distinct mitochondrial DNA clade from P. machaon was fixed in three hybrid taxa (P. brevicauda, P. joanae, and P. m. kahli), while one hybrid swarm (P. zelicaon x machaon) exhibited this hybrid mtDNA clade as well as widespread parental mtDNA haplotypes from both parental species. Microsatellite markers and morphology showed variable admixture and intermediacy, ranging from signatures of prolonged differential introgression from the paternal species (P. polyxenes/P. zelicaon) to current gene flow with both parental species. Divergences of the hybrid lineages dated to early- to mid-Pleistocene, suggesting that repeated glaciations and subsequent range shifts of parental species, particularly P. machaon hudsonianus, facilitated initial hybridization. Although each lineage is distinct, P. joanae is the only taxon with sufficient evidence (ecological separation from parental species) to define it as a homoploid hybrid species. The repetition of hybridization in this group provides a valuable foundation for future research on hybridization, and these results emphasize the potential for hybridization to drive speciation in diverse ways. PMID:26517268

Comparison of the decomposition characteristics of aromatic VOCs using an electron beam hybrid system

NASA Astrophysics Data System (ADS)

Son, Youn-Suk; Kim, Ki-Joon; Kim, Ji-Yong; Kim, Jo-Chun

2010-12-01

We applied a hybrid technique to assess the decomposition characteristics of ethylbenzene and toluene that annexed the catalyst technique with existing electron beam (EB) technology. The removal efficiency of ethylbenzene in the EB-catalyst hybrid turned out to be 30% greater than that of EB-only treatment. We concluded that ethylbenzene was decomposed more easily than toluene by EB irradiation. We compared the independent effects of the EB-catalyst hybrid and catalyst-only methods, and observed that the efficiency of the EB-catalyst hybrid demonstrated approximately 6% improvement for decomposing toluene and 20% improvement for decomposing ethylbenzene. The G-values for ethylbenzene increased with initial concentration and reactor type: for example, the G-values by reactor type at 2800 ppmC were 7.5-10.9 (EB-only) and 12.9-25.7 (EB-catalyst hybrid). We also observed a significant decrease in by-products as well as in the removal efficiencies associated with the EB-catalyst hybrid technique.

Hybrid Organic/Inorganic Nanocomposites for Photovoltaic Cells

PubMed Central

Liu, Ruchuan

2014-01-01

Inorganic/organic hybrid solar cells have attracted a lot of interest due to their potential in combining the advantages of both components. To understand the key issues in association with photoinduced charge separation/transportation processes and to improve overall power conversion efficiency, various combinations with nanostructures of hybrid systems have been investigated. Here, we briefly review the structures of hybrid nanocomposites studied so far, and attempt to associate the power conversion efficiency with these nanostructures. Subsequently, we are then able to summarize the factors for optimizing the performance of inorganic/organic hybrid solar cells. PMID:28788591

The hybrid BCI system for movement control by combining motor imagery and moving onset visual evoked potential.

PubMed

Ma, Teng; Li, Hui; Deng, Lili; Yang, Hao; Lv, Xulin; Li, Peiyang; Li, Fali; Zhang, Rui; Liu, Tiejun; Yao, Dezhong; Xu, Peng

2017-04-01

Movement control is an important application for EEG-BCI (EEG-based brain-computer interface) systems. A single-modality BCI cannot provide an efficient and natural control strategy, but a hybrid BCI system that combines two or more different tasks can effectively overcome the drawbacks encountered in single-modality BCI control. In the current paper, we developed a new hybrid BCI system by combining MI (motor imagery) and mVEP (motion-onset visual evoked potential), aiming to realize the more efficient 2D movement control of a cursor. The offline analysis demonstrates that the hybrid BCI system proposed in this paper could evoke the desired MI and mVEP signal features simultaneously, and both are very close to those evoked in the single-modality BCI task. Furthermore, the online 2D movement control experiment reveals that the proposed hybrid BCI system could provide more efficient and natural control commands. The proposed hybrid BCI system is compensative to realize efficient 2D movement control for a practical online system, especially for those situations in which P300 stimuli are not suitable to be applied.

Hybrid and Plug-In Electric Vehicles (Spanish Version); Clean Cities, Energy Efficiency & Renewable Energy (EERE) (in Spanish)

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

None

This is a Spanish-language brochure about hybrid and plug-in electric vehicles, which use electricity as their primary fuel or to improve the efficiency of conventional vehicle designs. These vehicles can be divided into three categories: hybrid electric vehicles (HEVs), plug-in hybrid electric vehicles (PHEVs), all-electric vehicles (EVs). Together, they have great potential to cut U.S. petroleum use and vehicle emissions.

Hybrid morphology dependence of CdTe:CdSe bulk-heterojunction solar cells

PubMed Central

2014-01-01

A nanocrystal thin-film solar cell operating on an exciton splitting pattern requires a highly efficient separation of electron-hole pairs and transportation of separated charges. A hybrid bulk-heterojunction (HBH) nanostructure providing a large contact area and interpenetrated charge channels is favorable to an inorganic nanocrystal solar cell with high performance. For this freshly appeared structure, here in this work, we have firstly explored the influence of hybrid morphology on the photovoltaic performance of CdTe:CdSe bulk-heterojunction solar cells with variation in CdSe nanoparticle morphology. Quantum dot (QD) or nanotetrapod (NT)-shaped CdSe nanocrystals have been employed together with CdTe NTs to construct different hybrid structures. The solar cells with the two different hybrid active layers show obvious difference in photovoltaic performance. The hybrid structure with densely packed and continuously interpenetrated two phases generates superior morphological and electrical properties for more efficient inorganic bulk-heterojunction solar cells, which could be readily realized in the NTs:QDs hybrid. This proved strategy is applicable and promising in designing other highly efficient inorganic hybrid solar cells. PMID:25386107

Hybrid morphology dependence of CdTe:CdSe bulk-heterojunction solar cells.

PubMed

Tan, Furui; Qu, Shengchun; Zhang, Weifeng; Wang, Zhanguo

2014-01-01

A nanocrystal thin-film solar cell operating on an exciton splitting pattern requires a highly efficient separation of electron-hole pairs and transportation of separated charges. A hybrid bulk-heterojunction (HBH) nanostructure providing a large contact area and interpenetrated charge channels is favorable to an inorganic nanocrystal solar cell with high performance. For this freshly appeared structure, here in this work, we have firstly explored the influence of hybrid morphology on the photovoltaic performance of CdTe:CdSe bulk-heterojunction solar cells with variation in CdSe nanoparticle morphology. Quantum dot (QD) or nanotetrapod (NT)-shaped CdSe nanocrystals have been employed together with CdTe NTs to construct different hybrid structures. The solar cells with the two different hybrid active layers show obvious difference in photovoltaic performance. The hybrid structure with densely packed and continuously interpenetrated two phases generates superior morphological and electrical properties for more efficient inorganic bulk-heterojunction solar cells, which could be readily realized in the NTs:QDs hybrid. This proved strategy is applicable and promising in designing other highly efficient inorganic hybrid solar cells.

Applicability of major histocompatibility complex DRB1 alleles as markers to detect vertebrate hybridization: a case study from Iberian ibex × domestic goat in southern Spain

PubMed Central

2012-01-01

Background Hybridization between closely related wild and domestic species is of great concern because it can alter the evolutionary integrity of the affected populations. The high allelic variability of Major Histocompatibility Complex (MHC) loci usually excludes them from being used in studies to detect hybridization events. However, if a) the parental species don’t share alleles, and b) one of the parental species possesses an exceptionally low number of alleles (to facilitate analysis), then even MHC loci have the potential to detect hybrids. Results By genotyping the exon2 of the MHC class II DRB1 locus, we were able to detect hybridization between domestic goats (Capra hircus) and free-ranging Iberian ibex (Capra pyrenaica hispanica) by molecular means. Conclusions This is the first documentation of a Capra pyrenaica × Capra hircus hybridization, which presented us the opportunity to test the applicability of MHC loci as new, simple, cost-effective, and time-saving approach to detect hybridization between wild species and their domesticated relatives, thus adding value to MHC genes role in animal conservation and management. PMID:23006678

13.2% efficiency Si nanowire/PEDOT:PSS hybrid solar cell using a transfer-imprinted Au mesh electrode

PubMed Central

Park, Kwang-Tae; Kim, Han-Jung; Park, Min-Joon; Jeong, Jun-Ho; Lee, Jihye; Choi, Dae-Geun; Lee, Jung-Ho; Choi, Jun-Hyuk

2015-01-01

In recent years, inorganic/organic hybrid solar cell concept has received growing attention for alternative energy solution because of the potential for facile and low-cost fabrication and high efficiency. Here, we report highly efficient hybrid solar cells based on silicon nanowires (SiNWs) and poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) using transfer-imprinted metal mesh front electrodes. Such a structure increases the optical absorption and shortens the carrier transport distance, thus, it greatly increases the charge carrier collection efficiency. Compared with hybrid cells formed using indium tin oxide (ITO) electrodes, we find an increase in power conversion efficiency from 5.95% to 13.2%, which is attributed to improvements in both the electrical and optical properties of the Au mesh electrode. Our fabrication strategy for metal mesh electrode is suitable for the large-scale fabrication of flexible transparent electrodes, paving the way towards low-cost, high-efficiency, flexible solar cells. PMID:26174964

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

PubMed

Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh; Ohkuma, Moriya; Sugita, Takashi; Iwasaki, Wataru

2018-01-01

To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Spatio-temporal changes in the structure of an Australian frog hybrid zone: a 40-year perspective.

PubMed

Smith, Katie L; Hale, Joshua M; Gay, Laurène; Kearney, Michael; Austin, Jeremy J; Parris, Kirsten M; Melville, Jane

2013-12-01

Spatio-temporal studies of hybrid zones provide an opportunity to test evolutionary hypotheses of hybrid zone maintenance and movement. We conducted a landscape genetics study on a classic hybrid zone of the south-eastern Australian frogs, Litoria ewingii and Litoria paraewingi. This hybrid zone has been comprehensively studied since the 1960s, providing the unique opportunity to directly assess changes in hybrid zone structure across time. We compared both mtDNA and male advertisement call data from two time periods (present and 1960s). Clinal analysis of the coincidence (same center) and concordance (same width) of these traits indicated that the center of the hybrid zone has shifted 1 km south over the last 40 years, although the width of the zone and the rate of introgression remained unchanged. The low frequency of hybrids, the strong concordance of clines within a time period, and the small but significant movement across the study period despite significant anthropogenic changes through the region, suggest the hybrid zone is a tension zone located within a low-density trough. Hybrid zone movement has not been considered common in the past but our findings highlight that it should be considered a crucial component to our understanding of evolution. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Bucking the Trend in Wolf-Dog Hybridization: First Evidence from Europe of Hybridization between Female Dogs and Male Wolves

PubMed Central

Hindrikson, Maris; Männil, Peep; Ozolins, Janis; Krzywinski, Andrzej; Saarma, Urmas

2012-01-01

Studies on hybridization have proved critical for understanding key evolutionary processes such as speciation and adaptation. However, from the perspective of conservation, hybridization poses a concern, as it can threaten the integrity and fitness of many wild species, including canids. As a result of habitat fragmentation and extensive hunting pressure, gray wolf (Canis lupus) populations have declined dramatically in Europe and elsewhere during recent centuries. Small and fragmented populations have persisted, but often only in the presence of large numbers of dogs, which increase the potential for hybridization and introgression to deleteriously affect wolf populations. Here, we demonstrate hybridization between wolf and dog populations in Estonia and Latvia, and the role of both genders in the hybridization process, using combined analysis of maternal, paternal and biparental genetic markers. Eight animals exhibiting unusual external characteristics for wolves - six from Estonia and two from Latvia - proved to be wolf-dog hybrids. However, one of the hybridization events was extraordinary. Previous field observations and genetic studies have indicated that mating between wolves and dogs is sexually asymmetrical, occurring predominantly between female wolves and male dogs. While this was also the case among the Estonian hybrids, our data revealed the existence of dog mitochondrial genomes in the Latvian hybrids and, together with Y chromosome and autosomal microsatellite data, thus provided the first evidence from Europe of mating between male wolves and female dogs. We discuss patterns of sexual asymmetry in wolf-dog hybridization. PMID:23056315

Bucking the trend in wolf-dog hybridization: first evidence from europe of hybridization between female dogs and male wolves.

PubMed

Hindrikson, Maris; Männil, Peep; Ozolins, Janis; Krzywinski, Andrzej; Saarma, Urmas

2012-01-01

Studies on hybridization have proved critical for understanding key evolutionary processes such as speciation and adaptation. However, from the perspective of conservation, hybridization poses a concern, as it can threaten the integrity and fitness of many wild species, including canids. As a result of habitat fragmentation and extensive hunting pressure, gray wolf (Canis lupus) populations have declined dramatically in Europe and elsewhere during recent centuries. Small and fragmented populations have persisted, but often only in the presence of large numbers of dogs, which increase the potential for hybridization and introgression to deleteriously affect wolf populations. Here, we demonstrate hybridization between wolf and dog populations in Estonia and Latvia, and the role of both genders in the hybridization process, using combined analysis of maternal, paternal and biparental genetic markers. Eight animals exhibiting unusual external characteristics for wolves - six from Estonia and two from Latvia - proved to be wolf-dog hybrids. However, one of the hybridization events was extraordinary. Previous field observations and genetic studies have indicated that mating between wolves and dogs is sexually asymmetrical, occurring predominantly between female wolves and male dogs. While this was also the case among the Estonian hybrids, our data revealed the existence of dog mitochondrial genomes in the Latvian hybrids and, together with Y chromosome and autosomal microsatellite data, thus provided the first evidence from Europe of mating between male wolves and female dogs. We discuss patterns of sexual asymmetry in wolf-dog hybridization.

Reticulate evolution in stick insects: the case of Clonopsis (Insecta Phasmida).

PubMed

Milani, Liliana; Ghiselli, Fabrizio; Pellecchia, Marco; Scali, Valerio; Passamonti, Marco

2010-08-25

Phasmids show noteworthy abilities to overcome species-specific reproductive isolation mechanisms, including hybridization, polyploidy, parthenogenesis, hybridogenesis and androgenesis. From an evolutionary standpoint, such tangled reproductive interactions lead to the complex phyletic relationships known as "reticulate evolution". Moroccan stick insects of the genus Clonopsis include one bisexual (C. felicitatis) and two closely related parthenogenetic forms (C. gallica, C. soumiae), which represent a polyploid series in chromosome number, but with apparent diploid karyotypes. Moreover, two Clonopsis strains of ameiotic males have been described, C. androgenes-35 and C. androgenes-53. As a consequence, Clonopsis stick insects may have experienced complex micro-evolutionary events, which we try to disentangle in this study. Mitochondrial cox2 analysis supports a recent divergence of Clonopsis, while AFLPs evidence genetic differentiation not linked to karyotypes, so that parthenogenetic C. gallica and C. soumiae appear to be a mix of strains of polyphyletic origin rather than single parthenogenetic species. Moreover, an admixed hybrid origin seems to be confirmed for C. androgenes. On the whole, Clonopsis is an intriguing case of reticulate evolution. Actually, complex cladogenetic events should be taken into account to explain the observed genetic structure, including diploidization of polyploid karyotypes, possibly coupled with hybridization and androgenesis. We also proposed a "working hypothesis" to account for the observed data, which deserves further studies, but fits the observed data very well.

Adaptive introgression as a resource for management and genetic conservation in a changing climate.

PubMed

Hamilton, Jill A; Miller, Joshua M

2016-02-01

Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species' and populations' ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species' ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced-generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate. © 2015 Society for Conservation Biology.

Reticulate evolution in stick insects: the case of Clonopsis (Insecta Phasmida)

PubMed Central

2010-01-01

Background Phasmids show noteworthy abilities to overcome species-specific reproductive isolation mechanisms, including hybridization, polyploidy, parthenogenesis, hybridogenesis and androgenesis. From an evolutionary standpoint, such tangled reproductive interactions lead to the complex phyletic relationships known as "reticulate evolution". Moroccan stick insects of the genus Clonopsis include one bisexual (C. felicitatis) and two closely related parthenogenetic forms (C. gallica, C. soumiae), which represent a polyploid series in chromosome number, but with apparent diploid karyotypes. Moreover, two Clonopsis strains of ameiotic males have been described, C. androgenes-35 and C. androgenes-53. As a consequence, Clonopsis stick insects may have experienced complex micro-evolutionary events, which we try to disentangle in this study. Results Mitochondrial cox2 analysis supports a recent divergence of Clonopsis, while AFLPs evidence genetic differentiation not linked to karyotypes, so that parthenogenetic C. gallica and C. soumiae appear to be a mix of strains of polyphyletic origin rather than single parthenogenetic species. Moreover, an admixed hybrid origin seems to be confirmed for C. androgenes. Conclusion On the whole, Clonopsis is an intriguing case of reticulate evolution. Actually, complex cladogenetic events should be taken into account to explain the observed genetic structure, including diploidization of polyploid karyotypes, possibly coupled with hybridization and androgenesis. We also proposed a "working hypothesis" to account for the observed data, which deserves further studies, but fits the observed data very well. PMID:20738851

Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2.

PubMed

Curk, Franck; Ancillo, Gema; Garcia-Lor, Andres; Luro, François; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Navarro, Luis; Ollitrault, Patrick

2014-12-29

The most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity. Modern breeding of these species is hampered by their complex heterozygous genomic structures that determine species phenotype and are broken by sexual hybridisation. Nevertheless, a large amount of diversity is present in the citrus gene pool, and breeding to allow inclusion of desirable traits is of paramount importance. However, the efficient mobilization of citrus biodiversity in innovative breeding schemes requires previous understanding of Citrus origins and genomic structures. Haplotyping of multiple gene fragments along the whole genome is a powerful approach to reveal the admixture genomic structure of current species and to resolve the evolutionary history of the gene pools. In this study, the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species was assessed by analysis of 16 gene fragments on chromosome 2. 454 amplicon libraries were established using the Fluidigm array system for 48 genotypes and 16 gene fragments from chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed using the haplotypic data for each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins, (ii) was consistent with previous hypotheses regarding the origin of secondary species, and (iii) provided a new picture of the evolution of chromosome 2. 454 sequencing was an efficient strategy to establish haplotypes with significant phylogenetic assignations in Citrus, providing a new picture of the mixed structure on chromosome 2 in 48 citrus genotypes.

Novel brewing yeast hybrids: creation and application.

PubMed

Krogerus, Kristoffer; Magalhães, Frederico; Vidgren, Virve; Gibson, Brian

2017-01-01

The natural interspecies Saccharomyces cerevisiae × Saccharomyces eubayanus hybrid yeast is responsible for global lager beer production and is one of the most important industrial microorganisms. Its success in the lager brewing environment is due to a combination of traits not commonly found in pure yeast species, principally low-temperature tolerance, and maltotriose utilization. Parental transgression is typical of hybrid organisms and has been exploited previously for, e.g., the production of wine yeast with beneficial properties. The parental strain S. eubayanus has only been discovered recently and newly created lager yeast strains have not yet been applied industrially. A number of reports attest to the feasibility of this approach and artificially created hybrids are likely to have a significant impact on the future of lager brewing. De novo S. cerevisiae × S. eubayanus hybrids outperform their parent strains in a number of respects, including, but not restricted to, fermentation rate, sugar utilization, stress tolerance, and aroma formation. Hybrid genome function and stability, as well as different techniques for generating hybrids and their relative merits are discussed. Hybridization not only offers the possibility of generating novel non-GM brewing yeast strains with unique properties, but is expected to aid in unraveling the complex evolutionary history of industrial lager yeast.

The genetic basis of postzygotic reproductive isolation between Drosophila santomea and D. yakuba due to hybrid male sterility.

PubMed

Moehring, Amanda J; Llopart, Ana; Elwyn, Susannah; Coyne, Jerry A; Mackay, Trudy F C

2006-05-01

A major unresolved challenge of evolutionary biology is to determine the nature of the allelic variants of "speciation genes": those alleles whose interaction produces inviable or infertile interspecific hybrids but does not reduce fitness in pure species. Here we map quantitative trait loci (QTL) affecting fertility of male hybrids between D. yakuba and its recently discovered sibling species, D. santomea. We mapped three to four X chromosome QTL and two autosomal QTL with large effects on the reduced fertility of D. yakuba and D. santomea backcross males. We observed epistasis between the X-linked QTL and also between the X and autosomal QTL. The X chromosome had a disproportionately large effect on hybrid sterility in both reciprocal backcross hybrids. However, the genetics of hybrid sterility differ between D. yakuba and D. santomea backcross males, both in terms of the magnitude of main effects and in the epistatic interactions. The QTL affecting hybrid fertility did not colocalize with QTL affecting sexual isolation in this species pair, but did colocalize with QTL affecting the marked difference in pigmentation between D. yakuba and D. santomea. These results provide the basis for future high-resolution mapping and ultimately, molecular cloning, of the interacting genes that contribute to hybrid sterility.

Invasive hybridization in a threatened species is accelerated by climate change

NASA Astrophysics Data System (ADS)

Muhlfeld, Clint C.; Kovach, Ryan P.; Jones, Leslie A.; Al-Chokhachy, Robert; Boyer, Matthew C.; Leary, Robb F.; Lowe, Winsor H.; Luikart, Gordon; Allendorf, Fred W.

2014-07-01

Climate change will decrease worldwide biodiversity through a number of potential pathways, including invasive hybridization (cross-breeding between invasive and native species). How climate warming influences the spread of hybridization and loss of native genomes poses difficult ecological and evolutionary questions with little empirical information to guide conservation management decisions. Here we combine long-term genetic monitoring data with high-resolution climate and stream temperature predictions to evaluate how recent climate warming has influenced the spatio-temporal spread of human-mediated hybridization between threatened native westslope cutthroat trout (Oncorhynchus clarkii lewisi) and non-native rainbow trout (Oncorhynchus mykiss), the world's most widely introduced invasive fish. Despite widespread release of millions of rainbow trout over the past century within the Flathead River system, a large relatively pristine watershed in western North America, historical samples revealed that hybridization was prevalent only in one (source) population. During a subsequent 30-year period of accelerated warming, hybridization spread rapidly and was strongly linked to interactions between climatic drivers--precipitation and temperature--and distance to the source population. Specifically, decreases in spring precipitation and increases in summer stream temperature probably promoted upstream expansion of hybridization throughout the system. This study shows that rapid climate warming can exacerbate interactions between native and non-native species through invasive hybridization, which could spell genomic extinction for many species.

Report on Hybrid Rocket Cold Flow Experiments

NASA Technical Reports Server (NTRS)

Haapanen, Siina

2004-01-01

The discovery of paraffin based fuels has lead to renewed interest in hybrid rocket research. Experiments have shown that they burn 3-5 times faster than conventional hybrid fuels. High thrust level that would have required a multi-port design in the past can now be achieved with a single-port motor. While tests performed in Stanford and NASA Ames have demonstrated the paraffin hybrids to be a promising technology, one of the major challenges has been the relatively low efficiency. The c* efficiency has ranged between 80% and 90% in experiments conducted at the Ames Hybrid Combustion Facility (HCF). The test motor in these experiments had a 45 inch long fuel grain with the initial port diameter ranging between 3 and 5_inches. The c* efficiency is defined as the ratio of measured and theoretical characteristic velocities and is related to how completely the fuel and oxidizer are converted to combustion products. A low efficiency means that the reactants burn incompletely, and the reaction does not release the maximum possible amount of energy.

Elucidation and short-term forecasting of microcystin concentrations in Lake Suwa (Japan) by means of artificial neural networks and evolutionary algorithms.

PubMed

Chan, Wai Sum; Recknagel, Friedrich; Cao, Hongqing; Park, Ho-Dong

2007-05-01

Non-supervised artificial neural networks (ANN) and hybrid evolutionary algorithms (EA) were applied to analyse and model 12 years of limnological time-series data of the shallow hypertrophic Lake Suwa in Japan. The results have improved understanding of relationships between changing microcystin concentrations, Microcystis species abundances and annual rainfall intensity. The data analysis by non-supervised ANN revealed that total Microcystis abundance and extra-cellular microcystin concentrations in typical dry years are much higher than those in typical wet years. It also showed that high microcystin concentrations in dry years coincided with the dominance of the toxic Microcystis viridis whilst in typical wet years non-toxic Microcystis ichthyoblabe were dominant. Hybrid EA were used to discover rule sets to explain and forecast the occurrence of high microcystin concentrations in relation to water quality and climate conditions. The results facilitated early warning by 3-days-ahead forecasting of microcystin concentrations based on limnological and meteorological input data, achieving an r(2)=0.74 for testing.

Zeolite-loaded poly(dimethylsiloxane) hybrid films for highly efficient thin-film microextraction of organic volatiles in water.

PubMed

Wang, Tao; Ansai, Toshihiro; Lee, Seung-Woo

2017-01-15

ZSM-5 zeolite-loaded poly(dimethylsiloxane) (PDMS) hybrid thin films were demonstrated for efficient thin-film microextraction (TFME) coupled with gas chromatography-mass spectrometry for analyzing organic volatiles in water. The extraction efficiency for a series of aliphatic alcohols and two aromatic compounds was significantly improved owing to the presence of ZSM-5 zeolites. The extraction efficiency of the hybrid films was increased in proportion to the content of ZSM-5 in the PDMS film, with 20wt% of ZSM-5 showing the best results. The 20wt% ZSM-5/PDMS hybrid film exhibited higher volatile organic content extraction compared with the single-component PDMS film or PDMS hybrid films containing other types of zeolite (e.g., SAPO-34). Limits of detection and limits of quantitation for individual analytes were in the range of 0.0034-0.049ppb and of 0.010-0.15 ppb, respectively. The effects of experimental parameters such as extraction time and temperature were optimized, and the molecular dispersion of the zeolites in/on the hybrid film matrix was confirmed with scanning electron microscopy and atomic force microscopy. Furthermore, the optimized hybrid film was preliminarily tested for the analysis of organic volatiles contained in commercially available soft drinks. Copyright © 2016 Elsevier B.V. All rights reserved.

Fuzzy control based engine sizing optimization for a fuel cell/battery hybrid mini-bus

NASA Astrophysics Data System (ADS)

Kim, Minjin; Sohn, Young-Jun; Lee, Won-Yong; Kim, Chang-Soo

The fuel cell/battery hybrid vehicle has been focused for the alternative engine of the existing internal-combustion engine due to the following advantages of the fuel cell and the battery. Firstly, the fuel cell is highly efficient and eco-friendly. Secondly, the battery has the fast response for the changeable power demand. However, the competitive efficiency of the hybrid fuel cell vehicle is necessary to successfully alternate the conventional vehicles with the fuel cell hybrid vehicle. The most relevant factor which affects the overall efficiency of the hybrid fuel cell vehicle is the relative engine sizing between the fuel cell and the battery. Therefore the design method to optimize the engine sizing of the fuel cell hybrid vehicle has been proposed. The target system is the fuel cell/battery hybrid mini-bus and its power distribution is controlled based on the fuzzy logic. The optimal engine sizes are determined based on the simulator developed in this paper. The simulator includes the several models for the fuel cell, the battery, and the major balance of plants. After the engine sizing, the system efficiency and the stability of the power distribution are verified based on the well-known driving schedule. Consequently, the optimally designed mini-bus shows good performance.

Hybrid Intrusion Forecasting Framework for Early Warning System

NASA Astrophysics Data System (ADS)

Kim, Sehun; Shin, Seong-Jun; Kim, Hyunwoo; Kwon, Ki Hoon; Han, Younggoo

Recently, cyber attacks have become a serious hindrance to the stability of Internet. These attacks exploit interconnectivity of networks, propagate in an instant, and have become more sophisticated and evolutionary. Traditional Internet security systems such as firewalls, IDS and IPS are limited in terms of detecting recent cyber attacks in advance as these systems respond to Internet attacks only after the attacks inflict serious damage. In this paper, we propose a hybrid intrusion forecasting system framework for an early warning system. The proposed system utilizes three types of forecasting methods: time-series analysis, probabilistic modeling, and data mining method. By combining these methods, it is possible to take advantage of the forecasting technique of each while overcoming their drawbacks. Experimental results show that the hybrid intrusion forecasting method outperforms each of three forecasting methods.

Highly Efficient Simplified Single-Emitting-Layer Hybrid WOLEDs with Low Roll-off and Good Color Stability through Enhanced Förster Energy Transfer.

PubMed

Zhang, Dongdong; Cai, Minghan; Zhang, Yunge; Zhang, Deqiang; Duan, Lian

2015-12-30

Single-emitting layer hybrid white organic light-emitting diodes (SEL-hybrid-WOLEDs) usually suffer from low efficiency, significant roll-off, and poor color stability, attributed to the incomplete energy transfer from the triplet states of the blue fluorophores to the phosphors. Here, we demonstrate highly efficient SEL-hybrid-WOLEDs with low roll-off and good color-stability utilizing blue thermally activated delayed fluorescence (TADF) materials as the host emitters. The triplet states of the blue TADF host emitter can be up-converted into its singlet states, and then the energy is transferred to the complementary phosphors through the long-range Förster energy transfer, enhancing the energy transfer from the host to the dopant. Simplified SEL-hybrid-WOLEDs achieve the highest forward-viewing external quantum efficiency (EQE) of 20.8% and power efficiency of 51.2 lm/W with CIE coordinates of (0.398, 0.456) at a luminance of 500 cd/m(2). The device EQE only slightly drops to 19.6% at a practical luminance of 1000 cd/m(2) with a power efficiency of 38.7 lm/W. Furthermore, the spectra of the device are rather stable with the raising voltage. The reason can be assigned to the enhanced Förster energy transfer, wide charge recombination zone, as well as the bipolar charge transporting ability of the host emitter. We believe that our work may shed light on the future development of highly efficient SEL-hybrid-WOLEDs with simultaneous low roll-off and good color stability.

Natural gas applications for hybrid vehicles. Final report, October 1992-July 1993

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

Bentley, J.M.

1993-08-01

Hybrid vehicle technology holds the potential for improved efficiency and emissions compared with internal combustion (IC) engines and improved range and refueling convenience over electric vehicles. This study evaluated the potential for using natural gas as a hybrid vehicle fuel. Potential regulatory and market drivers were evaluated for hybrids generally and natural gas hybrids in specific. Heat engine options and other configuration issues were investigated to determine efficiency, emissions or other benefits of light- and heavy-duty hybrids. Several hybrid vehicle configurations were evaluated to determine the specific packaging attributes of natural gas in a hybrid configuration. Generally, conventional IC enginesmore » appear adequate for most emissions-sensitive hybrid applications with no great advantage being gained from using turbines or other more advanced heat engines. The largest technology barrier to a near-term hybrid is the weight of available or near-term batteries. Smaller, light-duty hybrid vehicles will be more sensitive to this weight handicap than larger vehicles such as the urban transit bus.« less

Neuronal boost to evolutionary dynamics.

PubMed

de Vladar, Harold P; Szathmáry, Eörs

2015-12-06

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

Evolutionary branching under multi-dimensional evolutionary constraints.

PubMed

Ito, Hiroshi; Sasaki, Akira

2016-10-21

The fitness of an existing phenotype and of a potential mutant should generally depend on the frequencies of other existing phenotypes. Adaptive evolution driven by such frequency-dependent fitness functions can be analyzed effectively using adaptive dynamics theory, assuming rare mutation and asexual reproduction. When possible mutations are restricted to certain directions due to developmental, physiological, or physical constraints, the resulting adaptive evolution may be restricted to subspaces (constraint surfaces) with fewer dimensionalities than the original trait spaces. To analyze such dynamics along constraint surfaces efficiently, we develop a Lagrange multiplier method in the framework of adaptive dynamics theory. On constraint surfaces of arbitrary dimensionalities described with equality constraints, our method efficiently finds local evolutionarily stable strategies, convergence stable points, and evolutionary branching points. We also derive the conditions for the existence of evolutionary branching points on constraint surfaces when the shapes of the surfaces can be chosen freely. Copyright © 2016 Elsevier Ltd. All rights reserved.

a New Hybrid Yin-Yang Swarm Optimization Algorithm for Uncapacitated Warehouse Location Problems

NASA Astrophysics Data System (ADS)

Heidari, A. A.; Kazemizade, O.; Hakimpour, F.

2017-09-01

Yin-Yang-pair optimization (YYPO) is one of the latest metaheuristic algorithms (MA) proposed in 2015 that tries to inspire the philosophy of balance between conflicting concepts. Particle swarm optimizer (PSO) is one of the first population-based MA inspired by social behaviors of birds. In spite of PSO, the YYPO is not a nature inspired optimizer. It has a low complexity and starts with only two initial positions and can produce more points with regard to the dimension of target problem. Due to unique advantages of these methodologies and to mitigate the immature convergence and local optima (LO) stagnation problems in PSO, in this work, a continuous hybrid strategy based on the behaviors of PSO and YYPO is proposed to attain the suboptimal solutions of uncapacitated warehouse location (UWL) problems. This efficient hierarchical PSO-based optimizer (PSOYPO) can improve the effectiveness of PSO on spatial optimization tasks such as the family of UWL problems. The performance of the proposed PSOYPO is verified according to some UWL benchmark cases. These test cases have been used in several works to evaluate the efficacy of different MA. Then, the PSOYPO is compared to the standard PSO, genetic algorithm (GA), harmony search (HS), modified HS (OBCHS), and evolutionary simulated annealing (ESA). The experimental results demonstrate that the PSOYPO can reveal a better or competitive efficacy compared to the PSO and other MA.

A Structural Model Decomposition Framework for Hybrid Systems Diagnosis

NASA Technical Reports Server (NTRS)

Daigle, Matthew; Bregon, Anibal; Roychoudhury, Indranil

2015-01-01

Nowadays, a large number of practical systems in aerospace and industrial environments are best represented as hybrid systems that consist of discrete modes of behavior, each defined by a set of continuous dynamics. These hybrid dynamics make the on-line fault diagnosis task very challenging. In this work, we present a new modeling and diagnosis framework for hybrid systems. Models are composed from sets of user-defined components using a compositional modeling approach. Submodels for residual generation are then generated for a given mode, and reconfigured efficiently when the mode changes. Efficient reconfiguration is established by exploiting causality information within the hybrid system models. The submodels can then be used for fault diagnosis based on residual generation and analysis. We demonstrate the efficient causality reassignment, submodel reconfiguration, and residual generation for fault diagnosis using an electrical circuit case study.

Single- and Multiple-Objective Optimization with Differential Evolution and Neural Networks

NASA Technical Reports Server (NTRS)

Rai, Man Mohan

2006-01-01

Genetic and evolutionary algorithms have been applied to solve numerous problems in engineering design where they have been used primarily as optimization procedures. These methods have an advantage over conventional gradient-based search procedures became they are capable of finding global optima of multi-modal functions and searching design spaces with disjoint feasible regions. They are also robust in the presence of noisy data. Another desirable feature of these methods is that they can efficiently use distributed and parallel computing resources since multiple function evaluations (flow simulations in aerodynamics design) can be performed simultaneously and independently on ultiple processors. For these reasons genetic and evolutionary algorithms are being used more frequently in design optimization. Examples include airfoil and wing design and compressor and turbine airfoil design. They are also finding increasing use in multiple-objective and multidisciplinary optimization. This lecture will focus on an evolutionary method that is a relatively new member to the general class of evolutionary methods called differential evolution (DE). This method is easy to use and program and it requires relatively few user-specified constants. These constants are easily determined for a wide class of problems. Fine-tuning the constants will off course yield the solution to the optimization problem at hand more rapidly. DE can be efficiently implemented on parallel computers and can be used for continuous, discrete and mixed discrete/continuous optimization problems. It does not require the objective function to be continuous and is noise tolerant. DE and applications to single and multiple-objective optimization will be included in the presentation and lecture notes. A method for aerodynamic design optimization that is based on neural networks will also be included as a part of this lecture. The method offers advantages over traditional optimization methods. It is more flexible than other methods in dealing with design in the context of both steady and unsteady flows, partial and complete data sets, combined experimental and numerical data, inclusion of various constraints and rules of thumb, and other issues that characterize the aerodynamic design process. Neural networks provide a natural framework within which a succession of numerical solutions of increasing fidelity, incorporating more realistic flow physics, can be represented and utilized for optimization. Neural networks also offer an excellent framework for multiple-objective and multi-disciplinary design optimization. Simulation tools from various disciplines can be integrated within this framework and rapid trade-off studies involving one or many disciplines can be performed. The prospect of combining neural network based optimization methods and evolutionary algorithms to obtain a hybrid method with the best properties of both methods will be included in this presentation. Achieving solution diversity and accurate convergence to the exact Pareto front in multiple objective optimization usually requires a significant computational effort with evolutionary algorithms. In this lecture we will also explore the possibility of using neural networks to obtain estimates of the Pareto optimal front using non-dominated solutions generated by DE as training data. Neural network estimators have the potential advantage of reducing the number of function evaluations required to obtain solution accuracy and diversity, thus reducing cost to design.

Genetic analysis of hybridization and introgression between wild mongoose and brown lemurs.

PubMed

Pastorini, Jennifer; Zaramody, Alphonse; Curtis, Deborah J; Nievergelt, Caroline M; Mundy, Nicholas I

2009-02-05

Hybrid zones generally represent areas of secondary contact after speciation. The nature of the interaction between genes of individuals in a hybrid zone is of interest in the study of evolutionary processes. In this study, data from nuclear microsatellites and mitochondrial DNA sequences were used to genetically characterize hybridization between wild mongoose lemurs (Eulemur mongoz) and brown lemurs (E. fulvus) at Anjamena in west Madagascar. Two segments of mtDNA have been sequenced and 12 microsatellite loci screened in 162 brown lemurs and mongoose lemurs. Among the mongoose lemur population at Anjamena, we identified two F1 hybrids (one also having the mtDNA haplotype of E. fulvus) and six other individuals with putative introgressed alleles in their genotype. Principal component analysis groups both hybrids as intermediate between E. mongoz and E. fulvus and admixture analyses revealed an admixed genotype for both animals. Paternity testing proved one F1 hybrid to be fertile. Of the eight brown lemurs genotyped, all have either putative introgressed microsatellite alleles and/or the mtDNA haplotype of E. mongoz. Introgression is bidirectional for the two species, with an indication that it is more frequent in brown lemurs than in mongoose lemurs. We conclude that this hybridization occurs because mongoose lemurs have expanded their range relatively recently. Introgressive hybridization may play an important role in the unique lemur radiation, as has already been shown in other rapidly evolving animals.

