Evolutionary Paths to Corrupt Societies of Artificial Agents

NASA Astrophysics Data System (ADS)

Nasrallah, Walid

Virtual corrupt societies can be defined as groups of interacting computer-generated agents who predominantly choose behavior that gives short term personal gain at the expense of a higher aggregate cost to others. This paper focuses on corrupt societies that, unlike published models in which cooperation must evolve in order for the society to continue to survive, do not naturally die out as the corrupt class siphons off the resources. For example, a very computationally simple strategy of avoiding confrontation can allow a majority of "unethical" individuals to survive off the efforts of an "ethical" but productive minority. Analogies are drawn to actual human societies in which similar conditions gave rise to behavior traditionally defined as economic or political corruption.

Linking species habitat and past palaeoclimatic events to evolution of the teleost innate immune system.

PubMed

Solbakken, Monica Hongrø; Voje, Kjetil Lysne; Jakobsen, Kjetill Sigurd; Jentoft, Sissel

2017-04-26

Host-intrinsic factors as well as environmental changes are known to be strong evolutionary drivers defining the genetic foundation of immunity. Using a novel set of teleost genomes and a time-calibrated phylogeny, we here investigate the family of Toll-like receptor ( TLR ) genes and address the underlying evolutionary processes shaping the diversity of the first-line defence. Our findings reveal remarkable flexibility within the evolutionary design of teleost innate immunity characterized by prominent TLR gene losses and expansions. In the order of Gadiformes, expansions correlate with the loss of major histocompatibility complex class II ( MHCII ) and diversifying selection analyses support that this has fostered new immunological innovations in TLR s within this lineage. In teleosts overall, TLRs expansions correlate with species latitudinal distributions and maximum depth. By contrast, lineage-specific gene losses overlap with well-described changes in palaeoclimate (global ocean anoxia) and past Atlantic Ocean geography. In conclusion, we suggest that the evolvability of the teleost immune system has most likely played a prominent role in the survival and successful radiation of this lineage. © 2017 The Authors.

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

PubMed Central

Dolja, Valerian V.

2014-01-01

SUMMARY Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus “self” that defines the identity of deep, ancient viral lineages. However, several other widespread viral “hallmark genes” encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host. PMID:24847023

Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus).

PubMed

Castro-Prieto, Aines; Wachter, Bettina; Melzheimer, Joerg; Thalwitzer, Susanne; Sommer, Simone

2011-01-01

The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.

Precraniate origin of cranial motoneurons

PubMed Central

Dufour, Héloïse D.; Chettouh, Zoubida; Deyts, Carole; de Rosa, Renaud; Goridis, Christo; Joly, Jean-Stéphane; Brunet, Jean-François

2006-01-01

The craniate head is innervated by cranial sensory and motor neurons. Cranial sensory neurons stem from the neurogenic placodes and neural crest and are seen as evolutionary innovations crucial in fulfilling the feeding and respiratory needs of the craniate “new head.” In contrast, cranial motoneurons that are located in the hindbrain and motorize the head have an unclear phylogenetic status. Here we show that these motoneurons are in fact homologous to the motoneurons of the sessile postmetamorphic form of ascidians. The motoneurons of adult Ciona intestinalis, located in the cerebral ganglion and innervating muscles associated with the huge “branchial basket,” express the transcription factors CiPhox2 and CiTbx20, whose vertebrate orthologues collectively define cranial motoneurons of the branchiovisceral class. Moreover, Ciona's postmetamorphic motoneurons arise from a hindbrain set aside during larval life and defined as such by its position (caudal to the prosensephalic sensory vesicle) and coexpression of CiPhox2 and CiHox1, whose orthologues collectively mark the vertebrate hindbrain. These data unveil that the postmetamorphic ascidian brain, assumed to be a derived feature, in fact corresponds to the vertebrate hindbrain and push back the evolutionary origin of cranial nerves to before the origin of craniates. PMID:16735475

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences.

PubMed

Mizianty, Marcin J; Kurgan, Lukasz

2009-12-13

Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/.

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences

PubMed Central

2009-01-01

Background Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. Results The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. Conclusions The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/. PMID:20003388

Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding

PubMed Central

Chappell, Paul E; Meziane, El Kahina; Harrison, Michael; Magiera, Łukasz; Hermann, Clemens; Mears, Laura; Wrobel, Antoni G; Durant, Charlotte; Nielsen, Lise Lotte; Buus, Søren; Ternette, Nicola; Mwangi, William; Butter, Colin; Nair, Venugopal; Ahyee, Trudy; Duggleby, Richard; Madrigal, Alejandro; Roversi, Pietro; Lea, Susan M; Kaufman, Jim

2015-01-01

Highly polymorphic major histocompatibility complex (MHC) molecules are at the heart of adaptive immune responses, playing crucial roles in many kinds of disease and in vaccination. We report that breadth of peptide presentation and level of cell surface expression of class I molecules are inversely correlated in both chickens and humans. This relationship correlates with protective responses against infectious pathogens including Marek's disease virus leading to lethal tumours in chickens and human immunodeficiency virus infection progressing to AIDS in humans. We propose that differences in peptide binding repertoire define two groups of MHC class I molecules strategically evolved as generalists and specialists for different modes of pathogen resistance. We suggest that differences in cell surface expression level ensure the development of optimal peripheral T cell responses. The inverse relationship of peptide repertoire and expression is evidently a fundamental property of MHC molecules, with ramifications extending beyond immunology and medicine to evolutionary biology and conservation. DOI: http://dx.doi.org/10.7554/eLife.05345.001 PMID:25860507

Multiplicity in Early Stellar Evolution

NASA Astrophysics Data System (ADS)

Reipurth, B.; Clarke, C. J.; Boss, A. P.; Goodwin, S. P.; Rodríguez, L. F.; Stassun, K. G.; Tokovinin, A.; Zinnecker, H.

Observations from optical to centimeter wavelengths have demonstrated that multiple systems of two or more bodies is the norm at all stellar evolutionary stages. Multiple systems are widely agreed to result from the collapse and fragmentation of cloud cores, despite the inhibiting influence of magnetic fields. Surveys of class 0 protostars with millimeter interferometers have revealed a very high multiplicity frequency of about 2/3, even though there are observational difficulties in resolving close protobinaries, thus supporting the possibility that all stars could be born in multiple systems. Near-infrared adaptive optics observations of class I protostars show a lower binary frequency relative to the class 0 phase, a declining trend that continues through the class II/III stages to the field population. This loss of companions is a natural consequence of dynamical interplay in small multiple systems, leading to ejection of members. We discuss observational consequences of this dynamical evolution, and its influence on circumstellar disks, and we review the evolution of circumbinary disks and their role in defining binary mass ratios. Special attention is paid to eclipsing PMS binaries, which allow for observational tests of evolutionary models of early stellar evolution. Many stars are born in clusters and small groups, and we discuss how interactions in dense stellar environments can significantly alter the distribution of binary separations through dissolution of wider binaries. The binaries and multiples we find in the field are the survivors of these internal and external destructive processes, and we provide a detailed overview of the multiplicity statistics of the field, which form a boundary condition for all models of binary evolution. Finally, we discuss various formation mechanisms for massive binaries, and the properties of massive trapezia.

Punctuated equilibrium in the large-scale evolution of programming languages†

PubMed Central

Valverde, Sergi; Solé, Ricard V.

2015-01-01

The analogies and differences between biological and cultural evolution have been explored by evolutionary biologists, historians, engineers and linguists alike. Two well-known domains of cultural change are language and technology. Both share some traits relating the evolution of species, but technological change is very difficult to study. A major challenge in our way towards a scientific theory of technological evolution is how to properly define evolutionary trees or clades and how to weight the role played by horizontal transfer of information. Here, we study the large-scale historical development of programming languages, which have deeply marked social and technological advances in the last half century. We analyse their historical connections using network theory and reconstructed phylogenetic networks. Using both data analysis and network modelling, it is shown that their evolution is highly uneven, marked by innovation events where new languages are created out of improved combinations of different structural components belonging to previous languages. These radiation events occur in a bursty pattern and are tied to novel technological and social niches. The method can be extrapolated to other systems and consistently captures the major classes of languages and the widespread horizontal design exchanges, revealing a punctuated evolutionary path. PMID:25994298

Virus world as an evolutionary network of viruses and capsidless selfish elements.

PubMed

Koonin, Eugene V; Dolja, Valerian V

2014-06-01

Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Research and Teaching: Analyzing Upper Level Undergraduate Knowledge of Evolutionary Processes-- Can Class Discussions Help?

ERIC Educational Resources Information Center

Tran, Mark V.; Weigel, Emily G.; Richmond, Gail

2014-01-01

For biologists, a proper understanding of evolutionary processes is fundamentally important. However, undergraduate biology students often struggle to understand evolutionary processes, replacing factual knowledge with misconceptions on the subject. Classroom discussions can be effective active learning tools used to address these misconceptions…

Are there ergodic limits to evolution? Ergodic exploration of genome space and convergence

PubMed Central

McLeish, Tom C. B.

2015-01-01

We examine the analogy between evolutionary dynamics and statistical mechanics to include the fundamental question of ergodicity—the representative exploration of the space of possible states (in the case of evolution this is genome space). Several properties of evolutionary dynamics are identified that allow a generalization of the ergodic dynamics, familiar in dynamical systems theory, to evolution. Two classes of evolved biological structure then arise, differentiated by the qualitative duration of their evolutionary time scales. The first class has an ergodicity time scale (the time required for representative genome exploration) longer than available evolutionary time, and has incompletely explored the genotypic and phenotypic space of its possibilities. This case generates no expectation of convergence to an optimal phenotype or possibility of its prediction. The second, more interesting, class exhibits an evolutionary form of ergodicity—essentially all of the structural space within the constraints of slower evolutionary variables have been sampled; the ergodicity time scale for the system evolution is less than the evolutionary time. In this case, some convergence towards similar optima may be expected for equivalent systems in different species where both possess ergodic evolutionary dynamics. When the fitness maximum is set by physical, rather than co-evolved, constraints, it is additionally possible to make predictions of some properties of the evolved structures and systems. We propose four structures that emerge from evolution within genotypes whose fitness is induced from their phenotypes. Together, these result in an exponential speeding up of evolution, when compared with complete exploration of genomic space. We illustrate a possible case of application and a prediction of convergence together with attaining a physical fitness optimum in the case of invertebrate compound eye resolution. PMID:26640648

Are there ergodic limits to evolution? Ergodic exploration of genome space and convergence.

PubMed

McLeish, Tom C B

2015-12-06

We examine the analogy between evolutionary dynamics and statistical mechanics to include the fundamental question of ergodicity-the representative exploration of the space of possible states (in the case of evolution this is genome space). Several properties of evolutionary dynamics are identified that allow a generalization of the ergodic dynamics, familiar in dynamical systems theory, to evolution. Two classes of evolved biological structure then arise, differentiated by the qualitative duration of their evolutionary time scales. The first class has an ergodicity time scale (the time required for representative genome exploration) longer than available evolutionary time, and has incompletely explored the genotypic and phenotypic space of its possibilities. This case generates no expectation of convergence to an optimal phenotype or possibility of its prediction. The second, more interesting, class exhibits an evolutionary form of ergodicity-essentially all of the structural space within the constraints of slower evolutionary variables have been sampled; the ergodicity time scale for the system evolution is less than the evolutionary time. In this case, some convergence towards similar optima may be expected for equivalent systems in different species where both possess ergodic evolutionary dynamics. When the fitness maximum is set by physical, rather than co-evolved, constraints, it is additionally possible to make predictions of some properties of the evolved structures and systems. We propose four structures that emerge from evolution within genotypes whose fitness is induced from their phenotypes. Together, these result in an exponential speeding up of evolution, when compared with complete exploration of genomic space. We illustrate a possible case of application and a prediction of convergence together with attaining a physical fitness optimum in the case of invertebrate compound eye resolution.

Cooperative combinatorial optimization: evolutionary computation case study.

PubMed

Burgin, Mark; Eberbach, Eugene

2008-01-01

This paper presents a formalization of the notion of cooperation and competition of multiple systems that work toward a common optimization goal of the population using evolutionary computation techniques. It is proved that evolutionary algorithms are more expressive than conventional recursive algorithms, such as Turing machines. Three classes of evolutionary computations are introduced and studied: bounded finite, unbounded finite, and infinite computations. Universal evolutionary algorithms are constructed. Such properties of evolutionary algorithms as completeness, optimality, and search decidability are examined. A natural extension of evolutionary Turing machine (ETM) model is proposed to properly reflect phenomena of cooperation and competition in the whole population.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

PubMed

2004-12-09

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Tumor immunology viewed from alternative animal models—the Xenopus story

PubMed Central

Banach, Maureen; Robert, Jacques

2017-01-01

a) Purpose of review Nonmammalian comparative animal models are important not only to gain fundamental evolutionary understanding of the complex interactions of tumors with the immune system, but also to better predict the applicability of novel immunotherapeutic approaches to humans. After reviewing recent advances in developing alternative models, we focus on the amphibian Xenopus laevis and its usefulness in deciphering the perplexing roles of MHC class I-like molecules and innate (i)T cells in tumor immunity. b) Recent findings Experiments using MHC-defined inbred and cloned animals, tumor cell lines, effective reagents, sequenced genomes, and adapted gene editing techniques in Xenopus, have revealed that the critical involvement of class I-like molecules and iT cells in tumor immunity has been conserved during evolution. c) Summary Comparative studies with the X. laevis tumor immunity model can contribute to the development of better and more efficient cancer immunotherapies. PMID:28944105

Structural, Functional and Evolutionary Aspects of Seed Globulins.

PubMed

Kesari, Pooja; Neetu; Sharma, Anchal; Katiki, Madhusudhanarao; Kumar, Pramod; Gurjar, Bhola R; Tomar, Shailly; Sharma, Ashwani K; Kumar, Pravindra

2017-01-01

Globulins are a major class of seed storage proteins which were thought to be enzymatically inactive. These proteins belong to the most ancient cupin superfamily. They can be graded into 11S legumin type and 7S vicilin type based on their sedimentation coefficients. Members from both classes share structural homology are thought to have evolved from either one-domain germin predecessor by duplication or by horizontal gene transfer of two-domain gene from bacteria to eukaryotes. Globulins are known to define the nutritional quality of the seeds, however, they are also involved in sucrose binding, desiccation, defense against microbes, hormone binding and oxidative stress etc. Major drawback with globulins is their tendency to bind to IgE. Studying structural-functional behavior of such protein can help in modifying proteins for enhanced functionality in food processing industries. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The topological requirements for robust perfect adaptation in networks of any size.

PubMed

Araujo, Robyn P; Liotta, Lance A

2018-05-01

Robustness, and the ability to function and thrive amid changing and unfavorable environments, is a fundamental requirement for living systems. Until now it has been an open question how large and complex biological networks can exhibit robust behaviors, such as perfect adaptation to a variable stimulus, since complexity is generally associated with fragility. Here we report that all networks that exhibit robust perfect adaptation (RPA) to a persistent change in stimulus are decomposable into well-defined modules, of which there exist two distinct classes. These two modular classes represent a topological basis for all RPA-capable networks, and generate the full set of topological realizations of the internal model principle for RPA in complex, self-organizing, evolvable bionetworks. This unexpected result supports the notion that evolutionary processes are empowered by simple and scalable modular design principles that promote robust performance no matter how large or complex the underlying networks become.

Constraints in Genetic Programming

NASA Technical Reports Server (NTRS)

Janikow, Cezary Z.

1996-01-01

Genetic programming refers to a class of genetic algorithms utilizing generic representation in the form of program trees. For a particular application, one needs to provide the set of functions, whose compositions determine the space of program structures being evolved, and the set of terminals, which determine the space of specific instances of those programs. The algorithm searches the space for the best program for a given problem, applying evolutionary mechanisms borrowed from nature. Genetic algorithms have shown great capabilities in approximately solving optimization problems which could not be approximated or solved with other methods. Genetic programming extends their capabilities to deal with a broader variety of problems. However, it also extends the size of the search space, which often becomes too large to be effectively searched even by evolutionary methods. Therefore, our objective is to utilize problem constraints, if such can be identified, to restrict this space. In this publication, we propose a generic constraint specification language, powerful enough for a broad class of problem constraints. This language has two elements -- one reduces only the number of program instances, the other reduces both the space of program structures as well as their instances. With this language, we define the minimal set of complete constraints, and a set of operators guaranteeing offspring validity from valid parents. We also show that these operators are not less efficient than the standard genetic programming operators if one preprocesses the constraints - the necessary mechanisms are identified.

Punctuated equilibrium in the large-scale evolution of programming languages.

PubMed

Valverde, Sergi; Solé, Ricard V

2015-06-06

The analogies and differences between biological and cultural evolution have been explored by evolutionary biologists, historians, engineers and linguists alike. Two well-known domains of cultural change are language and technology. Both share some traits relating the evolution of species, but technological change is very difficult to study. A major challenge in our way towards a scientific theory of technological evolution is how to properly define evolutionary trees or clades and how to weight the role played by horizontal transfer of information. Here, we study the large-scale historical development of programming languages, which have deeply marked social and technological advances in the last half century. We analyse their historical connections using network theory and reconstructed phylogenetic networks. Using both data analysis and network modelling, it is shown that their evolution is highly uneven, marked by innovation events where new languages are created out of improved combinations of different structural components belonging to previous languages. These radiation events occur in a bursty pattern and are tied to novel technological and social niches. The method can be extrapolated to other systems and consistently captures the major classes of languages and the widespread horizontal design exchanges, revealing a punctuated evolutionary path. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

TAS3 miR390-dependent loci in non-vascular land plants: towards a comprehensive reconstruction of the gene evolutionary history.

PubMed

Morozov, Sergey Y; Milyutina, Irina A; Erokhina, Tatiana N; Ozerova, Liudmila V; Troitsky, Alexey V; Solovyev, Andrey G

2018-01-01

Trans-acting small interfering RNAs (ta-siRNAs) are transcribed from protein non-coding genomic TAS loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants, gymnosperms, ferns and mosses. In this study, bioinformatic and experimental PCR-based approaches were used as tools to analyze TAS3 and TAS6 loci in transcriptomes and genomic DNAs from representatives of evolutionary distant non-vascular plant taxa such as Bryophyta, Marchantiophyta and Anthocerotophyta. We revealed previously undiscovered TAS3 loci in plant classes Sphagnopsida and Anthocerotopsida, as well as TAS6 loci in Bryophyta classes Tetraphidiopsida, Polytrichopsida, Andreaeopsida and Takakiopsida. These data further unveil the evolutionary pathway of the miR390-dependent TAS3 loci in land plants. We also identified charophyte alga sequences coding for SUPPRESSOR OF GENE SILENCING 3 (SGS3), which is required for generation of ta-siRNAs in plants, and hypothesized that the appearance of TAS3-related sequences could take place at a very early step in evolutionary transition from charophyte algae to an earliest common ancestor of land plants.

Automated discovery of local search heuristics for satisfiability testing.

PubMed

Fukunaga, Alex S

2008-01-01

The development of successful metaheuristic algorithms such as local search for a difficult problem such as satisfiability testing (SAT) is a challenging task. We investigate an evolutionary approach to automating the discovery of new local search heuristics for SAT. We show that several well-known SAT local search algorithms such as Walksat and Novelty are composite heuristics that are derived from novel combinations of a set of building blocks. Based on this observation, we developed CLASS, a genetic programming system that uses a simple composition operator to automatically discover SAT local search heuristics. New heuristics discovered by CLASS are shown to be competitive with the best Walksat variants, including Novelty+. Evolutionary algorithms have previously been applied to directly evolve a solution for a particular SAT instance. We show that the heuristics discovered by CLASS are also competitive with these previous, direct evolutionary approaches for SAT. We also analyze the local search behavior of the learned heuristics using the depth, mobility, and coverage metrics proposed by Schuurmans and Southey.

Physical characteristics and evolutionary trends of continental rifts

NASA Technical Reports Server (NTRS)

Ramberg, I. B.; Morgan, P.

1984-01-01

Rifts may be defined as zones beneath which the entire lithosphere has ruptured in extension. They are widespread and occur in a variety of tectonic settings, and range up to 2,600 m.y. in age. The object of this review is to highlight characteristic features of modern and ancient rifts, to emphasize differences and similarities in order to help characterize evolutionary trends, to identify physical conditions favorable for initiation as well as termination of rifting, and to provide constraints for future modeling studies of rifting. Rifts are characterized on the basis of their structural, geomorphic, magmatic and geophysical features and the diverse character of these features and their evolutionary trends through time are discussed. Mechanisms of rifting are critically examined in terms of the physical characteristics and evolutionary trends of rifts, and it is concluded that while simple models can give valuable insight into specific processes of rifting, individual rifts can rarely, if ever, be characterized by well defined trends predicted by these models. More data are required to clearly define evolutionary trends, and the models require development to incorporate the effects of lithospheric heterogeneities and complex geologic histories.

Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques

PubMed Central

Campbell, Kevin J.; Detmer, Ann M.; Karl, Julie A.; Wiseman, Roger W.; Blasky, Alex J.; Hughes, Austin L.; Bimber, Benjamin N.; O’Connor, Shelby L.; O’Connor, David H.

2009-01-01

Cynomolgus macaques (Macaca fascicularis) provide increasingly common models for infectious disease research. Several geographically distinct populations of these macaques from Southeast Asia and the Indian Ocean island of Mauritius are available for pathogenesis studies. Though host genetics may profoundly impact results of such studies, similarities and differences between populations are often overlooked. In this study we identified 47 full-length MHC class I nucleotide sequences in 16 cynomolgus macaques of Filipino origin. The majority of MHC class I sequences characterized (39 of 47) were unique to this regional population. However, we discovered eight sequences with perfect identity and six sequences with close similarity to previously defined MHC class I sequences from other macaque populations. We identified two ancestral MHC haplotypes that appear to be shared between Filipino and Mauritian cynomolgus macaques, notably a Mafa-B haplotype that has previously been shown to protect Mauritian cynomolgus macaques against challenge with a simian/human immunodeficiency virus, SHIV89.6P. We also identified a Filipino cynomolgus macaque MHC class I sequence for which the predicted protein sequence differs from Mamu-B*17 by a single amino acid. This is important because Mamu-B*17 is strongly associated with protection against simian immunodeficiency virus (SIV) challenge in Indian rhesus macaques. These findings have implications for the evolutionary history of Filipino cynomolgus macaques as well as for the use of this model in SIV/SHIV research protocols. PMID:19107381

TAS3 miR390-dependent loci in non-vascular land plants: towards a comprehensive reconstruction of the gene evolutionary history

PubMed Central

Milyutina, Irina A.; Erokhina, Tatiana N.; Ozerova, Liudmila V.; Troitsky, Alexey V.; Solovyev, Andrey G.

2018-01-01

Trans-acting small interfering RNAs (ta-siRNAs) are transcribed from protein non-coding genomic TAS loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants, gymnosperms, ferns and mosses. In this study, bioinformatic and experimental PCR-based approaches were used as tools to analyze TAS3 and TAS6 loci in transcriptomes and genomic DNAs from representatives of evolutionary distant non-vascular plant taxa such as Bryophyta, Marchantiophyta and Anthocerotophyta. We revealed previously undiscovered TAS3 loci in plant classes Sphagnopsida and Anthocerotopsida, as well as TAS6 loci in Bryophyta classes Tetraphidiopsida, Polytrichopsida, Andreaeopsida and Takakiopsida. These data further unveil the evolutionary pathway of the miR390-dependent TAS3 loci in land plants. We also identified charophyte alga sequences coding for SUPPRESSOR OF GENE SILENCING 3 (SGS3), which is required for generation of ta-siRNAs in plants, and hypothesized that the appearance of TAS3-related sequences could take place at a very early step in evolutionary transition from charophyte algae to an earliest common ancestor of land plants. PMID:29682420

Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria).

PubMed

Fukami, Hironobu; Chen, Chaolun Allen; Budd, Ann F; Collins, Allen; Wallace, Carden; Chuang, Yao-Yang; Chen, Chienhsun; Dai, Chang-Feng; Iwao, Kenji; Sheppard, Charles; Knowlton, Nancy

2008-09-16

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ss-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.

Molecular characterization of classical and nonclassical MHC class I genes from the golden pheasant (Chrysolophus pictus).

PubMed

Zeng, Q-Q; Zhong, G-H; He, K; Sun, D-D; Wan, Q-H

2016-02-01

Classical major histocompatibility complex (MHC) class I allelic polymorphism is essential for competent antigen presentation. To improve the genotyping efforts in the golden pheasant, it is necessary to differentiate more accurately between classical and nonclassical class I molecules. In our study, all MHC class I genes were isolated from one golden pheasant based on two overlapping PCR amplifications. In total, six full-length class I nucleotide sequences (A-F) were identified, and four were novel. Two (A and C) belonged to the IA1 gene, two (B and D) were alleles derived from the IA2 gene through transgene amplification, and two (E and F) comprised a third novel locus, IA3 that was excluded from the core region of the golden pheasant MHC-B. IA1 and IA2 exhibited the broad expression profiles characteristic of classical loci, while IA3 showed no expression in multiple tissues and was therefore defined as a nonclassical gene. Phylogenetic analysis indicated that the three IA genes in the golden pheasant share a much closer evolutionary relationship than the corresponding sequences in other galliform species. This observation was consistent with high sequence similarity among them, which likely arises from the homogenizing effect of recombination. Our careful distinction between the classical and nonclassical MHC class I genes in the golden pheasant lays the foundation for developing locus-specific genotyping and establishing a good molecular marker system of classical MHC I loci. © 2015 John Wiley & Sons Ltd.

Evolutionary history of the ABCB2 genomic region in teleosts

USGS Publications Warehouse

Palti, Y.; Rodriguez, M.F.; Gahr, S.A.; Hansen, J.D.

2007-01-01

Gene duplication, silencing and translocation have all been implicated in shaping the unique genomic architecture of the teleost MH regions. Previously, we demonstrated that trout possess five unlinked regions encoding MH genes. One of these regions harbors ABCB2 which in all other vertebrate classes is found in the MHC class II region. In this study, we sequenced a BAC contig for the trout ABCB2 region. Analysis of this region revealed the presence of genes homologous to those located in the human class II (ABCB2, BRD2, ??DAA), extended class II (RGL2, PHF1, SYGP1) and class III (PBX2, Notch-L) regions. The organization and syntenic relationships of this region were then compared to similar regions in humans, Tetraodon and zebrafish to learn more about the evolutionary history of this region. Our analysis indicates that this region was generated during the teleost-specific duplication event while also providing insight about potential MH paralogous regions in teleosts. ?? 2006 Elsevier Ltd. All rights reserved.

Let the social sciences evolve.

PubMed

Smaldino, Paul E; Waring, Timothy M

2014-08-01

We agree that evolutionary perspectives may help us organize many divergent realms of the science of human behavior. Nevertheless, an imperative to unite all social science under an evolutionary framework risks turning off researchers who have their own theoretical perspectives that can be informed by evolutionary theory without being exclusively defined by it. We propose a few considerations for scholars interested in joining the evolutionary and social sciences.

Quasistatic Evolution in Perfect Plasticity for General Heterogeneous Materials

NASA Astrophysics Data System (ADS)

Solombrino, Francesco

2014-04-01

Inspired by some recent developments in the theory of small-strain heterogeneous elastoplasticity, we both revisit and generalize the formulation of the quasistatic evolutionary problem in perfect plasticity given by Francfort and Giacomini (Commun Pure Appl Math, 65:1185-1241, 2012). We show that their definition of the plastic dissipation measure is equivalent to an abstract one, where it is defined as the supremum of the dualities between the deviatoric parts of admissible stress fields and the plastic strains. By means of this abstract definition, a viscoplastic approximation and variational techniques from the theory of rate-independent processes give the existence of an evolution satisfying an energy-dissipation balance and consequently Hill's maximum plastic work principle for an abstract and very large class of yield conditions.

Scientific Method & Evolutionary Theory Elucidated by the Ivory-Billed Woodpecker Story

ERIC Educational Resources Information Center

Krupa, James J.

2014-01-01

Large, introductory, nonmajors biology classes present challenges when trying to encourage class discussion to help reinforce important concepts. Lively in-class discussion involving hundreds of students is more successful when a relevant story told with passion is used to introduce a topic. In my courses, each semester begins with thorough…

Phenotypic and genotypic expression of self-incompatibility haplotypes in Arabidopsis lyrata suggests unique origin of alleles in different dominance classes.

PubMed

Prigoda, Nadia L; Nassuth, Annette; Mable, Barbara K

2005-07-01

The highly divergent alleles of the SRK gene in outcrossing Arabidopsis lyrata have provided important insights into the evolutionary history of self-incompatibility (SI) alleles and serve as an ideal model for studies of the evolutionary and molecular interactions between alleles in cell-cell recognition systems in general. One tantalizing question is how new specificities arise in systems that require coordination between male and female components. Allelic recruitment via gene conversion has been proposed as one possibility, based on the division of DNA sequences at the SRK locus into two distinctive groups: (1) sequences whose relationships are not well resolved and display the long branch lengths expected for a gene under balancing selection (Class A); and (2) sequences falling into a well-supported group with shorter branch lengths (Class B) that are closely related to an unlinked paralogous locus. The purpose of this study was to determine if differences in phenotype (site of expression assayed using allele-specific reverse transcription-polymerase chain reaction) or function (dominance relationships assayed through controlled pollinations) accompany the sequence-based classification. Expression of Class A alleles was restricted to floral tissues, as predicted for genes involved in the SI response. In contrast, Class B alleles, despite being tightly linked to the SI phenotype, were unexpectedly expressed in both leaves and floral tissues; the same pattern found for a related unlinked paralogous sequence. Whereas Class A included haplotypes in three different dominance classes, all Class B haplotypes were found to be recessive to all except one Class A haplotype. In addition, mapping of expression and dominance patterns onto an S-domain-based genealogy suggested that allelic dominance may be determined more by evolutionary history than by frequency-dependent selection for lowered dominance as some theories suggest. The possibility that interlocus gene conversion might have contributed to allelic diversity is discussed.

The Great Struggles of Life: Darwin and the Emergence of Evolutionary Psychology

ERIC Educational Resources Information Center

Buss, David M.

2009-01-01

Darwin envisioned a scientific revolution for psychology. His theories of natural and sexual selection identified two classes of struggles--the struggle for existence and the struggle for mates. The emergence of evolutionary psychology and related disciplines signals the fulfillment of Darwin's vision. Natural selection theory guides scientists to…

Protein 3D Structure Computed from Evolutionary Sequence Variation

PubMed Central

Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

2011-01-01

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes. PMID:22163331

Mitochondrial and Nuclear Genes Suggest that Stony Corals Are Monophyletic but Most Families of Stony Corals Are Not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

PubMed Central

Fukami, Hironobu; Chen, Chaolun Allen; Budd, Ann F.; Collins, Allen; Wallace, Carden; Chuang, Yao-Yang; Chen, Chienhsun; Dai, Chang-Feng; Iwao, Kenji; Sheppard, Charles; Knowlton, Nancy

2008-01-01

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ß-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent “robust” and “complex” clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils. PMID:18795098

Comparing Evolutionary Programs and Evolutionary Pattern Search Algorithms: A Drug Docking Application

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

Hart, W.E.

1999-02-10

Evolutionary programs (EPs) and evolutionary pattern search algorithms (EPSAS) are two general classes of evolutionary methods for optimizing on continuous domains. The relative performance of these methods has been evaluated on standard global optimization test functions, and these results suggest that EPSAs more robustly converge to near-optimal solutions than EPs. In this paper we evaluate the relative performance of EPSAs and EPs on a real-world application: flexible ligand binding in the Autodock docking software. We compare the performance of these methods on a suite of docking test problems. Our results confirm that EPSAs and EPs have comparable performance, and theymore » suggest that EPSAs may be more robust on larger, more complex problems.« less

Evolutionary dynamics of enzymes.

PubMed

Demetrius, L

1995-08-01

This paper codifies and rationalizes the large diversity in reaction rates and substrate specificity of enzymes in terms of a model which postulates that the kinetic properties of present-day enzymes are the consequence of the evolutionary force of mutation and selection acting on a class of primordial enzymes with poor catalytic activity and broad substrate specificity. Enzymes are classified in terms of their thermodynamic parameters, activation enthalpy delta H* and activation entropy delta S*, in their kinetically significant transition states as follows: type 1, delta H* > 0, delta S* < 0; type 2, delta H* < or = 0, delta S* < or = 0; type 3, delta H* > 0, delta S* > 0. We study the evolutionary dynamics of these three classes of enzymes subject to mutation, which acts at the level of the gene which codes for the enzyme and selection, which acts on the organism that contains the enzyme. Our model predicts the following evolutionary trends in the reaction rate and binding specificity for the three classes of molecules. In type 1 enzymes, evolution results in random, non-directional changes in the reaction rate and binding specificity. In type 2 and 3 enzymes, evolution results in a unidirectional increase in both the reaction rate and binding specificity. We exploit these results in order to codify the diversity in functional properties of present-day enzymes. Type 1 molecules will be described by intermediate reaction rates and broad substrate specificity. Type 2 enzymes will be characterized by diffusion-controlled rates and absolute substrate specificity. The type 3 catalysts can be further subdivided in terms of their activation enthalpy into two classes: type 3a (delta H* small) and type 3b (delta H* large). We show that type 3a will be represented by the same functional properties that identify type 2, namely, diffusion-controlled rates and absolute substrate specificity, whereas type 3b will be characterized by non-diffusion-controlled rates and absolute substrate specificity. We infer from this depiction of the three classes of enzymes, a general relation between the two functional properties, reaction rate and substrate specificity, namely, enzymes with diffusion-controlled rates have absolute substrate specificity. By appealing to energetic considerations, we furthermore show that enzymes with diffusion-controlled rates (types 2 and 3a) form a small subset of the class of all enzymes. This codification of present-day enzymes derived from an evolutionary model, essentially relates the structural properties of enzymes, as described by their thermodynamic parameters, to their functional properties, as represented by the reaction rate and substrate specificity.

Dynamic and scalable audio classification by collective network of binary classifiers framework: an evolutionary approach.

PubMed

Kiranyaz, Serkan; Mäkinen, Toni; Gabbouj, Moncef

2012-10-01

In this paper, we propose a novel framework based on a collective network of evolutionary binary classifiers (CNBC) to address the problems of feature and class scalability. The main goal of the proposed framework is to achieve a high classification performance over dynamic audio and video repositories. The proposed framework adopts a "Divide and Conquer" approach in which an individual network of binary classifiers (NBC) is allocated to discriminate each audio class. An evolutionary search is applied to find the best binary classifier in each NBC with respect to a given criterion. Through the incremental evolution sessions, the CNBC framework can dynamically adapt to each new incoming class or feature set without resorting to a full-scale re-training or re-configuration. Therefore, the CNBC framework is particularly designed for dynamically varying databases where no conventional static classifiers can adapt to such changes. In short, it is entirely a novel topology, an unprecedented approach for dynamic, content/data adaptive and scalable audio classification. A large set of audio features can be effectively used in the framework, where the CNBCs make appropriate selections and combinations so as to achieve the highest discrimination among individual audio classes. Experiments demonstrate a high classification accuracy (above 90%) and efficiency of the proposed framework over large and dynamic audio databases. Copyright © 2012 Elsevier Ltd. All rights reserved.

ATLASGAL-selected massive clumps in the inner Galaxy. III. Dust continuum characterization of an evolutionary sample

NASA Astrophysics Data System (ADS)

König, C.; Urquhart, J. S.; Csengeri, T.; Leurini, S.; Wyrowski, F.; Giannetti, A.; Wienen, M.; Pillai, T.; Kauffmann, J.; Menten, K. M.; Schuller, F.

2017-03-01

Context. Massive-star formation and the processes involved are still poorly understood. The ATLASGAL survey provides an ideal basis for detailed studies of large numbers of massive-star forming clumps covering the whole range of evolutionary stages. The ATLASGAL Top100 is a sample of clumps selected by their infrared and radio properties to be representative for the whole range of evolutionary stages. Aims: The ATLASGAL Top100 sources are the focus of a number of detailed follow-up studies that will be presented in a series of papers. In the present work we use the dust continuum emission to constrain the physical properties of this sample and identify trends as a function of source evolution. Methods: We determine flux densities from mid-infrared to submillimeter wavelength (8-870 μm) images and use these values to fit their spectral energy distributions and determine their dust temperature and flux. Combining these with recent distances from the literature including maser parallax measurements we determine clump masses, luminosities and column densities. Results: We define four distinct source classes from the available continuum data and arrange these into an evolutionary sequence. This begins with sources found to be dark at 70 μm, followed by 24 μm weak sources with an embedded 70 μm source, continues through mid-infrared bright sources and ends with infrared bright sources associated with radio emission (I.e., H II regions). We find trends for increasing temperature, luminosity, and column density with the proposed evolution sequence, confirming that this sample is representative of different evolutionary stages of massive star formation. Our sources span temperatures from approximately 11 to 41 K, with bolometric luminosities in the range 57 L⊙-3.8 × 106L⊙. The highest masses reach 4.3 × 104M⊙ and peak column densities up to 1.1 × 1024 cm-1, and therefore have the potential to form the most massive O-type stars. We show that at least 93 sources (85%) of this sample have the ability to form massive stars and that most are gravitationally unstable and hence likely to be collapsing. Conclusions: The highest column density ATLASGAL sources cover the whole range of evolutionary stages from the youngest to the most evolved high-mass-star forming clumps. Study of these clumps provides a unique starting point for more in-depth research on massive-star formation in four distinct evolutionary stages whose well defined physical parameters afford more detailed studies. As most of the sample is closer than 5 kpc, these sources are also ideal for follow-up observations with high spatial resolution. Full Table 1, including fluxes, is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/599/A139

MHC class I diversity in chimpanzees and bonobos.

PubMed

Maibach, Vincent; Hans, Jörg B; Hvilsom, Christina; Marques-Bonet, Tomas; Vigilant, Linda

2017-10-01

Major histocompatibility complex (MHC) class I genes are critically involved in the defense against intracellular pathogens. MHC diversity comparisons among samples of closely related taxa may reveal traces of past or ongoing selective processes. The bonobo and chimpanzee are the closest living evolutionary relatives of humans and last shared a common ancestor some 1 mya. However, little is known concerning MHC class I diversity in bonobos or in central chimpanzees, the most numerous and genetically diverse chimpanzee subspecies. Here, we used a long-read sequencing technology (PacBio) to sequence the classical MHC class I genes A, B, C, and A-like in 20 and 30 wild-born bonobos and chimpanzees, respectively, with a main focus on central chimpanzees to assess and compare diversity in those two species. We describe in total 21 and 42 novel coding region sequences for the two species, respectively. In addition, we found evidence for a reduced MHC class I diversity in bonobos as compared to central chimpanzees as well as to western chimpanzees and humans. The reduced bonobo MHC class I diversity may be the result of a selective process in their evolutionary past since their split from chimpanzees.

Profile analysis and prediction of tissue-specific CpG island methylation classes

PubMed Central

2009-01-01

Background The computational prediction of DNA methylation has become an important topic in the recent years due to its role in the epigenetic control of normal and cancer-related processes. While previous prediction approaches focused merely on differences between methylated and unmethylated DNA sequences, recent experimental results have shown the presence of much more complex patterns of methylation across tissues and time in the human genome. These patterns are only partially described by a binary model of DNA methylation. In this work we propose a novel approach, based on profile analysis of tissue-specific methylation that uncovers significant differences in the sequences of CpG islands (CGIs) that predispose them to a tissue- specific methylation pattern. Results We defined CGI methylation profiles that separate not only between constitutively methylated and unmethylated CGIs, but also identify CGIs showing a differential degree of methylation across tissues and cell-types or a lack of methylation exclusively in sperm. These profiles are clearly distinguished by a number of CGI attributes including their evolutionary conservation, their significance, as well as the evolutionary evidence of prior methylation. Additionally, we assess profile functionality with respect to the different compartments of protein coding genes and their possible use in the prediction of DNA methylation. Conclusion Our approach provides new insights into the biological features that determine if a CGI has a functional role in the epigenetic control of gene expression and the features associated with CGI methylation susceptibility. Moreover, we show that the ability to predict CGI methylation is based primarily on the quality of the biological information used and the relationships uncovered between different sources of knowledge. The strategy presented here is able to predict, besides the constitutively methylated and unmethylated classes, two more tissue specific methylation classes conserving the accuracy provided by leading binary methylation classification methods. PMID:19383127

Physiological functions of the alpha class of carbonic anhydrases.

PubMed

Frost, Susan C

2014-01-01

Carbonic anhydrases are ubiquitous enzymes that catalyze the reversible hydration of carbon dioxide. These enzymes are of ancient origin as they are found in the deepest of branches of the evolutionary tree. Of the five different classes of carbonic anhydrases, the alpha class has perhaps received the most attention because of its role in human pathology. This review focuses on the physiological function of this class of carbonic anhydrases organized by their cellular location.

Time: The Biggest Pattern in Natural History Research

NASA Astrophysics Data System (ADS)

Gontier, Nathalie

2016-10-01

We distinguish between four cosmological transitions in the history of Western intellectual thought, and focus on how these cosmologies differentially define matter, space and time. We demonstrate that how time is conceptualized significantly impacts a cosmology's notion on causality, and hone in on how time is conceptualized differentially in modern physics and evolutionary biology. The former conflates time with space into a single space-time continuum and focuses instead on the movement of matter, while the evolutionary sciences have a tradition to understand time as a given when they cartography how organisms change across generations over or in time, thereby proving the phenomenon of evolution. The gap becomes more fundamental when we take into account that phenomena studied by chrono-biologists demonstrate that numerous organisms, including humans, have evolved a "sense" of time. And micro-evolutionary/genetic, meso-evolutionary/developmental and macro-evolutionary phenomena including speciation and extinction not only occur by different evolutionary modes and at different rates, they are also timely phenomena that follow different periodicities. This article focusses on delineating the problem by finding its historical roots. We conclude that though time might be an obsolete concept for the physical sciences, it is crucial for the evolutionary sciences where evolution is defined as the change that biological individuals undergo in/over or through time.

On origin and evolution of carbonic anhydrase isozymes: A phylogenetic analysis from whole-enzyme to active site.

PubMed

Banerjee, Srijoni; Deshpande, Parag A

2016-04-01

Genetic evolution of carbonic anhydrase enzyme provides an interesting instance of functional similarity in spite of structural diversity of the members of a given family of enzymes. Phylogenetic analysis of α-, β- and γ-carbonic anhydrase was carried out to determine the evolutionary relationships among various members of the family with the enzyme marking its presence in a wide range of cellular and chromosomal locations. The presence of more than one class of enzymes in a particular organism was revealed by phylogenetic time tree. The evolutionary relationships among the members of animal, plant and microbial kingdom were developed. The study revises a long-established notion of kingdom-specificity of the different classes of carbonic anhydrases and provides a new version of the presence of multiple classes of carbonic anhydrases in a single organism and the presence of a given class of carbonic anhydrase across different kingdoms. Copyright © 2016 Elsevier Ltd. All rights reserved.

EvoBuild: A Quickstart Toolkit for Programming Agent-Based Models of Evolutionary Processes

NASA Astrophysics Data System (ADS)

Wagh, Aditi; Wilensky, Uri

2018-04-01

Extensive research has shown that one of the benefits of programming to learn about scientific phenomena is that it facilitates learning about mechanisms underlying the phenomenon. However, using programming activities in classrooms is associated with costs such as requiring additional time to learn to program or students needing prior experience with programming. This paper presents a class of programming environments that we call quickstart: Environments with a negligible threshold for entry into programming and a modest ceiling. We posit that such environments can provide benefits of programming for learning without incurring associated costs for novice programmers. To make this claim, we present a design-based research study conducted to compare programming models of evolutionary processes with a quickstart toolkit with exploring pre-built models of the same processes. The study was conducted in six seventh grade science classes in two schools. Students in the programming condition used EvoBuild, a quickstart toolkit for programming agent-based models of evolutionary processes, to build their NetLogo models. Students in the exploration condition used pre-built NetLogo models. We demonstrate that although students came from a range of academic backgrounds without prior programming experience, and all students spent the same number of class periods on the activities including the time students took to learn programming in this environment, EvoBuild students showed greater learning about evolutionary mechanisms. We discuss the implications of this work for design research on programming environments in K-12 science education.

Universality of long-range correlations in expansion randomization systems

NASA Astrophysics Data System (ADS)

Messer, P. W.; Lässig, M.; Arndt, P. F.

2005-10-01

We study the stochastic dynamics of sequences evolving by single-site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of non-equilibrium 1D expansion-randomization systems with generic stationary long-range correlations in a regime of growing sequence length. We obtain explicitly the two-point correlation function of the sequence composition and the distribution function of the composition bias in sequences of finite length. The characteristic exponent χ of these quantities is determined by the ratio of two effective rates, which are explicitly calculated for several specific sequence evolution dynamics of the universality class. Depending on the value of χ, we find two different scaling regimes, which are distinguished by the detectability of the initial composition bias. All analytic results are accurately verified by numerical simulations. We also discuss the non-stationary build-up and decay of correlations, as well as more complex evolutionary scenarios, where the rates of the processes vary in time. Our findings provide a possible example for the emergence of universality in molecular biology.

Evolution of high-mass star-forming regions .

NASA Astrophysics Data System (ADS)

Giannetti, A.; Leurini, S.; Wyrowski, F.; Urquhart, J.; König, C.; Csengeri, T.; Güsten, R.; Menten, K. M.

Observational identification of a coherent evolutionary sequence for high-mass star-forming regions is still missing. We use the progressive heating of the gas caused by the feedback of high-mass young stellar objects to prove the statistical validity of the most common schemes used to observationally define an evolutionary sequence for high-mass clumps, and identify which physical process dominates in the different phases. From the spectroscopic follow-ups carried out towards the TOP100 sample between 84 and 365 km s^-1 giga hertz, we selected several multiplets of CH3CN, CH3CCH, and CH3OH lines to derive the physical properties of the gas in the clumps along the evolutionary sequence. We demonstrate that the evolutionary sequence is statistically valid, and we define intervals in L/M separating the compression, collapse and accretion, and disruption phases. The first hot cores and ZAMS stars appear at L/M≈10usk {L_ȯ}msun-1

The importance of offshore origination revealed through ophiuroid phylogenomics.

PubMed

Bribiesca-Contreras, Guadalupe; Verbruggen, Heroen; Hugall, Andrew F; O'Hara, Timothy D

2017-07-12

Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome. Despite this, bathymetric shifts have occurred. We inferred from ancestral reconstructions that eurybathic or intermediate distributions across both biomes were a transitional state and direct changes between shallow and deep sea did not occur. The macro-evolutionary pattern of bathome shift appeared to reflect micro-evolutionary processes of bathymetric speciation. Results suggest that most of the oldest clades have a deep-sea origin, but multiple colonization events indicate that the evolution of this group conforms neither to a simple onshore-offshore hypothesis, nor the opposite pattern. Both shallow and deep bathomes have played an important role in generating the current diversity of this major benthic class. © 2017 The Author(s).

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.

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective.

PubMed

Lion, Sébastien

2018-01-01

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

An evolutionary algorithm that constructs recurrent neural networks.

PubMed

Angeline, P J; Saunders, G M; Pollack, J B

1994-01-01

Standard methods for simultaneously inducing the structure and weights of recurrent neural networks limit every task to an assumed class of architectures. Such a simplification is necessary since the interactions between network structure and function are not well understood. Evolutionary computations, which include genetic algorithms and evolutionary programming, are population-based search methods that have shown promise in many similarly complex tasks. This paper argues that genetic algorithms are inappropriate for network acquisition and describes an evolutionary program, called GNARL, that simultaneously acquires both the structure and weights for recurrent networks. GNARL's empirical acquisition method allows for the emergence of complex behaviors and topologies that are potentially excluded by the artificial architectural constraints imposed in standard network induction methods.

"I'm Like You Not": Intergenerational Mobility of Working Class Students from a Cultural-Evolutionary Perspective

ERIC Educational Resources Information Center

Lovett, Trevor

2016-01-01

This retrospective narrative investigation challenges aspects of structural determinism. The biographical data generated in the study revealed that the baby-boomer, male participants were not academically constrained by their working class identities. Interpersonal relationships experienced within an individual's unique communities of practice…

Molecular interactions of orthologues of floral homeotic proteins from the gymnosperm Gnetum gnemon provide a clue to the evolutionary origin of 'floral quartets'.

PubMed

Wang, Yong-Qiang; Melzer, Rainer; Theissen, Günter

2010-10-01

Several lines of evidence suggest that the identity of floral organs in angiosperms is specified by multimeric transcription factor complexes composed of MADS-domain proteins. These bind to specific cis-regulatory elements ('CArG-boxes') of their target genes involving DNA-loop formation, thus constituting 'floral quartets'. Gymnosperms, angiosperms' closest relatives, contain orthologues of floral homeotic genes, but when and how the interactions constituting floral quartets were established during evolution has remained unknown. We have comprehensively studied the dimerization and DNA-binding of several classes of MADS-domain proteins from the gymnosperm Gnetum gnemon. Determination of protein-protein and protein-DNA interactions by yeast two-hybrid, in vitro pull-down and electrophoretic mobility shift assays revealed complex patterns of homo- and heterodimerization among orthologues of floral homeotic class B, class C and class E proteins and B(sister) proteins. Using DNase I footprint assays we demonstrate that both orthologues of class B with C proteins, and orthologues of class C proteins alone, but not orthologues of class B proteins alone can loop DNA in floral quartet-like complexes. This is in contrast to class B and class C proteins from angiosperms, which require other factors such as class E floral homeotic proteins to 'glue' them together in multimeric complexes. Our findings suggest that the evolutionary origin of floral quartet formation is based on the interaction of different DNA-bound homodimers, does not depend on class E proteins, and predates the origin of angiosperms. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

PubMed

Taylor, James; Tyekucheva, Svitlana; King, David C; Hardison, Ross C; Miller, Webb; Chiaromonte, Francesca

2006-12-01

Genomic sequence signals - such as base composition, presence of particular motifs, or evolutionary constraint - have been used effectively to identify functional elements. However, approaches based only on specific signals known to correlate with function can be quite limiting. When training data are available, application of computational learning algorithms to multispecies alignments has the potential to capture broader and more informative sequence and evolutionary patterns that better characterize a class of elements. However, effective exploitation of patterns in multispecies alignments is impeded by the vast number of possible alignment columns and by a limited understanding of which particular strings of columns may characterize a given class. We have developed a computational method, called ESPERR (evolutionary and sequence pattern extraction through reduced representations), which uses training examples to learn encodings of multispecies alignments into reduced forms tailored for the prediction of chosen classes of functional elements. ESPERR produces a greatly improved Regulatory Potential score, which can discriminate regulatory regions from neutral sites with excellent accuracy ( approximately 94%). This score captures strong signals (GC content and conservation), as well as subtler signals (with small contributions from many different alignment patterns) that characterize the regulatory elements in our training set. ESPERR is also effective for predicting other classes of functional elements, as we show for DNaseI hypersensitive sites and highly conserved regions with developmental enhancer activity. Our software, training data, and genome-wide predictions are available from our Web site (http://www.bx.psu.edu/projects/esperr).

Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein–Protein Interactions

PubMed Central

Bartlett, Madelaine; Thompson, Beth; Brabazon, Holly; Del Gizzi, Robert; Zhang, Thompson; Whipple, Clinton

2016-01-01

Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PIL) and AP3-like (AP3L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PIL protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PIL homodimerization is an anomaly or indicative of broader trends, we characterized PIL dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PIL homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PIL homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PIL protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PIL dimerization activity. Furthermore, ectopic expression of a Joinvillea PIL homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner. PMID:26908583

Dynamic species classification of microorganisms across time, abiotic and biotic environments—A sliding window approach

PubMed Central

Griffiths, Jason I.; Fronhofer, Emanuel A.; Garnier, Aurélie; Seymour, Mathew; Altermatt, Florian; Petchey, Owen L.

2017-01-01

The development of video-based monitoring methods allows for rapid, dynamic and accurate monitoring of individuals or communities, compared to slower traditional methods, with far reaching ecological and evolutionary applications. Large amounts of data are generated using video-based methods, which can be effectively processed using machine learning (ML) algorithms into meaningful ecological information. ML uses user defined classes (e.g. species), derived from a subset (i.e. training data) of video-observed quantitative features (e.g. phenotypic variation), to infer classes in subsequent observations. However, phenotypic variation often changes due to environmental conditions, which may lead to poor classification, if environmentally induced variation in phenotypes is not accounted for. Here we describe a framework for classifying species under changing environmental conditions based on the random forest classification. A sliding window approach was developed that restricts temporal and environmentally conditions to improve the classification. We tested our approach by applying the classification framework to experimental data. The experiment used a set of six ciliate species to monitor changes in community structure and behavior over hundreds of generations, in dozens of species combinations and across a temperature gradient. Differences in biotic and abiotic conditions caused simplistic classification approaches to be unsuccessful. In contrast, the sliding window approach allowed classification to be highly successful, as phenotypic differences driven by environmental change, could be captured by the classifier. Importantly, classification using the random forest algorithm showed comparable success when validated against traditional, slower, manual identification. Our framework allows for reliable classification in dynamic environments, and may help to improve strategies for long-term monitoring of species in changing environments. Our classification pipeline can be applied in fields assessing species community dynamics, such as eco-toxicology, ecology and evolutionary ecology. PMID:28472193

New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines.

PubMed

Balasubramaniam, Shandiya; Bray, Rebecca D; Mulder, Raoul A; Sunnucks, Paul; Pavlova, Alexandra; Melville, Jane

2016-05-21

The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune system and has been extensively studied across vertebrate taxa. Although the function of MHC genes appears to be conserved across taxa, there is great variation in the number and organisation of these genes. Among avian species, for instance, there are notable differences in MHC structure between passerine and non-passerine lineages: passerines typically have a high number of highly polymorphic MHC paralogs whereas non-passerines have fewer loci and lower levels of polymorphism. Although the occurrence of highly polymorphic MHC paralogs in passerines is well documented, their evolutionary origins are relatively unexplored. The majority of studies have focussed on the more derived passerine lineages and there is very little empirical information on the diversity of the MHC in basal passerine lineages. We undertook a study of MHC diversity and evolutionary relationships across seven species from four families (Climacteridae, Maluridae, Pardalotidae, Meliphagidae) that comprise a prominent component of the basal passerine lineages. We aimed to determine if highly polymorphic MHC paralogs have an early evolutionary origin within passerines or are a more derived feature of the infraorder Passerida. We identified 177 alleles of the MHC class II β exon 2 in seven basal passerine species, with variation in numbers of alleles across individuals and species. Overall, we found evidence of multiple gene loci, pseudoalleles, trans-species polymorphism and high allelic diversity in these basal lineages. Phylogenetic reconstruction of avian lineages based on MHC class II β exon 2 sequences strongly supported the monophyletic grouping of basal and derived passerine species. Our study provides evidence of a large number of highly polymorphic MHC paralogs in seven basal passerine species, with strong similarities to the MHC described in more derived passerine lineages rather than the simpler MHC in non-passerine lineages. These findings indicate an early evolutionary origin of highly polymorphic MHC paralogs in passerines and shed light on the evolutionary forces shaping the avian MHC.

The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis

PubMed Central

Ryan, Joseph F; Burton, Patrick M; Mazza, Maureen E; Kwong, Grace K; Mullikin, James C; Finnerty, John R

2006-01-01

Background Homeodomain transcription factors are key components in the developmental toolkits of animals. While this gene superclass predates the evolutionary split between animals, plants, and fungi, many homeobox genes appear unique to animals. The origin of particular homeobox genes may, therefore, be associated with the evolution of particular animal traits. Here we report the first near-complete set of homeodomains from a basal (diploblastic) animal. Results Phylogenetic analyses were performed on 130 homeodomains from the sequenced genome of the sea anemone Nematostella vectensis along with 228 homeodomains from human and 97 homeodomains from Drosophila. The Nematostella homeodomains appear to be distributed among established homeodomain classes in the following fashion: 72 ANTP class; one HNF class; four LIM class; five POU class; 33 PRD class; five SINE class; and six TALE class. For four of the Nematostella homeodomains, there is disagreement between neighbor-joining and Bayesian trees regarding their class membership. A putative Nematostella CUT class gene is also identified. Conclusion The homeodomain superclass underwent extensive radiations prior to the evolutionary split between Cnidaria and Bilateria. Fifty-six homeodomain families found in human and/or fruit fly are also found in Nematostella, though seventeen families shared by human and fly appear absent in Nematostella. Homeodomain loss is also apparent in the bilaterian taxa: eight homeodomain families shared by Drosophila and Nematostella appear absent from human (CG13424, EMXLX, HOMEOBRAIN, MSXLX, NK7, REPO, ROUGH, and UNC4), and six homeodomain families shared by human and Nematostella appear absent from fruit fly (ALX, DMBX, DUX, HNF, POU1, and VAX). PMID:16867185

Adaptive evolutionary conservation: towards a unified concept for defining conservation units.

PubMed

Fraser, D J; Bernatchez, L

2001-12-01

Recent years have seen a debate over various methods that could objectively prioritize conservation value below the species level. Most prominent among these has been the evolutionarily significant unit (ESU). We reviewed ESU concepts with the aim of proposing a more unified concept that would reconcile opposing views. Like species concepts, conflicting ESU concepts are all essentially aiming to define the same thing: segments of species whose divergence can be measured or evaluated by putting differential emphasis on the role of evolutionary forces at varied temporal scales. Thus, differences between ESU concepts lie more in the criteria used to define the ESUs themselves rather than in their fundamental essence. We provide a context-based framework for delineating ESUs which circumvents much of this situation. Rather than embroil in a befuddled debate over an optimal criterion, the key to a solution is accepting that differing criteria will work more dynamically than others and can be used alone or in combination depending on the situation. These assertions constitute the impetus behind adaptive evolutionary conservation.

The exaptive excellence of spandrels as a term and prototype

PubMed Central

Gould, Stephen Jay

1997-01-01

In 1979, Lewontin and I borrowed the architectural term “spandrel” (using the pendentives of San Marco in Venice as an example) to designate the class of forms and spaces that arise as necessary byproducts of another decision in design, and not as adaptations for direct utility in themselves. This proposal has generated a large literature featuring two critiques: (i) the terminological claim that the spandrels of San Marco are not true spandrels at all and (ii) the conceptual claim that they are adaptations and not byproducts. The features of the San Marco pendentives that we explicitly defined as spandrel-properties—their necessary number (four) and shape (roughly triangular)—are inevitable architectural byproducts, whatever the structural attributes of the pendentives themselves. The term spandrel may be extended from its particular architectural use for two-dimensional byproducts to the generality of “spaces left over,” a definition that properly includes the San Marco pendentives. Evolutionary biology needs such an explicit term for features arising as byproducts, rather than adaptations, whatever their subsequent exaptive utility. The concept of biological spandrels—including the examples here given of masculinized genitalia in female hyenas, exaptive use of an umbilicus as a brooding chamber by snails, the shoulder hump of the giant Irish deer, and several key features of human mentality—anchors the critique of overreliance upon adaptive scenarios in evolutionary explanation. Causes of historical origin must always be separated from current utilities; their conflation has seriously hampered the evolutionary analysis of form in the history of life. PMID:11038582

Variation in MHC class II B genes in marbled murrelets: implications for delineating conservation units

Treesearch

C. Vásquez-Carrillo; V. Friesen; L. Hall; M.Z. Peery

2013-01-01

Conserving genetic variation is critical for maintaining the evolutionary potential and viability of a species. Genetic studies seeking to delineate conservation units, however, typically focus on characterizing neutral genetic variation and may not identify populations harboring local adaptations. Here, variation at two major histocompatibility complex (MHC) class II...

In-Space Radiator Shape Optimization using Genetic Algorithms

NASA Technical Reports Server (NTRS)

Hull, Patrick V.; Kittredge, Ken; Tinker, Michael; SanSoucie, Michael

2006-01-01

Future space exploration missions will require the development of more advanced in-space radiators. These radiators should be highly efficient and lightweight, deployable heat rejection systems. Typical radiators for in-space heat mitigation commonly comprise a substantial portion of the total vehicle mass. A small mass savings of even 5-10% can greatly improve vehicle performance. The objective of this paper is to present the development of detailed tools for the analysis and design of in-space radiators using evolutionary computation techniques. The optimality criterion is defined as a two-dimensional radiator with a shape demonstrating the smallest mass for the greatest overall heat transfer, thus the end result is a set of highly functional radiator designs. This cross-disciplinary work combines topology optimization and thermal analysis design by means of a genetic algorithm The proposed design tool consists of the following steps; design parameterization based on the exterior boundary of the radiator, objective function definition (mass minimization and heat loss maximization), objective function evaluation via finite element analysis (thermal radiation analysis) and optimization based on evolutionary algorithms. The radiator design problem is defined as follows: the input force is a driving temperature and the output reaction is heat loss. Appropriate modeling of the space environment is added to capture its effect on the radiator. The design parameters chosen for this radiator shape optimization problem fall into two classes, variable height along the width of the radiator and a spline curve defining the -material boundary of the radiator. The implementation of multiple design parameter schemes allows the user to have more confidence in the radiator optimization tool upon demonstration of convergence between the two design parameter schemes. This tool easily allows the user to manipulate the driving temperature regions thus permitting detailed design of in-space radiators for unique situations. Preliminary results indicate an optimized shape following that of the temperature distribution regions in the "cooler" portions of the radiator. The results closely follow the expected radiator shape.

Stationary stability for evolutionary dynamics in finite populations

DOE PAGES

Harper, Marc; Fryer, Dashiell

2016-08-25

Here, we demonstrate a vast expansion of the theory of evolutionary stability to finite populations with mutation, connecting the theory of the stationary distribution of the Moran process with the Lyapunov theory of evolutionary stability. We define the notion of stationary stability for the Moran process with mutation and generalizations, as well as a generalized notion of evolutionary stability that includes mutation called an incentive stable state (ISS) candidate. For sufficiently large populations, extrema of the stationary distribution are ISS candidates and we give a family of Lyapunov quantities that are locally minimized at the stationary extrema and at ISSmore » candidates. In various examples, including for the Moran andWright–Fisher processes, we show that the local maxima of the stationary distribution capture the traditionally-defined evolutionarily stable states. The classical stability theory of the replicator dynamic is recovered in the large population limit. Finally we include descriptions of possible extensions to populations of variable size and populations evolving on graphs.« less

Evolutionary space platform concept study. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1982-01-01

The Evolutionary Space Platform Concept Study encompassed a 10 month effort to define, evaluate and compare approaches and concepts for evolving unmanned and manned capability platforms beyond the current Space Platform concepts to an evolutionary goal of establishing a permanent manned presence in space. Areas addressed included: special emphasis trade studies on the current unmanned concept, assessment of manned platform concepts, and utility analysis of a manned platform for defense related missions.

Joint scaling laws in functional and evolutionary categories in prokaryotic genomes

PubMed Central

Grilli, J.; Bassetti, B.; Maslov, S.; Cosentino Lagomarsino, M.

2012-01-01

We propose and study a class-expansion/innovation/loss model of genome evolution taking into account biological roles of genes and their constituent domains. In our model, numbers of genes in different functional categories are coupled to each other. For example, an increase in the number of metabolic enzymes in a genome is usually accompanied by addition of new transcription factors regulating these enzymes. Such coupling can be thought of as a proportional ‘recipe’ for genome composition of the type ‘a spoonful of sugar for each egg yolk’. The model jointly reproduces two known empirical laws: the distribution of family sizes and the non-linear scaling of the number of genes in certain functional categories (e.g. transcription factors) with genome size. In addition, it allows us to derive a novel relation between the exponents characterizing these two scaling laws, establishing a direct quantitative connection between evolutionary and functional categories. It predicts that functional categories that grow faster-than-linearly with genome size to be characterized by flatter-than-average family size distributions. This relation is confirmed by our bioinformatics analysis of prokaryotic genomes. This proves that the joint quantitative trends of functional and evolutionary classes can be understood in terms of evolutionary growth with proportional recipes. PMID:21937509

Evolution of vertebrate visual pigments.

PubMed

Bowmaker, James K

2008-09-01

The visual pigments of vertebrates evolved about 500 million years ago, before the major evolutionary step of the development of jaws. Four spectrally distinct classes of cone opsin evolved through gene duplication, followed by the rod opsin class that arose from the duplication of the middle-wave-sensitive cone opsin. All four cone classes are present in many extant teleost fish, reptiles and birds, but one or more classes have been lost in primitive fish, amphibians and mammals. Gene duplication within the cone classes, especially in teleosts, has resulted in multiple opsins being available, both temporally and spatially, during development.

Ecological and evolutionary consequences of explicit spatial structure in exploiter-victim systems

NASA Astrophysics Data System (ADS)

Klopfer, Eric David

One class of spatial model which has been widely used in ecology has been termed "pseudo-spatial models" and classically employs various types of aggregation in studying the coexistence of competing parasitoids. Yet, little is known about the relative effects of each of these aggregation behaviors. Thus, in Chapter 1 I chose to examine three types of aggregation and explore their relative strengths in promoting coexistence of two competing parasitoids. A striking shortcoming of spatial models in ecology to date is that there is a relative lack of use of spatial models to investigate problems on the evolutionary as opposed to ecological time scale. Consequently, in Chapter 2 I chose to start with a classic problem of evolutionary time scale--the evolution of virulence and predation rates. Debate about this problem has continued through several decades, yet many instances are not adequately explained by current models. In this study I explored the effect of explicit spatial structure on exploitation rates by comparing a cellular automata (CA) exploiter-victim model which incorporates local dynamics to a metapopulation model which does not include such dynamics. One advantage of CA models is that they are defined by simple rules rather than the often complex equations of other types of spatial models. This is an extremely useful attribute when one wants to convey results of models to an audience with an applied bent that is often uncomfortable with hard-to-understand equations. Thus, in Chapter 3, through the use of CA models I show that there are spatial phenomena which alter the impact of introduced predators and that these phenomena are potentially important in the implementation of biocontrol programs. The relatively recent incorporation of spatial models into the ecological literature has left most ecologists and evolutionary biologists without the ability to understand, let alone employ, spatial models in evolutionary problems. In order to give the next generation of potential ecologists a better understanding of these models, in Chapter 4 I present an interactive tutorial in which students are able to explore the most well studied of these models (the evolution of cooperation in a spatial environment).

Animal evolution: stiff or squishy notochord origins?

PubMed

Hejnol, Andreas; Lowe, Christopher J

2014-12-01

The notochord is considered an evolutionary novelty and one of the defining characters of chordates. A new study of an annelid challenges this view and proposes an earlier evolutionary origin in the most recent common ancestor of chordates and annelids. Copyright © 2014 Elsevier Ltd. All rights reserved.

The "Space" of Friendship: Young Children's Understandings and Expressions of Friendship in a Reception Class

ERIC Educational Resources Information Center

Papadopoulou, Marianna

2016-01-01

The purpose of this study has been to explore young children's understandings and experiences of friendship as these manifested in children's behaviours, in a reception class setting. Drawing on an evolutionary, ecological framework, friendship is seen as not only the expression and further development of social understandings and cognitive…

Evolutionary profiles from the QR factorization of multiple sequence alignments

PubMed Central

Sethi, Anurag; O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-01-01

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS. PMID:15741270

Evolution of Collective Behaviour in an Artificial World Using Linguistic Fuzzy Rule-Based Systems

PubMed Central

Lebar Bajec, Iztok

2017-01-01

Collective behaviour is a fascinating and easily observable phenomenon, attractive to a wide range of researchers. In biology, computational models have been extensively used to investigate various properties of collective behaviour, such as: transfer of information across the group, benefits of grouping (defence against predation, foraging), group decision-making process, and group behaviour types. The question ‘why,’ however remains largely unanswered. Here the interest goes into which pressures led to the evolution of such behaviour, and evolutionary computational models have already been used to test various biological hypotheses. Most of these models use genetic algorithms to tune the parameters of previously presented non-evolutionary models, but very few attempt to evolve collective behaviour from scratch. Of these last, the successful attempts display clumping or swarming behaviour. Empirical evidence suggests that in fish schools there exist three classes of behaviour; swarming, milling and polarized. In this paper we present a novel, artificial life-like evolutionary model, where individual agents are governed by linguistic fuzzy rule-based systems, which is capable of evolving all three classes of behaviour. PMID:28045964

Evolution of Collective Behaviour in an Artificial World Using Linguistic Fuzzy Rule-Based Systems.

PubMed

Demšar, Jure; Lebar Bajec, Iztok

2017-01-01

Collective behaviour is a fascinating and easily observable phenomenon, attractive to a wide range of researchers. In biology, computational models have been extensively used to investigate various properties of collective behaviour, such as: transfer of information across the group, benefits of grouping (defence against predation, foraging), group decision-making process, and group behaviour types. The question 'why,' however remains largely unanswered. Here the interest goes into which pressures led to the evolution of such behaviour, and evolutionary computational models have already been used to test various biological hypotheses. Most of these models use genetic algorithms to tune the parameters of previously presented non-evolutionary models, but very few attempt to evolve collective behaviour from scratch. Of these last, the successful attempts display clumping or swarming behaviour. Empirical evidence suggests that in fish schools there exist three classes of behaviour; swarming, milling and polarized. In this paper we present a novel, artificial life-like evolutionary model, where individual agents are governed by linguistic fuzzy rule-based systems, which is capable of evolving all three classes of behaviour.

Neural circuitry coordinating male copulation

PubMed Central

Pavlou, Hania J; Lin, Andrew C; Neville, Megan C; Nojima, Tetsuya; Diao, Fengqiu; Chen, Brian E; White, Benjamin H; Goodwin, Stephen F

2016-01-01

Copulation is the goal of the courtship process, crucial to reproductive success and evolutionary fitness. Identifying the circuitry underlying copulation is a necessary step towards understanding universal principles of circuit operation, and how circuit elements are recruited into the production of ordered action sequences. Here, we identify key sex-specific neurons that mediate copulation in Drosophila, and define a sexually dimorphic motor circuit in the male abdominal ganglion that mediates the action sequence of initiating and terminating copulation. This sexually dimorphic circuit composed of three neuronal classes – motor neurons, interneurons and mechanosensory neurons – controls the mechanics of copulation. By correlating the connectivity, function and activity of these neurons we have determined the logic for how this circuitry is coordinated to generate this male-specific behavior, and sets the stage for a circuit-level dissection of active sensing and modulation of copulatory behavior. DOI: http://dx.doi.org/10.7554/eLife.20713.001 PMID:27855059

Elements of an algorithm for optimizing a parameter-structural neural network

NASA Astrophysics Data System (ADS)

Mrówczyńska, Maria

2016-06-01

The field of processing information provided by measurement results is one of the most important components of geodetic technologies. The dynamic development of this field improves classic algorithms for numerical calculations in the aspect of analytical solutions that are difficult to achieve. Algorithms based on artificial intelligence in the form of artificial neural networks, including the topology of connections between neurons have become an important instrument connected to the problem of processing and modelling processes. This concept results from the integration of neural networks and parameter optimization methods and makes it possible to avoid the necessity to arbitrarily define the structure of a network. This kind of extension of the training process is exemplified by the algorithm called the Group Method of Data Handling (GMDH), which belongs to the class of evolutionary algorithms. The article presents a GMDH type network, used for modelling deformations of the geometrical axis of a steel chimney during its operation.

Toward a unifying framework for evolutionary processes.

PubMed

Paixão, Tiago; Badkobeh, Golnaz; Barton, Nick; Çörüş, Doğan; Dang, Duc-Cuong; Friedrich, Tobias; Lehre, Per Kristian; Sudholt, Dirk; Sutton, Andrew M; Trubenová, Barbora

2015-10-21

The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Space Station

NASA Image and Video Library

1982-01-01

McDornel Douglas performed an Evolutionary Space Platform Concept Study for the Marshall Space Flight Center in the early 1980's. The 10-month study was designed to define, evaluate, and compare approaches and concepts for evolving unmanned and manned capability platforms beyond the then current space platform concepts to an evolutionary goal of establishing a permanent-manned presence in space.

The evolutionary language game: an orthogonal approach.

PubMed

Lenaerts, Tom; Jansen, Bart; Tuyls, Karl; De Vylder, Bart

2005-08-21

Evolutionary game dynamics have been proposed as a mathematical framework for the cultural evolution of language and more specifically the evolution of vocabulary. This article discusses a model that is mutually exclusive in its underlying principals with some previously suggested models. The model describes how individuals in a population culturally acquire a vocabulary by actively participating in the acquisition process instead of passively observing and communicate through peer-to-peer interactions instead of vertical parent-offspring relations. Concretely, a notion of social/cultural learning called the naming game is first abstracted using learning theory. This abstraction defines the required cultural transmission mechanism for an evolutionary process. Second, the derived transmission system is expressed in terms of the well-known selection-mutation model defined in the context of evolutionary dynamics. In this way, the analogy between social learning and evolution at the level of meaning-word associations is made explicit. Although only horizontal and oblique transmission structures will be considered, extensions to vertical structures over different genetic generations can easily be incorporated. We provide a number of simplified experiments to clarify our reasoning.

Advanced Targeting Cost Function Design for Evolutionary Optimization of Control of Logistic Equation

NASA Astrophysics Data System (ADS)

Senkerik, Roman; Zelinka, Ivan; Davendra, Donald; Oplatkova, Zuzana

2010-06-01

This research deals with the optimization of the control of chaos by means of evolutionary algorithms. This work is aimed on an explanation of how to use evolutionary algorithms (EAs) and how to properly define the advanced targeting cost function (CF) securing very fast and precise stabilization of desired state for any initial conditions. As a model of deterministic chaotic system, the one dimensional Logistic equation was used. The evolutionary algorithm Self-Organizing Migrating Algorithm (SOMA) was used in four versions. For each version, repeated simulations were conducted to outline the effectiveness and robustness of used method and targeting CF.

Application of stochastic processes in random growth and evolutionary dynamics

NASA Astrophysics Data System (ADS)

Oikonomou, Panagiotis

We study the effect of power-law distributed randomness on the dynamical behavior of processes such as stochastic growth patterns and evolution. First, we examine the geometrical properties of random shapes produced by a generalized stochastic Loewner Evolution driven by a superposition of a Brownian motion and a stable Levy process. The situation is defined by the usual stochastic Loewner Evolution parameter, kappa, as well as alpha which defines the power-law tail of the stable Levy distribution. We show that the properties of these patterns change qualitatively and singularly at critical values of kappa and alpha. It is reasonable to call such changes "phase transitions". These transitions occur as kappa passes through four and as alpha passes through one. Numerical simulations are used to explore the global scaling behavior of these patterns in each "phase". We show both analytically and numerically that the growth continues indefinitely in the vertical direction for alpha greater than 1, goes as logarithmically with time for alpha equals to 1, and saturates for alpha smaller than 1. The probability density has two different scales corresponding to directions along and perpendicular to the boundary. Scaling functions for the probability density are given for various limiting cases. Second, we study the effect of the architecture of biological networks on their evolutionary dynamics. In recent years, studies of the architecture of large networks have unveiled a common topology, called scale-free, in which a majority of the elements are poorly connected except for a small fraction of highly connected components. We ask how networks with distinct topologies can evolve towards a pre-established target phenotype through a process of random mutations and selection. We use networks of Boolean components as a framework to model a large class of phenotypes. Within this approach, we find that homogeneous random networks and scale-free networks exhibit drastically different evolutionary paths. While homogeneous random networks accumulate neutral mutations and evolve by sparse punctuated steps, scale-free networks evolve rapidly and continuously towards the target phenotype. Moreover, we show that scale-free networks always evolve faster than homogeneous random networks; remarkably, this property does not depend on the precise value of the topological parameter. By contrast, homogeneous random networks require a specific tuning of their topological parameter in order to optimize their fitness. This model suggests that the evolutionary paths of biological networks, punctuated or continuous, may solely be determined by the network topology.

The concept of ageing in evolutionary algorithms: Discussion and inspirations for human ageing.

PubMed

Dimopoulos, Christos; Papageorgis, Panagiotis; Boustras, George; Efstathiades, Christodoulos

2017-04-01

This paper discusses the concept of ageing as this applies to the operation of Evolutionary Algorithms, and examines its relationship to the concept of ageing as this is understood for human beings. Evolutionary Algorithms constitute a family of search algorithms which base their operation on an analogy from the evolution of species in nature. The paper initially provides the necessary knowledge on the operation of Evolutionary Algorithms, focusing on the use of ageing strategies during the implementation of the evolutionary process. Background knowledge on the concept of ageing, as this is defined scientifically for biological systems, is subsequently presented. Based on this information, the paper provides a comparison between the two ageing concepts, and discusses the philosophical inspirations which can be drawn for human ageing based on the operation of Evolutionary Algorithms. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolutionary and mechanistic theories of aging.

PubMed

Hughes, Kimberly A; Reynolds, Rose M

2005-01-01

Senescence (aging) is defined as a decline in performance and fitness with advancing age. Senescence is a nearly universal feature of multicellular organisms, and understanding why it occurs is a long-standing problem in biology. Here we present a concise review of both evolutionary and mechanistic theories of aging. We describe the development of the general evolutionary theory, along with the mutation accumulation, antagonistic pleiotropy, and disposable soma versions of the evolutionary model. The review of the mechanistic theories focuses on the oxidative stress resistance, cellular signaling, and dietary control mechanisms of life span extension. We close with a discussion of how an approach that makes use of both evolutionary and molecular analyses can address a critical question: Which of the mechanisms that can cause variation in aging actually do cause variation in natural populations?

Probing the Evolution of Massive Young Stellar Objects using Weak Class II 6.7GHz Methanol Maser Emission

NASA Astrophysics Data System (ADS)

Ludwig, Bethany Ann; Cunningham, Nichol

2017-01-01

We present results from an investigation of class II 6.7GHz methanol masers towards four Massive Young Stellar Objects (MYSOs). The sources, selected from the Red MSX Source (RMS) Survey (Lumsden et al. 2013), were previously understood to be non-detections for class II methanol maser emission in the methanol multi-beam (MMB) Survey (Caswell et al. 2010.) Class II methanol masers are a well-known sign post of massive star forming regions and may be utilized to probe their relatively poorly understood formation. It is possible that these non-detections are simply weak masers that are potentially associated with a younger evolutionary phase of MYSOs as hypothesized by Olmi et al. (2014). The sources were chosen to sample various stages of evolution, having similar 21 to 8 micron flux ratios and bolometric luminosities as other MYSOs with previous class II methanol maser detections. We observed all 4 MYSOs with ATCA (~2" resolution) at 10 times deeper sensitivity than previously obtained with the MMB survey and have a spectral resolution of 0.087kms^-1 . The raw data is reduced using the program Miriad (Sault, R. J., et al., 1995) and deconvolutioned using the program CASA (McMullin, J. P., et al. 2007.) We determine one of the four observed MYSOs is harboring a weak class II methanol maser. We discuss the possibility of sensitivity limitations on the remaining sources as well as environmental and evolutionary differences between the sources.

Diversity and evolution of class 2 CRISPR–Cas systems

PubMed Central

Shmakov, Sergey; Smargon, Aaron; Scott, David; Cox, David; Pyzocha, Neena; Yan, Winston; Abudayyeh, Omar O.; Gootenberg, Jonathan S.; Makarova, Kira S.; Wolf, Yuri I.; Severinov, Konstantin; Zhang, Feng; Koonin, Eugene V.

2018-01-01

Class 2 CRISPR–Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR–Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR–Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR–Cas. PMID:28111461

Virus dynamics in the presence of synaptic transmission

PubMed Central

Komarova, Natalia L.; Wodarz, Dominik

2014-01-01

Traditionally, virus dynamics models consider populations of infected and target cells, and a population of free virus that can infect susceptible cells. In recent years, however, it has become clear that direct cell-to-cell transmission can also play an important role for the in vivo spread of viruses, especially retroviruses such as human T lymphotropic virus-1 (HTLV-1) and Human immundeficeincy virus (HIV). Such cell-to-cell transmission is thought to occur through the formation of virological synapses that are formed between an infected source cell and a susceptible target cell. Here we formulate and analyze a class of virus dynamics models that include such cell-cell synaptic transmission. We explore different ”strategies” of the virus defined by the number of viruses passed per synapse, and determine how the choice of strategy influences the basic reproductive ratio, R0, of the virus and thus its ability to establish a persistent infection. We show that depending on specific assumptions about the viral kinetics, strategies with low or intermediate numbers of viruses transferred may correspond to the highest values of R0. We also explore the evolutionary competition of viruses of different strains, which differ by their synaptic strategy, and show that viruses characterized by synaptic strategies with the highest R0 win the evolutionary competition and exclude other, inferior, strains. PMID:23357287

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.

Selection and paucity of phylogenetic signal challenge the utility of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans (Protista, Ciliophora).

PubMed

Rajter, Ľubomír; Vďačný, Peter

2018-05-12

The class Litostomatea represents a highly diverse but monophyletic group, uniting both free-living and endosymbiotic ciliates. Ribosomal RNA genes and ITS-region sequences helped to recognize and define the main litostomatean lineages, but did not provide enough phylogenetic signal to unambiguously resolve their interrelationships. In this study, we attempted to improve the resolution among main free-living predatory lineages by adding the gene coding for alpha-tubulin. However, our phylogenetic analyses challenged the performance of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans. We identified several mutually interconnected problems associated with the ciliate alpha-tubulin gene: the paucity of phylogenetic signal, molecular homoplasies and non-neutral evolution. Positive selection may generate molecular homoplasies (parallel evolution), while negative selection may cause a small number of changes and hence little phylogenetic informativness. Both problems were encountered in nucleotide and amino acid alpha-tubulin alignments, indicating an action of various selective pressures. Taking into account the involvement of alpha-tubulin in many essential biological processes, this protein could be so strongly affected by purifying selection that it even might have become an inappropriate molecular marker for reconstruction of phylogenetic relationships. Therefore, a great caution should be paid when tubulin genes are included in phylogenetic and/or phylogenomic analyses. Copyright © 2018 Elsevier Inc. All rights reserved.

Functional Constructivism: In Search of Formal Descriptors.

PubMed

Trofimova, Irina

2017-10-01

The Functional Constructivism (FC) paradigm is an alternative to behaviorism and considers behavior as being generated every time anew, based on an individual's capacities, environmental resources and demands. Walter Freeman's work provided us with evidence supporting the FC principles. In this paper we make parallels between gradual construction processes leading to the formation of individual behavior and habits, and evolutionary processes leading to the establishment of biological systems. Referencing evolutionary theory, several formal descriptors of such processes are proposed. These FC descriptors refer to the most universal aspects for constructing consistent structures: expansion of degrees of freedom, integration processes based on internal and external compatibility between systems and maintenance processes, all given in four different classes of systems: (a) Zone of Proximate Development (poorly defined) systems; (b) peer systems with emerging reproduction of multiple siblings; (c) systems with internalized integration of behavioral elements ('cruise controls'); and (d) systems capable of handling low-probability, not yet present events. The recursive dynamics within this set of descriptors acting on (traditional) downward, upward and horizontal directions of evolution, is conceptualized as diagonal evolution, or di-evolution. Two examples applying these FC descriptors to taxonomy are given: classification of the functionality of neuro-transmitters and temperament traits; classification of mental disorders. The paper is an early step towards finding a formal language describing universal tendencies in highly diverse, complex and multi-level transient systems known in ecology and biology as 'contingency cycles.'

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases

PubMed Central

Das, Sayoni; Dawson, Natalie L.; Dobrijevic, Dragana; Orengo, Christine

2016-01-01

Beta-lactamases represent the main bacterial mechanism of resistance to beta-lactam antibiotics and are a significant challenge to modern medicine. We have developed an automated classification and analysis protocol that exploits structure- and sequence-based approaches and which allows us to propose a grouping of serine beta-lactamases that more consistently captures and rationalizes the existing three classification schemes: Classes, (A, C and D, which vary in their implementation of the mechanism of action); Types (that largely reflect evolutionary distance measured by sequence similarity); and Variant groups (which largely correspond with the Bush-Jacoby clinical groups). Our analysis platform exploits a suite of in-house and public tools to identify Functional Determinants (FDs), i.e. residue sites, responsible for conferring different phenotypes between different classes, different types and different variants. We focused on Class A beta-lactamases, the most highly populated and clinically relevant class, to identify FDs implicated in the distinct phenotypes associated with different Class A Types and Variants. We show that our FunFHMMer method can separate the known beta-lactamase classes and identify those positions likely to be responsible for the different implementations of the mechanism of action in these enzymes. Two novel algorithms, ASSP and SSPA, allow detection of FD sites likely to contribute to the broadening of the substrate profiles. Using our approaches, we recognise 151 Class A types in UniProt. Finally, we used our beta-lactamase FunFams and ASSP profiles to detect 4 novel Class A types in microbiome samples. Our platforms have been validated by literature studies, in silico analysis and some targeted experimental verification. Although developed for the serine beta-lactamases they could be used to classify and analyse any diverse protein superfamily where sub-families have diverged over both long and short evolutionary timescales. PMID:27332861

Multi-target drugs to address multiple checkpoints in complex inflammatory pathologies: evolutionary cues for novel "first-in-class" anti-inflammatory drug candidates: a reviewer's perspective.

PubMed

Mathew, Geetha; Unnikrishnan, M K

2015-10-01

Inflammation is a complex, metabolically expensive process involving multiple signaling pathways and regulatory mechanisms which have evolved over evolutionary timescale. Addressing multiple targets of inflammation holistically, in moderation, is probably a more evolutionarily viable strategy, as compared to current therapy which addresses drug targets in isolation. Polypharmacology, addressing multiple targets, is commonly used in complex ailments, suggesting the superior safety and efficacy profile of multi-target (MT) drugs. Phenotypic drug discovery, which generated successful MT and first-in-class drugs in the past, is now re-emerging. A multi-pronged approach, which modulates the evolutionarily conserved, robust and pervasive cellular mechanisms of tissue repair, with AMPK at the helm, regulating the complex metabolic/immune/redox pathways underlying inflammation, is perhaps a more viable strategy than addressing single targets in isolation. Molecules that modulate multiple molecular mechanisms of inflammation in moderation (modulating TH cells toward the anti-inflammatory phenotype, activating AMPK, stimulating Nrf2 and inhibiting NFκB) might serve as a model for a novel Darwinian "first-in-class" therapeutic category that holistically addresses immune, redox and metabolic processes associated with inflammatory repair. Such a multimodal biological activity is supported by the fact that several non-calorific pleiotropic natural products with anti-inflammatory action have been incorporated into diet (chiefly guided by the adaptive development of olfacto-gustatory preferences over evolutionary timescales) rendering such molecules, endowed with evolutionarily privileged molecular scaffolds, naturally oriented toward multiple targets.

Everything You Always Wanted to Know About Maturity Models

DTIC Science & Technology

2014-01-23

path of experience, wisdom, perfection, or acculturation . Depicts an evolutionary progression of an attribute, characteristic, pattern, or...Processes are acculturated , defined, measured, and governed • Defined Level 3 •Managed Level 2 • Performed Level 1 • Incomplete Level 0

A comparative study of diversification events: the early Paleozoic versus the Mesozoic

NASA Technical Reports Server (NTRS)

Erwin, D. H.; Valentine, J. W.; Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

1987-01-01

We compare two major long-term diversifications of marine animal families that began during periods of low diversity but produced strikingly different numbers of phyla, classes, and orders. The first is the early-Paleozoic diversification (late Vendian-Ordovician; 182 MY duration) and the other the Mesozoic phase of the post-Paleozoic diversification (183 MY duration). The earlier diversification was associated with a great burst of morphological invention producing many phyla, classes, and orders and displaying high per taxon rates of family origination. The later diversification lacked novel morphologies recognized as phyla and classes, produced fewer orders, and displayed lower per taxon rates of family appearances. The chief difference between the diversifications appears to be that the earlier one proceeded from relatively narrow portions of adaptive space, whereas the latter proceeded from species widely scattered among adaptive zones and representing a variety of body plans. This difference is believed to explain the major differences in the products of these great radiations. Our data support those models that hold that evolutionary opportunity is a major factor in the outcome of evolutionary processes.

Asymmetric Evolutionary Games.

PubMed

McAvoy, Alex; Hauert, Christoph

2015-08-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

Analysis of convergence of an evolutionary algorithm with self-adaptation using a stochastic Lyapunov function.

PubMed

Semenov, Mikhail A; Terkel, Dmitri A

2003-01-01

This paper analyses the convergence of evolutionary algorithms using a technique which is based on a stochastic Lyapunov function and developed within the martingale theory. This technique is used to investigate the convergence of a simple evolutionary algorithm with self-adaptation, which contains two types of parameters: fitness parameters, belonging to the domain of the objective function; and control parameters, responsible for the variation of fitness parameters. Although both parameters mutate randomly and independently, they converge to the "optimum" due to the direct (for fitness parameters) and indirect (for control parameters) selection. We show that the convergence velocity of the evolutionary algorithm with self-adaptation is asymptotically exponential, similar to the velocity of the optimal deterministic algorithm on the class of unimodal functions. Although some martingale inequalities have not be proved analytically, they have been numerically validated with 0.999 confidence using Monte-Carlo simulations.

Evolutionary dynamics of group interactions on structured populations: a review

PubMed Central

Perc, Matjaž; Gómez-Gardeñes, Jesús; Szolnoki, Attila; Floría, Luis M.; Moreno, Yamir

2013-01-01

Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and non-living matter. Group interactions are a particularly important and widespread class, representative of which is the public goods game. In addition, methods of statistical physics have proved valuable for studying pattern formation, equilibrium selection and self-organization in evolutionary games. Here, we review recent advances in the study of evolutionary dynamics of group interactions on top of structured populations, including lattices, complex networks and coevolutionary models. We also compare these results with those obtained on well-mixed populations. The review particularly highlights that the study of the dynamics of group interactions, like several other important equilibrium and non-equilibrium dynamical processes in biological, economical and social sciences, benefits from the synergy between statistical physics, network science and evolutionary game theory. PMID:23303223

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein

NASA Technical Reports Server (NTRS)

Gaucher, Eric A.; Miyamoto, Michael M.; Benner, Steven A.

2003-01-01

The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.

Manager’s Guide to Technology Transition in an Evolutionary Acquisition Environment

DTIC Science & Technology

2005-06-01

program managers, product managers, staffs, and organizations that manage the development , procurement, production, and fielding of systems...rapidly advancing technologies. Technology transitions can occur during the development of systems, or even after a system has been in the field ...Documentation Evolutionary acquisition is an acquisition strategy that defines, develops , produces or acquires, and fields an initial hardware or software

Synthetic transitions: towards a new synthesis

PubMed Central

Solé, Ricard

2016-01-01

The evolution of life in our biosphere has been marked by several major innovations. Such major complexity shifts include the origin of cells, genetic codes or multicellularity to the emergence of non-genetic information, language or even consciousness. Understanding the nature and conditions for their rise and success is a major challenge for evolutionary biology. Along with data analysis, phylogenetic studies and dedicated experimental work, theoretical and computational studies are an essential part of this exploration. With the rise of synthetic biology, evolutionary robotics, artificial life and advanced simulations, novel perspectives to these problems have led to a rather interesting scenario, where not only the major transitions can be studied or even reproduced, but even new ones might be potentially identified. In both cases, transitions can be understood in terms of phase transitions, as defined in physics. Such mapping (if correct) would help in defining a general framework to establish a theory of major transitions, both natural and artificial. Here, we review some advances made at the crossroads between statistical physics, artificial life, synthetic biology and evolutionary robotics. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431516

Antigen processing and presentation: evolution from a bird's eye view.

PubMed

Kaufman, Jim

2013-09-01

Most detailed knowledge of the MHC outside of mammals has come from studies of chickens, originally due to the economic importance of the poultry industry. We have used our discoveries about the chicken MHC to develop a framework for understanding the evolution of the MHC, based on the importance of genomic organisation for gene co-evolution. In humans, MHC class I molecules are polymorphic and determine the specificity of peptide presentation, while the molecules involved in antigen processing are functionally monomorphic. The genes for tapasin, transporters associated with antigen presentation (TAPs) and inducible proteasome components (LMPs) are located in and beyond the class II region, far away from the class I genes in the class I region. In contrast, chickens express only one class I locus at high levels, which can result in strong MHC associations with resistance to particular infectious pathogens. The chicken TAP and tapasin genes are located very close to the class I genes, and have high levels of allelic polymorphism and moderate sequence diversity, co-evolving their specificities to work optimally with the dominantly expressed class I molecule. The salient features of the chicken MHC are found in many if not most non-mammalian species examined, and are likely to represent the ancestral organisation of the MHC. Comparison with the MHC organisation of humans and typical mammals suggests that a large inversion brought the class III region into the middle of the MHC, separating the antigen processing genes from the class I gene, breaking the co-evolutionary relationships and allowing a multigene family of well-expressed class I genes. Such co-evolution in the primordial MHC was likely responsible for the appearance of the antigen presentation pathways and receptor-ligand interactions at the birth of the adaptive immune system. Of course, much further work is required to understand this evolutionary framework in more detail. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.

PubMed

Krishnan, Arunkumar; Mustafa, Arshi; Almén, Markus Sällman; Fredriksson, Robert; Williams, Michael J; Schiöth, Helgi B

2015-10-01

Heterotrimeric G proteins perform a crucial role as molecular switches controlling various cellular responses mediated by G protein-coupled receptor (GPCR) signaling pathway. Recent data have shown that the vertebrate-like G protein families are found across metazoans and their closest unicellular relatives. However, an overall evolutionary hierarchy of vertebrate-like G proteins, including gene family annotations and in particular mapping individual gene gain/loss events across diverse holozoan lineages is still incomplete. Here, with more expanded invertebrate taxon sampling, we have reconstructed phylogenetic trees for each of the G protein classes/families and provide a robust classification and hierarchy of vertebrate-like heterotrimeric G proteins. Our results further extend the evidence that the common ancestor (CA) of holozoans had at least five ancestral Gα genes corresponding to all major vertebrate Gα classes and contain a total of eight genes including two Gβ and one Gγ. Our results also indicate that the GNAI/O-like gene likely duplicated in the last CA of metazoans to give rise to GNAI- and GNAO-like genes, which are conserved across invertebrates. Moreover, homologs of GNB1-4 paralogon- and GNB5 family-like genes are found in most metazoans and that the unicellular holozoans encode two ancestral Gβ genes. Similarly, most bilaterian invertebrates encode two Gγ genes which include a representative of the GNG gene cluster and a putative homolog of GNG13. Interestingly, our results also revealed key evolutionary events such as the Drosophila melanogaster eye specific Gβ subunit that is found conserved in most arthropods and several previously unidentified species specific expansions within Gαi/o, Gαs, Gαq, Gα12/13 classes and the GNB1-4 paralogon. Also, we provide an overall proposed evolutionary scenario on the expansions of all G protein families in vertebrate tetraploidizations. Our robust classification/hierarchy is essential to further understand the differential roles of GPCR/G protein mediated intracellular signaling system across various metazoan lineages. Copyright © 2015 Elsevier Inc. All rights reserved.

The evolutionary ecology of molecular replicators

PubMed Central

2016-01-01

By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology. PMID:27853598

The evolutionary ecology of molecular replicators.

PubMed

Nee, Sean

2016-08-01

By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.

Air cargo market outlook and impact via the NASA CLASS project. [Cargo/Logistics Airlift Systems Study

NASA Technical Reports Server (NTRS)

Winston, M. M.; Conner, D. W.

1980-01-01

An overview is given of the Cargo/Logistics Airlift Systems Study (CLASS) project which was a 10 man-year effort carried out by two contractor teams, aimed at defining factors impacting future system growth and obtaining market requirements and design guidelines for future air freighters. Growth projection was estimated by two approaches: one, an optimal systems approach with a more efficient and cost effective system considered as being available in 1990; and the other, an evolutionary approach with an econometric behavior model used to predict long term evolution from the present system. Both approaches predict significant growth in demand for international air freighter services and less growth for U.S. domestic services. Economic analysis of air freighter fleet options indicate very strong market appeal of derivative widebody transports in 1990 with little incentive to develop all new dedicated air freighters utilizing the 1990's technology until sometime beyond the year 2000. Advanced air freighters would be economically attractive for a wide range of payload sizes (to 500 metric tons), however, if a government would share in the RD and T costs by virtue of its needs for a slightly modified version of a civil air freighter design (a.g. military airlifter).

Coevolution in the Galapagos: An Example for the Biology Classroom.

ERIC Educational Resources Information Center

Biggs, Alton L.

1990-01-01

Several examples of coevolution which can be used in biology classes are presented. Discussed are evolutionary processes in general, giant cacti, and reptile and cacti association. The effects of human interference are briefly described. (CW)

Nonbinary Tree-Based Phylogenetic Networks.

PubMed

Jetten, Laura; van Iersel, Leo

2018-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.

Deep Space Mission Applications for NEXT: NASA's Evolutionary Xenon Thruster

NASA Technical Reports Server (NTRS)

Oh, David; Benson, Scott; Witzberger, Kevin; Cupples, Michael

2004-01-01

NASA's Evolutionary Xenon Thruster (NEXT) is designed to address a need for advanced ion propulsion systems on certain future NASA deep space missions. This paper surveys seven potential missions that have been identified as being able to take advantage of the unique capabilities of NEXT. Two conceptual missions to Titan and Neptune are analyzed, and it is shown that ion thrusters could decrease launch mass and shorten trip time, to Titan compared to chemical propulsion. A potential Mars Sample return mission is described, and compassion made between a chemical mission and a NEXT based mission. Four possible near term applications to New Frontiers and Discovery class missions are described, and comparisons are made to chemical systems or existing NSTAR ion propulsion system performance. The results show that NEXT has potential performance and cost benefits for missions in the Discovery, New Frontiers, and larger mission classes.

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.

Star formation history: Modeling of visual binaries

NASA Astrophysics Data System (ADS)

Gebrehiwot, Y. M.; Tessema, S. B.; Malkov, O. Yu.; Kovaleva, D. A.; Sytov, A. Yu.; Tutukov, A. V.

2018-05-01

Most stars form in binary or multiple systems. Their evolution is defined by masses of components, orbital separation and eccentricity. In order to understand star formation and evolutionary processes, it is vital to find distributions of physical parameters of binaries. We have carried out Monte Carlo simulations in which we simulate different pairing scenarios: random pairing, primary-constrained pairing, split-core pairing, and total and primary pairing in order to get distributions of binaries over physical parameters at birth. Next, for comparison with observations, we account for stellar evolution and selection effects. Brightness, radius, temperature, and other parameters of components are assigned or calculated according to approximate relations for stars in different evolutionary stages (main-sequence stars, red giants, white dwarfs, relativistic objects). Evolutionary stage is defined as a function of system age and component masses. We compare our results with the observed IMF, binarity rate, and binary mass-ratio distributions for field visual binaries to find initial distributions and pairing scenarios that produce observed distributions.

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

Evolution and Classification of Myosins, a Paneukaryotic Whole-Genome Approach

PubMed Central

Sebé-Pedrós, Arnau; Grau-Bové, Xavier; Richards, Thomas A.; Ruiz-Trillo, Iñaki

2014-01-01

Myosins are key components of the eukaryotic cytoskeleton, providing motility for a broad diversity of cargoes. Therefore, understanding the origin and evolutionary history of myosin classes is crucial to address the evolution of eukaryote cell biology. Here, we revise the classification of myosins using an updated taxon sampling that includes newly or recently sequenced genomes and transcriptomes from key taxa. We performed a survey of eukaryotic genomes and phylogenetic analyses of the myosin gene family, reconstructing the myosin toolkit at different key nodes in the eukaryotic tree of life. We also identified the phylogenetic distribution of myosin diversity in terms of number of genes, associated protein domains and number of classes in each taxa. Our analyses show that new classes (i.e., paralogs) and domain architectures were continuously generated throughout eukaryote evolution, with a significant expansion of myosin abundance and domain architectural diversity at the stem of Holozoa, predating the origin of animal multicellularity. Indeed, single-celled holozoans have the most complex myosin complement among eukaryotes, with paralogs of most myosins previously considered animal specific. We recover a dynamic evolutionary history, with several lineage-specific expansions (e.g., the myosin III-like gene family diversification in choanoflagellates), convergence in protein domain architectures (e.g., fungal and animal chitin synthase myosins), and important secondary losses. Overall, our evolutionary scheme demonstrates that the ancestral eukaryote likely had a complex myosin repertoire that included six genes with different protein domain architectures. Finally, we provide an integrative and robust classification, useful for future genomic and functional studies on this crucial eukaryotic gene family. PMID:24443438

Cooperation in two-person evolutionary games with complex personality profiles.