Distribution of 45S rDNA in Modern Rose Cultivars (Rosa hybrida), Rosa rugosa, and Their Interspecific Hybrids Revealed by Fluorescence in situ Hybridization.

PubMed

Ding, Xiao-Liu; Xu, Ting-Liang; Wang, Jing; Luo, Le; Yu, Chao; Dong, Gui-Min; Pan, Hui-Tang; Zhang, Qi-Xiang

2016-01-01

To elucidate the evolutionary dynamics of the location and number of rDNA loci in the process of polyploidization in the genus Rosa, we examined 45S rDNA sites in the chromosomes of 6 modern rose cultivars (R. hybrida), 5 R. rugosa cultivars, and 20 hybrid progenies by fluorescence in situ hybridization. Variation in the number of rDNA sites in parents and their interspecific hybrids was detected. As expected, 4 rDNA sites were observed in the genomes of 4 modern rose cultivars, while 3 hybridization sites were observed in the 2 others. Two expected rDNA sites were found in 2 R. rugosa cultivars, while in the other 3 R. rugosa cultivars 4 sites were present. Among the 20 R. hybrida × R. rugosa offspring, 13 carried the expected number of rDNA sites, and 1 had 6 hybridization sites, which exceeded the expected number by far. The other 6 offspring had either 2 or 3 hybridization sites, which was less than expected. Differences in the number of rDNA loci were observed in interspecific offspring, indicating that rDNA loci exhibit instability after distant hybridization events. Abnormal chromosome pairing may be the main factor explaining the variation in rDNA sites during polyploidization. © 2016 S. Karger AG, Basel.

Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins

PubMed Central

2012-01-01

Background Interspecific hybrids between S. cerevisiae × S. kudriavzevii have frequently been detected in wine and beer fermentations. Significant physiological differences among parental and hybrid strains under different stress conditions have been evidenced. In this study, we used comparative genome hybridization analysis to evaluate the genome composition of different S. cerevisiae × S. kudriavzevii natural hybrids isolated from wine and beer fermentations to infer their evolutionary origins and to figure out the potential role of common S. kudriavzevii gene fraction present in these hybrids. Results Comparative genomic hybridization (CGH) and ploidy analyses carried out in this study confirmed the presence of individual and differential chromosomal composition patterns for most S. cerevisiae × S. kudriavzevii hybrids from beer and wine. All hybrids share a common set of depleted S. cerevisiae genes, which also are depleted or absent in the wine strains studied so far, and the presence a common set of S. kudriavzevii genes, which may be associated with their capability to grow at low temperatures. Finally, a maximum parsimony analysis of chromosomal rearrangement events, occurred in the hybrid genomes, indicated the presence of two main groups of wine hybrids and different divergent lineages of brewing strains. Conclusion Our data suggest that wine and beer S. cerevisiae × S. kudriavzevii hybrids have been originated by different rare-mating events involving a diploid wine S. cerevisiae and a haploid or diploid European S. kudriavzevii strains. Hybrids maintain several S. kudriavzevii genes involved in cold adaptation as well as those related to S. kudriavzevii mitochondrial functions. PMID:22906207

Three state-of-the-art individual electric and hybrid vehicle test reports, volume 2

NASA Technical Reports Server (NTRS)

1978-01-01

Procedures used in determining the energy efficiency and economy of a gasoline-electric hybrid taxi, an electric passenger car, and an electric van are described. Tabular and graphic data show results of driving cycle and constant speed tests, energy distribution to various components, efficiency of the components, and, for the hybrid vehicle, the emissions.

The hybrid BCI system for movement control by combining motor imagery and moving onset visual evoked potential

NASA Astrophysics Data System (ADS)

Ma, Teng; Li, Hui; Deng, Lili; Yang, Hao; Lv, Xulin; Li, Peiyang; Li, Fali; Zhang, Rui; Liu, Tiejun; Yao, Dezhong; Xu, Peng

2017-04-01

Objective. Movement control is an important application for EEG-BCI (EEG-based brain-computer interface) systems. A single-modality BCI cannot provide an efficient and natural control strategy, but a hybrid BCI system that combines two or more different tasks can effectively overcome the drawbacks encountered in single-modality BCI control. Approach. In the current paper, we developed a new hybrid BCI system by combining MI (motor imagery) and mVEP (motion-onset visual evoked potential), aiming to realize the more efficient 2D movement control of a cursor. Main result. The offline analysis demonstrates that the hybrid BCI system proposed in this paper could evoke the desired MI and mVEP signal features simultaneously, and both are very close to those evoked in the single-modality BCI task. Furthermore, the online 2D movement control experiment reveals that the proposed hybrid BCI system could provide more efficient and natural control commands. Significance. The proposed hybrid BCI system is compensative to realize efficient 2D movement control for a practical online system, especially for those situations in which P300 stimuli are not suitable to be applied.

Using hybridization networks to retrace the evolution of Indo-European languages.

PubMed

Willems, Matthieu; Lord, Etienne; Laforest, Louise; Labelle, Gilbert; Lapointe, François-Joseph; Di Sciullo, Anna Maria; Makarenkov, Vladimir

2016-09-06

Curious parallels between the processes of species and language evolution have been observed by many researchers. Retracing the evolution of Indo-European (IE) languages remains one of the most intriguing intellectual challenges in historical linguistics. Most of the IE language studies use the traditional phylogenetic tree model to represent the evolution of natural languages, thus not taking into account reticulate evolutionary events, such as language hybridization and word borrowing which can be associated with species hybridization and horizontal gene transfer, respectively. More recently, implicit evolutionary networks, such as split graphs and minimal lateral networks, have been used to account for reticulate evolution in linguistics. Striking parallels existing between the evolution of species and natural languages allowed us to apply three computational biology methods for reconstruction of phylogenetic networks to model the evolution of IE languages. We show how the transfer of methods between the two disciplines can be achieved, making necessary methodological adaptations. Considering basic vocabulary data from the well-known Dyen's lexical database, which contains word forms in 84 IE languages for the meanings of a 200-meaning Swadesh list, we adapt a recently developed computational biology algorithm for building explicit hybridization networks to study the evolution of IE languages and compare our findings to the results provided by the split graph and galled network methods. We conclude that explicit phylogenetic networks can be successfully used to identify donors and recipients of lexical material as well as the degree of influence of each donor language on the corresponding recipient languages. We show that our algorithm is well suited to detect reticulate relationships among languages, and present some historical and linguistic justification for the results obtained. Our findings could be further refined if relevant syntactic, phonological and morphological data could be analyzed along with the available lexical data.

Hybridization of decomposition and local search for multiobjective optimization.

PubMed

Ke, Liangjun; Zhang, Qingfu; Battiti, Roberto

2014-10-01

Combining ideas from evolutionary algorithms, decomposition approaches, and Pareto local search, this paper suggests a simple yet efficient memetic algorithm for combinatorial multiobjective optimization problems: memetic algorithm based on decomposition (MOMAD). It decomposes a combinatorial multiobjective problem into a number of single objective optimization problems using an aggregation method. MOMAD evolves three populations: 1) population P(L) for recording the current solution to each subproblem; 2) population P(P) for storing starting solutions for Pareto local search; and 3) an external population P(E) for maintaining all the nondominated solutions found so far during the search. A problem-specific single objective heuristic can be applied to these subproblems to initialize the three populations. At each generation, a Pareto local search method is first applied to search a neighborhood of each solution in P(P) to update P(L) and P(E). Then a single objective local search is applied to each perturbed solution in P(L) for improving P(L) and P(E), and reinitializing P(P). The procedure is repeated until a stopping condition is met. MOMAD provides a generic hybrid multiobjective algorithmic framework in which problem specific knowledge, well developed single objective local search and heuristics and Pareto local search methods can be hybridized. It is a population based iterative method and thus an anytime algorithm. Extensive experiments have been conducted in this paper to study MOMAD and compare it with some other state-of-the-art algorithms on the multiobjective traveling salesman problem and the multiobjective knapsack problem. The experimental results show that our proposed algorithm outperforms or performs similarly to the best so far heuristics on these two problems.

Efficient triplet harvesting of hybrid white organic light-emitting diodes using thermally activated delayed fluorescence green emitter

NASA Astrophysics Data System (ADS)

Lee, Song Eun; Lee, Ho Won; Baek, Hyun Jung; Yun, Tae Jun; Yun, Geum Jae; Kim, Woo Young; Kim, Young Kwan

2016-10-01

Hybrid white organic light-emitting diodes (WOLEDs) were fabricated by applying triplet harvesting (TH) using a green thermally activated delayed fluorescence (TADF) emitter. The triplet exciton of the green TADF emitter can be upconverted to its singlet state. The TH involved energy transfer of triplet exciton from a blue fluorescent emitter to a green TADF and red phosphorescent emitters, where they can decay radiatively. In addition, the triplet exciton of the green TADF emitter was energy transferred to its singlet state for a reverse intersystem crossing by green emission. Enhanced hybrid WOLEDs were demonstrated using an efficient green TADF emitter combined with red phosphorescent and blue fluorescent emitters. Hybrid WOLEDs were fabricated with various hole-electron recombination zones as changing blue emitting layer thicknesses. Among these, hybrid WOLEDs showed a maximum external quantum efficiency of 11.23%, luminous efficiency of 29.20 cd/A, and a power efficiency of 26.21 lm/W. Moreover, the WOLED exhibited electroluminescence spectra with Commission International de L'Éclairage chromaticity of (0.38, 0.36) at 1000 cd/m2 and a color rendering index of 82 at a practical brightness of 20,000 cd/m2.

Optimality and stability of symmetric evolutionary games with applications in genetic selection.

PubMed

Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun

2015-06-01

Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders.

An Orthogonal Evolutionary Algorithm With Learning Automata for Multiobjective Optimization.

PubMed

Dai, Cai; Wang, Yuping; Ye, Miao; Xue, Xingsi; Liu, Hailin

2016-12-01

Research on multiobjective optimization problems becomes one of the hottest topics of intelligent computation. In order to improve the search efficiency of an evolutionary algorithm and maintain the diversity of solutions, in this paper, the learning automata (LA) is first used for quantization orthogonal crossover (QOX), and a new fitness function based on decomposition is proposed to achieve these two purposes. Based on these, an orthogonal evolutionary algorithm with LA for complex multiobjective optimization problems with continuous variables is proposed. The experimental results show that in continuous states, the proposed algorithm is able to achieve accurate Pareto-optimal sets and wide Pareto-optimal fronts efficiently. Moreover, the comparison with the several existing well-known algorithms: nondominated sorting genetic algorithm II, decomposition-based multiobjective evolutionary algorithm, decomposition-based multiobjective evolutionary algorithm with an ensemble of neighborhood sizes, multiobjective optimization by LA, and multiobjective immune algorithm with nondominated neighbor-based selection, on 15 multiobjective benchmark problems, shows that the proposed algorithm is able to find more accurate and evenly distributed Pareto-optimal fronts than the compared ones.

Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights.

PubMed

Liston, Aaron; Cronn, Richard; Ashman, Tia-Lynn

2014-10-01

The cultivated strawberry, Fragaria ×ananassa, is one of the youngest domesticated plants. Its 18th century origin via hybridization in Europe between the North American F. virginiana and the South American F. chiloensis was documented by the botanist Antoine Nicolas Duchesne. His 1766 "Natural History of Strawberries" is an extraordinary work that integrates fundamental discoveries on the biology, ecology, and phylogeny of Fragaria with applied information on cultivation and ethnobotanical uses, serving as an inspiration for current research in the genus. Fragaria species exhibit the full range of sexual systems in the gynodioecy pathway from hermaphroditism to dioecy (and back again), as well as variation in self-compatibility, and evidence of sex chromosomes with female heterogamety. The genus is also characterized by interspecific hybridization and polyploidy, with a natural range of ploidy levels from diploids to decaploids. This biological diversity, combined with the availability of genomic resources and the ease of growing and experimenting with the plants, makes Fragaria a very attractive system for ecological and evolutionary genomics. The goal of this review is to introduce Fragaria as a model genus and to provide a roadmap for future integrative research. These research directions will deepen our understanding of the ecological and evolutionary context that shaped the ancestors of the cultivated strawberry, not only providing information that can be applied to efforts to shape the future of this important fruit crop but also our understanding of key transitions in plant evolution. © 2014 Botanical Society of America, Inc.

PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination

PubMed Central

Baker, Christopher L.; Kajita, Shimpei; Walker, Michael; Saxl, Ruth L.; Raghupathy, Narayanan; Choi, Kwangbom; Petkov, Petko M.; Paigen, Kenneth

2015-01-01

Meiotic recombination generates new genetic variation and assures the proper segregation of chromosomes in gametes. PRDM9, a zinc finger protein with histone methyltransferase activity, initiates meiotic recombination by binding DNA at recombination hotspots and directing the position of DNA double-strand breaks (DSB). The DSB repair mechanism suggests that hotspots should eventually self-destruct, yet genome-wide recombination levels remain constant, a conundrum known as the hotspot paradox. To test if PRDM9 drives this evolutionary erosion, we measured activity of the Prdm9 Cst allele in two Mus musculus subspecies, M.m. castaneus, in which Prdm9Cst arose, and M.m. domesticus, into which Prdm9Cst was introduced experimentally. Comparing these two strains, we find that haplotype differences at hotspots lead to qualitative and quantitative changes in PRDM9 binding and activity. Using Mus spretus as an outlier, we found most variants affecting PRDM9Cst binding arose and were fixed in M.m. castaneus, suppressing hotspot activity. Furthermore, M.m. castaneus×M.m. domesticus F1 hybrids exhibit novel hotspots, with large haplotype biases in both PRDM9 binding and chromatin modification. These novel hotspots represent sites of historic evolutionary erosion that become activated in hybrids due to crosstalk between one parent's Prdm9 allele and the opposite parent's chromosome. Together these data support a model where haplotype-specific PRDM9 binding directs biased gene conversion at hotspots, ultimately leading to hotspot erosion. PMID:25568937

PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination.

PubMed

Baker, Christopher L; Kajita, Shimpei; Walker, Michael; Saxl, Ruth L; Raghupathy, Narayanan; Choi, Kwangbom; Petkov, Petko M; Paigen, Kenneth

2015-01-01

Meiotic recombination generates new genetic variation and assures the proper segregation of chromosomes in gametes. PRDM9, a zinc finger protein with histone methyltransferase activity, initiates meiotic recombination by binding DNA at recombination hotspots and directing the position of DNA double-strand breaks (DSB). The DSB repair mechanism suggests that hotspots should eventually self-destruct, yet genome-wide recombination levels remain constant, a conundrum known as the hotspot paradox. To test if PRDM9 drives this evolutionary erosion, we measured activity of the Prdm9Cst allele in two Mus musculus subspecies, M.m. castaneus, in which Prdm9Cst arose, and M.m. domesticus, into which Prdm9Cst was introduced experimentally. Comparing these two strains, we find that haplotype differences at hotspots lead to qualitative and quantitative changes in PRDM9 binding and activity. Using Mus spretus as an outlier, we found most variants affecting PRDM9Cst binding arose and were fixed in M.m. castaneus, suppressing hotspot activity. Furthermore, M.m. castaneus×M.m. domesticus F1 hybrids exhibit novel hotspots, with large haplotype biases in both PRDM9 binding and chromatin modification. These novel hotspots represent sites of historic evolutionary erosion that become activated in hybrids due to crosstalk between one parent's Prdm9 allele and the opposite parent's chromosome. Together these data support a model where haplotype-specific PRDM9 binding directs biased gene conversion at hotspots, ultimately leading to hotspot erosion.

A quantitative and spatially resolved analysis of the performance-bottleneck in high efficiency, planar hybrid perovskite solar cells

DOE PAGES

Draguta, Sergiu; Christians, Jeffrey A.; Morozov, Yurii V.; ...

2018-01-01

Hybrid perovskites represent a potential paradigm shift for the creation of low-cost solar cells. Current power conversion efficiencies (PCEs) exceed 22%. However, despite this, record PCEs are still far from their theoretical Shockley–Queisser limit of 31%. To increase these PCE values, there is a pressing need to understand, quantify and microscopically model charge recombination processes in full working devices. Here, we present a complete microscopic account of charge recombination processes in high efficiency (18–19% PCE) hybrid perovskite (mixed cation and methylammonium lead iodide) solar cells. We employ diffraction-limited optical measurements along with relevant kinetic modeling to establish, for the firstmore » time, local photoluminescence quantum yields, trap densities, trapping efficiencies, charge extraction efficiencies, quasi-Fermi-level splitting, and effective PCE estimates. Correlations between these spatially resolved parameters, in turn, allow us to conclude that intrinsic electron traps in the perovskite active layers limit the performance of these state-of-the-art hybrid perovskite solar cells.« less

A quantitative and spatially resolved analysis of the performance-bottleneck in high efficiency, planar hybrid perovskite solar cells

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

Draguta, Sergiu; Christians, Jeffrey A.; Morozov, Yurii V.

Hybrid perovskites represent a potential paradigm shift for the creation of low-cost solar cells. Current power conversion efficiencies (PCEs) exceed 22%. However, despite this, record PCEs are still far from their theoretical Shockley–Queisser limit of 31%. To increase these PCE values, there is a pressing need to understand, quantify and microscopically model charge recombination processes in full working devices. Here, we present a complete microscopic account of charge recombination processes in high efficiency (18–19% PCE) hybrid perovskite (mixed cation and methylammonium lead iodide) solar cells. We employ diffraction-limited optical measurements along with relevant kinetic modeling to establish, for the firstmore » time, local photoluminescence quantum yields, trap densities, trapping efficiencies, charge extraction efficiencies, quasi-Fermi-level splitting, and effective PCE estimates. Correlations between these spatially resolved parameters, in turn, allow us to conclude that intrinsic electron traps in the perovskite active layers limit the performance of these state-of-the-art hybrid perovskite solar cells.« less

General fuel cell hybrid synergies and hybrid system testing status

NASA Astrophysics Data System (ADS)

Winkler, Wolfgang; Nehter, Pedro; Williams, Mark C.; Tucker, David; Gemmen, Randy

FCT hybrid power systems offer the highest efficiency and the cleanest emissions of all fossil fuelled power. The engineering for the highest possible efficiency at lowest cost and weight depends on general system architecture issues and the performance of the components. Presented in this paper are system studies which provide direction for the most efficient path toward achieving the most beneficial result for this technology. Ultimately, fuel cell-turbine (FCT) hybrid systems applicable to integrated gasification combined cycle power systems will form the basis for reaching the goals for advanced coal-based power generation. The FCT hybrid power island will also be important for the FutureGen plant and will provide new options for carbon dioxide capture and sequestration as well as power and hydrogen generation. The system studies presented in this paper provide insight to current technology 'benchmarks' versus expected benefits from hybrid applications. Discussion is also presented on the effects of different balance of plant arrangements and approaches. Finally, we discuss the status of US DOE is sponsored projects that are looking to help understand the unique requirements for these systems. One of these projects, Hyper, will provide information on FCT dynamics and will help identify technical needs and opportunities for cycle advancement. The methods studied show promise for effective control of a hybrid system without the direct intervention of isolation valves or check valves in the main pressure loop of the system, which introduce substantial pressure losses, allowing for realization of the full potential efficiency of the hybrid system.

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

PubMed Central

Blanco-Pastor, José Luis; Vargas, Pablo; Pfeil, Bernard E.

2012-01-01

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora. PMID:22768061

Evolution in situ: hybrid origin and establishment of willows (Salix L.) on alpine glacier forefields

PubMed Central

Gramlich, S; Sagmeister, P; Dullinger, S; Hadacek, F; Hörandl, E

2016-01-01

Little attention has been paid to the evolutionary consequences of the colonizing dynamics and succession processes following glacier retreat. Here we studied hybrid populations that have recently formed and established on glacier forefields of the European Alps owing to secondary contact of a lowland colonizer with a subalpine species. We analyzed the composition of two hybrid populations between Salix purpurea and Salix helvetica with nine microsatellite markers by using Bayesian methods (structure and NewHybrids), and simulations. We also studied niche differentiation between the hybrids and the parental species based on indicator values, soil pH and water retention potential measurements. Allelic structure of hybrids confirms the assumed parentage and in situ origin of the crosses on two independent sites within the last decades. Both hybrid populations comprised F1 and later generation hybrids (F2 and backcrosses), confirming hybrid fertility. The parental species showed significant differences in niche characteristics for temperature, soil pH, nutrients and moisture. Remarkably, the hybrids exhibited a higher tolerance to cold temperatures, nutrient-poor and acidic soils than either parent. Our results show that willow hybrids originated after glacier retreat and have established persistent populations within a few decades. One factor contributing to hybrid establishment in sympatry with their parents is their ability to occupy more extreme niches than either parental species within a mosaic-like pattern of microhabitats on the forefield. Introgression and/or transgressive segregation may have resulted in novel genotypes that are able to expand the ecological spectrum of either parent. PMID:26980342

Genetic architecture of male sterility and segregation distortion in Drosophila pseudoobscura Bogota-USA hybrids.

PubMed

Phadnis, Nitin

2011-11-01

Understanding the genetic basis of reproductive isolation between recently diverged species is a central problem in evolutionary genetics. Here, I present analyses of the genetic architecture underlying hybrid male sterility and segregation distortion between the Bogota and USA subspecies of Drosophila pseudoobscura. Previously, a single gene, Overdrive (Ovd), was shown to be necessary but not sufficient for both male sterility and segregation distortion in F(1) hybrids between these subspecies, requiring several interacting partner loci for full manifestation of hybrid phenomena. I map these partner loci separately on the Bogota X chromosome and USA autosomes using a combination of different mapping strategies. I find that hybrid sterility involves a single hybrid incompatibility of at least seven interacting partner genes that includes three large-effect loci. Segregation distortion involves three loci on the Bogota X chromosome and one locus on the autosomes. The genetic bases of hybrid sterility and segregation distortion are at least partially--but not completely--overlapping. My results lay the foundation for fine-mapping experiments to identify the complete set of genes that interact with Overdrive. While individual genes that cause hybrid sterility or inviability have been identified in a few cases, my analysis provides a comprehensive look at the genetic architecture of all components of a hybrid incompatibility underlying F(1) hybrid sterility. Such an analysis would likely be unfeasible for most species pairs due to their divergence time and emphasizes the importance of young species pairs such as the D. pseudoobscura subspecies studied here.

An efficient method for hybrid density functional calculation with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Wang, Maoyuan; Liu, Gui-Bin; Guo, Hong; Yao, Yugui

2018-03-01

In first-principles calculations, hybrid functional is often used to improve accuracy from local exchange correlation functionals. A drawback is that evaluating the hybrid functional needs significantly more computing effort. When spin-orbit coupling (SOC) is taken into account, the non-collinear spin structure increases computing effort by at least eight times. As a result, hybrid functional calculations with SOC are intractable in most cases. In this paper, we present an approximate solution to this problem by developing an efficient method based on a mixed linear combination of atomic orbital (LCAO) scheme. We demonstrate the power of this method using several examples and we show that the results compare very well with those of direct hybrid functional calculations with SOC, yet the method only requires a computing effort similar to that without SOC. The presented technique provides a good balance between computing efficiency and accuracy, and it can be extended to magnetic materials.

Life history traits and phenotypic selection among sunflower crop–wild hybrids and their wild counterpart: implications for crop allele introgression

PubMed Central

Kost, Matthew A; Alexander, Helen M; Jason Emry, D; Mercer, Kristin L

2015-01-01

Hybridization produces strong evolutionary forces. In hybrid zones, selection can differentially occur on traits and selection intensities may differ among hybrid generations. Understanding these dynamics in crop–wild hybrid zones can clarify crop-like traits likely to introgress into wild populations and the particular hybrid generations through which introgression proceeds. In a field experiment with four crop–wild hybrid Helianthus annuus (sunflower) cross types, we measured growth and life history traits and performed phenotypic selection analysis on early season traits to ascertain the likelihood, and routes, of crop allele introgression into wild sunflower populations. All cross types overwintered, emerged in the spring, and survived until flowering, indicating no early life history barriers to crop allele introgression. While selection indirectly favored earlier seedling emergence and taller early season seedlings, direct selection only favored greater early season leaf length. Further, there was cross type variation in the intensity of selection operating on leaf length. Thus, introgression of multiple early season crop-like traits, due to direct selection for greater early season leaf length, should not be impeded by any cross type and may proceed at different rates among generations. In sum, alleles underlying early season sunflower crop-like traits are likely to introgress into wild sunflower populations. PMID:26029263

Ancestral chloroplast polymorphism and historical secondary contact in a broad hybrid zone of Aesculus (Sapindaceae).

PubMed

Modliszewski, Jennifer L; Thomas, David T; Fan, Chuanzhu; Crawford, Daniel J; Depamphilis, Claude W; Xiang, Qiu-Yun Jenny

2006-03-01

Knowledge regarding the origin and maintenance of hybrid zones is critical for understanding the evolutionary outcomes of natural hybridization. To evaluate the contribution of historical contact vs. long-distance gene flow in the formation of a broad hybrid zone in central and northern Georgia that involves Aesculus pavia, A. sylvatica, and A. flava, three cpDNA regions (matK, trnD-trnT, and trnH-trnK) were analyzed. The maternal inheritance of cpDNA in Aesculus was confirmed via sequencing of matK from progeny of controlled crosses. Restriction site analyses identified 21 unique haplotypes among 248 individuals representing 29 populations from parental species and hybrids. Haplotypes were sequenced for all cpDNA regions. Restriction site and sequence data were subjected to phylogeographic and population genetic analyses. Considerable cpDNA variation was detected in the hybrid zone, as well as ancestral cpDNA polymorphism; furthermore, the distribution of haplotypes indicates limited interpopulation gene flow via seeds. The genealogy and structure of genetic variation further support the historical presence of A. pavia in the Piedmont, although they are at present locally extinct. In conjunction with previous allozyme studies, the cpDNA data suggest that the hybrid zone originated through historical local gene flow, yet is maintained by periodic long-distance pollen dispersal.

High-resolution genome-wide dissection of the two rules of speciation in Drosophila.

PubMed

Masly, John P; Presgraves, Daven C

2007-09-01

Postzygotic reproductive isolation is characterized by two striking empirical patterns. The first is Haldane's rule--the preferential inviability or sterility of species hybrids of the heterogametic (XY) sex. The second is the so-called large X effect--substitution of one species's X chromosome for another's has a disproportionately large effect on hybrid fitness compared to similar substitution of an autosome. Although the first rule has been well-established, the second rule remains controversial. Here, we dissect the genetic causes of these two rules using a genome-wide introgression analysis of Drosophila mauritiana chromosome segments in an otherwise D. sechellia genetic background. We find that recessive hybrid incompatibilities outnumber dominant ones and that hybrid male steriles outnumber all other types of incompatibility, consistent with the dominance and faster-male theories of Haldane's rule, respectively. We also find that, although X-linked and autosomal introgressions are of similar size, most X-linked introgressions cause hybrid male sterility (60%) whereas few autosomal introgressions do (18%). Our results thus confirm the large X effect and identify its proximate cause: incompatibilities causing hybrid male sterility have a higher density on the X chromosome than on the autosomes. We evaluate several hypotheses for the evolutionary cause of this excess of X-linked hybrid male sterility.

High-Resolution Genome-Wide Dissection of the Two Rules of Speciation in Drosophila

PubMed Central

2007-01-01

Postzygotic reproductive isolation is characterized by two striking empirical patterns. The first is Haldane's rule—the preferential inviability or sterility of species hybrids of the heterogametic (XY) sex. The second is the so-called large X effect—substitution of one species's X chromosome for another's has a disproportionately large effect on hybrid fitness compared to similar substitution of an autosome. Although the first rule has been well-established, the second rule remains controversial. Here, we dissect the genetic causes of these two rules using a genome-wide introgression analysis of Drosophila mauritiana chromosome segments in an otherwise D. sechellia genetic background. We find that recessive hybrid incompatibilities outnumber dominant ones and that hybrid male steriles outnumber all other types of incompatibility, consistent with the dominance and faster-male theories of Haldane's rule, respectively. We also find that, although X-linked and autosomal introgressions are of similar size, most X-linked introgressions cause hybrid male sterility (60%) whereas few autosomal introgressions do (18%). Our results thus confirm the large X effect and identify its proximate cause: incompatibilities causing hybrid male sterility have a higher density on the X chromosome than on the autosomes. We evaluate several hypotheses for the evolutionary cause of this excess of X-linked hybrid male sterility. PMID:17850182

Life history traits and phenotypic selection among sunflower crop-wild hybrids and their wild counterpart: implications for crop allele introgression.

PubMed

Kost, Matthew A; Alexander, Helen M; Jason Emry, D; Mercer, Kristin L

2015-06-01

Hybridization produces strong evolutionary forces. In hybrid zones, selection can differentially occur on traits and selection intensities may differ among hybrid generations. Understanding these dynamics in crop-wild hybrid zones can clarify crop-like traits likely to introgress into wild populations and the particular hybrid generations through which introgression proceeds. In a field experiment with four crop-wild hybrid Helianthus annuus (sunflower) cross types, we measured growth and life history traits and performed phenotypic selection analysis on early season traits to ascertain the likelihood, and routes, of crop allele introgression into wild sunflower populations. All cross types overwintered, emerged in the spring, and survived until flowering, indicating no early life history barriers to crop allele introgression. While selection indirectly favored earlier seedling emergence and taller early season seedlings, direct selection only favored greater early season leaf length. Further, there was cross type variation in the intensity of selection operating on leaf length. Thus, introgression of multiple early season crop-like traits, due to direct selection for greater early season leaf length, should not be impeded by any cross type and may proceed at different rates among generations. In sum, alleles underlying early season sunflower crop-like traits are likely to introgress into wild sunflower populations.

Impact of parental Bos taurus and Bos indicus origins on copy number variation in traditional Chinese cattle breeds

USDA-ARS?s Scientific Manuscript database

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution o...

Introgression among three rockfish species (Sebastes spp.) in the Salish Sea, northeast Pacific Ocean

PubMed Central

Park, Linda K.; Hauser, Lorenz

2018-01-01

Interspecific hybridization is often seen as a major conservation issue, potentially threatening endangered species and decreasing biodiversity. In natural populations, the conservation implications of hybridization depends on both on anthropogenic factors and the evolutionary processes maintaining the hybrid zone. However, the timeline and patterns of hybridization in the hybrid zone are often not known. Therefore, species conservation becomes a concern when recent anthropogenic changes influence hybridization and not if hybridization is part of a long-term process. Here, we use sequence data from one mitochondrial gene, three nuclear introns and one nuclear exon to estimate the direction, geographic extent, frequency and possible timeline of hybridization between three rockfish species (Sebastes auriculatus, S. caurinus, S. maliger) in the Salish Sea, Washington, USA. We show that (i) introgression occurred much more frequently in the Salish Sea than on the outer coast, (ii) introgression was highly asymmetrical from S. maliger into the other two species, (iii) almost 40% of individuals in the Salish Sea were hybrids, with frequency of hybrids increasing with isolation from the coast, and (iv) all hybrids were later generation backcrosses rather than F1 hybrids. Our results suggest long-standing low-level hybridization rather than recent onset of interbreeding because of human induced environmental change, possibly facilitated by specific environmental conditions in the sub-basins of the Salish Sea, and by differences in population sizes during recolonization of the area after the last glaciation. This rockfish hybrid system, with asymmetrical introgression and the maintenance of parental species, may prove useful to study both mechanisms that maintain species boundaries and that facilitate speciation in the presence of rapid environmental change. PMID:29566070

Hybrid carbon nanoparticles modified core-shell silica: a high efficiency carbon-based phase for hydrophilic interaction liquid chromatography.

PubMed

Ibrahim, Mohammed E A; Wahab, M Farooq; Lucy, Charles A

2014-04-11

Hydrophilic interaction liquid chromatography (HILIC) is a fast growing separation technique for hydrophilic and polar analytes. In this work, we combine the unique selectivity of carbon surfaces with the high efficiency of core-shell silica. First, 5 μm core-shell silica is electrostatically coated with 105 nm cationic latex bearing quaternary ammonium groups. Then 50 nm anionic carbon nanoparticles are anchored onto the surface of the latex coated core-shell silica particles to produce a hybrid carbon-silica phase. The hybrid phase shows different selectivity than ten previously classified HILIC column chemistries and 36 stationary phases. The hybrid HILIC phase has shape selectivity for positional isomeric pairs (phthalic/isophthalic and 1-naphthoic/2-naphthoic acids). Fast and high efficiency HILIC separations of biologically important carboxylates, phenols and pharmaceuticals are reported with efficiencies up to 85,000 plates m(-1). Reduced plate height of 1.9 (95,000 plates m(-1)) can be achieved. The hybrid phase is stable for at least 3 months of usage and storage under typical HILIC eluents. Copyright © 2014 Elsevier B.V. All rights reserved.

Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?

PubMed

Gambette, Philippe; van Iersel, Leo; Kelk, Steven; Pardi, Fabio; Scornavacca, Celine

2016-09-01

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental questions that arise in this context is whether the evolution of a gene with one copy in all species can be explained by a given network. In mathematical terms, this is often translated in the following way: is a given phylogenetic tree contained in a given phylogenetic network? Recently this tree containment problem has been widely investigated from a computational perspective, but most studies have only focused on the topology of the phylogenies, ignoring a piece of information that, in the case of phylogenetic trees, is routinely inferred by evolutionary analyses: branch lengths. These measure the amount of change (e.g., nucleotide substitutions) that has occurred along each branch of the phylogeny. Here, we study a number of versions of the tree containment problem that explicitly account for branch lengths. We show that, although length information has the potential to locate more precisely a tree within a network, the problem is computationally hard in its most general form. On a positive note, for a number of special cases of biological relevance, we provide algorithms that solve this problem efficiently. This includes the case of networks of limited complexity, for which it is possible to recover, among the trees contained by the network with the same topology as the input tree, the closest one in terms of branch lengths.

Classification of Two Class Motor Imagery Tasks Using Hybrid GA-PSO Based K-Means Clustering.

PubMed

Suraj; Tiwari, Purnendu; Ghosh, Subhojit; Sinha, Rakesh Kumar

2015-01-01

Transferring the brain computer interface (BCI) from laboratory condition to meet the real world application needs BCI to be applied asynchronously without any time constraint. High level of dynamism in the electroencephalogram (EEG) signal reasons us to look toward evolutionary algorithm (EA). Motivated by these two facts, in this work a hybrid GA-PSO based K-means clustering technique has been used to distinguish two class motor imagery (MI) tasks. The proposed hybrid GA-PSO based K-means clustering is found to outperform genetic algorithm (GA) and particle swarm optimization (PSO) based K-means clustering techniques in terms of both accuracy and execution time. The lesser execution time of hybrid GA-PSO technique makes it suitable for real time BCI application. Time frequency representation (TFR) techniques have been used to extract the feature of the signal under investigation. TFRs based features are extracted and relying on the concept of event related synchronization (ERD) and desynchronization (ERD) feature vector is formed.

Classification of Two Class Motor Imagery Tasks Using Hybrid GA-PSO Based K-Means Clustering

PubMed Central

Suraj; Tiwari, Purnendu; Ghosh, Subhojit; Sinha, Rakesh Kumar

2015-01-01

Transferring the brain computer interface (BCI) from laboratory condition to meet the real world application needs BCI to be applied asynchronously without any time constraint. High level of dynamism in the electroencephalogram (EEG) signal reasons us to look toward evolutionary algorithm (EA). Motivated by these two facts, in this work a hybrid GA-PSO based K-means clustering technique has been used to distinguish two class motor imagery (MI) tasks. The proposed hybrid GA-PSO based K-means clustering is found to outperform genetic algorithm (GA) and particle swarm optimization (PSO) based K-means clustering techniques in terms of both accuracy and execution time. The lesser execution time of hybrid GA-PSO technique makes it suitable for real time BCI application. Time frequency representation (TFR) techniques have been used to extract the feature of the signal under investigation. TFRs based features are extracted and relying on the concept of event related synchronization (ERD) and desynchronization (ERD) feature vector is formed. PMID:25972896

A superhard sp3 microporous carbon with direct bandgap

NASA Astrophysics Data System (ADS)

Pan, Yilong; Xie, Chenlong; Xiong, Mei; Ma, Mengdong; Liu, Lingyu; Li, Zihe; Zhang, Shuangshuang; Gao, Guoying; Zhao, Zhisheng; Tian, Yongjun; Xu, Bo; He, Julong

2017-12-01

Carbon allotropes with distinct sp, sp2, and sp3 hybridization possess various different properties. Here, a novel all-sp3 hybridized tetragonal carbon, namely the P carbon, was predicted by the evolutionary particle swarm structural search. It demonstrated a low density among all-sp3 carbons, due to the corresponding distinctive microporous structure. P carbon is thermodynamically stable than the known C60 and could be formed through the single-walled carbon nanotubes (SWCNTs) compression. P carbon is a direct bandgap semiconductor displaying a strong and superhard nature. The unique combination of electrical and mechanical properties constitutes P carbon a potential superhard material for semiconductor industrial fields.

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.

PubMed

Schröder, Markus S; Martinez de San Vicente, Kontxi; Prandini, Tâmara H R; Hammel, Stephen; Higgins, Desmond G; Bagagli, Eduardo; Wolfe, Kenneth H; Butler, Geraldine

2016-11-01

Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.

Invasive hybridization in a threatened species is accelerated by climate change

USGS Publications Warehouse

Muhlfeld, Clint C.; Kovach, Ryan P.; Jones, Leslie A.; Al-Chokhachy, Robert K.; Boyer, Matthew C.; Leary, Robb F.; Lowe, Winsor H.; Luikart, Gordon; Allendorf, Fred W.

2014-01-01

Climate change will decrease worldwide biodiversity through a number of potential pathways, including invasive hybridization (cross-breeding between invasive and native species). How climate warming influences the spread of hybridization and loss of native genomes poses difficult ecological and evolutionary questions with little empirical information to guide conservation management decisions. Here we combine long-term genetic monitoring data with high-resolution climate and stream temperature predictions to evaluate how recent climate warming has influenced the spatio-temporal spread of human-mediated hybridization between threatened native westslope cutthroat trout (Oncorhynchus clarkii lewisi) and non-native rainbow trout (Oncorhynchus mykiss), the world’s most widely introduced invasive fish. Despite widespread release of millions of rainbow trout over the past century within the Flathead River system, a large relatively pristine watershed in western North America, historical samples revealed that hybridization was prevalent only in one (source) population. During a subsequent 30-year period of accelerated warming, hybridization spread rapidly and was strongly linked to interactions between climatic drivers—precipitation and temperature—and distance to the source population. Specifically, decreases in spring precipitation and increases in summer stream temperature probably promoted upstream expansion of hybridization throughout the system. This study shows that rapid climate warming can exacerbate interactions between native and non-native species through invasive hybridization, which could spell genomic extinction for many species.

Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids.

PubMed

Meier, Joana Isabel; Marques, David Alexander; Wagner, Catherine Elise; Excoffier, Laurent; Seehausen, Ole

2018-06-01

The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case is blue and red-backed Pundamilia species, for which we recently showed that a young species pair may have evolved through "hybrid parallel speciation". Coalescent simulations suggested that the older species P. pundamilia (blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new "nyererei-like" and "pundamilia-like" species evolved from the admixed population. Here, we use genome scans to study the genomic architecture of differentiation, and assess the influence of hybridization on the evolution of the younger species pair. For each of the two species pairs, we find over 300 genomic regions, widespread across the genome, which are highly differentiated. A subset of the most strongly differentiated regions of the older pair are also differentiated in the younger pair. These shared differentiated regions often show parallel allele frequency differences, consistent with the hypothesis that admixture-derived alleles were targeted by divergent selection in the hybrid population. However, two-thirds of the genomic regions that are highly differentiated between the younger species are not highly differentiated between the older species, suggesting independent evolutionary responses to selection pressures. Our analyses reveal how divergent selection on admixture-derived genetic variation can facilitate new speciation events.

Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons.

PubMed

Qi, L L; Wu, J J; Friebe, B; Qian, C; Gu, Y Q; Fu, D L; Gill, B S

2013-08-01

Brachypodium distachyon is a wild annual grass belonging to the Pooideae, more closely related to wheat, barley, and forage grasses than rice and maize. As an experimental model, the completed genome sequence of B. distachyon provides a unique opportunity to study centromere evolution during the speciation of grasses. Centromeric satellite sequences have been identified in B. distachyon, but little is known about centromeric retrotransposons in this species. In the present study, bacterial artificial chromosome (BAC)-fluorescence in situ hybridization was conducted in maize, rice, barley, wheat, and rye using B. distachyon (Bd) centromere-specific BAC clones. Eight Bd centromeric BAC clones gave no detectable fluorescence in situ hybridization (FISH) signals on the chromosomes of rice and maize, and three of them also did not yield any FISH signals in barley, wheat, and rye. In addition, four of five Triticeae centromeric BAC clones did not hybridize to the B. distachyon centromeres, implying certain unique features of Brachypodium centromeres. Analysis of Brachypodium centromeric BAC sequences identified a long terminal repeat (LTR)-centromere retrotransposon of B. distachyon (CRBd1). This element was found in high copy number accounting for 1.6 % of the B. distachyon genome, and is enriched in Brachypodium centromeric regions. CRBd1 accumulated in active centromeres, but was lost from inactive ones. The LTR of CRBd1 appears to be specific to B. distachyon centromeres. These results reveal different evolutionary events of this retrotransposon family across grass species.

Hybridization between mouse lemurs in an ecological transition zone in southern Madagascar.

PubMed

Gligor, M; Ganzhorn, J U; Rakotondravony, D; Ramilijaona, O R; Razafimahatratra, E; Zischler, H; Hapke, A

2009-02-01

Hybrid zones in ecotones can be useful model systems for the study of evolutionary processes that shape the distribution and discreteness of species. Such studies could be important for an improved understanding of the complex biogeography of Madagascar, which is renowned for its outstanding degree of small-scale endemism. Certain forest remnants in central Madagascar indicate that transitional corridors across the island could have connected microendemics in different forest types in the past. Evolutionary processes in such corridors are difficult to study because most of these corridors have disappeared due to deforestation in central Madagascar. We studied a hybrid zone in one of the few remaining ecotonal corridors between dry and humid forests in Madagascar, which connects two species of mouse lemurs, Microcebus griseorufus in dry spiny forest and Microcebus murinus in humid littoral forest. We sampled 162 mouse lemurs at nine sites across this boundary. Morphometric analyses revealed intermediate morphotypes of many individuals in transitional habitat. Bayesian clustering of microsatellite genotypes and assignment tests yielded evidence for a mixed ancestry of mouse lemurs in the ecotone, where we also observed significant linkage disequilibria and heterozygote deficiency. In contrast to these observations, mitochondrial haplotypes displayed a sharply delimited boundary at the eastern edge of spiny forest, which was noncoincident with the signals from microsatellite data. Among several alternative scenarios, we propose asymmetric nuclear introgression due to male-biased dispersal, divergent environmental selection, and an expansion of dry spiny forest in the course of aridification as a probable explanation of our observations.

Efficient hybrid white organic light-emitting diodes for application of triplet harvesting with simple structure

NASA Astrophysics Data System (ADS)

Hwang, Kyo Min; Lee, Song Eun; Lee, Sungkyu; Yoo, Han Kyu; Baek, Hyun Jung; Kim, Young Kwan; Kim, Jwajin; Yoon, Seung Soo

2016-08-01

In this study, we fabricated hybrid white organic light-emitting diodes (WOLEDs) based on triplet harvesting with a simple structure. All the hole transporting material and host in the emitting layer (EML) of devices utilized the same material N,N'-di-1-naphthalenyl-N,N'-diphenyl [1,1':4',1″:4″,1‴-quaterphenyl]-4,4‴-diamine (4P-NPD), which is known to be blue fluorescent material. Simple hybrid WOLEDs were fabricated with blue fluorescent, green and red phosphorescent materials. We investigated the effect of triplet harvesting (TH) by an exciton generation zone on simple hybrid WOLEDs. The simple hybrid WOLEDs characteristically had a dominant hole mobility, so an exciton generation zone was expected in the EML. Additionally, the optimal the thickness of the hole transporting layer and electron transporting layer was fabricated a simple hybrid WOLEDs. The simple hybrid WOLED exhibits a maximum luminous efficiency of 29.3 cd/A and a maximum external quantum efficiency of 11.2%. The Commission Internationale de l'Éclairage (International Commission on Illumination) coordinates were (0.45, 0.43) at about 10,000 cd/m2.

Asymmetrical Gene Flow in a Hybrid Zone of Hawaiian Schiedea (Caryophyllaceae) Species with Contrasting Mating Systems

PubMed Central

Wallace, Lisa E.; Culley, Theresa M.; Weller, Stephen G.; Sakai, Ann K.; Kuenzi, Ashley; Roy, Tilottama; Wagner, Warren L.; Nepokroeff, Molly

2011-01-01

Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1) putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2) gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3) in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s) of S. menziesii. PMID:21949765

Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum

PubMed Central

Cara, Nicolás; Marfil, Carlos F; Masuelli, Ricardo W

2013-01-01

Interspecific hybridization is known for triggering genetic and epigenetic changes, such as modifications on DNA methylation patterns and impact on phenotypic plasticity and ecological adaptation. Wild potatoes (Solanum, section Petota) are adapted to multiple habitats along the Andes, and natural hybridizations have proven to be a common feature among species of this group. Solanum × rechei, a recently formed hybrid that grows sympatrically with the parental species S. kurtzianum and S. microdontum, represents an ideal model for studying the ecologically and evolutionary importance of hybridization in generating of epigenetic variability. Genetic and epigenetic variability and their correlation with morphological variation were investigated in wild and ex situ conserved populations of these three wild potato species using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques. We observed that novel methylation patterns doubled the number of novel genetic patterns in the hybrid and that the morphological variability measured on 30 characters had a higher correlation with the epigenetic than with the genetic variability. Statistical comparison of methylation levels suggested that the interspecific hybridization induces genome demethylation in the hybrids. A Bayesian analysis of the genetic data reveled the hybrid nature of S. × rechei, with genotypes displaying high levels of admixture with the parental species, while the epigenetic information assigned S. × rechei to its own cluster with low admixture. These findings suggested that after the hybridization event, a novel epigenetic pattern was rapidly established, which might influence the phenotypic plasticity and adaptation of the hybrid to new environments. PMID:24198938

An Improved Solution for Integrated Array Optics in Quasi-Optical mm and Submm Receivers: the Hybrid Antenna

NASA Technical Reports Server (NTRS)

Buttgenbach, Thomas H.

1993-01-01

The hybrid antenna discussed here is defined as a dielectric lens-antenna as a special case of an extended hemi-spherical dielectric lens that is operated in the diffraction limited regime. It is a modified version of the planar antenna on a lens scheme developed by Rutledge. The dielectric lens-antenna is fed by a planar-structure antenna, which is mounted on the flat side of the dielectric lens-antenna using it as a substrate, and the combination is termed a hybrid antenna. Beam pattern and aperture efficiency measurements were made at millimeter and submillimeter wavelengths as a function of extension of the hemi- spherical lens and different lens sizes. An optimum extension distance is found experimentally and numerically for which excellent beam patterns and simultaneously high aperture efficiencies can be achieved. At 115 GHz the aperture efficiency was measured to be (76 4 +/- 6) % for a diffraction limited beam with sidelobes below -17 dB. Results of a single hybrid antenna with an integrated Superconductor-Insulator-Superconductor (SIS) detector and a broad-band matching structure at submillimeter wavelengths are presented. The hybrid antenna is diffraction limited, space efficient in an array due to its high aperture efficiency, and is easily mass produced, thus being well suited for focal plane heterodyne receiver arrays.

Solution processable inverted structure ZnO-organic hybrid heterojuction white LEDs

NASA Astrophysics Data System (ADS)

Bano, N.; Hussain, I.; Soomro, M. Y.; EL-Naggar, A. M.; Albassam, A. A.

2018-05-01

Improving luminance efficiency and colour purity are the most important challenges for zinc oxide (ZnO)-organic hybrid heterojunction light emitting diodes (LEDs), affecting their large area applications. If ZnO-organic hybrid heterojunction white LEDs are fabricated by a hydrothermal method, it is difficult to obtain pure and stable blue emission from PFO due to the presence of an undesirable green emission. In this paper, we present an inverted-structure ZnO-organic hybrid heterojunction LED to avoid green emission from PFO, which mainly originates during device processing. With this configuration, each ZnO nanorod (NR) forms a discrete p-n junction; therefore, large-area white LEDs can be designed without compromising the junction area. The configuration used for this novel structure is glass/ZnO NRs/PFO/PEDOT:PSS/L-ITO, which enables the development of efficient, large-area and low-cost hybrid heterojunction LEDs. Inverted-structure ZnO-organic hybrid heterojunction white LEDs offer several improvements in terms of brightness, size, colour, external quantum efficiency and a wider applicability as compared to normal architecture LEDs.

Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

PubMed Central

Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

2015-01-01

Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

Hybrid Particle Swarm Optimization for Hybrid Flowshop Scheduling Problem with Maintenance Activities

PubMed Central

Li, Jun-qing; Pan, Quan-ke; Mao, Kun

2014-01-01

A hybrid algorithm which combines particle swarm optimization (PSO) and iterated local search (ILS) is proposed for solving the hybrid flowshop scheduling (HFS) problem with preventive maintenance (PM) activities. In the proposed algorithm, different crossover operators and mutation operators are investigated. In addition, an efficient multiple insert mutation operator is developed for enhancing the searching ability of the algorithm. Furthermore, an ILS-based local search procedure is embedded in the algorithm to improve the exploitation ability of the proposed algorithm. The detailed experimental parameter for the canonical PSO is tuning. The proposed algorithm is tested on the variation of 77 Carlier and Néron's benchmark problems. Detailed comparisons with the present efficient algorithms, including hGA, ILS, PSO, and IG, verify the efficiency and effectiveness of the proposed algorithm. PMID:24883414

Estimating the efficiency of fish cross-species cDNA microarray hybridization.

PubMed

Cohen, Raphael; Chalifa-Caspi, Vered; Williams, Timothy D; Auslander, Meirav; George, Stephen G; Chipman, James K; Tom, Moshe

2007-01-01

Using an available cross-species cDNA microarray is advantageous for examining multigene expression patterns in non-model organisms, saving the need for construction of species-specific arrays. The aim of the present study was to estimate relative efficiency of cross-species hybridizations across bony fishes, using bioinformatics tools. The methodology may serve also as a model for similar evaluations in other taxa. The theoretical evaluation was done by substituting comparative whole-transcriptome sequence similarity information into the thermodynamic hybridization equation. Complementary DNA sequence assemblages of nine fish species belonging to common families or suborders and distributed across the bony fish taxonomic branch were selected for transcriptome-wise comparisons. Actual cross-species hybridizations among fish of different taxonomic distances were used to validate and eventually to calibrate the theoretically computed relative efficiencies.

Neuronal boost to evolutionary dynamics

PubMed Central

de Vladar, Harold P.; Szathmáry, Eörs

2015-01-01

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

Efficient Generation of Long-Lived Triplet Excitons in 2D Hybrid Perovskite.

PubMed

Younts, Robert; Duan, Hsin-Sheng; Gautam, Bhoj; Saparov, Bayrammurad; Liu, Jie; Mongin, Cedric; Castellano, Felix N; Mitzi, David B; Gundogdu, Kenan

2017-03-01

Triplet excitons form in quasi-2D hybrid inorganic-organic perovskites and diffuse over 100 nm before radiating with >11% photoluminescence quantum efficiency (PLQE) at low temperatures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolutionary and ecological implications of genome size in the North American endemic sagebrushes and allies (Artemisia, Asteraceae)

Treesearch

Sonia Garcia; Miguel A. Canela; Teresa Garnatje; E. Durant McArthur; Jaume Pellicer; Stewart C. Sanderson; Joan Valles

2008-01-01

The genome size of 51 populations of 20 species of the North American endemic sagebrushes (subgenus Tridentatae), related species, and some hybrid taxa were assessed by flow cytometry, and were analysed in a phylogenetic framework. Results were similar for most Tridentatae species, with the exception of three taxonomically conflictive species: Artemisia bigelovii Gray...

Hybridisation and diversification in the adaptive radiation of clownfishes.

PubMed

Litsios, Glenn; Salamin, Nicolas

2014-11-30

The importance of hybridisation during species diversification has long been debated among evolutionary biologists. It is increasingly recognised that hybridisation events occurred during the evolutionary history of numerous species, especially during the early stages of adaptive radiation. We study the effect of hybridisation on diversification in the clownfishes, a clade of coral reef fish that diversified through an adaptive radiation process. While two species of clownfish are likely to have been described from hybrid specimens, the occurrence and effect of hybridisation on the clade diversification is yet unknown. We generate sequences of three mitochondrial genes to complete an existing dataset of nuclear sequences and document cytonuclear discordance at a node, which shows a drastic increase of diversification rate. Then, using a tree-based jack-knife method, we identify clownfish species likely stemming from hybridisation events. Finally, we use molecular cloning and identify the putative parental species of four clownfish specimens that display the morphological characteristics of hybrids. Our results show that consistently with the syngameon hypothesis, hybridisation events are linked with a burst of diversification in the clownfishes. Moreover, several recently diverged clownfish lineages likely originated through hybridisation, which indicates that diversification, catalysed by hybridisation events, may still be happening.

Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago.

PubMed

Matute, D R; Ayroles, J F

2014-06-01

Drosophila simulans and D. sechellia are sister species that serve as a model to study the evolution of reproductive isolation. While D. simulans is a human commensal that has spread all over the world, D. sechellia is restricted to the Seychelles archipelago and is found to breed exclusively on the toxic fruit of Morinda citrifolia. We surveyed the relative frequency of males from these two species in a variety of substrates found on five islands of the Seychelles archipelago. We sampled different fruits and found that putative D. simulans can be found in a variety of substrates, including, surprisingly, M. citrifolia. Putative D. sechellia was found preferentially on M. citrifolia fruits, but a small proportion was found in other substrates. Our survey also shows the existence of putative hybrid males in areas where D. simulans is present in Seychelles. The results from this field survey support the hypothesis of current interbreeding between these species in the central islands of Seychelles and open the possibility for fine measurements of admixture between these two Drosophila species to be made. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Cannibalism in single-batch hybrid catfish production ponds

USDA-ARS?s Scientific Manuscript database

Hybrid catfish are more efficiently harvested by seining than are Channel Catfish. Due to that, and their faster growth, hybrids are typically produced in “single-batch” production systems, either in intensively-aerated commercial ponds or in split-pond systems. In either production system, hybrids...

Predicting protein complexes from weighted protein-protein interaction graphs with a novel unsupervised methodology: Evolutionary enhanced Markov clustering.

PubMed

Theofilatos, Konstantinos; Pavlopoulou, Niki; Papasavvas, Christoforos; Likothanassis, Spiros; Dimitrakopoulos, Christos; Georgopoulos, Efstratios; Moschopoulos, Charalampos; Mavroudi, Seferina

2015-03-01

Proteins are considered to be the most important individual components of biological systems and they combine to form physical protein complexes which are responsible for certain molecular functions. Despite the large availability of protein-protein interaction (PPI) information, not much information is available about protein complexes. Experimental methods are limited in terms of time, efficiency, cost and performance constraints. Existing computational methods have provided encouraging preliminary results, but they phase certain disadvantages as they require parameter tuning, some of them cannot handle weighted PPI data and others do not allow a protein to participate in more than one protein complex. In the present paper, we propose a new fully unsupervised methodology for predicting protein complexes from weighted PPI graphs. The proposed methodology is called evolutionary enhanced Markov clustering (EE-MC) and it is a hybrid combination of an adaptive evolutionary algorithm and a state-of-the-art clustering algorithm named enhanced Markov clustering. EE-MC was compared with state-of-the-art methodologies when applied to datasets from the human and the yeast Saccharomyces cerevisiae organisms. Using public available datasets, EE-MC outperformed existing methodologies (in some datasets the separation metric was increased by 10-20%). Moreover, when applied to new human datasets its performance was encouraging in the prediction of protein complexes which consist of proteins with high functional similarity. In specific, 5737 protein complexes were predicted and 72.58% of them are enriched for at least one gene ontology (GO) function term. EE-MC is by design able to overcome intrinsic limitations of existing methodologies such as their inability to handle weighted PPI networks, their constraint to assign every protein in exactly one cluster and the difficulties they face concerning the parameter tuning. This fact was experimentally validated and moreover, new potentially true human protein complexes were suggested as candidates for further validation using experimental techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Influence of electrical and hybrid heating on bread quality during baking.

PubMed

Chhanwal, N; Ezhilarasi, P N; Indrani, D; Anandharamakrishnan, C

2015-07-01

Energy efficiency and product quality are the key factors for any food processing industry. The aim of the study was to develop energy and time efficient baking process. The hybrid heating (Infrared + Electrical) oven was designed and fabricated using two infrared lamps and electric heating coils. The developed oven can be operated in serial or combined heating modes. The standardized baking conditions were 18 min at 220°C to produce the bread from hybrid heating oven. Effect of baking with hybrid heating mode (H-1 and H-2, hybrid oven) on the quality characteristics of bread as against conventional heating mode (C-1, pilot scale oven; C-2, hybrid oven) was studied. The results showed that breads baked in hybrid heating mode (H-2) had higher moisture content (28.87%), higher volume (670 cm(3)), lower crumb firmness value (374.6 g), and overall quality score (67.0) comparable to conventional baking process (68.5). Moreover, bread baked in hybrid heating mode showed 28% reduction in baking time.

Natural and Anthropogenic Hybridization in Two Species of Eastern Brazilian Marmosets (Callithrix jacchus and C. penicillata)

PubMed Central

Malukiewicz, Joanna; Boere, Vanner; Fuzessy, Lisieux F.; Grativol, Adriana D.; de Oliveira e Silva, Ita; Pereira, Luiz C. M.; Ruiz-Miranda, Carlos R.; Valença, Yuri M.; Stone, Anne C.

2015-01-01

Animal hybridization is well documented, but evolutionary outcomes and conservation priorities often differ for natural and anthropogenic hybrids. Among primates, an order with many endangered species, the two contexts can be hard to disentangle from one another, which carries important conservation implications. Callithrix marmosets give us a unique glimpse of genetic hybridization effects under distinct natural and human-induced contexts. Here, we use a 44 autosomal microsatellite marker panel to examine genome-wide admixture levels and introgression at a natural C. jacchus and C. penicillata species border along the São Francisco River in NE Brazil and in an area of Rio de Janeiro state where humans introduced these species exotically. Additionally, we describe for the first time autosomal genetic diversity in wild C. penicillata and expand previous C. jacchus genetic data. We characterize admixture within the natural zone as bimodal where hybrid ancestry is biased toward one parental species or the other. We also show evidence that São Francisco River islands are gateways for bidirectional gene flow across the species border. In the anthropogenic zone, marmosets essentially form a hybrid swarm with intermediate levels of admixture, likely from the absence of strong physical barriers to interspecific breeding. Our data show that while hybridization can occur naturally, the presence of physical, even if leaky, barriers to hybridization is important for maintaining species genetic integrity. Thus, we suggest further study of hybridization under different contexts to set well informed conservation guidelines for hybrid populations that often fit somewhere between “natural” and “man-made.” PMID:26061111

Genetic Architecture of Male Sterility and Segregation Distortion in Drosophila pseudoobscura Bogota–USA Hybrids

PubMed Central

Phadnis, Nitin

2011-01-01

Understanding the genetic basis of reproductive isolation between recently diverged species is a central problem in evolutionary genetics. Here, I present analyses of the genetic architecture underlying hybrid male sterility and segregation distortion between the Bogota and USA subspecies of Drosophila pseudoobscura. Previously, a single gene, Overdrive (Ovd), was shown to be necessary but not sufficient for both male sterility and segregation distortion in F1 hybrids between these subspecies, requiring several interacting partner loci for full manifestation of hybrid phenomena. I map these partner loci separately on the Bogota X chromosome and USA autosomes using a combination of different mapping strategies. I find that hybrid sterility involves a single hybrid incompatibility of at least seven interacting partner genes that includes three large-effect loci. Segregation distortion involves three loci on the Bogota X chromosome and one locus on the autosomes. The genetic bases of hybrid sterility and segregation distortion are at least partially—but not completely—overlapping. My results lay the foundation for fine-mapping experiments to identify the complete set of genes that interact with Overdrive. While individual genes that cause hybrid sterility or inviability have been identified in a few cases, my analysis provides a comprehensive look at the genetic architecture of all components of a hybrid incompatibility underlying F1 hybrid sterility. Such an analysis would likely be unfeasible for most species pairs due to their divergence time and emphasizes the importance of young species pairs such as the D. pseudoobscura subspecies studied here. PMID:21900263

The chromosomal constitution of fish hybrid lineage revealed by 5S rDNA FISH.

PubMed

Zhang, Chun; Ye, Lihai; Chen, Yiyi; Xiao, Jun; Wu, Yanhong; Tao, Min; Xiao, Yamei; Liu, Shaojun

2015-12-03

The establishment of the bisexual fertile fish hybrid lineage including the allodiploid and allotetraploid hybrids, from interspecific hybridization of red crucian carp (Carassius auratus red var. 2n = 100, 2n = AA) (♀) × common carp (Cyprinus carpio L. 2n = 100, 2n = BB) (♂), provided a good platform to investigate genetic relationship between the parents and their hybrid progenies. The chromosomal inheritance of diploid and allotetraploid hybrid progenies in successive generations, was studied by applying 5S rDNA fluorescence in situ hybridization. Signals of 5S rDNA distinguished the chromosomal constitution of common carp (B-genome) from red crucian carp (A-genome), in which two strong signals were observed on the first submetacentric chromosome, while no major signal was found in common carp. After fish hybridization, one strong signal of 5S rDNA was detected in the same locus on the chromosome of diploid hybrids. As expected, two strong signals were observed in 4nF3 tetraploid hybrids offspring and it is worth mentioning that two strong signals were detected in a separating bivalent of a primary spermatocyte in 4nF3. Furthermore, the mitosis of heterozygous chromosomes was shown normal and stable with blastular tissue histological studies. We revealed that 5S rDNA signal can be applied to discern A-genome from B-genome, and that 5S rDNA bearing chromosomes can be stably passed down in successive generations. Our work provided a significant method in fish breeding and this is important for studies in fish evolutionary biology.

Experimental Crossing of Two Distinct Species of Leopard Geckos, Eublepharis angramainyu and E. macularius: Viability, Fertility and Phenotypic Variation of the Hybrids

PubMed Central

Jančúchová-Lásková, Jitka; Landová, Eva; Frynta, Daniel

2015-01-01

Hybridization between distinct species of animals and subsequent genetic introgression plays a considerable role in the speciation process and the emergence of adaptive characters. Fitness of between-species hybrids usually sharply decreases with the divergence time of the concerned species and the divergence depth, which still allows for a successful crossing differs among principal clades of vertebrates. Recently, a review of hybridization events among distinct lizard species revealed that lizards belong to vertebrates with a highly developed ability to hybridize. In spite of this, reliable reports of experimental hybridizations between genetically fairly divergent species are only exceptional. Here, we show the results of the crossing of two distinct allopatric species of eyelid geckos possessing temperature sex determination and lacking sex chromosomes: Eublepharis macularius distributed in Pakistan/Afghanistan area and E. angramainyu, which inhabits Mesopotamia and adjacent areas. We demonstrated that F1 hybrids were viable and fertile, and the introgression of E. angramainyu genes into the E. macularius genome can be enabled via a backcrossing. The examined hybrids (except those of the F2 generation) displayed neither malformations nor a reduced survival. Analyses of morphometric and coloration traits confirmed phenotypic distinctness of both parental species and their F1 hybrids. These findings contrast with long-term geographic and an evolutionary separation of the studied species. Thus, the occurrence of fertile hybrids of comparably divergent species, such as E. angramainyu and E. macularius, may also be expected in other taxa of squamates. This would violate the current estimates of species diversity in lizards. PMID:26633648

High-efficiency and conveniently recyclable photo-catalysts for dye degradation based on urchin-like CuO microparticle/polymer hybrid composites

NASA Astrophysics Data System (ADS)

Liu, Xiong; Cheng, Yuming; Li, Xuefeng; Dong, Jinfeng

2018-05-01

In this work, we developed a new type of photo-catalysts composed of the urchin-like cupric oxide (CuO) microparticle and polyvinylidene fluoride (PVDF) hybrid composites by the convenient organic-inorganic hybrid strategy, which show high-efficiency and conveniently recyclable for dye degradation including methylene blue (MB), Congo red (CR), and malachite green (MG) by visible light irradiation. The micro-structural characteristics of urchin-like CuO microparticles are crucial and dominant over the photo-degrading efficiency of hybrid catalyst because of their highly exposed {0 0 2} facet and larger specific surface area. Simultaneously, the intrinsic porous framework of PVDF membrane not only remains the excellent photo-catalytic activity of urchin-like CuO microparticles but also facilitates the enrichment of dyes on the membrane, and thereby synergistically contributing to the photo-catalytic efficiency. The microstructures of both urchin-like CuO microparticles and hybrid catalysts are systematically characterized by various techniques including scanning electron microscopy (SEM), transmission electron microscope (TEM), high-resolution transmission electron microscope (HRTEM), powder X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and nitrogen adsorption/desorption isotherms, which evidently support the mentioned mechanism.

Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

PubMed Central

Tennessen, Jacob A.; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron

2014-01-01

Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes. PMID:25477420

Highly Efficient Porphyrin-Based OPV/Perovskite Hybrid Solar Cells with Extended Photoresponse and High Fill Factor.

PubMed

Gao, Ke; Zhu, Zonglong; Xu, Bo; Jo, Sae Byeok; Kan, Yuanyuan; Peng, Xiaobin; Jen, Alex K-Y

2017-12-01

Employing a layer of bulk-heterojunction (BHJ) organic semiconductors on top of perovskite to further extend its photoresponse is considered as a simple and promising way to enhance the efficiency of perovskite-based solar cells, instead of using tandem devices or near infrared (NIR)-absorbing Sn-containing perovskites. However, the progress made from this approach is quite limited because very few such hybrid solar cells can simultaneously show high short-circuit current (J SC ) and fill factor (FF). To find an appropriate NIR-absorbing BHJ is essential for highly efficient, organic, photovoltaics (OPV)/perovskite hybrid solar cells. The materials involved in the BHJ layer not only need to have broad photoresponse to increase J SC , but also possess suitable energy levels and high mobility to afford high V OC and FF. In this work, a new porphyrin is synthesized and blended with [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) to function as an efficient BHJ for OPV/perovskite hybrid solar cells. The extended photoresponse, well-matched energy levels, and high hole mobility from optimized BHJ morphology afford a very high power conversion efficiency (PCE) (19.02%) with high V oc , J SC , and FF achieved simultaneously. This is the highest value reported so far for such hybrid devices, which demonstrates the feasibility of further improving the efficiency of perovskite devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chromosomal rearrangements and gene flow over time in an inter-specific hybrid zone of the Sorex araneus group.

PubMed

Yannic, G; Basset, P; Hausser, J

2009-06-01

Most hybrid zones have existed for hundreds or thousands of years but have generally been observed for only a short time period. Studies extending over periods long enough to track evolutionary changes in the zones or assess the ultimate outcome of hybridization are scarce. Here, we describe the evolution over time of the level of genetic isolation between two karyotypically different species of shrews (Sorex araneus and Sorex antinorii) at a hybrid zone located in the Swiss Alps. We first evaluated hybrid zone movement by contrasting patterns of gene flow and changes in cline parameters (centre and width) using 24 microsatellite loci, between two periods separated by 10 years apart. Additionally, we tested the role of chromosomal rearrangements on gene flow by analysing microsatellite loci located on both rearranged and common chromosomes to both species. We did not detect any movement of the hybrid zone during the period analysed, suggesting that the zone is a typical tension zone. However, the gene flow was significantly lower among the rearranged than the common chromosomes for the second period, whereas the difference was only marginally significant for the first period. This further supports the role of chromosomal rearrangements on gene flow between these taxa.

Synthesis of clonality and polyploidy in vertebrate animals by hybridization between two sexual species.

PubMed

Choleva, Lukáš; Janko, Karel; De Gelas, Koen; Bohlen, Jörg; Šlechtová, Věra; Rábová, Marie; Ráb, Petr

2012-07-01

Because most clonal vertebrates have hybrid genomic constitutions, tight linkages are assumed among hybridization, clonality, and polyploidy. However, predictions about how these processes mechanistically relate during the switch from sexual to clonal reproduction have not been validated. Therefore, we performed a crossing experiment to test the hypothesis that interspecific hybridization per se initiated clonal diploid and triploid spined loaches (Cobitis) and their gynogenetic reproduction. We reared two F1 families resulting from the crossing of 14 pairs of two sexual species, and found their diploid hybrid constitution and a 1:1 sex ratio. While males were infertile, females produced unreduced nonrecombinant eggs (100%). Synthetic triploid females and males (96.3%) resulted in each of nine backcrossed families from eggs of synthesized diploid F1s fertilized by haploid sperm from sexual males. Five individuals (3.7%) from one backcross family were genetically identical to the somatic cells of the mother and originated via gynogenesis; the sperm of the sexual male only triggered clonal development of the egg. Our reconstruction of the evolutionary route from sexuality to clonality and polyploidy in these fish shows that clonality and gynogenesis may have been directly triggered by interspecific hybridization and that polyploidy is a consequence, not a cause, of clonality. © 2012 The Author(s).

The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts

PubMed Central

Baker, EmilyClare; Wang, Bing; Bellora, Nicolas; Peris, David; Hulfachor, Amanda Beth; Koshalek, Justin A.; Adams, Marie; Libkind, Diego; Hittinger, Chris Todd

2015-01-01

The dramatic phenotypic changes that occur in organisms during domestication leave indelible imprints on their genomes. Although many domesticated plants and animals have been systematically compared with their wild genetic stocks, the molecular and genomic processes underlying fungal domestication have received less attention. Here, we present a nearly complete genome assembly for the recently described yeast species Saccharomyces eubayanus and compare it to the genomes of multiple domesticated alloploid hybrids of S. eubayanus × S. cerevisiae (S. pastorianus syn. S. carlsbergensis), which are used to brew lager-style beers. We find that the S. eubayanus subgenomes of lager-brewing yeasts have experienced increased rates of evolution since hybridization, and that certain genes involved in metabolism may have been particularly affected. Interestingly, the S. eubayanus subgenome underwent an especially strong shift in selection regimes, consistent with more extensive domestication of the S. cerevisiae parent prior to hybridization. In contrast to recent proposals that lager-brewing yeasts were domesticated following a single hybridization event, the radically different neutral site divergences between the subgenomes of the two major lager yeast lineages strongly favor at least two independent origins for the S. cerevisiae × S. eubayanus hybrids that brew lager beers. Our findings demonstrate how this industrially important hybrid has been domesticated along similar evolutionary trajectories on multiple occasions. PMID:26269586

Molecular evidence of hybrid zones of Cedrela (Meliaceae) in the Yungas of Northwestern Argentina.

PubMed

Zelener, Noga; Tosto, Daniela; de Oliveira, Luiz Orlando; Soldati, María Cristina; Inza, María Virginia; Fornes, Luis Fernando

2016-09-01

In the Yungas of Northwestern Argentina, three endangered species of Cedrela (C. angustifolia, C. saltensis, and C. balansae) follow altitudinal gradients of distribution with contact zones between them. We sampled 210 individuals from 20 populations that spanned most of Cedrela's geographical range in the Yungas, and used Amplified Fragment Length Polymorphism (AFLP) markers and DNA sequences of the nuclear Internal Transcribed Spacer (ITS) to investigate hybrid zones. Data analyses employed an array of complementary methods, including principal coordinate analyses, Bayesian clustering analyses, maximum likelihood tree-building, and network techniques. Both nuclear molecular systems - AFLP and ITS - provided insights into the evolutionary history of Cedrela in the Yungas in a congruent manner. We uncovered strong support for the occurrence of natural hybridization between C. balansae and C. saltensis. Additionally, we identified hybrid zones in areas of sympatry (at both the Calilegua National Park and the San Andrés farm) and in transition zones from 820 to 1100meters above sea level (localities of Pintascayo and Acambuco). There was no evidence for hybridization of either C. balansae or C. saltensis with C. angustifolia. The role of hybrid populations in conservation and use of genetic resources in the Yungas were discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

PubMed Central

Dasmahapatra, Kanchon K; Walters, James R.; Briscoe, Adriana D.; Davey, John W.; Whibley, Annabel; Nadeau, Nicola J.; Zimin, Aleksey V.; Hughes, Daniel S. T.; Ferguson, Laura C.; Martin, Simon H.; Salazar, Camilo; Lewis, James J.; Adler, Sebastian; Ahn, Seung-Joon; Baker, Dean A.; Baxter, Simon W.; Chamberlain, Nicola L.; Chauhan, Ritika; Counterman, Brian A.; Dalmay, Tamas; Gilbert, Lawrence E.; Gordon, Karl; Heckel, David G.; Hines, Heather M.; Hoff, Katharina J.; Holland, Peter W.H.; Jacquin-Joly, Emmanuelle; Jiggins, Francis M.; Jones, Robert T.; Kapan, Durrell D.; Kersey, Paul; Lamas, Gerardo; Lawson, Daniel; Mapleson, Daniel; Maroja, Luana S.; Martin, Arnaud; Moxon, Simon; Palmer, William J.; Papa, Riccardo; Papanicolaou, Alexie; Pauchet, Yannick; Ray, David A.; Rosser, Neil; Salzberg, Steven L.; Supple, Megan A.; Surridge, Alison; Tenger-Trolander, Ayse; Vogel, Heiko; Wilkinson, Paul A.; Wilson, Derek; Yorke, James A.; Yuan, Furong; Balmuth, Alexi L.; Eland, Cathlene; Gharbi, Karim; Thomson, Marian; Gibbs, Richard A.; Han, Yi; Jayaseelan, Joy C.; Kovar, Christie; Mathew, Tittu; Muzny, Donna M.; Ongeri, Fiona; Pu, Ling-Ling; Qu, Jiaxin; Thornton, Rebecca L.; Worley, Kim C.; Wu, Yuan-Qing; Linares, Mauricio; Blaxter, Mark L.; Constant, Richard H. ffrench; Joron, Mathieu; Kronforst, Marcus R.; Mullen, Sean P.; Reed, Robert D.; Scherer, Steven E.; Richards, Stephen; Mallet, James; McMillan, W. Owen; Jiggins, Chris D.

2012-01-01

The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation. PMID:22722851

Biparental inheritance of organelles in Pelargonium: evidence for intergenomic recombination of mitochondrial DNA.