PubMed

Płatkowski, Tadeusz

2010-10-21

We propose a theory of evolution of social systems which generalizes the standard proportional fitness rule of the evolutionary game theory. The formalism is applied to describe the dynamics of two-person one-shot population games. In particular it predicts the non-zero level of cooperation in the long run for the Prisoner's Dilemma games, the increase of the fraction of cooperators for general classes of the Snow-Drift game, and stable nonzero cooperation level for coordination games. Copyright © 2010 Elsevier Ltd. All rights reserved.

Mission Advantages of NEXT: Nasa's Evolutionary Xenon Thruster

NASA Technical Reports Server (NTRS)

Oleson, Steven; Gefert, Leon; Benson, Scott; Patterson, Michael; Noca, Muriel; Sims, Jon

2002-01-01

With the demonstration of the NSTAR propulsion system on the Deep Space One mission, the range of the Discovery class of NASA missions can now be expanded. NSTAR lacks, however, sufficient performance for many of the more challenging Office of Space Science (OSS) missions. Recent studies have shown that NASA's Evolutionary Xenon Thruster (NEXT) ion propulsion system is the best choice for many exciting potential OSS missions including outer planet exploration and inner solar system sample returns. The NEXT system provides the higher power, higher specific impulse, and higher throughput required by these science missions.

Evolutionary transitions in symbioses: dramatic reductions in bathymetric and geographic ranges of Zoanthidea coincide with loss of symbioses with invertebrates.

PubMed

Swain, Timothy D

2010-06-01

Two fundamental symbiosis-based trophic types are recognized among Zoanthidea (Cnidaria, Anthozoa): fixed carbon is either obtained directly from zooxanthellae photosymbionts or from environmental sources through feeding with the assistance of host-invertebrate behaviour and structure. Each trophic type is characteristic of the suborders of Zoanthidea and is associated with substantial distributional asymmetries: suborder Macrocnemina are symbionts of invertebrates and have global geographic and bathymetric distributions and suborder Brachycnemina are hosts of endosymbiotic zooxanthellae and are restricted to tropical photic zones. While exposure to solar radiation could explain the bathymetric asymmetry it does not explain the geographic asymmetry, nor is it clear why evolutionary transitions to the zooxanthellae-free state have apparently occurred within Macrocnemina but not within Brachycnemina. To better understand the transitions between symbiosis-based trophic types of Zoanthidea, a concatenated data set of nuclear and mitochondrial nucleotide sequences were used to test hypotheses of monophyly for groups defined by morphology and symbiosis, and to reconstruct the evolutionary transitions of morphological and symbiotic characters. The results indicate that the morphological characters that define Macrocnemina are plesiomorphic and the characters that define its subordinate taxa are homoplasious. Symbioses with invertebrates have ancient and recent transitions with a general pattern of stability in host associations through evolutionary time. The reduction in distribution of Zoanthidea is independent of the evolution of zooxanthellae symbiosis and consistent with hypotheses of the benefits of invertebrate symbioses, indicating that the ability to persist in most habitats may have been lost with the termination of symbioses with invertebrates.

Naturalizing semiotics: The triadic sign of Charles Sanders Peirce as a systems property.

PubMed

Kilstrup, Mogens

2015-12-01

The father of pragmatism, Charles Sanders Peirce, gave in 1903 the following definition of a sign: "A Sign, or Representamen, is a First which stands in such a genuine triadic relation to a Second, called its Object, as to be capable of determining a Third, called its Interpretant, to assume the same triadic relation to its Object in which it stands itself to the same Object. The triadic relation is genuine, that is its three members are bound together by it in a way that does not consist in any complexus of dyadic relations". Despite its cult status and its pragmatic foundation, the Peircean sign has never revealed its true potential by being integrated into a formal system. In the present report, a reconstruction of the sign model is presented, which may at first appear somewhat obvious and superficial. However by use of the reconstructed model, the above statement and the majority of Peirce's other statements about the nature of signs fall into place. Instead of defining three links between Object (O), Representamen (R), and Interpretant (I), the sign is described as having a single three-dimensional link, specifying its location in a three dimensional (O,R,I) linkage space. To understand and explain sign function, the process of sign utilization (semiosis) has to be divided into two temporally separated phases, a sign-establishment phase where a three-dimensional link (Ψ(O,R,I)) is formed between three sign elements, and a later sign-interpretation phase where the established linkage is used for inferring significance to a novel phenomenon, if this satisfies the criteria for being a Representamen for the sign. Numerous statements from Peirce indicate that he used a two-staged semiosis paradigm although he did not state that explicitly. The three-dimensional model was primarily constructed for use in biosemiotics, as an exploratory frame for mapping the evolutionary establishment of sign links, which logically must have preceded the fixation of any regulatory process in molecular biological systems. It became clear, however, that the model is able to clarify many of the difficult explanations offered by Peirce about his sign model. I make no claim that Peirce used a similar type of three-dimensional model, because he explicitly used the chemical atom as naturalization (natural scientific explanation) for his sign model, an interesting but problematic analogy. In order to discuss common versus specific semiotic scaffolds for molecular biosemiotics, biosemiotics and semiotics proper, I start with a generic definition of the three-dimensional sign system, using human semiosis as examples. After this, the major part of the paper, I define the specific biochemical and evolutionary scaffolds that is used for obtaining the evolutionary memory that is needed for sign establishment. To exemplify semiosis according to the present model I present a typical situation where a Representamen (RE) and an object (OE) in the establishment phase are frequently encountered together by a sign interpreter. The process that links specific Representamens to specific Objects will first involve the recognition of the specific traits that distinguish the two sign elements. Subsequently the establishment process leads to the creation of a specific systems-state, called the Interpretant, which links the two traits in a way that allows retrieval of the information (a memory function). During a later interpretation phase, a hypothetical Object will be inferred by the interpreter when a Representamen (RI) harboring the required characteristics is encountered. This inference happens through a memory retrieval process, irrespective of the fact that relevant Objects of the sign may never be encountered after establishment. A simplified scheme for computer neural network algorithms is introduced as an example of such a system. Since the Peircean sign according to this definition is a systems property, there can be no sign without a sign interpreting systems or without some kind of memory function. A sign interpreter will thus harbor a semiotic scaffold that consists of at least an input sensor and an interpreting system coupled to a memory function. Further border conditions for semiotic scaffolds will be introduced. Peirce published a comprehensive sign definition system, but he allowed only ten sign classes, selected from the twenty-seven sign classes that result from his three main subdivisions, each containing three classes. His allowed sign classes are here identified as those which do not infer more significance during interpretation than was warranted during establishment. The excluded sign classes are either undefinable in his system or are of such a nature that the objects during interpretation are inferred to be much more significant than what was warranted during establishment. Occult signs are of these forbidden free-wheeling types, and it is postulated that they were omitted because Peirce defined his sign classes for use in a novel sign based logical system, where such over-signification would be detrimental. Copyright © 2015. Published by Elsevier Ltd.

Distribution of taxonomic classes and the compositional structure of the asteroid belt

NASA Technical Reports Server (NTRS)

Gradie, Jonathan C.; Chapman, Clark R.; Tedesco, Edward F.

1989-01-01

This paper reviews previous studies on the distribution of the asteroid taxonomic classes and analyzes the techniques, results, and interpretations of these studies, with special attention given to the strong and weak points of these studies and the important caveat for their interpretation. It is concluded that, in spite of the differences in class definition, the rather ordered heliocentric distribution of the composition is real and must be due to either primordial, evolutionary, or dynamical processes, or to a combination of all three. In general, the distribution of asteroid taxonomic classes is characterized by moderate-albedo asteroids dominant in the inner asteroid belt, and low-albedo asteroids prevalent in the outer belt and beyond.

Do Hypervolumes Have Holes?

PubMed

Blonder, Benjamin

2016-04-01

Hypervolumes are used widely to conceptualize niches and trait distributions for both species and communities. Some hypervolumes are expected to be convex, with boundaries defined by only upper and lower limits (e.g., fundamental niches), while others are expected to be maximal, with boundaries defined by the limits of available space (e.g., potential niches). However, observed hypervolumes (e.g., realized niches) could also have holes, defined as unoccupied hyperspace representing deviations from these expectations that may indicate unconsidered ecological or evolutionary processes. Detecting holes in more than two dimensions has to date not been possible. I develop a mathematical approach, implemented in the hypervolume R package, to infer holes in large and high-dimensional data sets. As a demonstration analysis, I assess evidence for vacant niches in a Galapagos finch community on Isabela Island. These mathematical concepts and software tools for detecting holes provide approaches for addressing contemporary research questions across ecology and evolutionary biology.

Psychotraumatology: What researchers and clinicians can learn from an evolutionary perspective.

PubMed

Troisi, Alfonso

2018-05-01

This review outlines the contribution of evolutionary science to experimental and clinical psychotraumatology. From an evolutionary perspective, traumatic and psychosocial stressors are conceived of as events or circumstances that thwart the achievement of biological goals. The more important is the adaptive value of the goal, the more painful is the emotional impact of the life event that endangers goal achievement. Life history theory and sexual selection theory help to explain why goal priorities differ between the sexes and across age groups. Cultural values and social learning interact with evolved inclinations in determining the hierarchy of goals for a specific person in a specific phase of his or her life. To illustrate the applicability of the evolutionary model, epidemiological and clinical data concerning individual differences in stress sensitivity and stress generation are reviewed and discussed. The final part of the review summarizes new hypotheses that explain how early and current psychosocial stressors can activate a series of adaptive mechanisms including developmental plasticity, predictive adaptive responses and differential susceptibility. Ultimately, the contribution of evolutionary science to psychotraumatology is the idea that experimental and clinical studies should shift the focus of research from the external environment (defined as all stressful factors external to the subjects under investigation) to the ecological environment (defined as those stressful factors of the external environment that have a greater potential to threaten the adaptive equilibrium of the subjects under investigation because of their evolved inclinations). Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapidly rotating polytropes in general relativity

NASA Technical Reports Server (NTRS)

Cook, Gregory B.; Shapiro, Stuart L.; Teukolsky, Saul A.

1994-01-01

We construct an extensive set of equilibrium sequences of rotating polytropes in general relativity. We determine a number of important physical parameters of such stars, including maximum mass and maximum spin rate. The stability of the configurations against quasi-radial perturbations is diagnosed. Two classes of evolutionary sequences of fixed rest mass and entropy are explored: normal sequences which behave very much like Newtonian evolutionary sequences, and supramassive sequences which exist solely because of relativistic effects. Dissipation leading to loss of angular momentum causes a star to evolve in a quasi-stationary fashion along an evolutionary sequence. Supramassive sequences evolve towards eventual catastrophic collapse to a black hole. Prior to collapse, the star must spin up as it loses angular momentum, an effect which may provide an observational precursor to gravitational collapse to a black hole.

Evolution and Christian Faith

NASA Astrophysics Data System (ADS)

Roughgarden, J. E.

2006-12-01

My recent book, Evolution and Christian Faith explores how evolutionary biology can be portrayed from the religious perspective of Christianity. The principal metaphors for evolutionary biology---differential success at breeding and random mutation, probably originate with the dawn of agriculture and clearly occur in the Bible. The central narrative of evolutionary biology can be presented using Biblical passages, providing an account of evolution that is inherently friendly to a Christian perspective. Still, evolutionary biology is far from complete, and problematic areas pertain to species in which the concept of an individual is poorly defined, and to species in which the expression of gender and sexuality depart from Darwin's sexual-selection templates. The present- day controversy in the US about teaching evolution in the schools provides an opportunity to engage the public about science education.

Evolutionary distances in the twilight zone--a rational kernel approach.

PubMed

Schwarz, Roland F; Fletcher, William; Förster, Frank; Merget, Benjamin; Wolf, Matthias; Schultz, Jörg; Markowetz, Florian

2010-12-31

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.

Cambrian Evolutionary Radiation: Context, correlation, and chronostratigraphy—Overcoming deficiencies of the first appearance datum (FAD) concept

NASA Astrophysics Data System (ADS)

Landing, Ed; Geyer, Gerd; Brasier, Martin D.; Bowring, Samuel A.

2013-08-01

Use of the first appearance datum (FAD) of a fossil to define a global chronostratigraphic unit's base can lead to intractable correlation and stability problems. FADs are diachronous—they reflect species' evolutionary history, dispersal, biofacies, preservation, collection, and taxonomy. The Cambrian Evolutionary Radiation is characterised by diachronous FADs, biofacies controls, and provincialism of taxa and ecological communities that confound a stable Lower Cambrian chronostratigraphy. Cambrian series and stage definitions require greater attention to assemblage zone successions and non-biostratigraphic, particularly carbon isotope, correlation techniques such as those that define the Ediacaran System base. A redefined, basal Cambrian Trichophycus pedum Assemblage Zone lies above the highest Ediacaran-type biotas (vendobionts, putative metazoans, and calcareous problematica such as Cloudina) and the basal Asteridium tornatum-Comasphaeridium velvetum Zone (acritarchs). This definition and the likely close correspondence of evolutionary origin and local FAD of T. pedum preserves the Fortune Head, Newfoundland, GSSP of the Cambrian base and allows the presence of sub-Cambrian, branched ichnofossils. The sub-Tommotian-equivalent base of Stage 2 (a suggested "Laolinian Stage") should be defined by the I'/L4/ZHUCE δ13C positive peak, bracketed by the lower ranges of Watsonella crosbyi and Aldanella attleborensis (molluscs) and the Skiagia ornata-Fimbrioglomerella membranacea Zone (acritarchs). The W. crosbyi and A. attleborensis FADs cannot define a Stage 2 base as they are diachronous even in the Newfoundland "type" W. crosbyi Zone. The Series 2 base cannot be based on a species' FAD owing to the provincialism of skeletalised metazoans in the Terreneuvian-Series 2 boundary interval and global heterochrony of the oldest trilobites. A Series 2 and Stage 3 (a suggested "Lenaldanian Series" and "Zhurinskyan Stage," new) GSSP base is proposed at the Siberian lower Atdabanian δ13C IV peak—which correlates into South China, Avalonia, and Morocco and assigns the oldest trilobites to the terminal Terreneuvian Series.

IRAS 23385 & 6053: A Prototype Massive Class O Object

NASA Technical Reports Server (NTRS)

Molinari, S.; Testi, L.; Brand, J.; Cesaroni, R.; Palla, F.

1998-01-01

The last few years have seen a rapid growth in observations aimed at identifying intermediate and high-mass star forming sites in a wide range of evolutionary stages ranging from Hot Cores to ultracompact regions, to proto-Ae/Be stars.

Evolutionary games on graphs

NASA Astrophysics Data System (ADS)

Szabó, György; Fáth, Gábor

2007-07-01

Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.

Evolutionary Design and Simulation of a Tube Crawling Inspection Robot

NASA Technical Reports Server (NTRS)

Craft, Michael; Howsman, Tom; ONeil, Daniel; Howell, Joe T. (Technical Monitor)

2002-01-01

The Space Robotics Assembly Team Simulation (SpaceRATS) is an expansive concept that will hopefully lead to a space flight demonstration of a robotic team cooperatively assembling a system from its constitutive parts. A primary objective of the SpaceRATS project is to develop a generalized evolutionary design approach for multiple classes of robots. The portion of the overall SpaceRats program associated with the evolutionary design and simulation of an inspection robot's morphology is the subject of this paper. The vast majority of this effort has concentrated on the use and modification of Darwin2K, a robotic design and simulation software package, to analyze the design of a tube crawling robot. This robot is designed for carrying out inspection duties in relatively inaccessible locations within a liquid rocket engine similar to the SSME. A preliminary design of the tube crawler robot was completed, and the mechanical dynamics of the system were simulated. An evolutionary approach to optimizing a few parameters of the system was utilized, resulting in a more optimum design.

Asymmetric Evolutionary Games

PubMed Central

McAvoy, Alex; Hauert, Christoph

2015-01-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

Are there laws of genome evolution?

PubMed

Koonin, Eugene V

2011-08-01

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.

Marching to the beat of Moore's Law

NASA Astrophysics Data System (ADS)

Borodovsky, Yan

2006-03-01

Area density scaling in integrated circuits, defined as transistor count per unit area, has followed the famous observation-cum-prediction by Gordon Moore for many generations. Known as "Moore's Law" which predicts density doubling every 18-24 month, it has provided all important synchronizing guidance and reference for tools and materials suppliers, IC manufacturers and their customers as to what minimal requirements their products and services need to meet to satisfy technical and financial expectations in support of the infrastructure required for the development and manufacturing of corresponding technology generation nodes. Multiple lithography solutions are usually under considerations for any given node. In general, three broad classes of solutions are considered: evolutionary - technology that is extension of existing technology infrastructure at similar or slightly higher cost and risk to schedule; revolutionary - technology that discards significant parts of the existing infrastructure at similar cost, higher risk to schedule but promises higher capability as compared to the evolutionary approach; and last but not least, disruptive - approach that as a rule promises similar or better capabilities, much lower cost and wholly unpredictable risk to schedule and products yields. This paper examines various lithography approaches, their respective merits against criteria of respective infrastructure availability, affordability and risk to IC manufacturer's schedules and strategy involved in developing and selecting best solution in an attempt to sort out key factors that will impact the decision on the lithography choice for large-scale manufacturing for the future technology nodes.

Microsatellites: Evolutionary and methodological background and empirical applications at individual, population, and phylogenetic levels

USGS Publications Warehouse

Scribner, Kim T.; Pearce, John M.; Baker, Allan J.

2000-01-01

The recent proliferation and greater accessibility of molecular genetic markers has led to a growing appreciation of the ecological and evolutionary inferences that can be drawn from molecular characterizations of individuals and populations (Burke et al. 1992, Avise 1994). Different techniques have the ability to target DNA sequences which have different patterns of inheritance, different modes and rates of evolution and, concomitantly, different levels of variation. In the quest for 'the right marker for the right job', microsatellites have been widely embraced as the marker of choice for many empirical genetic studies. The proliferation of microsatellite loci for various species and the voluminous literature compiled in very few years associated with their evolution and use in various research applications, exemplifies their growing importance as a research tool in the biological sciences.The ability to define allelic states based on variation at the nucleotide level has afforded unparalleled opportunities to document the actual mutational process and rates of evolution at individual microsatellite loci. The scrutiny to which these loci have been subjected has resulted in data that raise issues pertaining to assumptions formerly stated, but largely untestable for other marker classes. Indeed this is an active arena for theoretical and empirical work. Given the extensive and ever-increasing literature on various statistical methodologies and cautionary notes regarding the uses of microsatellites, some consideration should be given to the unique characteristics of these loci when determining how and under what conditions they can be employed.

A Spur to Atavism: Placing Platypus Poison.

PubMed

Hobbins, Peter

2015-11-01

For over two centuries, the platypus (Ornithorhynchus anatinus) has been constructed and categorized in multiple ways. An unprecedented mélange of anatomical features and physiological functions, it long remained a systematic quandary. Nevertheless, since 1797, naturalists and biologists have pursued two recurring obsessions. Investigations into platypus reproduction and lactation have focused attention largely upon females of the species. Despite its apparent admixture of avian, reptilian and mammalian characters, the platypus was soon placed as a rudimentary mammal--primitive, naïve and harmless. This article pursues a different taxonomic trajectory, concentrating on a specifically male anatomical development: the crural spur and venom gland on the hind legs. Once the defining characteristic of both the platypus and echidna (Tachyglossus aculeatus), by 1830 this sexed spur had been largely dismissed as inactive and irrelevant. For a creature regularly depicted as a biological outlier, the systematic and evolutionary implications of platypus poison have remained largely overlooked. In Australia, however, sporadic cases of 'spiking' led to consistent homologies being remarked between the platypus crural system and the venom glands of snakes. As with its reproductive reliance upon eggs, possession of an endogenous poison suggested significant reptilian affinities, yet the platypus has rarely been classed as an advanced reptile. Indeed, ongoing uncertainty regarding the biological purpose of the male's spur has ostensibly posed a directional puzzle. As with so many of its traits, however, platypus poison has been consistently described as a redundant remnant, rather than an emergent feature indicating evolutionary advance.

Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements

PubMed Central

Brunet, Tyler D.P.; Doolittle, W. Ford

2015-01-01

One of several issues at play in the renewed debate over “junk DNA” is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to “speed evolution” or as an “evolutionary repository” could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness—or are instead junk— is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. PMID:26253318

The evolution of cell types in animals: emerging principles from molecular studies.

PubMed

Arendt, Detlev

2008-11-01

Cell types are fundamental units of multicellular life but their evolution is obscure. How did the first cell types emerge and become distinct in animal evolution? What were the sets of cell types that existed at important evolutionary nodes that represent eumetazoan or bilaterian ancestors? How did these ancient cell types diversify further during the evolution of organ systems in the descending evolutionary lines? The recent advent of cell type molecular fingerprinting has yielded initial insights into the evolutionary interrelationships of cell types between remote animal phyla and has allowed us to define some first principles of cell type diversification in animal evolution.

Reconciliation of Gene and Species Trees

PubMed Central

Rusin, L. Y.; Lyubetskaya, E. V.; Gorbunov, K. Y.; Lyubetsky, V. A.

2014-01-01

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree. PMID:24800245

Symbiosis: An Evolutionary Innovator.

ERIC Educational Resources Information Center

Case, Emily

2003-01-01

Defines symbiosis and describes the connection between symbiosis and evolution, how it is described in science textbooks, and genetic variability. Discusses educational policy and science curriculum content. (YDS)

Designing Class Methods from Dataflow Diagrams

NASA Astrophysics Data System (ADS)

Shoval, Peretz; Kabeli-Shani, Judith

A method for designing the class methods of an information system is described. The method is part of FOOM - Functional and Object-Oriented Methodology. In the analysis phase of FOOM, two models defining the users' requirements are created: a conceptual data model - an initial class diagram; and a functional model - hierarchical OO-DFDs (object-oriented dataflow diagrams). Based on these models, a well-defined process of methods design is applied. First, the OO-DFDs are converted into transactions, i.e., system processes that supports user task. The components and the process logic of each transaction are described in detail, using pseudocode. Then, each transaction is decomposed, according to well-defined rules, into class methods of various types: basic methods, application-specific methods and main transaction (control) methods. Each method is attached to a proper class; messages between methods express the process logic of each transaction. The methods are defined using pseudocode or message charts.

Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

PubMed Central

2011-01-01

Background Several susceptibility genetic variants for autoimmune diseases have been identified. A subset of these polymorphisms displays an opposite risk profile in different autoimmune conditions. This observation open interesting questions on the evolutionary forces shaping the frequency of these alleles in human populations. We aimed at testing the hypothesis whereby balancing selection has shaped the frequency of opposite risk alleles. Results Since balancing selection signatures are expected to extend over short genomic portions, we focused our analyses on 11 regions carrying putative functional polymorphisms that may represent the disease variants (and the selection targets). No exceptional nucleotide diversity was observed for ZSCAN23, HLA-DMB, VARS2, PTPN22, BAT3, C6orf47, and IL10; summary statistics were consistent with evolutionary neutrality for these gene regions. Conversely, CDSN/PSORS1C1, TRIM10/TRIM40, BTNL2, and TAP2 showed extremely high nucleotide diversity and most tests rejected neutrality, suggesting the action of balancing selection. For TAP2 and BTNL2 these signatures are not secondary to linkage disequilibrium with HLA class II genes. Nonetheless, with the exception of variants in TRIM40 and CDSN, our data suggest that opposite risk SNPs are not selection targets but rather have accumulated as neutral variants. Conclusion Data herein indicate that balancing selection is common within the extended MHC region and involves several non-HLA loci. Yet, the evolutionary history of most SNPs with an opposite effect for autoimmune diseases is consistent with evolutionary neutrality. We suggest that variants with an opposite effect on autoimmune diseases should not be considered a distinct class of disease alleles from the evolutionary perspective and, in a few cases, the opposite effect on distinct diseases may derive from complex haplotype structures in regions with high genetic diversity. PMID:21682861

Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.

PubMed

Inglin, Raffael C; Meile, Leo; Stevens, Marc J A

2018-04-24

Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events. We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class "genetic information processing" is conserved in the core-genome but that "signaling and cellular processes" is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation. Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed by the environment and HGT.

The kW power module evolution study: Executive summary

NASA Technical Reports Server (NTRS)

1979-01-01

Using the Marshall Space Flight Center 25 kW Power Module (PM) reference design as a point of departure, the study defined evolutionary growth paths to 100 kW and above. A recommended development approach and initial configurations were described. Specific hardware changes from the reference design are recommended for the initial PM configuration to ensure evolutionary growth, improved replicability, and reduced cost. Certain functional changes are also recommended to enhance system capabilities.

Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways

PubMed Central

Woods, Kristina N.; Pfeffer, Jürgen; Klein-Seetharaman, Judith

2017-01-01

Retinal is the light-absorbing chromophore that is responsible for the activation of visual pigments and light-driven ion pumps. Evolutionary changes in the intermolecular interactions of the retinal with specific amino acids allow for adaptation of the spectral characteristics, referred to as spectral tuning. However, it has been proposed that a specific species of dragon fish has bypassed the adaptive evolutionary process of spectral tuning and replaced it with a single evolutionary event: photosensitization of rhodopsin by chlorophyll derivatives. Here, by using a combination of experimental measurements and computational modeling to probe retinal-receptor interactions in rhodopsin, we show how the binding of the chlorophyll derivative, chlorin-e6 (Ce6) in the intracellular domain (ICD) of the receptor allosterically excites G-protein coupled receptor class A (GPCR-A) conserved long-range correlated fluctuations that connect distant parts of the receptor. These long-range correlated motions are associated with regulating the dynamics and intermolecular interactions of specific amino acids in the retinal ligand-binding pocket that have been associated with shifts in the absorbance peak maximum (λmax) and hence, spectral sensitivity of the visual system. Moreover, the binding of Ce6 affects the overall global properties of the receptor. Specifically, we find that Ce6-induced dynamics alter the thermal stability of rhodopsin by adjusting hydrogen-bonding interactions near the receptor active-site that consequently also influences the intrinsic conformational equilibrium of the receptor. Due to the conservation of the ICD residues amongst different receptors in this class and the fact that all GPCR-A receptors share a common mechanism of activation, it is possible that the allosteric associations excited in rhodopsin with Ce6 binding are a common feature in all class A GPCRs. PMID:29312953

Estado evolutivo de estrellas con fenómeno B[e

NASA Astrophysics Data System (ADS)

Aidelman, Y. J.; Cidale, L.; Borges Fernandes, M.; Kraus, M.

The B[e] phenomenon is related to certain peculiar features observed in the spectrum of some B stars, which are mainly linked to the physical conditions of their circumstellar medium. As these stars are embedded in dense and optically thick circumstellar media, the determination of the spectral type and luminosity class of the central objects is quite difficult. As a consequence, their evolutionary stage and distances present huge uncertainties. In this work we study 4 B[e] stars and discuss their stellar fundamental parameters and evolutionary stages using the BCD spectrophotometric system. FULL TEXT IN SPANISH

Improving Search Properties in Genetic Programming

NASA Technical Reports Server (NTRS)

Janikow, Cezary Z.; DeWeese, Scott

1997-01-01

With the advancing computer processing capabilities, practical computer applications are mostly limited by the amount of human programming required to accomplish a specific task. This necessary human participation creates many problems, such as dramatically increased cost. To alleviate the problem, computers must become more autonomous. In other words, computers must be capable to program/reprogram themselves to adapt to changing environments/tasks/demands/domains. Evolutionary computation offers potential means, but it must be advanced beyond its current practical limitations. Evolutionary algorithms model nature. They maintain a population of structures representing potential solutions to the problem at hand. These structures undergo a simulated evolution by means of mutation, crossover, and a Darwinian selective pressure. Genetic programming (GP) is the most promising example of an evolutionary algorithm. In GP, the structures that evolve are trees, which is a dramatic departure from previously used representations such as strings in genetic algorithms. The space of potential trees is defined by means of their elements: functions, which label internal nodes, and terminals, which label leaves. By attaching semantic interpretation to those elements, trees can be interpreted as computer programs (given an interpreter), evolved architectures, etc. JSC has begun exploring GP as a potential tool for its long-term project on evolving dextrous robotic capabilities. Last year we identified representation redundancies as the primary source of inefficiency in GP. Subsequently, we proposed a method to use problem constraints to reduce those redundancies, effectively reducing GP complexity. This method was implemented afterwards at the University of Missouri. This summer, we have evaluated the payoff from using problem constraints to reduce search complexity on two classes of problems: learning boolean functions and solving the forward kinematics problem. We have also developed and implemented methods to use additional problem heuristics to fine-tune the searchable space, and to use typing information to further reduce the search space. Additional improvements have been proposed, but they are yet to be explored and implemented.

Autoimmunity as a Driving Force of Cognitive Evolution

PubMed Central

Nataf, Serge

2017-01-01

In the last decades, increasingly robust experimental approaches have formally demonstrated that autoimmunity is a physiological process involved in a large range of functions including cognition. On this basis, the recently enunciated “brain superautoantigens” theory proposes that autoimmunity has been a driving force of cognitive evolution. It is notably suggested that the immune and nervous systems have somehow co-evolved and exerted a mutual selection pressure benefiting to both systems. In this two-way process, the evolutionary-determined emergence of neurons expressing specific immunogenic antigens (brain superautoantigens) has exerted a selection pressure on immune genes shaping the T-cell repertoire. Such a selection pressure on immune genes has translated into the emergence of a finely tuned autoimmune T-cell repertoire that promotes cognition. In another hand, the evolutionary-determined emergence of brain-autoreactive T-cells has exerted a selection pressure on neural genes coding for brain superautoantigens. Such a selection pressure has translated into the emergence of a neural repertoire (defined here as the whole of neurons, synapses and non-neuronal cells involved in cognitive functions) expressing brain superautoantigens. Overall, the brain superautoantigens theory suggests that cognitive evolution might have been primarily driven by internal cues rather than external environmental conditions. Importantly, while providing a unique molecular connection between neural and T-cell repertoires under physiological conditions, brain superautoantigens may also constitute an Achilles heel responsible for the particular susceptibility of Homo sapiens to “neuroimmune co-pathologies” i.e., disorders affecting both neural and T-cell repertoires. These may notably include paraneoplastic syndromes, multiple sclerosis as well as autism, schizophrenia and neurodegenerative diseases. In the context of this theoretical frame, a specific emphasis is given here to the potential evolutionary role exerted by two families of genes, namely the MHC class II genes, involved in antigen presentation to T-cells, and the Foxp genes, which play crucial roles in language (Foxp2) and the regulation of autoimmunity (Foxp3). PMID:29123465

Detecting and Analyzing Genetic Recombination Using RDP4.

PubMed

Martin, Darren P; Murrell, Ben; Khoosal, Arjun; Muhire, Brejnev

2017-01-01

Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. The evolutionary value of recombination has been widely debated and so too has its influence on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. When nucleic acids recombine, the evolution of the daughter or recombinant molecule cannot be accurately described by a single phylogeny. This simple fact can seriously undermine the accuracy of any phylogenetics-based analytical approach which assumes that the evolutionary history of a set of recombining sequences can be adequately described by a single phylogenetic tree. There are presently a large number of available methods and associated computer programs for analyzing and characterizing recombination in various classes of nucleotide sequence datasets. Here we examine the use of some of these methods to derive and test recombination hypotheses using multiple sequence alignments.

Yellow evolved stars in open clusters

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

Sowell, J.R.

1987-05-01

This paper describes a program in which Galactic cluster post-AGB candidates were first identified and then analyzed for cluster membership via radial velocities, monitored for possible photometric variations, examined for evidence of mass loss, and classified as completely as possible in terms of their basic stellar parameters. The intrinsically brightest supergiants are found in the youngest clusters. With increasing cluster age, the absolute luminosities attained by the supergiants decline. It appears that the evolutionary tracks of luminosity class II stars are more similar to those of class I than of class III. Only two superluminous giant star candidates are foundmore » in open clusters. 154 references.« less

Diversification and enrichment of clinical biomaterials inspired by Darwinian evolution.

PubMed

Green, D W; Watson, G S; Watson, J A; Lee, D-J; Lee, J-M; Jung, H-S

2016-09-15

Regenerative medicine and biomaterials design are driven by biomimicry. There is the essential requirement to emulate human cell, tissue, organ and physiological complexity to ensure long-lasting clinical success. Biomimicry projects for biomaterials innovation can be re-invigorated with evolutionary insights and perspectives, since Darwinian evolution is the original dynamic process for biological organisation and complexity. Many existing human inspired regenerative biomaterials (defined as a nature generated, nature derived and nature mimicking structure, produced within a biological system, which can deputise for, or replace human tissues for which it closely matches) are without important elements of biological complexity such as, hierarchy and autonomous actions. It is possible to engineer these essential elements into clinical biomaterials via bioinspired implementation of concepts, processes and mechanisms played out during Darwinian evolution; mechanisms such as, directed, computational, accelerated evolutions and artificial selection contrived in the laboratory. These dynamos for innovation can be used during biomaterials fabrication, but also to choose optimal designs in the regeneration process. Further evolutionary information can help at the design stage; gleaned from the historical evolution of material adaptations compared across phylogenies to changes in their environment and habitats. Taken together, harnessing evolutionary mechanisms and evolutionary pathways, leading to ideal adaptations, will eventually provide a new class of Darwinian and evolutionary biomaterials. This will provide bioengineers with a more diversified and more efficient innovation tool for biomaterial design, synthesis and function than currently achieved with synthetic materials chemistry programmes and rational based materials design approach, which require reasoned logic. It will also inject further creativity, diversity and richness into the biomedical technologies that we make. All of which are based on biological principles. Such evolution-inspired biomaterials have the potential to generate innovative solutions, which match with existing bioengineering problems, in vital areas of clinical materials translation that include tissue engineering, gene delivery, drug delivery, immunity modulation, and scar-less wound healing. Evolution by natural selection is a powerful generator of innovations in molecular, materials and structures. Man has influenced evolution for thousands of years, to create new breeds of farm animals and crop plants, but now molecular and materials can be molded in the same way. Biological molecules and simple structures can be evolved, literally in the laboratory. Furthermore, they are re-designed via lessons learnt from evolutionary history. Through a 3-step process to (1) create variants in material building blocks, (2) screen the variants with beneficial traits/properties and (3) select and support their self-assembly into usable materials, improvements in design and performance can emerge. By introducing biological molecules and small organisms into this process, it is possible to make increasingly diversified, sophisticated and clinically relevant materials for multiple roles in biomedicine. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Markov-modulated Markov chains and the covarion process of molecular evolution.

PubMed

Galtier, N; Jean-Marie, A

2004-01-01

The covarion (or site specific rate variation, SSRV) process of biological sequence evolution is a process by which the evolutionary rate of a nucleotide/amino acid/codon position can change in time. In this paper, we introduce time-continuous, space-discrete, Markov-modulated Markov chains as a model for representing SSRV processes, generalizing existing theory to any model of rate change. We propose a fast algorithm for diagonalizing the generator matrix of relevant Markov-modulated Markov processes. This algorithm makes phylogeny likelihood calculation tractable even for a large number of rate classes and a large number of states, so that SSRV models become applicable to amino acid or codon sequence datasets. Using this algorithm, we investigate the accuracy of the discrete approximation to the Gamma distribution of evolutionary rates, widely used in molecular phylogeny. We show that a relatively large number of classes is required to achieve accurate approximation of the exact likelihood when the number of analyzed sequences exceeds 20, both under the SSRV and among site rate variation (ASRV) models.

Employment of Both Mn I and II Transitions to Determine the Abundance Trend and Ionization Balance in Three Stellar Evolutionary Classes

NASA Astrophysics Data System (ADS)

Sobeck, Jennifer; Den Hartog, B.; Lawler, J.; Sneden, C.

2010-01-01

Several prior investigations have repeatedly found that Manganese is under-abundant with respect to solar in metal-deficient stars. However a recent study, which employed a non-LTE approach/methodology, found that the [Mn/Fe] abundance ratio remains solar in the range -2.5 < [Fe/H] < 0 (results which stand in direct contrast to previous data). We will re-determine the [Mn/Fe] ratio over a large range of metallicity in a statistically significant sample consisting of stars from three evolutionary classes (dwarf, turnoff, and giant). We will employ new laboratory work (reported also at this meeting) to analyze the transitions of *both* the neutral (Mn I) and the first-ionized species (Mn II) in stellar spectra. We intend to determine the ionization equilibrium within each star and identify departures from LTE in each stellar group. We will explore the Mn abundance trend with metallicity and provide insight into its astrophysical origin (with special emphasis on the explosive nucleosynthetic contribution).

Sex in an Evolutionary Perspective: Just Another Reaction Norm

PubMed Central

Nylin, Sören

2010-01-01

It is common to refer to all sorts of clear-cut differences between the sexes as something that is biologically almost inevitable. Although this does not reflect the status of evolutionary theory on sex determination and sexual dimorphism, it is probably a common view among evolutionary biologists as well, because of the impact of sexual selection theory. To get away from thinking about biological sex and traits associated with a particular sex as something static, it should be recognized that in an evolutionary perspective sex can be viewed as a reaction norm, with sex attributes being phenotypically plastic. Sex determination itself is fundamentally plastic, even when it is termed “genetic”. The phenotypic expression of traits that are statistically associated with a particular sex always has a plastic component. This plasticity allows for much more variation in the expression of traits according to sex and more overlap between the sexes than is typically acknowledged. Here we review the variation and frequency of evolutionary changes in sex, sex determination and sex roles and conclude that sex in an evolutionary time-frame is extremely variable. We draw on recent findings in sex determination mechanisms, empirical findings of morphology and behaviour as well as genetic and developmental models to explore the concept of sex as a reaction norm. From this point of view, sexual differences are not expected to generally fall into neat, discrete, pre-determined classes. It is important to acknowledge this variability in order to increase objectivity in evolutionary research. PMID:21170116

Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species.

PubMed

Rodríguez-Quilón, Isabel; Santos-Del-Blanco, Luis; Serra-Varela, María Jesús; Koskela, Jarkko; González-Martínez, Santiago C; Alía, Ricardo

2016-10-01

Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available. © 2016 by the Ecological Society of America.

Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus.

PubMed

Mohammed, Jaaved; Flynt, Alex S; Panzarino, Alexandra M; Mondal, Md Mosharrof Hossein; DeCruz, Matthew; Siepel, Adam; Lai, Eric C

2018-01-01

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5' end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3' untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution. © 2018 Mohammed et al.; Published by Cold Spring Harbor Laboratory Press.

Phylogenetic relationships of the ciliate class Heterotrichea (Protista, Ciliophora, Postciliodesmatophora) inferred from multiple molecular markers and multifaceted analysis strategy.

PubMed

Shazib, Shahed Uddin Ahmed; Vd'ačný, Peter; Kim, Ji Hye; Jang, Seok Won; Shin, Mann Kyoon

2014-09-01

The ciliate class Heterotrichea is defined by somatic dikinetids bearing postciliodesmata, by an oral apparatus consisting of a paroral membrane and an adoral zone of membranelles, as well as by features of nuclear division involving extramacronuclear microtubules. Although phylogenetic interrelationships among heterotrichs have been analyzed several times, deeper nodes of the heterotrichean tree of life remain poorly resolved. To cast more light on the evolutionary history of heterotricheans, we performed phylogenetic analyses of multiple loci (18S rRNA gene, ITS1-5.8S rRNA-ITS2 region, and 28S rRNA gene) using traditional tree-building phylogenetic methods and statistical tree topology tests as well as phylogenetic networks, split spectrum analysis and quartet likelihood mapping. This multifaceted approach has shown that (1) Peritromus is very likely an adelphotaxon of all other heterotrichs; (2) Spirostomum and Anigsteinia are sister taxa and their common monophyletic origin is strongly supported by a uniquely posteriorly-thickened paroral membrane; (3) the monotypic family Chattonidiidae should be suppressed because its type genus clusters within the family Condylostomatidae; and (4) new families are needed for Gruberia and Fabrea because their affiliation with Spirostomidae and Climacostomidae, respectively, is not supported by molecular phylogenies nor the fine structure of the paroral membrane. Copyright © 2014 Elsevier Inc. All rights reserved.

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

Singleton, Jr., Robert

This report documents the implementation of several related 1D heat flow problems in the verification package ExactPack [1]. In particular, the planar sandwich class defined in Ref. [2], as well as the classes PlanarSandwichHot, PlanarSandwichHalf, and other generalizations of the planar sandwich problem, are defined and documented here. A rather general treatment of 1D heat flow is presented, whose main results have been implemented in the class Rod1D. All planar sandwich classes are derived from the parent class Rod1D.

Genomic V exons from whole genome shotgun data in reptiles.

PubMed

Olivieri, D N; von Haeften, B; Sánchez-Espinel, C; Faro, J; Gambón-Deza, F

2014-08-01

Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

Fixation of competing strategies when interacting agents differ in the time scale of strategy updating

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Weissing, Franz J.; Cao, Ming

2016-09-01

A commonly used assumption in evolutionary game theory is that natural selection acts on individuals in the same time scale; e.g., players use the same frequency to update their strategies. Variation in learning rates within populations suggests that evolutionary game theory may not necessarily be restricted to uniform time scales associated with the game interaction and strategy adaption evolution. In this study, we remove this restricting assumption by dividing the population into fast and slow groups according to the players' strategy updating frequencies and investigate how different strategy compositions of one group influence the evolutionary outcome of the other's fixation probabilities of strategies within its own group. Analytical analysis and numerical calculations are performed to study the evolutionary dynamics of strategies in typical classes of two-player games (prisoner's dilemma game, snowdrift game, and stag-hunt game). The introduction of the heterogeneity in strategy-update time scales leads to substantial changes in the evolution dynamics of strategies. We provide an approximation formula for the fixation probability of mutant types in finite populations and study the outcome of strategy evolution under the weak selection. We find that although heterogeneity in time scales makes the collective evolutionary dynamics more complicated, the possible long-run evolutionary outcome can be effectively predicted under technical assumptions when knowing the population composition and payoff parameters.

Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata.

PubMed

Suvorov, Anton; Jensen, Nicholas O; Sharkey, Camilla R; Fujimoto, M Stanley; Bodily, Paul; Wightman, Haley M Cahill; Ogden, T Heath; Clement, Mark J; Bybee, Seth M

2017-03-01

Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Several evolutionary models have been proposed for gene duplication to explain how new gene copies are preserved by natural selection, but these models have rarely been tested using empirical data. Opsin proteins, when combined with a chromophore, form a photopigment that is responsible for the absorption of light, the first step in the phototransduction cascade. Adaptive gene duplications have occurred many times within the animal opsins' gene family, leading to novel wavelength sensitivities. Consequently, opsins are an attractive choice for the study of gene duplication evolutionary models. Odonata (dragonflies and damselflies) have the largest opsin repertoire of any insect currently known. Additionally, there is tremendous variation in opsin copy number between species, particularly in the long-wavelength-sensitive (LWS) class. Using comprehensive phylotranscriptomic and statistical approaches, we tested various evolutionary models of gene duplication. Our results suggest that both the blue-sensitive (BS) and LWS opsin classes were subjected to strong positive selection that greatly weakens after multiple duplication events, a pattern that is consistent with the permanent heterozygote model. Due to the immense interspecific variation and duplicability potential of opsin genes among odonates, they represent a unique model system to test hypotheses regarding opsin gene duplication and diversification at the molecular level. © 2016 John Wiley & Sons Ltd.

Evolutionary cell biology: two origins, one objective.

PubMed

Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

2014-12-02

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

Evolutionary cell biology: Two origins, one objective

PubMed Central

Lynch, Michael; Field, Mark C.; Goodson, Holly V.; Malik, Harmit S.; Pereira-Leal, José B.; Roos, David S.; Turkewitz, Aaron P.; Sazer, Shelley

2014-01-01

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology. PMID:25404324

Extreme halophilic archaea derive from two distinct methanogen Class II lineages.

PubMed

Aouad, Monique; Taib, Najwa; Oudart, Anne; Lecocq, Michel; Gouy, Manolo; Brochier-Armanet, Céline

2018-04-20

Phylogenetic analyses of conserved core genes have disentangled most of the ancient relationships in Archaea. However, some groups remain debated, like the DPANN, a deep-branching super-phylum composed of nanosized archaea with reduced genomes. Among these, the Nanohaloarchaea require high-salt concentrations for growth. Their discovery in 2012 was significant because they represent, together with Halobacteria (a Class belonging to Euryarchaeota), the only two described lineages of extreme halophilic archaea. The phylogenetic position of Nanohaloarchaea is highly debated, being alternatively proposed as the sister-lineage of Halobacteria or a member of the DPANN super-phylum. Pinpointing the phylogenetic position of extreme halophilic archaea is important to improve our knowledge of the deep evolutionary history of Archaea and the molecular adaptive processes and evolutionary paths that allowed their emergence. Using comparative genomic approaches, we identified 258 markers carrying a reliable phylogenetic signal. By combining strategies limiting the impact of biases on phylogenetic inference, we showed that Nanohaloarchaea and Halobacteria represent two independent lines that derived from two distinct but related methanogens Class II lineages. This implies that adaptation to high salinity emerged twice independently in Archaea and indicates that their emergence within DPANN in previous studies is likely the consequence of a tree reconstruction artifact, challenging the existence of this super-phylum. Copyright © 2018. Published by Elsevier Inc.

Phylogeny of Eutardigrada: new molecular data and their morphological support lead to the identification of new evolutionary lineages.

PubMed

Bertolani, Roberto; Guidetti, Roberto; Marchioro, Trevor; Altiero, Tiziana; Rebecchi, Lorena; Cesari, Michele

2014-07-01

An extensive study of the phylogeny of Eutardigrada, the largest class of Tardigrada, has been performed analyzing one hundred and forty sequences (eighty of which newly obtained) representative of one hundred and twenty-nine specimens belonging to all families (except Necopinatidae) of this class. The molecular (18S and 28S rRNA) results were compared with new and previous morphological data, allowing us to find new phylogenetic relationships, to identify new phylogenetic lineages, to erect new taxa for some lineages, and to find several morphological synapomorphies supporting the identified clusters. The class Eutardigrada has been confirmed and, within it, the orders Apochela and Parachela, the superfamilies Macrobiotoidea, Hypsibioidea, Isohypsibioidea, and Eohypsibioidea, and all the families and subfamilies considered, although with emended diagnoses in several cases. In addition, new taxa have been erected: the new subfamily Pilatobiinae (Hypsibiidae) with the new genus Pilatobius, as well as an upgrading of Diphascon and Adropion to genus level, previously considered subgenera of Diphascon. Our results demonstrate that while molecular analysis is an important tool for understanding phylogeny, an integrative and comparative approach using both molecular and morphological data is necessary to better elucidate evolutionary relationships. Copyright © 2014 Elsevier Inc. All rights reserved.

Generative Representations for Evolving Families of Designs

NASA Technical Reports Server (NTRS)

Hornby, Gregory S.

2003-01-01

Since typical evolutionary design systems encode only a single artifact with each individual, each time the objective changes a new set of individuals must be evolved. When this objective varies in a way that can be parameterized, a more general method is to use a representation in which a single individual encodes an entire class of artifacts. In addition to saving time by preventing the need for multiple evolutionary runs, the evolution of parameter-controlled designs can create families of artifacts with the same style and a reuse of parts between members of the family. In this paper an evolutionary design system is described which uses a generative representation to encode families of designs. Because a generative representation is an algorithmic encoding of a design, its input parameters are a way to control aspects of the design it generates. By evaluating individuals multiple times with different input parameters the evolutionary design system creates individuals in which the input parameter controls specific aspects of a design. This system is demonstrated on two design substrates: neural-networks which solve the 3/5/7-parity problem and three-dimensional tables of varying heights.

Structural symmetry in evolutionary games.

PubMed

McAvoy, Alex; Hauert, Christoph

2015-10-06

In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be 'evolutionarily equivalent' in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term 'homogeneous' should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. © 2015 The Author(s).

Structural symmetry in evolutionary games

PubMed Central

McAvoy, Alex; Hauert, Christoph

2015-01-01

In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be ‘evolutionarily equivalent’ in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term ‘homogeneous’ should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. PMID:26423436

The Generation of Variation and The Developmental Basis for Evolutionary Novelty

PubMed Central

Hallgrímsson, Benedikt; Jamniczky, Heather A.; Young, Nathan M.; Rolian, Campbell; Schmidt-Ott, Urs; Marcucio, Ralph S.

2013-01-01

Organisms exhibit an incredible diversity of form, a fact that makes the evolution of novelty seemingly self-evident. However, despite the “obvious” case for novelty, defining this concept in evolutionary terms is highly problematic, so much so that some have suggested discarding it altogether. Approaches to this problem tend to take either an adaptation or development-based perspective, but we argue here that an exclusive focus on either of these misses the original intent of the novelty concept and undermines its practical utility. We instead propose that for a feature to be novel it must have evolved both by a transition between adaptive peaks on the fitness landscape and that this transition must have overcome a previous developmental constraint. This definition focuses novelty on the explanation of apparently difficult or low probability evolutionary transitions and highlights how the integration of developmental and functional considerations is necessary to evolutionary explanation. It further reinforces that novelty is a central concern not just of evolutionary developmental biology (i.e., “evo-devo”) but of evolutionary biology more generally. We explore this definition of novelty in light of four examples that range from the obvious to subtle. PMID:22649039

The growth of birdwings

NASA Technical Reports Server (NTRS)

Meunier, K.

1980-01-01

Growth and order allometry is defined and applied to the growth of bird effects of negative wing allometry discussed with regard to body size and flight power. Transposition and evolutionary significance are explained.

Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques.

PubMed

Creager, Hannah M; Becker, Ericka A; Sandman, Kelly K; Karl, Julie A; Lank, Simon M; Bimber, Benjamin N; Wiseman, Roger W; Hughes, Austin L; O'Connor, Shelby L; O'Connor, David H

2011-09-01

In recent years, the use of cynomolgus macaques in biomedical research has increased greatly. However, with the exception of the Mauritian population, knowledge of the MHC class II genetics of the species remains limited. Here, using cDNA cloning and Sanger sequencing, we identified 127 full-length MHC class II alleles in a group of 12 Indonesian and 12 Vietnamese cynomolgus macaques. Forty two of these were completely novel to cynomolgus macaques while 61 extended the sequence of previously identified alleles from partial to full length. This more than doubles the number of full-length cynomolgus macaque MHC class II alleles available in GenBank, significantly expanding the allele library for the species and laying the groundwork for future evolutionary and functional studies.

Quantum information and the problem of mechanisms of biological evolution.

PubMed

Melkikh, Alexey V

2014-01-01

One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Evolutionary dynamics on any population structure

NASA Astrophysics Data System (ADS)

Allen, Benjamin; Lippner, Gabor; Chen, Yu-Ting; Fotouhi, Babak; Momeni, Naghmeh; Yau, Shing-Tung; Nowak, Martin A.

2017-03-01

Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve. Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours. The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm. Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times of random walks. We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure—graph surgery—affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.

An Analytical Framework for Runtime of a Class of Continuous Evolutionary Algorithms.

PubMed

Zhang, Yushan; Hu, Guiwu

2015-01-01

Although there have been many studies on the runtime of evolutionary algorithms in discrete optimization, relatively few theoretical results have been proposed on continuous optimization, such as evolutionary programming (EP). This paper proposes an analysis of the runtime of two EP algorithms based on Gaussian and Cauchy mutations, using an absorbing Markov chain. Given a constant variation, we calculate the runtime upper bound of special Gaussian mutation EP and Cauchy mutation EP. Our analysis reveals that the upper bounds are impacted by individual number, problem dimension number n, searching range, and the Lebesgue measure of the optimal neighborhood. Furthermore, we provide conditions whereby the average runtime of the considered EP can be no more than a polynomial of n. The condition is that the Lebesgue measure of the optimal neighborhood is larger than a combinatorial calculation of an exponential and the given polynomial of n.

Life as a Cosmic Phenomenon: 2. the Panspermic Trajectory of Homo Sapiens

NASA Astrophysics Data System (ADS)

Tokoro, Gensuke; Wickramasinghe, N. Chandra

We discuss the origin and evolution of Homo sapiens in a cosmic context, and in relation to the Hoyle-Wickramasinghe theory of panspermia for which there is now overwhelming evidence. It is argued that the first bacteria (archea) incident on the Earth via the agency of comets 3.8-4 billion years ago continued at later times to be augmented by viral genes (DNA, RNA) from space that eventually led to the evolutionary patterns we see in present-day biology. We argue that the current evolutionary status of Homo sapiens as well as its future trajectory is circumscribed by evolutionary processes that were pre-determined on a cosmic scale -- over vast distances and enormous spans of cosmic time. Based on this teleological hypothesis we postulate that two distinct classes of cosmic viruses (cosmic viral genes) are involved in accounting for the facts relating to the evolution of life.

Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1

USDA-ARS?s Scientific Manuscript database

In order to characterize the evolutionary adaptations of avian paramyxovirus 1 (APMV-1) genomes, we have compared codon usage and codon adaptation indexes among groups of Newcastle disease viruses that differ in biological, ecological, and genetic characteristics. We have used available GenBank com...

Exploring an Alternative Model of Human Reproductive Capability: A Creative Learning Activity

ERIC Educational Resources Information Center

Cherif, Abour H.; Jedlicka, Dianne M.

2012-01-01

Biological and social evolutionary processes, along with social and cultural developments, have allowed humans to separate procreation from pleasurable/recreational sexual activity. As a class learning project, an alternative, hypothetical reproductive scenario is presented: "What if humans were biologically ready to conceive only during one…

General survey of hAT transposon superfamily with highlight on hobo element in Drosophila.

PubMed

Ladevèze, Véronique; Chaminade, Nicole; Lemeunier, Françoise; Periquet, Georges; Aulard, Sylvie

2012-09-01

The hAT transposons, very abundant in all kingdoms, have a common evolutionary origin probably predating the plant-fungi-animal divergence. In this paper we present their general characteristics. Members of this superfamily belong to Class II transposable elements. hAT elements share transposase, short terminal inverted repeats and eight base-pairs duplication of genomic target. We focus on hAT elements in Drosophila, especially hobo. Its distribution, dynamics and impact on genome restructuring in laboratory strains as well as in natural populations are reported. Finally, the evolutionary history of hAT elements, their domestication and use as transgenic tools are discussed.

Perspective: Evolutionary design of granular media and block copolymer patterns

NASA Astrophysics Data System (ADS)

Jaeger, Heinrich M.; de Pablo, Juan J.

2016-05-01

The creation of new materials "by design" is a process that starts from desired materials properties and proceeds to identify requirements for the constituent components. Such process is challenging because it inverts the typical modeling approach, which starts from given micro-level components to predict macro-level properties. We describe how to tackle this inverse problem using concepts from evolutionary computation. These concepts have widespread applicability and open up new opportunities for design as well as discovery. Here we apply them to design tasks involving two very different classes of soft materials, shape-optimized granular media and nanopatterned block copolymer thin films.

The repABC plasmids with quorum-regulated transfer systems in members of the Rhizobiales divide into two structurally and separately evolving groups

DOE PAGES

Wetzel, Margaret E.; Olsen, Gary J.; Chakravartty, Vandana; ...

2015-11-19

The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary relationships. In an analysis of 18 such plasmids these elements fall into two organizational classes, Group I and Group II, based on the sites at which cargo DNA is located. Cladograms constructed from proteins of the transfer and quorum-sensing components indicated that those of the Group I plasmids, while coevolving, have diverged from thosemore » coevolving proteins of the Group II plasmids. Moreover, within these groups the phylogenies of the proteins usually occupy similar, if not identical, tree topologies. Remarkably, such relationships were not seen among proteins of the replication system; although RepA and RepB coevolve, RepC does not. Nor do the replication proteins coevolve with the proteins of the transfer and quorum-sensing systems. Functional analysis was mostly consistent with phylogenies. TraR activated promoters from plasmids within its group, but not between groups and dimerized with TraR proteins from within but not between groups. However, oriT sequences, which are highly conserved, were processed by the transfer system of plasmids regardless of group. Here, we conclude that these plasmids diverged into two classes based on the locations at which cargo DNA is inserted, that the quorum-sensing and transfer functions are coevolving within but not between the two groups, and that this divergent evolution extends to function.« less

The repABC plasmids with quorum-regulated transfer systems in members of the Rhizobiales divide into two structurally and separately evolving groups

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

Wetzel, Margaret E.; Olsen, Gary J.; Chakravartty, Vandana

The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary relationships. In an analysis of 18 such plasmids these elements fall into two organizational classes, Group I and Group II, based on the sites at which cargo DNA is located. Cladograms constructed from proteins of the transfer and quorum-sensing components indicated that those of the Group I plasmids, while coevolving, have diverged from thosemore » coevolving proteins of the Group II plasmids. Moreover, within these groups the phylogenies of the proteins usually occupy similar, if not identical, tree topologies. Remarkably, such relationships were not seen among proteins of the replication system; although RepA and RepB coevolve, RepC does not. Nor do the replication proteins coevolve with the proteins of the transfer and quorum-sensing systems. Functional analysis was mostly consistent with phylogenies. TraR activated promoters from plasmids within its group, but not between groups and dimerized with TraR proteins from within but not between groups. However, oriT sequences, which are highly conserved, were processed by the transfer system of plasmids regardless of group. Here, we conclude that these plasmids diverged into two classes based on the locations at which cargo DNA is inserted, that the quorum-sensing and transfer functions are coevolving within but not between the two groups, and that this divergent evolution extends to function.« less

Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements.

PubMed

Brunet, Tyler D P; Doolittle, W Ford

2015-08-06

One of several issues at play in the renewed debate over "junk DNA" is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to "speed evolution" or as an "evolutionary repository" could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness--or are instead junk--is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Space station needs, attributes and architectural options. Volume 1: Executive summary NASA

NASA Technical Reports Server (NTRS)

1983-01-01

The uses alignment plan was implemented. The existing data bank was used to define a large number of station requirements. Ten to 20 valid mission scenarios were developed. Architectural options as they are influenced by communications operations, subsystem evolvability, and required technology growth are defined. Costing of evolutionary concepts, alternative approaches, and options, was based on minimum design details.

Definition of technology development missions for early space station satellite servicing, volume 1

NASA Technical Reports Server (NTRS)

1983-01-01

The testbed role of an early manned space station in the context of a satellite servicing evolutionary development and flight demonstration technology plan which results in a satellite servicing operational capability is defined. A satellite servicing technology development mission (a set of missions) to be performed on an early manned space station is conceptually defined.

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

PubMed Central

Pires, Nuno; Dolan, Liam

2010-01-01

Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use whole-genome sequences from nine species of land plants and algae to define the relationships between these proteins in plants. We show that few (less than 5) bHLH proteins are encoded in the genomes of chlorophytes and red algae. In contrast, many bHLH proteins (100–170) are encoded in the genomes of land plants (embryophytes). Phylogenetic analyses suggest that plant bHLH proteins are monophyletic and constitute 26 subfamilies. Twenty of these subfamilies existed in the common ancestors of extant mosses and vascular plants, whereas six further subfamilies evolved among the vascular plants. In addition to the conserved bHLH domains, most subfamilies are characterized by the presence of highly conserved short amino acid motifs. We conclude that much of the diversity of plant bHLH proteins was established in early land plants, over 440 million years ago. PMID:19942615

[Genetic mechanism and evolutionary significance of the origin of parthenogenetic insects].

PubMed

Wang, Cheng-Ye

2011-12-01

There is a high proportion of parthenogenesis in insecta, and the parthenogenetic potential of insects is an important but often ignored threaten factor for the agricultural and forestry production. The maintenance of parthenogenetic species is a puzzling issue in evolutionary biology. In recent years, although the cellular mechanisms during parthenogenesis in some species have been well studied, the underlying genetic mechanisms that cause the switch from sexual reproduction to parthenogenesis have not been defined. While, understanding the genetic mechanism and evolutionary significance of the origin of parthenogenetic insects is crucial for preventing the pests in agricultural and forestry production. Here we summarized recent studies aimed at identifying the underlying genetic mechanism of parthenogenesis in insects, and briefly discussed its potential application in this filed.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.

PubMed

Gagniuc, Paul; Ionescu-Tirgoviste, Constantin

2012-09-28

The main function of gene promoters appears to be the integration of different gene products in their biological pathways in order to maintain homeostasis. Generally, promoters have been classified in two major classes, namely TATA and CpG. Nevertheless, many genes using the same combinatorial formation of transcription factors have different gene expression patterns. Accordingly, we tried to ask ourselves some fundamental questions: Why certain genes have an overall predisposition for higher gene expression levels than others? What causes such a predisposition? Is there a structural relationship of these sequences in different tissues? Is there a strong phylogenetic relationship between promoters of closely related species? In order to gain valuable insights into different promoter regions, we obtained a series of image-based patterns which allowed us to identify 10 generic classes of promoters. A comprehensive analysis was undertaken for promoter sequences from Arabidopsis thaliana, Drosophila melanogaster, Homo sapiens and Oryza sativa, and a more extensive analysis of tissue-specific promoters in humans. We observed a clear preference for these species to use certain classes of promoters for specific biological processes. Moreover, in humans, we found that different tissues use distinct classes of promoters, reflecting an emerging promoter network. Depending on the tissue type, comparisons made between these classes of promoters reveal a complementarity between their patterns whereas some other classes of promoters have been observed to occur in competition. Furthermore, we also noticed the existence of some transitional states between these classes of promoters that may explain certain evolutionary mechanisms, which suggest a possible predisposition for specific levels of gene expression and perhaps for a different number of factors responsible for triggering gene expression. Our conclusions are based on comprehensive data from three different databases and a new computer model whose core is using Kappa index of coincidence. To fully understand the connections between gene promoters and gene expression, we analyzed thousands of promoter sequences using our Kappa Index of Coincidence method and a specialized Optical Character Recognition (OCR) neural network. Under our criteria, 10 classes of promoters were detected. In addition, the existence of "transitional" promoters suggests that there is an evolutionary weighted continuum between classes, depending perhaps upon changes in their gene products.

Atmospheric lidar multi-user instrument system definition study

NASA Technical Reports Server (NTRS)

Greco, R. V. (Editor)

1980-01-01

A spaceborne lidar system for atmospheric studies was defined. The primary input was the Science Objectives Experiment Description and Evolutionary Flow Document. The first task of the study was to perform an experiment evolutionary analysis of the SEED. The second task was the system definition effort of the instrument system. The third task was the generation of a program plan for the hardware phase. The fourth task was the supporting studies which included a Shuttle deficiency analysis, a preliminary safety hazard analysis, the identification of long lead items, and development studies required. As a result of the study an evolutionary Lidar Multi-User Instrument System (MUIS) was defined. The MUIS occupies a full Spacelab pallet and has a weight of 1300 kg. The Lidar MUIS laser provides a 2 joule frequency doubled Nd:YAG laser that can also pump a tuneable dye laser wide frequency range and bandwidth. The MUIS includes a 1.25 meter diameter aperture Cassegrain receiver, with a moveable secondary mirror to provide precise alignment with the laser. The receiver can transmit the return signal to three single and multiple photomultiple tube detectors by use of a rotating fold mirror. It is concluded that the Lidar MUIS proceed to program implementation.

Space industrialization. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1978-01-01

Potential goals for space industrialization were identified, and evolutionary program options for the realization of those goals were developed and assessed. Program support demands were defined, and recommendations were made in relation to program implementation.

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

PubMed Central

Mohammed, Jaaved; Flynt, Alex S.; Siepel, Adam; Lai, Eric C.

2013-01-01

The molecular evolutionary signatures of miRNAs inform our understanding of their emergence, biogenesis, and function. The known signatures of miRNA evolution have derived mostly from the analysis of deeply conserved, canonical loci. In this study, we examine the impact of age, biogenesis pathway, and genomic arrangement on the evolutionary properties of Drosophila miRNAs. Crucial to the accuracy of our results was our curation of high-quality miRNA alignments, which included nearly 150 corrections to ortholog calls and nucleotide sequences of the global 12-way Drosophilid alignments currently available. Using these data, we studied primary sequence conservation, normalized free-energy values, and types of structure-preserving substitutions. We expand upon common miRNA evolutionary patterns that reflect fundamental features of miRNAs that are under functional selection. We observe that melanogaster-subgroup-specific miRNAs, although recently emerged and rapidly evolving, nonetheless exhibit evolutionary signatures that are similar to well-conserved miRNAs and distinct from other structured noncoding RNAs and bulk conserved non-miRNA hairpins. This provides evidence that even young miRNAs may be selected for regulatory activities. More strikingly, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs, even after controlling for sequence depth. These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class. PMID:23882112

Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid.

PubMed

Turcotte, Martin M; Reznick, David N; Daniel Hare, J

2013-05-01

An eco-evolutionary feedback loop is defined as the reciprocal impacts of ecology on evolutionary dynamics and evolution on ecological dynamics on contemporary timescales. We experimentally tested for an eco-evolutionary feedback loop in the green peach aphid, Myzus persicae, by manipulating initial densities and evolution. We found strong evidence that initial aphid density alters the rate and direction of evolution, as measured by changes in genotype frequencies through time. We also found that evolution of aphids within only 16 days, or approximately three generations, alters the rate of population growth and predicts density compared to nonevolving controls. The impact of evolution on population dynamics also depended on density. In one evolution treatment, evolution accelerated population growth by up to 10.3% at high initial density or reduced it by up to 6.4% at low initial density. The impact of evolution on population growth was as strong as or stronger than that caused by a threefold change in intraspecific density. We found that, taken together, ecological condition, here intraspecific density, alters evolutionary dynamics, which in turn alter concurrent population growth rate (ecological dynamics) in an eco-evolutionary feedback loop. Our results suggest that ignoring evolution in studies predicting population dynamics might lead us to over- or underestimate population density and that we cannot predict the evolutionary outcome within aphid populations without considering population size.

VizieR Online Data Catalog: Torun catalog of post-AGB and related objects (Szczerba+, 2007)

NASA Astrophysics Data System (ADS)

Szczerba, R.; Siodmiak, N.; Stasinska, G.; Borkowski, J.

2007-09-01

With the ongoing AKARI infrared sky survey, of much greater sensitivity than IRAS, a wealth of post-AGB objects may be discovered. It is thus time to organize our present knowledge of known post-AGB stars in the galaxy with a view to using it to search for new post-AGB objects among AKARI sources. We searched the literature available on the NASA Astrophysics Data System up to 1 October 2006, and defined criteria for classifying sources into three categories: very likely, possible and disqualified post-AGB objects. The category of very likely post-AGB objects is made up of several classes. We have created an evolutionary, on-line catalogue of Galactic post-AGB objects, to be referred to as the Torun catalogue of Galactic post-AGB and related objects. The present version of the catalogue contains 326 very likely, 107 possible and 64 disqualified objects. For the very likely post-AGB objects, the catalogue gives the available optical and infrared photometry, infrared spectroscopy and spectral types, and links to finding charts and bibliography. (3 data files).

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

Cauquelin, C.

This paper presents an overview of the use of leak-before-break (LBB) analysis for EPR reactors. EPR is an evolutionary Nuclear Island of the 4 loop x 1500 Mwe class currently in the design phase. Application of LBB to the main coolant lines and resulting design impacts are summarized. Background information on LBB analysis in France and Germany is also presented.

Evolutionary relationships of a plant-pathogenic mycoplasmalike organism and Acholeplasma laidlawii deduced from two ribosomal protein gene sequences.

PubMed Central

Lim, P O; Sears, B B

1992-01-01

The families within the class Mollicutes are distinguished by their morphologies, nutritional requirements, and abilities to metabolize certain compounds. Biosystematic classification of the plant-pathogenic mycoplasmalike organisms (MLOs) has been difficult because these organisms have not been cultured in vitro, and hence their nutritional requirements have not been determined nor have physiological characterizations been possible. To investigate the evolutionary relationship of the MLOs to other members of the class Mollicutes, a segment of a ribosomal protein operon was cloned and sequenced from an aster yellows-type MLO which is pathogenic for members of the genus Oenothera and from Acholeplasma laidlawii. The deduced amino acid sequence data from the rpl22 and rps3 genes indicate that the MLOs are more closely related to A. laidlawii than to animal mycoplasmas, confirming previous results from 16S rRNA sequence comparisons. This conclusion is also supported by the finding that the UGA codon is not read as a tryptophan codon in the MLO and A. laidlawii, in contrast to its usage in Mycoplasma capricolum. PMID:1556079

The evolution of highly variable immunity genes across a passerine bird radiation.

PubMed

O'Connor, E A; Strandh, M; Hasselquist, D; Nilsson, J-Å; Westerdahl, H

2016-02-01

To survive, individuals must be able to recognize and eliminate pathogens. The genes of the major histocompatibility complex (MHC) play an essential role in this process in vertebrates as their diversity affects the repertoire of pathogens that can be recognized by the immune system. Emerging evidence suggests that birds within the parvorder Passerida possess an exceptionally high number of MHC genes. However, this has yet to be directly investigated using a consistent framework, and the question of how this MHC diversity has evolved has not been addressed. We used next-generation sequencing to investigate how MHC class I gene copy number and sequence diversity varies across the Passerida radiation using twelve species chosen to represent the phylogenetic range of this group. Additionally, we performed phylogenetic analyses on this data to identify, for the first time, the evolutionary model that best describes how MHC class I gene diversity has evolved within Passerida. We found evidence of multiple MHC class I genes in every family tested, with an extremely broad range in gene copy number across Passerida. There was a strong phylogenetic signal in MHC gene copy number and diversity, and these traits appear to have evolved through a process of Brownian motion in the species studied, that is following the pattern of genetic drift or fluctuating selection, as opposed to towards a single optimal value or through evolutionary 'bursts'. By characterizing MHC class I gene diversity across Passerida in a systematic framework, this study provides a first step towards understanding this huge variation. © 2016 John Wiley & Sons Ltd.

Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis

PubMed Central

Kümpers, Britta M. C.; Smith-Unna, Richard D.; Hibberd, Julian M.

2014-01-01

With at least 60 independent origins spanning monocotyledons and dicotyledons, the C4 photosynthetic pathway represents one of the most remarkable examples of convergent evolution. The recurrent evolution of this highly complex trait involving alterations to leaf anatomy, cell biology and biochemistry allows an increase in productivity by ∼50% in tropical and subtropical areas. The extent to which separate lineages of C4 plants use the same genetic networks to maintain C4 photosynthesis is unknown. We developed a new informatics framework to enable deep evolutionary comparison of gene expression in species lacking reference genomes. We exploited this to compare gene expression in species representing two independent C4 lineages (Cleome gynandra and Zea mays) whose last common ancestor diverged ∼140 million years ago. We define a cohort of 3,335 genes that represent conserved components of leaf and photosynthetic development in these species. Furthermore, we show that genes encoding proteins of the C4 cycle are recruited into networks defined by photosynthesis-related genes. Despite the wide evolutionary separation and independent origins of the C4 phenotype, we report that these species use homologous transcription factors to both induce C4 photosynthesis and to maintain the cell specific gene expression required for the pathway to operate. We define a core molecular signature associated with leaf and photosynthetic maturation that is likely shared by angiosperm species derived from the last common ancestor of the monocotyledons and dicotyledons. We show that deep evolutionary comparisons of gene expression can reveal novel insight into the molecular convergence of highly complex phenotypes and that parallel evolution of trans-factors underpins the repeated appearance of C4 photosynthesis. Thus, exploitation of extant natural variation associated with complex traits can be used to identify regulators. Moreover, the transcription factors that are shared by independent C4 lineages are key targets for engineering the C4 pathway into C3 crops such as rice. PMID:24901697

Systems Operation Studies for Automated Guideway Transit Systems - Classification and Definition of AGT Systems

DOT National Transportation Integrated Search

1980-02-01

The report describes the development of an AGT classification structure. Five classes are defined based on three system characteristics: service type, minimum travelling unit capacity, and maximum operating velocity. The five classes defined are: Per...

The effects of historical fragmentation on major histocompatibility complex class II β and microsatellite variation in the Aegean island reptile, Podarcis erhardii.

PubMed

Santonastaso, Trent; Lighten, Jackie; van Oosterhout, Cock; Jones, Kenneth L; Foufopoulos, Johannes; Anthony, Nicola M

2017-07-01

The major histocompatibility complex (MHC) plays a key role in disease resistance and is the most polymorphic gene region in vertebrates. Although habitat fragmentation is predicted to lead to a loss in MHC variation through drift, the impact of other evolutionary forces may counter this effect. Here we assess the impact of selection, drift, migration, and recombination on MHC class II and microsatellite variability in 14 island populations of the Aegean wall lizard Podarcis erhardii . Lizards were sampled from islands within the Cyclades (Greece) formed by rising sea levels as the last glacial maximum approximately 20,000 before present. Bathymetric data were used to determine the area and age of each island, allowing us to infer the corresponding magnitude and timing of genetic bottlenecks associated with island formation. Both MHC and microsatellite variation were positively associated with island area, supporting the hypothesis that drift governs neutral and adaptive variation in this system. However, MHC but not microsatellite variability declined significantly with island age. This discrepancy is likely due to the fact that microsatellites attain mutation-drift equilibrium more rapidly than MHC. Although we detected signals of balancing selection, recombination and migration, the effects of these evolutionary processes appeared negligible relative to drift. This study demonstrates how land bridge islands can provide novel insights into the impact of historical fragmentation on genetic diversity as well as help disentangle the effects of different evolutionary forces on neutral and adaptive diversity.

Ascidian and amphioxus Adh genes correlate functional and molecular features of the ADH family expansion during vertebrate evolution.

PubMed

Cañestro, Cristian; Albalat, Ricard; Hjelmqvist, Lars; Godoy, Laura; Jörnvall, Hans; Gonzàlez-Duarte, Roser

2002-01-01

The alcohol dehydrogenase (ADH) family has evolved into at least eight ADH classes during vertebrate evolution. We have characterized three prevertebrate forms of the parent enzyme of this family, including one from an urochordate (Ciona intestinalis) and two from cephalochordates (Branchiostoma floridae and Branchiostoma lanceolatum). An evolutionary analysis of the family was performed gathering data from protein and gene structures, exon-intron distribution, and functional features through chordate lines. Our data strongly support that the ADH family expansion occurred 500 million years ago, after the cephalochordate/vertebrate split, probably in the gnathostome subphylum line of the vertebrates. Evolutionary rates differ between the ancestral, ADH3 (glutathione-dependent formaldehyde dehydrogenase), and the emerging forms, including the classical alcohol dehydrogenase, ADH1, which has an evolutionary rate 3.6-fold that of the ADH3 form. Phylogenetic analysis and chromosomal mapping of the vertebrate Adh gene cluster suggest that family expansion took place by tandem duplications, probably concurrent with the extensive isoform burst observed before the fish/tetrapode split, rather than through the large-scale genome duplications also postulated in early vertebrate evolution. The absence of multifunctionality in lower chordate ADHs and the structures compared argue in favor of the acquisition of new functions in vertebrate ADH classes. Finally, comparison between B. floridae and B. lanceolatum Adhs provides the first estimate for a cephalochordate speciation, 190 million years ago, probably concomitant with the beginning of the drifting of major land masses from the Pangea.

Size selection from fishways and potential evolutionary responses in a threatened Atlantic salmon population

USGS Publications Warehouse

Maynard, George A.; Kinnison, M.T.; Zydlewski, Joseph D.

2017-01-01

The evolutionary effects of harvest on wild fish populations have been documented around the world; however, sublethal selective pressures can also cause evolutionary changes in phenotypes. For migratory fishes, passage facilities may represent instances of nonlethal selective pressure. Our analysis of 6 years of passage data suggests that certain fish passage facilities on the Penobscot River have been exerting selective pressure against large-bodied, anadromous Atlantic salmon (Salmo salar). At the second and third dams in the river, a 91-cm salmon was 21%–27% and 12%–16% less likely to pass than a 45-cm salmon, respectively. Fish size positively influences egg survival and number and is a heritable trait. Therefore, in a wild-reproducing population, exclusion of large fish from spawning areas may have population-level impacts. In the Penobscot River, most returning adults derive from a hatchery program that collects its broodstock after passing the first dam in the river. Analysis of fork lengths of salmon returning to the Penobscot River from 1978 to 2012 provided mixed support for evolution of size at maturity in different age classes in a pattern that may be expected from interactions with conservation hatchery operations. Additionally, slow-maturing and iteroparous individuals that represent the largest salmon size classes were essentially lost from the population during that time, and Penobscot River fish have shorter fork lengths at maturity than Atlantic salmon in undammed systems.

A teleofunctional account of evolutionary mismatch.

PubMed

Cofnas, Nathan

When the environment in which an organism lives deviates in some essential way from that to which it is adapted, this is described as "evolutionary mismatch," or "evolutionary novelty." The notion of mismatch plays an important role, explicitly or implicitly, in evolution-informed cognitive psychology, clinical psychology, and medicine. The evolutionary novelty of our contemporary environment is thought to have significant implications for our health and well-being. However, scientists have generally been working without a clear definition of mismatch. This paper defines mismatch as deviations in the environment that render biological traits unable, or impaired in their ability, to produce their selected effects (i.e., to perform their proper functions in Neander's sense). The machinery developed by Millikan in connection with her account of proper function, and with her related teleosemantic account of representation, is used to identify four major types, and several subtypes, of evolutionary mismatch. While the taxonomy offered here does not in itself resolve any scientific debates, the hope is that it can be used to better formulate empirical hypotheses concerning the effects of mismatch. To illustrate, it is used to show that the controversial hypothesis that general intelligence evolved as an adaptation to handle evolutionary novelty can, contra some critics, be formulated in a conceptually coherent way.

Plumage polymorphism and fitness in Swainson's hawks.

PubMed

Briggs, C W; Collopy, M W; Woodbridge, B

2011-10-01

We examine the maintenance of a plumage polymorphism, variation in plumages among the same age and sex class within a population, in a population of Swainson's Hawks. We take advantage of 32 years of data to examine two prevalent hypotheses used to explain the persistence of morphs: apostatic selection and heterozygous advantage. We investigate differences in fitness among three morph classes of a melanistic trait in Swainson's Hawks: light (7% of the local breeding population), intermediate (57%) and dark (36%). Specifically, we examined morph differences in adult apparent survival, breeding success, annual number of fledglings produced, probability of offspring recruitment into the breeding population and lifetime reproductive success (LRS). If apostatic selection were a factor in maintaining morphs, we would expect that individuals with the least frequent morph would perform best in one or more of these fitness categories. Alternatively, if heterozygous advantage played a role in the maintenance of this polymorphism, we would expect heterozygotes (i.e. intermediate morphs) to have one or more increased rates in these categories. We found no difference in adult apparent survival between morph classes. Similarly, there were no differences in breeding success, nest productivity, LRS or probability of recruitment of offspring between parental morph. We conclude that neither apostatic selection nor heterozygous advantage appear to play a role in maintaining morphs in this population. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Eco-evolutionary factors drive induced plant volatiles: a meta-analysis.

PubMed

Rowen, Elizabeth; Kaplan, Ian

2016-04-01

Herbivore-induced plant volatiles (HIPVs) mediate critical ecological functions, but no studies have quantitatively synthesized data published on HIPVs to evaluate broad patterns. We tested three hypotheses that use eco-evolutionary theory to predict volatile induction: feeding guild (chewing arthropods > sap feeders), diet breadth (specialist herbivores > generalists), and selection history (domesticated plants < wild species). To test these hypotheses, we extracted data from 236 experiments that report volatiles produced by herbivore-damaged and undamaged plants. These data were subjected to meta-analysis, including effects on total volatiles and major biochemical classes. Overall, we found that chewers induced more volatiles than sap feeders, for both total volatiles and most volatile classes (e.g. green leaf volatiles, monoterpenes). Although specialist herbivores induced more total volatiles than generalists, this was inconsistent across chemical classes. Contrary to our expectation, domesticated species induced stronger volatile responses than wild species, even when controlling for plant taxonomy. Surprisingly, this is the first quantitative synthesis of published studies on HIPVs. Our analysis provides support for perceptions in the published literature (chewers > sap feeders), while challenging other commonly held notions (wild > crop). Despite the large number of experiments, we identified several gaps in the existing literature that should guide future investigations. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Evaluation of solar electric propulsion technologies for discovery class missions

NASA Technical Reports Server (NTRS)

Oh, David Y.

2005-01-01

A detailed study examines the potential benefits that advanced electric propulsion (EP) technologies offer to the cost-capped missions in NASA's Discovery program. The study looks at potential cost and performance benefits provided by three EP technologies that are currently in development: NASA's Evolutionary Xenon Thruster (NEXT), an Enhanced NSTAR system, and a Low Power Hall effect thruster. These systems are analyzed on three straw man Discovery class missions and their performance is compared to a state of the art system using the NSTAR ion thruster. An electric propulsion subsystem cost model is used to conduct a cost-benefit analysis for each option. The results show that each proposed technology offers a different degree of performance and/or cost benefit for Discovery class missions.

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

FINAL ECOSYSTEM GOODS AND SERVICES CLASSIFICATION SYSTEM (FEGS-CS)

EPA Science Inventory

This document defines and classifies 338 Final Ecosystem Goods and Services (FEGS), each defined and uniquely numbered by a combination of environmental class or sub-class and a beneficiary category or sub-category. The introductory section provides the rationale and conceptual ...

Fitness and Individuality in Complex Life Cycles.

PubMed

Herron, Matthew D

2016-12-01

Complex life cycles are common in the eukaryotic world, and they complicate the question of how to define individuality. Using a bottom-up, gene-centric approach, I consider the concept of fitness in the context of complex life cycles. I analyze the fitness effects of an allele (or a trait) on different biological units within a complex life history and how these effects drive evolutionary change within populations. Based on these effects, I attempt to construct a concept of fitness that accurately predicts evolutionary change in the context of complex life cycles.

Evolutionary space platform concept study. Volume 2, part A: SASP special emphasis trade studies

NASA Technical Reports Server (NTRS)

1982-01-01

Efforts are in progress to define an approach to provide a simple and cost effective solution to the problem of long duration space flight. This approach involves a Space Platform in low Earth orbit, which can be tended by the Space Shuttle and which will provide, for extended periods of time, stability, utilities and access for a variety of replaceable payloads. The feasibility of an evolutionary space system which would cost effectively support unmanned payloads in groups, using a Space Platform which provides centralized basic subsystems is addressed.

Bell-Curve Based Evolutionary Optimization Algorithm

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, J.; Laba, K.; Kincaid, R.

1998-01-01

The paper presents an optimization algorithm that falls in the category of genetic, or evolutionary algorithms. While the bit exchange is the basis of most of the Genetic Algorithms (GA) in research and applications in America, some alternatives, also in the category of evolutionary algorithms, but use a direct, geometrical approach have gained popularity in Europe and Asia. The Bell-Curve Based Evolutionary Algorithm (BCB) is in this alternative category and is distinguished by the use of a combination of n-dimensional geometry and the normal distribution, the bell-curve, in the generation of the offspring. The tool for creating a child is a geometrical construct comprising a line connecting two parents and a weighted point on that line. The point that defines the child deviates from the weighted point in two directions: parallel and orthogonal to the connecting line, the deviation in each direction obeying a probabilistic distribution. Tests showed satisfactory performance of BCB. The principal advantage of BCB is its controllability via the normal distribution parameters and the geometrical construct variables.

Observational evidence of dust evolution in galactic extinction curves

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

Cecchi-Pestellini, Cesare; Casu, Silvia; Mulas, Giacomo

Although structural and optical properties of hydrogenated amorphous carbons are known to respond to varying physical conditions, most conventional extinction models are basically curve fits with modest predictive power. We compare an evolutionary model of the physical properties of carbonaceous grain mantles with their determination by homogeneously fitting observationally derived Galactic extinction curves with the same physically well-defined dust model. We find that a large sample of observed Galactic extinction curves are compatible with the evolutionary scenario underlying such a model, requiring physical conditions fully consistent with standard density, temperature, radiation field intensity, and average age of diffuse interstellar clouds.more » Hence, through the study of interstellar extinction we may, in principle, understand the evolutionary history of the diffuse interstellar clouds.« less

Evolution of the indoor biome.

PubMed

Martin, Laura J; Adams, Rachel I; Bateman, Ashley; Bik, Holly M; Hawks, John; Hird, Sarah M; Hughes, David; Kembel, Steven W; Kinney, Kerry; Kolokotronis, Sergios-Orestis; Levy, Gabriel; McClain, Craig; Meadow, James F; Medina, Raul F; Mhuireach, Gwynne; Moreau, Corrie S; Munshi-South, Jason; Nichols, Lauren M; Palmer, Clare; Popova, Laura; Schal, Coby; Täubel, Martin; Trautwein, Michelle; Ugalde, Juan A; Dunn, Robert R

2015-04-01

Few biologists have studied the evolutionary processes at work in indoor environments. Yet indoor environments comprise approximately 0.5% of ice-free land area--an area as large as the subtropical coniferous forest biome. Here we review the emerging subfield of 'indoor biome' studies. After defining the indoor biome and tracing its deep history, we discuss some of its evolutionary dimensions. We restrict our examples to the species found in human houses--a subset of the environments constituting the indoor biome--and offer preliminary hypotheses to advance the study of indoor evolution. Studies of the indoor biome are situated at the intersection of evolutionary ecology, anthropology, architecture, and human ecology and are well suited for citizen science projects, public outreach, and large-scale international collaborations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hamilton's rule, inclusive fitness maximization, and the goal of individual behaviour in symmetric two-player games.

PubMed

Okasha, S; Martens, J

2016-03-01

Hamilton's original work on inclusive fitness theory assumed additivity of costs and benefits. Recently, it has been argued that an exact version of Hamilton's rule for the spread of a pro-social allele (rb > c) holds under nonadditive pay-offs, so long as the cost and benefit terms are defined as partial regression coefficients rather than pay-off parameters. This article examines whether one of the key components of Hamilton's original theory can be preserved when the rule is generalized to the nonadditive case in this way, namely that evolved organisms will behave as if trying to maximize their inclusive fitness in social encounters. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Chaos and unpredictability in evolution.

PubMed

Doebeli, Michael; Ispolatov, Iaroslav

2014-05-01

The possibility of complicated dynamic behavior driven by nonlinear feedbacks in dynamical systems has revolutionized science in the latter part of the last century. Yet despite examples of complicated frequency dynamics, the possibility of long-term evolutionary chaos is rarely considered. The concept of "survival of the fittest" is central to much evolutionary thinking and embodies a perspective of evolution as a directional optimization process exhibiting simple, predictable dynamics. This perspective is adequate for simple scenarios, when frequency-independent selection acts on scalar phenotypes. However, in most organisms many phenotypic properties combine in complicated ways to determine ecological interactions, and hence frequency-dependent selection. Therefore, it is natural to consider models for evolutionary dynamics generated by frequency-dependent selection acting simultaneously on many different phenotypes. Here we show that complicated, chaotic dynamics of long-term evolutionary trajectories in phenotype space is very common in a large class of such models when the dimension of phenotype space is large, and when there are selective interactions between the phenotypic components. Our results suggest that the perspective of evolution as a process with simple, predictable dynamics covers only a small fragment of long-term evolution. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Evolutionary and mechanistic drivers of laterality: A review and new synthesis.

PubMed

Wiper, Mallory L

2017-11-01

Laterality, best understood as asymmetries of bilateral structures or biases in behaviour, has been demonstrated in species from all major vertebrate classes, and in many invertebrates, showing a large degree of evolutionary conservation across vertebrate groups. Despite the establishment of this phenomenon in so many species, however, the evolutionary and mechanistic study of laterality is uneven with numerous areas in this field requiring greater attention. Here, I present a partial review of how far the study of laterality has come, outlining previous pioneering work, I discuss the hypothesized costs and benefits of a lateralized brain and the suggested path of the evolution of laterality for populations and individuals. I propose an expansion of laterality research into areas that have been touched upon in the past but require stronger evidence from which the field will greatly benefit. Namely, I suggest a continuation of the phylogenetic approach to investigating laterality to better understand its evolutionary path; and a further focus on mechanistic drivers, with special attention to genetic and environmental effects. Putting together the puzzle of laterality using as many pieces as possible will provide a stronger understanding of this field, allowing us to continue to expand the field in novel ways.

A Case-by-Case Evolutionary Analysis of Four Imprinted Retrogenes

PubMed Central

McCole, Ruth B; Loughran, Noeleen B; Chahal, Mandeep; Fernandes, Luis P; Roberts, Roland G; Fraternali, Franca; O'Connell, Mary J; Oakey, Rebecca J

2011-01-01

Retroposition is a widespread phenomenon resulting in the generation of new genes that are initially related to a parent gene via very high coding sequence similarity. We examine the evolutionary fate of four retrogenes generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of parental imprinting. We first provide new data on the age of these retrogene insertions. Using codon-based models of sequence evolution, we show these retrogenes have diverse evolutionary trajectories, including divergence from the parent coding sequence under positive selection pressure, purifying selection pressure maintaining parent-retrogene similarity, and neutral evolution. Examination of the expression pattern of retrogenes shows an atypical, broad pattern across multiple tissues. Protein 3D structure modeling reveals that a positively selected residue in U2af1-rs1, not shared by its parent, may influence protein conformation. Our case-by-case analysis of the evolution of four imprinted retrogenes reveals that this interesting class of imprinted genes, while similar in regulation and sequence characteristics, follow very varied evolutionary paths. PMID:21166792

A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes

PubMed Central

2013-01-01

Background Ribonucleotide reductase (RNR), the enzyme responsible for the formation of deoxyribonucleotides from ribonucleotides, is found in all domains of life and many viral genomes. RNRs are also amongst the most abundant genes identified in environmental metagenomes. This study focused on understanding the distribution, diversity, and evolution of RNRs in phages (viruses that infect bacteria). Hidden Markov Model profiles were used to analyze the proteins encoded by 685 completely sequenced double-stranded DNA phages and 22 environmental viral metagenomes to identify RNR homologs in cultured phages and uncultured viral communities, respectively. Results RNRs were identified in 128 phage genomes, nearly tripling the number of phages known to encode RNRs. Class I RNR was the most common RNR class observed in phages (70%), followed by class II (29%) and class III (28%). Twenty-eight percent of the phages contained genes belonging to multiple RNR classes. RNR class distribution varied according to phage type, isolation environment, and the host’s ability to utilize oxygen. The majority of the phages containing RNRs are Myoviridae (65%), followed by Siphoviridae (30%) and Podoviridae (3%). The phylogeny and genomic organization of phage and host RNRs reveal several distinct evolutionary scenarios involving horizontal gene transfer, co-evolution, and differential selection pressure. Several putative split RNR genes interrupted by self-splicing introns or inteins were identified, providing further evidence for the role of frequent genetic exchange. Finally, viral metagenomic data indicate that RNRs are prevalent and highly dynamic in uncultured viral communities, necessitating future research to determine the environmental conditions under which RNRs provide a selective advantage. Conclusions This comprehensive study describes the distribution, diversity, and evolution of RNRs in phage genomes and environmental viral metagenomes. The distinct distributions of specific RNR classes amongst phages, combined with the various evolutionary scenarios predicted from RNR phylogenies suggest multiple inheritance sources and different selective forces for RNRs in phages. This study significantly improves our understanding of phage RNRs, providing insight into the diversity and evolution of this important auxiliary metabolic gene as well as the evolution of phages in response to their bacterial hosts and environments. PMID:23391036

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly

PubMed Central

Hanski, Ilkka A.

2011-01-01

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time. PMID:21788506

Partial protein domains: evolutionary insights and bioinformatics challenges.

PubMed

Kelley, Lawrence A; Sternberg, Michael J E

2015-05-19

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.

Unexpected amino acid composition of modern Reptilia and its implications in molecular mechanisms of dinosaur extinction.

PubMed

Wang, Guang-Zhong; Ma, Bin-Guang; Yang, Yan; Zhang, Hong-Yu

2005-08-12

Dinosaur extinction is a great challenge to evolutionary biology. Although accumulating evidence suggests that an abrupt change of environment, such as a long period of low temperature induced by asteroid hit or other disasters, may be responsible for dinosaur extinction, little is known about the underlying molecular mechanisms. By analyzing the amino acid compositions of 13 biological classes, we found that the charged amino acid content of modern Reptilia, the sibling of dinosaur, is strikingly different from those of other classes, which inspires us to propose a possible molecular mechanism for dinosaur extinction.

A Framework for Empirical Discovery.

DTIC Science & Technology

1986-09-24

history of science reveal distinct classes of defined terms. Some systems have focused on one subset of these classes, while other programs have...the operators in detail, presenting examples of each from the history of science . 2.1 Defining Numeric Terms The most obvious operator for defining...laws; they can also simplify the process of discovering such laws. Let us consider some examples from the history of science in which the definition of

Changes from 2000 to 2009 in the Prevalence of HIV-1 Containing Drug Resistance-associated Mutations from Antiretroviral Therapy-naïve, HIV-1-infected Patients in the United States.

PubMed

Ross, Lisa L; Shortino, Denise; Shaefer, Mark S

2018-05-05

Background: Pre-existing HIV drug resistance can jeopardize first-line antiretroviral therapy (ART) success. Changes in the prevalence of drug-resistance-associated mutations (DRMs) were analyzed from HIV-infected, ART-naïve, United States (USA) individuals seeking ART treatment from 2000-2009. Methods: HIV DRM data from 3,829 ART-naïve subjects were analyzed by year of sample collection using International Antiviral Society (IAS-USA) and World Health Organization (WHO) "surveillance" DRM definitions; minor IAS-USA-defined DRMs were excluded. Results: IAS-USA DRM prevalence between 2000-2009 was 14%; beginning with 8% in 2000, 13% in 2009. The greatest incidence was observed in 2007 (17%). Overall, IAS-USA-defined non-nucleoside reverse transcriptase (NNRTI) DRMs were 9.5%; NRTI: 4% and major protease inhibitor (PI):3%. The most frequently detected IAS-USA-defined DRMs by class were NNRTI: K103N/S (4%); NRTI: M41L (1.5%) and PI: L90M (1%). Overall WHO-defined DRM prevalence was 13% (5% in 2000; 13% in 2009). By class, NNRTI prevalence was 6%, NRTI: 6%, and PI: 3.2%. The most frequent WHO-defined DRMs were NRTI: codon T215 (3.0%); NNRTI: K103N/S (4%) and PI: L90M (1%). WHO-defined NNRTI DRMs declined significantly (p=0.0412) from 2007 to 2009. The overall prevalence of HIV-1-containing major IAS-USA or WHO-defined DRMs to ≥2 or ≥3 classes was 2% and <1%, respectively. The prevalence of HIV-1 with WHO-defined dual or triple-class resistance significantly declined (p=0.0461) from 2008 (4%) to 2009 (<1%). Conclusions: In this USA cohort, prevalence of HIV-1 DRMs increased from 2000 onwards, peaked between 2005-2007 and then declined in 2008-2009; the detection of WHO-defined dual or triple-class DRM similarly decreased from 2008 to 2009.

The Paradox of Isochrony in the Evolution of Human Rhythm

PubMed Central

Ravignani, Andrea; Madison, Guy

2017-01-01

Isochrony is crucial to the rhythm of human music. Some neural, behavioral and anatomical traits underlying rhythm perception and production are shared with a broad range of species. These may either have a common evolutionary origin, or have evolved into similar traits under different evolutionary pressures. Other traits underlying rhythm are rare across species, only found in humans and few other animals. Isochrony, or stable periodicity, is common to most human music, but isochronous behaviors are also found in many species. It appears paradoxical that humans are particularly good at producing and perceiving isochronous patterns, although this ability does not conceivably confer any evolutionary advantage to modern humans. This article will attempt to solve this conundrum. To this end, we define the concept of isochrony from the present functional perspective of physiology, cognitive neuroscience, signal processing, and interactive behavior, and review available evidence on isochrony in the signals of humans and other animals. We then attempt to resolve the paradox of isochrony by expanding an evolutionary hypothesis about the function that isochronous behavior may have had in early hominids. Finally, we propose avenues for empirical research to examine this hypothesis and to understand the evolutionary origin of isochrony in general. PMID:29163252

On the path to genetic novelties: insights from programmed DNA elimination and RNA splicing.

PubMed

Catania, Francesco; Schmitz, Jürgen

2015-01-01

Understanding how genetic novelties arise is a central goal of evolutionary biology. To this end, programmed DNA elimination and RNA splicing deserve special consideration. While programmed DNA elimination reshapes genomes by eliminating chromatin during organismal development, RNA splicing rearranges genetic messages by removing intronic regions during transcription. Small RNAs help to mediate this class of sequence reorganization, which is not error-free. It is this imperfection that makes programmed DNA elimination and RNA splicing excellent candidates for generating evolutionary novelties. Leveraging a number of these two processes' mechanistic and evolutionary properties, which have been uncovered over the past years, we present recently proposed models and empirical evidence for how splicing can shape the structure of protein-coding genes in eukaryotes. We also chronicle a number of intriguing similarities between the processes of programmed DNA elimination and RNA splicing, and highlight the role that the variation in the population-genetic environment may play in shaping their target sequences. © 2015 Wiley Periodicals, Inc.

Geologic map of the Agnesi quadrangle (V-45), Venus

USGS Publications Warehouse

Hansen, Vicki L.; Tharalson, Erik R.

2014-01-01

Two general classes of hypotheses have emerged to address the near random spatial distribution of ~970 apparently pristine impact craters across the surface of Venus: (1) catastrophic/episodic resurfacing and (2) equilibrium/evolutionary resurfacing. Catastrophic/episodic hypotheses propose that a global-scale, temporally punctuated event or events dominated Venus’ evolution and that the generally uniform impact crater distribution (Schaber and others, 1992; Phillips and others, 1992; Herrick and others, 1997) reflects craters that accumulated during relative global quiescence since that event (for example, Strom and others, 1994; Herrick, 1994; Turcotte and others, 1999). Equilibrium/evolutionary hypotheses suggest instead that the near random crater distribution results from relatively continuous, but spatially localized, resurfacing in which volcanic and (or) tectonic processes occur across the planet through time, although the style of operative processes may have varied temporally and spatially (for example, Phillips and others, 1992; Guest and Stofan, 1999; Hansen and Young, 2007). Geologic relations within the map area allow us to test the catastrophic/episodic versus equilibrium/evolutionary resurfacing hypotheses.

The Changing Pattern of Nutrition Intake by Social Class in Contemporary China, 1991-2011.

PubMed

Xu, Zhun; Zhang, Wei

2017-11-01

To explore the changing pattern of nutrition intake by social class in contemporary China. We defined social class in 2 ways. The first definition was based on employment, and the second definition was based on per capita household income levels. We used China Health and Nutrition Survey data from 1991 to 2011 to show the changes in the relation between social class and nutrition intake. The relation between social class and nutrition intake in China changed significantly within the 2 decades. For example, in the early 1990s, the lowest social class (defined by employment or income) had more caloric intake than did the highest social class; 20 years later, however, the relation reversed, and the lowest social class consumed significantly fewer calories. China has seen a great reversal in its social class-nutrition relationship since the early 1990s. Our study calls for wider recognition that insufficient consumption of food and nutrition is increasingly an issue for people in the lower social classes in China.

Evolutionary and Cognitive Motivations for Fractal Art in Art and Design Education

ERIC Educational Resources Information Center

Joye, Yannick

2005-01-01

Humans are endowed with cognitive modules specialised in processing information about the class of natural things. Due to their naturalness, fractal art and design can contribute to developing these modules, and trigger affective responses that are associated with certain natural objects. It is argued that exposure to fractals in an art and design…

Darwin versus Intelligent Design in US Courts: Does Teaching Intelligent Design in Biology Classes Violate the US Constitution?