PubMed

Apitz, Janina; Weihe, Andreas; Pohlheim, Frank; Börner, Thomas

2013-02-01

While uniparental transmission of mtDNA is widespread and dominating in eukaryotes leaving mutation as the major source of genotypic diversity, recently, biparental inheritance of mitochondrial genes has been demonstrated in reciprocal crosses of Pelargonium zonale and P. inquinans. The thereby arising heteroplasmy carries the potential for recombination between mtDNAs of different descent, i.e. between the parental mitochondrial genomes. We have analyzed these Pelargonium hybrids for mitochondrial intergenomic recombination events by examining differences in DNA blot hybridization patterns of the mitochondrial genes atp1 and cob. Further investigation of these genes and their flanking regions using nucleotide sequence polymorphisms and PCR revealed DNA segments in the progeny, which contained both P. zonale and P. inquinans sequences suggesting an intergenomic recombination in hybrids of Pelargonium. This turns Pelargonium into an interesting subject for studies of recombination and evolutionary dynamics of mitochondrial genomes.

Evolutionary analysis of Pinus densata Masters, a putative Tertiary hybrid : 1. Allozyme variation.

PubMed

Wang, X R; Szmidt, A E; Lewandowski, A; Wang, Z R

1990-11-01

Allozyme differentiation at 13 loci was studied in populations of Pinus tabulaeformis, P. densata, and P. yunnanensis from China. It was previously suggested that P. densata represents a Tertiary hybrid between P. tabulaeformis and P. yunnanensis. The observed levels of allozyme variation within and among the investigated species were comparable to those of other conifers. P. tabulaeformis differed markedly from P. yunnanensis with respect to allozyme frequencies, while P. densata was intermediate between the two putative parents. There was evidence of homozygote excess in embryos from all investigated species, as compared to Hardy-Weinberg expectations. The observed allozyme composition of P. densata conformed to earlier morphological and molecular evidence indicating hybrid origin of this taxon. It was proposed that fusion of gene pools from P. tabulaeformis and P. yunnanensis has led to adaptive evolution of a new species, P. densata.

Evolutionary fuzzy ARTMAP neural networks for classification of semiconductor defects.

PubMed

Tan, Shing Chiang; Watada, Junzo; Ibrahim, Zuwairie; Khalid, Marzuki

2015-05-01

Wafer defect detection using an intelligent system is an approach of quality improvement in semiconductor manufacturing that aims to enhance its process stability, increase production capacity, and improve yields. Occasionally, only few records that indicate defective units are available and they are classified as a minority group in a large database. Such a situation leads to an imbalanced data set problem, wherein it engenders a great challenge to deal with by applying machine-learning techniques for obtaining effective solution. In addition, the database may comprise overlapping samples of different classes. This paper introduces two models of evolutionary fuzzy ARTMAP (FAM) neural networks to deal with the imbalanced data set problems in a semiconductor manufacturing operations. In particular, both the FAM models and hybrid genetic algorithms are integrated in the proposed evolutionary artificial neural networks (EANNs) to classify an imbalanced data set. In addition, one of the proposed EANNs incorporates a facility to learn overlapping samples of different classes from the imbalanced data environment. The classification results of the proposed evolutionary FAM neural networks are presented, compared, and analyzed using several classification metrics. The outcomes positively indicate the effectiveness of the proposed networks in handling classification problems with imbalanced data sets.

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

PubMed Central

Hou, Beiwei; Luo, Jing; Zhang, Yusi; Niu, Zhitao; Xue, Qingyun; Ding, Xiaoyu

2017-01-01

The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species’ diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange. PMID:28262789

Organic-Inorganic Composites of Semiconductor Nanocrystals for Efficient Excitonics.

PubMed

Guzelturk, Burak; Demir, Hilmi Volkan

2015-06-18

Nanocomposites of colloidal semiconductor nanocrystals integrated into conjugated polymers are the key to soft-material hybrid optoelectronics, combining advantages of both plastics and particles. Synergic combination of the favorable properties in the hybrids of colloidal nanocrystals and conjugated polymers offers enhanced performance and new functionalities in light-generation and light-harvesting applications, where controlling and mastering the excitonic interactions at the nanoscale are essential. In this Perspective, we highlight and critically consider the excitonic interactions in the organic-inorganic nanocomposites to achieve highly efficient exciton transfer through rational design of the nanocomposites. The use of strong excitonic interactions in optoelectronic devices can trigger efficiency breakthroughs in hybrid optoelectronics.

Conditions for optimal efficiency of PCBM-based terahertz modulators

NASA Astrophysics Data System (ADS)

Yoo, Hyung Keun; Lee, Hanju; Lee, Kiejin; Kang, Chul; Kee, Chul-Sik; Hwang, In-Wook; Lee, Joong Wook

2017-10-01

We demonstrate the conditions for optimal modulation efficiency of active terahertz modulators based on phenyl-C61-butyric acid methyl ester (PCBM)-silicon hybrid structures. Highly efficient active control of the terahertz wave modulation was realized by controlling organic film thickness, annealing temperature, and laser excitation wavelength. Under the optimal conditions, the modulation efficiency reached nearly 100%. Charge distributions measured with a near-field scanning microwave microscanning technique corroborated the fact that the increase of photo-excited carriers due to the PCBM-silicon hybrid structure enables the enhancement of active modulation efficiency.

The population genetics of sporophytic self-incompatibility in three hybridizing senecio (asteraceae) species with contrasting population histories.

PubMed

Brennan, Adrian C; Harris, Stephen A; Hiscock, Simon J

2013-05-01

Hybridization generates evolutionary novelty and spreads adaptive variation. By promoting outcrossing, plant self-incompatibility (SI) systems also favor interspecific hybridization because the S locus is under strong negative frequency-dependent balancing selection. This study investigates the SI mating systems of three hybridizing Senecio species with contrasting population histories. Senecio aethnensis and S. chrysanthemifolius native to Sicily, form a hybrid zone at intermediate altitudes on Mount Etna, and their neo-homoploid hybrid species, S. squalidus, has colonized disturbed urban habitats in the UK during the last 150 years. We show that all three species express sporophytic SI (SSI), where pollen incompatibility is controlled by the diploid parental genome, and that SSI is inherited and functions normally in hybrids. Large-scale crossing studies of wild sampled populations allowed direct comparison of SSI between species and found that the main impacts of colonization in S. squalidus compared to Sicilian Senecio was a reduced number of S alleles, increased S allele frequencies, and increased interpopulation S allele sharing. In general, many S alleles were shared between species and the S locus showed reduced intra- and interspecific population genetic structure compared to molecular genetic markers, indicative of enhanced effective gene flow due to balancing selection. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Introgressive hybridization and latitudinal admixture clines in North Atlantic eels

PubMed Central

2014-01-01

Background Hybridization, the interbreeding of diagnosably divergent species, is a major focus in evolutionary studies. Eels, both from North America and Europe migrate through the Atlantic to mate in a vast, overlapping area in the Sargasso Sea. Due to the lack of direct observation, it is unknown how these species remain reproductively isolated. The detection of inter-species hybrids in Iceland suggests on-going gene flow, but few studies to date have addressed the influence of introgression on genetic differentiation in North Atlantic eels. Results Here, we show that while mitochondrial lineages remain completely distinct on both sides of the Atlantic, limited hybridization is detectable with nuclear DNA markers. The nuclear hybridization signal peaks in the northern areas and decreases towards the southern range limits on both continents according to Bayesian assignment analyses. By simulating increasing proportions of both F1 hybrids and admixed individuals from the southern to the northern-most locations, we were able to generate highly significant isolation-by-distance patterns in both cases, reminiscent of previously published data for the European eel. Finally, fitting an isolation-with-migration model to our data supports the hypothesis of recent asymmetric introgression and refutes the alternative hypothesis of ancient polymorphism. Conclusions Fluctuating degrees of introgressive hybridization between Atlantic eel species are sufficient to explain temporally varying correlations of geographic and genetic distances reported for populations of the European eel. PMID:24674242

An introduced and a native vertebrate hybridize to form a genetic bridge to a second native species

USGS Publications Warehouse

McDonald, D.B.; Parchman, T.L.; Bower, M.R.; Hubert, W.A.; Rahel, F.J.

2008-01-01

The genetic impacts of hybridization between native and introduced species are of considerable conservation concern, while the possibility of reticulate evolution affects our basic understanding of how species arise and shapes how we use genetic data to understand evolutionary diversification. By using mitochondrial NADH dehydrogenase subunit 2 (ND2) sequences and 467 amplified fragment-length polymorphism nuclear DNA markers, we show that the introduced white sucker (Catostomus commersoni) has hybridized with two species native to the Colorado River Basin - the flannelmouth sucker (Catostomus latipinnis) and the bluehead sucker (Catostomus discobolus). Hybrids between the flannelmouth sucker and white sucker have facilitated introgression between the two native species, previously isolated by reproductive barriers, such that individuals exist with contributions from all three genomes. Most hybrids had the mitochondrial haplotype of the introduced white sucker, emphasizing its pivotal role in this three-way hybridization. Our findings highlight how introduced species can threaten the genetic integrity of not only one species but also multiple previously reproductively isolated species. Furthermore, this complex three-way reticulate (as opposed to strictly bifurcating) evolution suggests that seeking examples in other vertebrate systems might be productive. Although the present study involved an introduced species, similar patterns of hybridization could result from natural processes, including stream capture or geological formations (e.g., the Bering land bridge). ?? 2008 by The National Academy of Sciences of the USA.

Hybrid engineered materials with high water-collecting efficiency inspired by Namib Desert beetles.

PubMed

Zhu, Hai; Guo, Zhiguang

2016-05-21

Inspired by Namib Desert beetles, a hybrid superhydrophobic surface was fabricated, showing highly efficient fog harvesting with a water collection rate (WCR) of 1309.9 mg h(-1) cm(-2). And, the surface possessed an excellent robustness and self-cleaning property.

Interspecific competition, hybridization, and reproductive isolation in secondary contact: missing perspectives on males and females

PubMed Central

2018-01-01

Abstract Research on sexual selection and hybridization has focused on female mate choice and male–male competition. While the evolutionary outcomes of interspecific female preference have been well explored, we are now gaining a better understanding of the processes by which male–male competition between species in secondary contact promotes reproductive isolation versus hybridization. What is relatively unexplored is the interaction between female choice and male competition, as they can oppose one another or align with similar outcomes for reproductive isolation. The role of female–female competition in hybridization is also not well understood, but could operate similarly to male–male competition in polyandrous and other systems where costs to heterospecific mating are low for females. Reproductive competition between either sex of sympatric species can cause the divergence and/or convergence of sexual signals and recognition, which in turn influences the likelihood for interspecific mating. Future work on species interactions in secondary contact should test the relative influences of both mate choice and competition for mates on hybridization outcomes, and should not ignore the possibilities that females can compete over mating resources, and males can exercise mate choice. PMID:29492041

Morphological and genetic evidence of contemporary intersectional hybridisation in Mediterranean Helichrysum (Asteraceae, Gnaphalieae).

PubMed

Galbany-Casals, M; Carnicero-Campmany, P; Blanco-Moreno, J M; Smissen, R D

2012-09-01

Hybridisation is considered an important evolutionary phenomenon in Gnaphalieae, but contemporary hybridisation has been little explored within the tribe. Here, hybridisation between Helichrysum orientale and Helichrysum stoechas is studied at two different localities in the islands of Crete and Rhodes (Greece). Using three different types of molecular data (AFLP, nrDNA ITS sequences and cpDNA ndhF sequences) and morphological data, the aim is to provide simultaneous and direct comparisons between molecular and morphological variation among the parental species and the studied hybrid populations. AFLP profiles, ITS sequences and morphological data support the existence of hybrids at the two localities studied, shown as morphological and genetic intermediates between the parental species. Chloroplast DNA sequences show that both parental species can act either as pollen donor or as maternal parent. Fertility of hybrids is demonstrated by the viability of seeds produced by hybrids from both localities, and the detection of a backcross specimen to H. orientale. Although there is general congruence of morphological and molecular data, the analysis of morphology and ITS sequences can fail to detect backcross hybrids. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

Multiobjective synchronization of coupled systems

NASA Astrophysics Data System (ADS)

Tang, Yang; Wang, Zidong; Wong, W. K.; Kurths, Jürgen; Fang, Jian-an

2011-06-01

In this paper, multiobjective synchronization of chaotic systems is investigated by especially simultaneously minimizing optimization of control cost and convergence speed. The coupling form and coupling strength are optimized by an improved multiobjective evolutionary approach that includes a hybrid chromosome representation. The hybrid encoding scheme combines binary representation with real number representation. The constraints on the coupling form are also considered by converting the multiobjective synchronization into a multiobjective constraint problem. In addition, the performances of the adaptive learning method and non-dominated sorting genetic algorithm-II as well as the effectiveness and contributions of the proposed approach are analyzed and validated through the Rössler system in a chaotic or hyperchaotic regime and delayed chaotic neural networks.

The Hybrid Automobile and the Atkinson Cycle

ERIC Educational Resources Information Center

Feldman, Bernard J.

2008-01-01

The hybrid automobile is a strikingly new automobile technology with a number of new technological features that dramatically improve energy efficiency. This paper will briefly describe how hybrid automobiles work; what are these new technological features; why the Toyota Prius hybrid internal combustion engine operates on the Atkinson cycle…

Asymmetric Hybridization in Cattails (Typha spp.) and Its Implications for the Evolutionary Maintenance of Native Typha latifolia.

PubMed

Pieper, Sara J; Nicholls, Allison A; Freeland, Joanna R; Dorken, Marcel E

2017-07-01

Cattails (Typha spp.) have become an increasingly dominant component of wetlands in eastern North America and this dominance is largely attributable to the high frequency of Typha × glauca, the hybrid of native Typha latifolia and putatively introduced Typha angustifolia. Hybridization in this group is asymmetric, with T. angustifolia nearly always the maternal parent of F1 hybrids. However, the magnitude of hybrid infertility and whether mating asymmetries extend to the formation of advanced-generation hybrids have not been examined. We used hand-crosses to measure seed set and germination success. We found that mating asymmetries extend to the formation of back-crosses, with ~0 seeds set when T. latifolia was pollinated by hybrid cattails. Seed set was unaffected by pollen source for T. × glauca or T. angustifolia. However, seed production by T. angustifolia was consistently high while that of T. × glauca was variable and when pollinated by other T. × glauca more than 75% lower than for any other intraspecific cross indicating reduced hybrid fertility. We used these results to parameterize a model of hybrid zone evolution in which mating patterns and fertility were governed by interactions between alleles at nuclear and cytoplasmic loci. The model revealed that asymmetric mating and reduced hybrid fertility should favor the maintenance of T. latifolia over T. angustifolia compared to null expectations. However, the model also indicated restrictive conditions for the long-term maintenance of T. latifolia within populations, indicating that asymmetric mating might only stall rather than prevent the displacement of native cattails by hybrids. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genome-scale transcriptional study of hybrid effects and regulatory divergence in an F1 hybrid Ruellia (Wild Petunias: Acanthaceae) and its parents.

PubMed

Zhuang, Yongbin; Tripp, Erin A

2017-01-17

New combinations of divergent genomes can give rise to novel genetic functions in resulting hybrid progeny. Such functions may yield opportunities for ecological divergence, contributing ultimately to reproductive isolation and evolutionary longevity of nascent hybrid lineages. In plants, the degree to which transgressive genotypes contribute to floral novelty remains a question of key interest. Here, we generated an F 1 hybrid plant between the red-flowered Ruellia elegans and yellow flowered R. speciosa. RNA-seq technology was used to explore differential gene expression between the hybrid and its two parents, with emphasis on genetic elements involved in the production of floral anthocyanin pigments. The hybrid was purple flowered and produced novel floral delphinidin pigments not manufactured by either parent. We found that nearly a fifth of all 86,475 unigenes expressed were unique to the hybrid. The majority of hybrid unigenes (80.97%) showed a pattern of complete dominance to one parent or the other although this ratio was uneven, suggesting asymmetrical influence of parental genomes on the progeny transcriptome. However, 8.87% of all transcripts within the hybrid were expressed at significantly higher or lower mean levels than observed for either parent. A total of 28 unigenes coding putatively for eight core enzymes in the anthocyanin pathway were recovered, along with three candidate MYBs involved in anthocyanin regulation. Our results suggest that models of gene evolution that explain phenotypic novelty and hybrid establishment in plants may need to include transgressive effects. Additionally, our results lend insight into the potential for floral novelty that derives from unions of divergent genomes. These findings serve as a starting point to further investigate molecular mechanisms involved in flower color transitions in Ruellia.

Wiener-Hammerstein system identification - an evolutionary approach

NASA Astrophysics Data System (ADS)

Naitali, Abdessamad; Giri, Fouad

2016-01-01

The problem of identifying parametric Wiener-Hammerstein (WH) systems is addressed within the evolutionary optimisation context. Specifically, a hybrid culture identification method is developed that involves model structure adaptation using genetic recombination and model parameter learning using particle swarm optimisation. The method enjoys three interesting features: (1) the risk of premature convergence of model parameter estimates to local optima is significantly reduced, due to the constantly maintained diversity of model candidates; (2) no prior knowledge is needed except for upper bounds on the system structure indices; (3) the method is fully autonomous as no interaction is needed with the user during the optimum search process. The performances of the proposed method will be illustrated and compared to alternative methods using a well-established WH benchmark.

Simple structured hybrid WOLEDs based on incomplete energy transfer mechanism: from blue exciplex to orange dopant.

PubMed

Zhang, Tianyou; Zhao, Bo; Chu, Bei; Li, Wenlian; Su, Zisheng; Yan, Xingwu; Liu, Chengyuan; Wu, Hairuo; Gao, Yuan; Jin, Fangming; Hou, Fuhua

2015-05-15

Exciplex is well known as a charge transfer state formed between electron-donating and electron-accepting molecules. However, exciplex based organic light emitting diodes (OLED) often performed low efficiencies relative to pure phosphorescent OLED and could hardly be used to construct white OLED (WOLED). In this work, a new mechanism is developed to realize efficient WOLED with extremely simple structure by redistributing the energy of triplet exciplex to both singlet exciplex and the orange dopant. The micro process of energy transfer could be directly examined by detailed photoluminescence decay measurement and time resolved photoluminescence analysis. This strategy overcomes the low reverse intersystem crossing efficiency of blue exciplex and complicated device structure of traditional WOLED, enables us to achieve efficient hybrid WOLEDs. Based on this mechanism, we have successfully constructed both exciplex-fluorescence and exciplex-phosphorescence hybrid WOLEDs with remarkable efficiencies.

Simple structured hybrid WOLEDs based on incomplete energy transfer mechanism: from blue exciplex to orange dopant

NASA Astrophysics Data System (ADS)

Zhang, Tianyou; Zhao, Bo; Chu, Bei; Li, Wenlian; Su, Zisheng; Yan, Xingwu; Liu, Chengyuan; Wu, Hairuo; Gao, Yuan; Jin, Fangming; Hou, Fuhua

2015-05-01

Exciplex is well known as a charge transfer state formed between electron-donating and electron-accepting molecules. However, exciplex based organic light emitting diodes (OLED) often performed low efficiencies relative to pure phosphorescent OLED and could hardly be used to construct white OLED (WOLED). In this work, a new mechanism is developed to realize efficient WOLED with extremely simple structure by redistributing the energy of triplet exciplex to both singlet exciplex and the orange dopant. The micro process of energy transfer could be directly examined by detailed photoluminescence decay measurement and time resolved photoluminescence analysis. This strategy overcomes the low reverse intersystem crossing efficiency of blue exciplex and complicated device structure of traditional WOLED, enables us to achieve efficient hybrid WOLEDs. Based on this mechanism, we have successfully constructed both exciplex-fluorescence and exciplex-phosphorescence hybrid WOLEDs with remarkable efficiencies.

Simple structured hybrid WOLEDs based on incomplete energy transfer mechanism: from blue exciplex to orange dopant

PubMed Central

Zhang, Tianyou; Zhao, Bo; Chu, Bei; Li, Wenlian; Su, Zisheng; Yan, Xingwu; Liu, Chengyuan; Wu, Hairuo; Gao, Yuan; Jin, Fangming; Hou, Fuhua

2015-01-01

Exciplex is well known as a charge transfer state formed between electron-donating and electron-accepting molecules. However, exciplex based organic light emitting diodes (OLED) often performed low efficiencies relative to pure phosphorescent OLED and could hardly be used to construct white OLED (WOLED). In this work, a new mechanism is developed to realize efficient WOLED with extremely simple structure by redistributing the energy of triplet exciplex to both singlet exciplex and the orange dopant. The micro process of energy transfer could be directly examined by detailed photoluminescence decay measurement and time resolved photoluminescence analysis. This strategy overcomes the low reverse intersystem crossing efficiency of blue exciplex and complicated device structure of traditional WOLED, enables us to achieve efficient hybrid WOLEDs. Based on this mechanism, we have successfully constructed both exciplex-fluorescence and exciplex-phosphorescence hybrid WOLEDs with remarkable efficiencies. PMID:25975371

Highly Conductive PEDOT:PSS Transparent Hole Transporting Layer with Solvent Treatment for High Performance Silicon/Organic Hybrid Solar Cells.

PubMed

Li, Qingduan; Yang, Jianwei; Chen, Shuangshuang; Zou, Jizhao; Xie, Weiguang; Zeng, Xierong

2017-08-23

Efficient Si/organic hybrid solar cells were fabricated with dimethyl sulfoxide (DMSO) and surfactant-doped poly(3,4-ethylenedioxythiophene): polystyrene (PEDOT:PSS). A post-treatment on PEDOT:PSS films with polar solvent was performed to increase the device performance. We found that the performance of hybrid solar cells increase with the polarity of solvent. A high conductivity of 1105 S cm - 1 of PEDOT:PSS was achieved by adopting methanol treatment, and the best efficiency of corresponding hybrid solar cells reaches 12.22%. X-ray photoelectron spectroscopy (XPS) and RAMAN spectroscopy were utilized to conform to component changes of PEDOT:PSS films after solvent treatment. It was found that the removal of the insulator PSS from the film and the conformational changes are the determinants for the device performance enhancement. Electrochemical impedance spectroscopy (EIS) was used to investigate the recombination resistance and capacitance of methanol-treated and untreated hybrid solar cells, indicating that methanol-treated devices had a larger recombination resistance and capacitance. Our findings bring a simple and efficient way for improving the performance of hybrid solar cell.

EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

PubMed

Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

2012-01-01

Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

Remanagement of Singlet and Triplet Excitons in Single-Emissive-Layer Hybrid White Organic Light-Emitting Devices Using Thermally Activated Delayed Fluorescent Blue Exciplex.

PubMed

Liu, Xiao-Ke; Chen, Zhan; Qing, Jian; Zhang, Wen-Jun; Wu, Bo; Tam, Hoi Lam; Zhu, Furong; Zhang, Xiao-Hong; Lee, Chun-Sing

2015-11-25

A high-performance hybrid white organic light-emitting device (WOLED) is demonstrated based on an efficient novel thermally activated delayed fluorescence (TADF) blue exciplex system. This device shows a low turn-on voltage of 2.5 V and maximum forward-viewing external quantum efficiency of 25.5%, which opens a new avenue for achieving high-performance hybrid WOLEDs with simple structures. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A hybrid framework for coupling arbitrary summation-by-parts schemes on general meshes

NASA Astrophysics Data System (ADS)

Lundquist, Tomas; Malan, Arnaud; Nordström, Jan

2018-06-01

We develop a general interface procedure to couple both structured and unstructured parts of a hybrid mesh in a non-collocated, multi-block fashion. The target is to gain optimal computational efficiency in fluid dynamics simulations involving complex geometries. While guaranteeing stability, the proposed procedure is optimized for accuracy and requires minimal algorithmic modifications to already existing schemes. Initial numerical investigations confirm considerable efficiency gains compared to non-hybrid calculations of up to an order of magnitude.

Nanotetrapods: quantum dot hybrid for bulk heterojunction solar cells

PubMed Central

2013-01-01

Hybrid thin film solar cell based on all-inorganic nanoparticles is a new member in the family of photovoltaic devices. In this work, a novel and performance-efficient inorganic hybrid nanostructure with continuous charge transportation and collection channels is demonstrated by introducing CdTe nanotetropods (NTs) and CdSe quantum dots (QDs). Hybrid morphology is characterized, demonstrating an interpenetration and compacted contact of NTs and QDs. Electrical measurements show enhanced charge transfer at the hybrid bulk heterojunction interface of NTs and QDs after ligand exchange which accordingly improves the performance of solar cells. Photovoltaic and light response tests exhibit a combined optic-electric contribution from both CdTe NTs and CdSe QDs through a formation of interpercolation in morphology as well as a type II energy level distribution. The NT and QD hybrid bulk heterojunction is applicable and promising in other highly efficient photovoltaic materials such as PbS QDs. PMID:24139059

Why is population information crucial for taxonomy? A case study involving a hybrid swarm and related varieties

PubMed Central

Marczewski, Tobias; Ma, Yong-Peng; Zhang, Xue-Mei; Sun, Wei-Bang; Marczewski, A. Jane

2016-01-01

Hybridization has become a focal topic in evolutionary biology, and many taxonomists are aware that the process occurs more frequently than previously assumed. Nonetheless many species and varieties are still described without explicitly considering the possibility of hybridization, especially in countries that have relatively short scientific histories, but which often possess the highest species diversities. Furthermore, new taxa are often described based only on herbarium specimens, not taking into account information from wild populations, significantly decreasing the potential to detect morphologies arising from hybridization at this crucial descriptive stage. We used morphological data from a hybrid swarm involving two Rhododendron species to showcase possible character combinations in intermediates. Certain characters used to distinguish taxa were more variable within the same individual than between species, emphasizing the importance of population information for an adequate choice of characters. Most described varieties of the two species fell within the spectrum of hybrid morphology, suggesting that these taxa would be unlikely to have merited formal description if contemporary standards had been employed. In all investigated cases the hybrid nature of described varieties seems to have been detectable with adequate morphological data alone, if populations had been assessed. A post hoc assessment of taxa is often complicated, especially if certain types of information are not provided. To avoid accumulation of such invalid taxa, careful scrutiny should be employed for new descriptions. Hybrids (not hybrid species) described as taxa obscure valuable information about natural processes and impact negatively on further research that depends on taxonomic data. PMID:27758764

A constraint-based evolutionary learning approach to the expectation maximization for optimal estimation of the hidden Markov model for speech signal modeling.

PubMed

Huda, Shamsul; Yearwood, John; Togneri, Roberto

2009-02-01

This paper attempts to overcome the tendency of the expectation-maximization (EM) algorithm to locate a local rather than global maximum when applied to estimate the hidden Markov model (HMM) parameters in speech signal modeling. We propose a hybrid algorithm for estimation of the HMM in automatic speech recognition (ASR) using a constraint-based evolutionary algorithm (EA) and EM, the CEL-EM. The novelty of our hybrid algorithm (CEL-EM) is that it is applicable for estimation of the constraint-based models with many constraints and large numbers of parameters (which use EM) like HMM. Two constraint-based versions of the CEL-EM with different fusion strategies have been proposed using a constraint-based EA and the EM for better estimation of HMM in ASR. The first one uses a traditional constraint-handling mechanism of EA. The other version transforms a constrained optimization problem into an unconstrained problem using Lagrange multipliers. Fusion strategies for the CEL-EM use a staged-fusion approach where EM has been plugged with the EA periodically after the execution of EA for a specific period of time to maintain the global sampling capabilities of EA in the hybrid algorithm. A variable initialization approach (VIA) has been proposed using a variable segmentation to provide a better initialization for EA in the CEL-EM. Experimental results on the TIMIT speech corpus show that CEL-EM obtains higher recognition accuracies than the traditional EM algorithm as well as a top-standard EM (VIA-EM, constructed by applying the VIA to EM).

Phenotypic variation and covariation indicate high evolvability of acoustic communication in crickets.

PubMed

Blankers, T; Lübke, A K; Hennig, R M

2015-09-01

Studying the genetic architecture of sexual traits provides insight into the rate and direction at which traits can respond to selection. Traits associated with few loci and limited genetic and phenotypic constraints tend to evolve at high rates typically observed for secondary sexual characters. Here, we examined the genetic architecture of song traits and female song preferences in the field crickets Gryllus rubens and Gryllus texensis. Song and preference data were collected from both species and interspecific F1 and F2 hybrids. We first analysed phenotypic variation to examine interspecific differentiation and trait distributions in parental and hybrid generations. Then, the relative contribution of additive and additive-dominance variation was estimated. Finally, phenotypic variance-covariance (P) matrices were estimated to evaluate the multivariate phenotype available for selection. Song traits and preferences had unimodal trait distributions, and hybrid offspring were intermediate with respect to the parents. We uncovered additive and dominance variation in song traits and preferences. For two song traits, we found evidence for X-linked inheritance. On the one hand, the observed genetic architecture does not suggest rapid divergence, although sex linkage may have allowed for somewhat higher evolutionary rates. On the other hand, P matrices revealed that multivariate variation in song traits aligned with major dimensions in song preferences, suggesting a strong selection response. We also found strong covariance between the main traits that are sexually selected and traits that are not directly selected by females, providing an explanation for the striking multivariate divergence in male calling songs despite limited divergence in female preferences. © 2015 European Society For Evolutionary Biology.

Simulation of hybrid solar power plants

NASA Astrophysics Data System (ADS)

Dieckmann, Simon; Dersch, Jürgen

2017-06-01

Hybrid solar power plants have the potential to combine advantages of two different technologies at the cost of increased complexity. The present paper shows the potential of the software greenius for the techno-economic evaluation of hybrid solar power plants and discusses two exemplary scenarios. Depreciated Concentrated Solar Power (CSP) plants based on trough technology can be retrofitted with solar towers in order to reach higher steam cycle temperatures and hence efficiencies. Compared to a newly built tower plant the hybridization of a depreciated trough plant causes about 30% lower LCOE reaching 104 /MWh. The second hybrid scenario combines cost-efficient photovoltaics with dispatchable CSP technology. This hybrid plant offers very high capacity factors up to 69% based on 100% load from 8am to 11pm. The LCOE of the hybrid plant are only slightly lower (174 vs. 186 /MWh) compared to the pure CSP plant because the capital expenditure for thermal storage and power block remains the same while the electricity output is much lower.

A hybrid fuzzy logic and extreme learning machine for improving efficiency of circulating water systems in power generation plant

NASA Astrophysics Data System (ADS)

Aziz, Nur Liyana Afiqah Abdul; Siah Yap, Keem; Afif Bunyamin, Muhammad

2013-06-01

This paper presents a new approach of the fault detection for improving efficiency of circulating water system (CWS) in a power generation plant using a hybrid Fuzzy Logic System (FLS) and Extreme Learning Machine (ELM) neural network. The FLS is a mathematical tool for calculating the uncertainties where precision and significance are applied in the real world. It is based on natural language which has the ability of "computing the word". The ELM is an extremely fast learning algorithm for neural network that can completed the training cycle in a very short time. By combining the FLS and ELM, new hybrid model, i.e., FLS-ELM is developed. The applicability of this proposed hybrid model is validated in fault detection in CWS which may help to improve overall efficiency of power generation plant, hence, consuming less natural recourses and producing less pollutions.

A rapid and efficient branched DNA hybridization assay to titer lentiviral vectors.

PubMed

Nair, Ayyappan; Xie, Jinger; Joshi, Sarasijam; Harden, Paul; Davies, Joan; Hermiston, Terry

2008-11-01

A robust assay to titer lentiviral vectors is imperative to qualifying their use in drug discovery, target validation and clinical applications. In this study, a novel branched DNA based hybridization assay was developed to titer lentiviral vectors by quantifying viral RNA genome copy numbers from viral lysates without having to purify viral RNA, and this approach was compared with other non-functional (p24 protein ELISA and viral RT-qPCR) and a functional method (reporter gene expression) used commonly. The RT-qPCR method requires purification of viral RNA and the accuracy of titration therefore depends on the efficiency of purification; this requirement is ameliorated in the hybridization assay as RNA is measured directly in viral lysates. The present study indicates that the hybridization based titration assay performed on viral lysates was more accurate and has additional advantages of being rapid, robust and not dependent on transduction efficiency in different cell types.

Hybrid photonic-plasmonic near-field probe for efficient light conversion into the nanoscale hot spot.

PubMed

Koshelev, Alexander; Munechika, Keiko; Cabrini, Stefano

2017-11-01

In this Letter, we present a design and simulations of the novel hybrid photonic-plasmonic near-field probe. Near-field optics is a unique imaging tool that provides optical images with resolution down to tens of nanometers. One of the main limitations of this technology is its low light sensitivity. The presented hybrid probe solves this problem by combining a campanile plasmonic probe with the photonic layer, consisting of the diffractive optic element (DOE). The DOE is designed to match the plasmonic field at the broad side of the campanile probe with the fiber mode. This makes it possible to optimize the size of the campanile tip to convert light efficiently into the hot spot. The simulations show that the hybrid probe is ∼540 times more efficient compared with the conventional campanile on average in the 600-900 nm spectral range.

Saccharomyces pastorianus: genomic insights inspiring innovation for industry.

PubMed

Gibson, Brian; Liti, Gianni

2015-01-01

A combination of biological and non-biological factors has led to the interspecific hybrid yeast species Saccharomyces pastorianus becoming one of the world's most important industrial organisms. This yeast is used in the production of lager-style beers, the fermentation of which requires very low temperatures compared to other industrial fermentation processes. This group of organisms has benefited from both the whole-genome duplication in its ancestral lineage and the subsequent hybridization event between S. cerevisiae and S. eubayanus, resulting in strong fermentative ability. The hybrid has key traits, such as cold tolerance and good maltose- and maltotriose-utilizing ability, inherited either from the parental species or originating from genetic interactions between the parent genomes. Instability in the nascent allopolyploid hybrid genome may have contributed to rapid evolution of the yeast to tolerate conditions prevalent in the brewing environment. The recent discovery of S. eubayanus has provided new insights into the evolutionary history of S. pastorianus and may offer new opportunities for generating novel industrially-beneficial lager yeast strains. Copyright © 2014 John Wiley & Sons, Ltd.

Maximizing coupling-efficiency of high-power diode lasers utilizing hybrid assembly technology

NASA Astrophysics Data System (ADS)

Zontar, D.; Dogan, M.; Fulghum, S.; Müller, T.; Haag, S.; Brecher, C.

2015-03-01

In this paper, we present hybrid assembly technology to maximize coupling efficiency for spatially combined laser systems. High quality components, such as center-turned focusing units, as well as suitable assembly strategies are necessary to obtain highest possible output ratios. Alignment strategies are challenging tasks due to their complexity and sensitivity. Especially in low-volume production fully automated systems are economically at a disadvantage, as operator experience is often expensive. However reproducibility and quality of automatically assembled systems can be superior. Therefore automated and manual assembly techniques are combined to obtain high coupling efficiency while preserving maximum flexibility. The paper will describe necessary equipment and software to enable hybrid assembly processes. Micromanipulator technology with high step-resolution and six degrees of freedom provide a large number of possible evaluation points. Automated algorithms are necess ary to speed-up data gathering and alignment to efficiently utilize available granularity for manual assembly processes. Furthermore, an engineering environment is presented to enable rapid prototyping of automation tasks with simultaneous data ev aluation. Integration with simulation environments, e.g. Zemax, allows the verification of assembly strategies in advance. Data driven decision making ensures constant high quality, documents the assembly process and is a basis for further improvement. The hybrid assembly technology has been applied on several applications for efficiencies above 80% and will be discussed in this paper. High level coupling efficiency has been achieved with minimized assembly as a result of semi-automated alignment. This paper will focus on hybrid automation for optimizing and attaching turning mirrors and collimation lenses.

A strategy with novel evolutionary features for the iterated prisoner's dilemma.

PubMed

Li, Jiawei; Kendall, Graham

2009-01-01

In recent iterated prisoner's dilemma tournaments, the most successful strategies were those that had identification mechanisms. By playing a predetermined sequence of moves and learning from their opponents' responses, these strategies managed to identify their opponents. We believe that these identification mechanisms may be very useful in evolutionary games. In this paper one such strategy, which we call collective strategy, is analyzed. Collective strategies apply a simple but efficient identification mechanism (that just distinguishes themselves from other strategies), and this mechanism allows them to only cooperate with their group members and defect against any others. In this way, collective strategies are able to maintain a stable population in evolutionary iterated prisoner's dilemma. By means of an invasion barrier, this strategy is compared with other strategies in evolutionary dynamics in order to demonstrate its evolutionary features. We also find that this collective behavior assists the evolution of cooperation in specific evolutionary environments.

A study on optimization of hybrid drive train using Advanced Vehicle Simulator (ADVISOR)

NASA Astrophysics Data System (ADS)

Same, Adam; Stipe, Alex; Grossman, David; Park, Jae Wan

This study investigates the advantages and disadvantages of three hybrid drive train configurations: series, parallel, and "through-the-ground" parallel. Power flow simulations are conducted with the MATLAB/Simulink-based software ADVISOR. These simulations are then applied in an application for the UC Davis SAE Formula Hybrid vehicle. ADVISOR performs simulation calculations for vehicle position using a combined backward/forward method. These simulations are used to study how efficiency and agility are affected by the motor, fuel converter, and hybrid configuration. Three different vehicle models are developed to optimize the drive train of a vehicle for three stages of the SAE Formula Hybrid competition: autocross, endurance, and acceleration. Input cycles are created based on rough estimates of track geometry. The output from these ADVISOR simulations is a series of plots of velocity profile and energy storage State of Charge that provide a good estimate of how the Formula Hybrid vehicle will perform on the given course. The most noticeable discrepancy between the input cycle and the actual velocity profile of the vehicle occurs during deceleration. A weighted ranking system is developed to organize the simulation results and to determine the best drive train configuration for the Formula Hybrid vehicle. Results show that the through-the-ground parallel configuration with front-mounted motors achieves an optimal balance of efficiency, simplicity, and cost. ADVISOR is proven to be a useful tool for vehicle power train design for the SAE Formula Hybrid competition. This vehicle model based on ADVISOR simulation is applicable to various studies concerning performance and efficiency of hybrid drive trains.

Research related to improved computer aided design software package. [comparative efficiency of finite, boundary, and hybrid element methods in elastostatics

NASA Technical Reports Server (NTRS)

Walston, W. H., Jr.

1986-01-01

The comparative computational efficiencies of the finite element (FEM), boundary element (BEM), and hybrid boundary element-finite element (HVFEM) analysis techniques are evaluated for representative bounded domain interior and unbounded domain exterior problems in elastostatics. Computational efficiency is carefully defined in this study as the computer time required to attain a specified level of solution accuracy. The study found the FEM superior to the BEM for the interior problem, while the reverse was true for the exterior problem. The hybrid analysis technique was found to be comparable or superior to both the FEM and BEM for both the interior and exterior problems.

Recent progress in efficient hybrid lead halide perovskite solar cells

PubMed Central

Cui, Jin; Yuan, Huailiang; Li, Junpeng; Xu, Xiaobao; Shen, Yan; Lin, Hong; Wang, Mingkui

2015-01-01

The efficiency of perovskite solar cells (PSCs) has been improved from 9.7 to 19.3%, with the highest value of 20.1% achieved in 2014. Such a high photovoltaic performance can be attributed to optically high absorption characteristics and balanced charge transport properties with long diffusion lengths of the hybrid lead halide perovskite materials. In this review, some fundamental details of hybrid lead iodide perovskite materials, various fabrication techniques and device structures are described, aiming for a better understanding of these materials and thus highly efficient PSC devices. In addition, some advantages and open issues are discussed here to outline the prospects and challenges of using perovskites in commercial photovoltaic devices. PMID:27877815

High-efficiency second harmonic generation from a single hybrid ZnO nanowire/Au plasmonic nano-oligomer.

PubMed

Grinblat, Gustavo; Rahmani, Mohsen; Cortés, Emiliano; Caldarola, Martín; Comedi, David; Maier, Stefan A; Bragas, Andrea V

2014-11-12

We introduce a plasmonic-semiconductor hybrid nanosystem, consisting of a ZnO nanowire coupled to a gold pentamer oligomer by crossing the hot-spot. It is demonstrated that the hybrid system exhibits a second harmonic (SH) conversion efficiency of ∼3 × 10(-5)%, which is among the highest values for a nanoscale object at optical frequencies reported so far. The SH intensity was found to be ∼1700 times larger than that from the same nanowire excited outside the hot-spot. Placing high nonlinear susceptibility materials precisely in plasmonic confined-field regions to enhance SH generation opens new perspectives for highly efficient light frequency up-conversion on the nanoscale.

Decentralized diagnostics based on a distributed micro-genetic algorithm for transducer networks monitoring large experimental systems.

PubMed

Arpaia, P; Cimmino, P; Girone, M; La Commara, G; Maisto, D; Manna, C; Pezzetti, M

2014-09-01

Evolutionary approach to centralized multiple-faults diagnostics is extended to distributed transducer networks monitoring large experimental systems. Given a set of anomalies detected by the transducers, each instance of the multiple-fault problem is formulated as several parallel communicating sub-tasks running on different transducers, and thus solved one-by-one on spatially separated parallel processes. A micro-genetic algorithm merges evaluation time efficiency, arising from a small-size population distributed on parallel-synchronized processors, with the effectiveness of centralized evolutionary techniques due to optimal mix of exploitation and exploration. In this way, holistic view and effectiveness advantages of evolutionary global diagnostics are combined with reliability and efficiency benefits of distributed parallel architectures. The proposed approach was validated both (i) by simulation at CERN, on a case study of a cold box for enhancing the cryogeny diagnostics of the Large Hadron Collider, and (ii) by experiments, under the framework of the industrial research project MONDIEVOB (Building Remote Monitoring and Evolutionary Diagnostics), co-funded by EU and the company Del Bo srl, Napoli, Italy.

Controlling Tensegrity Robots Through Evolution

NASA Technical Reports Server (NTRS)

Iscen, Atil; Agogino, Adrian; SunSpiral, Vytas; Tumer, Kagan

2013-01-01

Tensegrity structures (built from interconnected rods and cables) have the potential to offer a revolutionary new robotic design that is light-weight, energy-efficient, robust to failures, capable of unique modes of locomotion, impact tolerant, and compliant (reducing damage between the robot and its environment). Unfortunately robots built from tensegrity structures are difficult to control with traditional methods due to their oscillatory nature, nonlinear coupling between components and overall complexity. Fortunately this formidable control challenge can be overcome through the use of evolutionary algorithms. In this paper we show that evolutionary algorithms can be used to efficiently control a ball-shaped tensegrity robot. Experimental results performed with a variety of evolutionary algorithms in a detailed soft-body physics simulator show that a centralized evolutionary algorithm performs 400 percent better than a hand-coded solution, while the multi-agent evolution performs 800 percent better. In addition, evolution is able to discover diverse control solutions (both crawling and rolling) that are robust against structural failures and can be adapted to a wide range of energy and actuation constraints. These successful controls will form the basis for building high-performance tensegrity robots in the near future.

An efficient enzyme-powered micromotor device fabricated by cyclic alternate hybridization assembly for DNA detection.

PubMed

Fu, Shizhe; Zhang, Xueqing; Xie, Yuzhe; Wu, Jie; Ju, Huangxian

2017-07-06

An efficient enzyme-powered micromotor device was fabricated by assembling multiple layers of catalase on the inner surface of a poly(3,4-ethylenedioxythiophene and sodium 4-styrenesulfonate)/Au microtube (PEDOT-PSS/Au). The catalase assembly was achieved by programmed DNA hybridization, which was performed by immobilizing a designed sandwich DNA structure as the sensing unit on the PEDOT-PSS/Au, and then alternately hybridizing with two assisting DNA to bind the enzyme for efficient motor motion. The micromotor device showed unique features of good reproducibility, stability and motion performance. Under optimal conditions, it showed a speed of 420 μm s -1 in 2% H 2 O 2 and even 51 μm s -1 in 0.25% H 2 O 2 . In the presence of target DNA, the sensing unit hybridized with target DNA to release the multi-layer DNA as well as the multi-catalase, resulting in a decrease of the motion speed. By using the speed as a signal, the micromotor device could detect DNA from 10 nM to 1 μM. The proposed micromotor device along with the cyclic alternate DNA hybridization assembly technique provided a new path to fabricate efficient and versatile micromotors, which would be an exceptional tool for rapid and simple detection of biomolecules.

Post-silking Factor Consequences for N Efficiency Changes Over 38 Years of Commercial Maize Hybrids.

PubMed

Chen, Keru; Vyn, Tony J

2017-01-01

Hybrid selection in maize ( Zea mays L.) over the decades has increased post-silking dry matter (PostDM) and nitrogen (PostN) accumulation, often with an accompanying increase in one or more N use efficiency (NUE) metrics such as partial factor productivity (PFP), N conversion efficiency (NCE), and N internal efficiency (NIE). More certainty on the underlying mechanisms of how PostDM and PostN changes over time have contributed to NUE gains or losses in modern-era hybrids can only be realized by directly comparing hybrids of different eras in the context of production-system-relevant management systems. A two-year and two-location field study was conducted in Indiana with two N rates (55 and 220 kg N ha -1 ), three plant densities (54,000, 79,000, and 104,000 plants ha -1 ) and eight commercial hybrids that were released by a single seed company from 1967 to 2005. The main treatment effects of N rate, density, and hybrid dominated the PostDM and PostN responses, and there were no significant two-way or three-way interactions. Total dry matter at maturity gains averaged 80 kg ha -1 year -1 of hybrid release when averaged over locations, plant densities and N rates. Total N contents at maturity increased 0.68 kg ha -1 year -1 , primarily due to annual increases in grain N content (0.8 kg ha -1 year -1 ). Post-silking N uptake rate increased 0.44 kg ha -1 year -1 for these era hybrids in more favorable production site-years. Slopes of grain N concentration increases per unit PostN gain were similar for all hybrids. Gains in average PFP over time were considerably higher at the low N rate (0.9 kg ha -1 year -1 ) than at the high N rate (0.3 kg kg -1 year -1 ). Hybrid gains in NIE were evident from 1967 to 1994, but not thereafter. The low N rate and higher plant densities also increased relative NIE and NCE values, but without hybrid interactions. There was no consistent trend of NIE or NCE gains in these hybrids primarily because grain and whole-plant N concentrations didn't decline over the decades at either N rate, and because NIE and NCE were often plant-density dependent.

Genetic structure of Plasmodium vivax using the merozoite surface protein 1 icb5-6 fragment reveals new hybrid haplotypes in southern Mexico

PubMed Central

2014-01-01

Background Plasmodium vivax is a protozoan parasite with an extensive worldwide distribution, being highly prevalent in Asia as well as in Mesoamerica and South America. In southern Mexico, P. vivax transmission has been endemic and recent studies suggest that these parasites have unique biological and genetic features. The msp1 gene has shown high rate of nucleotide substitutions, deletions, insertions, and its mosaic structure reveals frequent events of recombination, maybe between highly divergent parasite isolates. Methods The nucleotide sequence variation in the polymorphic icb5-6 fragment of the msp1 gene of Mexican and worldwide isolates was analysed. To understand how genotype diversity arises, disperses and persists in Mexico, the genetic structure and genealogical relationships of local isolates were examined. To identify new sequence hybrids and their evolutionary relationships with other P. vivax isolates circulating worldwide two haplotype networks were constructed questioning that two portions of the icb5-6 have different evolutionary history. Results Twelve new msp1 icb5-6 haplotypes of P. vivax from Mexico were identified. These nucleotide sequences show mosaic structure comprising three partially conserved and two variable subfragments and resulted into five different sequence types. The variable subfragment sV1 has undergone recombination events and resulted in hybrid sequences and the haplotype network allocated the Mexican haplotypes to three lineages, corresponding to the Sal I and Belem types, and other more divergent group. In contrast, the network from icb5-6 fragment but not sV1 revealed that the Mexican haplotypes belong to two separate lineages, none of which are closely related to Sal I or Belem sequences. Conclusions These results suggest that the new hybrid haplotypes from southern Mexico were the result of at least three different recombination events. These rearrangements likely resulted from the recombination between haplotypes of highly divergent lineages that are frequently distributed in South America and Asia and diversified rapidly. PMID:24472213

Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression

PubMed Central

Dunn, Barbara; Paulish, Terry; Stanbery, Alison; Piotrowski, Jeff; Koniges, Gregory; Kroll, Evgueny; Louis, Edward J.; Liti, Gianni; Sherlock, Gavin; Rosenzweig, Frank

2013-01-01

Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ∼1-kb region of chromosome 14, and all producing an “interspecific fusion junction” within the MEP2 gene coding sequence, such that the 5′ portion derives from S. cerevisiae and the 3′ portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in numerous eukaryotic phyla, that does not require repeated backcrossing to one of the parental species. PMID:23555283

Evolutionary relevance facilitates visual information processing.

PubMed

Jackson, Russell E; Calvillo, Dusti P

2013-11-03

Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

Molecular evidence of hybridization in sympatric populations of the Enantia jethys complex (Lepidoptera: Pieridae).

PubMed

Jasso-Martínez, Jovana M; Machkour-M'Rabet, Salima; Vila, Roger; Rodríguez-Arnaiz, Rosario; Castañeda-Sortibrán, América Nitxin

2018-01-01

Hybridization events are frequently demonstrated in natural butterfly populations. One interesting butterfly complex species is the Enantia jethys complex that has been studied for over a century; many debates exist regarding the species composition of this complex. Currently, three species that live sympatrically in the Gulf slope of Mexico (Enantia jethys, E. mazai, and E. albania) are recognized in this complex (based on morphological and molecular studies). Where these species live in sympatry, some cases of interspecific mating have been observed, suggesting hybridization events. Considering this, we employed a multilocus approach (analyses of mitochondrial and nuclear sequences: COI, RpS5, and Wg; and nuclear dominant markers: inter-simple sequence repeat (ISSRs) to study hybridization in sympatric populations from Veracruz, Mexico. Genetic diversity parameters were determined for all molecular markers, and species identification was assessed by different methods such as analyses of molecular variance (AMOVA), clustering, principal coordinate analysis (PCoA), gene flow, and PhiPT parameters. ISSR molecular markers were used for a more profound study of hybridization process. Although species of the Enantia jethys complex have a low dispersal capacity, we observed high genetic diversity, probably reflecting a high density of individuals locally. ISSR markers provided evidence of a contemporary hybridization process, detecting a high number of hybrids (from 17% to 53%) with significant differences in genetic diversity. Furthermore, a directional pattern of hybridization was observed from E. albania to other species. Phylogenetic study through DNA sequencing confirmed the existence of three clades corresponding to the three species previously recognized by morphological and molecular studies. This study underlines the importance of assessing hybridization in evolutionary studies, by tracing the lineage separation process that leads to the origin of new species. Our research demonstrates that hybridization processes have a high occurrence in natural populations.

Comparison of Moringa stenopetala seed extract as a clean coagulant with Alum and Moringa stenopetala-Alum hybrid coagulant to remove direct dye from Textile Wastewater.

PubMed

Dalvand, Arash; Gholibegloo, Elham; Ganjali, Mohammad Reza; Golchinpoor, Najmeh; Khazaei, Mohammad; Kamani, Hossein; Hosseini, Sara Sadat; Mahvi, Amir Hossein

2016-08-01

In this study, the efficiency of Moringa stenopetala seed extract was compared with alum and M. stenopetala-alum hybrid coagulant to remove Direct Red 23 azo dye from textile wastewater. The effects of parameters such as pH, coagulant dose, type of salt used for the extraction of coagulant and initial dye concentration on dye removal efficiency were investigated. Moreover, the existing functional groups on the structure of M. stenopetala coagulant (MSC) were determined by Fourier transform infrared spectroscopy, and the morphology of sludge produced by MSC, alum, and hybrid coagulant was characterized by scanning electron microscopy. Ninhydrin test was also used to determine the quantity of primary amines in the MSC and Moringa oleifera coagulant (MOC). According to the results, with increasing the coagulant dose and decreasing the initial dye concentration, dye removal efficiency has increased. The maximum dye removal of 98.5, 98.2, and 98.3 % were obtained by using 240, 120, and 80 mg/L MSC, alum and hybrid coagulant at pH 7, respectively. The results also showed MSC was much more effective than MOC for dye removal. The volume of sludge produced by MSC was one fourth and half of those produced by alum and hybrid coagulant, respectively. Based on the results, hybrid coagulant was the most efficient coagulant for direct dye removal from colored wastewater.

AIEgens-Functionalized Inorganic-Organic Hybrid Materials: Fabrications and Applications.

PubMed

Li, Dongdong; Yu, Jihong

2016-12-01

Inorganic materials functionalized with organic fluorescent molecules combine advantages of them both, showing potential applications in biomedicine, chemosensors, light-emitting, and so on. However, when more traditional organic dyes are doped into the inorganic materials, the emission of resulting hybrid materials may be quenched, which is not conducive to the efficiency and sensitivity of detection. In contrast to the aggregation-caused quenching (ACQ) system, the aggregation-induced emission luminogens (AIEgens) with high solid quantum efficiency, offer new potential for developing highly efficient inorganic-organic hybrid luminescent materials. So far, many AIEgens have been incorporated into inorganic materials through either physical doping caused by aggregation induced emission (AIE) or chemical bonding (e.g., covalent bonding, ionic bonding, and coordination bonding) caused by bonding induced emission (BIE) strategy. The hybrid materials exhibit excellent photoactive properties due to the intramolecular motion of AIEgens is restricted by inorganic matrix. Recent advances in the fabrication of AIEgens-functionalized inorganic-organic hybrid materials and their applications in biomedicine, chemical sensing, and solid-state light emitting are presented. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fuel economy and life-cycle cost analysis of a fuel cell hybrid vehicle

NASA Astrophysics Data System (ADS)

Jeong, Kwi Seong; Oh, Byeong Soo

The most promising vehicle engine that can overcome the problem of present internal combustion is the hydrogen fuel cell. Fuel cells are devices that change chemical energy directly into electrical energy without combustion. Pure fuel cell vehicles and fuel cell hybrid vehicles (i.e. a combination of fuel cell and battery) as energy sources are studied. Considerations of efficiency, fuel economy, and the characteristics of power output in hybridization of fuel cell vehicle are necessary. In the case of Federal Urban Driving Schedule (FUDS) cycle simulation, hybridization is more efficient than a pure fuel cell vehicle. The reason is that it is possible to capture regenerative braking energy and to operate the fuel cell system within a more efficient range by using battery. Life-cycle cost is largely affected by the fuel cell size, fuel cell cost, and hydrogen cost. When the cost of fuel cell is high, hybridization is profitable, but when the cost of fuel cell is less than 400 US$/kW, a pure fuel cell vehicle is more profitable.

Two-component signal transduction systems of Xanthomonas spp.: a lesson from genomics.

PubMed

Qian, Wei; Han, Zhong-Ji; He, Chaozu

2008-02-01

The two-component signal transduction systems (TCSTSs), consisting of a histidine kinase sensor (HK) and a response regulator (RR), are the dominant molecular mechanisms by which prokaryotes sense and respond to environmental stimuli. Genomes of Xanthomonas generally contain a large repertoire of TCSTS genes (approximately 92 to 121 for each genome), which encode diverse structural groups of HKs and RRs. Among them, although a core set of 70 TCSTS genes (about two-thirds in total) which accumulates point mutations with a slow rate are shared by these genomes, the other genes, especially hybrid HKs, experienced extensive genetic recombination, including genomic rearrangement, gene duplication, addition or deletion, and fusion or fission. The recombinations potentially promote the efficiency and complexity of TCSTSs in regulating gene expression. In addition, our analysis suggests that a co-evolutionary model, rather than a selfish operon model, is the major mechanism for the maintenance and microevolution of TCSTS genes in the genomes of Xanthomonas. Genomic annotation, secondary protein structure prediction, and comparative genomic analyses of TCSTS genes reviewed here provide insights into our understanding of signal networks in these important phytopathogenic bacteria.

The positioning logic and copy number control of genes in bacteria under stress

NASA Astrophysics Data System (ADS)

Zhang, Qiucen; Austin, Robert; Vyawahare, Saurabh; Lau, Alexandra

2013-03-01

Escherichia coli (E. coli) cells when challenged with sublethal concentrations of the genotoxic antibiotic ciprofloxacin cease to divide and form long filaments which contain multiple bacterial chromosomes. These filaments are individual mesoscopic environmental niches which provide protection for a community of chromosomes (as opposed to cells) under mutagenic stress and can provide an evolutionary fitness advantage within the niche. We use comparative genomic hybridization to show that the mesoscopic niche evolves within 20 minutes of ciprofloxacin exposure via replication of multiple copies of genes expressing ATP dependent transporters. We show that this rapid genomic amplification is done in a time efficient manner via placement of the genes encoding the pumps near the origin of replication on the bacterial chromosome. The de-amplification of multiple copies back to the wild type number is a function of the duration is a function of the ciprofloxacin exposure duration: the longer the exposure, the slower the removal of the multiple copies. The project described was supported by the National Science Foundation and the National Cancer Institute

Thermodynamic Modeling and Dispatch of Distributed Energy Technologies including Fuel Cell -- Gas Turbine Hybrids

NASA Astrophysics Data System (ADS)

McLarty, Dustin Fogle

Distributed energy systems are a promising means by which to reduce both emissions and costs. Continuous generators must be responsive and highly efficiency to support building dynamics and intermittent on-site renewable power. Fuel cell -- gas turbine hybrids (FC/GT) are fuel-flexible generators capable of ultra-high efficiency, ultra-low emissions, and rapid power response. This work undertakes a detailed study of the electrochemistry, chemistry and mechanical dynamics governing the complex interaction between the individual systems in such a highly coupled hybrid arrangement. The mechanisms leading to the compressor stall/surge phenomena are studied for the increased risk posed to particular hybrid configurations. A novel fuel cell modeling method introduced captures various spatial resolutions, flow geometries, stack configurations and novel heat transfer pathways. Several promising hybrid configurations are analyzed throughout the work and a sensitivity analysis of seven design parameters is conducted. A simple estimating method is introduced for the combined system efficiency of a fuel cell and a turbine using component performance specifications. Existing solid oxide fuel cell technology is capable of hybrid efficiencies greater than 75% (LHV) operating on natural gas, and existing molten carbonate systems greater than 70% (LHV). A dynamic model is calibrated to accurately capture the physical coupling of a FC/GT demonstrator tested at UC Irvine. The 2900 hour experiment highlighted the sensitivity to small perturbations and a need for additional control development. Further sensitivity studies outlined the responsiveness and limits of different control approaches. The capability for substantial turn-down and load following through speed control and flow bypass with minimal impact on internal fuel cell thermal distribution is particularly promising to meet local demands or provide dispatchable support for renewable power. Advanced control and dispatch heuristics are discussed using a case study of the UCI central plant. Thermal energy storage introduces a time horizon into the dispatch optimization which requires novel solution strategies. Highly efficient and responsive generators are required to meet the increasingly dynamic loads of today's efficient buildings and intermittent local renewable wind and solar power. Fuel cell gas turbine hybrids will play an integral role in the complex and ever-changing solution to local electricity production.

Performance analysis of hybrid vibrational energy harvesters with experimental verification

NASA Astrophysics Data System (ADS)

Sriramdas, Rammohan; Pratap, Rudra

2018-07-01

In the present work, performance indices for a hybrid energy harvester (HEH) that is composed of piezoelectric and electrodynamic or electromagnetic mechanisms of energy conversion are analyzed. Performance of a HEH is defined in terms of Q-normalized power factor and efficiency of conversion. They are observed to acutely depend on coupling strength or figures of merit in both piezoelectric and electrodynamic domains. The influence of figures of merit on the Q-normalized power factor, and the limits of conversion efficiency are explored. Based on the studies, a suitable range for figures of merit that would maximize both Q-normalized power factor and conversion efficiency in hybrid harvesters is proposed. The proposed idea is verified experimentally for the appropriate values of figures of merit and efficiencies by fabricating and testing four experimental models of the HEHs.

Nonimaging optics maximizing exergy for hybrid solar system

NASA Astrophysics Data System (ADS)

Winston, Roland; Jiang, Lun; Abdelhamid, Mahmoud; Widyolar, Bennett K.; Ferry, Jonathan; Cygan, David; Abbasi, Hamid; Kozlov, Alexandr; Kirk, Alexander; Elarde, Victor; Osowski, Mark

2016-09-01

The project team of University of California at Merced (UC-Merced), Gas Technology Institute (GTI) and MicroLink Devices Inc. (MicroLink) are developing a hybrid solar system using a nonimaging compound parabolic concentrator (CPC) that maximizes the exergy by delivering direct electricity and on-demand heat. The hybrid solar system technology uses secondary optics in a solar receiver to achieve high efficiency at high temperature, collects heat in particles and uses reflective liftoff cooled double junction (2J) InGaP/GaAs solar cells with backside infrared (IR) reflectors on the secondary optical element to raise exergy efficiency. The nonimaging optics provides additional concentration towards the high temperature thermal stream and enables it to operate efficiently at 650 °C while the solar cell is maintained at 40 °C to operate as efficiently as possible.

Caracterisation des mecanismes d'usure en cavitation de revetements HVOF a base de CaviTec

NASA Astrophysics Data System (ADS)

Lavigne, Sebastien

The increasing demand for high performance power conversion systems continuously pushes for improvement in efficiency and power density. This dissertation focuses on a topological effort to efficiently utilize the active and passive devices. In particular, a hybrid approach is adopted, where both capacitors and inductors are used in the voltage conversion and power transfer process. Conventional capacitor-based converters, called switched-capacitor (SC) converters, suffer from poor efficiency due to the inevitable charge redistribution process. With a strategic placement of one or more inductors, the charge redistribution loss can be eliminated by inductively charging/discharging the capacitors, a process called soft-charging operation. As a result, the capacitor size can be greatly reduced without reducing the efficiency. A general analytical framework is presented, which determines whether an arbitrary SC topology is able to achieve full soft-charging operation with a single inductor. For topologies that cannot, a split-phase control technique is introduced, which amends existing two-phase controls to completely eliminate the charge redistribution loss. In addition, alternative placements of inductors are explored to extend the family of hybrid converters. The hybrid converters can have two modes of operation, the fixed-ratio mode and pulse width modulated (PWM) mode. The fixed-conversion-ratio hybrid converters operate in a similar manner to that of a conventional SC converter, with the addition of a soft-charging inductor. The switching frequency of such converters can be adjusted to operate in either zero current switching (ZCS) mode or continuous conduction mode (CCM), which allows for the trade-off of switching loss and conduction loss. It is shown that the capacitor and inductor values can be selected to achieve a minimal passive component volume, which can be significantly smaller than that of a conventional SC converter or a magnetic-based converter. On the other hand, PWM-based hybrid converters generate a PWM rectangular wave as the terminal voltage to the inductor, similar to the operation of a buck converter. In contrast to conventional SC converters, such hybrid converters can achieve lossless and continuous regulation of the output voltage. Compared to buck converters, the required inductor is greatly reduced, as well as the switch stress. A 80-170 V input, 12-24 V output prototype PWM Dickson converter is implemented using GaN switches. The measured peak efficiency is 97%, and high efficiency can be maintained over the entire input and output operating range. In addition, the similarity between multilevel converters (for example, flying capacitor multilevel (FCML) converters) and the PWM-based hybrid SC converters is discussed. Both types of converters can be seen as a hybrid converter which uses both capacitors and inductors for energy transfer. A general framework to compare these converters, along with conventional buck converters, is proposed. In this framework, the power losses (including conduction loss and switching loss) are kept constant, while the total passive component volume is used as the figure of merit. Based on the principle of maximizing energy utilization of passive components, a 7-level FCML converter and an active energy buffer are designed and implemented for single phase dc-ac applications. In addition, the stand-alone system includes a start-up circuitry, EMC filter and auxiliary power supply. The enclosed box achieves a combined power density of 216 W/in3 and an efficiency of 97.4%, and compares favorably against the state-of-the-art designs under the same specification. To further improve the efficiency and power density, soft-switching techniques are investigated and applied on the hybrid converters. A zero voltage switching (ZVS) technique is introduced for both the fixed-ratio mode and the PWM mode operated hybrid converters. The previous hardware prototypes are modified for ZVS operation, and prove the feasibility of simultaneous soft-charging and soft-switching operation. Last but not the least, some of the practical issues associated with the hybrid converter are discussed, such as practical capacitor selection, capacitor voltage balancing and other circuit implementation challenges. Future work based on these topics is given. In summary, these hybrid converters are suited for applications where extreme efficiency and power density are critical. Through efficient utilization of active and passive devices, the hybrid topologies can offer a greater optimization opportunity and ability to take advantage of technology improvement than is possible with conventional designs.

Recent Natural Hybridization between Two Allopolyploid Wheatgrasses (Elytrigia, Poaceae): Ecological and Evolutionary Implications

PubMed Central

Mahelka, Václav; Fehrer, Judith; Krahulec, František; Jarolímová, Vlasta

2007-01-01

Background and Aims Natural hybridization was investigated between two predominantly allohexaploid wheatgrasses, weedy Elytrigia repens and steppic E. intermedia, with respect to habitats characterized by different degrees of anthropogenic disturbance. Methods Using flow cytometry (relative DNA content), 269 plants from three localities were analysed. Hybrids were further analysed using nuclear ribosomal (ITS1-5·8S-ITS2 region) and chloroplast (trnT-F region) DNA markers in addition to absolute DNA content and chromosome numbers. Key Results Weedy E. repens was rare in a steppic locality whereas E. intermedia was almost absent at two sites of agricultural land-use. Nevertheless, hybrids were common there whereas none were found at the steppic locality, underlining the importance of different ecological conditions for hybrid formation or establishment. At one highly disturbed site, > 16 % of randomly collected plants were hybrids. Hexaploid hybrids showed intermediate genome size compared with the parents and additive patterns of parental ITS copies. Some evidence of backcrosses was found. The direction of hybridization was highly asymmetric as cpDNA identified E. intermedia as the maternal parent in 61 out of 63 cases. Out of nine nonaploid cytotypes (2n = 9x = 63) which likely originated by fusion of unreduced and reduced gametes of hexaploids, eight were hybrids whereas one was a nonaploid cytotype of E. repens. The progeny of one nonaploid hybrid demonstrated gene flow between hexaploid and nonaploid cytotypes. Conclusions The results show that E. repens and E. intermedia frequently cross at places where they co-occur. Hybrid frequency is likely influenced by habitat type; sites disturbed by human influence sustain hybrid formation and/or establishment. Hexaploid and nonaploid hybrid fertility is not negligible, backcrossing is possible, and the progeny is variable. The frequent production of new at least partially fertile cyto- and genotypes provides ample raw material for evolution and adaptation. PMID:17562679

HRSSA - Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

NASA Astrophysics Data System (ADS)

Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong

2016-07-01

This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

Cooling/grounding mount for hybrid circuits

NASA Technical Reports Server (NTRS)

Bagstad, B.; Estrada, R.; Mandel, H.

1981-01-01

Extremely short input and output connections, adequate grounding, and efficient heat removal for hybrid integrated circuits are possible with mounting. Rectangular clamp holds hybrid on printed-circuit board, in contact with heat-conductive ground plate. Clamp is attached to ground plane by bolts.

Standardization and optimization of fluorescence in situ hybridization (FISH) for HER-2 assessment in breast cancer: A single center experience.

PubMed

Bogdanovska-Todorovska, Magdalena; Petrushevska, Gordana; Janevska, Vesna; Spasevska, Liljana; Kostadinova-Kunovska, Slavica

2018-05-20

Accurate assessment of human epidermal growth factor receptor 2 (HER-2) is crucial in selecting patients for targeted therapy. Commonly used methods for HER-2 testing are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Here we presented the implementation, optimization and standardization of two FISH protocols using breast cancer samples and assessed the impact of pre-analytical and analytical factors on HER-2 testing. Formalin fixed paraffin embedded (FFPE) tissue samples from 70 breast cancer patients were tested for HER-2 using PathVysion™ HER-2 DNA Probe Kit and two different paraffin pretreatment kits, Vysis/Abbott Paraffin Pretreatment Reagent Kit (40 samples) and DAKO Histology FISH Accessory Kit (30 samples). The concordance between FISH and IHC results was determined. Pre-analytical and analytical factors (i.e., fixation, baking, digestion, and post-hybridization washing) affected the efficiency and quality of hybridization. The overall hybridization success in our study was 98.6% (69/70); the failure rate was 1.4%. The DAKO pretreatment kit was more time-efficient and resulted in more uniform signals that were easier to interpret, compared to the Vysis/Abbott kit. The overall concordance between IHC and FISH was 84.06%, kappa coefficient 0.5976 (p < 0.0001). The greatest discordance (82%) between IHC and FISH was observed in IHC 2+ group. A standardized FISH protocol for HER-2 assessment, with high hybridization efficiency, is necessary due to variability in tissue processing and individual tissue characteristics. Differences in the pre-analytical and analytical steps can affect the hybridization quality and efficiency. The use of DAKO pretreatment kit is time-saving and cost-effective.

Modeling of hybrid vehicle fuel economy and fuel engine efficiency

NASA Astrophysics Data System (ADS)

Wu, Wei

"Near-CV" (i.e., near-conventional vehicle) hybrid vehicles, with an internal combustion engine, and a supplementary storage with low-weight, low-energy but high-power capacity, are analyzed. This design avoids the shortcoming of the "near-EV" and the "dual-mode" hybrid vehicles that need a large energy storage system (in terms of energy capacity and weight). The small storage is used to optimize engine energy management and can provide power when needed. The energy advantage of the "near-CV" design is to reduce reliance on the engine at low power, to enable regenerative braking, and to provide good performance with a small engine. The fuel consumption of internal combustion engines, which might be applied to hybrid vehicles, is analyzed by building simple analytical models that reflect the engines' energy loss characteristics. Both diesel and gasoline engines are modeled. The simple analytical models describe engine fuel consumption at any speed and load point by describing the engine's indicated efficiency and friction. The engine's indicated efficiency and heat loss are described in terms of several easy-to-obtain engine parameters, e.g., compression ratio, displacement, bore and stroke. Engine friction is described in terms of parameters obtained by fitting available fuel measurements on several diesel and spark-ignition engines. The engine models developed are shown to conform closely to experimental fuel consumption and motored friction data. A model of the energy use of "near-CV" hybrid vehicles with different storage mechanism is created, based on simple algebraic description of the components. With powertrain downsizing and hybridization, a "near-CV" hybrid vehicle can obtain a factor of approximately two in overall fuel efficiency (mpg) improvement, without considering reductions in the vehicle load.

Sleeping Beauty-baculovirus hybrid vectors for long-term gene expression in the eye.

PubMed

Turunen, Tytteli Anni Kaarina; Laakkonen, Johanna Päivikki; Alasaarela, Laura; Airenne, Kari Juhani; Ylä-Herttuala, Seppo

2014-01-01

A baculovirus vector is capable of efficiently transducing many nondiving and diving cell types. However, the potential of baculovirus is restricted for many gene delivery applications as a result of the transient gene expression that it mediates. The plasmid-based Sleeping Beauty (SB) transposon system integrates transgenes into target cell genome efficiently with a genomic integration pattern that is generally considered safer than the integration of many other integrating vectors; yet efficient delivery of therapeutic genes into cells of target tissues in vivo is a major challenge for nonviral gene therapy. In the present study, SB was introduced into baculovirus to obtain novel hybrid vectors that would combine the best features of the two vector systems (i.e. effective gene delivery and efficient integration into the genome), thus circumventing the major limitations of these vectors. We constructed and optimized SB-baculovirus hybrid vectors that bear either SB100x transposase or SB transposon in the forward or reverse orientations with respect to the viral backbone The functionality of the novel hybrid vectors was investigated in cell cultures and in a proof-of-concept study in the mouse eye. The hybrid vectors showed high and sustained transgene expression that remained stable and demonstrated no signs of decline during the 2 months follow-up in vitro. These results were verified in the mouse eye where persistent transgene expression was detected two months after intravitreal injection. Our results confirm that (i) SB-baculovirus hybrid vectors mediate long-term gene expression in vitro and in vivo, and (ii) the hybrid vectors are potential new tools for the treatment of ocular diseases. Copyright © 2014 John Wiley & Sons, Ltd.

Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

PubMed

Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

2015-12-01

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

Patterns of reproductive isolation in a haplodiploid - strong post-mating, prezygotic barriers among three forms of a social spider mite.

PubMed

Sato, Yukie; Sakamoto, Hironori; Gotoh, Tetsuo; Saito, Yutaka; Chao, Jung-Tai; Egas, Martijn; Mochizuki, Atsushi

2018-06-01

In speciation research, much attention is paid to the evolution of reproductive barriers, preventing diverging groups from hybridizing back into one gene pool. The prevalent view is that reproductive barriers evolve gradually as a by-product of genetic changes accumulated by natural selection and genetic drift in groups that are segregated spatially and/or temporally. Reproductive barriers, however, can also be reinforced by natural selection against maladaptive hybridization. These mutually compatible theories are both empirically supported by studies, analysing relationships between intensity of reproductive isolation and genetic distance in sympatric taxa and allopatric taxa. Here, we present the - to our knowledge - first comparative study in a haplodiploid organism, the social spider mite Stigmaeopsis miscanthi, by measuring premating and post-mating, pre- and post-zygotic components of reproductive isolation, using three recently diverged forms of the mite that partly overlap in home range. We carried out cross-experiments and measured genetic distances (mitochondrial DNA and nuclear DNA) among parapatric and allopatric populations of the three forms. Our results show that the three forms are reproductively isolated, despite the absence of premating barriers, and that the post-mating, prezygotic component contributes most to reproductive isolation. As expected, the strength of post-mating reproductive barriers positively correlated with genetic distance. We did not find a clear pattern of prezygotic barriers evolving faster in parapatry than in allopatry, although one form did show a trend in line with the ecological and behavioural relationships between the forms. Our study advocates the versatility of haplodiploid animals for investigating the evolution of reproductive barriers. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes.

PubMed

Parsons, Kevin J; Concannon, Moira; Navon, Dina; Wang, Jason; Ea, Ilene; Groveas, Kiran; Campbell, Calum; Albertson, R Craig

2016-12-01

Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F 3 hybrid mapping population. At early juvenile stages, hybrid families were split and reared in alternate foraging environments that mimicked benthic/scraping or limnetic/sucking modes of feeding. These alternate treatments produced a variation in morphology that was broadly similar to the major axis of divergence among Malawi cichlids, providing support for the flexible stem theory of adaptive radiation. Next, we found that the genetic architecture of several morphological traits was highly sensitive to the environment. In particular, of 22 significant quantitative trait loci (QTL), only one was shared between the environments. In addition, we identified QTL acting across environments with alternate alleles being differentially sensitive to the environment. Thus, our data suggest that while plasticity is largely determined by loci specific to a given environment, it may also be influenced by loci operating across environments. Finally, our mapping data provide evidence for the evolution of plasticity via genetic assimilation at an important regulatory locus, ptch1. In all, our data address long-standing discussions about the genetic basis and evolution of plasticity. They also underscore the importance of the environment in affecting developmental outcomes, genetic architectures, morphological diversity and evolutionary potential. © 2016 John Wiley & Sons Ltd.

Evaluating and Improving Automatic Sleep Spindle Detection by Using Multi-Objective Evolutionary Algorithms

PubMed Central

Liu, Min-Yin; Huang, Adam; Huang, Norden E.