ERIC Educational Resources Information Center

Bradt, Patricia T.

2006-01-01

Darwinian evolution is accepted by the great majority of scientists as the method by which the diversity of earth's organisms, including humans, evolved. Current research continues to expand our knowledge of evolutionary mechanisms. However, certain religious groups, supporting teaching the creation of earth's species as outlined in Genesis…

Evolutionary Steps: A Stairway-Created Display of the History of Life.

ERIC Educational Resources Information Center

Hedeen, Stanley E.

1997-01-01

Describes an exercise whereby a biology class used a stairway to illustrate how fossiliferous rock strata were deposited, the oldest on the bottom and most recent at the top. Each step represents a dated boundary between adjacent geological ages, and each riser is labeled as a geological unit. Geological time is compressed to 365 days. Offers…

Hox3/zen and the evolution of extraembryonic epithelia in insects.

PubMed

Schmidt-Ott, Urs; Rafiqi, Ab Matteen; Lemke, Steffen

2010-01-01

Insects have undergone dramatic evolutionary changes in extraembryonic development, which correlate with changes in the expression of the class-3 Hox gene zen. Here, we review the evolution of this gene in insects and point out how changes in zen expression may have affected extraembryonic development at the morphological and the genetic level.

Insights into the Diversity of Attitudes Concerning Evolution and Creation: A Multidimensional Approach

ERIC Educational Resources Information Center

Konneman, Christiane; Asshoff, Roman; Hammann, Marcus

2016-01-01

The main aim of this paper is to describe high school students' attitudes concerning evolution and creation, with a focus on (1) attitudes toward evolutionary theory, (2) attitudes toward the Biblical accounts of creation, (3) creationist beliefs, and (4) scientistic beliefs. Latent class analyses revealed seven attitude profiles in a sample of…

Origins of Allostery and Evolvability in Proteins: A Case Study.

PubMed

Raman, Arjun S; White, K Ian; Ranganathan, Rama

2016-07-14

Proteins display the capacity for adaptation to new functions, a property critical for evolvability. But what structural principles underlie the capacity for adaptation? Here, we show that adaptation to a physiologically distinct class of ligand specificity in a PSD95, DLG1, ZO-1 (PDZ) domain preferentially occurs through class-bridging intermediate mutations located distant from the ligand-binding site. These mutations provide a functional link between ligand classes and demonstrate the principle of "conditional neutrality" in mediating evolutionary adaptation. Structures show that class-bridging mutations work allosterically to open up conformational plasticity at the active site, permitting novel functions while retaining existing function. More generally, the class-bridging phenotype arises from mutations in an evolutionarily conserved network of coevolving amino acids in the PDZ family (the sector) that connects the active site to distant surface sites. These findings introduce the concept that allostery in proteins could have its origins not in protein function but in the capacity to adapt. Copyright © 2016 Elsevier Inc. All rights reserved.

Tracking the Molecular Evolution of Calcium Permeability in a Nicotinic Acetylcholine Receptor

PubMed Central

Lipovsek, Marcela; Fierro, Angélica; Pérez, Edwin G.; Boffi, Juan C.; Millar, Neil S.; Fuchs, Paul A.; Katz, Eleonora; Elgoyhen, Ana Belén

2014-01-01

Nicotinic acetylcholine receptors are a family of ligand-gated nonselective cationic channels that participate in fundamental physiological processes at both the central and the peripheral nervous system. The extent of calcium entry through ligand-gated ion channels defines their distinct functions. The α9α10 nicotinic cholinergic receptor, expressed in cochlear hair cells, is a peculiar member of the family as it shows differences in the extent of calcium permeability across species. In particular, mammalian α9α10 receptors are among the ligand-gated ion channels which exhibit the highest calcium selectivity. This acquired differential property provides the unique opportunity of studying how protein function was shaped along evolutionary history, by tracking its evolutionary record and experimentally defining the amino acid changes involved. We have applied a molecular evolution approach of ancestral sequence reconstruction, together with molecular dynamics simulations and an evolutionary-based mutagenesis strategy, in order to trace the molecular events that yielded a high calcium permeable nicotinic α9α10 mammalian receptor. Only three specific amino acid substitutions in the α9 subunit were directly involved. These are located at the extracellular vestibule and at the exit of the channel pore and not at the transmembrane region 2 of the protein as previously thought. Moreover, we show that these three critical substitutions only increase calcium permeability in the context of the mammalian but not the avian receptor, stressing the relevance of overall protein structure on defining functional properties. These results highlight the importance of tracking evolutionarily acquired changes in protein sequence underlying fundamental functional properties of ligand-gated ion channels. PMID:25193338

Models of performance of evolutionary program induction algorithms based on indicators of problem difficulty.

PubMed

Graff, Mario; Poli, Riccardo; Flores, Juan J

2013-01-01

Modeling the behavior of algorithms is the realm of evolutionary algorithm theory. From a practitioner's point of view, theory must provide some guidelines regarding which algorithm/parameters to use in order to solve a particular problem. Unfortunately, most theoretical models of evolutionary algorithms are difficult to apply to realistic situations. However, in recent work (Graff and Poli, 2008, 2010), where we developed a method to practically estimate the performance of evolutionary program-induction algorithms (EPAs), we started addressing this issue. The method was quite general; however, it suffered from some limitations: it required the identification of a set of reference problems, it required hand picking a distance measure in each particular domain, and the resulting models were opaque, typically being linear combinations of 100 features or more. In this paper, we propose a significant improvement of this technique that overcomes the three limitations of our previous method. We achieve this through the use of a novel set of features for assessing problem difficulty for EPAs which are very general, essentially based on the notion of finite difference. To show the capabilities or our technique and to compare it with our previous performance models, we create models for the same two important classes of problems-symbolic regression on rational functions and Boolean function induction-used in our previous work. We model a variety of EPAs. The comparison showed that for the majority of the algorithms and problem classes, the new method produced much simpler and more accurate models than before. To further illustrate the practicality of the technique and its generality (beyond EPAs), we have also used it to predict the performance of both autoregressive models and EPAs on the problem of wind speed forecasting, obtaining simpler and more accurate models that outperform in all cases our previous performance models.

Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1

PubMed Central

Brumme, Chanson J.; Martin, Eric; Listgarten, Jennifer; Brockman, Mark A.; Le, Anh Q.; Chui, Celia K. S.; Cotton, Laura A.; Knapp, David J. H. F.; Riddler, Sharon A.; Haubrich, Richard; Nelson, George; Pfeifer, Nico; DeZiel, Charles E.; Heckerman, David; Apps, Richard; Carrington, Mary; Mallal, Simon; Harrigan, P. Richard; John, Mina

2012-01-01

HLA class I-associated polymorphisms identified at the population level mark viral sites under immune pressure by individual HLA alleles. As such, analysis of their distribution, frequency, location, statistical strength, sequence conservation, and other properties offers a unique perspective from which to identify correlates of protective cellular immunity. We analyzed HLA-associated HIV-1 subtype B polymorphisms in 1,888 treatment-naïve, chronically infected individuals using phylogenetically informed methods and identified characteristics of HLA-associated immune pressures that differentiate protective and nonprotective alleles. Over 2,100 HLA-associated HIV-1 polymorphisms were identified, approximately one-third of which occurred inside or within 3 residues of an optimally defined cytotoxic T-lymphocyte (CTL) epitope. Differential CTL escape patterns between closely related HLA alleles were common and increased with greater evolutionary distance between allele group members. Among 9-mer epitopes, mutations at HLA-specific anchor residues represented the most frequently detected escape type: these occurred nearly 2-fold more frequently than expected by chance and were computationally predicted to reduce peptide-HLA binding nearly 10-fold on average. Characteristics associated with protective HLA alleles (defined using hazard ratios for progression to AIDS from natural history cohorts) included the potential to mount broad immune selection pressures across all HIV-1 proteins except Nef, the tendency to drive multisite and/or anchor residue escape mutations within known CTL epitopes, and the ability to strongly select mutations in conserved regions within HIV's structural and functional proteins. Thus, the factors defining protective cellular immune responses may be more complex than simply targeting conserved viral regions. The results provide new information to guide vaccine design and immunogenicity studies. PMID:23055555

FY98 Class Convening Schedule for Coast Guard Class

DOT National Transportation Integrated Search

1998-08-12

This Notice publishes the FY98 class convening schedule of Coast Guard Class "A" : and "C" resident and exportable training courses defined by program/force : managers as essential or directly related to mission accomplishment for : achievement of pr...

High-resolution 25 μm Imaging of the Disks around Herbig Ae/Be Stars

NASA Astrophysics Data System (ADS)

Honda, M.; Maaskant, K.; Okamoto, Y. K.; Kataza, H.; Yamashita, T.; Miyata, T.; Sako, S.; Fujiyoshi, T.; Sakon, I.; Fujiwara, H.; Kamizuka, T.; Mulders, G. D.; Lopez-Rodriguez, E.; Packham, C.; Onaka, T.

2015-05-01

We imaged circumstellar disks around 22 Herbig Ae/Be stars at 25 μm using Subaru/COMICS and Gemini/T-ReCS. Our sample consists of an equal number of objects from each of the two categories defined by Meeus et al.; 11 group I (flaring disk) and II (flat disk) sources. We find that group I sources tend to show more extended emission than group II sources. Previous studies have shown that the continuous disk is difficult to resolve with 8 m class telescopes in the Q band due to the strong emission from the unresolved innermost region of the disk. This indicates that the resolved Q-band sources require a hole or gap in the disk material distribution to suppress the contribution from the innermost region of the disk. As many group I sources are resolved at 25 μm, we suggest that many, but not all, group I Herbig Ae/Be disks have a hole or gap and are (pre-)transitional disks. On the other hand, the unresolved nature of many group II sources at 25 μm supports the idea that group II disks have a continuous flat disk geometry. It has been inferred that group I disks may evolve into group II through the settling of dust grains into the mid-plane of the protoplanetary disk. However, considering the growing evidence for the presence of a hole or gap in the disk of group I sources, such an evolutionary scenario is unlikely. The difference between groups I and II may reflect different evolutionary pathways of protoplanetary disks. Based on data collected at the Subaru Telescope, via the time exchange program between Subaru and the Gemini Observatory. The Subaru Telescope is operated by the National Astronomical Observatory of Japan.

The Potential Feasibility of Chlorinic Photosynthesis on Exoplanets

NASA Astrophysics Data System (ADS)

Haas, Johnson R.

2010-11-01

The modern search for life-bearing exoplanets emphasizes the potential detection of O2 and O3 absorption spectra in exoplanetary atmospheres as ideal signatures of biology. However, oxygenic photosynthesis may not arise ubiquitously in exoplanetary biospheres. Alternative evolutionary paths may yield planetary atmospheres tinted with the waste products of other dominant metabolisms, including potentially exotic biochemistries. This paper defines chlorinic photosynthesis (CPS) as biologically mediated photolytic oxidation of aqueous Cl- to form halocarbon or dihalogen products, coupled with CO2 assimilation. This hypothetical metabolism appears to be feasible energetically, physically, and geochemically, and could potentially develop under conditions that approximate the terrestrial Archean. It is hypothesized that an exoplanetary biosphere in which chlorinic photosynthesis dominates primary production would tend to evolve a strongly oxidizing, halogen-enriched atmosphere over geologic time. It is recommended that astronomical observations of exoplanetary outgoing thermal emission spectra consider signs of halogenated chemical species as likely indicators of the presence of a chlorinic biosphere. Planets that favor the evolution of CPS would probably receive equivalent or greater surface UV flux than is produced by the Sun, which would promote stronger abiotic UV photolysis of aqueous halides than occurred during Earth's Archean era and impose stronger evolutionary selection pressures on endemic life to accommodate and utilize halogenated compounds. Ocean-bearing planets of stars with metallicities equivalent to, or greater than, the Sun should especially favor the evolution of chlorinic biospheres because of the higher relative seawater abundances of Cl, Br, and I such planets would tend to host. Directed searches for chlorinic biospheres should probably focus on G0-G2, F, and A spectral class stars that have bulk metallicities of +0.0 Dex or greater.

The potential feasibility of chlorinic photosynthesis on exoplanets.

PubMed

Haas, Johnson R

2010-11-01

The modern search for life-bearing exoplanets emphasizes the potential detection of O(2) and O(3) absorption spectra in exoplanetary atmospheres as ideal signatures of biology. However, oxygenic photosynthesis may not arise ubiquitously in exoplanetary biospheres. Alternative evolutionary paths may yield planetary atmospheres tinted with the waste products of other dominant metabolisms, including potentially exotic biochemistries. This paper defines chlorinic photosynthesis (CPS) as biologically mediated photolytic oxidation of aqueous Cl(-) to form halocarbon or dihalogen products, coupled with CO(2) assimilation. This hypothetical metabolism appears to be feasible energetically, physically, and geochemically, and could potentially develop under conditions that approximate the terrestrial Archean. It is hypothesized that an exoplanetary biosphere in which chlorinic photosynthesis dominates primary production would tend to evolve a strongly oxidizing, halogen-enriched atmosphere over geologic time. It is recommended that astronomical observations of exoplanetary outgoing thermal emission spectra consider signs of halogenated chemical species as likely indicators of the presence of a chlorinic biosphere. Planets that favor the evolution of CPS would probably receive equivalent or greater surface UV flux than is produced by the Sun, which would promote stronger abiotic UV photolysis of aqueous halides than occurred during Earth's Archean era and impose stronger evolutionary selection pressures on endemic life to accommodate and utilize halogenated compounds. Ocean-bearing planets of stars with metallicities equivalent to, or greater than, the Sun should especially favor the evolution of chlorinic biospheres because of the higher relative seawater abundances of Cl, Br, and I such planets would tend to host. Directed searches for chlorinic biospheres should probably focus on G0-G2, F, and A spectral class stars that have bulk metallicities of +0.0 Dex or greater.

Evolutionary method for finding communities in bipartite networks.

PubMed

Zhan, Weihua; Zhang, Zhongzhi; Guan, Jihong; Zhou, Shuigeng

2011-06-01

An important step in unveiling the relation between network structure and dynamics defined on networks is to detect communities, and numerous methods have been developed separately to identify community structure in different classes of networks, such as unipartite networks, bipartite networks, and directed networks. Here, we show that the finding of communities in such networks can be unified in a general framework-detection of community structure in bipartite networks. Moreover, we propose an evolutionary method for efficiently identifying communities in bipartite networks. To this end, we show that both unipartite and directed networks can be represented as bipartite networks, and their modularity is completely consistent with that for bipartite networks, the detection of modular structure on which can be reformulated as modularity maximization. To optimize the bipartite modularity, we develop a modified adaptive genetic algorithm (MAGA), which is shown to be especially efficient for community structure detection. The high efficiency of the MAGA is based on the following three improvements we make. First, we introduce a different measure for the informativeness of a locus instead of the standard deviation, which can exactly determine which loci mutate. This measure is the bias between the distribution of a locus over the current population and the uniform distribution of the locus, i.e., the Kullback-Leibler divergence between them. Second, we develop a reassignment technique for differentiating the informative state a locus has attained from the random state in the initial phase. Third, we present a modified mutation rule which by incorporating related operations can guarantee the convergence of the MAGA to the global optimum and can speed up the convergence process. Experimental results show that the MAGA outperforms existing methods in terms of modularity for both bipartite and unipartite networks.

Issues in the classification of disease instances with ontologies.

PubMed

Burgun, Anita; Bodenreider, Olivier; Jacquelinet, Christian

2005-01-01

Ontologies define classes of entities and their interrelations. They are used to organize data according to a theory of the domain. Towards that end, ontologies provide class definitions (i.e., the necessary and sufficient conditions for defining class membership). In medical ontologies, it is often difficult to establish such definitions for diseases. We use three examples (anemia, leukemia and schizophrenia) to illustrate the limitations of ontologies as classification resources. We show that eligibility criteria are often more useful than the Aristotelian definitions traditionally used in ontologies. Examples of eligibility criteria for diseases include complex predicates such as ' x is an instance of the class C when at least n criteria among m are verified' and 'symptoms must last at least one month if not treated, but less than one month, if effectively treated'. References to normality and abnormality are often found in disease definitions, but the operational definition of these references (i.e., the statistical and contextual information necessary to define them) is rarely provided. We conclude that knowledge bases that include probabilistic and statistical knowledge as well as rule-based criteria are more useful than Aristotelian definitions for representing the predicates defined by necessary and sufficient conditions. Rich knowledge bases are needed to clarify the relations between individuals and classes in various studies and applications. However, as ontologies represent relations among classes, they can play a supporting role in disease classification services built primarily on knowledge bases.

The extended evolutionary synthesis: its structure, assumptions and predictions

PubMed Central

Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

2015-01-01

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

On the preservation of cooperation in two-strategy games with nonlocal interactions.

PubMed

Aydogmus, Ozgur; Zhou, Wen; Kang, Yun

2017-03-01

Nonlocal interactions such as spatial interaction are ubiquitous in nature and may alter the equilibrium in evolutionary dynamics. Models including nonlocal spatial interactions can provide a further understanding on the preservation and emergence of cooperation in evolutionary dynamics. In this paper, we consider a variety of two-strategy evolutionary spatial games with nonlocal interactions based on an integro-differential replicator equation. By defining the invasion speed and minimal traveling wave speed for the derived model, we study the effects of the payoffs, the selection pressure and the spatial parameter on the preservation of cooperation. One of our most interesting findings is that, for the Prisoners Dilemma games in which the defection is the only evolutionary stable strategy for unstructured populations, analyses on its asymptotic speed of propagation suggest that, in contrast with spatially homogeneous games, the cooperators can invade the habitat under proper conditions. Other two-strategy evolutionary spatial games are also explored. Both our theoretical and numerical studies show that the nonlocal spatial interaction favors diversity in strategies in a population and is able to preserve cooperation in a competing environment. A real data application in a virus mutation study echoes our theoretical observations. In addition, we compare the results of our model to the partial differential equation approach to demonstrate the importance of including non-local interaction component in evolutionary game models. Copyright © 2016 Elsevier Inc. All rights reserved.

The Plasmodium gaboni genome illuminates allelic dimorphism of immunologically important surface antigens in P. falciparum.

PubMed

Roy, Scott William

2015-12-01

In the deadly human malaria parasite Plasmodium falciparum, several major merozoite surface proteins (MSPs) show a striking pattern of allelic diversity called allelic dimorphism (AD). In AD, the vast majority of observed alleles fall into two highly divergent allelic classes, with recombinant alleles being rare or not observed, presumably due to repression by natural selection (recombination suppression, or RS). The three AD loci, merozoite surface proteins (MSPs) 1, 2, and 6, along with MSP3, which also exhibits RS among four allelic classes, can be collectively called AD/RS. The causes of AD/RS and the evolutionary history of allelic diversity at these loci remain mysterious. The few available sequences from a single closely related chimpanzee parasite, P. reichenowi, have suggested that for 3/4 loci, AD/RS is an ancient state that has been retained in P. falciparum since well before the P. falciparum-P. reichenowi ancestor. On the other hand, based on comparative sequence analysis, we recently suggested that (i) AD/RS P. falciparum loci have undergone interallelic recombination over longer evolutionary times (on the timescale of recent speciation events), and thus (ii) AD/RS may be a recent phenomenon. The recent publication of genomic sequencing efforts for P. gaboni, an outgroup to P. falciparum and P. reichenowi, allows for improved reconstruction of the evolutionary history of these loci. In this work, I report genic sequence for P. gaboni for all four AD/RS P. falciparum loci (MSP1, 2, 3, and 6). Comparison of these sequences with available P. falciparum and P. reichenowi data strengthens the evidence for interallelic recombination over the evolutionary history of these species and also strengthens the case that AD/RS at these loci is ancient. Combined with previous results, these data provide evidence that AD/RS at different loci has evolved at several different times in the evolutionary history of P. falciparum: (i) before the P. gaboni-P. falciparum divergence, for much of MSP1 and MSP3; (ii) between the P. gaboni-P. falciparum and P. reichenowi-P. falciparum divergences, for the 5' end of the AD region of MSP6 and block 3 of MSP1; (iii) near the P. reichenowi-P. falciparum divergence, for the 3' end of the AD region of MSP6; and (iv) after the P. reichenowi-P. falciparum divergence, for MSP2. Based on these results, I suggest a new hypothesis for long-term evolutionary maintenance of AD/RS by recombination within allelic groups. Copyright © 2015 Elsevier B.V. All rights reserved.

The roles of gene duplication, gene conversion and positive selection in rodent Esp and Mup pheromone gene families with comparison to the Abp family.

PubMed

Karn, Robert C; Laukaitis, Christina M

2012-01-01

Three proteinaceous pheromone families, the androgen-binding proteins (ABPs), the exocrine-gland secreting peptides (ESPs) and the major urinary proteins (MUPs) are encoded by large gene families in the genomes of Mus musculus and Rattus norvegicus. We studied the evolutionary histories of the Mup and Esp genes and compared them with what is known about the Abp genes. Apparently gene conversion has played little if any role in the expansion of the mouse Class A and Class B Mup genes and pseudogenes, and the rat Mups. By contrast, we found evidence of extensive gene conversion in many Esp genes although not in all of them. Our studies of selection identified at least two amino acid sites in β-sheets as having evolved under positive selection in the mouse Class A and Class B MUPs and in rat MUPs. We show that selection may have acted on the ESPs by determining K(a)/K(s) for Exon 3 sequences with and without the converted sequence segment. While it appears that purifying selection acted on the ESP signal peptides, the secreted portions of the ESPs probably have undergone much more rapid evolution. When the inner gene converted fragment sequences were removed, eleven Esp paralogs were present in two or more pairs with K(a)/K(s) >1.0 and thus we propose that positive selection is detectable by this means in at least some mouse Esp paralogs. We compare and contrast the evolutionary histories of all three mouse pheromone gene families in light of their proposed functions in mouse communication.

There must be a prokaryote somewhere: microbiology's search for itself

NASA Technical Reports Server (NTRS)

Woese, C. R.

1994-01-01

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.

Parametric Sensitivity Analysis of Oscillatory Delay Systems with an Application to Gene Regulation.

PubMed

Ingalls, Brian; Mincheva, Maya; Roussel, Marc R

2017-07-01

A parametric sensitivity analysis for periodic solutions of delay-differential equations is developed. Because phase shifts cause the sensitivity coefficients of a periodic orbit to diverge, we focus on sensitivities of the extrema, from which amplitude sensitivities are computed, and of the period. Delay-differential equations are often used to model gene expression networks. In these models, the parametric sensitivities of a particular genotype define the local geometry of the evolutionary landscape. Thus, sensitivities can be used to investigate directions of gradual evolutionary change. An oscillatory protein synthesis model whose properties are modulated by RNA interference is used as an example. This model consists of a set of coupled delay-differential equations involving three delays. Sensitivity analyses are carried out at several operating points. Comments on the evolutionary implications of the results are offered.

Evolutionary Game Model Study of Construction Green Supply Chain Management under the Government Intervention

NASA Astrophysics Data System (ADS)

Xing, Yuanzhi; Deng, Xiaoyi

2017-11-01

The paper first has defined the concepts of green supply chain management and evolution game theory, and pointed out the characteristics of green supply chain management in construction. The main participants and key links of the construction green supply chain management are determined by constructing the organization framework. This paper established the evolutionary game model between construction enterprises and recycling enterprises for the green supply chain closed-loop structure. The waste recycling evolutionary stability equilibrium solution is obtained to explore the principle and effective scope of government policy intervention. This paper put forward the relevant countermeasures to the green supply chain management in construction recycling stage from the government point of view. The conclusion has reference value and guidance to the final product construction enterprises, recycling enterprises and the government during green supply chain.

Nephrogenic systemic fibrosis and class labeling of gadolinium-based contrast agents by the Food and Drug Administration.

PubMed

Yang, Lucie; Krefting, Ira; Gorovets, Alex; Marzella, Louis; Kaiser, James; Boucher, Robert; Rieves, Dwaine

2012-10-01

In 2007, the Food and Drug Administration requested that manufacturers of all approved gadolinium-based contrast agents (GBCAs), drugs widely used in magnetic resonance imaging, use nearly identical text in their product labeling to describe the risk of nephrogenic systemic fibrosis (NSF). Accumulating information about NSF risks led to revision of the labeling text for all of these drugs in 2010. The present report summarizes the basis and purpose of this class-labeling approach and describes some of the related challenges, given the evolutionary nature of the NSF risk evidence. The class-labeling approach for presentation of product risk is designed to decrease the occurrence of NSF and to enhance the safe use of GBCAs in radiologic practice. © RSNA, 2012.

Contrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion

USGS Publications Warehouse

Minias, Piotr; Bateson, Zachary W.; Whittingham, Linda A.; Johnson, Jeff A.; Oyler-McCance, Sara J.; Dunn, Peter O.

2016-01-01

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

Contrasting evolutionary histories of MHC class I and class II loci in grouse—effects of selection and gene conversion

PubMed Central

Minias, P; Bateson, Z W; Whittingham, L A; Johnson, J A; Oyler-McCance, S; Dunn, P O

2016-01-01

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens. PMID:26860199

Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches.

PubMed

Siver, Peter A; Jo, Bok Yeon; Kim, Jong Im; Shin, Woongghi; Lott, Anne Marie; Wolfe, Alexander P

2015-06-01

Heterokont algae of the class Synurophyceae, characterized by distinctive siliceous scales that cover the surface of the cell, are ecologically important in inland waters, yet their evolutionary history remains enigmatic. We explore phylogenetic relationships within this group of algae relative to geologic time, with a focus on evolution of siliceous components. We combined an expansive five-gene and time-calibrated molecular phylogeny of synurophyte algae with an extensive array of fossil specimens from the middle Eocene to infer evolutionary trends within the group. The group originated in the Jurassic approximately 157 million years ago (Ma), with the keystone genera Mallomonas and Synura diverging during the Early Cretaceous at 130 Ma. Mallomonas further splits into two major subclades, signaling the evolution of the V-rib believed to aid in the spacing and organization of scales on the cell covering. Synura also diverges into two primary subclades, separating taxa with forward-projecting spines on the scale from those with a keel positioned on the scale proper. Approximately one third of the fossil species are extinct, whereas the remaining taxa are linked to modern congeners. The taxonomy of synurophytes, which relies extensively on the morphology of the siliceous components, is largely congruent with molecular analyses. Scales of extinct synurophytes were significantly larger than those of modern taxa and may have played a role in their demise. In contrast, many fossil species linked to modern lineages were smaller in the middle Eocene, possibly reflecting growth in the greenhouse climatic state that characterized this geologic interval. © 2015 Botanical Society of America, Inc.

Automatic feature design for optical character recognition using an evolutionary search procedure.

PubMed

Stentiford, F W

1985-03-01

An automatic evolutionary search is applied to the problem of feature extraction in an OCR application. A performance measure based on feature independence is used to generate features which do not appear to suffer from peaking effects [17]. Features are extracted from a training set of 30 600 machine printed 34 class alphanumeric characters derived from British mail. Classification results on the training set and a test set of 10 200 characters are reported for an increasing number of features. A 1.01 percent forced decision error rate is obtained on the test data using 316 features. The hardware implementation should be cheap and fast to operate. The performance compares favorably with current low cost OCR page readers.

Comparison of Evolutionary (Genetic) Algorithm and Adjoint Methods for Multi-Objective Viscous Airfoil Optimizations

NASA Technical Reports Server (NTRS)

Pulliam, T. H.; Nemec, M.; Holst, T.; Zingg, D. W.; Kwak, Dochan (Technical Monitor)

2002-01-01

A comparison between an Evolutionary Algorithm (EA) and an Adjoint-Gradient (AG) Method applied to a two-dimensional Navier-Stokes code for airfoil design is presented. Both approaches use a common function evaluation code, the steady-state explicit part of the code,ARC2D. The parameterization of the design space is a common B-spline approach for an airfoil surface, which together with a common griding approach, restricts the AG and EA to the same design space. Results are presented for a class of viscous transonic airfoils in which the optimization tradeoff between drag minimization as one objective and lift maximization as another, produces the multi-objective design space. Comparisons are made for efficiency, accuracy and design consistency.

Comparative genomics reveals insights into avian genome evolution and adaptation

PubMed Central

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

2015-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

The Practice Pattern of Percutaneous Coronary Intervention in Korea: Based on Year 2014 Cohort of Korean Percutaneous Coronary Intervention (K-PCI) Registry.

PubMed

Gwon, Hyeon-Cheol; Jeon, Dong Woon; Kang, Hyun-Jae; Jang, Jae-Sik; Park, Duk-Woo; Shin, Dong-Ho; Moon, Keon-Woong; Kim, Jung-Sun; Kim, Juhan; Bae, Jang-Whan; Hur, Seung-Ho; Kim, Byung Ok; Choi, Donghoon; Han, Kyoo-Rok; Kim, Hyo-Soo

2017-05-01

Appropriate use criteria (AUC) was developed to improve the quality of percutaneous coronary intervention (PCI). However, these criteria should consider the current practice pattern in the country where they are being applied. The algorithm for the Korean PCI practice pattern (KP3) was developed by modifying the United States-derived AUC in expert consensus meetings. KP3 class A was defined as any strategy with evidence from randomized trials that was more conservative for PCI than medical therapy or coronary artery bypass graft (CABG). Class C was defined as any strategy with less evidence from randomized trials and more aggressive for PCI than medical therapy or CABG. Class B was defined as a strategy that was partly class A and partly class C. We applied the KP3 classification system to the Korean PCI registry. The KP3 class A was noted in 67.7% of patients, class B in 28.8%, and class C in 3.5%. The median proportion of class C cases per center was 2.0%. The distribution of KP3 classes varied significantly depending on clinical and angiographic characteristics. The proportion of KP3 class C cases per center was not significantly dependent on PCI volume, but rather on the percentage of ACS cases in each center. We report the current PCI practice pattern by applying the new KP3 classification in a nationwide PCI registry. The results should be interpreted carefully with due regard for the complex relationships between the determining variables and the healthcare system in Korea.

Nuclear technology and the space exploration missions

NASA Technical Reports Server (NTRS)

Brandhorst, Henry W.; Sovie, Ronald J.

1990-01-01

The strategy for a major exploration initiative leading to permanent human presence beyond earth orbit is still being developed; however enough is known to begin defining the role of nuclear technologies. Three broad areas are discussed: low power (less than 10 kWe) rover/vehicle power systems; integrated, evolutionary base power systems (25 to 100 kW) and nuclear energy for electric propulsion (2 to 100 MWe); and direct thermal propulsion (1000s MW). A phased, evolutionary approach is described for both the moon and Mars, and the benefits of nuclear technologies relative to solar and their integration are described.

Defining Social Class Across Time and Between Groups.

PubMed

Cohen, Dov; Shin, Faith; Liu, Xi; Ondish, Peter; Kraus, Michael W

2017-11-01

We examined changes over four decades and between ethnic groups in how people define their social class. Changes included the increasing importance of income, decreasing importance of occupational prestige, and the demise of the "Victorian bargain," in which poor people who subscribed to conservative sexual and religious norms could think of themselves as middle class. The period also saw changes (among Whites) and continuity (among Black Americans) in subjective status perceptions. For Whites (and particularly poor Whites), their perceptions of enhanced social class were greatly reduced. Poor Whites now view their social class as slightly but significantly lower than their poor Black and Latino counterparts. For Black respondents, a caste-like understanding of social class persisted, as they continued to view their class standing as relatively independent of their achieved education, income, and occupation. Such achievement indicators, however, predicted Black respondents' self-esteem more than they predicted self-esteem for any other group.

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 4 2014-10-01 2014-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 4 2011-10-01 2011-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 4 2010-10-01 2010-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 4 2012-10-01 2012-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

42 CFR 433.56 - Classes of health care services and providers defined.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 4 2013-10-01 2013-10-01 false Classes of health care services and providers defined. 433.56 Section 433.56 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION General Administrative Requirements State Financial...

A Generalized Approach to Defining Item Discrimination for DCMs

ERIC Educational Resources Information Center

Henson, Robert; DiBello, Lou; Stout, Bill

2018-01-01

Diagnostic classification models (DCMs, also known as cognitive diagnosis models) hold the promise of providing detailed classroom information about the skills a student has or has not mastered. Specifically, DCMs are special cases of constrained latent class models where classes are defined based on mastery/nonmastery of a set of attributes (or…

Symbiotic lifestyle expression by fungal endophytes and the adaptation of plants to stress: unraveling the complexities of intimacy

USGS Publications Warehouse

Redman, Regina S.; Henson, Joan M.; Rodriguez, Russell J.

2005-01-01

The fossil record indicates that fungal symbionts have been associated with plants since the Ordovician period (approximately 400 million years ago), when plants first became established on land (Pirozynski and Malloch, 1975; Redecker et al., 2000; Remy et al., 1994; Simon et al., 1993). Transitioning from aquatic to terrestrial habitats likely presented plants with new stresses, including periods of desiccation. Since symbiotic fungi are known to confer drought tolerance to plants (Bacon, 1993; Read and Camp, 1986), it has been suggested that fungal symbiosis was involved with or responsible for the establishment of land plants (Pirozynski and Malloch, 1975). Symbiosis was first defined by De Bary in 1879, and since that time, all plants in natural ecosystems have been found to be colonized with fungal and bacterial symbionts. It is clear that individual plants represent symbiotic communities with microorganisms associated in or on tissues below- and aboveground.There are two major classes of fungal symbionts associated with internal plant tissues: fungal endophytes that reside entirely within plants and may be associated with roots, stems leaves, or flowers; and mycorrhizal fungi that reside only in roots but extend out into the rhizosphere. In addition, fungal endophytes may be divided into two classes: (1) a relatively small number of fastidious species that are limited to a few monocot hosts (Clay and Schardl, 2002), and (2) a large number of tractable species with broad host ranges, including both monocots and eudicots (Stone et al., 2000). While significant resources and research have been invested in mycorrhizae and class 1 endophytes, comparatively little is known about class 2 endophytes, which may represent the largest group of fungal symbionts. This is partially because the symbiotic functionalities of class 2 endophytes have only recently been elucidated and shown to be responsible for the adaptation of some plants to high-stress environments (Redman et al., 1999, 2001, 2002a; Arnold et al., 2003; Dingle and McGee, 2003; Ernst et al., 2003).In this chapter, we focus on symbiotic interactions between class 2 endophytes and a variety of monocot and eudicot host species. Specifically, we will discuss the ability of endophytes to express more than one symbiotic lifestyle, fungal taxonomy vs. lifestyle expression, the adaptive nature of symbioses, mechanisms of symbiotically conferred stress tolerance, and the evolutionary implications of adaptive symbiosis. We will refer to class 2 endophytes as fungal endophytes throughout the text.

Isolation and characterization of major histocompatibility class IIβ genes in an endangered North American cyprinid fish, the Rio Grande silvery minnow (Hybognathus amarus).

PubMed

Osborne, Megan J; Turner, Thomas F

2011-06-01

The major histocompatibility complex (MHC) is a critical component of the adaptive immune response in vertebrates. Due to the role that MHC plays in immunity, absence of variation within these genes may cause species to be vulnerable to emerging diseases. The freshwater fish family Cyprinidae comprises the most diverse and species-rich group of freshwater fish in the world, but some are imperiled. Despite considerable species richness and the long evolutionary history of the family, there are very few reports of MHC sequences (apart from a few model species), and no sequences are reported from endemic North American cyprinids (subfamily Leuciscinae). Here we isolate and characterize the MH Class II beta genes from complementary DNA and genomic DNA of the non-model, endangered Rio Grande silvery minnow (Hybognathus amarus), a North American cyprinid. Phylogenetic reconstruction revealed two groups of divergent MH alleles that are paralogous to previously described loci found in deeply divergent cyprinid taxa including common carp, zebrafish, African large barb and bream. Both groups of alleles were under the influence of diversifying selection yet not all individuals had alleles belonging to both allelic groups. We concluded that the general organization and pattern of variation of MH class II genes in Rio Grande silvery minnow is similar to that identified in other cyprinid fishes studied to date, despite distant evolutionary relationships and evidence of a severe genetic bottleneck. Copyright © 2011 Elsevier Ltd. All rights reserved.

Understanding Randomness and Its Impact on Student Learning: Lessons Learned from Building the Biology Concept Inventory (BCI)

ERIC Educational Resources Information Center

Garvin-Doxas, Kathy; Klymkowsky, Michael W.

2008-01-01

While researching student assumptions for the development of the Biology Concept Inventory (BCI; http://bioliteracy.net), we found that a wide class of student difficulties in molecular and evolutionary biology appears to be based on deep-seated, and often unaddressed, misconceptions about random processes. Data were based on more than 500…

Crystal structure of Pistol, a class of self-cleaving ribozyme

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

Nguyen, Laura A.; Wang, Jimin; Steitz, Thomas A.

2017-01-17

Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile bymore » deprotonating the 2'-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5' leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.« less

Evolution of extortion in Iterated Prisoner's Dilemma games.

PubMed

Hilbe, Christian; Nowak, Martin A; Sigmund, Karl

2013-04-23

Iterated games are a fundamental component of economic and evolutionary game theory. They describe situations where two players interact repeatedly and have the ability to use conditional strategies that depend on the outcome of previous interactions, thus allowing for reciprocation. Recently, a new class of strategies has been proposed, so-called "zero-determinant" strategies. These strategies enforce a fixed linear relationship between one's own payoff and that of the other player. A subset of those strategies allows "extortioners" to ensure that any increase in one player's own payoff exceeds that of the other player by a fixed percentage. Here, we analyze the evolutionary performance of this new class of strategies. We show that in reasonably large populations, they can act as catalysts for the evolution of cooperation, similar to tit-for-tat, but that they are not the stable outcome of natural selection. In very small populations, however, extortioners hold their ground. Extortion strategies do particularly well in coevolutionary arms races between two distinct populations. Significantly, they benefit the population that evolves at the slower rate, an example of the so-called "Red King" effect. This may affect the evolution of interactions between host species and their endosymbionts.

Evolution of extortion in Iterated Prisoner’s Dilemma games

PubMed Central

Hilbe, Christian; Nowak, Martin A.; Sigmund, Karl

2013-01-01

Iterated games are a fundamental component of economic and evolutionary game theory. They describe situations where two players interact repeatedly and have the ability to use conditional strategies that depend on the outcome of previous interactions, thus allowing for reciprocation. Recently, a new class of strategies has been proposed, so-called “zero-determinant” strategies. These strategies enforce a fixed linear relationship between one’s own payoff and that of the other player. A subset of those strategies allows “extortioners” to ensure that any increase in one player’s own payoff exceeds that of the other player by a fixed percentage. Here, we analyze the evolutionary performance of this new class of strategies. We show that in reasonably large populations, they can act as catalysts for the evolution of cooperation, similar to tit-for-tat, but that they are not the stable outcome of natural selection. In very small populations, however, extortioners hold their ground. Extortion strategies do particularly well in coevolutionary arms races between two distinct populations. Significantly, they benefit the population that evolves at the slower rate, an example of the so-called “Red King” effect. This may affect the evolution of interactions between host species and their endosymbionts. PMID:23572576

Prediction and explanation in the multiverse

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

Garriga, J.; Vilenkin, A.

2008-02-15

Probabilities in the multiverse can be calculated by assuming that we are typical representatives in a given reference class. But is this class well defined? What should be included in the ensemble in which we are supposed to be typical? There is a widespread belief that this question is inherently vague, and that there are various possible choices for the types of reference objects which should be counted in. Here we argue that the 'ideal' reference class (for the purpose of making predictions) can be defined unambiguously in a rather precise way, as the set of all observers with identicalmore » information content. When the observers in a given class perform an experiment, the class branches into subclasses who learn different information from the outcome of that experiment. The probabilities for the different outcomes are defined as the relative numbers of observers in each subclass. For practical purposes, wider reference classes can be used, where we trace over all information which is uncorrelated to the outcome of the experiment, or whose correlation with it is beyond our current understanding. We argue that, once we have gathered all practically available evidence, the optimal strategy for making predictions is to consider ourselves typical in any reference class we belong to, unless we have evidence to the contrary. In the latter case, the class must be correspondingly narrowed.« less

Gender and the Construction of Class.

ERIC Educational Resources Information Center

Acker, Joan

Only by recognizing that class is not gender neutral can the processes of class formation and reproduction be understood. Class is defined as a process in which human beings take an active part, rather than a structure of categories into which individuals may be inserted. Gender organizes or structures class in many different ways. For example,…

The Ia.2 Epitope Defines a Subset of Lipid Raft Resident MHC Class II Molecules Crucial to Effective Antigen Presentation1

PubMed Central

Busman-Sahay, Kathleen; Sargent, Elizabeth; Harton, Jonathan A.; Drake, James R.

2016-01-01

Previous work has established that binding of the 11-5.2 anti-I-Ak mAb, which recognizes the Ia.2 epitope on I-Ak class II molecules, elicits MHC class II signaling, whereas binding of two other anti-I-Ak mAb that recognize the Ia.17 epitope fail to elicit signaling. Using a biochemical approach, we establish that the Ia.2 epitope recognized by the widely used 11-5.2 mAb defines a subset of cell surface I-Ak molecules predominantly found within membrane lipid rafts. Functional studies demonstrate that the Ia.2 bearing subset of I-Ak class II molecules is critically necessary for effective B cell–T cell interactions especially at low antigen doses, a finding consistent with published studies on the role of raft-resident class II molecules in CD4 T cell activation. Interestingly, B cells expressing recombinant I-Ak class II molecules possessing a β chain-tethered HEL peptide lack the Ia.2 epitope and fail to partition into lipid rafts. Moreover, cells expressing Ia.2 negative tethered peptide-class II molecules are severely impaired in their ability to present both tethered peptide or peptide derived from exogenous antigen to CD4 T cells. These results establish the Ia.2 epitope as defining a lipid raft-resident MHC class II confomer vital to the initiation of MHC class II restricted B cell–T cell interactions. PMID:21543648

Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism.

PubMed

Veprinskiy, Valery; Heizinger, Leonhard; Plach, Maximilian G; Merkl, Rainer

2017-01-26

Microbes, plants, and fungi synthesize an enormous number of metabolites exhibiting rich chemical diversity. For a high-level classification, metabolism is subdivided into primary (PM) and secondary (SM) metabolism. SM products are often not essential for survival of the organism and it is generally assumed that SM enzymes stem from PM homologs. We wanted to assess evolutionary relationships and function of bona fide bacterial PM and SM enzymes. Thus, we analyzed the content of 1010 biosynthetic gene clusters (BGCs) from the MIBiG dataset; the encoded bacterial enzymes served as representatives of SM. The content of 15 bacterial genomes known not to harbor BGCs served as a representation of PM. Enzymes were categorized on their EC number and for these enzyme functions, frequencies were determined. The comparison of PM/SM frequencies indicates a certain preference for hydrolases (EC class 3) and ligases (EC class 6) in PM and of oxidoreductases (EC class 1) and lyases (EC class 4) in SM. Based on BLAST searches, we determined pairs of PM/SM homologs and their functional diversity. Oxidoreductases, transferases (EC class 2), lyases and isomerases (EC class 5) form a tightly interlinked network indicating that many protein folds can accommodate different functions in PM and SM. In contrast, the functional diversity of hydrolases and especially ligases is significantly limited in PM and SM. For the most direct comparison of PM/SM homologs, we restricted for each BGC the search to the content of the genome it comes from. For each homologous hit, the contribution of the genomic neighborhood to metabolic pathways was summarized in BGC-specific html-pages that are interlinked with KEGG; this dataset can be downloaded from https://www.bioinf.ur.de . Only few reaction chemistries are overrepresented in bacterial SM and at least 55% of the enzymatic functions present in BGCs possess PM homologs. Many SM enzymes arose in PM and Nature utilized the evolvability of enzymes similarly to establish novel functions both in PM and SM. Future work aimed at the elucidation of evolutionary routes that have interconverted a PM enzyme into an SM homolog can profit from our BGC-specific annotations.

Theoretical Analysis of Local Search and Simple Evolutionary Algorithms for the Generalized Travelling Salesperson Problem.

PubMed

Pourhassan, Mojgan; Neumann, Frank

2018-06-22

The generalized travelling salesperson problem is an important NP-hard combinatorial optimization problem for which meta-heuristics, such as local search and evolutionary algorithms, have been used very successfully. Two hierarchical approaches with different neighbourhood structures, namely a Cluster-Based approach and a Node-Based approach, have been proposed by Hu and Raidl (2008) for solving this problem. In this paper, local search algorithms and simple evolutionary algorithms based on these approaches are investigated from a theoretical perspective. For local search algorithms, we point out the complementary abilities of the two approaches by presenting instances where they mutually outperform each other. Afterwards, we introduce an instance which is hard for both approaches when initialized on a particular point of the search space, but where a variable neighbourhood search combining them finds the optimal solution in polynomial time. Then we turn our attention to analysing the behaviour of simple evolutionary algorithms that use these approaches. We show that the Node-Based approach solves the hard instance of the Cluster-Based approach presented in Corus et al. (2016) in polynomial time. Furthermore, we prove an exponential lower bound on the optimization time of the Node-Based approach for a class of Euclidean instances.

Our Social Roots: How Local Ecology Shapes Our Social Structures

NASA Astrophysics Data System (ADS)

Mace, Ruth

There is overwhelming evidence that wide-ranging aspects of human biology and human behavior can be considered as adaptations to different subsistence systems. Wider environmental and ecological correlates of behavioral and cultural traits are generally best understood as being mediated by differences in subsistence strategies. Modes of subsistence profoundly influence both human biology, as documented in genetic changes, and human social behavior and cultural norms, such as kinship, marriage, descent, wealth inheritance, and political systems. Thus both cultural and biological factors usually need to be considered together in studies of human evolutionary ecology, combined in specifically defined evolutionary models. Models of cultural adaptation to environmental conditions can be subjected to the same or similar tests that behavioral ecologists have used to seek evidence for adaptive behavior in other species. Phylogenetic comparative methods are proving useful, both for studying co-evolutionary hypotheses (cultural and/or gene-culture co-evolution), and for estimating ancestral states of prehistoric societies. This form of formal cross-cultural comparison is helping to put history back into anthropology, and helping us to understand cultural evolutionary processes at a number of levels.

Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains.

PubMed

Angelini, A; Amato, A; Bianconi, G; Bassetti, B; Cosentino Lagomarsino, M

2010-02-01

We present a combined mean-field and simulation approach to different models describing the dynamics of classes formed by elements that can appear, disappear, or copy themselves. These models, related to a paradigm duplication-innovation model known as Chinese restaurant process, are devised to reproduce the scaling behavior observed in the genome-wide repertoire of protein domains of all known species. In view of these data, we discuss the qualitative and quantitative differences of the alternative model formulations, focusing in particular on the roles of element loss and of the specificity of empirical domain classes.

Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains

NASA Astrophysics Data System (ADS)

Angelini, A.; Amato, A.; Bianconi, G.; Bassetti, B.; Cosentino Lagomarsino, M.

2010-02-01

We present a combined mean-field and simulation approach to different models describing the dynamics of classes formed by elements that can appear, disappear, or copy themselves. These models, related to a paradigm duplication-innovation model known as Chinese restaurant process, are devised to reproduce the scaling behavior observed in the genome-wide repertoire of protein domains of all known species. In view of these data, we discuss the qualitative and quantitative differences of the alternative model formulations, focusing in particular on the roles of element loss and of the specificity of empirical domain classes.

Issues in the Classification of Disease Instances with Ontologies

PubMed Central

Burgun, Anita; Bodenreider, Olivier; Jacquelinet, Christian

2006-01-01

Ontologies define classes of entities and their interrelations. They are used to organize data according to a theory of the domain. Towards that end, ontologies provide class definitions (i.e., the necessary and sufficient conditions for defining class membership). In medical ontologies, it is often difficult to establish such definitions for diseases. We use three examples (anemia, leukemia and schizophrenia) to illustrate the limitations of ontologies as classification resources. We show that eligibility criteria are often more useful than the Aristotelian definitions traditionally used in ontologies. Examples of eligibility criteria for diseases include complex predicates such as ‘ x is an instance of the class C when at least n criteria among m are verified’ and ‘symptoms must last at least one month if not treated, but less than one month, if effectively treated’. References to normality and abnormality are often found in disease definitions, but the operational definition of these references (i.e., the statistical and contextual information necessary to define them) is rarely provided. We conclude that knowledge bases that include probabilistic and statistical knowledge as well as rule-based criteria are more useful than Aristotelian definitions for representing the predicates defined by necessary and sufficient conditions. Rich knowledge bases are needed to clarify the relations between individuals and classes in various studies and applications. However, as ontologies represent relations among classes, they can play a supporting role in disease classification services built primarily on knowledge bases. PMID:16160339

Climatic niche evolution is faster in sympatric than allopatric lineages of the butterfly genus Pyrgus

PubMed Central

Pitteloud, Camille; Arrigo, Nils; Suchan, Tomasz; Mastretta-Yanes, Alicia; Dincă, Vlad; Hernández-Roldán, Juan; Brockmann, Ernst; Chittaro, Yannick; Kleckova, Irena; Fumagalli, Luca; Buerki, Sven; Pellissier, Loïc

2017-01-01

Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare the magnitude of climatic niche shifts between sympatric versus allopatric divergence of lineages in butterflies. By combining next-generation sequencing, parametric biogeography and ecological niche analyses applied to a genus-wide phylogeny of Palaearctic Pyrgus butterflies, we compare evolutionary rates along eight climatic dimensions across sister lineages that diverged in large-scale sympatry versus allopatry. In order to examine the possible effects of the spatial scale at which sympatry is defined, we considered three sets of biogeographic assignments, ranging from narrow to broad definition. Our findings suggest higher rates of niche evolution along all climatic dimensions for sister lineages that diverge in sympatry, when using a narrow delineation of biogeographic areas. This result contrasts with significantly lower rates of climatic niche evolution found in cases of allopatric speciation, despite the biogeographic regions defined here being characterized by significantly different climates. Higher rates in allopatry are retrieved when biogeographic areas are too widely defined—in such a case allopatric events may be recorded as sympatric. Our results reveal the macro-evolutionary significance of abiotic niche differentiation involved in speciation processes within biogeographic regions, and illustrate the importance of the spatial scale chosen to define areas when applying parametric biogeographic analyses. PMID:28404781

Representations and evolutionary operators for the scheduling of pump operations in water distribution networks.