2017-01-01

Sleep spindles are brief bursts of brain activity in the sigma frequency range (11–16 Hz) measured by electroencephalography (EEG) mostly during non-rapid eye movement (NREM) stage 2 sleep. These oscillations are of great biological and clinical interests because they potentially play an important role in identifying and characterizing the processes of various neurological disorders. Conventionally, sleep spindles are identified by expert sleep clinicians via visual inspection of EEG signals. The process is laborious and the results are inconsistent among different experts. To resolve the problem, numerous computerized methods have been developed to automate the process of sleep spindle identification. Still, the performance of these automated sleep spindle detection methods varies inconsistently from study to study. There are two reasons: (1) the lack of common benchmark databases, and (2) the lack of commonly accepted evaluation metrics. In this study, we focus on tackling the second problem by proposing to evaluate the performance of a spindle detector in a multi-objective optimization context and hypothesize that using the resultant Pareto fronts for deriving evaluation metrics will improve automatic sleep spindle detection. We use a popular multi-objective evolutionary algorithm (MOEA), the Strength Pareto Evolutionary Algorithm (SPEA2), to optimize six existing frequency-based sleep spindle detection algorithms. They include three Fourier, one continuous wavelet transform (CWT), and two Hilbert-Huang transform (HHT) based algorithms. We also explore three hybrid approaches. Trained and tested on open-access DREAMS and MASS databases, two new hybrid methods of combining Fourier with HHT algorithms show significant performance improvement with F1-scores of 0.726–0.737. PMID:28572762

Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies.

PubMed

Kumar, S; Gadagkar, S R

2000-12-01

The neighbor-joining (NJ) method is widely used in reconstructing large phylogenies because of its computational speed and the high accuracy in phylogenetic inference as revealed in computer simulation studies. However, most computer simulation studies have quantified the overall performance of the NJ method in terms of the percentage of branches inferred correctly or the percentage of replications in which the correct tree is recovered. We have examined other aspects of its performance, such as the relative efficiency in correctly reconstructing shallow (close to the external branches of the tree) and deep branches in large phylogenies; the contribution of zero-length branches to topological errors in the inferred trees; and the influence of increasing the tree size (number of sequences), evolutionary rate, and sequence length on the efficiency of the NJ method. Results show that the correct reconstruction of deep branches is no more difficult than that of shallower branches. The presence of zero-length branches in realized trees contributes significantly to the overall error observed in the NJ tree, especially in large phylogenies or slowly evolving genes. Furthermore, the tree size does not influence the efficiency of NJ in reconstructing shallow and deep branches in our simulation study, in which the evolutionary process is assumed to be homogeneous in all lineages.

Efficient hybrid white polymer light-emitting devices with electroluminescence covered the entire visible range and reduced efficiency roll-off

NASA Astrophysics Data System (ADS)

Hu, Sujun; Zhu, Minrong; Zou, Qinghua; Wu, Hongbin; Yang, Chuluo; Wong, Wai-Yeung; Yang, Wei; Peng, Junbiao; Cao, Yong

2012-02-01

We report efficient hybrid white polymer light emitting devices (WPLEDs) fabricated via simple solution-proceeded process from a newly synthesized wide band-gap fluorene-co-dibenzothiophene-S,S-dioxide copolymer, which dually function as fluorescent blue emitter and host material for electrophosphorescent sky-blue, yellow, and saturated-red dyes. The Commission Internationale d'Énclairage coordinates of the best devices are (0.356, 0.334), with electroluminescence covered the entire visible light spectrum from 400 to 780 nm, resulting in a high color rendering index of 90. Incorporation of a bilayer electrode consisting of water/alcohol-soluble conjugated polymer and Al as electron-injection cathode boosts an enhancement of 50% in device efficiency, leading to external quantum efficiency of 12.6%, and peak power efficiency of 21.4 l m W-1 as measured in an integrating sphere. Both the efficiency and the color quality of the obtained device are ranking among one of the highest values for WPLEDs reported to date. Furthermore, as compared with those all-phosphorescent WPLEDs, the hybrid WPLEDs studied here exhibit a significantly reduced efficiency roll-off due to the very low doping concentration.

Solving SAT Problem Based on Hybrid Differential Evolution Algorithm

NASA Astrophysics Data System (ADS)

Liu, Kunqi; Zhang, Jingmin; Liu, Gang; Kang, Lishan

Satisfiability (SAT) problem is an NP-complete problem. Based on the analysis about it, SAT problem is translated equally into an optimization problem on the minimum of objective function. A hybrid differential evolution algorithm is proposed to solve the Satisfiability problem. It makes full use of strong local search capacity of hill-climbing algorithm and strong global search capability of differential evolution algorithm, which makes up their disadvantages, improves the efficiency of algorithm and avoids the stagnation phenomenon. The experiment results show that the hybrid algorithm is efficient in solving SAT problem.

Superior photoelectrochemical properties of ZnO nanorods/poly(3-hexylthiophene) hybrid photoanodes

NASA Astrophysics Data System (ADS)

Majumder, T.; Hmar, J. J. L.; Dhar, S.; Mondal, S. P.

2017-06-01

Photoelectrochemical properties of ZnO nanorods (ZnO NRs) and poly(3-hexylthiophene) (P3HT) polymer hybrid photoanodes have been studied. The hybrid photoanodes demonstrated higher photoconversion efficiency, incident photon to current conversion efficiency (IPCE) and lower interfacial resistance compared to pristine ZnO nanorods and P3HT based electrodes. The origin of superior photoelectrochemical properties of ZnO/P3HT photoanodes has been explained using carrier transport mechanism at semiconductor/electrolyte junction. The stability of ZnO NRs/P3HT photoanode has been demonstrated.

From hybrid swarms to swarms of hybrids

USGS Publications Warehouse

Stohlgren, Thomas J.; Szalanski, Allen L; Gaskin, John F.; Young, Nicholas E.; West, Amanda; Jarnevich, Catherine S.; Tripodi, Amber

2014-01-01

Science has shown that the introgression or hybridization of modern humans (Homo sapiens) with Neanderthals up to 40,000 YBP may have led to the swarm of modern humans on earth. However, there is little doubt that modern trade and transportation in support of the humans has continued to introduce additional species, genotypes, and hybrids to every country on the globe. We assessed the utility of species distributions modeling of genotypes to assess the risk of current and future invaders. We evaluated 93 locations of the genus Tamarix for which genetic data were available. Maxent models of habitat suitability showed that the hybrid, T. ramosissima x T. chinensis, was slightly greater than the parent taxa (AUCs > 0.83). General linear models of Africanized honey bees, a hybrid cross of Tanzanian Apis mellifera scutellata and a variety of European honey bee including A. m. ligustica, showed that the Africanized bees (AUC = 0.81) may be displacing European honey bees (AUC > 0.76) over large areas of the southwestern U.S. More important, Maxent modeling of sub-populations (A1 and A26 mitotypes based on mDNA) could be accurately modeled (AUC > 0.9), and they responded differently to environmental drivers. This suggests that rapid evolutionary change may be underway in the Africanized bees, allowing the bees to spread into new areas and extending their total range. Protecting native species and ecosystems may benefit from risk maps of harmful invasive species, hybrids, and genotypes.

Wolves in the Great Lakes region: a phylogeographic puzzle.

PubMed

Randi, Ettore

2010-10-01

Empirical studies demonstrate that natural hybridization in animals is more common than thought so far (Mallet 2005), particularly among species that originated recently through cycles of population contraction-expansion arising from climate changes over the last glacial period, the Pleistocene. In addition, the post-glacial global growth of human populations has fostered anthropogenic hybridization events, mediated by habitat changes, the persecution of large predators and the introduction of alien species (Allendorf et al. 2001). The Canis lineage shows cases of both natural and anthropogenic hybridization, exacerbating the controversy about the number of species that should be formally validated in the taxonomic lists, the evolutionary role of genetic introgression and the ways to manage hybrids with invading wild or domesticated populations. The study by Wheeldon et al. (2010), published in this issue of Molecular Ecology, adds a new piece to the intricate puzzle of evolution and taxonomy of Canis in North America. They show that sympatric wolves (C. lupus) and coyotes (C. latrans) are not (extensively) hybridizing in the western North American Great Lakes region (GLR). Widespread hybridization between coyotes and a genetically distinct, but closely related, wolf-like population (the eastern wolf) occurred in the northeastern regions of North America. In Wheeldon et al.'s (2010) opinion, these data should prove definitely that two different species of wolf (the western gray wolf C. lupus and the eastern wolf C. lycaon) and their hybrids are distributed across the GLR. © 2010 Blackwell Publishing Ltd.

Performance of hybrid progeny formed between genetically modified herbicide-tolerant soybean and its wild ancestor

PubMed Central

Guan, Zheng-Jun; Zhang, Peng-Fei; Wei, Wei; Mi, Xiang-Cheng; Kang, Ding-Ming; Liu, Biao

2015-01-01

Gene flow from genetically modified (GM) crops to wild relatives might affect the evolutionary dynamics of weedy populations and result in the persistence of escaped genes. To examine the effects of this gene flow, the growth of F1 hybrids that were formed by pollinating wild soybean (Glycine soja) with glyphosate-tolerant GM soybean (G. max) or its non-GM counterpart was examined in a greenhouse. The wild soybean was collected from two geographical populations in China. The performance of the wild soybean and the F2 hybrids was further explored in a field trial. Performance was measured by several vegetative and reproductive growth parameters, including the vegetative growth period, pod number, seed number, above-ground biomass and 100-seed weight. The pod setting percentage was very low in the hybrid plants. Genetically modified hybrid F1 plants had a significantly longer period of vegetative growth, higher biomass and lower 100-seed weight than the non-GM ones. The 100-seed weight of both F1 and F2 hybrids was significantly higher than that of wild soybean in both the greenhouse and the field trial. No difference in plant growth was found between GM and non-GM F2 hybrids in the field trial. The herbicide-resistant gene appeared not to adversely affect the growth of introgressed wild soybeans, suggesting that the escaped transgene could persist in nature in the absence of herbicide use. PMID:26507568

A Bright Future for Evolutionary Methods in Drug Design.

PubMed

Le, Tu C; Winkler, David A

2015-08-01

Most medicinal chemists understand that chemical space is extremely large, essentially infinite. Although high-throughput experimental methods allow exploration of drug-like space more rapidly, they are still insufficient to fully exploit the opportunities that such large chemical space offers. Evolutionary methods can synergistically blend automated synthesis and characterization methods with computational design to identify promising regions of chemical space more efficiently. We describe how evolutionary methods are implemented, and provide examples of published drug development research in which these methods have generated molecules with increased efficacy. We anticipate that evolutionary methods will play an important role in future drug discovery. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Double positive effect of adding hexaethyelene glycol when optimizing the hybridization efficiency of a microring DNA detection assay

NASA Astrophysics Data System (ADS)

Van Eeghem, Anabelle; Werquin, Sam; Hoste, Jan-Willem; Goes, Arne; Vanderleyden, Els; Bienstman, Peter; Dubruel, Peter

2017-05-01

In this paper, a method for detection of DNA molecules using silicon-on-insulator (SOI) microring resonators is described. The influence of temperature and the use of formamide on the hybridization efficiency were studied. It was shown that 50 v/v% of formamide in the hybridization buffer can ensure hybridization when working close to physiological temperature. Furthermore, the use of hexaethylene glycol (HEG) as backfilling agent was studied in order to resolve issues of non-specific adsorption to the surface. The results indicated that not only non-specific binding was reduced significantly but also that HEG improves the orientation of the DNA probes on the surface. This led to a 4-fold increase in hybridization efficiency and thus in an equal decrease in the detection limit, compared to hybridization without the use of HEG. An improvement in robustness of the assay was also observed. This DNA reorientation hypothesis was confirmed by studying the thickness and density of the layers by using dual polarization microring sensing. Finally, the different steps in the sensing experiment were characterized in more detail by static contact angle (SCA) and X-ray photoelectron spectroscopy (XPS) analysis. The results showed quantitatively that the surface modifications were successful.

Continuous Morphological Variation Correlated with Genome Size Indicates Frequent Introgressive Hybridization among Diphasiastrum Species (Lycopodiaceae) in Central Europe

PubMed Central

Hanušová, Kristýna; Ekrt, Libor; Vít, Petr; Kolář, Filip; Urfus, Tomáš

2014-01-01

Introgressive hybridization is an important evolutionary process frequently contributing to diversification and speciation of angiosperms. Its extent in other groups of land plants has only rarely been studied, however. We therefore examined the levels of introgression in the genus Diphasiastrum, a taxonomically challenging group of Lycopodiophytes, using flow cytometry and numerical and geometric morphometric analyses. Patterns of morphological and cytological variation were evaluated in an extensive dataset of 561 individuals from 57 populations of six taxa from Central Europe, the region with the largest known taxonomic complexity. In addition, genome size values of 63 individuals from Northern Europe were acquired for comparative purposes. Within Central European populations, we detected a continuous pattern in both morphological variation and genome size (strongly correlated together) suggesting extensive levels of interspecific gene flow within this region, including several large hybrid swarm populations. The secondary character of habitats of Central European hybrid swarm populations suggests that man-made landscape changes might have enhanced unnatural contact of species, resulting in extensive hybridization within this area. On the contrary, a distinct pattern of genome size variation among individuals from other parts of Europe indicates that pure populations prevail outside Central Europe. All in all, introgressive hybridization among Diphasiastrum species in Central Europe represents a unique case of extensive interspecific gene flow among spore producing vascular plants that cause serious complications of taxa delimitation. PMID:24932509

The genome sequence of Saccharomyces eubayanus and the domestication of lager-brewing yeasts

DOE PAGES

Baker, Emily Clare; Wang, Bing; Bellora, Nicolas; ...

2015-08-11

The dramatic phenotypic changes that occur in organisms during domestication leave indelible imprints on their genomes. Although many domesticated plants and animals have been systematically compared with their wild genetic stocks, the molecular and genomic processes underlying fungal domestication have received less attention. Here, we present a nearly complete genome assembly for the recently described yeast species Saccharomyces eubayanus and compare it to the genomes of multiple domesticated alloploid hybrids of S. eubayanus × S. cerevisiae ( S. pastorianus syn. S. carlsbergensis), which are used to brew lager-style beers. We find that the S. eubayanus subgenomes of lager-brewing yeasts havemore » experienced increased rates of evolution since hybridization, and that certain genes involved in metabolism may have been particularly affected. Interestingly, the S. eubayanus subgenome underwent an especially strong shift in selection regimes, consistent with more extensive domestication of the S. cerevisiae parent prior to hybridization. In contrast to recent proposals that lager-brewing yeasts were domesticated following a single hybridization event, the radically different neutral site divergences between the subgenomes of the two major lager yeast lineages strongly favor at least two independent origins for the S. cerevisiae × S. eubayanus hybrids that brew lager beers. In conclusion, our findings demonstrate how this industrially important hybrid has been domesticated along similar evolutionary trajectories on multiple occasions.« less

Two closely related species differ in their regional genetic differentiation despite admixing

PubMed Central

Fischer, Markus; Oja, Tatjana

2018-01-01

Abstract Regional genetic differentiation within species is often addressed in evolutionary ecology and conservation biology. Here, we address regional differentiation in two closely related hybridizing taxa, the perennial sedges Carex flava and C. viridula and their hybrid C. × subviridula in 37 populations in the north and centre of their distribution range in Europe (Estonia, Lowland (<1000 m a.s.l.) and Highland Switzerland) using 10 putative microsatellite loci. We ask whether regional differentiation was larger in the less common taxon C. viridula or whether, possibly due to hybridization, it was similar between taxa. Our results showed similar, low to moderate genetic diversity for the three studied taxa. In total, we found 12 regional species-specific alleles. Analysis of molecular variance (AMOVA), STRUCTURE and multidimensional scaling analysis showed regional structure in genetic variation, where intraspecific differentiation between regions was lower for C. flava (AMOVA: 6.84 %) than for C. viridula (20.77 %) or C. × subviridula (18.27 %) populations. Hybrids differed from the parental taxa in the two regions where they occurred, i.e. in Estonia and Lowland Switzerland. We conclude that C. flava and C. viridula clearly differ from each other genetically, that there is pronounced regional differentiation and that, despite hybridization, this regional differentiation is more pronounced in the less common taxon, C. viridula. We encourage future studies on hybridizing taxa to work with plant populations from more than one region. PMID:29479408

The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts.

PubMed

Baker, EmilyClare; Wang, Bing; Bellora, Nicolas; Peris, David; Hulfachor, Amanda Beth; Koshalek, Justin A; Adams, Marie; Libkind, Diego; Hittinger, Chris Todd

2015-11-01

The dramatic phenotypic changes that occur in organisms during domestication leave indelible imprints on their genomes. Although many domesticated plants and animals have been systematically compared with their wild genetic stocks, the molecular and genomic processes underlying fungal domestication have received less attention. Here, we present a nearly complete genome assembly for the recently described yeast species Saccharomyces eubayanus and compare it to the genomes of multiple domesticated alloploid hybrids of S. eubayanus × S. cerevisiae (S. pastorianus syn. S. carlsbergensis), which are used to brew lager-style beers. We find that the S. eubayanus subgenomes of lager-brewing yeasts have experienced increased rates of evolution since hybridization, and that certain genes involved in metabolism may have been particularly affected. Interestingly, the S. eubayanus subgenome underwent an especially strong shift in selection regimes, consistent with more extensive domestication of the S. cerevisiae parent prior to hybridization. In contrast to recent proposals that lager-brewing yeasts were domesticated following a single hybridization event, the radically different neutral site divergences between the subgenomes of the two major lager yeast lineages strongly favor at least two independent origins for the S. cerevisiae × S. eubayanus hybrids that brew lager beers. Our findings demonstrate how this industrially important hybrid has been domesticated along similar evolutionary trajectories on multiple occasions. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Hybrid Robust Multi-Objective Evolutionary Optimization Algorithm

DTIC Science & Technology

2009-03-10

pp. 594-606. 8. Inverse Approaches to Drying of Thin Bodies With Significant Shrinkage Effects (with G. H. Kanevce, L. P. Kanevce, V. B. Mitrevski ...Kanevce, L. Kanevce, V. Mitrevski ), ICCES󈧌: International Conference on Computational & Experimental Engineering and Sciences, Honolulu, Hawaii, March 17...Miami Beach, FL, April 16-18, 2007. 16. Inverse Approaches to Drying of Sliced Foods (with Kanevce, G. H., Kanevce, Lj. P., and Mitrevski , V. B

Hybrid Architectures for Evolutionary Computing Algorithms

DTIC Science & Technology

2008-01-01

other EC algorithms to FPGA Core Burns P1026/MAPLD 200532 Genetic Algorithm Hardware References S. Scott, A. Samal , and S. Seth, “HGA: A Hardware Based...on Parallel and Distributed Processing (IPPS/SPDP 󈨦), pp. 316-320, Proceedings. IEEE Computer Society 1998. [12] Scott, S. D. , Samal , A., and...Algorithm Hardware References S. Scott, A. Samal , and S. Seth, “HGA: A Hardware Based Genetic Algorithm”, Proceedings of the 1995 ACM Third

Comparative mapping of human alphoid centromeric sequences in great apes

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

Archidiacono, N.; Antonacci, R.; Marzella, R.

1994-09-01

Metaphase spreads from chimpanzees (Pan troglodytes and Pan paniscus) and gorilla (Gorilla gorilla) have been hybridized in situ with 27 alphoid DNA probes specific for the centromere of human chromosomes, to investigate the evolutionary relationship between centromeric regions of human and great apes. The results showed that most human probes do not recognize their corresponding homologs in great apes. Chromosome X is the only chromosome showing localization consistency in all the four species. Each suprachromosomal family (SCF) exhibits a distinct and peculiar evolutionary history. SCF1 (chromosomes 1, 3, 6, 7, 19, 12, 16) is very heterogeneous: some probes gave intensemore » signals, but always on non-homologous chromosomes; others did not produce any hybridization signal. All probes localized on SCF2 (chromosomes 2, 4, 8, 9, 13, 14, 15, 18, 20, 21, and 22) recognize a single chromosome: chromosome 11 (phylogenetic IX) in PTR and PPA; chromosome 4 (phylogenetic V) in GGO. SCF3 subsets (chromosomes 1, 11, 17, X) are substantially conserved in PTR and PPA, but not in GGO, with the exception restricted to chromosome X. No signals have been detected on PPA chromosomes I, III, IV, V, VI and in PTR chromosomes V, suggesting that the centromeric region of some chromsomes have probably lost homology with human alphoid sequences.« less

Hybridization of Strength Pareto Multiobjective Optimization with Modified Cuckoo Search Algorithm for Rectangular Array

NASA Astrophysics Data System (ADS)

Abdul Rani, Khairul Najmy; Abdulmalek, Mohamedfareq; A. Rahim, Hasliza; Siew Chin, Neoh; Abd Wahab, Alawiyah

2017-04-01

This research proposes the various versions of modified cuckoo search (MCS) metaheuristic algorithm deploying the strength Pareto evolutionary algorithm (SPEA) multiobjective (MO) optimization technique in rectangular array geometry synthesis. Precisely, the MCS algorithm is proposed by incorporating the Roulette wheel selection operator to choose the initial host nests (individuals) that give better results, adaptive inertia weight to control the positions exploration of the potential best host nests (solutions), and dynamic discovery rate to manage the fraction probability of finding the best host nests in 3-dimensional search space. In addition, the MCS algorithm is hybridized with the particle swarm optimization (PSO) and hill climbing (HC) stochastic techniques along with the standard strength Pareto evolutionary algorithm (SPEA) forming the MCSPSOSPEA and MCSHCSPEA, respectively. All the proposed MCS-based algorithms are examined to perform MO optimization on Zitzler-Deb-Thiele’s (ZDT’s) test functions. Pareto optimum trade-offs are done to generate a set of three non-dominated solutions, which are locations, excitation amplitudes, and excitation phases of array elements, respectively. Overall, simulations demonstrates that the proposed MCSPSOSPEA outperforms other compatible competitors, in gaining a high antenna directivity, small half-power beamwidth (HPBW), low average side lobe level (SLL) suppression, and/or significant predefined nulls mitigation, simultaneously.

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

PubMed Central

Vogt, Günter

2017-01-01

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

Characterization of a chromosome-specific chimpanzee alpha satellite subset: Evolutionary relationship to subsets on human chromosomes

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

Warburton, P.E.; Gosden, J.; Lawson, D.

1996-04-15

Alpha satellite DNA is a tandemly repeated DNA family found at the centromeres of all primate chromosomes examined. The fundamental repeat units of alpha satellite DNA are diverged 169- to 172-bp monomers, often found to be organized in chromosome-specific higher-order repeat units. The chromosomes of human (Homo sapiens (HSA)), chimpanzee (Pan troglodytes (PTR) and Pan paniscus), and gorilla (Gorilla gorilla) share a remarkable similarity and synteny. It is of interest to ask if alpha satellite arrays at centromeres of homologous chromosomes between these species are closely related (evolving in an orthologous manner) or if the evolutionary processes that homogenize andmore » spread these arrays within and between chromosomes result in nonorthologous evolution of arrays. By using PCR primers specific for human chromosome 17-specific alpha satellite DNA, we have amplified, cloned, and characterized a chromosome-specific subset from the PTR chimpanzee genome. Hybridization both on Southern blots and in situ as well as sequence analysis show that this subset is most closely related, as expected, to sequences on HSA 17. However, in situ hybridization reveals that this subset is not found on the homologous chromosome in chimpanzee (PTR 19), but instead on PTR 12, which is homologous to HSA 2p. 40 refs., 3 figs.« less

Ramgen Power Systems-Supersonic Component Technology for Military Engine Applications

DTIC Science & Technology

2006-11-01

turbine efficiency power (kW) LHV efficiency HHV efficiency notes **Current Design Point 0.45 1700 1013 84.4% 220.1 35.4% 31.8% - Rampressor...tor (such as a standalone power-only mode device), or to a fuel cell in a hybrid configuration. This paper presents the development of the RPS gas...turbine technology and potential applications to the two specific engine cycle configurations, i.e., an indirect fuel cell / RPS turbine hybrid-cycle

Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids.

PubMed

Shivrain, Vinod K; Burgos, Nilda R; Gealy, David R; Sales, Marites A; Smith, Kenneth L

2009-10-01

Gene transfer from weeds to crops could produce weedy individuals that might impact upon the evolutionary dynamics of weedy populations, the persistence of escaped genes in agroecosystems and approaches to weed management and containment of transgenic crops. The present aim was to quantify the gene flowrate from weedy red rice to cultivated rice, and evaluate the morphology, phenology and fecundity of resulting hybrids. Field experiments were conducted at Stuttgart and Rohwer, Arkansas, USA. Twelve red rice accessions and an imazethapyr-resistant rice (Imi-R; Clearfield) were used. Hybrids between Imi-R rice x red rice were 138-150 cm tall and flowered 1-5 days later than the rice parent, regardless of the red rice parent. Hybrids produced 20-50% more seed than the rice parent, but had equivalent seed production to the majority of red rice parents. Seeds of all hybrids were red, pubescent and dehisced at maturity. For the majority of hybrids, seed germination was higher than that of the red rice parent. The gene flowrate from red rice to rice was 0.01-0.2% and differed by red rice biotype. The hybrids had higher fecundity and potential competitive ability than the rice parent, and in some cases also the red rice parent. Red rice plants are vectors of gene flow back to cultivated rice and other weedy populations. The progeny of red rice hybrids from cultivated rice mother plants have higher chances of persistence than those from red rice mother plants. Gene flow mitigation strategies should consider this scenario. Copyright 2009 Society of Chemical Industry.

Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility

PubMed Central

2013-01-01

Background Interspecific hybridization creates individuals harboring diverged genomes. The interaction of these genomes can generate successful evolutionary novelty or disadvantageous genomic conflict. Annual sunflowers Helianthus annuus and H. petiolaris have a rich history of hybridization in natural populations. Although first-generation hybrids generally have low fertility, hybrid swarms that include later generation and fully fertile backcross plants have been identified, as well as at least three independently-originated stable hybrid taxa. We examine patterns of transcript accumulation in the earliest stages of hybridization of these species via analyses of transcriptome sequences from laboratory-derived F1 offspring of an inbred H. annuus cultivar and a wild H. petiolaris accession. Results While nearly 14% of the reference transcriptome showed significant accumulation differences between parental accessions, total F1 transcript levels showed little evidence of dominance, as midparent transcript levels were highly predictive of transcript accumulation in F1 plants. Allelic bias in F1 transcript accumulation was detected in 20% of transcripts containing sufficient polymorphism to distinguish parental alleles; however the magnitude of these biases were generally smaller than differences among parental accessions. Conclusions While analyses of allelic bias suggest that cis regulatory differences between H. annuus and H. petiolaris are common, their effect on transcript levels may be more subtle than trans-acting regulatory differences. Overall, these analyses found little evidence of regulatory incompatibility or dominance interactions between parental genomes within F1 hybrid individuals, although it is unclear whether this is a legacy or an enabler of introgression between species. PMID:23701699

Regulatory Divergence between Parental Alleles Determines Gene Expression Patterns in Hybrids

PubMed Central

Combes, Marie-Christine; Hueber, Yann; Dereeper, Alexis; Rialle, Stéphanie; Herrera, Juan-Carlos; Lashermes, Philippe

2015-01-01

Both hybridization and allopolyploidization generate novel phenotypes by conciliating divergent genomes and regulatory networks in the same cellular context. To understand the rewiring of gene expression in hybrids, the total expression of 21,025 genes and the allele-specific expression of over 11,000 genes were quantified in interspecific hybrids and their parental species, Coffea canephora and Coffea eugenioides using RNA-seq technology. Between parental species, cis- and trans-regulatory divergences affected around 32% and 35% of analyzed genes, respectively, with nearly 17% of them showing both. The relative importance of trans-regulatory divergences between both species could be related to their low genetic divergence and perennial habit. In hybrids, among divergently expressed genes between parental species and hybrids, 77% was expressed like one parent (expression level dominance), including 65% like C. eugenioides. Gene expression was shown to result from the expression of both alleles affected by intertwined parental trans-regulatory factors. A strong impact of C. eugenioides trans-regulatory factors on the upregulation of C. canephora alleles was revealed. The gene expression patterns appeared determined by complex combinations of cis- and trans-regulatory divergences. In particular, the observed biased expression level dominance seemed to be derived from the asymmetric effects of trans-regulatory parental factors on regulation of alleles. More generally, this study illustrates the effects of divergent trans-regulatory parental factors on the gene expression pattern in hybrids. The characteristics of the transcriptional response to hybridization appear to be determined by the compatibility of gene regulatory networks and therefore depend on genetic divergences between the parental species and their evolutionary history. PMID:25819221

The Evolution of Polymorphic Hybrid Incompatibilities in House Mice.

PubMed

Larson, Erica L; Vanderpool, Dan; Sarver, Brice A J; Callahan, Colin; Keeble, Sara; Provencio, Lorraine P; Kessler, Michael D; Stewart, Vanessa; Nordquist, Erin; Dean, Matthew D; Good, Jeffrey M

2018-04-24

Resolving the mechanistic and genetic bases of reproductive barriers between species is essential to understanding the evolutionary forces that shape speciation. Intrinsic hybrid incompatibilities are often treated as fixed between species, yet there can be considerable variation in the strength of reproductive isolation between populations. The extent and causes of this variation remain poorly understood in most systems. We investigated the genetic basis of variable hybrid male sterility (HMS) between two recently diverged subspecies of house mice, Mus musculus domesticus and M. m. musculus We found that polymorphic HMS has a surprisingly complex genetic basis, with contributions from at least five autosomal loci segregating between two closely related wild-derived strains of M. m. musculus One of the HMS-linked regions on Chromosome 4 also showed extensive introgression among inbred laboratory strains and transmission ratio distortion (TRD) in hybrid crosses. Using additional crosses and whole genome sequencing of sperm pools, we showed that TRD was limited to hybrid crosses and was not due to differences in sperm motility between M. m. musculus strains. Based on these results, we argue that TRD likely reflects additional incompatibilities that reduce hybrid embryonic viability. In some common inbred strains of mice, selection against deleterious interactions appears to have unexpectedly driven introgression at loci involved in epistatic hybrid incompatibilities. The highly variable genetic basis to F1 hybrid incompatibilities between closely related mouse lineages argues that a thorough dissection of reproductive isolation will require much more extensive sampling of natural variation than has been commonly utilized in mice and other model systems. Copyright © 2018, Genetics.

Recovery Act: Tennessee Energy Efficient Schools Initiative Ground Source Heat Pump Program

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

Townsend, Terry; Slusher, Scott

The Tennessee Energy Efficient Schools Initiative (EESI) Hybrid-Water Source Heat Pump (HY-GSHP) Program sought to provide installation costs and operation costs for different Hybrid water source heat pump systems’ configurations so that other State of Tennessee School Districts will have a resource for comparison purposes if considering a geothermal system.

A High-Efficiency Si Nanowire Array/Perovskite Hybrid Solar Cell.

PubMed

Yan, Xin; Zhang, Chen; Wang, Jiamin; Zhang, Xia; Ren, Xiaomin

2017-12-01

A low-cost Si nanowire array/perovskite hybrid solar cell is proposed and simulated. The solar cell consists of a Si p-i-n nanowire array filled with CH 3 NH 3 PbI 3 , in which both the nanowires and perovskite absorb the incident light while the nanowires act as the channels for transporting photo-generated electrons and holes. The hybrid structure has a high absorption efficiency in a broad wavelength range of 300~800 nm. A large short-circuit current density of 28.8 mA/cm 2 and remarkable conversion efficiency of 13.3% are obtained at a thin absorber thickness of 1.6 μm, which are comparable to the best results of III-V nanowire solar cells.

Interfacial engineering of CuO nanorod/ZnO nanowire hybrid nanostructure photoanode in dye-sensitized solar cell

NASA Astrophysics Data System (ADS)

Kilic, Bayram; Turkdogan, Sunay; Astam, Aykut; Baran, Sümeyra Seniha; Asgin, Mansur; Gur, Emre; Kocak, Yusuf

2018-01-01

Developing efficient and cost-effective photoanode plays a vital role determining the photocurrent and photovoltage in dye-sensitized solar cells (DSSCs). Here, we demonstrate DSSCs that achieve relatively high power conversion efficiencies (PCEs) by using one-dimensional (1D) zinc oxide (ZnO) nanowires and copper (II) oxide (CuO) nanorods hybrid nanostructures. CuO nanorod-based thin films were prepared by hydrothermal method and used as a blocking layer on top of the ZnO nanowires' layer. The use of 1D ZnO nanowire/CuO nanorod hybrid nanostructures led to an exceptionally high photovoltaic performance of DSSCs with a remarkably high open-circuit voltage (0.764 V), short current density (14.76 mA/cm2 under AM1.5G conditions), and relatively high solar to power conversion efficiency (6.18%) . The enhancement of the solar to power conversion efficiency can be explained in terms of the lag effect of the interfacial recombination dynamics of CuO nanorod-blocking layer on ZnO nanowires. This work shows more economically feasible method to bring down the cost of the nano-hybrid cells and promises for the growth of other important materials to further enhance the solar to power conversion efficiency.

Evolutionary genomics of yeast pathogens in the Saccharomycotina

PubMed Central

Naranjo-Ortíz, Miguel A.; Marcet-Houben, Marina

2016-01-01

Saccharomycotina comprises a diverse group of yeasts that includes numerous species of industrial or clinical relevance. Opportunistic pathogens within this clade are often assigned to the genus Candida but belong to phylogenetically distant lineages that also comprise non-pathogenic species. This indicates that the ability to infect humans has evolved independently several times among Saccharomycotina. Although the mechanisms of infection of the main groups of Candida pathogens are starting to be unveiled, we still lack sufficient understanding of the evolutionary paths that led to a virulent phenotype in each of the pathogenic lineages. Deciphering what genomic changes underlie the evolutionary emergence of a virulence trait will not only aid the discovery of novel virulence mechanisms but it will also provide valuable information to understand how new pathogens emerge, and what clades may pose a future danger. Here we review recent comparative genomics efforts that have revealed possible evolutionary paths to pathogenesis in different lineages, focusing on the main three agents of candidiasis worldwide: Candida albicans, C. parapsilosis and C. glabrata. We will discuss what genomic traits may facilitate the emergence of virulence, and focus on two different genome evolution mechanisms able to generate drastic phenotypic changes and which have been associated to the emergence of virulence: gene family expansion and interspecies hybridization. PMID:27493146

The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data

PubMed Central

Sun, Keping; Kimball, Rebecca T.; Liu, Tong; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Lin, Aiqing; Feng, Jiang

2016-01-01

Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization. PMID:27748429

Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences.

PubMed

Zheng, Xiaoyan; Cai, Danying; Potter, Daniel; Postman, Joseph; Liu, Jing; Teng, Yuanwen

2014-11-01

Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus. Copyright © 2014 Elsevier Inc. All rights reserved.

Invisible hand effect in an evolutionary minority game model

NASA Astrophysics Data System (ADS)

Sysi-Aho, Marko; Saramäki, Jari; Kaski, Kimmo

2005-03-01

In this paper, we study the properties of a minority game with evolution realized by using genetic crossover to modify fixed-length decision-making strategies of agents. Although the agents in this evolutionary game act selfishly by trying to maximize their own performances only, it turns out that the whole society will eventually be rewarded optimally. This “invisible hand” effect is what Adam Smith over two centuries ago expected to take place in the context of free market mechanism. However, this behaviour of the society of agents is realized only under idealized conditions, where all agents are utilizing the same efficient evolutionary mechanism. If on the other hand part of the agents are adaptive, but not evolutionary, the system does not reach optimum performance, which is also the case if part of the evolutionary agents form a uniformly acting “cartel”.

Efficiency of a hybrid-type plasma-assisted fuel reformation system

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

Matveev, I.B.; Serbin, S.I.; Lux, S.M.

2008-12-15

The major advantages of a new plasma-assisted fuel reformation system are its cost effectiveness and technical efficiency. Applied Plasma Technologies has proposed its new highly efficient hybrid-type plasma-assisted system for organic fuel combustion and gasification. The system operates as a multimode multipurpose reactor in a wide range of plasma feedstock gases and turndown ratios. This system also has convenient and simultaneous feeding of several reagents in the reaction zone such as liquid fuels, coal, steam, and air. A special methodology has been developed for such a system in terms of heat balance evaluation and optimization. This methodology considers all existingmore » and possible energy streams, which could influence the system's efficiency. The developed hybrid-type plasma system could be suitable for combustion applications, mobile and autonomous small- to mid-size liquid fuel and coal gasification modules, hydrogen-rich gas generators, waste-processing facilities, and plasma chemical reactors.« less

Hybrid perovskite films approaching the radiative limit with over 90% photoluminescence quantum efficiency

NASA Astrophysics Data System (ADS)

Braly, Ian L.; deQuilettes, Dane W.; Pazos-Outón, Luis M.; Burke, Sven; Ziffer, Mark E.; Ginger, David S.; Hillhouse, Hugh W.

2018-06-01

Reducing non-radiative recombination in semiconducting materials is a prerequisite for achieving the highest performance in light-emitting and photovoltaic applications. Here, we characterize both external and internal photoluminescence quantum efficiency and quasi-Fermi-level splitting of surface-treated hybrid perovskite (CH3NH3PbI3) thin films. With respect to the material bandgap, these passivated films exhibit the highest quasi-Fermi-level splitting measured to date, reaching 97.1 ± 0.7% of the radiative limit, approaching that of the highest performing GaAs solar cells. We confirm these values with independent measurements of internal photoluminescence quantum efficiency of 91.9 ± 2.7% under 1 Sun illumination intensity, setting a new benchmark for these materials. These results suggest hybrid perovskite solar cells are inherently capable of further increases in power conversion efficiency if surface passivation can be combined with optimized charge carrier selective interfaces.

Silicon Nanowire/Polymer Hybrid Solar Cell-Supercapacitor: A Self-Charging Power Unit with a Total Efficiency of 10.5.

PubMed

Liu, Ruiyuan; Wang, Jie; Sun, Teng; Wang, Mingjun; Wu, Changsheng; Zou, Haiyang; Song, Tao; Zhang, Xiaohong; Lee, Shuit-Tong; Wang, Zhong Lin; Sun, Baoquan

2017-07-12

An integrated self-charging power unit, combining a hybrid silicon nanowire/polymer heterojunction solar cell with a polypyrrole-based supercapacitor, has been demonstrated to simultaneously harvest solar energy and store it. By efficiency enhancement of the hybrid nanowire solar cells and a dual-functional titanium film serving as conjunct electrode of the solar cell and supercapacitor, the integrated system is able to yield a total photoelectric conversion to storage efficiency of 10.5%, which is the record value in all the integrated solar energy conversion and storage system. This system may not only serve as a buffer that diminishes the solar power fluctuations from light intensity, but also pave its way toward cost-effective high efficiency self-charging power unit. Finally, an integrated device based on ultrathin Si substrate is demonstrated to expand its feasibility and potential application in flexible energy conversion and storage devices.

Improving the sampling efficiency of Monte Carlo molecular simulations: an evolutionary approach

NASA Astrophysics Data System (ADS)

Leblanc, Benoit; Braunschweig, Bertrand; Toulhoat, Hervé; Lutton, Evelyne

We present a new approach in order to improve the convergence of Monte Carlo (MC) simulations of molecular systems belonging to complex energetic landscapes: the problem is redefined in terms of the dynamic allocation of MC move frequencies depending on their past efficiency, measured with respect to a relevant sampling criterion. We introduce various empirical criteria with the aim of accounting for the proper convergence in phase space sampling. The dynamic allocation is performed over parallel simulations by means of a new evolutionary algorithm involving 'immortal' individuals. The method is bench marked with respect to conventional procedures on a model for melt linear polyethylene. We record significant improvement in sampling efficiencies, thus in computational load, while the optimal sets of move frequencies are liable to allow interesting physical insights into the particular systems simulated. This last aspect should provide a new tool for designing more efficient new MC moves.

Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes

PubMed Central

Scriber, Jon Mark

2013-01-01

Comprising 50%–75% of the world’s fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including “invasive species” in various ecosystems as they may become disrupted in different ways by rapid climate change. “Invasive genes” (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. “Genetic rescue” via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced “reshuffling” (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge. PMID:26462579

Nuclear microsatellite variation in Malagasy baobabs (Adansonia, Bombacoideae, Malvaceae) reveals past hybridization and introgression.

PubMed

Leong Pock Tsy, Jean-Michel; Lumaret, Roselyne; Flaven-Noguier, Elodie; Sauve, Mathieu; Dubois, Marie-Pierre; Danthu, Pascal

2013-12-01

Adansonia comprises nine species, six of which are endemic to Madagascar. Genetic relationships between the Malagasy species remain unresolved due to conflicting results between nuclear and plastid DNA variation. Morphologically intermediate individuals between distinct species have been identified, indicative of interspecific hybridization. In this paper, microsatellite data are used to identify potential cases of hybridization and to provide insights into the evolutionary history of the genus on Madagascar. Eleven microsatellites amplified with new primers developed for Adansonia rubrostipa were used to analyse 672 individuals collected at 27 sites for the six Malagasy species and morphologically intermediate individuals. Rates of individual admixture were examined using three Bayesian clustering programs, STRUCTURE, BAPS and NewHybrids, with no a priori species assignment. Population differentiation was coherent, with recognized species boundaries. In the four Malagasy species of section Longitubae, 8·0, 9·0 and 9·5 % of individuals with mixed genotypes were identified by BAPS, NewHybrids and STRUCTURE, respectively. At sites with sympatric populations of A. rubrostipa and A. za, NewHybrids indicated these individuals to be F2 and, predominantly, backcrosses with both parental species. In northern Madagascar, two populations of trees combining A. za and A. perrieri morphology and microsatellite alleles were identified in the current absence of the parental species. The clear genetic differentiation observed between the six species may reflect their adaptation to different assortments of climate regimes and habitats during the colonization of the island. Microsatellite variation reveals that hybridization probably occurred in secondary contact between species of section Longitubae. This type of hybridization may also have been involved in the differentiation of a local new stabilized entity showing specific microsatellite alleles and morphological characters, suggesting a potential role of hybridization in the recent history of diversification on Madagascar.

Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes.

PubMed

Scriber, Jon Mark

2013-12-24

Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.

Lager Yeast Comes of Age

PubMed Central

2014-01-01

Alcoholic fermentations have accompanied human civilizations throughout our history. Lager yeasts have a several-century-long tradition of providing fresh beer with clean taste. The yeast strains used for lager beer fermentation have long been recognized as hybrids between two Saccharomyces species. We summarize the initial findings on this hybrid nature, the genomics/transcriptomics of lager yeasts, and established targets of strain improvements. Next-generation sequencing has provided fast access to yeast genomes. Its use in population genomics has uncovered many more hybridization events within Saccharomyces species, so that lager yeast hybrids are no longer the exception from the rule. These findings have led us to propose network evolution within Saccharomyces species. This “web of life” recognizes the ability of closely related species to exchange DNA and thus drain from a combined gene pool rather than be limited to a gene pool restricted by speciation. Within the domesticated lager yeasts, two groups, the Saaz and Frohberg groups, can be distinguished based on fermentation characteristics. Recent evidence suggests that these groups share an evolutionary history. We thus propose to refer to the Saaz group as Saccharomyces carlsbergensis and to the Frohberg group as Saccharomyces pastorianus based on their distinct genomes. New insight into the hybrid nature of lager yeast will provide novel directions for future strain improvement. PMID:25084862

Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays

PubMed Central

2010-01-01

Background Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. However, although commercial microarrays are available for most common laboratory models, transcriptome analysis in non-traditional model species still remains a challenge. Indeed, the signal resulting from heterologous hybridization is low and difficult to interpret because of the weak complementarity between probe and target sequences, especially when no microarray dedicated to a genetically close species is available. Results We show here that transcriptome analysis in a species genetically distant from laboratory models is made possible by using MAXRS, a new method of analyzing heterologous hybridization on microarrays. This method takes advantage of the design of several commercial microarrays, with different probes targeting the same transcript. To illustrate and test this method, we analyzed the transcriptome of king penguin pectoralis muscle hybridized to Affymetrix chicken microarrays, two organisms separated by an evolutionary distance of approximately 100 million years. The differential gene expression observed between different physiological situations computed by MAXRS was confirmed by real-time PCR on 10 genes out of 11 tested. Conclusions MAXRS appears to be an appropriate method for gene expression analysis under heterologous hybridization conditions. PMID:20509979

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

PubMed Central

Dujon, Bernard

2012-01-01

Summary: Forced interspecific hybridization has been used in yeasts for many years to study speciation or to construct artificial strains with novel fermentative and metabolic properties. Recent genome analyses indicate that natural hybrids are also generated spontaneously between yeasts belonging to distinct species, creating lineages with novel phenotypes, varied genetic stability, or altered virulence in the case of pathogens. Large segmental introgressions from evolutionarily distant species are also visible in some yeast genomes, suggesting that interspecific genetic exchanges occur during evolution. The origin of this phenomenon remains unclear, but it is likely based on weak prezygotic barriers, limited Dobzhansky-Muller (DM) incompatibilities, and rapid clonal expansions. Newly formed interspecies hybrids suffer rapid changes in the genetic contribution of each parent, including chromosome loss or aneuploidy, translocations, and loss of heterozygosity, that, except in a few recently studied cases, remain to be characterized more precisely at the genomic level by use of modern technologies. We review here known cases of natural or artificially formed interspecies hybrids between yeasts and discuss their potential importance in terms of genome evolution. Problems of meiotic fertility, ploidy constraint, gene and gene product compatibility, and nucleomitochondrial interactions are discussed and placed in the context of other known mechanisms of yeast genome evolution as a model for eukaryotes. PMID:23204364

Multiple Origins and Nested Cycles of Hybridization Result in High Tetraploid Diversity in the Monocot Prospero.

PubMed

Jang, Tae-Soo; Parker, John S; Emadzade, Khatere; Temsch, Eva M; Leitch, Andrew R; Weiss-Schneeweiss, Hanna

2018-01-01

Polyploidy is a major driving force in angiosperm evolution, but our understanding of establishment and early diversification processes following allo- vs. auto-polyploidy is limited. An excellent system to address such questions is the monocot plant Prospero autumnale , as it comprises several genomically and chromosomally distinct diploid cytotypes and their auto- and allotetraploid derivatives. To infer origins and evolutionary trajectories of the tetraploids, we use genome size data, in situ hybridization with parental genomic DNAs and specific probes (satDNA, rDNAs), as well as molecular-phylogenetic analyses. Thus, we demonstrate that an astounding range of allotetraploid lineages has been formed recurrently by chromosomal re-patterning, interactions of chromosomally variable parental genomes and nested cycles of extensive hybridization, whereas autotetraploids have originated at least twice and are cytologically stable. During the recurrent formation and establishment across wide geographic areas hybridization in some populations could have inhibited lineage diversification and nascent speciation of such a hybrid swarm. However, cytotypes that became fixed in populations enhanced the potential for species diversification, possibly exploiting the extended allelic base, and fixed heterozygosity that polyploidy confers. The time required for polyploid cytotype fixation may in part reflect the lag phase reported for polyploids between their formation and species diversification.

Conceptual Design and Optimal Power Control Strategy for AN Eco-Friendly Hybrid Vehicle

NASA Astrophysics Data System (ADS)

Nasiri, N. Mir; Chieng, Frederick T. A.

2011-06-01

This paper presents a new concept for a hybrid vehicle using a torque and speed splitting technique. It is implemented by the newly developed controller in combination with a two degree of freedom epicyclic gear transmission. This approach enables optimization of the power split between the less powerful electrical motor and more powerful engine while driving a car load. The power split is fundamentally a dual-energy integration mechanism as it is implemented by using the epicyclic gear transmission that has two inputs and one output for a proper power distribution. The developed power split control system manages the operation of both the inputs to have a known output with the condition of maintaining optimum operating efficiency of the internal combustion engine and electrical motor. This system has a huge potential as it is possible to integrate all the features of hybrid vehicle known to-date such as the regenerative braking system, series hybrid, parallel hybrid, series/parallel hybrid, and even complex hybrid (bidirectional). By using the new power split system it is possible to further reduce fuel consumption and increase overall efficiency.

Optimal design of hybrid electric-human powered lightweight transportation

DOT National Transportation Integrated Search

2001-07-01

The goal of this project was to develop a lightweight and efficient hybrid bicycle design. A series approach to design of the hybrid bicycle was used to allow for more technical advances to be made. This approach required the project to be divided in...

Developing a Shuffled Complex-Self Adaptive Hybrid Evolution (SC-SAHEL) Framework for Water Resources Management and Water-Energy System Optimization

NASA Astrophysics Data System (ADS)

Rahnamay Naeini, M.; Sadegh, M.; AghaKouchak, A.; Hsu, K. L.; Sorooshian, S.; Yang, T.

2017-12-01

Meta-Heuristic optimization algorithms have gained a great deal of attention in a wide variety of fields. Simplicity and flexibility of these algorithms, along with their robustness, make them attractive tools for solving optimization problems. Different optimization methods, however, hold algorithm-specific strengths and limitations. Performance of each individual algorithm obeys the "No-Free-Lunch" theorem, which means a single algorithm cannot consistently outperform all possible optimization problems over a variety of problems. From users' perspective, it is a tedious process to compare, validate, and select the best-performing algorithm for a specific problem or a set of test cases. In this study, we introduce a new hybrid optimization framework, entitled Shuffled Complex-Self Adaptive Hybrid EvoLution (SC-SAHEL), which combines the strengths of different evolutionary algorithms (EAs) in a parallel computing scheme, and allows users to select the most suitable algorithm tailored to the problem at hand. The concept of SC-SAHEL is to execute different EAs as separate parallel search cores, and let all participating EAs to compete during the course of the search. The newly developed SC-SAHEL algorithm is designed to automatically select, the best performing algorithm for the given optimization problem. This algorithm is rigorously effective in finding the global optimum for several strenuous benchmark test functions, and computationally efficient as compared to individual EAs. We benchmark the proposed SC-SAHEL algorithm over 29 conceptual test functions, and two real-world case studies - one hydropower reservoir model and one hydrological model (SAC-SMA). Results show that the proposed framework outperforms individual EAs in an absolute majority of the test problems, and can provide competitive results to the fittest EA algorithm with more comprehensive information during the search. The proposed framework is also flexible for merging additional EAs, boundary-handling techniques, and sampling schemes, and has good potential to be used in Water-Energy system optimal operation and management.

Efficient light emission from inorganic and organic semiconductor hybrid structures by energy-level tuning

PubMed Central

Schlesinger, R.; Bianchi, F.; Blumstengel, S.; Christodoulou, C.; Ovsyannikov, R.; Kobin, B.; Moudgil, K.; Barlow, S.; Hecht, S.; Marder, S.R.; Henneberger, F.; Koch, N.

2015-01-01

The fundamental limits of inorganic semiconductors for light emitting applications, such as holographic displays, biomedical imaging and ultrafast data processing and communication, might be overcome by hybridization with their organic counterparts, which feature enhanced frequency response and colour range. Innovative hybrid inorganic/organic structures exploit efficient electrical injection and high excitation density of inorganic semiconductors and subsequent energy transfer to the organic semiconductor, provided that the radiative emission yield is high. An inherent obstacle to that end is the unfavourable energy level offset at hybrid inorganic/organic structures, which rather facilitates charge transfer that quenches light emission. Here, we introduce a technologically relevant method to optimize the hybrid structure's energy levels, here comprising ZnO and a tailored ladder-type oligophenylene. The ZnO work function is substantially lowered with an organometallic donor monolayer, aligning the frontier levels of the inorganic and organic semiconductors. This increases the hybrid structure's radiative emission yield sevenfold, validating the relevance of our approach. PMID:25872919

Graphene-cobaltite-Pd hybrid materials for use as efficient bifunctional electrocatalysts in alkaline direct methanol fuel cells.

PubMed

Sharma, Chandra Shekhar; Awasthi, Rahul; Singh, Ravindra Nath; Sinha, Akhoury Sudhir Kumar

2013-12-14

Hybrid materials comprising of Pd, MCo2O4 (where M = Mn, Co or Ni) and graphene have been prepared for use as efficient bifunctional electrocatalysts in alkaline direct methanol fuel cells. Structural and electrochemical characterizations were carried out using X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, chronoamperometry and cyclic, CO stripping, and linear sweep voltammetries. The study revealed that all the three hybrid materials are active for both methanol oxidation (MOR) and oxygen reduction (ORR) reactions in 1 M KOH. However, the Pd-MnCo2O4/GNS hybrid electrode exhibited the greatest MOR and ORR activities. This active hybrid electrode has also outstanding stability under both MOR and ORR conditions, while Pt- and other Pd-based catalysts undergo degradation under similar experimental conditions. The Pd-MnCo2O4/GNS hybrid catalyst exhibited superior ORR activity and stability compared to even Pt in alkaline solutions.

Using Protein Dimers to Maximize the Protein Hybridization Efficiency with Multisite DNA Origami Scaffolds

PubMed Central

Verma, Vikash; Mallik, Leena; Hariadi, Rizal F.; Sivaramakrishnan, Sivaraj; Skiniotis, Georgios; Joglekar, Ajit P.

2015-01-01

DNA origami provides a versatile platform for conducting ‘architecture-function’ analysis to determine how the nanoscale organization of multiple copies of a protein component within a multi-protein machine affects its overall function. Such analysis requires that the copy number of protein molecules bound to the origami scaffold exactly matches the desired number, and that it is uniform over an entire scaffold population. This requirement is challenging to satisfy for origami scaffolds with many protein hybridization sites, because it requires the successful completion of multiple, independent hybridization reactions. Here, we show that a cleavable dimerization domain on the hybridizing protein can be used to multiplex hybridization reactions on an origami scaffold. This strategy yields nearly 100% hybridization efficiency on a 6-site scaffold even when using low protein concentration and short incubation time. It can also be developed further to enable reliable patterning of a large number of molecules on DNA origami for architecture-function analysis. PMID:26348722

Efficient light emission from inorganic and organic semiconductor hybrid structures by energy-level tuning.

PubMed

Schlesinger, R; Bianchi, F; Blumstengel, S; Christodoulou, C; Ovsyannikov, R; Kobin, B; Moudgil, K; Barlow, S; Hecht, S; Marder, S R; Henneberger, F; Koch, N

2015-04-15

The fundamental limits of inorganic semiconductors for light emitting applications, such as holographic displays, biomedical imaging and ultrafast data processing and communication, might be overcome by hybridization with their organic counterparts, which feature enhanced frequency response and colour range. Innovative hybrid inorganic/organic structures exploit efficient electrical injection and high excitation density of inorganic semiconductors and subsequent energy transfer to the organic semiconductor, provided that the radiative emission yield is high. An inherent obstacle to that end is the unfavourable energy level offset at hybrid inorganic/organic structures, which rather facilitates charge transfer that quenches light emission. Here, we introduce a technologically relevant method to optimize the hybrid structure's energy levels, here comprising ZnO and a tailored ladder-type oligophenylene. The ZnO work function is substantially lowered with an organometallic donor monolayer, aligning the frontier levels of the inorganic and organic semiconductors. This increases the hybrid structure's radiative emission yield sevenfold, validating the relevance of our approach.

Hybrid and Plug-in Electric Vehicles

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

None

2014-05-20

Hybrid and plug-in electric vehicles use electricity either as their primary fuel or to improve the efficiency of conventional vehicle designs. This new generation of vehicles, often called electric drive vehicles, can be divided into three categories: hybrid electric vehicles (HEVs), plug-in hybrid electric vehicles(PHEVs), and all-electric vehicles (EVs). Together, they have great potential to reduce U.S. petroleum use.

Organic and Hybrid Organic Solid-State Photovoltaic Materials and Devices

DTIC Science & Technology

2014-02-19

hybrids have potential applications in solar cells and may thus provide mobile energy sources for aircraft and soldier technologies. Modeling and...modeling and simulation developed in this project are encouraging further development. 2. Technical Activities Hybrid organic solar cells are an...between surface-modified semiconducting nanoparticles and polymers often contributes to the limited efficiency of hybrid photovoltaic cells and

Periodic imidazolium-bridged hybrid monolith for high-efficiency capillary liquid chromatography with enhanced selectivity.

PubMed

Qiao, Xiaoqiang; Zhang, Niu; Han, Manman; Li, Xueyun; Qin, Xinying; Shen, Shigang

2017-03-01

A novel periodic imidazolium-bridged hybrid monolithic column was developed. With diene imidazolium ionic liquid 1-allyl-3-vinylimidazolium bromide as both cross-linker and organic functionalized reagent, a new periodic imidazolium-bridged hybrid monolithic column was facilely prepared in capillary with homogeneously distributed cationic imidazolium by a one-step free-radical polymerization with polyhedral oligomeric silsesquioxane methacryl substituted. The successful preparation of the new column was verified by Fourier transform infrared spectroscopy, scanning electron microscopy, elemental analysis, and surface area analysis. Most interestingly, the bonded amount of 1-allyl-3-vinylimidazolium bromide of the new column is three times higher than that of the conventional imidazolium-embedded hybrid monolithic column and the specific surface area of the column reached 478 m 2 /g. The new column exhibited high stability, excellent separation efficiency, and enhanced separation selectivity. The column efficiency reached 151 000 plates/m for alkylbenzenes. Furthermore, the new column was successfully used for separation of highly polar nucleosides and nucleic acid bases with pure water as mobile phase and even bovine serum albumin tryptic digest. All these results demonstrate the periodic imidazolium-bridged hybrid monolithic column is a good separation media and can be used for chromatographic separation of small molecules and complex biological samples with high efficiency. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient hybrid white organic light-emitting diodes with extremely long lifetime: the effect of n-type interlayer

PubMed Central

Liu, Baiquan; Wang, Lei; Xu, Miao; Tao, Hong; Zou, Jianhua; Gao, Dongyu; Lan, Linfeng; Ning, Honglong; Peng, Junbiao; Cao, Yong

2014-01-01

The effect of n-type interlayer in hybrid white organic light-emitting diodes (WOLEDs) has been systematically investigated by using various n-type materials. A new finding, that the triplet energy rather than electron mobility or hole-blocking ability of interlayer plays a more positive role in the performance of hybrid WOLEDs, is demonstrated. Based on the new finding, a more efficient n-type interlayer bis[2-(2-hydroxyphenyl)-pyridine] beryllium has been employed to realize a high-performance hybrid WOLED. The resulting device (without n-doping technology) exhibits low voltages (i.e., 2.8 V for 1 cd/m2, 3.9 V for 100 cd/m2) and low efficiency roll-off (i.e., 11.5 cd/A at 100 cd/m2 and 11.2 cd/A at 1000 cd/m2). At the display-relevant luminance of 100 cd/m2, a total power efficiency of 16.0 lm/W, a color rendering index of 73 and an extremely long lifetime of 12596265 h are obtained. Such superior results not only comprehensively indicate that the n-type materials are effective interlayers to develop high-performance hybrid WOLEDs but also demonstrate a significant step towards real commercialization in WOLEDs. PMID:25425090

Intracellular trafficking of hybrid gene delivery vectors.

PubMed

Keswani, Rahul K; Lazebnik, Mihael; Pack, Daniel W

2015-06-10

Viral and non-viral gene delivery vectors are in development for human gene therapy, but both exhibit disadvantages such as inadequate efficiency, lack of cell-specific targeting or safety concerns. We have recently reported the design of hybrid delivery vectors combining retrovirus-like particles with synthetic polymers or lipids that are efficient, provide sustained gene expression and are more stable compared to native retroviruses. To guide further development of this promising class of gene delivery vectors, we have investigated their mechanisms of intracellular trafficking. Moloney murine leukemia virus-like particles (M-VLPs) were complexed with chitosan (Chi) or liposomes (Lip) comprising DOTAP, DOPE and cholesterol to form the hybrid vectors (Chi/M-VLPs and Lip/M-VLPs, respectively). Transfection efficiency and cellular internalization of the vectors were quantified in the presence of a panel of inhibitors of various endocytic pathways. Intracellular transport and trafficking kinetics of the hybrid vectors were dependent on the synthetic component and used a combination of clathrin- and caveolar-dependent endocytosis and macropinocytosis. Chi/M-VLPs were slower to transfect compared to Lip/M-VLPs due to the delayed detachment of the synthetic component. The synthetic component of hybrid gene delivery vectors plays a significant role in their cellular interactions and processing and is a key parameter for the design of more efficient gene delivery vehicles. Copyright © 2015 Elsevier B.V. All rights reserved.

HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

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

Marchetti, Luca, E-mail: marchetti@cosbi.eu; Priami, Corrado, E-mail: priami@cosbi.eu; University of Trento, Department of Mathematics

This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance andmore » accuracy of HRSSA against other state of the art algorithms.« less

Efficient Flexible Organic/Inorganic Hybrid Perovskite Light-Emitting Diodes Based on Graphene Anode.

PubMed

Seo, Hong-Kyu; Kim, Hobeom; Lee, Jaeho; Park, Min-Ho; Jeong, Su-Hun; Kim, Young-Hoon; Kwon, Sung-Joo; Han, Tae-Hee; Yoo, Seunghyup; Lee, Tae-Woo

2017-03-01

Highly efficient organic/inorganic hybrid perovskite light-emitting diodes (PeLEDs) based on graphene anode are developed for the first time. Chemically inert graphene avoids quenching of excitons by diffused metal atom species from indium tin oxide. The flexible PeLEDs with graphene anode on plastic substrate show good bending stability; they provide an alternative and reliable flexible electrode for highly efficient flexible PeLEDs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Novel Interfacing Technique for Distributed Hybrid Simulations Combining EMT and Transient Stability Models

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

Shu, Dewu; Xie, Xiaorong; Jiang, Qirong

With steady increase of power electronic devices and nonlinear dynamic loads in large scale AC/DC systems, the traditional hybrid simulation method, which incorporates these components into a single EMT subsystem and hence causes great difficulty for network partitioning and significant deterioration in simulation efficiency. To resolve these issues, a novel distributed hybrid simulation method is proposed in this paper. The key to realize this method is a distinct interfacing technique, which includes: i) a new approach based on the two-level Schur complement to update the interfaces by taking full consideration of the couplings between different EMT subsystems; and ii) amore » combined interaction protocol to further improve the efficiency while guaranteeing the simulation accuracy. The advantages of the proposed method in terms of both efficiency and accuracy have been verified by using it for the simulation study of an AC/DC hybrid system including a two-terminal VSC-HVDC and nonlinear dynamic loads.« less

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

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

Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn

2015-03-28

The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much lessmore » computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.« less

Potential Evaluation of Solar Heat Assisted Desiccant Hybrid Air Conditioning System

NASA Astrophysics Data System (ADS)

Tran, Thien Nha; Hamamoto, Yoshinori; Akisawa, Atsushi; Kashiwagi, Takao

The solar thermal driven desiccant dehumidification-absorption cooling hybrid system has superior advantage in hot-humid climate regions. The reasonable air processing of desiccant hybrid air conditioning system and the utility of clean and free energy make the system environment friendly and energy efficient. The study investigates the performance of the desiccant dehumidification air conditioning systems with solar thermal assistant. The investigation is performed for three cases which are combinations of solar thermal and absorption cooling systems with different heat supply temperature levels. Two solar thermal systems are used in the study: the flat plate collector (FPC) and the vacuum tube with compound parabolic concentrator (CPC). The single-effect and high energy efficient double-, triple-effect LiBr-water absorption cooling cycles are considered for cooling systems. COP of desiccant hybrid air conditioning systems are determined. The evaluation of these systems is subsequently performed. The single effect absorption cooling cycle combined with the flat plate collector solar system is found to be the most energy efficient air conditioning system.

An on-chip polarization splitter based on the radiation loss in the bending hybrid plasmonic waveguide structure

NASA Astrophysics Data System (ADS)

Sun, Chengwei; Rong, Kexiu; Gan, Fengyuan; Chu, Saisai; Gong, Qihuang; Chen, Jianjun

2017-09-01

Polarization beam splitters (PBSs) are one of the key components in the integrated photonic circuits. To increase the integration density, various complex hybrid plasmonic structures have been numerically designed to shrink the footprints of the PBSs. Here, to decrease the complexity of the small hybrid structures and the difficulty of the hybrid micro-nano fabrications, the radiation losses are utilized to experimentally demonstrate an ultra-small, broadband, and efficient PBS in a simple bending hybrid plasmonic waveguide structure. The hybrid plasmonic waveguide comprising a dielectric strip on the metal surface supports both the transverse-magnetic (TM) and transverse-electric (TE) waveguide modes. Because of the different field confinements, the TE waveguide mode has larger radiation loss than the TM waveguide mode in the bending hybrid strip waveguide. Based on the different radiation losses, the two incident waveguide modes of orthogonal polarization states are efficiently split in the proposed structure with a footprint of only about 2.2 × 2.2 μm2 on chips. Since there is no resonance or interference in the splitting process, the operation bandwidth is as broad as Δλ = 70 nm. Moreover, the utilization of the strongly confined waveguide modes instead of the bulk free-space light (with the spot size of at least a few wavelengths) as the incident source considerably increases the coupling efficiency, resulting in a low insertion loss of <3 dB.

Discovery radiomics via evolutionary deep radiomic sequencer discovery for pathologically proven lung cancer detection.

PubMed

Shafiee, Mohammad Javad; Chung, Audrey G; Khalvati, Farzad; Haider, Masoom A; Wong, Alexander

2017-10-01

While lung cancer is the second most diagnosed form of cancer in men and women, a sufficiently early diagnosis can be pivotal in patient survival rates. Imaging-based, or radiomics-driven, detection methods have been developed to aid diagnosticians, but largely rely on hand-crafted features that may not fully encapsulate the differences between cancerous and healthy tissue. Recently, the concept of discovery radiomics was introduced, where custom abstract features are discovered from readily available imaging data. We propose an evolutionary deep radiomic sequencer discovery approach based on evolutionary deep intelligence. Motivated by patient privacy concerns and the idea of operational artificial intelligence, the evolutionary deep radiomic sequencer discovery approach organically evolves increasingly more efficient deep radiomic sequencers that produce significantly more compact yet similarly descriptive radiomic sequences over multiple generations. As a result, this framework improves operational efficiency and enables diagnosis to be run locally at the radiologist's computer while maintaining detection accuracy. We evaluated the evolved deep radiomic sequencer (EDRS) discovered via the proposed evolutionary deep radiomic sequencer discovery framework against state-of-the-art radiomics-driven and discovery radiomics methods using clinical lung CT data with pathologically proven diagnostic data from the LIDC-IDRI dataset. The EDRS shows improved sensitivity (93.42%), specificity (82.39%), and diagnostic accuracy (88.78%) relative to previous radiomics approaches.

Complex Ancestries of Isoprenoid Synthesis in Dinoflagellates.

PubMed

Bentlage, Bastian; Rogers, Travis S; Bachvaroff, Tsvetan R; Delwiche, Charles F

2016-01-01

Isoprenoid metabolism occupies a central position in the anabolic metabolism of all living cells. In plastid-bearing organisms, two pathways may be present for de novo isoprenoid synthesis, the cytosolic mevalonate pathway (MVA) and nuclear-encoded, plastid-targeted nonmevalonate pathway (DOXP). Using transcriptomic data we find that dinoflagellates apparently make exclusive use of the DOXP pathway. Using phylogenetic analyses of all DOXP genes we inferred the evolutionary origins of DOXP genes in dinoflagellates. Plastid replacements led to a DOXP pathway of multiple evolutionary origins. Dinoflagellates commonly referred to as dinotoms due to their relatively recent acquisition of a diatom plastid, express two completely redundant DOXP pathways. Dinoflagellates with a tertiary plastid of haptophyte origin, by contrast, express a hybrid pathway of dual evolutionary origin. Here, changes in the targeting motif of signal/transit peptide likely allow for targeting the new plastid by the proteins of core isoprenoid metabolism proteins. Parasitic dinoflagellates of the Amoebophyra species complex appear to have lost the DOXP pathway, suggesting that they may rely on their host for sterol synthesis. © 2015 The Author(s) Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.

PubMed

Abdullah, Afnizanfaizal; Deris, Safaai; Anwar, Sohail; Arjunan, Satya N V

2013-01-01

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.

An Evolutionary Firefly Algorithm for the Estimation of Nonlinear Biological Model Parameters

PubMed Central

Abdullah, Afnizanfaizal; Deris, Safaai; Anwar, Sohail; Arjunan, Satya N. V.

2013-01-01

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test. PMID:23469172

Perspective for Fibre-Hybrid Composites in Wind Energy Applications

PubMed Central

2017-01-01

Increasing the efficiency of wind turbines will be vital for the wind energy sector to continue growing. The drive for increased efficiency is pushing turbine manufacturers to shift from glass fibre composite blades towards carbon/glass fibre-hybrid composite blades. This shift brings significant challenges in terms of optimising the design and understanding the failure of these new blade materials. This review therefore surveys the literature on fibre-hybrid composites, with an emphasis on aspects that are relevant for turbine blade materials. The literature on tensile, flexural, compressive, and fatigue performance is critically assessed and areas for future research are identified. Numerical simulations of fibre-hybrid composites have reached a reasonable maturity for tensile failure, but significant progress is required for flexural, compressive, and fatigue failure. Fatigue failure of fibre-hybrid composites in particular, requires more careful attention from both a modelling and experimental point of view. PMID:29117126

0D-2D and 1D-2D Semiconductor Hybrids Composed of All Inorganic Perovskite Nanocrystals and Single-Layer Graphene with Improved Light Harvesting

DOE PAGES

Chen, Jia-Shiang; Doane, Tennyson L.; Li, Mingxing; ...

2017-12-27

In this study, inorganic cesium lead iodide (CsPbI 3) perovskite nanoparticles (PNPs) and perovskite nanowires (PNWs) with single-layer graphene (SLG) are combined to obtain 0D–2D PNP–SLG and 1D–2D PNW–SLG hybrids with improved light harvesting. Time-resolved single-nanostructure photoluminescence studies of PNPs, PNWs, and related hybrids reveal (i) quasi-two-state photoluminescence blinking in PNPs, (ii) highly polarized photoluminescence emitted by PNWs and (iii) efficient interfacial electron transfer between perovskite nanostructures and SLG in both PNP–SLG and PNW–SLG hybrids. Thus, doping of poorly absorbing, highly conductive SLG with perovskite nanocrystals and nanowires provides a simple, yet efficient path to obtain hybrids with increased light-harvestingmore » properties for potential utilization in the next-generation photodetectors and photovoltaic devices, including polarization sensitive photodetectors.« less

0D-2D and 1D-2D Semiconductor Hybrids Composed of All Inorganic Perovskite Nanocrystals and Single-Layer Graphene with Improved Light Harvesting

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

Chen, Jia-Shiang; Doane, Tennyson L.; Li, Mingxing

In this study, inorganic cesium lead iodide (CsPbI 3) perovskite nanoparticles (PNPs) and perovskite nanowires (PNWs) with single-layer graphene (SLG) are combined to obtain 0D–2D PNP–SLG and 1D–2D PNW–SLG hybrids with improved light harvesting. Time-resolved single-nanostructure photoluminescence studies of PNPs, PNWs, and related hybrids reveal (i) quasi-two-state photoluminescence blinking in PNPs, (ii) highly polarized photoluminescence emitted by PNWs and (iii) efficient interfacial electron transfer between perovskite nanostructures and SLG in both PNP–SLG and PNW–SLG hybrids. Thus, doping of poorly absorbing, highly conductive SLG with perovskite nanocrystals and nanowires provides a simple, yet efficient path to obtain hybrids with increased light-harvestingmore » properties for potential utilization in the next-generation photodetectors and photovoltaic devices, including polarization sensitive photodetectors.« less

Hybrid daylight/light-emitting diode illumination system for indoor lighting.

PubMed

Ge, Aiming; Qiu, Peng; Cai, Jinlin; Wang, Wei; Wang, Junwei

2014-03-20

A hybrid illumination method using both daylight and light-emitting diodes (LEDs) for indoor lighting is presented in this study. The daylight can be introduced into the indoor space by a panel-integration system. The daylight part and LEDs are combined within a specific luminaire that can provide uniform illumination. The LEDs can be turned on and dimmed through closed-loop control when the daylight illuminance is inadequate. We simulated the illumination and calculated the indoor lighting efficiency of our hybrid daylight and LED lighting system, and compared this with that of LED and fluorescent lighting systems. Simulation results show that the efficiency of the hybrid daylight/LED illumination method is better than that of LED and traditional lighting systems, under the same lighting conditions and lighting time; the method has hybrid lighting average energy savings of T5 66.28%, and that of the LEDs is 41.62%.

Perspective for Fibre-Hybrid Composites in Wind Energy Applications.

PubMed

Swolfs, Yentl

2017-11-08

Increasing the efficiency of wind turbines will be vital for the wind energy sector to continue growing. The drive for increased efficiency is pushing turbine manufacturers to shift from glass fibre composite blades towards carbon/glass fibre-hybrid composite blades. This shift brings significant challenges in terms of optimising the design and understanding the failure of these new blade materials. This review therefore surveys the literature on fibre-hybrid composites, with an emphasis on aspects that are relevant for turbine blade materials. The literature on tensile, flexural, compressive, and fatigue performance is critically assessed and areas for future research are identified. Numerical simulations of fibre-hybrid composites have reached a reasonable maturity for tensile failure, but significant progress is required for flexural, compressive, and fatigue failure. Fatigue failure of fibre-hybrid composites in particular, requires more careful attention from both a modelling and experimental point of view.

Behavior differentiation between wild Japanese quail, domestic quail, and their first filial generation.

PubMed

Chang, G B; Liu, X P; Chang, H; Chen, G H; Zhao, W M; Ji, D J; Chen, R; Qin, Y R; Shi, X K; Hu, G S

2009-06-01

The number of wild quail has dramatically reduced in China and reached a state of endangerment with the deterioration of the environment in recent years. In this study, we examined the ecological behaviors of quails in the cage to determine the differentiation level between wild Japanese quail and domestic quail, to detect the relationship between quail behavior and evolutionary differentiation and to analyze the possibility of restoring effective size of wild population. With the on-the-spot observations and measurements, the behaviors of 3 categories of quail, namely wild Japanese quail from the Weishan Lake area in China, domestic quail, and their first filial generation (F(1)) were studied. Domestic quail differed from wild Japanese quail in morphological pattern and ecological behaviors, including some indexes of figure type and egg, vocalization, aggression and fighting, and mating, but wild Japanese quail and domestic quail could succeed in mating and reproducing fertile hybrid offspring. There were significant differences between domestic quail and wild Japanese quail in reproductive traits, involved mating times, fertility rate, hatching rate, and hatching rate of fertilized eggs (P < 0.05). The first filial generation presented significant difference from the wild Japanese quail in vocalization, aggression and fighting, mating, hatching rate, hatching rate of fertilized eggs, and some egg indexes (P < 0.05) and significantly differ from the domestic quail in vocalization, hatching rate, and hatching rate of fertilized eggs (P < 0.05). Evolutionary differentiation between wild quail and domestic quail was still at a relatively low level because no reproductive isolation existed. The advantages of the F(1) hybrids in reproductive capacity, fertilization, and hatching recommend that releasing hybrids instead of domestic quails to the wild would be a more effective way to restore the effective size of wild quail population if necessary.

Whole Mitochondrial Genomic and Y-Chromosomal Phylogenies of Burmese Long-Tailed Macaque (Macaca fascicularis aurea) Suggest Ancient Hybridization between fascicularis and sinica Species Groups.