PubMed

López-Ibáñez, Manuel; Prasad, T Devi; Paechter, Ben

2011-01-01

Reducing the energy consumption of water distribution networks has never had more significance. The greatest energy savings can be obtained by carefully scheduling the operations of pumps. Schedules can be defined either implicitly, in terms of other elements of the network such as tank levels; or explicitly, by specifying the time during which each pump is on/off. The traditional representation of explicit schedules is a string of binary values with each bit representing pump on/off status during a particular time interval. In this paper, we formally define and analyze two new explicit representations based on time-controlled triggers, where the maximum number of pump switches is established beforehand and the schedule may contain fewer than the maximum number of switches. In these representations, a pump schedule is divided into a series of integers with each integer representing the number of hours for which a pump is active/inactive. This reduces the number of potential schedules compared to the binary representation, and allows the algorithm to operate on the feasible region of the search space. We propose evolutionary operators for these two new representations. The new representations and their corresponding operations are compared with the two most-used representations in pump scheduling, namely, binary representation and level-controlled triggers. A detailed statistical analysis of the results indicates which parameters have the greatest effect on the performance of evolutionary algorithms. The empirical results show that an evolutionary algorithm using the proposed representations is an improvement over the results obtained by a recent state of the art hybrid genetic algorithm for pump scheduling using level-controlled triggers.

Phages of lactic acid bacteria: The role of genetics in understanding phage-host interactions and their co-evolutionary processes

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

Mahony, Jennifer, E-mail: j.mahony@ucc.ie; Ainsworth, Stuart; Stockdale, Stephen

Dairy fermentations are among the oldest food processing applications, aimed at preservation and shelf-life extension through the use of lactic acid bacteria (LAB) starter cultures, in particular strains of Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. and Leuconostoc spp. Traditionally this was performed by continuous passaging of undefined cultures from a finished fermentation to initiate the next fermentation. More recently, consumer demands on consistent and desired flavours and textures of dairy products have led to a more defined approach to such processes. Dairy (starter) companies have responded to the need to define the nature and complexity of the starter culture mixes,more » and dairy fermentations are now frequently based on defined starter cultures of low complexity, where each starter component imparts specific technological properties that are desirable to the product. Both mixed and defined starter culture approaches create the perfect environment for the proliferation of (bacterio)phages capable of infecting these LAB. The repeated use of the same starter cultures in a single plant, coupled to the drive towards higher and consistent production levels, increases the risk and negative impact of phage infection. In this review we will discuss recent advances in tracking the adaptation of phages to the dairy industry, the advances in understanding LAB phage-host interactions, including evolutionary and genomic aspects.« less

Cellulose synthase 'class specific regions' are intrinsically disordered and functionally undifferentiated.

PubMed

Scavuzzo-Duggan, Tess R; Chaves, Arielle M; Singh, Abhishek; Sethaphong, Latsavongsakda; Slabaugh, Erin; Yingling, Yaroslava G; Haigler, Candace H; Roberts, Alison W

2018-06-01

Cellulose synthases (CESAs) are glycosyltransferases that catalyze formation of cellulose microfibrils in plant cell walls. Seed plant CESA isoforms cluster in six phylogenetic clades, whose non-interchangeable members play distinct roles within cellulose synthesis complexes (CSCs). A 'class specific region' (CSR), with higher sequence similarity within versus between functional CESA classes, has been suggested to contribute to specific activities or interactions of different isoforms. We investigated CESA isoform specificity in the moss, Physcomitrella patens (Hedw.) B. S. G. to gain evolutionary insights into CESA structure/function relationships. Like seed plants, P. patens has oligomeric rosette-type CSCs, but the PpCESAs diverged independently and form a separate CESA clade. We showed that P. patens has two functionally distinct CESAs classes, based on the ability to complement the gametophore-negative phenotype of a ppcesa5 knockout line. Thus, non-interchangeable CESA classes evolved separately in mosses and seed plants. However, testing of chimeric moss CESA genes for complementation demonstrated that functional class-specificity is not determined by the CSR. Sequence analysis and computational modeling showed that the CSR is intrinsically disordered and contains predicted molecular recognition features, consistent with a possible role in CESA oligomerization and explaining the evolution of class-specific sequences without selection for class-specific function. © 2018 Institute of Botany, Chinese Academy of Sciences.

Conceptualizing "Homework" in Flipped Mathematics Classes

ERIC Educational Resources Information Center

de Araujo, Zandra; Otten, Samuel; Birisci, Salih

2017-01-01

Flipped instruction is becoming more common in the United States, particularly in mathematics classes. One of the defining characteristics of this increasingly popular instructional format is the homework teachers assign. In contrast to traditional mathematics classes in which homework consists of problem sets, homework in flipped classes often…

76 FR 68058 - Classes of Poultry

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-03

... characteristics of poultry in the market today. Poultry classes are defined primarily in terms of the age and sex... sex of the bird. \\1\\ Ready-to-cook poultry at 9 CFR 381.1 is defined as any slaughtered poultry free... are female while the definition states that the birds may be of either sex. The comment suggested that...

77 FR 32157 - Self-Regulatory Organizations; NYSE Amex LLC; Notice of Filing of Proposed Rule Change Defining a...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-31

... Specialist in Each Options Class and Modifying the Specialist Entitlement Accordingly May 24, 2012. Pursuant... of Substance of the Proposed Rule Change The Exchange proposes to define a Primary Specialist in each options class and modify the Specialist entitlement accordingly. The text of the proposed rule change is...

Integrating instance selection, instance weighting, and feature weighting for nearest neighbor classifiers by coevolutionary algorithms.

PubMed

Derrac, Joaquín; Triguero, Isaac; Garcia, Salvador; Herrera, Francisco

2012-10-01

Cooperative coevolution is a successful trend of evolutionary computation which allows us to define partitions of the domain of a given problem, or to integrate several related techniques into one, by the use of evolutionary algorithms. It is possible to apply it to the development of advanced classification methods, which integrate several machine learning techniques into a single proposal. A novel approach integrating instance selection, instance weighting, and feature weighting into the framework of a coevolutionary model is presented in this paper. We compare it with a wide range of evolutionary and nonevolutionary related methods, in order to show the benefits of the employment of coevolution to apply the techniques considered simultaneously. The results obtained, contrasted through nonparametric statistical tests, show that our proposal outperforms other methods in the comparison, thus becoming a suitable tool in the task of enhancing the nearest neighbor classifier.

Genomic insights into the evolution of hybrid isoprenoid biosynthetic gene clusters in the MAR4 marine streptomycete clade

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

Gallagher, Kelley A.; Jensen, Paul R.

Background: Considerable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into the diversity and distributions of secondary metabolite biosynthetic gene clusters and the evolutionary processes that generate them. Here we examine the distribution of gene clusters predicted to encode the biosynthesis of a structurally diverse class of molecules called hybrid isoprenoids (HIs) in the genus Streptomyces. These compounds are derived from a mixed biosynthetic origin that is characterized by the incorporation of a terpene moiety onto a variety of chemicalmore » scaffolds and include many potent antibiotic and cytotoxic agents. Results: One hundred and twenty Streptomyces genomes were searched for HI biosynthetic gene clusters using ABBA prenyltransferases (PTases) as queries. These enzymes are responsible for a key step in HI biosynthesis. The strains included 12 that belong to the ‘MAR4’ clade, a largely marine-derived lineage linked to the production of diverse HI secondary metabolites. We found ABBA PTase homologs in all of the MAR4 genomes, which averaged five copies per strain, compared with 21 % of the non-MAR4 genomes, which averaged one copy per strain. Phylogenetic analyses suggest that MAR4 PTase diversity has arisen by a combination of horizontal gene transfer and gene duplication. Furthermore, there is evidence that HI gene cluster diversity is generated by the horizontal exchange of orthologous PTases among clusters. Many putative HI gene clusters have not been linked to their secondary metabolic products, suggesting that MAR4 strains will yield additional new compounds in this structure class. Finally, we confirm that the mevalonate pathway is not always present in genomes that contain HI gene clusters and thus is not a reliable query for identifying strains with the potential to produce HI secondary metabolites. In conclusion: We found that marine-derived MAR4 streptomycetes possess a relatively high genetic potential for HI biosynthesis. The combination of horizontal gene transfer, duplication, and rearrangement indicate that complex evolutionary processes account for the high level of HI gene cluster diversity in these bacteria, the products of which may provide a yet to be defined adaptation to the marine environment.« less

Genomic insights into the evolution of hybrid isoprenoid biosynthetic gene clusters in the MAR4 marine streptomycete clade

DOE PAGES

Gallagher, Kelley A.; Jensen, Paul R.

2015-11-17

Background: Considerable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into the diversity and distributions of secondary metabolite biosynthetic gene clusters and the evolutionary processes that generate them. Here we examine the distribution of gene clusters predicted to encode the biosynthesis of a structurally diverse class of molecules called hybrid isoprenoids (HIs) in the genus Streptomyces. These compounds are derived from a mixed biosynthetic origin that is characterized by the incorporation of a terpene moiety onto a variety of chemicalmore » scaffolds and include many potent antibiotic and cytotoxic agents. Results: One hundred and twenty Streptomyces genomes were searched for HI biosynthetic gene clusters using ABBA prenyltransferases (PTases) as queries. These enzymes are responsible for a key step in HI biosynthesis. The strains included 12 that belong to the ‘MAR4’ clade, a largely marine-derived lineage linked to the production of diverse HI secondary metabolites. We found ABBA PTase homologs in all of the MAR4 genomes, which averaged five copies per strain, compared with 21 % of the non-MAR4 genomes, which averaged one copy per strain. Phylogenetic analyses suggest that MAR4 PTase diversity has arisen by a combination of horizontal gene transfer and gene duplication. Furthermore, there is evidence that HI gene cluster diversity is generated by the horizontal exchange of orthologous PTases among clusters. Many putative HI gene clusters have not been linked to their secondary metabolic products, suggesting that MAR4 strains will yield additional new compounds in this structure class. Finally, we confirm that the mevalonate pathway is not always present in genomes that contain HI gene clusters and thus is not a reliable query for identifying strains with the potential to produce HI secondary metabolites. In conclusion: We found that marine-derived MAR4 streptomycetes possess a relatively high genetic potential for HI biosynthesis. The combination of horizontal gene transfer, duplication, and rearrangement indicate that complex evolutionary processes account for the high level of HI gene cluster diversity in these bacteria, the products of which may provide a yet to be defined adaptation to the marine environment.« less

Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models.

PubMed

Borchert, Nadine; Krug, Karsten; Gnad, Florian; Sinha, Amit; Sommer, Ralf J; Macek, Boris

2012-12-01

Pristionchus pacificus is a nematode that is increasingly used as a model organism in evolutionary biology. The genome of P. pacificus differs markedly from that of C. elegans, with a high number of orphan genes that are restricted to P. pacificus and have no homologs in other species. To gain insight into the architecture of signal transduction networks in model nematodes, we performed a large-scale qualitative phosphoproteome analysis of P. pacificus. Using two-stage enrichment of phosphopeptides from a digest of P. pacificus proteins and their subsequent analysis via high accuracy MS, we detected and localized 6,809 phosphorylation events on 2,508 proteins. We compared the detected P. pacificus phosphoproteome to the recently published phosphoproteome of C. elegans. The overall numbers and functional classes of phosphoproteins were similar between the two organisms. Interestingly, the products of orphan genes were significantly underrepresented among the detected P. pacificus phosphoproteins. We defined the theoretical kinome of P. pacificus and compared it to that of C. elegans. While tyrosine kinases were slightly underrepresented in the kinome of P. pacificus, all major classes of kinases were present in both organisms. Application of our kinome annotation to a recent transcriptomic study of dauer and mixed stage populations showed that Ser/Thr and Tyr kinases show similar expression levels in P. pacificus but not in C. elegans. This study presents the first systematic comparison of phosphoproteomes and kinomes of two model nematodes and, as such, will be a useful resource for comparative studies of their signal transduction networks.

Spatial self-organization in hybrid models of multicellular adhesion

NASA Astrophysics Data System (ADS)

Bonforti, Adriano; Duran-Nebreda, Salva; Montañez, Raúl; Solé, Ricard

2016-10-01

Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically cellular automata or reaction-diffusion systems. A different class of dynamical processes involves the correlated movement of agents over space, which can be mediated through chemotactic movement or minimization of cell-cell interaction energy. A classic example of the latter is given by the formation of spatially segregated assemblies when cells display differential adhesion. Here, we consider a new class of dynamical models, involving cell adhesion among two stochastically exchangeable cell states as a minimal model capable of exhibiting well-defined, ordered spatial patterns. Our results suggest that a whole space of pattern-forming rules is hosted by the combination of physical differential adhesion and the value of probabilities modulating cell phenotypic switching, showing that Turing-like patterns can be obtained without resorting to reaction-diffusion processes. If the model is expanded allowing cells to proliferate and die in an environment where diffusible nutrient and toxic waste are at play, different phases are observed, characterized by regularly spaced patterns. The analysis of the parameter space reveals that certain phases reach higher population levels than other modes of organization. A detailed exploration of the mean-field theory is also presented. Finally, we let populations of cells with different adhesion matrices compete for reproduction, showing that, in our model, structural organization can improve the fitness of a given cell population. The implications of these results for ecological and evolutionary models of pattern formation and the emergence of multicellularity are outlined.

Poverty and Depression among Men: The Social Class Worldview Model and Counseling Implications.

ERIC Educational Resources Information Center

Liu, William M.

This paper outlines a theory for understanding social class in men's lives, and argues that poverty and depression are a function of social class and internalized classism. It begins by defining poverty, then explains the Social Class Worldview Model, which is a subjective social class model, and the Modern Classism Theory, which allows clinicians…

A differential CDM model for fatigue of unidirectional metal matrix composites

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Kruch, S.

1992-01-01

A multiaxial, isothermal, continuum damage mechanics (CDM) model for fatigue of a unidirectional metal matrix composite volume element is presented. The model is phenomenological, stress based, and assumes a single scalar internal damage variable, the evolution of which is anisotropic. The development of the fatigue damage model, (i.e., evolutionary law) is based on the definition of an initially transversely isotropic fatigue limit surface, a static fracture surface, and a normalized stress amplitude function. The anisotropy of these surfaces and function, and therefore the model, is defined through physically meaningful invariants reflecting the local stress and material orientation. This transversely isotropic model is shown, when taken to it's isotropic limit, to directly simplify to a previously developed and validated isotropic fatigue continuum damage model. Results of a nondimensional parametric study illustrate (1) the flexibility of the present formulation in attempting to characterize a class of composite materials, and (2) the capability of the formulation in predicting anticipated qualitative trends in the fatigue behavior of unidirectional metal matrix composites. Also, specific material parameters representing an initial characterization of the composite system SiC/Ti 15-3 and the matrix material (Ti 15-3) are reported.

An analysis of the currently available calibrations in Strömgren photometry by using open clusters

NASA Astrophysics Data System (ADS)

Jordi, C.; Masana, E.; Figueras, F.; Torra, J.

1997-05-01

In recent years, several authors have revised the calibrations used to compute physical parameters (Mv, Teff, log g, [Fe/H]) from intrinsic colours in the uvby H_beta photometric system. For reddened stars, these intrinsic colours can be computed through the standard relations among colour indices for each of the regions defined by \\cite[Stromgren (1966)]{str66} on the HR diagram. We present a discussion of the coherence of these calibrations for main-sequence stars. Stars from open clusters are used to carry out this analysis. Assuming that individual reddening values and distances should be similar for all the members of a given open cluster, systematic differences among the calibrations used in each of the photometric regions might arise when comparing mean reddening values and distances for the members of each region. To classify the stars into Stromgren's regions we extended the algorithm presented by \\cite[Figueras et al. (1991)]{fig91} to a wider range of spectral types and luminosity classes. The observational ZAMS are compared with the theoretical ZAMS from stellar evolutionary models, in the range 6500-30000 K. The discrepancies are also discussed.

Origin and Evolution of the Sponge Aggregation Factor Gene Family

PubMed Central

Grice, Laura F.; Gauthier, Marie E.A.; Roper, Kathrein E.; Fernàndez-Busquets, Xavier; Degnan, Sandie M.

2017-01-01

Although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. Here, we characterize the Aggregation Factor (AF) gene family, which encodes putative allorecognition factors in the demosponge Amphimedon queenslandica, and trace its evolution across 24 sponge (Porifera) species. The AF locus in Amphimedon is comprised of a cluster of five similar genes that encode Calx-beta and Von Willebrand domains and a newly defined Wreath domain, and are highly polymorphic. Further AF variance appears to be generated through individualistic patterns of RNA editing. The AF gene family varies between poriferans, with protein sequences and domains diagnostic of the AF family being present in Amphimedon and other demosponges, but absent from other sponge classes. Within the demosponges, AFs vary widely with no two species having the same AF repertoire or domain organization. The evolution of AFs suggests that their diversification occurs via high allelism, and the continual and rapid gain, loss and shuffling of domains over evolutionary time. Given the marked differences in metazoan allorecognition genes, we propose the rapid evolution of AFs in sponges provides a model for understanding the extensive diversification of self–nonself recognition systems in the animal kingdom. PMID:28104746

Latent Class Analysis of Differential Item Functioning on the Peabody Picture Vocabulary Test-III

ERIC Educational Resources Information Center

Webb, Mi-young Lee; Cohen, Allan S.; Schwanenflugel, Paula J.

2008-01-01

This study investigated the use of latent class analysis for the detection of differences in item functioning on the Peabody Picture Vocabulary Test-Third Edition (PPVT-III). A two-class solution for a latent class model appeared to be defined in part by ability because Class 1 was lower in ability than Class 2 on both the PPVT-III and the…

Conservation of transcription factor binding events predicts gene expression across species

PubMed Central

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to function, defined as expression of the target genes. We show that (i) there is a significantly higher degree of conservation of TFBEs when the target gene is expressed in both species; (ii) there is increased conservation of binding events for groups of TFs compared to individual TFs; and (iii) conserved TFBEs have a greater impact on the expression of their target genes than non-conserved ones. These results link conservation of structural elements (TFBEs) to conservation of function (gene expression) and suggest a higher degree of functional conservation than implied by previous studies. PMID:21622661

phyloXML: XML for evolutionary biology and comparative genomics

PubMed Central

Han, Mira V; Zmasek, Christian M

2009-01-01

Background Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. Results We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. Conclusion PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at . PMID:19860910

Ranking Mammal Species for Conservation and the Loss of Both Phylogenetic and Trait Diversity.

PubMed

Redding, David W; Mooers, Arne O

2015-01-01

The 'edge of existence' (EDGE) prioritisation scheme is a new approach to rank species for conservation attention that aims to identify species that are both isolated on the tree of life and at imminent risk of extinction as defined by the World Conservation Union (IUCN). The self-stated benefit of the EDGE system is that it effectively captures unusual 'unique' species, and doing so will preserve the total evolutionary history of a group into the future. Given the EDGE metric was not designed to capture total evolutionary history, we tested this claim. Our analyses show that the total evolutionary history of mammals preserved is indeed much higher if EDGE species are protected than if at-risk species are chosen randomly. More of the total tree is also protected by EDGE species than if solely threat status or solely evolutionary distinctiveness were used for prioritisation. When considering how much trait diversity is captured by IUCN and EDGE prioritisation rankings, interestingly, preserving the highest-ranked EDGE species, or indeed just the most threatened species, captures more total trait diversity compared to sets of randomly-selected at-risk species. These results suggest that, as advertised, EDGE mammal species contribute evolutionary history to the evolutionary tree of mammals non-randomly, and EDGE-style rankings among endangered species can also capture important trait diversity. If this pattern holds for other groups, the EDGE prioritisation scheme has greater potential to be an efficient method to allocate scarce conservation effort.

Differences in evolutionary pressure acting within highly conserved ortholog groups.

PubMed

Przytycka, Teresa M; Jothi, Raja; Aravind, L; Lipman, David J

2008-07-17

In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes). Using correlations in entropy measures as a proxy for evolutionary pressure, we observed two distinct behaviors within our ortholog collection. The first subset of ortholog groups, called here informational, consisted mostly of proteins associated with information processing (i.e. translation, transcription, DNA replication) and the second, the non-informational ortholog groups, mostly comprised of proteins involved in metabolic pathways. The evolutionary pressure acting on non-informational proteins is more uniform relative to their informational counterparts. The non-informational proteins show higher level of correlation between entropy profiles and more uniformity across subgroups. The low correlation of entropy profiles in the informational ortholog groups suggest that the evolutionary pressure acting on the informational ortholog groups is not uniform across different clades considered this study. This might suggest "fine-tuning" of informational proteins in each lineage leading to lineage-specific differences in selection. This, in turn, could make these proteins less exchangeable between lineages. In contrast, the uniformity of the selective pressure acting on the non-informational groups might allow the exchange of the genetic material via lateral gene transfer.

New Insight into the Colonization Processes of Common Voles: Inferences from Molecular and Fossil Evidence

PubMed Central

Tougard, Christelle; Renvoisé, Elodie; Petitjean, Amélie; Quéré, Jean-Pierre

2008-01-01

Elucidating the colonization processes associated with Quaternary climatic cycles is important in order to understand the distribution of biodiversity and the evolutionary potential of temperate plant and animal species. In Europe, general evolutionary scenarios have been defined from genetic evidence. Recently, these scenarios have been challenged with genetic as well as fossil data. The origins of the modern distributions of most temperate plant and animal species could predate the Last Glacial Maximum. The glacial survival of such populations may have occurred in either southern (Mediterranean regions) and/or northern (Carpathians) refugia. Here, a phylogeographic analysis of a widespread European small mammal (Microtus arvalis) is conducted with a multidisciplinary approach. Genetic, fossil and ecological traits are used to assess the evolutionary history of this vole. Regardless of whether the European distribution of the five previously identified evolutionary lineages is corroborated, this combined analysis brings to light several colonization processes of M. arvalis. The species' dispersal was relatively gradual with glacial survival in small favourable habitats in Western Europe (from Germany to Spain) while in the rest of Europe, because of periglacial conditions, dispersal was less regular with bottleneck events followed by postglacial expansions. Our study demonstrates that the evolutionary history of European temperate small mammals is indeed much more complex than previously suggested. Species can experience heterogeneous evolutionary histories over their geographic range. Multidisciplinary approaches should therefore be preferentially chosen in prospective studies, the better to understand the impact of climatic change on past and present biodiversity. PMID:18958287

Evolution of column density distributions within Orion A⋆

NASA Astrophysics Data System (ADS)

Stutz, A. M.; Kainulainen, J.

2015-05-01

We compare the structure of star-forming molecular clouds in different regions of Orion A to determine how the column density probability distribution function (N-PDF) varies with environmental conditions such as the fraction of young protostars. A correlation between the N-PDF slope and Class 0 protostar fraction has been previously observed in a low-mass star-formation region (Perseus); here we test whether a similar correlation is observed in a high-mass star-forming region. We used Herschel PACS and SPIRE cold dust emission observations to derive a column density map of Orion A. We used the Herschel Orion Protostar Survey catalog to accurately identify and classify the Orion A young stellar object content, including the cold and relatively short-lived Class 0 protostars (with a lifetime of ~0.14 Myr). We divided Orion A into eight independent regions of 0.25 square degrees (13.5 pc2); in each region we fit the N-PDF distribution with a power law, and we measured the fraction of Class 0 protostars. We used a maximum-likelihood method to measure the N-PDF power-law index without binning the column density data. We find that the Class 0 fraction is higher in regions with flatter column density distributions. We tested the effects of incompleteness, extinction-driven misclassification of Class 0 sources, resolution, and adopted pixel-scales. We show that these effects cannot account for the observed trend. Our observations demonstrate an association between the slope of the power-law N-PDF and the Class 0 fractions within Orion A. Various interpretations are discussed, including timescales based on the Class 0 protostar fraction assuming a constant star-formation rate. The observed relation suggests that the N-PDF can be related to an evolutionary state of the gas. If universal, such a relation permits evaluating the evolutionary state from the N-PDF power-law index at much greater distances than those accessible with protostar counts. Appendices are available in electronic form at http://www.aanda.orgThe N(H) map as a FITS file is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/577/L6

A global evolutionary and metabolic analysis of human obesity gene risk variants.

PubMed

Castillo, Joseph J; Hazlett, Zachary S; Orlando, Robert A; Garver, William S

2017-09-05

It is generally accepted that the selection of gene variants during human evolution optimized energy metabolism that now interacts with our obesogenic environment to increase the prevalence of obesity. The purpose of this study was to perform a global evolutionary and metabolic analysis of human obesity gene risk variants (110 human obesity genes with 127 nearest gene risk variants) identified using genome-wide association studies (GWAS) to enhance our knowledge of early and late genotypes. As a result of determining the mean frequency of these obesity gene risk variants in 13 available populations from around the world our results provide evidence for the early selection of ancestral risk variants (defined as selection before migration from Africa) and late selection of derived risk variants (defined as selection after migration from Africa). Our results also provide novel information for association of these obesity genes or encoded proteins with diverse metabolic pathways and other human diseases. The overall results indicate a significant differential evolutionary pattern for the selection of obesity gene ancestral and derived risk variants proposed to optimize energy metabolism in varying global environments and complex association with metabolic pathways and other human diseases. These results are consistent with obesity genes that encode proteins possessing a fundamental role in maintaining energy metabolism and survival during the course of human evolution. Copyright © 2017. Published by Elsevier B.V.

37 GHz Methanol Masers : Horsemen of the Apocalypse for the Class II Methanol Maser Phase?

NASA Astrophysics Data System (ADS)

Ellingsen, S. P.; Breen, S. L.; Sobolev, A. M.; Voronkov, M. A.; Caswell, J. L.; Lo, N.

2011-12-01

We report the results of a search for class II methanol masers at 37.7, 38.3, and 38.5 GHz toward a sample of 70 high-mass star formation regions. We primarily searched toward regions known to show emission either from the 107 GHz class II methanol maser transition, or from the 6.035 GHz excited OH transition. We detected maser emission from 13 sources in the 37.7 GHz transition, eight of these being new detections. We detected maser emission from three sources in the 38 GHz transitions, one of which is a new detection. We find that 37.7 GHz methanol masers are only associated with the most luminous 6.7 and 12.2 GHz methanol maser sources, which in turn are hypothesized to be the oldest class II methanol sources. We suggest that the 37.7 GHz methanol masers are associated with a brief evolutionary phase (of 1000-4000 years) prior to the cessation of class II methanol maser activity in the associated high-mass star formation region.

Root hairs, trichomes and the evolution of duplicate genes.

PubMed

Kellogg, E A

2001-12-01

The MYB-class proteins WEREWOLF and GLABRA1 are functionally interchangeable, even though one is normally expressed solely in roots and the other only in shoots. This shows that their different functions are the result of the modification of cis-regulatory sequences over evolutionary time. The two genes thus provide an example of morphological diversification created by gene duplication and changes in regulation.

Herschel Shines Light on the Episodic Evolutionary Sequence of Protostars

NASA Astrophysics Data System (ADS)

Green, Joel D.; DIGIT; FOOSH; COPS Teams

2014-01-01

New far-infrared and submillimeter spectroscopic capabilities, along with moderate spatial and spectral resolution, provide the opportunity to study the diversity of shocks, accretion processes, and compositions of the envelopes of developing protostellar objects in nearby molecular clouds. We present the "COPS" (CO in Protostars) sample; a statistical analysis of the full sample of 30 Class 0/I protostars from the "DIGIT" Key project using Herschel-PACS/SPIRE 50-700 micron spectroscopy. We consider the sample as a whole in characteristic spectral lines, using a standardized data reduction procedure for all targets, and analyze the differences in the continuum and gas over the full sample, presenting an overview of trends. We compare the sources in evolutionary state, envelope mass, and gas properties to more evolved sources from the"FOOSH'' (FUor) samples.

Supercooperation in evolutionary games on correlated weighted networks.

PubMed

Buesser, Pierre; Tomassini, Marco

2012-01-01

In this work we study the behavior of classical two-person, two-strategies evolutionary games on a class of weighted networks derived from Barabási-Albert and random scale-free unweighted graphs. Using customary imitative dynamics, our numerical simulation results show that the presence of link weights that are correlated in a particular manner with the degree of the link end points leads to unprecedented levels of cooperation in the whole games' phase space, well above those found for the corresponding unweighted complex networks. We provide intuitive explanations for this favorable behavior by transforming the weighted networks into unweighted ones with particular topological properties. The resulting structures help us to understand why cooperation can thrive and also give ideas as to how such supercooperative networks might be built.

Comparative genomics reveals insights into avian genome evolution and adaptation.

PubMed

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S; Gatesy, John; Hoffmann, Federico G; Opazo, Juan C; Håstad, Olle; Sawyer, Roger H; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A; Green, Richard E; O'Brien, Stephen J; Griffin, Darren; Johnson, Warren E; Haussler, David; Ryder, Oliver A; Willerslev, Eske; Graves, Gary R; Alström, Per; Fjeldså, Jon; Mindell, David P; Edwards, Scott V; Braun, Edward L; Rahbek, Carsten; Burt, David W; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D; Gilbert, M Thomas P; Wang, Jun

2014-12-12

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. Copyright © 2014, American Association for the Advancement of Science.

Hunting for swinging millisecond pulsars with XMM-Newton

NASA Astrophysics Data System (ADS)

Papitto, Alessandro

2013-10-01

The recent XMM discovery of a millisecond pulsar swinging between an accretion- powered (X-ray) and a rotation-powered (radio) pulsar state provided the final evidence of the evolutionary link between these two classes, demonstrating that transitions between the two states can be observed over of a few weeks. We propose a ToO program (made of 3 triggers of 60 ks, over a 3years timescale) aimed at detecting X-ray accretion powered pulsations in sources already known as ms radio pulsars. Candidates are restricted to black widows and redbacks, systems in an evolutionary phase that allows state transitions. Enlarging the number of systems in this transitional phase is crucial to test binary evolution theories, and to study the disk-field interaction over a large range of mass accretion rates.

Chemosystematics in the Opiliones (Arachnida): a comment on the evolutionary history of alkylphenols and benzoquinones in the scent gland secretions of Laniatores

PubMed Central

Raspotnig, Günther; Bodner, Michaela; Schäffer, Sylvia; Koblmüller, Stephan; Schönhofer, Axel; Karaman, Ivo

2015-01-01

Large prosomal scent glands constitute a major synapomorphic character of the arachnid order Opiliones. These glands produce a variety of chemicals very specific to opilionid taxa of different taxonomic levels, and thus represent a model system to investigate the evolutionary traits in exocrine secretion chemistry across a phylogenetically old group of animals. The chemically best-studied opilionid group is certainly Laniatores, and currently available chemical data allow first hypotheses linking the phylogeny of this group to the evolution of major chemical classes of secretion chemistry. Such hypotheses are essential to decide upon a best-fitting explanation of the distribution of scent-gland secretion compounds across extant laniatorean taxa, and hence represent a key toward a well-founded opilionid chemosystematics. PMID:26074662

Chemosystematics in the Opiliones (Arachnida): a comment on the evolutionary history of alkylphenols and benzoquinones in the scent gland secretions of Laniatores.

PubMed

Raspotnig, Günther; Bodner, Michaela; Schäffer, Sylvia; Koblmüller, Stephan; Schönhofer, Axel; Karaman, Ivo

2015-04-01

Large prosomal scent glands constitute a major synapomorphic character of the arachnid order Opiliones. These glands produce a variety of chemicals very specific to opilionid taxa of different taxonomic levels, and thus represent a model system to investigate the evolutionary traits in exocrine secretion chemistry across a phylogenetically old group of animals. The chemically best-studied opilionid group is certainly Laniatores, and currently available chemical data allow first hypotheses linking the phylogeny of this group to the evolution of major chemical classes of secretion chemistry. Such hypotheses are essential to decide upon a best-fitting explanation of the distribution of scent-gland secretion compounds across extant laniatorean taxa, and hence represent a key toward a well-founded opilionid chemosystematics.

Computational architecture of the yeast regulatory network

NASA Astrophysics Data System (ADS)

Maslov, Sergei; Sneppen, Kim

2005-12-01

The topology of regulatory networks contains clues to their overall design principles and evolutionary history. We find that while in- and out-degrees of a given protein in the regulatory network are not correlated with each other, there exists a strong negative correlation between the out-degree of a regulatory protein and in-degrees of its targets. Such correlation positions large regulatory modules on the periphery of the network and makes them rather well separated from each other. We also address the question of relative importance of different classes of proteins quantified by the lethality of null-mutants lacking one of them as well as by the level of their evolutionary conservation. It was found that in the yeast regulatory network highly connected proteins are in fact less important than their low-connected counterparts.

Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

PubMed

Di, Chao; Xu, Wenying; Su, Zhen; Yuan, Joshua S

2010-10-07

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out to dissect the PHB gene function. The conserved gene evolution indicated that the study in the model species can be translated to human and mammalian studies.

Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles.

PubMed

Orozco-terWengel, Pablo; Kapun, Martin; Nolte, Viola; Kofler, Robert; Flatt, Thomas; Schlötterer, Christian

2012-10-01

The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome-wide false discovery rates < 0.005%) deviating from neutral expectation. Importantly, the evolutionary trajectories of the selected alleles were heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects. © 2012 Blackwell Publishing Ltd.

"Asia's missing women" as a problem in applied evolutionary psychology?

PubMed

Brooks, Robert

2012-12-20

In many parts of Asia, the Middle East and North Africa, women and children are so undervalued, neglected, abused, and so often killed, that sex ratios are now strongly male biased. In recent decades, sex-biased abortion has exacerbated the problem. In this article I highlight several important insights from evolutionary biology into both the origin and the severe societal consequences of "Asia's missing women", paying particular attention to interactions between evolution, economics and culture. Son preferences and associated cultural practices like patrilineal inheritance, patrilocality and the Indian Hindu dowry system arise among the wealthy and powerful elites for reasons consistent with models of sex-biased parental investment. Those practices then spread via imitation as technology gets cheaper and economic development allows the middle class to grow rapidly. I will consider evidence from India, China and elsewhere that grossly male-biased sex ratios lead to increased crime, violence, local warfare, political instability, drug abuse, prostitution and trafficking of women. The problem of Asia's missing women presents a challenge for applied evolutionary psychology to help us understand and ameliorate sex ratio biases and their most severe consequences.

Unifying measures of gene function and evolution.

PubMed

Wolf, Yuri I; Carmel, Liran; Koonin, Eugene V

2006-06-22

Recent genome analyses revealed intriguing correlations between variables characterizing the functioning of a gene, such as expression level (EL), connectivity of genetic and protein-protein interaction networks, and knockout effect, and variables describing gene evolution, such as sequence evolution rate (ER) and propensity for gene loss. Typically, variables within each of these classes are positively correlated, e.g. products of highly expressed genes also have a propensity to be involved in many protein-protein interactions, whereas variables between classes are negatively correlated, e.g. highly expressed genes, on average, evolve slower than weakly expressed genes. Here, we describe principal component (PC) analysis of seven genome-related variables and propose biological interpretations for the first three PCs. The first PC reflects a gene's 'importance', or the 'status' of a gene in the genomic community, with positive contributions from knockout lethality, EL, number of protein-protein interaction partners and the number of paralogues, and negative contributions from sequence ER and gene loss propensity. The next two PCs define a plane that seems to reflect the functional and evolutionary plasticity of a gene. Specifically, PC2 can be interpreted as a gene's 'adaptability' whereby genes with high adaptability readily duplicate, have many genetic interaction partners and tend to be non-essential. PC3 also might reflect the role of a gene in organismal adaptation albeit with a negative rather than a positive contribution of genetic interactions; we provisionally designate this PC 'reactivity'. The interpretation of PC2 and PC3 as measures of a gene's plasticity is compatible with the observation that genes with high values of these PCs tend to be expressed in a condition- or tissue-specific manner. Functional classes of genes substantially vary in status, adaptability and reactivity, with the highest status characteristic of the translation system and cytoskeletal proteins, highest adaptability seen in cellular processes and signalling genes, and top reactivity characteristic of metabolic enzymes.

Crystal structure of PnpCD, a two-subunit hydroquinone 1,2-dioxygenase, reveals a novel structural class of Fe2+-dependent dioxygenases.

PubMed

Liu, Shiheng; Su, Tiantian; Zhang, Cong; Zhang, Wen-Mao; Zhu, Deyu; Su, Jing; Wei, Tiandi; Wang, Kang; Huang, Yan; Guo, Liming; Xu, Sujuan; Zhou, Ning-Yi; Gu, Lichuan

2015-10-02

Aerobic microorganisms have evolved a variety of pathways to degrade aromatic and heterocyclic compounds. However, only several classes of oxygenolytic fission reaction have been identified for the critical ring cleavage dioxygenases. Among them, the most well studied dioxygenases proceed via catecholic intermediates, followed by noncatecholic hydroxy-substituted aromatic carboxylic acids. Therefore, the recently reported hydroquinone 1,2-dioxygenases add to the diversity of ring cleavage reactions. Two-subunit hydroquinone 1,2-dioxygenase PnpCD, the key enzyme in the hydroquinone pathway of para-nitrophenol degradation, catalyzes the ring cleavage of hydroquinone to γ-hydroxymuconic semialdehyde. Here, we report three PnpCD structures, named apo-PnpCD, PnpCD-Fe(3+), and PnpCD-Cd(2+)-HBN (substrate analog hydroxyenzonitrile), respectively. Structural analysis showed that both the PnpC and the C-terminal domains of PnpD comprise a conserved cupin fold, whereas PnpC cannot form a competent metal binding pocket as can PnpD cupin. Four residues of PnpD (His-256, Asn-258, Glu-262, and His-303) were observed to coordinate the iron ion. The Asn-258 coordination is particularly interesting because this coordinating residue has never been observed in the homologous cupin structures of PnpCD. Asn-258 is proposed to play a pivotal role in binding the iron prior to the enzymatic reaction, but it might lose coordination to the iron when the reaction begins. PnpD also consists of an intriguing N-terminal domain that might have functions other than nucleic acid binding in its structural homologs. In summary, PnpCD has no apparent evolutionary relationship with other iron-dependent dioxygenases and therefore defines a new structural class. The study of PnpCD might add to the understanding of the ring cleavage of dioxygenases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Crystal Structure of PnpCD, a Two-subunit Hydroquinone 1,2-Dioxygenase, Reveals a Novel Structural Class of Fe2+-dependent Dioxygenases*

PubMed Central

Liu, Shiheng; Su, Tiantian; Zhang, Cong; Zhang, Wen-Mao; Zhu, Deyu; Su, Jing; Wei, Tiandi; Wang, Kang; Huang, Yan; Guo, Liming; Xu, Sujuan; Zhou, Ning-Yi; Gu, Lichuan

2015-01-01

Aerobic microorganisms have evolved a variety of pathways to degrade aromatic and heterocyclic compounds. However, only several classes of oxygenolytic fission reaction have been identified for the critical ring cleavage dioxygenases. Among them, the most well studied dioxygenases proceed via catecholic intermediates, followed by noncatecholic hydroxy-substituted aromatic carboxylic acids. Therefore, the recently reported hydroquinone 1,2-dioxygenases add to the diversity of ring cleavage reactions. Two-subunit hydroquinone 1,2-dioxygenase PnpCD, the key enzyme in the hydroquinone pathway of para-nitrophenol degradation, catalyzes the ring cleavage of hydroquinone to γ-hydroxymuconic semialdehyde. Here, we report three PnpCD structures, named apo-PnpCD, PnpCD-Fe3+, and PnpCD-Cd2+-HBN (substrate analog hydroxyenzonitrile), respectively. Structural analysis showed that both the PnpC and the C-terminal domains of PnpD comprise a conserved cupin fold, whereas PnpC cannot form a competent metal binding pocket as can PnpD cupin. Four residues of PnpD (His-256, Asn-258, Glu-262, and His-303) were observed to coordinate the iron ion. The Asn-258 coordination is particularly interesting because this coordinating residue has never been observed in the homologous cupin structures of PnpCD. Asn-258 is proposed to play a pivotal role in binding the iron prior to the enzymatic reaction, but it might lose coordination to the iron when the reaction begins. PnpD also consists of an intriguing N-terminal domain that might have functions other than nucleic acid binding in its structural homologs. In summary, PnpCD has no apparent evolutionary relationship with other iron-dependent dioxygenases and therefore defines a new structural class. The study of PnpCD might add to the understanding of the ring cleavage of dioxygenases. PMID:26304122

Coastal change analysis program implemented in Louisiana

USGS Publications Warehouse

Ramsey, Elijah W.; Nelson, G.A.; Sapkota, S.K.

2001-01-01

Landsat Thematic Mapper images from 1990 to 1996 and collateral data sources were used to classify the land cover of the Mermentau River Basin (MRB) within the Chenier Plain of coastal Louisiana. Landcover classes followed the definition of the National Oceanic and Atmospheric Administration's Coastal Change Analysis Program; however, classification methods had to be developed as part of this study for attainment of these national classification standards. Classification method developments were especially important when classes were spectrally inseparable, when classes were part of spatial and spectral continuums, when the spatial resolution of the sensor included more than one landcover type, and when human activities caused abnormal transitions in the landscape. Most classification problems were overcome by using one or a combination of techniques, such as separating the MRB into subregions of commonality, applying masks to specific land mixtures, and highlighting class transitions between years that were highly unlikely. Overall, 1990, 1993, and 1996 classification accuracy percentages (associated kappa statistics) were 80% (0.79), 78% (0.76), and 86% (0.84), respectively. Most classification errors were associated with confusion between managed (cultivated land) and unmanaged grassland classes; scrub shrub, grasslands and forest classes; water, unconsolidated shore and bare land classes; and especially in 1993, between water and floating vegetation classes. Combining cultivated land and grassland classes and water and floating vegetation classes into single classes accuracies for 1990, 1993, and 1996 increased to 82%, 83%, and 90%, respectively. To improve the interpretation of landcover change, three indicators of landcover class stability were formulated. Location stability was defined as the percentage of a landcover class that remained as the same class in the same location at the beginning and the end of the monitoring period. Residence stability was defined as the percent change in each class within the entire MRB during the monitoring period. Turnover was defined as the addition of other landcover classes to the target landcover class during the defined monitoring period. These indicators allowed quick assessment of the dynamic nature of landcover classes, both in reference to a spatial location and to retaining their presence throughout the MRB. Examining the landcover changes between 1990 to 1993 and 1993 to 1996, led us to five principal findings: (1) Landcover turnover is maintaining a near stable logging cycle, although the locations of grassland, scrub shrub, and forest areas involved in the cycle appeared to change. (2) Planting of seedlings is critical to maintaining cycle stability. (3) Logging activities tend to replace woody land mixed forests with woody land evergreen forests. (4) Wetland estuarine marshes are expanding slightly. (5) Wetland palustrine marshes and mature forested wetlands in the MRB are relatively stable.

Protein 8-class secondary structure prediction using conditional neural fields.

PubMed

Wang, Zhiyong; Zhao, Feng; Peng, Jian; Xu, Jinbo

2011-10-01

Compared with the protein 3-class secondary structure (SS) prediction, the 8-class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8-class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non-evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic cluster generation for a fuzzy classifier with ellipsoidal regions.

PubMed

Abe, S

1998-01-01

In this paper, we discuss a fuzzy classifier with ellipsoidal regions that dynamically generates clusters. First, for the data belonging to a class we define a fuzzy rule with an ellipsoidal region. Namely, using the training data for each class, we calculate the center and the covariance matrix of the ellipsoidal region for the class. Then we tune the fuzzy rules, i.e., the slopes of the membership functions, successively until there is no improvement in the recognition rate of the training data. Then if the number of the data belonging to a class that are misclassified into another class exceeds a prescribed number, we define a new cluster to which those data belong and the associated fuzzy rule. Then we tune the newly defined fuzzy rules in the similar way as stated above, fixing the already obtained fuzzy rules. We iterate generation of clusters and tuning of the newly generated fuzzy rules until the number of the data belonging to a class that are misclassified into another class does not exceed the prescribed number. We evaluate our method using thyroid data, Japanese Hiragana data of vehicle license plates, and blood cell data. By dynamic cluster generation, the generalization ability of the classifier is improved and the recognition rate of the fuzzy classifier for the test data is the best among the neural network classifiers and other fuzzy classifiers if there are no discrete input variables.

Gene Expression in Class 2 Integrons Is SOS-Independent and Involves Two Pc Promoters.

PubMed

Jové, Thomas; Da Re, Sandra; Tabesse, Aurore; Gassama-Sow, Amy; Ploy, Marie-Cécile

2017-01-01

Integrons are powerful bacterial genetic elements that permit the expression and dissemination of antibiotic-resistance gene cassettes. They contain a promoter Pc that allows the expression of gene cassettes captured through site-specific recombination catalyzed by IntI, the integron-encoded integrase. Class 1 and 2 integrons are found in both clinical and environmental settings. The regulation of intI and of Pc promoters has been extensively studied in class 1 integrons and the regulatory role of the SOS response on intI expression has been shown. Here we investigated class 2 integrons. We characterized the P intI2 promoter and showed that intI2 expression is not regulated via the SOS response. We also showed that, unlike class 1 integrons, class 2 integrons possess not one but two active Pc promoters that are located within the attI2 region that seem to contribute equally to gene cassette expression. Class 2 integrons mostly encode an inactive truncated integrase, but the rare class 2 integrons that encode an active integrase are associated with less efficient Pc2 promoter variants. We propose an evolutionary model for class 2 integrons in which the absence of repression of the integrase gene expression led to mutations resulting in either inactive integrase or Pc variants of weaker activity, thereby reducing the potential fitness cost of these integrons.

Effects of directional migration on prisoner's dilemma game in a square domain

NASA Astrophysics Data System (ADS)

Cheng, Hongyan; Dai, Qionglin; Li, Haihong; Qian, Xiaolan; Zhang, Mei; Yang, Junzhong

2013-04-01

We introduce a new migration rule, the directional migration, into evolutionary prisoner's dilemma games defined in a square domain with periodic boundary conditions. We find that cooperation can be enhanced to a much higher level than the case in the absence of migration. Additionally, the presence of the directional migration has profound impact on the population structure: the directional migration drives individuals to form a number of dense clusters which resembles social cohesion. The evolutionary game theory incorporating the directional migration can reproduce some real characteristics of populations in human society and may shed light on the problem of social cohesion.

Latent classes of resilience and psychological response among only-child loss parents in China.

PubMed

Wang, An-Ni; Zhang, Wen; Zhang, Jing-Ping; Huang, Fei-Fei; Ye, Man; Yao, Shu-Yu; Luo, Yuan-Hui; Li, Zhi-Hua; Zhang, Jie; Su, Pan

2017-10-01

Only-child loss parents in China recently gained extensive attention as a newly defined social group. Resilience could be a probable solution out of the psychological dilemma. Using a sample of 185 only-child loss people, this study employed latent class analysis (a) to explore whether different classes of resilience could be identified, (b) to determine socio-demographic characteristics of each class, and (c) to compare the depression and the subjective well-being of each class. The results supported a three-class solution, defined as 'high tenacity-strength but moderate optimism class', 'moderate resilience but low self-efficacy class' and 'low tenacity but moderate adaption-dependence class'. Parents with low income and medical insurance of low reimbursement type and without endowment insurance occupied more proportions in the latter two classes. The latter two classes also had a significant higher depression scores and lower subjective well-being scores than high tenacity-strength but moderate optimism class. Future work should care those socio-economically vulnerable bereaved parents, and an elastic economic assistance policy was needed. To develop targeted resilience interventions, the emphasis of high tenacity-strength but moderate optimism class should be the optimism. Moderate resilience but low self-efficacy class should be self-efficacy, and low tenacity but moderate adaption-dependence class should be tenacity. Copyright © 2016 John Wiley & Sons, Ltd.

Classification and global distribution of ocean precipitation types based on satellite passive microwave signatures

NASA Astrophysics Data System (ADS)

Gautam, Nitin

The main objectives of this thesis are to develop a robust statistical method for the classification of ocean precipitation based on physical properties to which the SSM/I is sensitive and to examine how these properties vary globally and seasonally. A two step approach is adopted for the classification of oceanic precipitation classes from multispectral SSM/I data: (1)we subjectively define precipitation classes using a priori information about the precipitating system and its possible distinct signature on SSM/I data such as scattering by ice particles aloft in the precipitating cloud, emission by liquid rain water below freezing level, the difference of polarization at 19 GHz-an indirect measure of optical depth, etc.; (2)we then develop an objective classification scheme which is found to reproduce the subjective classification with high accuracy. This hybrid strategy allows us to use the characteristics of the data to define and encode classes and helps retain the physical interpretation of classes. The classification methods based on k-nearest neighbor and neural network are developed to objectively classify six precipitation classes. It is found that the classification method based neural network yields high accuracy for all precipitation classes. An inversion method based on minimum variance approach was used to retrieve gross microphysical properties of these precipitation classes such as column integrated liquid water path, column integrated ice water path, and column integrated min water path. This classification method is then applied to 2 years (1991-92) of SSM/I data to examine and document the seasonal and global distribution of precipitation frequency corresponding to each of these objectively defined six classes. The characteristics of the distribution are found to be consistent with assumptions used in defining these six precipitation classes and also with well known climatological patterns of precipitation regions. The seasonal and global distribution of these six classes is also compared with the earlier results obtained from Comprehensive Ocean Atmosphere Data Sets (COADS). It is found that the gross pattern of the distributions obtained from SSM/I and COADS data match remarkably well with each other.