PubMed

Matsudaira, Kazunari; Hamada, Yuzuru; Bunlungsup, Srichan; Ishida, Takafumi; San, Aye Mi; Malaivijitnond, Suchinda

2018-05-11

Macaca fascicularis aurea (Burmese long-tailed macaque) is 1 of the 10 subspecies of Macaca fascicularis. Despite having few morphological differences from other subspecies, a recent phylogeographic study showed that M. f. aurea is clearly distinct genetically from Macaca fascicularis fascicularis (common long-tailed macaque) and suggests that M. f. aurea experienced a disparate evolutionary pathway versus other subspecies. To construct a detailed evolutionary history of M. f. aurea and its relationships with other macaque species, we performed phylogenetic analyses and divergence time estimation of whole mitochondrial genomes (2 M. f. aurea, 8 M. f. fascicularis, and 16 animals of 12 macaque species) and 2871 bp of the Y chromosome (1 M. f. aurea, 2 M. f. fascicularis, and 5 animals of 5 macaque species) and haplotype network analysis of 758 bp of the Y chromosome (1 M. f. aurea, 2 M. f. fascicularis, and 21 animals of 19 macaque species). Whereas the Y chromosome of M. f. aurea clustered with those of the fascicularis species group in the phylogenetic and haplotype network analyses, its mtDNA clustered within the clade of the sinica species group. Based on this phylogenetic incongruence and the estimated divergence times, we propose that proto-M. f. aurea underwent hybridization with a population of the sinica species group between 2.5 and 0.95 MYA after divergence from the common ancestor of M. fascicularis. Hybridization and introgression might have been central in the evolution of M. f. aurea, similar to what occurred in the evolution of other macaque species and subspecies.

Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander.

PubMed

Pereira, Ricardo J; Martínez-Solano, Iñigo; Buckley, David

2016-04-01

Ecological models predict that, in the face of climate change, taxa occupying steep altitudinal gradients will shift their distributions, leading to the contraction or extinction of the high-elevation (cold-adapted) taxa. However, hybridization between ecomorphologically divergent taxa commonly occurs in nature and may lead to alternative evolutionary outcomes, such as genetic merger or gene flow at specific genes. We evaluate this hypothesis by studying patterns of divergence and gene flow across three replicate contact zones between high- and low-elevation ecomorphs of the fire salamander (Salamandra salamandra) that have experienced altitudinal range shifts over the current postglacial period. Strong population structure with high genetic divergence in mitochondrial DNA suggests that vicariant evolution has occurred over several glacial-interglacial cycles and that it has led to cryptic differentiation within ecomorphs. In current parapatric boundaries, we do not find evidence for local extinction and replacement upon postglacial expansion. Instead, parapatric taxa recurrently show discordance between mitochondrial and nuclear markers, suggesting nuclear-mediated gene flow across contact zones. Isolation with migration models support this hypothesis by showing significant gene flow across all five parapatric boundaries. Together, our results suggest that, while some genomic regions, such as the mitochondria, may follow morphologic species traits and retreat to isolated mountain tops, other genomic regions, such as nuclear markers, may flow across parapatric boundaries, sometimes leading to a complete genetic merger. We show that despite high ecologic and morphologic divergence over prolonged periods of time, hybridization allows for evolutionary outcomes alternative to extinction and replacement of taxa in response to climate change. © 2016 John Wiley & Sons Ltd.

Specialized hybrid learners resolve Rogers' paradox about the adaptive value of social learning.

PubMed

Kharratzadeh, Milad; Montrey, Marcel; Metz, Alex; Shultz, Thomas R

2017-02-07

Culture is considered an evolutionary adaptation that enhances reproductive fitness. A common explanation is that social learning, the learning mechanism underlying cultural transmission, enhances mean fitness by avoiding the costs of individual learning. This explanation was famously contradicted by Rogers (1988), who used a simple mathematical model to show that cheap social learning can invade a population without raising its mean fitness. He concluded that some crucial factor remained unaccounted for, which would reverse this surprising result. Here we extend this model to include a more complex environment and limited resources, where individuals cannot reliably learn everything about the environment on their own. Under such conditions, cheap social learning evolves and enhances mean fitness, via hybrid learners capable of specializing their individual learning. We then show that while spatial or social constraints hinder the evolution of hybrid learners, a novel social learning strategy, complementary copying, can mitigate these effects. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimal design of structures for earthquake loads by a hybrid RBF-BPSO method

NASA Astrophysics Data System (ADS)

Salajegheh, Eysa; Gholizadeh, Saeed; Khatibinia, Mohsen

2008-03-01

The optimal seismic design of structures requires that time history analyses (THA) be carried out repeatedly. This makes the optimal design process inefficient, in particular, if an evolutionary algorithm is used. To reduce the overall time required for structural optimization, two artificial intelligence strategies are employed. In the first strategy, radial basis function (RBF) neural networks are used to predict the time history responses of structures in the optimization flow. In the second strategy, a binary particle swarm optimization (BPSO) is used to find the optimum design. Combining the RBF and BPSO, a hybrid RBF-BPSO optimization method is proposed in this paper, which achieves fast optimization with high computational performance. Two examples are presented and compared to determine the optimal weight of structures under earthquake loadings using both exact and approximate analyses. The numerical results demonstrate the computational advantages and effectiveness of the proposed hybrid RBF-BPSO optimization method for the seismic design of structures.

Hybrid General Pattern Search and Simulated Annealing for Industrail Production Planning Problems

NASA Astrophysics Data System (ADS)

Vasant, P.; Barsoum, N.

2010-06-01

In this paper, the hybridization of GPS (General Pattern Search) method and SA (Simulated Annealing) incorporated in the optimization process in order to look for the global optimal solution for the fitness function and decision variables as well as minimum computational CPU time. The real strength of SA approach been tested in this case study problem of industrial production planning. This is due to the great advantage of SA for being easily escaping from trapped in local minima by accepting up-hill move through a probabilistic procedure in the final stages of optimization process. Vasant [1] in his Ph. D thesis has provided 16 different techniques of heuristic and meta-heuristic in solving industrial production problems with non-linear cubic objective functions, eight decision variables and 29 constraints. In this paper, fuzzy technological problems have been solved using hybrid techniques of general pattern search and simulated annealing. The simulated and computational results are compared to other various evolutionary techniques.

Design and implementation of a hybrid sub-band acoustic echo canceller (AEC)

NASA Astrophysics Data System (ADS)

Bai, Mingsian R.; Yang, Cheng-Ken; Hur, Ker-Nan

2009-04-01

An efficient method is presented for implementing an acoustic echo canceller (AEC) that makes use of hybrid sub-band approach. The hybrid system is comprised of a fixed processor and an adaptive filter in each sub-band. The AEC aims at reducing the echo resulting from the acoustic feedback in loudspeaker-enclosure-microphone (LEM) systems such as teleconferencing and hands-free systems. In order to cancel the acoustical echo efficiently, various processing architectures including fixed filters, hybrid processors, and sub-band structure are investigated. A double-talk detector is incorporated into the proposed AEC to prevent the adaptive filter from diverging in double-talk situations. A de-correlation filter is also used alongside sub-band processing in order to enhance the performance and efficiency of AEC. All algorithms are implemented and verified on the platform of a fixed-point digital signal processor (DSP). The AECs are evaluated in terms of cancellation performance and computation complexity. In addition, listening tests are conducted to assess the subjective performance of the AECs. From the results, the proposed hybrid sub-band AEC was found to be the most effective among all methods in terms of echo reduction and timbral quality.

Hybrid tandem quantum dot/organic photovoltaic cells with complementary near infrared absorption

NASA Astrophysics Data System (ADS)

Kim, Taesoo; Palmiano, Elenita; Liang, Ru-Ze; Hu, Hanlin; Murali, Banavoth; Kirmani, Ahmad R.; Firdaus, Yuliar; Gao, Yangqin; Sheikh, Arif; Yuan, Mingjian; Mohammed, Omar F.; Hoogland, Sjoerd; Beaujuge, Pierre M.; Sargent, Edward H.; Amassian, Aram

2017-05-01

Monolithically integrated hybrid tandem solar cells that effectively combine solution-processed colloidal quantum dot (CQD) and organic bulk heterojunction subcells to achieve tandem performance that surpasses the individual subcell efficiencies have not been demonstrated to date. In this work, we demonstrate hybrid tandem cells with a low bandgap PbS CQD subcell harvesting the visible and near-infrared photons and a polymer:fullerene—poly (diketopyrrolopyrrole-terthiophene) (PDPP3T):[6,6]-phenyl-C60-butyric acid methyl ester (PC61BM)—top cell absorbing effectively the red and near-infrared photons of the solar spectrum in a complementary fashion. The two subcells are connected in series via an interconnecting layer (ICL) composed of a metal oxide layer, a conjugated polyelectrolyte, and an ultrathin layer of Au. The ultrathin layer of Au forms nano-islands in the ICL, reducing the series resistance, increasing the shunt resistance, and enhancing the device fill-factor. The hybrid tandems reach a power conversion efficiency (PCE) of 7.9%, significantly higher than the PCE of the corresponding individual single cells, representing one of the highest efficiencies reported to date for hybrid tandem solar cells based on CQD and polymer subcells.

High efficiency silicon nanowire/organic hybrid solar cells with two-step surface treatment.

PubMed

Wang, Jianxiong; Wang, Hao; Prakoso, Ari Bimo; Togonal, Alienor Svietlana; Hong, Lei; Jiang, Changyun; Rusli

2015-03-14

A simple two-step surface treatment process is proposed to boost the efficiency of silicon nanowire/PEDOT:PSS hybrid solar cells. The Si nanowires (SiNWs) are first subjected to a low temperature ozone treatment to form a surface sacrificial oxide, followed by a HF etching process to partially remove the oxide. TEM investigation demonstrates that a clean SiNW surface is achieved after the treatment, in contrast to untreated SiNWs that have Ag nanoparticles left on the surface from the metal-catalyzed etching process that is used to form the SiNWs. The cleaner SiNW surface achieved and the thin layer of residual SiO2 on the SiNWs have been found to improve the performance of the hybrid solar cells. Overall, the surface recombination of the hybrid SiNW solar cells is greatly suppressed, resulting in a remarkably improved open circuit voltage of 0.58 V. The power conversion efficiency has also increased from about 10% to 12.4%. The two-step surface treatment method is promising in enhancing the photovoltaic performance of the hybrid silicon solar cells, and can also be applied to other silicon nanostructure based solar cells.

FLIM and FCS detection in laser-scanning microscopes: increased efficiency by GaAsP hybrid detectors.

PubMed

Becker, W; Su, B; Holub, O; Weisshart, K

2011-09-01

Photon counting detectors currently used in fluorescence lifetime microscopy have a number of deficiencies that result in less-than-ideal signal-to-noise ratio of the lifetimes obtained: either the quantum efficiency is unsatisfactory or the active area is too small, and afterpulsing or tails in the temporal response contribute to overall timing inaccuracy. We have therefore developed a new FLIM detector based on a GaAsP hybrid photomultiplier. Compared with conventional PMTs and SPADs, GaAsP hybrid detectors have a number of advantages: The detection quantum efficiency reaches or surpasses the efficiency of fast SPADs, and the active area is on the order of 5 mm², compared with 2.5 10⁻³ mm² for a SPAD. The TCSPC response is clean, without the bumps and the diffusion tails typical for PMTs and SPADs. Most important, the hybrid detector is intrinsically free of afterpulsing. FLIM results are therefore free of signal-dependent background, and FCS curves are free of the known afterpulsing peak. We demonstrate the performance of the new detector for multiphoton NDD FLIM and for FCS. Copyright © 2010 Wiley-Liss, Inc.

Numerical solution of the Saint-Venant equations by an efficient hybrid finite-volume/finite-difference method

NASA Astrophysics Data System (ADS)

Lai, Wencong; Khan, Abdul A.

2018-04-01

A computationally efficient hybrid finite-volume/finite-difference method is proposed for the numerical solution of Saint-Venant equations in one-dimensional open channel flows. The method adopts a mass-conservative finite volume discretization for the continuity equation and a semi-implicit finite difference discretization for the dynamic-wave momentum equation. The spatial discretization of the convective flux term in the momentum equation employs an upwind scheme and the water-surface gradient term is discretized using three different schemes. The performance of the numerical method is investigated in terms of efficiency and accuracy using various examples, including steady flow over a bump, dam-break flow over wet and dry downstream channels, wetting and drying in a parabolic bowl, and dam-break floods in laboratory physical models. Numerical solutions from the hybrid method are compared with solutions from a finite volume method along with analytic solutions or experimental measurements. Comparisons demonstrates that the hybrid method is efficient, accurate, and robust in modeling various flow scenarios, including subcritical, supercritical, and transcritical flows. In this method, the QUICK scheme for the surface slope discretization is more accurate and less diffusive than the center difference and the weighted average schemes.

Recent advances of flexible hybrid perovskite solar cells

NASA Astrophysics Data System (ADS)

Shin, Dong Hee; Heo, Jin Hyuck; Im, Sang Hyuk

2017-11-01

Recently, hybrid perovskite solar cells have attracted great interest because they can be fabricated to low cost, flexible, and highly efficient solar cells. Here, we introduced recent advances of flexible hybrid perovskite solar cells. We introduced research background of flexible perovskite solar cells in introduction part. Then we composed the main body to i) structure and properties of hybrid perovskite solar cells, ii) why flexible hybrid perovskite solar cells are important?, iii) transparent conducting oxide (TCO) based flexible hybrid perovskite solar cells, and iv) TCO-free transparent conducting electrode (TCE) based flexible hybrid perovskite solar cells. Finally, we summarized research outlook of flexible hybrid perovskite solar cells.

Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

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

Nakhleh, Luay

I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbialmore » genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.« less

On the usefulness of gradient information in multi-objective deformable image registration using a B-spline-based dual-dynamic transformation model: comparison of three optimization algorithms

NASA Astrophysics Data System (ADS)

Pirpinia, Kleopatra; Bosman, Peter A. N.; Sonke, Jan-Jakob; van Herk, Marcel; Alderliesten, Tanja

2015-03-01

The use of gradient information is well-known to be highly useful in single-objective optimization-based image registration methods. However, its usefulness has not yet been investigated for deformable image registration from a multi-objective optimization perspective. To this end, within a previously introduced multi-objective optimization framework, we use a smooth B-spline-based dual-dynamic transformation model that allows us to derive gradient information analytically, while still being able to account for large deformations. Within the multi-objective framework, we previously employed a powerful evolutionary algorithm (EA) that computes and advances multiple outcomes at once, resulting in a set of solutions (a so-called Pareto front) that represents efficient trade-offs between the objectives. With the addition of the B-spline-based transformation model, we studied the usefulness of gradient information in multiobjective deformable image registration using three different optimization algorithms: the (gradient-less) EA, a gradientonly algorithm, and a hybridization of these two. We evaluated the algorithms to register highly deformed images: 2D MRI slices of the breast in prone and supine positions. Results demonstrate that gradient-based multi-objective optimization significantly speeds up optimization in the initial stages of optimization. However, allowing sufficient computational resources, better results could still be obtained with the EA. Ultimately, the hybrid EA found the best overall approximation of the optimal Pareto front, further indicating that adding gradient-based optimization for multiobjective optimization-based deformable image registration can indeed be beneficial

Algorithmic Mechanism Design of Evolutionary Computation.

PubMed

Pei, Yan

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.

Algorithmic Mechanism Design of Evolutionary Computation

PubMed Central

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

Evaluation of Generation Alternation Models in Evolutionary Robotics

NASA Astrophysics Data System (ADS)

Oiso, Masashi; Matsumura, Yoshiyuki; Yasuda, Toshiyuki; Ohkura, Kazuhiro

For efficient implementation of Evolutionary Algorithms (EA) to a desktop grid computing environment, we propose a new generation alternation model called Grid-Oriented-Deletion (GOD) based on comparison with the conventional techniques. In previous research, generation alternation models are generally evaluated by using test functions. However, their exploration performance on the real problems such as Evolutionary Robotics (ER) has not been made very clear yet. Therefore we investigate the relationship between the exploration performance of EA on an ER problem and its generation alternation model. We applied four generation alternation models to the Evolutionary Multi-Robotics (EMR), which is the package-pushing problem to investigate their exploration performance. The results show that GOD is more effective than the other conventional models.

Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve.

PubMed

Piotrowski, Jeff S; Nagarajan, Saisubramanian; Kroll, Evgueny; Stanbery, Alison; Chiotti, Kami E; Kruckeberg, Arthur L; Dunn, Barbara; Sherlock, Gavin; Rosenzweig, Frank

2012-04-02

Interspecific hybridization occurs in every eukaryotic kingdom. While hybrid progeny are frequently at a selective disadvantage, in some instances their increased genome size and complexity may result in greater stress resistance than their ancestors, which can be adaptively advantageous at the edges of their ancestors' ranges. While this phenomenon has been repeatedly documented in the field, the response of hybrid populations to long-term selection has not often been explored in the lab. To fill this knowledge gap we crossed the two most distantly related members of the Saccharomyces sensu stricto group, S. cerevisiae and S. uvarum, and established a mixed population of homoploid and aneuploid hybrids to study how different types of selection impact hybrid genome structure. As temperature was raised incrementally from 31°C to 46.5°C over 500 generations of continuous culture, selection favored loss of the S. uvarum genome, although the kinetics of genome loss differed among independent replicates. Temperature-selected isolates exhibited greater inherent and induced thermal tolerance than parental species and founding hybrids, and also exhibited ethanol resistance. In contrast, as exogenous ethanol was increased from 0% to 14% over 500 generations of continuous culture, selection favored euploid S. cerevisiae x S. uvarum hybrids. Ethanol-selected isolates were more ethanol tolerant than S. uvarum and one of the founding hybrids, but did not exhibit resistance to temperature stress. Relative to parental and founding hybrids, temperature-selected strains showed heritable differences in cell wall structure in the forms of increased resistance to zymolyase digestion and Micafungin, which targets cell wall biosynthesis. This is the first study to show experimentally that the genomic fate of newly-formed interspecific hybrids depends on the type of selection they encounter during the course of evolution, underscoring the importance of the ecological theatre in determining the outcome of the evolutionary play.

One-pot in situ redox synthesis of hexacyanoferrate/conductive polymer hybrids as lithium-ion battery cathodes.

PubMed

Wong, Min Hao; Zhang, Zixuan; Yang, Xianfeng; Chen, Xiaojun; Ying, Jackie Y

2015-09-14

An efficient and adaptable method is demonstrated for the synthesis of lithium hexacyanoferrate/conductive polymer hybrids for Li-ion battery cathodes. The hybrids were synthesized via a one-pot method, involving a redox-coupled reaction between pyrrole monomers and the Li3Fe(CN)6 precursor. The hybrids showed much better cyclability relative to reported Prussian Blue (PB) analogs.

FY 2007 Progress Report for Advanced Combustion Engine Technologies

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

None, None

2007-12-01

Advanced combustion engines have great potential for achieving dramatic energy efficiency improvements in light-duty vehicle applications, where it is suited to both conventional and hybrid- electric powertrain configurations. Light-duty vehicles with advanced combustion engines can compete directly with gasoline engine hybrid vehicles in terms of fuel economy and consumer-friendly driving characteristics; also, they are projected to have energy efficiencies that are competitive with hydrogen fuel cell vehicles when used in hybrid applications.Advanced engine technologies being researched and developed by the Advanced Combustion Engine R&D Sub-Program will also allow the use of hydrogen as a fuel in ICEs and will providemore » an energy-efficient interim hydrogen-based powertrain technology during the transition to hydrogen/fuelcell-powered transportation vehicles.« less

Investigation of Stability of Photosynthetic Reaction Center and Quantum Dot Hybrid Films.

PubMed

Lukashev, E P; Knox, P P; Oleinikov, I P; Seifullina, N Kh; Grishanova, N P

2016-01-01

The efficiency of interaction (efficiency of energy transfer) between various quantum dots (QDs) and photosynthetic reaction centers (RCs) from the purple bacterium Rhodobacter sphaeroides and conditions of long-term stability of functioning of such hybrid complexes in film preparations were investigated. It was found that dry films containing RCs and QDs and maintained at atmospheric humidity are capable to keep their functional activity for at least some months as judging by results of measurement of their spectral characteristics, efficiency of energy transfer from QDs to RCs, and RC electron-transport activity. Addition of trehalose to the films giving them still greater stability is especially expressed for films maintained at low humidity. These stable hybrid film structures are promising for further biotechnological studies for developing new phototransformation devices.

Enabling efficient vertical takeoff/landing and forward flight of unmanned aerial vehicles: Design and control of tandem wing-tip mounted rotor mechanisms

NASA Astrophysics Data System (ADS)

Mancuso, Peter Timothy

Fixed-wing unmanned aerial vehicles (UAVs) that offer vertical takeoff and landing (VTOL) and forward flight capability suffer from sub-par performance in both flight modes. Achieving the next generation of efficient hybrid aircraft requires innovations in: (i) power management, (ii) efficient structures, and (iii) control methodologies. Existing hybrid UAVs generally utilize one of three transitioning mechanisms: an external power mechanism to tilt the rotor-propulsion pod, separate propulsion units and rotors during hover and forward flight, or tilt body craft (smaller scale). Thus, hybrid concepts require more energy compared to dedicated fixed-wing or rotorcraft UAVs. Moreover, design trade-offs to reinforce the wing structure (typically to accommodate the propulsion systems and enable hover, i.e. tilt-rotor concepts) adversely impacts the aerodynamics, controllability and efficiency of the aircraft in both hover and forward flight modes. The goal of this research is to develop more efficient VTOL/ hover and forward flight UAVs. In doing so, the transition sequence, transition mechanism, and actuator performance are heavily considered. A design and control methodology was implemented to address these issues through a series of computer simulations and prototype benchtop tests to verify the proposed solution. Finally, preliminary field testing with a first-generation prototype was conducted. The methods used in this research offer guidelines and a new dual-arm rotor UAV concept to designing more efficient hybrid UAVs in both hover and forward flight.

Advanced EMT and Phasor-Domain Hybrid Simulation with Simulation Mode Switching Capability for Transmission and Distribution Systems

DOE PAGES

Huang, Qiuhua; Vittal, Vijay

2018-05-09

Conventional electromagnetic transient (EMT) and phasor-domain hybrid simulation approaches presently exist for trans-mission system level studies. Their simulation efficiency is generally constrained by the EMT simulation. With an increasing number of distributed energy resources and non-conventional loads being installed in distribution systems, it is imperative to extend the hybrid simulation application to include distribution systems and integrated transmission and distribution systems. Meanwhile, it is equally important to improve the simulation efficiency as the modeling scope and complexity of the detailed system in the EMT simulation increases. To meet both requirements, this paper introduces an advanced EMT and phasor-domain hybrid simulationmore » approach. This approach has two main features: 1) a comprehensive phasor-domain modeling framework which supports positive-sequence, three-sequence, three-phase and mixed three-sequence/three-phase representations and 2) a robust and flexible simulation mode switching scheme. The developed scheme enables simulation switching from hybrid simulation mode back to pure phasor-domain dynamic simulation mode to achieve significantly improved simulation efficiency. The proposed method has been tested on integrated transmission and distribution systems. In conclusion, the results show that with the developed simulation switching feature, the total computational time is significantly reduced compared to running the hybrid simulation for the whole simulation period, while maintaining good simulation accuracy.« less

Building America Case Study: Assessment of a Hybrid Retrofit Gas Water Heater

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

This project completed a modeling evaluation of a hybrid gas water heater that combines a reduced capacity tankless unit with a downsized storage tank. This product would meet a significant market need by providing a higher efficiency gas water heater solution for retrofit applications while maintaining compatibility with the half-inch gas lines and standard B vents found in most homes. The TRNSYS simulation tool was used to model a base case 0.60 EF atmospheric gas storage water, a 0.82 EF non-condensing gas tankless water heater, an existing (high capacity) hybrid unit on the market, and an alternative hybrid unit withmore » lower storage volume and reduced gas input requirements. Simulations were completed under a 'peak day' sizing scenario with 183 gpd hot water loads in a Minnesota winter climate case. Full-year simulations were then completed in three climates (ranging from Phoenix to Minneapolis) for three hot water load scenarios (36, 57, and 96 gpd). Model projections indicate that the alternative hybrid offers an average 4.5% efficiency improvement relative to the 0.60 EF gas storage unit across all scenarios modeled. The alternative hybrid water heater evaluated does show promise, but the current low cost of natural gas across much of the country and the relatively small incremental efficiency improvement poses challenges in initially building a market demand for the product.« less

Strategies for Energy Efficient Resource Management of Hybrid Programming Models

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

Li, Dong; Supinski, Bronis de; Schulz, Martin

2013-01-01

Many scientific applications are programmed using hybrid programming models that use both message-passing and shared-memory, due to the increasing prevalence of large-scale systems with multicore, multisocket nodes. Previous work has shown that energy efficiency can be improved using software-controlled execution schemes that consider both the programming model and the power-aware execution capabilities of the system. However, such approaches have focused on identifying optimal resource utilization for one programming model, either shared-memory or message-passing, in isolation. The potential solution space, thus the challenge, increases substantially when optimizing hybrid models since the possible resource configurations increase exponentially. Nonetheless, with the accelerating adoptionmore » of hybrid programming models, we increasingly need improved energy efficiency in hybrid parallel applications on large-scale systems. In this work, we present new software-controlled execution schemes that consider the effects of dynamic concurrency throttling (DCT) and dynamic voltage and frequency scaling (DVFS) in the context of hybrid programming models. Specifically, we present predictive models and novel algorithms based on statistical analysis that anticipate application power and time requirements under different concurrency and frequency configurations. We apply our models and methods to the NPB MZ benchmarks and selected applications from the ASC Sequoia codes. Overall, we achieve substantial energy savings (8.74% on average and up to 13.8%) with some performance gain (up to 7.5%) or negligible performance loss.« less

Advanced EMT and Phasor-Domain Hybrid Simulation with Simulation Mode Switching Capability for Transmission and Distribution Systems

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

Huang, Qiuhua; Vittal, Vijay

Conventional electromagnetic transient (EMT) and phasor-domain hybrid simulation approaches presently exist for trans-mission system level studies. Their simulation efficiency is generally constrained by the EMT simulation. With an increasing number of distributed energy resources and non-conventional loads being installed in distribution systems, it is imperative to extend the hybrid simulation application to include distribution systems and integrated transmission and distribution systems. Meanwhile, it is equally important to improve the simulation efficiency as the modeling scope and complexity of the detailed system in the EMT simulation increases. To meet both requirements, this paper introduces an advanced EMT and phasor-domain hybrid simulationmore » approach. This approach has two main features: 1) a comprehensive phasor-domain modeling framework which supports positive-sequence, three-sequence, three-phase and mixed three-sequence/three-phase representations and 2) a robust and flexible simulation mode switching scheme. The developed scheme enables simulation switching from hybrid simulation mode back to pure phasor-domain dynamic simulation mode to achieve significantly improved simulation efficiency. The proposed method has been tested on integrated transmission and distribution systems. In conclusion, the results show that with the developed simulation switching feature, the total computational time is significantly reduced compared to running the hybrid simulation for the whole simulation period, while maintaining good simulation accuracy.« less

Assessment of a Hybrid Retrofit Gas Water Heater

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

Hoeschele, Marc; Weitzel, Elizabeth; Backman, Christine

2017-02-28

This project completed a modeling evaluation of a hybrid gas water heater that combines a reduced capacity tankless unit with a downsized storage tank. This product would meet a significant market need by providing a higher efficiency gas water heater solution for retrofit applications while maintaining compatibility with the 1/2 inch gas lines and standard B vents found in most homes. The TRNSYS simulation tool was used to model a base case 0.60 EF atmospheric gas storage water, a 0.82 EF non-condensing gas tankless water heater, an existing (high capacity) hybrid unit on the market, and an alternative hybrid unitmore » with lower storage volume and reduced gas input requirements. Simulations were completed under a 'peak day' sizing scenario with 183 gpd hot water loads in a Minnesota winter climate case. Full-year simulations were then completed in three climates (ranging from Phoenix to Minneapolis) for three hot water load scenarios (36, 57, and 96 gpd). Model projections indicate that the alternative hybrid offers an average 4.5% efficiency improvement relative to the 0.60 EF gas storage unit across all scenarios modeled. The alternative hybrid water heater evaluated does show promise, but the current low cost of natural gas across much of the country and the relatively small incremental efficiency improvement poses challenges in initially building a market demand for the product.« less

Three-dimensional Nitrogen-Doped Graphene Supported Molybdenum Disulfide Nanoparticles as an Advanced Catalyst for Hydrogen Evolution Reaction

PubMed Central

Dong, Haifeng; Liu, Conghui; Ye, Haitao; Hu, Linping; Fugetsu, Bunshi; Dai, Wenhao; Cao, Yu; Qi, Xueqiang; Lu, Huiting; Zhang, Xueji

2015-01-01

An efficient three-dimensional (3D) hybrid material of nitrogen-doped graphene sheets (N-RGO) supporting molybdenum disulfide (MoS2) nanoparticles with high-performance electrocatalytic activity for hydrogen evolution reaction (HER) is fabricated by using a facile hydrothermal route. Comprehensive microscopic and spectroscopic characterizations confirm the resulting hybrid material possesses a 3D crumpled few-layered graphene network structure decorated with MoS2 nanoparticles. Electrochemical characterization analysis reveals that the resulting hybrid material exhibits efficient electrocatalytic activity toward HER under acidic conditions with a low onset potential of 112 mV and a small Tafel slope of 44 mV per decade. The enhanced mechanism of electrocatalytic activity has been investigated in detail by controlling the elemental composition, electrical conductance and surface morphology of the 3D hybrid as well as Density Functional Theory (DFT) calculations. This demonstrates that the abundance of exposed active sulfur edge sites in the MoS2 and nitrogen active functional moieties in N-RGO are synergistically responsible for the catalytic activity, whilst the distinguished and coherent interface in MoS2/N-RGO facilitates the electron transfer during electrocatalysis. Our study gives insights into the physical/chemical mechanism of enhanced HER performance in MoS2/N-RGO hybrids and illustrates how to design and construct a 3D hybrid to maximize the catalytic efficiency. PMID:26639026

Hybrid systems based on gold nanostructures and porphyrins as promising photosensitizers for photodynamic therapy.

PubMed

Ferreira, Daniele C; Monteiro, Camila S; Chaves, Claudilene R; Sáfar, Gustavo A M; Moreira, Roberto L; Pinheiro, Maurício V B; Martins, Dayse C S; Ladeira, Luiz Orlando; Krambrock, Klaus

2017-02-01

Gold nanostructures of two different shapes (spheres and rods) were synthesized to form a colloidal hybrid system with 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin tosylate salt (H 2 TM4PyP(OTs) 4 ) (POR) for applications in photodynamic therapy (PDT) using light in the visible spectral range. Electron paramagnetic resonance (EPR) experiments in combination with spin trapping were used for the detection of reactive oxygen species (ROS) and evaluation of the efficiency of these novel hybrid systems as photosensitizers. It is shown that the hybrid system consisting of gold nanorods (AuNR) and porphyrin (POR) is by far more efficient than its isolated components. This enhanced efficiency is explained by a synergetic effect between the AuNR and the porphyrin, wherein a rapid energy transfer from the former to the latter produces a large amount of singlet oxygen followed by its conversion into hydroxyl radicals. The mechanism was investigated using different spin traps and different ROS inhibitors. On the other hand, spherical gold nanoparticles (AuNP) do not show this synergetic effect. The synergetic effect for gold nanorods/POR hybrid is attributed to a larger field enhancement close to the gold nanorod surface in addition to the electrostatic attraction between the components of the hybrid system. Copyright © 2016 Elsevier B.V. All rights reserved.

A sodium–aluminum hybrid battery

DOE PAGES

Sun, Xiao-Guang; Zhang, Zhizhen; Guan, Hong Yu; ...

2017-03-07

We present novel hybrid batteries that are fabricated using an aluminum anode, a sodium intercalation cathode Na 3V 2(PO 4) 3 (NVP), and a sodium/aluminum dual salt electrolyte based on NaAlCl 4 and an eutectic mixture of 1-ethyl-3-methylimidazolium chloride (EMImC) and aluminum chloride. Cyclic voltammograms indicate that increasing the molar concentration of AlCl 3 in the electrolyte is beneficial to high coulombic efficiency of aluminum deposition/stripping, which, unfortunately, results in lower coulombic efficiency of sodium extraction/insertion in the cathode. Therefore, EMImC–AlCl 3 with a molar ratio of 1–1.1 is used for battery evaluation. The hybrid battery with 1.0 M NaAlClmore » 4 exhibits a discharge voltage of 1.25 V and a cathodic capacity of 99 mA h g -1 at a current rate of C/10. In addition, the hybrid battery exhibits good rate performance and long-term cycling stability while maintaining a high coulombic efficiency of 98%. It is also demonstrated that increasing salt concentration can further enhance the cycling performance of the hybrid battery. X-ray diffraction analysis of the NVP electrodes under different conditions confirms that the main cathode reaction is indeed Na extraction/insertion. Based on all earth-abundant elements, the new Na–Al hybrid battery is very attractive for stationary and grid energy storage applications.« less

A sodium–aluminum hybrid battery

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

Sun, Xiao-Guang; Zhang, Zhizhen; Guan, Hong Yu

We present novel hybrid batteries that are fabricated using an aluminum anode, a sodium intercalation cathode Na 3V 2(PO 4) 3 (NVP), and a sodium/aluminum dual salt electrolyte based on NaAlCl 4 and an eutectic mixture of 1-ethyl-3-methylimidazolium chloride (EMImC) and aluminum chloride. Cyclic voltammograms indicate that increasing the molar concentration of AlCl 3 in the electrolyte is beneficial to high coulombic efficiency of aluminum deposition/stripping, which, unfortunately, results in lower coulombic efficiency of sodium extraction/insertion in the cathode. Therefore, EMImC–AlCl 3 with a molar ratio of 1–1.1 is used for battery evaluation. The hybrid battery with 1.0 M NaAlClmore » 4 exhibits a discharge voltage of 1.25 V and a cathodic capacity of 99 mA h g -1 at a current rate of C/10. In addition, the hybrid battery exhibits good rate performance and long-term cycling stability while maintaining a high coulombic efficiency of 98%. It is also demonstrated that increasing salt concentration can further enhance the cycling performance of the hybrid battery. X-ray diffraction analysis of the NVP electrodes under different conditions confirms that the main cathode reaction is indeed Na extraction/insertion. Based on all earth-abundant elements, the new Na–Al hybrid battery is very attractive for stationary and grid energy storage applications.« less

Multi-objective optimization of an arch dam shape under static loads using an evolutionary game method

NASA Astrophysics Data System (ADS)

Meng, Rui; Cheong, Kang Hao; Bao, Wei; Wong, Kelvin Kian Loong; Wang, Lu; Xie, Neng-gang

2018-06-01

This article attempts to evaluate the safety and economic performance of an arch dam under the action of static loads. The geometric description of a crown cantilever section and the horizontal arch ring is presented. A three-objective optimization model of arch dam shape is established based on the arch dam volume, maximum principal tensile stress and total strain energy. The evolutionary game method is then applied to obtain the optimal solution. In the evolutionary game technique, a novel and more efficient exploration method of the game players' strategy space, named the 'sorting partition method under the threshold limit', is presented, with the game profit functions constructed according to both competitive and cooperative behaviour. By way of example, three optimization goals have all shown improvements over the initial solutions. In particular, the evolutionary game method has potentially faster convergence. This demonstrates the preliminary proof of principle of the evolutionary game method.

Ocean warming, a rapid distributional shift, and the hybridization of a coastal fish species.

PubMed

Potts, Warren M; Henriques, Romina; Santos, Carmen V; Munnik, Kate; Ansorge, Isabelle; Dufois, Francois; Booth, Anthony J; Kirchner, Carola; Sauer, Warwick H H; Shaw, Paul W

2014-09-01

Despite increasing awareness of large-scale climate-driven distribution shifts in the marine environment, no study has linked rapid ocean warming to a shift in distribution and consequent hybridization of a marine fish species. This study describes rapid warming (0.8 °C per decade) in the coastal waters of the Angola-Benguela Frontal Zone over the last three decades and a concomitant shift by a temperature sensitive coastal fish species (Argyrosomus coronus) southward from Angola into Namibia. In this context, rapid shifts in distribution across Economic Exclusive Zones will complicate the management of fishes, particularly when there is a lack of congruence in the fisheries policy between nations. Evidence for recent hybridization between A. coronus and a congener, A. inodorus, indicate that the rapid shift in distribution of A. coronus has placed adults of the two species in contact during their spawning events. Ocean warming may therefore revert established species isolation mechanisms and alter the evolutionary history of fishes. While the consequences of the hybridization on the production of the resource remain unclear, this will most likely introduce additional layers of complexity to their management. © 2014 John Wiley & Sons Ltd.

Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes.

PubMed

Wallis, Graham P; Cameron-Christie, Sophia R; Kennedy, Hannah L; Palmer, Gemma; Sanders, Tessa R; Winter, David J

2017-06-01

Classification, phylogeography and the testing of evolutionary hypotheses rely on correct estimation of species phylogeny. Early molecular phylogenies often relied on mtDNA alone, which acts as a single linkage group with one history. Over the last decade, the use of multiple nuclear sequences has often revealed conflict among gene trees. This observation can be attributed to hybridization, lineage sorting, paralogy or selection. Here, we use 54 groups of fishes from 48 studies to estimate the degree of concordance between mitochondrial and nuclear gene trees in two ecological grades of fishes: marine and freshwater. We test the hypothesis that freshwater fish phylogenies should, on average, show more discordance because of their higher propensity for hybridization in the past. In keeping with this idea, concordance between mitochondrial and nuclear gene trees (as measured by proportion of components shared) is on average 50% higher in marine fishes. We discuss why this difference almost certainly results from introgression caused by greater historical hybridization among lineages in freshwater groups, and further emphasize the need to use multiple nuclear genes, and identify conflict among them, in estimation of species phylogeny. © 2017 John Wiley & Sons Ltd.