On the Origin and Evolutionary History of NANOG

PubMed Central

Vivien, Céline; Kodjabachian, Laurent; Demeneix, Barbara; Coen, Laurent; Girardot, Fabrice

2014-01-01

Though pluripotency is well characterized in mammals, many questions remain to be resolved regarding its evolutionary history. A necessary prerequisite for addressing this issue is to determine the phylogenetic distributions and orthology relationships of the transcription factor families sustaining or modulating this property. In mammals, the NANOG homeodomain transcription factor is one of the core players in the pluripotency network. However, its evolutionary history has not been thoroughly studied, hindering the interpretation of comparative studies. To date, the NANOG family was thought to be monogenic, with numerous pseudogenes described in mammals, including a tandem duplicate in Hominidae. By examining a wide-array of craniate genomes, we provide evidence that the NANOG family arose at the latest in the most recent common ancestor of osteichthyans and that NANOG genes are frequently found as tandem duplicates in sarcopterygians and as a single gene in actinopterygians. Their phylogenetic distribution is thus reminiscent of that recently shown for Class V POU paralogues, another key family of pluripotency-controlling factors. However, while a single ancestral duplication has been reported for the Class V POU family, we suggest that multiple independent duplication events took place during evolution of the NANOG family. These multiple duplications could have contributed to create a layer of complexity in the control of cell competence and pluripotency, which could explain the discrepancies relative to the functional evolution of this important gene family. Further, our analysis does not support the hypothesis that loss of NANOG and emergence of the preformation mode of primordial germ cell specification are causally linked. Our study therefore argues for the need of further functional comparisons between NANOG paralogues, notably regarding the novel duplicates identified in sauropsids and non-eutherian mammals. PMID:24465486

Space Construction Experiment Definition Study (SCEDS), part 1. Volume 2: Study results

NASA Technical Reports Server (NTRS)

1981-01-01

A basic Space Shuttle flight experiment which will provide needed data on the construction of large space systems from the Orbiter was defined. The predicted dynamic behavior of a representative large structure, on-orbit construction operations, and Orbiter control during and after construction were studied. Evolutionary or supplemental flight experiments for the development or augmentation of a basic flight experiment were identified and defined. The study was divided into six major tasks with appropriate sub-tasks noted.

Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle

PubMed Central

Littlejohn, Mathew D.; Henty, Kristen M.; Tiplady, Kathryn; Johnson, Thomas; Harland, Chad; Lopdell, Thomas; Sherlock, Richard G.; Li, Wanbo; Lukefahr, Steven D.; Shanks, Bruce C.; Garrick, Dorian J.; Snell, Russell G.; Spelman, Richard J.; Davis, Stephen R.

2014-01-01

Lactation, hair development and homeothermy are characteristic evolutionary features that define mammals from other vertebrate species. Here we describe the discovery of two autosomal dominant mutations with antagonistic, pleiotropic effects on all three of these biological processes, mediated through the prolactin signalling pathway. Most conspicuously, mutations in prolactin (PRL) and its receptor (PRLR) have an impact on thermoregulation and hair morphology phenotypes, giving prominence to this pathway outside of its classical roles in lactation. PMID:25519203

A Review of Dendroctonus frontalis Zimmermann Systematics

Treesearch

Anthony I. Cognato

2011-01-01

The systematic history of the southern pine beetle, Dendroctonus frontalis Zimmermann, is reviewed. Morphological, biological, karyological, and molecular data clearly define and diagnose the species limits of D. frontalis. More complete phylogenetic analysis and characterization of population genetic variation will further clarify the evolutionary history of the D....

Space station automation study. Volume 2: Technical report. Autonomous systems and assembly

NASA Technical Reports Server (NTRS)

1984-01-01

The application of automation to space station functions is discussed. A summary is given of the evolutionary functions associated with long range missions and objectives. Mission tasks and requirements are defined. Space station sub-systems, mission models, assembly, and construction are discussed.

Long-Range Strategic Planning: The Rochester Experience.

ERIC Educational Resources Information Center

Schultz, John M.; Anthony, Deborah L.

The administration of Rochester Community Schools (Michigan) initiated a process for long-range strategic planning in 1984, described in this synopsis. Strategic planning is an ongoing, evolutionary process of defining the business one is in or should be in; establishing organizational goals and objectives; and developing and implementing…

A framework for evolutionary systems biology

PubMed Central

Loewe, Laurence

2009-01-01

Background Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects. Results Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions in silico. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism. Conclusion EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications. PMID:19239699

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

PubMed Central

Koonin, Eugene V.; Wolf, Yuri I.

2012-01-01

When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain “ribosomal Tree of Life” that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: (1) pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept, (2) Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and (3) evolution of evolvability, i.e., dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary biology. PMID:22993722

Characterization of swine leukocyte antigen alleles and haplotypes on a novel miniature pig line, Microminipig.

PubMed

Ando, A; Imaeda, N; Ohshima, S; Miyamoto, A; Kaneko, N; Takasu, M; Shiina, T; Kulski, J K; Inoko, H; Kitagawa, H

2014-12-01

Microminipigs are extremely small-sized, novel miniature pigs that were recently developed for medical research. The inbred Microminipigs with defined swine leukocyte antigen (SLA) haplotypes are expected to be useful for allo- and xenotransplantation studies and also for association analyses between SLA haplotypes and immunological traits. To establish SLA-defined Microminipig lines, we characterized the polymorphic SLA alleles for three class I (SLA-1, SLA-2 and SLA-3) and two class II (SLA-DRB1 and SLA-DQB1) genes of 14 parental Microminipigs using a high-resolution nucleotide sequence-based typing method. Eleven class I and II haplotypes, including three recombinant haplotypes, were found in the offspring of the parental Microminipigs. Two class I and class II haplotypes, Hp-31.0 (SLA-1*1502-SLA-3*070102-SLA-2*1601) and Hp-0.37 (SLA-DRB1*0701-SLA-DQB1*0502), are novel and have not so far been reported in other pig breeds. Crossover regions were defined by the analysis of 22 microsatellite markers within the SLA class III region of three recombinant haplotypes. The SLA allele and haplotype information of Microminipigs in this study will be useful to establish SLA homozygous lines including three recombinants for transplantation and immunological studies. © 2014 Stichting International Foundation for Animal Genetics.

White Middle-Class Privilege: Social Class Bias and Implications for Training and Practice

ERIC Educational Resources Information Center

Liu, William Ming; Pickett, Theodore, Jr.; Ivey, Allen E.

2007-01-01

Social class, classism, and privilege and their relationship to counseling have been given insufficient attention. This article defines and explores White middle-class privilege; it proffers support for its integration in a multicultural competency, as well as its intersection with race and other dimensions of multiculturalism and privilege.…

75 FR 39145 - Amendment of Class C Airspace; Flint, MI

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-08

...-0599; Airspace Docket No. 10-AWA-3] RIN 2120-AA66 Amendment of Class C Airspace; Flint, MI AGENCY... description of the Bishop International Airport, Flint, MI, Class C airspace area by amending the airport... defines the Class C airspace area's center point. The Rule This action amends Title 14 Code of Federal...

The Experiences of Working-Class College Students Who Became University Presidents

ERIC Educational Resources Information Center

Springer, Mary E.

2012-01-01

Working-class students enter college lacking necessary capital to predict their academic and personal success making college success less likely than for middle class students (Bufton, 2003; Mack, 2006; Paulsen & St. John, 2002; Rose, 1997; Wegner, 1973). This same social class origin helps to define experiences, provides context for…

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2013 CFR

2013-10-01

.... Class 1 (explosives) must be stowed as far away as practicable from any potential source of heat or... vertically. In addition to this separation, there must be insulation to Class A60 standard as defined in 46...

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2014 CFR

2014-10-01

.... Class 1 (explosives) must be stowed as far away as practicable from any potential source of heat or... vertically. In addition to this separation, there must be insulation to Class A60 standard as defined in 46...

Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities.

PubMed

Nagy, László G; Riley, Robert; Tritt, Andrew; Adam, Catherine; Daum, Chris; Floudas, Dimitrios; Sun, Hui; Yadav, Jagjit S; Pangilinan, Jasmyn; Larsson, Karl-Henrik; Matsuura, Kenji; Barry, Kerrie; Labutti, Kurt; Kuo, Rita; Ohm, Robin A; Bhattacharya, Sukanta S; Shirouzu, Takashi; Yoshinaga, Yuko; Martin, Francis M; Grigoriev, Igor V; Hibbett, David S

2016-04-01

Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

"Homo Pedagogicus": The Evolutionary Nature of Second Language Teaching

ERIC Educational Resources Information Center

Atkinson, Dwight

2017-01-01

Second language (SL) teacher educators tirelessly teach others how to teach. But how often do we actually define teaching? Without explicit definitional activity on this fundamental concept in second language teaching (SLT), it remains implicit and intuitive--the opposite of clear, productive understanding. I therefore explore the question,…

The Importance of Culture for Developmental Science

ERIC Educational Resources Information Center

Keller, Heidi

2012-01-01

In this essay, it is argued that a general understanding of human development needs a unified framework based on evolutionary theorizing and cross-cultural and cultural anthropological approaches. An eco-social model of development has been proposed that defines cultural milieus as adaptations to specific socio-demographic contexts. Ontogenetic…

First-Person Educational Psychology for Teacher Education Majors: A Biofunctional Understanding Intervention

ERIC Educational Resources Information Center

Iran-Nejad, Asghar; Stewart, William; Robinson, Cecil

2015-01-01

This is a semester-long study of the development of first-person biofunctional understanding in educational psychology for teacher education majors. We defined biofunctional understanding as a spontaneous intellectual capacity. To reach its deep biological levels, sculpted by countless evolutionary millennia, students identified and dwelled in…

Second interim briefing (D3). Evolutionary Science and Applications Space Platform. Characterization of concepts, tasks A and B

NASA Technical Reports Server (NTRS)

1981-01-01

The objectives were to define, evaluate, and select concepts for evolving a space station in conjunction with the Space Platform for NASA science, Applications, Technology and DOD; and a permanently manned presence in space early, with a maximum of existing technology.

Understanding Vegetative Desiccation Tolerance using Integrated Functional Genomics Approaches within a Comparative Evolutionary Framework

USDA-ARS?s Scientific Manuscript database

Desiccation tolerance (DT) is defined as the equilibration of protoplasmic water potential with that of the surrounding air (generally dry) without loss of viability upon rehydration. Vegetative DT is widespread amongst mosses and lichens, but is relatively rare in vascular plants (0.15%). Recent st...

Geometric quadratic stochastic operator on countable infinite set

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

Ganikhodjaev, Nasir; Hamzah, Nur Zatul Akmar

2015-02-03

In this paper we construct the family of Geometric quadratic stochastic operators defined on the countable sample space of nonnegative integers and investigate their trajectory behavior. Such operators can be reinterpreted in terms of of evolutionary operator of free population. We show that Geometric quadratic stochastic operators are regular transformations.

Darwinism Defined: The Difference Between Fact and Theory.

ERIC Educational Resources Information Center

Gould, Stephen Jay

1987-01-01

Discusses various developments in both science and theology following the work of Charles Darwin on evolution. Differentiates between the facts regarding evolution and the theory of natural selection as a mechanism for evolutionary change. Warns that the differences between facts and theory have not been adequately emphasized by scientists. (TW)

Evolutionary trade-offs in kidney injury and repair.

PubMed

Lei, Yutian; Anders, Hans-Joachim

2017-11-01

Evolutionary medicine has proven helpful to understand the origin of human disease, e.g. in identifying causal roles of recent environmental changes impacting on human physiology (environment-phenotype mismatch). In contrast, diseases affecting only a limited number of members of a species often originate from evolutionary trade-offs for usually physiologic adaptations assuring reproductive success in the context of extrinsic threats. For example, the G1 and G2 variants of the APOL1 gene supporting control of Trypanosoma infection come with the trade-off that they promote the progression of kidney disease. In this review we extend the concept of evolutionary nephrology by discussing how the physiologic adaptations (danger responses) to tissue injury create evolutionary trade-offs that drive histopathological changes underlying acute and chronic kidney diseases. The evolution of multicellular organisms positively selected a number of danger response programs for their overwhelming benefits in assuring survival such as clotting, inflammation, epithelial healing and mesenchymal healing, i.e. fibrosis and sclerosis. Upon kidney injury these danger programs often present as pathomechanisms driving persistent nephron loss and renal failure. We explore how classic kidney disease entities involve insufficient or overshooting activation of these danger response programs for which the underlying genetic basis remains largely to be defined. Dissecting the causative and hierarchical relationships between danger programs should help to identify molecular targets to control kidney injury and to improve disease outcomes.

Links between Evolution, Development, Human Anatomy, Pathology, and Medicine, with A Proposition of A Re-defined Anatomical Position and Notes on Constraints and Morphological "Imperfections".

PubMed

Diogo, Rui; Molnar, Julia

2016-06-01

Surprisingly the oldest formal discipline in medicine (anatomy) has not yet felt the full impact of evolutionary developmental biology. In medical anatomy courses and textbooks, the human body is still too often described as though it is a "perfect machine." In fact, the study of human anatomy predates evolutionary theory; therefore, many of its conventions continue to be outdated, making it difficult to study, understand, and treat the human body, and to compare it with that of other, nonbipedal animals, including other primates. Moreover, such an erroneous view of our anatomy as "perfect" can be used to fuel nonevolutionary ideologies such as intelligent design. In the section An Evolutionary and Developmental Approach to Human Anatomical Position of this paper, we propose the redefinition of the "human standard anatomical position" used in textbooks to be consistent with human evolutionary and developmental history. This redefined position also simplifies, for students and practitioners of the health professions, the study and learning of embryonic muscle groups (each group including muscles derived from the same/ontogenetically closely related primordium/primordia) and joint movements and highlights the topological correspondence between the upper and lower limbs. Section Evolutionary and Developmental Constraints, "Imperfections" and Sports Pathologies continues the theme by describing examples of apparently "illogical" characteristics of the human body that only make sense when one understands the developmental and evolutionary constraints that have accumulated over millions of years. We focus, in particular, on musculoskeletal functional problems and sports pathologies to emphasize the links with pathology and medicine. These examples demonstrate how incorporating evolutionary theory into anatomy education can be helpful for medical students, teachers, researchers, and physicians, as well as for anatomists, functional morphologists, and evolutionary and developmental biologists. © 2016 Wiley Periodicals, Inc.

Defined types of cortical interneurone structure space and spike timing in the hippocampus

PubMed Central

Somogyi, Peter; Klausberger, Thomas

2005-01-01

The cerebral cortex encodes, stores and combines information about the internal and external environment in rhythmic activity of multiple frequency ranges. Neurones of the cortex can be defined, recognized and compared on the comprehensive application of the following measures: (i) brain area- and cell domain-specific distribution of input and output synapses, (ii) expression of molecules involved in cell signalling, (iii) membrane and synaptic properties reflecting the expression of membrane proteins, (iv) temporal structure of firing in vivo, resulting from (i)–(iii). Spatial and temporal measures of neurones in the network reflect an indivisible unity of evolutionary design, i.e. neurones do not have separate structure or function. The blueprint of this design is most easily accessible in the CA1 area of the hippocampus, where a relatively uniform population of pyramidal cells and their inputs follow an instantly recognizable laminated pattern and act within stereotyped network activity patterns. Reviewing the cell types and their spatio-temporal interactions, we suggest that CA1 pyramidal cells are supported by at least 16 distinct types of GABAergic neurone. During a given behaviour-contingent network oscillation, interneurones of a given type exhibit similar firing patterns. During different network oscillations representing two distinct brain states, interneurones of the same class show different firing patterns modulating their postsynaptic target-domain in a brain-state-dependent manner. These results suggest roles for specific interneurone types in structuring the activity of pyramidal cells via their respective target domains, and accurately timing and synchronizing pyramidal cell discharge, rather than providing generalized inhibition. Finally, interneurones belonging to different classes may fire preferentially at distinct time points during a given oscillation. As different interneurones innervate distinct domains of the pyramidal cells, the different compartments will receive GABAergic input differentiated in time. Such a dynamic, spatio-temporal, GABAergic control, which evolves distinct patterns during different brain states, is ideally suited to regulating the input integration of individual pyramidal cells contributing to the formation of cell assemblies and representations in the hippocampus and, probably, throughout the cerebral cortex. PMID:15539390

Phylogenetics and evolution of Trx SET genes in fully sequenced land plants.

PubMed

Zhu, Xinyu; Chen, Caoyi; Wang, Baohua

2012-04-01

Plant Trx SET proteins are involved in H3K4 methylation and play a key role in plant floral development. Genes encoding Trx SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history of the Trx SET gene family, we made a comprehensive evolutionary analysis on this gene family from 13 major representatives of green plants. A novel clustering (here named as cpTrx clade), which included the III-1, III-2, and III-4 orthologous groups, previously resolved was identified. Our analysis showed that plant Trx proteins possessed a variety of domain organizations and gene structures among paralogs. Additional domains such as PHD, PWWP, and FYR were early integrated into primordial SET-PostSET domain organization of cpTrx clade. We suggested that the PostSET domain was lost in some members of III-4 orthologous group during the evolution of land plants. At least four classes of gene structures had been formed at the early evolutionary stage of land plants. Three intronless orphan Trx SET genes from the Physcomitrella patens (moss) were identified, and supposedly, their parental genes have been eliminated from the genome. The structural differences among evolutionary groups of plant Trx SET genes with different functions were described, contributing to the design of further experimental studies.

Female orgasm rates are largely independent of other traits: implications for "female orgasmic disorder" and evolutionary theories of orgasm.

PubMed

Zietsch, Brendan P; Miller, Geoffrey F; Bailey, J Michael; Martin, Nicholas G

2011-08-01

The criteria for "female orgasmic disorder" (FOD) assume that low rates of orgasm are dysfunctional, implying that high rates are functional. Evolutionary theories about the function of female orgasm predict correlations of orgasm rates with sexual attitudes and behavior and other fitness-related traits. To test hypothesized evolutionary functions of the female orgasm. We examined such correlations in a community sample of 2,914 adult female Australian twins who reported their orgasm rates during masturbation, intercourse, and other sexual activities, and who completed demographic, personality, and sexuality questionnaires. Orgasm rates during intercourse, other sex, and masturbation. Although orgasm rates showed high variance across women and substantial heritability, they were largely phenotypically and genetically independent of other important traits. We found zero to weak phenotypic correlations between all three orgasm rates and all other 19 traits examined, including occupational status, social class, educational attainment, extraversion, neuroticism, psychoticism, impulsiveness, childhood illness, maternal pregnancy stress, marital status, political liberalism, restrictive attitudes toward sex, libido, lifetime number of sex partners, risky sexual behavior, masculinity, orientation toward uncommitted sex, age of first intercourse, and sexual fantasy. Furthermore, none of the correlations had significant genetic components. These findings cast doubt on most current evolutionary theories about female orgasm's adaptive functions, and on the validity of FOD as a psychiatric construct. © 2011 International Society for Sexual Medicine.

Mode and tempo in the evolution of socio-political organization: reconciling 'Darwinian' and 'Spencerian' evolutionary approaches in anthropology.

PubMed

Currie, Thomas E; Mace, Ruth

2011-04-12

Traditional investigations of the evolution of human social and political institutions trace their ancestry back to nineteenth century social scientists such as Herbert Spencer, and have concentrated on the increase in socio-political complexity over time. More recent studies of cultural evolution have been explicitly informed by Darwinian evolutionary theory and focus on the transmission of cultural traits between individuals. These two approaches to investigating cultural change are often seen as incompatible. However, we argue that many of the defining features and assumptions of 'Spencerian' cultural evolutionary theory represent testable hypotheses that can and should be tackled within a broader 'Darwinian' framework. In this paper we apply phylogenetic comparative techniques to data from Austronesian-speaking societies of Island South-East Asia and the Pacific to test hypotheses about the mode and tempo of human socio-political evolution. We find support for three ideas often associated with Spencerian cultural evolutionary theory: (i) political organization has evolved through a regular sequence of forms, (ii) increases in hierarchical political complexity have been more common than decreases, and (iii) political organization has co-evolved with the wider presence of hereditary social stratification.

Mode and tempo in the evolution of socio-political organization: reconciling ‘Darwinian’ and ‘Spencerian’ evolutionary approaches in anthropology

PubMed Central

Currie, Thomas E.; Mace, Ruth

2011-01-01

Traditional investigations of the evolution of human social and political institutions trace their ancestry back to nineteenth century social scientists such as Herbert Spencer, and have concentrated on the increase in socio-political complexity over time. More recent studies of cultural evolution have been explicitly informed by Darwinian evolutionary theory and focus on the transmission of cultural traits between individuals. These two approaches to investigating cultural change are often seen as incompatible. However, we argue that many of the defining features and assumptions of ‘Spencerian’ cultural evolutionary theory represent testable hypotheses that can and should be tackled within a broader ‘Darwinian’ framework. In this paper we apply phylogenetic comparative techniques to data from Austronesian-speaking societies of Island South-East Asia and the Pacific to test hypotheses about the mode and tempo of human socio-political evolution. We find support for three ideas often associated with Spencerian cultural evolutionary theory: (i) political organization has evolved through a regular sequence of forms, (ii) increases in hierarchical political complexity have been more common than decreases, and (iii) political organization has co-evolved with the wider presence of hereditary social stratification. PMID:21357233

Deciphering the evolutionary history of open and closed mitosis

PubMed Central

Sazer, Shelley; Lynch, Michael; Needleman, Daniel

2014-01-01

Summary The origin of the nucleus at the prokaryote to eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the "closed" mitosis of some yeast but loses its integrity in the "open" mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and document patterns of mitotic nuclear variation within and among species and map them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. PMID:25458223

Local Nash equilibrium in social networks.

PubMed

Zhang, Yichao; Aziz-Alaoui, M A; Bertelle, Cyrille; Guan, Jihong

2014-08-29

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures.

Local Nash Equilibrium in Social Networks

PubMed Central

Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

2014-01-01

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures. PMID:25169150

Evolutionary plant physiology: Charles Darwin's forgotten synthesis

NASA Astrophysics Data System (ADS)

Kutschera, Ulrich; Niklas, Karl J.

2009-11-01

Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin’s son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin’s work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.

Local Nash Equilibrium in Social Networks

NASA Astrophysics Data System (ADS)

Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

2014-08-01

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures.

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

PubMed Central

Stark, Alexander; Kheradpour, Pouya; Parts, Leopold; Brennecke, Julius; Hodges, Emily; Hannon, Gregory J.; Kellis, Manolis

2007-01-01

MicroRNAs (miRNAs) are short regulatory RNAs that inhibit target genes by complementary binding in 3′ untranslated regions (3′ UTRs). They are one of the most abundant classes of regulators, targeting a large fraction of all genes, making their comprehensive study a requirement for understanding regulation and development. Here we use 12 Drosophila genomes to define structural and evolutionary signatures of miRNA hairpins, which we use for their de novo discovery. We predict >41 novel miRNA genes, which encompass many unique families, and 28 of which are validated experimentally. We also define signals for the precise start position of mature miRNAs, which suggest corrections of previously known miRNAs, often leading to drastic changes in their predicted target spectrum. We show that miRNA discovery power scales with the number and divergence of species compared, suggesting that such approaches can be successful in human as dozens of mammalian genomes become available. Interestingly, for some miRNAs sense and anti-sense hairpins score highly and mature miRNAs from both strands can indeed be found in vivo. Similarly, miRNAs with weak 5′ end predictions show increased in vivo processing of multiple alternate 5′ ends and have fewer predicted targets. Lastly, we show that several miRNA star sequences score highly and are likely functional. For mir-10 in particular, both arms show abundant processing, and both show highly conserved target sites in Hox genes, suggesting a possible cooperation of the two arms, and their role as a master Hox regulator. PMID:17989255

The continuous prisoner's dilemma and the evolution of cooperation through reciprocal altruism with variable investment.

PubMed

Killingback, Timothy; Doebeli, Michael

2002-10-01

Understanding the evolutionary origin and persistence of cooperative behavior is a fundamental biological problem. The standard "prisoner's dilemma," which is the most widely adopted framework for studying the evolution of cooperation through reciprocal altruism between unrelated individuals, does not allow for varying degrees of cooperation. Here we study the continuous iterated prisoner's dilemma, in which cooperative investments can vary continuously in each round. This game has been previously considered for a class of reactive strategies in which current investments are based on the partner's previous investment. In the standard iterated prisoner's dilemma, such strategies are inferior to strategies that take into account both players' previous moves, as is exemplified by the evolutionary dominance of "Pavlov" over "tit for tat." Consequently, we extend the analysis of the continuous prisoner's dilemma to a class of strategies in which current investments depend on previous payoffs and, hence, on both players' previous investments. We show, both analytically and by simulation, that payoff-based strategies, which embody the intuitively appealing idea that individuals invest more in cooperative interactions when they profit from these interactions, provide a natural explanation for the gradual evolution of cooperation from an initially noncooperative state and for the maintenance of cooperation thereafter.

Distinct evolutionary strategies of human leucocyte antigen loci in pathogen-rich environments

PubMed Central

Sanchez-Mazas, Alicia; Lemaître, Jean-François; Currat, Mathias

2012-01-01

Human leucocyte antigen (HLA) loci have a complex evolution where both stochastic (e.g. genetic drift) and deterministic (natural selection) forces are involved. Owing to their extraordinary level of polymorphism, HLA genes are useful markers for reconstructing human settlement history. However, HLA variation often deviates significantly from neutral expectations towards an excess of genetic diversity. Because HLA molecules play a crucial role in immunity, this observation is generally explained by pathogen-driven-balancing selection (PDBS). In this study, we investigate the PDBS model by analysing HLA allelic diversity on a large database of 535 populations in relation to pathogen richness. Our results confirm that geographical distances are excellent predictors of HLA genetic differentiation worldwide. We also find a significant positive correlation between genetic diversity and pathogen richness at two HLA class I loci (HLA-A and -B), as predicted by PDBS, and a significant negative correlation at one HLA class II locus (HLA-DQB1). Although these effects are weak, as shown by a loss of significance when populations submitted to rapid genetic drift are removed from the analysis, the inverse relationship between genetic diversity and pathogen richness at different loci indicates that HLA genes have adopted distinct evolutionary strategies to provide immune protection in pathogen-rich environments. PMID:22312050

Convergent and parallel evolution in life habit of the scallops (Bivalvia: Pectinidae)

PubMed Central

2011-01-01

Background We employed a phylogenetic framework to identify patterns of life habit evolution in the marine bivalve family Pectinidae. Specifically, we examined the number of independent origins of each life habit and distinguished between convergent and parallel trajectories of life habit evolution using ancestral state estimation. We also investigated whether ancestral character states influence the frequency or type of evolutionary trajectories. Results We determined that temporary attachment to substrata by byssal threads is the most likely ancestral condition for the Pectinidae, with subsequent transitions to the five remaining habit types. Nearly all transitions between life habit classes were repeated in our phylogeny and the majority of these transitions were the result of parallel evolution from byssate ancestors. Convergent evolution also occurred within the Pectinidae and produced two additional gliding clades and two recessing lineages. Furthermore, our analysis indicates that byssal attaching gave rise to significantly more of the transitions than any other life habit and that the cementing and nestling classes are only represented as evolutionary outcomes in our phylogeny, never as progenitor states. Conclusions Collectively, our results illustrate that both convergence and parallelism generated repeated life habit states in the scallops. Bias in the types of habit transitions observed may indicate constraints due to physical or ontogenetic limitations of particular phenotypes. PMID:21672233

Phylogenetic trends in phenolic metabolism of milkweeds (Asclepias): evidence for escalation.

PubMed

Agrawal, Anurag A; Salminen, Juha-Pekka; Fishbein, Mark

2009-03-01

Although plant-defense theory has long predicted patterns of chemical defense across taxa, we know remarkably little about the evolution of defense, especially in the context of directional phylogenetic trends. Here we contrast the production of phenolics and cardenolides in 35 species of milkweeds (Asclepias and Gomphocarpus). Maximum-likelihood analyses of character evolution revealed three major patterns. First, consistent with the defense-escalation hypothesis, the diversification of the milkweeds was associated with a trend for increasing phenolic production; this pattern was reversed (a declining evolutionary trend) for cardenolides, toxins sequestered by specialist herbivores. Second, phylogenetically independent correlations existed among phenolic classes across species. For example, coumaric acid derivatives showed negatively correlated evolution with caffeic acid derivatives, and this was likely driven by the fact that the former are used as precursors for the latter. In contrast, coumaric acid derivatives were positively correlated with flavonoids, consistent with competition for the precursor p-coumaric acid. Finally, of the phenolic classes, only flavonoids showed correlated evolution (positive) with cardenolides, consistent with a physiological and evolutionary link between the two via malonate. Thus, this study presents a rigorous test of the defense-escalation hypothesis and a novel phylogenetic approach to understanding the long-term persistence of physiological constraints on secondary metabolism.

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

PubMed Central

Haupt, V. Joachim; Schroeder, Michael; Labudde, Dirk

2018-01-01

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes. PMID:29659563

Biological Races in Humans

PubMed Central

Templeton, Alan R.

2013-01-01

Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race. PMID:23684745

49 CFR 1241.11 - Annual reports of class I railroads.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 9 2010-10-01 2010-10-01 false Annual reports of class I railroads. 1241.11... class I railroads. (a) Commencing with reports for the year ended December 31, 1973, and thereafter, until further order, all line-haul railroad companies of class I, as defined in § 1240.1 of this chapter...

Comparison of Group Cohesion, Class Participation, and Exam Performance in Live and Online Classes

ERIC Educational Resources Information Center

Galyon, Charles E.; Heaton, Eleanore C. T.; Best, Tiffany L.; Williams, Robert L.

2016-01-01

Though class participation and group cohesion have shown some potential to promote student performance in conventional classrooms, their efficacy has not yet been demonstrated in an online-class setting. Group cohesion, defined as member attraction to and self-identification with a group, is thought to promote positive interdependence and the…

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2012 CFR

2012-10-01

... stowage conditions for Class 1 (explosive) materials. (a) Heat and sources of ignition: (1) Class 1... on board. Stowage must be well away from all sources of heat, including steam pipes, heating coils... addition to this separation, there must be insulation to Class A60 standard as defined in 46 CFR 72.05-10(a...

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2011 CFR

2011-10-01

... stowage conditions for Class 1 (explosive) materials. (a) Heat and sources of ignition: (1) Class 1... on board. Stowage must be well away from all sources of heat, including steam pipes, heating coils... addition to this separation, there must be insulation to Class A60 standard as defined in 46 CFR 72.05-10(a...

49 CFR 176.116 - General stowage conditions for Class 1 (explosive) materials.

Code of Federal Regulations, 2010 CFR

2010-10-01

... stowage conditions for Class 1 (explosive) materials. (a) Heat and sources of ignition: (1) Class 1... on board. Stowage must be well away from all sources of heat, including steam pipes, heating coils... addition to this separation, there must be insulation to Class A60 standard as defined in 46 CFR 72.05-10(a...

Working-Class Women's Ways of Knowing: Effects of Gender, Race and Class.

ERIC Educational Resources Information Center

Luttrell, Wendy

1989-01-01

Analyzes the way black and white working-class women define and claim knowledge, challenging feminist analyses that have identified a single or universal mode of knowing for women. Contends that women speak to complex gender, racial, and class relations of power that shape how they think about learning and knowing. (Author/SLM)

Preparation guide for class B software specification documents

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1979-01-01

General conceptual requirements and specific application rules and procedures are provided for the production of software specification documents in conformance with deep space network software standards and class B standards. Class B documentation is identified as the appropriate level applicable to implementation, sustaining engineering, and operational uses by qualified personnel. Special characteristics of class B documents are defined.

Genetic Dissection of the Human Leukocyte Antigen Region by Use of Haplotypes of Tasmanians with Multiple Sclerosis

PubMed Central

Rubio, Justin P.; Bahlo, Melanie; Butzkueven, Helmut; van der Mei, Ingrid A. F.; Sale, Michèle M.; Dickinson, Joanne L.; Groom, Patricia; Johnson, Laura J.; Simmons, Rex D.; Tait, Brian; Varney, Mike; Taylor, Bruce; Dwyer, Terence; Williamson, Robert; Gough, Nicholas M.; Kilpatrick, Trevor J.; Speed, Terence P.; Foote, Simon J.

2002-01-01

Association of multiple sclerosis (MS) with the human leukocyte antigen (HLA) class II haplotype DRB1*1501-DQB1*0602 is the most consistently replicated finding of genetic studies of the disease. However, the high level of linkage disequilibrium (LD) in the HLA region has hindered the identification of other loci that single-marker tests for association are unlikely to resolve. In order to address this issue, we generated haplotypes spanning 14.754 Mb (5 cM) across the entire HLA region. The haplotypes, which were inferred by genotyping relatives of 152 patients with MS and 105 unaffected control subjects of Tasmanian ancestry, define a genomic segment from D6S276 to D6S291, including 13 microsatellite markers integrated with allele-typing data for DRB1 and DQB1. Association to the DRB1*1501-DQB1*0602 haplotype was replicated. In addition, we found that the class I/extended class I region, defined by a genomic segment of ∼400 kb between MOGCA and D6S265, harbors genes that independently increase risk of, or provide protection from, MS. Log-linear modeling analysis of constituent haplotypes that represent genomic regions containing class I (MOGCA-D6S265), class III (TNFa-TNFd-D6S273), and class II (DRB1-DQB1) genes indicated that having class I and class II susceptibility variants on the same haplotype provides an additive effect on risk. Moreover, we found no evidence for a disease locus in the class III region defined by a 150-kb genomic segment containing the TNF locus and 14 other genes. A global overview of LD performed using GOLD identified two discrete blocks of LD in the HLA region that correspond well with previous findings. We propose that the analysis of haplotypes, by use of the types of approaches outlined in the present article, should make it possible to more accurately define the contribution of the HLA to MS. PMID:11923913

MALT-45: A 7 mm survey of the southern Galaxy

NASA Astrophysics Data System (ADS)

Jordan, Christopher Harry

2015-09-01

The last decade has seen vast improvement in the knowledge of star formation within our Galaxy, largely owing to improvements in instrumentation, allowing astronomers to compile more data. However, despite the advances of technology, the quest for understanding high-mass star formation (HMSF) continues. As we go on, breakthroughs have occurred; a prime example is the discovery of the class II methanol maser, which exclusively signposts on-going sites of HMSF, but still lacks the detail necessary to identify HMSF in all forms. Once we have understood where, why and how HMSF can occur, we will be able to diagnose Galactic structure and evolution. Untargeted, large area surveys of molecular gas are ideal for identifying HMSF regions across a broad range of evolutionary phases. For example, searches for molecular species with a high critical density can highlight dense gases, which can then be used to probe Galactic structure and star formation. Because HMSF occurs in regions of dense molecular gas, mapping high-density tracers serves well to identify regions for study. The (1,1), (2,2) and (3,3) inversion transitions of ammonia (NH3) have been successfully mapped by the H2O Southern Galactic Plane Survey (HOPS), identifying previously unknown sites of star formation, as well as probing the structure of the Milky Way's spiral arms. Fortunately, HMSF can be identified by bright spectral lines in maser emission; HOPS also mapped the Galactic plane for water (H2O) masers and, perhaps more importantly, the Methanol MultiBeam survey identities class II methanol (CH3OH) masers, which are exclusively associated with HMSF. While class II CH3OH masers always signpost HMSF, they appear only in a specific evolutionary stage, and therefore other species (such as H2O masers) are required to identify other stages. Another, even higher density gas tracer useful for detecting HMSF and mapping the structure of our Galaxy is carbon monosulfide (CS). The ground state transition J = 1-0 for CS lies within the 7mm waveband, which also contains the poorly understood class I CH3OH maser. Unlike the class II variant, class I masers are not exclusively associated with HMSF, but do appear in star-forming regions across a wide range of evolutionary stages. A large problem for class I CH3OH maser studies is the bias in the targeted searches which have been used to find them; they have only been identified towards other masing regions (such as class II CH3OH), and therefore the properties of these masers are somewhat unclear. In this thesis, results focus on the MALT-45 survey using the Australia Telescope Compact Array (ATCA) in auto-correlation ('single-dish' mode). To date, MALT-45 has mapped the Galactic plane within 330° *lt; < l < 335°, jbj< 0:5°, which contains several known star-forming regions, including the G333 giant molecular cloud. MALT-45 surveys 12 spectral lines, but primarily CS (1-0), class I CH3OH masers and SiO (1-0) v = 0; 1; 2; 3. Bright, extended CS emission is detected across the survey region, and highlight two distinct velocities, due to different spiral arms of the Galaxy. In addition to the previously known 19 class I CH3OH masers, 58 new masers were detected. SiO masers were detected towards 47 regions, in various combinations of vibrational mode v = 1; 2; 3, all towards evolved infrared stars. Thermal SiO v = 0 emission is also detected across the survey region. Major science results from MALT-45 include: (i) A CS to NH3 comparison, which highlights cold, dense clumps as well as hot, evolved clumps. The cold and dense clumps appear to have self-absorption of CS emission in their centres and a relative over-abundance of NH3, while evolved clumps appear to have very little NH3 emission, despite being a dense gas tracer; (ii) Almost all (94 per cent) of ATLASGAL 870 um dust emission point sources are associated with at least a 3σ peak of CS emission; (iii) By comparing with peak CS velocities, class I CH3OH masers are good indicators of the systemic velocities of clouds; (iv) More than half (55 per cent) of the detected class I CH3OH masers are not associated with any other kind of maser; (v) Class II CH3OH, H2O and hydroxyl (OH) masers associate well with class I CH3OH masers, confirming that class I CH3OH masers occur towards a wide range of evolutionary stages in HMSF; (vi) Class I CH3OH masers appear to have no correlation in intensity or luminosity with other maser species; (vii) Class I CH3OH masers have typical projected linear distances from other masers associated with star formation, peaks of CS and 870 μm point sources within 0.5 pc; (viii) Class I CH3OH masers are spread over a larger area when also associated with class II CH3OH or OH masers, perhaps due to their more evolved state; (ix) Almost all (95 per cent) of class I CH3OH masers are associated with an ATLASGAL source; (x) Using ATLASGAL source parameters, a clump mass is calculated. The population of class I CH3OH masers has a broad range of associated masses (10^1.5 to 10^4.5M⊙), but peaks between 10^3.0 and 10^3.5M⊙. Higher masses tend to be associated with evolved regions of star formation, while lower masses tend to be non-evolved regions; (xi) SiO masers typically decrease in intensity with vibrational mode (v = 1; 2; 3), but eleven cases of stronger v = 2 than v = 1 emission were found, and two regions of only v = 2 emission were found; (xii) The relatively rare v = 3 vibrational mode of SiO (1-0) was detected towards three evolved infrared stars.

CRISPR-mediated HDAC2 disruption identifies two distinct classes of target genes in human cells.

PubMed

Somanath, Priyanka; Herndon Klein, Rachel; Knoepfler, Paul S

2017-01-01

The transcriptional functions of the class I histone deacetylases (HDACs) HDAC1 and HDAC2 are mainly viewed as both repressive and redundant based on murine knockout studies, but they may have additional independent roles and their physiological functions in human cells are not as clearly defined. To address the individual epigenomic functions of HDAC2, here we utilized CRISPR-Cas9 to disrupt HDAC2 in human cells. We find that while HDAC2 null cells exhibited signs of cross-regulation between HDAC1 and HDAC2, specific epigenomic phenotypes were still apparent using RNA-seq and ChIP assays. We identified specific targets of HDAC2 repression, and defined a novel class of genes that are actively expressed in a partially HDAC2-dependent manner. While HDAC2 was required for the recruitment of HDAC1 to repressed HDAC2-gene targets, HDAC2 was dispensable for HDAC1 binding to HDAC2-activated targets, supporting the notion of distinct classes of targets. Both active and repressed classes of gene targets demonstrated enhanced histone acetylation and methylation in HDAC2-null cells. Binding of the HDAC1/2-associated SIN3A corepressor was altered at most HDAC2-targets, but without a clear pattern. Overall, our study defines two classes of HDAC2 targets in human cells, with a dependence of HDAC1 on HDAC2 at one class of targets, and distinguishes unique functions for HDAC2.

Chemical and Physical Properties of Comets in the Lowell Database: Results from Four Decades of Narrowband Photometry

NASA Astrophysics Data System (ADS)

Schleicher, David G.; Bair, Allison Nicole

2016-10-01

As remnants from the epoch of early solar system formation, comet nuclei are less processed than any other class of objects currently available for detailed study. Compositional and physical studies can therefore be used to investigate primordial conditions across the region of comet formation and/or subsequent evolutionary effects. With these goals, a long duration program of comet narrowband photometry was begun in 1976 and results for 85 comets were published by A'Hearn et al. (1995; Icarus 118, 223). Observations continued and we performed a new set of analyses of data obtained through mid-2011. Following a hiatus due to lack of funding and other competing priorities, we have now resumed our efforts at completing this project while also incorporating the most recent five years of data. The database now includes 191 comets obtained over 848 nights. A restricted subset of 116 objects were observed multiple times and are considered well-determined; these form the basis of our compositional studies. Using a variety of taxonomic techniques, we identified seven compositional classes for the data up to 2011 and anticipate no changes with the newest additions. Several classes are simply sub-groups of the original carbon-chain depleted class found by A'Hearn et al.; all evidence continues to indicate that carbon-chain depletion reflects the primordial composition at the time and location of cometary accretion and is not associated with evolution. Another new class contains five comets depleted in ammonia but not depleted in carbon-chain molecules; it is unclear if this group is primordial or not. In comparison, clear evidence for evolutionary effects are seen in the active fractions for comet nuclei -- decreasing with age -- and with the dust-to-gas ratio -- decreasing with age and perihelion distance, implying an evolution of the surface of the nucleus associated with the peak temperature attained and how often such temperatures have been reached. Updates of these and other results including data from the last five years will be presented. Support was provided by NASA Planetary Atmospheres grant NNX08AG19G.

Origins and evolution of viruses of eukaryotes: The ultimate modularity

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

Koonin, Eugene V., E-mail: koonin@ncbi.nlm.nih.gov; Dolja, Valerian V., E-mail: doljav@science.oregonstate.edu; Krupovic, Mart, E-mail: krupovic@pasteur.fr

2015-05-15

Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangiblemore » clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes. - Highlights: • Eukaryotic virome dramatically differs from the viromes of bacteria and archaea. • Eukaryotic virome is dominated by RNA viruses and retroelements. • All classes of eukaryotic viruses evolved by gene module exchange. • Prokaryotic ancestry is traceable for core gene modules of most eukaryotic viruses. • Evolutionary histories of viruses and transposable elements are tightly linked.« less

Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms.

PubMed

Allen, Andrew E; Moustafa, Ahmed; Montsant, Anton; Eckert, Angelika; Kroth, Peter G; Bowler, Chris

2012-01-01

Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively.

Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes in Photosynthetic Marine Diatoms

PubMed Central

Allen, Andrew E.; Moustafa, Ahmed; Montsant, Anton; Eckert, Angelika; Kroth, Peter G.; Bowler, Chris

2012-01-01

Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively. PMID:21903677

The fighting hypothesis as an evolutionary explanation for the handedness polymorphism in humans: where are we?

PubMed

Faurie, Charlotte; Raymond, Michel

2013-06-01

The ubiquitous and persistent handedness polymorphism in humans requires an evolutionary explanation. It has been suggested that left-handers have a frequency-dependent advantage during a fight, such that this advantage decreases when their frequency increases. Many independent studies are providing data from interactive sports (a specific class of fights), and are very supportive of the fighting hypothesis. The only intercultural study on traditional societies is also consistent with the fighting hypothesis, although it has not yet been replicated. The frequencies of left-handers in the few remaining violent societies are likely to be rapidly decreasing, due to Western colonization (long-range weapons, religion, and money market) dramatically affecting the frequency-dependent selection associated with handedness. Clearly, more data are urgently needed outside the Western influence. © 2013 New York Academy of Sciences.

Evolutionary Consequences of DNA Methylation in a Basal Metazoan

PubMed Central

Dixon, Groves B.; Bay, Line K.; Matz, Mikhail V.

2016-01-01

Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower sequence evolution. We also find a strong correlation between gbM and codon bias, resulting from systematic replacement of CpG bearing codons. We conclude that gbM has strong effects on codon evolution and speculate that this may influence establishment of optimal codons. PMID:27189563

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.

PubMed

Studer, Romain A; Penel, Simon; Duret, Laurent; Robinson-Rechavi, Marc

2008-09-01

A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.

Characterization and classification of zebrafish brain morphology mutants

PubMed Central

Lowery, Laura Anne; De Rienzo, Gianluca; Gutzman, Jennifer H.; Sive, Hazel

2010-01-01

The mechanisms by which the vertebrate brain achieves its three-dimensional structure are clearly complex, requiring the functions of many genes. Using the zebrafish as a model, we have begun to define genes required for brain morphogenesis, including brain ventricle formation, by studying 16 mutants previously identified as having embryonic brain morphology defects. We report the phenotypic characterization of these mutants at several time-points, using brain ventricle dye injection, imaging, and immunohistochemistry with neuronal markers. Most of these mutants display early phenotypes, affecting initial brain shaping, while others show later phenotypes, affecting brain ventricle expansion. In the early phenotype group, we further define four phenotypic classes and corresponding functions required for brain morphogenesis. Although we did not use known genotypes for this classification, basing it solely on phenotypes, many mutants with defects in functionally related genes clustered in a single class. In particular, class 1 mutants show midline separation defects, corresponding to epithelial junction defects; class 2 mutants show reduced brain ventricle size; class 3 mutants show midbrain-hindbrain abnormalities, corresponding to basement membrane defects; and class 4 mutants show absence of ventricle lumen inflation, corresponding to defective ion pumping. Later brain ventricle expansion requires the extracellular matrix, cardiovascular circulation, and transcription/splicing-dependent events. We suggest that these mutants define processes likely to be used during brain morphogenesis throughout the vertebrates. PMID:19051268

Using Evolution to Guide Protein Engineering: The Devil IS in the Details.

PubMed

Swint-Kruse, Liskin

2016-07-12

For decades, protein engineers have endeavored to reengineer existing proteins for novel applications. Overall, protein folds and gross functions can be readily transferred from one protein to another by transplanting large blocks of sequence (i.e., domain recombination). However, predictably fine-tuning function (e.g., by adjusting ligand affinity, specificity, catalysis, and/or allosteric regulation) remains a challenge. One approach has been to use the sequences of protein families to identify amino acid positions that change during the evolution of functional variation. The rationale is that these nonconserved positions could be mutated to predictably fine-tune function. Evolutionary approaches to protein design have had some success, but the engineered proteins seldom replicate the functional performances of natural proteins. This Biophysical Perspective reviews several complexities that have been revealed by evolutionary and experimental studies of protein function. These include 1) challenges in defining computational and biological thresholds that define important amino acids; 2) the co-occurrence of many different patterns of amino acid changes in evolutionary data; 3) difficulties in mapping the patterns of amino acid changes to discrete functional parameters; 4) the nonconventional mutational outcomes that occur for a particular group of functionally important, nonconserved positions; 5) epistasis (nonadditivity) among multiple mutations; and 6) the fact that a large fraction of a protein's amino acids contribute to its overall function. To overcome these challenges, new goals are identified for future studies. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Pelvis morphology suggests that early Mesozoic birds were too heavy to contact incubate their eggs.

PubMed

Charles Deeming, D; Mayr, Gerald

2018-05-01

Numerous new fossils have driven an interest in reproduction of early birds, but direct evidence remains elusive. No Mesozoic avian eggs can be unambiguously assigned to a species, which hampers our understanding of the evolution of contact incubation, which is a defining feature of extant birds. Compared to living species, eggs of Mesozoic birds are relatively small, but whether the eggs of Mesozoic birds could actually have borne the weight of a breeding adult has not yet been investigated. We estimated maximal egg breadth for a range of Mesozoic avian taxa from the width of the pelvic canal defined by the pubic symphysis. Known elongation ratios of Mesozoic bird eggs allowed us to predict egg mass and hence the load mass an egg could endure before cracking. These values were compared to the predicted body masses of the adult birds based on skeletal remains. Based on 21 fossil species, we show that for nonornithothoracine birds body mass was 187% of the load mass of the eggs. For Enantiornithes, body mass was 127% greater than the egg load mass, but some early Cretaceous ornithuromorphs were 179% heavier than their eggs could support. Our indirect approach provides the best evidence yet that early birds could not have sat on their eggs without running the risk of causing damage. We suggest that contact incubation evolved comparatively late in birds. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Interferometric view of the circumstellar envelopes of northern FU Orionis-type stars

NASA Astrophysics Data System (ADS)

Fehér, O.; Kóspál, Á.; Ábrahám, P.; Hogerheijde, M. R.; Brinch, C.

2017-11-01

Context. FU Orionis-type objects are pre-main sequence, low-mass stars with large outbursts in visible light that last for several years or decades. They are thought to represent an evolutionary phase during the life of every young star when accretion from the circumstellar disk is enhanced during recurring time periods. These outbursts are able to rapidly build up the star while affecting the physical conditions inside the circumstellar disk and thus the ongoing or future planet formation. In many models, infall from a circumstellar envelope seems to be necessary to trigger the outbursts. Aims: We characterise the morphology and the physical parameters of the circumstellar material around FU Orionis-type stars using the emission of millimetre-wavelength molecular tracers. The high-spatial-resolution study provides insight into the evolutionary state of the objects, the distribution of parameters in the envelopes and the physical processes forming the environment of these stars. Methods: We observed the J = 1-0 rotational transition of 13CO and C18O towards eight northern FU Orionis-type stars (V1057 Cyg, V1515 Cyg, V2492 Cyg, V2493 Cyg, V1735 Cyg, V733 Cep, RNO 1B and RNO 1C) and determine the spatial and velocity structure of the circumstellar gas on a scale of a few thousand AU. We derive temperatures and envelope masses and discuss the kinematics of the circumstellar material. Results: We detected extended CO emission associated with all our targets. Smaller-scale CO clumps were found to be associated with five objects with radii of 2000-5000 AU and masses of 0.02-0.5 M⊙; these are clearly heated by the central stars. Three of these envelopes are also strongly detected in the 2.7 mm continuum. No central CO clumps were detected around V733 Cep and V710 Cas which can be interpreted as envelopes but there are many other clumps in their environments. Traces of outflow activity were observed towards V1735 Cyg, V733 Cep and V710 Cas. Conclusions: The diversity of the observed envelopes enables us to set up an evolutionary sequence between the objects. We find their evolutionary state to range from early, embedded Class I stage to late, Class II-type objects with very-low-mass circumstellar material. We also find evidence of larger-scale circumstellar material influencing the detected spectral features in the environment of our targets. These results reinforce the idea of FU Orionis-type stars as representatives of a transitory stage between embedded Class I young stellar objects and classical T Tauri stars.

Group adaptation, formal darwinism and contextual analysis.

PubMed

Okasha, S; Paternotte, C

2012-06-01

We consider the question: under what circumstances can the concept of adaptation be applied to groups, rather than individuals? Gardner and Grafen (2009, J. Evol. Biol.22: 659-671) develop a novel approach to this question, building on Grafen's 'formal Darwinism' project, which defines adaptation in terms of links between evolutionary dynamics and optimization. They conclude that only clonal groups, and to a lesser extent groups in which reproductive competition is repressed, can be considered as adaptive units. We re-examine the conditions under which the selection-optimization links hold at the group level. We focus on an important distinction between two ways of understanding the links, which have different implications regarding group adaptationism. We show how the formal Darwinism approach can be reconciled with G.C. Williams' famous analysis of group adaptation, and we consider the relationships between group adaptation, the Price equation approach to multi-level selection, and the alternative approach based on contextual analysis. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Metapopulation dynamics and the evolution of dispersal

NASA Astrophysics Data System (ADS)

Parvinen, Kalle

A metapopulation consists of local populations living in habitat patches. In this chapter metapopulation dynamics and the evolution of dispersal is studied in two metapopulation models defined in discrete time. In the first model there are finitely many patches, and in the other one there are infinitely many patches, which allows to incorporate catastrophes into the model. In the first model, cyclic local population dynamics can be either synchronized or not, and increasing dispersal both synchronizes and stabilizes metapopulation dynamics. On the other hand, the type of dynamics has a strong effect on the evolution of dispersal. In case of non-synchronized metapopulation dynamics, dispersal is much more beneficial than in the case of synchronized metapopulation dynamics. Local dynamics has a substantial effect also on the possibility of evolutionary branching in both models. Furthermore, with an Allee effect in the local dynamics of the second model, even evolutionary suicide can occur. It is an evolutionary process in which a viable population adapts in such a way that it can no longer persist.

The impact of rapid evolution on population dynamics in the wild: experimental test of eco-evolutionary dynamics.

PubMed

Turcotte, Martin M; Reznick, David N; Hare, J Daniel

2011-11-01

Rapid evolution challenges the assumption that evolution is too slow to impact short-term ecological dynamics. This insight motivates the study of 'Eco-Evolutionary Dynamics' or how evolution and ecological processes reciprocally interact on short time scales. We tested how rapid evolution impacts concurrent population dynamics using an aphid (Myzus persicae) and an undomesticated host (Hirschfeldia incana) in replicated wild populations. We manipulated evolvability by creating non-evolving (single clone) and potentially evolving (two-clone) aphid populations that contained genetic variation in intrinsic growth rate. We observed significant evolution in two-clone populations whether or not they were exposed to predators and competitors. Evolving populations grew up to 42% faster and attained up to 67% higher density, compared with non-evolving control populations but only in treatments exposed to competitors and predators. Increased density also correlates with relative fitness of competing clones suggesting a full eco-evolutionary dynamic cycle defined as reciprocal interactions between evolution and density. © 2011 Blackwell Publishing Ltd/CNRS.

Bridging the physical scales in evolutionary biology: From protein sequence space to fitness of organisms and populations

PubMed Central

Bershtein, Shimon; Serohijos, Adrian W.R.; Shakhnovich, Eugene I.

2016-01-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. PMID:27810574

Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

PubMed

Bershtein, Shimon; Serohijos, Adrian Wr; Shakhnovich, Eugene I

2017-02-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Woese on the received view of evolution.

PubMed

Sarkar, Sahotra

2014-01-01

As part of his attempt to reconstruct the earliest phase of the evolution of life on Earth, Woese produced a compelling critique of the received view of evolution from the 20th century. This paper explicitly articulates two related features of that critique that are fundamental but the first of which has not been sufficiently clearly recognized in the context of evolutionary theorizing: (1) according to Woese's scenario of communal evolution during life's earliest phase (roughly, the first billion years of life on Earth), well-defined biological individuals (and, thus, individual lineages) did not exist; and (2) during that phase, evolutionary change took place through ubiquitous horizontal gene transfer (HGT) rather than through vertical transmission of features (including genes) and the combinatorics of HGT was the dominant mechanism of evolutionary change. Both factors present serious challenges to the received view of evolution and that framework would have to be radically altered to incorporate these factors. The extent to which this will be necessary will depend on whether Woese's scenario of collective early evolution is correct.

Rumour propagation and the eco-evolutionary dynamics of social information use.

PubMed

Suire, Alexandre; van Baalen, Minus

2018-03-28

Information is a crucial currency for living organisms as it allows them to adjust their behaviour to environmental fluctuations. Thus, natural selection should have favoured the capacity of collecting information from different sources, including social interactions whereby individuals could quickly gain reliable information. However, such conditions may also favour the gathering of potentially detrimental information, such as false or misinterpreted accounts of environmental and social phenomena such as rumours, which may spread via informational cascades. We applied ecological and evolutionary principles to investigate how the propagation of social information at a populational level affects the propensity to assimilate it, here defined as the gullibilty. Our results show that the evolution of an individual's susceptibility to assimilate information strongly depends on eco-evolutionary feedbacks, in particular when both useful and detrimental information circulate. We discuss our results regarding the different information transmission mechanisms involved with particular attention to specific cases of social learning. © 2018 The Author(s).

49 CFR 232.207 - Class IA brake tests-1,000-mile inspection.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Class IA brake tests-1,000-mile inspection. 232... Class IA brake tests—1,000-mile inspection. (a) Except as provided in § 232.213, each train shall receive a Class IA brake test performed by a qualified person, as defined in § 232.5, at a location that...

49 CFR 232.207 - Class IA brake tests-1,000-mile inspection.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Class IA brake tests-1,000-mile inspection. 232... Class IA brake tests—1,000-mile inspection. (a) Except as provided in § 232.213, each train shall receive a Class IA brake test performed by a qualified person, as defined in § 232.5, at a location that...

Design of partially supervised classifiers for multispectral image data

NASA Technical Reports Server (NTRS)

Jeon, Byeungwoo; Landgrebe, David

1993-01-01

A partially supervised classification problem is addressed, especially when the class definition and corresponding training samples are provided a priori only for just one particular class. In practical applications of pattern classification techniques, a frequently observed characteristic is the heavy, often nearly impossible requirements on representative prior statistical class characteristics of all classes in a given data set. Considering the effort in both time and man-power required to have a well-defined, exhaustive list of classes with a corresponding representative set of training samples, this 'partially' supervised capability would be very desirable, assuming adequate classifier performance can be obtained. Two different classification algorithms are developed to achieve simplicity in classifier design by reducing the requirement of prior statistical information without sacrificing significant classifying capability. The first one is based on optimal significance testing, where the optimal acceptance probability is estimated directly from the data set. In the second approach, the partially supervised classification is considered as a problem of unsupervised clustering with initially one known cluster or class. A weighted unsupervised clustering procedure is developed to automatically define other classes and estimate their class statistics. The operational simplicity thus realized should make these partially supervised classification schemes very viable tools in pattern classification.

An iterative approach to optimize change classification in SAR time series data

NASA Astrophysics Data System (ADS)

Boldt, Markus; Thiele, Antje; Schulz, Karsten; Hinz, Stefan

2016-10-01

The detection of changes using remote sensing imagery has become a broad field of research with many approaches for many different applications. Besides the simple detection of changes between at least two images acquired at different times, analyses which aim on the change type or category are at least equally important. In this study, an approach for a semi-automatic classification of change segments is presented. A sparse dataset is considered to ensure the fast and simple applicability for practical issues. The dataset is given by 15 high resolution (HR) TerraSAR-X (TSX) amplitude images acquired over a time period of one year (11/2013 to 11/2014). The scenery contains the airport of Stuttgart (GER) and its surroundings, including urban, rural, and suburban areas. Time series imagery offers the advantage of analyzing the change frequency of selected areas. In this study, the focus is set on the analysis of small-sized high frequently changing regions like parking areas, construction sites and collecting points consisting of high activity (HA) change objects. For each HA change object, suitable features are extracted and a k-means clustering is applied as the categorization step. Resulting clusters are finally compared to a previously introduced knowledge-based class catalogue, which is modified until an optimal class description results. In other words, the subjective understanding of the scenery semantics is optimized by the data given reality. Doing so, an even sparsely dataset containing only amplitude imagery can be evaluated without requiring comprehensive training datasets. Falsely defined classes might be rejected. Furthermore, classes which were defined too coarsely might be divided into sub-classes. Consequently, classes which were initially defined too narrowly might be merged. An optimal classification results when the combination of previously defined key indicators (e.g., number of clusters per class) reaches an optimum.

Investigating Evolutionary Conservation of Dendritic Cell Subset Identity and Functions

PubMed Central

Vu Manh, Thien-Phong; Bertho, Nicolas; Hosmalin, Anne; Schwartz-Cornil, Isabelle; Dalod, Marc

2015-01-01

Dendritic cells (DCs) were initially defined as mononuclear phagocytes with a dendritic morphology and an exquisite efficiency for naïve T-cell activation. DC encompass several subsets initially identified by their expression of specific cell surface molecules and later shown to excel in distinct functions and to develop under the instruction of different transcription factors or cytokines. Very few cell surface molecules are expressed in a specific manner on any immune cell type. Hence, to identify cell types, the sole use of a small number of cell surface markers in classical flow cytometry can be deceiving. Moreover, the markers currently used to define mononuclear phagocyte subsets vary depending on the tissue and animal species studied and even between laboratories. This has led to confusion in the definition of DC subset identity and in their attribution of specific functions. There is a strong need to identify a rigorous and consensus way to define mononuclear phagocyte subsets, with precise guidelines potentially applicable throughout tissues and species. We will discuss the advantages, drawbacks, and complementarities of different methodologies: cell surface phenotyping, ontogeny, functional characterization, and molecular profiling. We will advocate that gene expression profiling is a very rigorous, largely unbiased and accessible method to define the identity of mononuclear phagocyte subsets, which strengthens and refines surface phenotyping. It is uniquely powerful to yield new, experimentally testable, hypotheses on the ontogeny or functions of mononuclear phagocyte subsets, their molecular regulation, and their evolutionary conservation. We propose defining cell populations based on a combination of cell surface phenotyping, expression analysis of hallmark genes, and robust functional assays, in order to reach a consensus and integrate faster the huge but scattered knowledge accumulated by different laboratories on different cell types, organs, and species. PMID:26082777

Structure and content of the major histocompatibility complex (MHC) class I regions of the great anthropoid apes.

PubMed

Venditti, C P; Lawlor, D A; Sharma, P; Chorney, M J

1996-09-01

The origins of the functional class I genes predated human speciation, a phenomenon known as trans-speciation. The retention of class Ia orthologues within the great apes, however, has not been paralleled by studies designed to examine the pseudogene content, organization, and structure of their class I regions. Therefore, we have begun the systematic characterization of the Old World primate MHCs. The numbers and sizes of fragments harboring class I sequences were similar among the chimpanzee, gorilla, and human genomes tested. Both of the gorillas included in our study possessed genomic fragments carrying orthologues of the recently evolved HLA-H pseudogene identical to those found in the human. The overall megabase restriction fragment patterns of humans and chimpanzees appeared slightly more similar to each other, although the HLA-A subregional megabase variants may have been generated following the emergence of Homo sapiens. Based on the results of this initial study, it is difficult to generate a firm species tree and to determine human's closest evolutionary neighbor. Nevertheless, an analysis of MHC subregional similarities and differences in the hominoid apes may ultimately aid in localizing and identifying MHC haplotype-associated disease genes such as idiopathic hemochromatosis.

CRYPTIC NEOGENE VICARIANCE AND QUATERNARY DISPERSAL OF THE RED-SPOTTED TOAD (BUFO PUNCTATUS) INSIGHTS ON THE EVOLUTION OF NORTH AMERICAN WARM DESERT BIOTAS

EPA Science Inventory

We define the geographic distributions of embedded evolutionary mitochondrial DNA (mtDNA) lineages (clades) within a broadly distributed, arid- dwelling toad, Bufo punctatus, and evaluate these patterns as they relate to hypothesized vicariant events leading to the formation of b...

A statistical test of unbiased evolution of body size in birds.

PubMed

Bokma, Folmer

2002-12-01

Of the approximately 9500 bird species, the vast majority is small-bodied. That is a general feature of evolutionary lineages, also observed for instance in mammals and plants. The avian interspecific body size distribution is right-skewed even on a logarithmic scale. That has previously been interpreted as evidence that body size evolution has been biased. However, a procedure to test for unbiased evolution from the shape of body size distributions was lacking. In the present paper unbiased body size evolution is defined precisely, and a statistical test is developed based on Monte Carlo simulation of unbiased evolution. Application of the test to birds suggests that it is highly unlikely that avian body size evolution has been unbiased as defined. Several possible explanations for this result are discussed. A plausible explanation is that the general model of unbiased evolution assumes that population size and generation time do not affect the evolutionary variability of body size; that is, that micro- and macroevolution are decoupled, which theory suggests is not likely to be the case.

The Three Domains of Conservation Genetics: Case Histories from Hawaiian Waters

PubMed Central

2016-01-01

The scientific field of conservation biology is dominated by 3 specialties: phylogenetics, ecology, and evolution. Under this triad, phylogenetics is oriented towards the past history of biodiversity, conserving the divergent branches in the tree of life. The ecological component is rooted in the present, maintaining the contemporary life support systems for biodiversity. Evolutionary conservation (as defined here) is concerned with preserving the raw materials for generating future biodiversity. All 3 domains can be documented with genetic case histories in the waters of the Hawaiian Archipelago, an isolated chain of volcanic islands with 2 types of biodiversity: colonists, and new species that arose from colonists. This review demonstrates that 1) phylogenetic studies have identified previously unknown branches in the tree of life that are endemic to Hawaiian waters; 2) population genetic surveys define isolated marine ecosystems as management units, and 3) phylogeographic analyses illustrate the pathways of colonization that can enhance future biodiversity. Conventional molecular markers have advanced all 3 domains in conservation biology over the last 3 decades, and recent advances in genomics are especially valuable for understanding the foundations of future evolutionary diversity. PMID:27001936

Evolutionary algorithm for vehicle driving cycle generation.

PubMed

Perhinschi, Mario G; Marlowe, Christopher; Tamayo, Sergio; Tu, Jun; Wayne, W Scott

2011-09-01

Modeling transit bus emissions and fuel economy requires a large amount of experimental data over wide ranges of operational conditions. Chassis dynamometer tests are typically performed using representative driving cycles defined based on vehicle instantaneous speed as sequences of "microtrips", which are intervals between consecutive vehicle stops. Overall significant parameters of the driving cycle, such as average speed, stops per mile, kinetic intensity, and others, are used as independent variables in the modeling process. Performing tests at all the necessary combinations of parameters is expensive and time consuming. In this paper, a methodology is proposed for building driving cycles at prescribed independent variable values using experimental data through the concatenation of "microtrips" isolated from a limited number of standard chassis dynamometer test cycles. The selection of the adequate "microtrips" is achieved through a customized evolutionary algorithm. The genetic representation uses microtrip definitions as genes. Specific mutation, crossover, and karyotype alteration operators have been defined. The Roulette-Wheel selection technique with elitist strategy drives the optimization process, which consists of minimizing the errors to desired overall cycle parameters. This utility is part of the Integrated Bus Information System developed at West Virginia University.

The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates.

PubMed

Stoeck, T; Przybos, E; Dunthorn, M

2014-05-01

Ciliates are a major evolutionary lineage within the alveolates, which are distributed in nearly all habitats on our planet and are an essential component for ecosystem function, processes and stability. Accurate identification of these unicellular eukaryotes through, for example, microscopy or mating type reactions is reserved to few specialists. To satisfy the demand for a DNA barcode for ciliates, which meets the standard criteria for DNA barcodes defined by the Consortium for the Barcode of Life (CBOL), we here evaluated the D1-D2 region of the ribosomal DNA large subunit (LSU-rDNA). Primer universality for the phylum Ciliophora was tested in silico with available database sequences as well as in the laboratory with 73 ciliate species, which represented nine of 12 ciliate classes. Primers tested in this study were successful for all tested classes. To test the ability of the D1-D2 region to resolve conspecific and congeneric sequence divergence, 63 Paramecium strains were sampled from 24 mating species. The average conspecific D1-D2 variation was 0.18%, whereas congeneric sequence divergence averaged 4.83%. In pairwise genetic distance analyses, we identified a D1-D2 sequence divergence of <0.6% as an ideal threshold to discriminate Paramecium species. Using this definition, only 3.8% of all conspecific and 3.9% of all congeneric sequence comparisons had the potential of false assignments. Neighbour-joining analyses inferred monophyly for all taxa but for two Paramecium octaurelia strains. Here, we present a protocol for easy DNA amplification of single cells and voucher deposition. In conclusion, the presented data pinpoint the D1-D2 region as an excellent candidate for an official CBOL barcode for ciliated protists. © 2013 John Wiley & Sons Ltd.

Evolutionary dynamics of an expressed MHC class IIβ locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing

USGS Publications Warehouse

Mulder, Kevin P.; Cortazar-Chinarro, Maria; Harris, D. James; Crottini, Angelica; Grant, Evan H. Campbell; Fleischer, Robert C.; Savage, Anna E.

2017-01-01

The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.

A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines.

PubMed

Toussaint, Nora C; Dönnes, Pierre; Kohlbacher, Oliver

2008-12-01

Epitope-based vaccines (EVs) have a wide range of applications: from therapeutic to prophylactic approaches, from infectious diseases to cancer. The development of an EV is based on the knowledge of target-specific antigens from which immunogenic peptides, so-called epitopes, are derived. Such epitopes form the key components of the EV. Due to regulatory, economic, and practical concerns the number of epitopes that can be included in an EV is limited. Furthermore, as the major histocompatibility complex (MHC) binding these epitopes is highly polymorphic, every patient possesses a set of MHC class I and class II molecules of differing specificities. A peptide combination effective for one person can thus be completely ineffective for another. This renders the optimal selection of these epitopes an important and interesting optimization problem. In this work we present a mathematical framework based on integer linear programming (ILP) that allows the formulation of various flavors of the vaccine design problem and the efficient identification of optimal sets of epitopes. Out of a user-defined set of predicted or experimentally determined epitopes, the framework selects the set with the maximum likelihood of eliciting a broad and potent immune response. Our ILP approach allows an elegant and flexible formulation of numerous variants of the EV design problem. In order to demonstrate this, we show how common immunological requirements for a good EV (e.g., coverage of epitopes from each antigen, coverage of all MHC alleles in a set, or avoidance of epitopes with high mutation rates) can be translated into constraints or modifications of the objective function within the ILP framework. An implementation of the algorithm outperforms a simple greedy strategy as well as a previously suggested evolutionary algorithm and has runtimes on the order of seconds for typical problem sizes.

Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases*♦

PubMed Central

Valencia-Sánchez, Marco Igor; Rodríguez-Hernández, Annia; Ferreira, Ruben; Santamaría-Suárez, Hugo Aníbal; Arciniega, Marcelino; Dock-Bregeon, Anne-Catherine; Moras, Dino; Beinsteiner, Brice; Brieba, Luis G.; Grøtli, Morten

2016-01-01

Glycyl tRNA synthetase (GlyRS) provides a unique case among class II aminoacyl tRNA synthetases, with two clearly widespread types of enzymes: a dimeric (α2) species present in some bacteria, archaea, and eukaryotes; and a heterotetrameric form (α2β2) present in most bacteria. Although the differences between both types of GlyRS at the anticodon binding domain level are evident, the extent and implications of the variations in the catalytic domain have not been described, and it is unclear whether the mechanism of amino acid recognition is also dissimilar. Here, we show that the α-subunit of the α2β2 GlyRS from the bacterium Aquifex aeolicus is able to perform the first step of the aminoacylation reaction, which involves the activation of the amino acid with ATP. The crystal structure of the α-subunit in the complex with an analog of glycyl adenylate at 2.8 Å resolution presents a conformational arrangement that properly positions the cognate amino acid. This work shows that glycine is recognized by a subset of different residues in the two types of GlyRS. A structural and sequence analysis of class II catalytic domains shows that bacterial GlyRS is closely related to alanyl tRNA synthetase, which led us to define a new subclassification of these ancient enzymes and to propose an evolutionary path of α2β2 GlyRS, convergent with α2 GlyRS and divergent from AlaRS, thus providing a possible explanation for the puzzling existence of two proteins sharing the same fold and function but not a common ancestor. PMID:27226617

Structural insights into the polyphyletic origins of glycyl tRNA synthetases

DOE PAGES

Valencia-Sánchez, Marco Igor; Rodríguez-Hernández, Annia; Ferreira, Ruben; ...

2016-05-23

Glycyl tRNA synthetase (GlyRS) provides a unique case among class II aminoacyl tRNA synthetases, with two clearly widespread types of enzymes: a dimeric (α 2) species present in some bacteria, archaea, and eukaryotes; and a heterotetrameric form (α 2β 2) present in most bacteria. Although the differences between both types of GlyRS at the anticodon binding domain level are evident, the extent and implications of the variations in the catalytic domain have not been described, and it is unclear whether the mechanism of amino acid recognition is also dissimilar. Here, we show that the α-subunit of the α 2β 2more » GlyRS from the bacterium Aquifex aeolicus is able to perform the first step of the aminoacylation reaction, which involves the activation of the amino acid with ATP. The crystal structure of the α-subunit in the complex with an analog of glycyl adenylate at 2.8 Å resolution presents a conformational arrangement that properly positions the cognate amino acid. This work shows that glycine is recognized by a subset of different residues in the two types of GlyRS. Furthermore, a structural and sequence analysis of class II catalytic domains shows that bacterial GlyRS is closely related to alanyl tRNA synthetase, which led us to define a new subclassification of these ancient enzymes and to propose an evolutionary path of α 2β 2 GlyRS, convergent with α 2 GlyRS and divergent from AlaRS, thus providing a possible explanation for the puzzling existence of two proteins sharing the same fold and function but not a common ancestor.« less

A Framework to Manage Information Models

NASA Astrophysics Data System (ADS)

Hughes, J. S.; King, T.; Crichton, D.; Walker, R.; Roberts, A.; Thieman, J.

2008-05-01

The Information Model is the foundation on which an Information System is built. It defines the entities to be processed, their attributes, and the relationships that add meaning. The development and subsequent management of the Information Model is the single most significant factor for the development of a successful information system. A framework of tools has been developed that supports the management of an information model with the rigor typically afforded to software development. This framework provides for evolutionary and collaborative development independent of system implementation choices. Once captured, the modeling information can be exported to common languages for the generation of documentation, application databases, and software code that supports both traditional and semantic web applications. This framework is being successfully used for several science information modeling projects including those for the Planetary Data System (PDS), the International Planetary Data Alliance (IPDA), the National Cancer Institute's Early Detection Research Network (EDRN), and several Consultative Committee for Space Data Systems (CCSDS) projects. The objective of the Space Physics Archive Search and Exchange (SPASE) program is to promote collaboration and coordination of archiving activity for the Space Plasma Physics community and ensure the compatibility of the architectures used for a global distributed system and the individual data centers. Over the past several years, the SPASE data model working group has made great progress in developing the SPASE Data Model and supporting artifacts including a data dictionary, XML Schema, and two ontologies. The authors have captured the SPASE Information Model in this framework. This allows the generation of documentation that presents the SPASE Information Model in object-oriented notation including UML class diagrams and class hierarchies. The modeling information can also be exported to semantic web languages such as OWL and RDF and written to XML Metadata Interchange (XMI) files for import into UML tools.

Evolutionary dynamics of an expressed MHC class IIβ locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing.

PubMed

Mulder, Kevin P; Cortazar-Chinarro, Maria; Harris, D James; Crottini, Angelica; Campbell Grant, Evan H; Fleischer, Robert C; Savage, Anna E

2017-11-01

The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa. Copyright © 2017 Elsevier Ltd. All rights reserved.

Information and Biological Revolutions: Global Governance Challenges Summary of a Study Group

DTIC Science & Technology

2000-01-01

instruction and organize the classes. This change will come about slowly and then only if it proves to increase learning in the classroom. See Thomas K...dendrites and to form synaptic connections, then help to maintain and regulate synaptic activity responsible for learning and cognitive functions...testosterone may foster violent behavior is by the promotion of positive illusions about competitive ability . 77 Thus, an evolutionary history of raiding

VERITAS: a Discovery-Class Venus Surface Geology and Geophysics Mission

NASA Technical Reports Server (NTRS)

Freeman, Anthony; Smrekar, Suzanne E.; Hensley, Scott; Wallace, Mark; Sotin, Christophe; Darrach, Murray; Xaypraseuth, Peter; Helbert, Joern; Mazarico, Erwan

2016-01-01

Our understanding of solar system evolution is limited by a great unanswered question: How Earthlike is Venus? We know that these "twin" planets formed with similar bulk composition and size. Yet the evolutionary path Venus followed has diverged from Earth's, in losing its surface water and becoming hotter than Mercury. What led to this? The answer has profound implications for how terrestrial planets become habitable and the potential for life in the universe.

Increasing Supercycle Lengths of Active SU UMa-type Dwarf Novae

NASA Astrophysics Data System (ADS)

Otulakowska-Hypka, M.; Olech, A.

2014-12-01

We present observational evidence that supercycle lengths of the most active SU UMa-type stars are increasing during the past decades. We analyzed a large number of photometric measurements from available archives and found that this effect is generic for this class of stars, independently of their evolutionary status. This finding is in agreement with previous predictions and the most recent work of Patterson et al. (2012) on BK Lyn.

Evolution of the α2-adrenoreceptors in vertebrates: ADRA2D is absent in mammals and crocodiles.

PubMed

Céspedes, Héctor A; Zavala, Kattina; Vandewege, Michael W; Opazo, Juan C

2017-09-01

Evolutionary studies of genes that have been functionally characterized and whose variation has been associated with pathological conditions represent an opportunity to understand the genetic basis of pathologies. α 2 -Adrenoreceptors (ADRA2) are a class of G protein-coupled receptors that regulate several physiological processes including blood pressure, platelet aggregation, insulin secretion, lipolysis, and neurotransmitter release. This gene family has been extensively studied from a molecular/physiological perspective, yet much less is known about its evolutionary history. Accordingly, the goal of this study was to investigate the evolutionary history of α 2 -adrenoreceptors (ADRA2) in vertebrates. Our results show that in addition to the three well-recognized α 2 -adrenoreceptor genes (ADRA2A, ADRA2B and ADRA2C), we recovered a clade that corresponds to the fourth member of the α 2 -adrenoreceptor gene family (ADRA2D). We also recovered a clade that possesses two ADRA2 sequences found in two lamprey species. Furthermore, our results show that mammals and crocodiles are characterized by possessing three α 2 -adrenoreceptor genes, whereas all other vertebrate groups possess the full repertoire of α 2 -adrenoreceptor genes. Among vertebrates ADRA2D seems to be a dispensable gene, as it was lost two independent times during the evolutionary history of the group. Additionally, we found that most examined species possess the most common alleles described for humans; however, there are cases in which non-human mammals possess the alternative variant. Finally, transcript abundance profiles revealed that during the early evolutionary history of gnathostomes, the expression of ADRA2D in different taxonomic groups became specialized to different tissues, but in the ancestor of sarcopterygians this specialization would have been lost. Copyright © 2017 Elsevier Inc. All rights reserved.

Aspiration dynamics of multi-player games in finite populations

PubMed Central

Du, Jinming; Wu, Bin; Altrock, Philipp M.; Wang, Long

2014-01-01

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics. PMID:24598208

Aspiration dynamics of multi-player games in finite populations.

PubMed

Du, Jinming; Wu, Bin; Altrock, Philipp M; Wang, Long

2014-05-06

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics.

48 CFR 211.275-2 - Policy.

Code of Federal Regulations, 2010 CFR

2010-10-01

... that— (1) Contain items in any of the following classes of supply, as defined in DoD 4140.1-R, DoD Supply Chain Materiel Management Regulation, AP1.1.11: (i) Subclass of Class I—Packaged operational... administrative and housekeeping supplies and equipment. (iii) Class IIIP—Packaged petroleum, lubricants, oils...

Measurement and Structural Model Class Separation in Mixture CFA: ML/EM versus MCMC

ERIC Educational Resources Information Center

Depaoli, Sarah

2012-01-01

Parameter recovery was assessed within mixture confirmatory factor analysis across multiple estimator conditions under different simulated levels of mixture class separation. Mixture class separation was defined in the measurement model (through factor loadings) and the structural model (through factor variances). Maximum likelihood (ML) via the…

Cyclic Peptides Arising by Evolutionary Parallelism via Asparaginyl-Endopeptidase–Mediated Biosynthesis[C][W

PubMed Central

Mylne, Joshua S.; Chan, Lai Yue; Chanson, Aurelie H.; Daly, Norelle L.; Schaefer, Hanno; Bailey, Timothy L.; Nguyencong, Philip; Cascales, Laura; Craik, David J.

2012-01-01

The cyclic miniprotein Momordica cochinchinensis Trypsin Inhibitor II (MCoTI-II) (34 amino acids) is a potent trypsin inhibitor (TI) and a favored scaffold for drug design. We have cloned the corresponding genes and determined that each precursor protein contains a tandem series of cyclic TIs terminating with the more commonly known, and potentially ancestral, acyclic TI. Expression of the precursor protein in Arabidopsis thaliana showed that production of the cyclic TIs, but not the terminal acyclic TI, depends on asparaginyl endopeptidase (AEP) for maturation. The nature of their repetitive sequences and the almost identical structures of emerging TIs suggest these cyclic peptides evolved by internal gene amplification associated with recruitment of AEP for processing between domain repeats. This is the third example of similar AEP-mediated processing of a class of cyclic peptides from unrelated precursor proteins in phylogenetically distant plant families. This suggests that production of cyclic peptides in angiosperms has evolved in parallel using AEP as a constraining evolutionary channel. We believe this is evolutionary evidence that, in addition to its known roles in proteolysis, AEP is especially suited to performing protein cyclization. PMID:22822203

The genomic landscape of rapid repeated evolutionary ...

EPA Pesticide Factsheets

Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediatinggenes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversityhas likely been a crucial substrate for selective sweeps to propel rapid adaptation. This manuscript describes genomic evaluations that contribute to our understanding of the ecological and evolutionary risks associated with chronic contaminant exposures to wildlife populations. Here, we assessed genetic patterns associated with long-term response to an important class of highly toxic environmental pollutants. Specifically, chemical-specific tolerance has rapidly and repeatedly evolved in an estuarine fish species resident to estuaries of the Atlantic U.S. coast. We used laboratory studies to ch

Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes.

PubMed

Sharma, S; Raina, S N

2005-01-01

A major component of the plant nuclear genome is constituted by different classes of repetitive DNA sequences. The structural, functional and evolutionary aspects of the satellite repetitive DNA families, and their organization in the chromosomes is reviewed. The tandem satellite DNA sequences exhibit characteristic chromosomal locations, usually at subtelomeric and centromeric regions. The repetitive DNA family(ies) may be widely distributed in a taxonomic family or a genus, or may be specific for a species, genome or even a chromosome. They may acquire large-scale variations in their sequence and copy number over an evolutionary time-scale. These features have formed the basis of extensive utilization of repetitive sequences for taxonomic and phylogenetic studies. Hybrid polyploids have especially proven to be excellent models for studying the evolution of repetitive DNA sequences. Recent studies explicitly show that some repetitive DNA families localized at the telomeres and centromeres have acquired important structural and functional significance. The repetitive elements are under different evolutionary constraints as compared to the genes. Satellite DNA families are thought to arise de novo as a consequence of molecular mechanisms such as unequal crossing over, rolling circle amplification, replication slippage and mutation that constitute "molecular drive". Copyright 2005 S. Karger AG, Basel.

A Pareto-based Ensemble with Feature and Instance Selection for Learning from Multi-Class Imbalanced Datasets.

PubMed

Fernández, Alberto; Carmona, Cristobal José; José Del Jesus, María; Herrera, Francisco

2017-09-01

Imbalanced classification is related to those problems that have an uneven distribution among classes. In addition to the former, when instances are located into the overlapped areas, the correct modeling of the problem becomes harder. Current solutions for both issues are often focused on the binary case study, as multi-class datasets require an additional effort to be addressed. In this research, we overcome these problems by carrying out a combination between feature and instance selections. Feature selection will allow simplifying the overlapping areas easing the generation of rules to distinguish among the classes. Selection of instances from all classes will address the imbalance itself by finding the most appropriate class distribution for the learning task, as well as possibly removing noise and difficult borderline examples. For the sake of obtaining an optimal joint set of features and instances, we embedded the searching for both parameters in a Multi-Objective Evolutionary Algorithm, using the C4.5 decision tree as baseline classifier in this wrapper approach. The multi-objective scheme allows taking a double advantage: the search space becomes broader, and we may provide a set of different solutions in order to build an ensemble of classifiers. This proposal has been contrasted versus several state-of-the-art solutions on imbalanced classification showing excellent results in both binary and multi-class problems.

Evolutionary Diversifaction of Aminopeptidase N in Lepidoptera by Conserved Clade-specific Amino Acid Residues

PubMed Central

Hughes, Austin L.

2015-01-01

Members of the aminopepidase N (APN) gene family of the insect order Lepidoptera (moths and butterflies) bind the naturally insecticidal Cry toxins produced by the bacterium Bacillus thuringiensis. Phylogenetic analysis of amino acid sequences of seven lepidopteran APN classes provided strong support for the hypothesis that lepidopteran APN2 class arose by gene duplication prior to the most recent common ancestor of Lepidoptera and Diptera. The Cry toxin-binding region (BR) of lepidopteran and dipteran APNs was subject to stronger purifying selection within APN classes than was the remainder of the molecule, reflecting conservation of catalytic site and adjoining residues within the BR. Of lepidopteran APN classes, APN2, APN6, and APN8 showed the strongest evidence of functional specialization, both in expression patterns and in the occurrence of conserved derived amino acid residues. The latter three APN classes also shared a convergently evolved conserved residue close to the catalytic site. APN8 showed a particularly strong tendency towards class-specific conserved residues, including one of the catalytic site residues in the BR and ten others in close vicinity to the catalytic site residues. The occurrence of class-specific sequences along with the conservation of enzymatic function is consistent with the hypothesis that the presence of Cry toxins in the environment has been a factor shaping the evolution of this multi-gene family. PMID:24675701

Summary and recommendations on nuclear electric propulsion technology for the space exploration initiative

NASA Technical Reports Server (NTRS)

Doherty, Michael P.; Holcomb, Robert S.

1993-01-01

A project in Nuclear Electric Propulsion (NEP) technology is being established to develop the NEP technologies needed for advanced propulsion systems. A paced approach has been suggested which calls for progressive development of NEP component and subsystem level technologies. This approach will lead to major facility testing to achieve TRL-5 for megawatt NEP for SEI mission applications. This approach is designed to validate NEP power and propulsion technologies from kilowatt class to megawatt class ratings. Such a paced approach would have the benefit of achieving the development, testing, and flight of NEP systems in an evolutionary manner. This approach may also have the additional benefit of synergistic application with SEI extraterrestrial surface nuclear power applications.

Evolution of the tRNALeu (UAA) Intron and Congruence of Genetic Markers in Lichen-Symbiotic Nostoc

PubMed Central

Kaasalainen, Ulla; Olsson, Sanna; Rikkinen, Jouko

2015-01-01

The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants. In lichen symbiotic Nostoc, the P6b stem-loop of trnL intron always involves one of two different repeat motifs, either Class I or Class II, both with unresolved evolutionary histories. Here we attempt to resolve the complex evolution of the two different trnL P6b region types. Our analysis indicates that the Class II repeat motif most likely appeared first and that independent and unidirectional shifts to the Class I motif have since taken place repeatedly. In addition, we compare our results with those obtained with other genetic markers and find strong evidence of recombination in the 16S rRNA gene, a marker widely used in phylogenetic studies on Bacteria. The congruence of the different genetic markers is successfully evaluated with the recently published software Saguaro, which has not previously been utilized in comparable studies. PMID:26098760

Evolution of the tRNALeu (UAA) Intron and Congruence of Genetic Markers in Lichen-Symbiotic Nostoc.

PubMed

Kaasalainen, Ulla; Olsson, Sanna; Rikkinen, Jouko

2015-01-01

The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants. In lichen symbiotic Nostoc, the P6b stem-loop of trnL intron always involves one of two different repeat motifs, either Class I or Class II, both with unresolved evolutionary histories. Here we attempt to resolve the complex evolution of the two different trnL P6b region types. Our analysis indicates that the Class II repeat motif most likely appeared first and that independent and unidirectional shifts to the Class I motif have since taken place repeatedly. In addition, we compare our results with those obtained with other genetic markers and find strong evidence of recombination in the 16S rRNA gene, a marker widely used in phylogenetic studies on Bacteria. The congruence of the different genetic markers is successfully evaluated with the recently published software Saguaro, which has not previously been utilized in comparable studies.

Automated simultaneous multiple feature classification of MTI data

NASA Astrophysics Data System (ADS)

Harvey, Neal R.; Theiler, James P.; Balick, Lee K.; Pope, Paul A.; Szymanski, John J.; Perkins, Simon J.; Porter, Reid B.; Brumby, Steven P.; Bloch, Jeffrey J.; David, Nancy A.; Galassi, Mark C.

2002-08-01

Los Alamos National Laboratory has developed and demonstrated a highly capable system, GENIE, for the two-class problem of detecting a single feature against a background of non-feature. In addition to the two-class case, however, a commonly encountered remote sensing task is the segmentation of multispectral image data into a larger number of distinct feature classes or land cover types. To this end we have extended our existing system to allow the simultaneous classification of multiple features/classes from multispectral data. The technique builds on previous work and its core continues to utilize a hybrid evolutionary-algorithm-based system capable of searching for image processing pipelines optimized for specific image feature extraction tasks. We describe the improvements made to the GENIE software to allow multiple-feature classification and describe the application of this system to the automatic simultaneous classification of multiple features from MTI image data. We show the application of the multiple-feature classification technique to the problem of classifying lava flows on Mauna Loa volcano, Hawaii, using MTI image data and compare the classification results with standard supervised multiple-feature classification techniques.

Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing.

PubMed

Stiebens, Victor A; Merino, Sonia E; Chain, Frédéric J J; Eizaguirre, Christophe

2013-04-30

In evolutionary and conservation biology, parasitism is often highlighted as a major selective pressure. To fight against parasites and pathogens, genetic diversity of the immune genes of the major histocompatibility complex (MHC) are particularly important. However, the extensive degree of polymorphism observed in these genes makes it difficult to conduct thorough population screenings. We utilized a genotyping protocol that uses 454 amplicon sequencing to characterize the MHC class I in the endangered loggerhead sea turtle (Caretta caretta) and to investigate their evolution at multiple relevant levels of organization. MHC class I genes revealed signatures of trans-species polymorphism across several reptile species. In the studied loggerhead turtle individuals, it results in the maintenance of two ancient allelic lineages. We also found that individuals carrying an intermediate number of MHC class I alleles are larger than those with either a low or high number of alleles. Multiple modes of evolution seem to maintain MHC diversity in the loggerhead turtles, with relatively high polymorphism for an endangered species.

Time-Dependent Rate Phenomenon in Viruses

PubMed Central

Aiewsakun, Pakorn

2016-01-01

ABSTRACT Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses. IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies. PMID:27252529

Bryozoans are returning home: recolonization of freshwater ecosystems inferred from phylogenetic relationships.

PubMed

Koletić, Nikola; Novosel, Maja; Rajević, Nives; Franjević, Damjan

2015-01-01

Bryozoans are aquatic invertebrates that inhabit all types of aquatic ecosystems. They are small animals that form large colonies by asexual budding. Colonies can reach the size of several tens of centimeters, while individual units within a colony are the size of a few millimeters. Each individual within a colony works as a separate zooid and is genetically identical to each other individual within the same colony. Most freshwater species of bryozoans belong to the Phylactolaemata class, while several species that tolerate brackish water belong to the Gymnolaemata class. Tissue samples for this study were collected in the rivers of Adriatic and Danube basin and in the wetland areas in the continental part of Croatia (Europe). Freshwater and brackish taxons of bryozoans were genetically analyzed for the purpose of creating phylogenetic relationships between freshwater and brackish taxons of the Phylactolaemata and Gymnolaemata classes and determining the role of brackish species in colonizing freshwater and marine ecosystems. Phylogenetic relationships inferred on the genes for 18S rRNA, 28S rRNA, COI, and ITS2 region confirmed Phylactolaemata bryozoans as radix bryozoan group. Phylogenetic analysis proved Phylactolaemata bryozoan's close relations with taxons from Phoronida phylum as well as the separation of the Lophopodidae family from other families within the Plumatellida genus. Comparative analysis of existing knowledge about the phylogeny of bryozoans and the expansion of known evolutionary hypotheses is proposed with the model of settlement of marine and freshwater ecosystems by the bryozoans group during their evolutionary past. In this case study, brackish bryozoan taxons represent a link for this ecological phylogenetic hypothesis. Comparison of brackish bryozoan species Lophopus crystallinus and Conopeum seurati confirmed a dual colonization of freshwater ecosystems throughout evolution of this group of animals.

Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies.

PubMed

Gangaiah, Dharanesh; Spinola, Stanley M

2016-12-01

Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities.

Review Guidelines for Software Languages for use in Nuclear Power Plant Safety Systems

DTIC Science & Technology

1997-10-01

desirable to segregate base classes from derived classes. Review is facilitated and safety is enhanced if project-specific guidance is provided on the... Segregate base from derived classes. In C++, it is desirable to segregate base classes from derived classes. 4.4.1.8 Minimizing Use of Literals...memory utilization. At the lowest level are base attributes, i.e., attributes xv NUREG/CR-6463 Rev. 1 sufficiently specific to define guidelines. An

Thematic accuracy of the National Land Cover Database (NLCD) 2001 land cover for Alaska

USGS Publications Warehouse

Selkowitz, D.J.; Stehman, S.V.

2011-01-01

The National Land Cover Database (NLCD) 2001 Alaska land cover classification is the first 30-m resolution land cover product available covering the entire state of Alaska. The accuracy assessment of the NLCD 2001 Alaska land cover classification employed a geographically stratified three-stage sampling design to select the reference sample of pixels. Reference land cover class labels were determined via fixed wing aircraft, as the high resolution imagery used for determining the reference land cover classification in the conterminous U.S. was not available for most of Alaska. Overall thematic accuracy for the Alaska NLCD was 76.2% (s.e. 2.8%) at Level II (12 classes evaluated) and 83.9% (s.e. 2.1%) at Level I (6 classes evaluated) when agreement was defined as a match between the map class and either the primary or alternate reference class label. When agreement was defined as a match between the map class and primary reference label only, overall accuracy was 59.4% at Level II and 69.3% at Level I. The majority of classification errors occurred at Level I of the classification hierarchy (i.e., misclassifications were generally to a different Level I class, not to a Level II class within the same Level I class). Classification accuracy was higher for more abundant land cover classes and for pixels located in the interior of homogeneous land cover patches. ?? 2011.

Extrapolating Weak Selection in Evolutionary Games

PubMed Central

Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

2013-01-01

In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species

PubMed Central

Hung, Li-Yuan; Chen, Yen-Ju; Mai, Te-Lun; Chen, Chia-Ying; Yang, Min-Yu; Chiang, Tai-Wei; Wang, Yi-Da

2018-01-01

Abstract Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization. PMID:29294013

Molecular Evolution of the Non-Coding Eosinophil Granule Ontogeny Transcript

PubMed Central

Rose, Dominic; Stadler, Peter F.

2011-01-01

Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs). The evolutionary history of mlncRNAs is still largely uncharted territory. In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT), an experimentally confirmed representative of an abundant class of totally intronic non-coding transcripts (TINs). EGOT is located antisense to an intron of the ITPR1 gene. We computationally identify putative EGOT orthologs in the genomes of 32 different amniotes, including orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans, as well as putative candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyze patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, may be present throughout the placental mammals, but most likely dates back even further. We demonstrate here for the first time that the whole EGOT locus is highly structured, containing several evolutionary conserved, and thermodynamic stable secondary structures. Our analyses allow us to postulate novel functional roles of a hitherto poorly understood region at the intron of EGO-B which is highly conserved at the sequence level. The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element. PMID:22303364

The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria.

PubMed

Ji, Boyang; Zhang, Sheng-Da; Zhang, Wei-Jia; Rouy, Zoe; Alberto, François; Santini, Claire-Lise; Mangenot, Sophie; Gagnot, Séverine; Philippe, Nadège; Pradel, Nathalie; Zhang, Lichen; Tempel, Sébastien; Li, Ying; Médigue, Claudine; Henrissat, Bernard; Coutinho, Pedro M; Barbe, Valérie; Talla, Emmanuel; Wu, Long-Fei

2017-03-01

Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared with other bacterial taxonomic groups remain to be illustrated. Here, we analysed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1. Detailed analyses of the ribosomal proteins and whole proteomes of 390 genomes reveal that, among the Proteobacteria analysed, only MO-1 and MC-1 have coding sequences (CDSs) with a similarly high proportion of origins from Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria and Gammaproteobacteria. Interestingly, a comparative metabolic network analysis with anoxic network enzymes from sequenced MTB and non-MTB successfully allows the eventual prediction of an organism with a metabolic profile compatible for magnetosome production. Altogether, our genomic analysis reveals multiple origins of MO-1 and M. marinus MC-1 genomes and suggests a metabolism-restriction model for explaining whether a bacterium could become an MTB upon acquisition of magnetosome encoding genes. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Families of Nuclear Receptors in Vertebrate Models: Characteristic and Comparative Toxicological Perspective

NASA Astrophysics Data System (ADS)

Zhao, Yanbin; Zhang, Kun; Giesy, John P.; Hu, Jianying

2015-02-01

Various synthetic chemicals are ligands for nuclear receptors (NRs) and can cause adverse effects in vertebrates mediated by NRs. While several model vertebrates, such as mouse, chicken, western clawed frog and zebrafish, are widely used in toxicity testing, few NRs have been well described for most of these classes. In this report, NRs in genomes of 12 vertebrates are characterized via bioinformatics approaches. Although numbers of NRs varied among species, with 40-42 genes in birds to 66-74 genes in teleost fishes, all NRs had clear homologs in human and could be categorized into seven subfamilies defined as NR0B-NR6A. Phylogenetic analysis revealed conservative evolutionary relationships for most NRs, which were consistent with traditional morphology-based systematics, except for some exceptions in Dolphin (Tursiops truncatus). Evolution of PXR and CAR exhibited unexpected multiple patterns and the existence of CAR possibly being traced back to ancient lobe-finned fishes and tetrapods (Sarcopterygii). Compared to the more conservative DBD of NRs, sequences of LBD were less conserved: Sequences of THRs, RARs and RXRs were >=90% similar to those of the human, ERs, AR, GR, ERRs and PPARs were more variable with similarities of 60%-100% and PXR, CAR, DAX1 and SHP were least conserved among species.

Methods for estimating dispersal probabilities and related parameters using marked animals

USGS Publications Warehouse

Bennetts, R.E.; Nichols, J.D.; Pradel, R.; Lebreton, J.D.; Kitchens, W.M.; Clobert, Jean; Danchin, Etienne; Dhondt, Andre A.; Nichols, James D.

2001-01-01

Deriving valid inferences about the causes and consequences of dispersal from empirical studies depends largely on our ability reliably to estimate parameters associated with dispersal. Here, we present a review of the methods available for estimating dispersal and related parameters using marked individuals. We emphasize methods that place dispersal in a probabilistic framework. In this context, we define a dispersal event as a movement of a specified distance or from one predefined patch to another, the magnitude of the distance or the definition of a `patch? depending on the ecological or evolutionary question(s) being addressed. We have organized the chapter based on four general classes of data for animals that are captured, marked, and released alive: (1) recovery data, in which animals are recovered dead at a subsequent time, (2) recapture/resighting data, in which animals are either recaptured or resighted alive on subsequent sampling occasions, (3) known-status data, in which marked animals are reobserved alive or dead at specified times with probability 1.0, and (4) combined data, in which data are of more than one type (e.g., live recapture and ring recovery). For each data type, we discuss the data required, the estimation techniques, and the types of questions that might be addressed from studies conducted at single and multiple sites.

Neither biased sex ratio nor spatial segregation of the sexes in the subtropical dioecious tree Eurycorymbus cavaleriei (Sapindaceae).

PubMed

Gao, Puxin; Kang, Ming; Wang, Jing; Ye, Qigang; Huang, Hongwen

2009-06-01

Knowledge of sex ratio and spatial distribution of males and females of dioecious species is both of evolutionary interest and of crucial importance for biological conservation. Eurycorymbus cavaleriei, the only species in the genus Eurycorymbus (Sapindaceae), is a dioecious tree endemic to subtropical montane forest in South China. Sex ratios were investigated in 15 natural populations for the two defined ages (young and old). Spatial distribution of males and females was further studied in six large populations occurring in different habitats (fragmented and continuous). The study revealed a slight trend of male-biased sex ratio in both ages of E. cavaleriei, but sex ratio of most populations (13 out of 15) did not display statistically significant deviation from equality. All of the four significantly male-biased populations in the young class shifted to equality or even female-biased. The Ripley's K analysis of the distribution of males with respect to females suggested that individuals of the opposite sexes were more randomly distributed rather than spatially structured. These results suggest that the male-biased sex ratio in E. cavaleriei may result from the precocity of males and habitat heterogeneity. The sex ratio and the sex spatial distribution pattern are unlikely to constitute a serious threat to the survival of the species.

Origin and Evolution of the Sponge Aggregation Factor Gene Family.

PubMed

Grice, Laura F; Gauthier, Marie E A; Roper, Kathrein E; Fernàndez-Busquets, Xavier; Degnan, Sandie M; Degnan, Bernard M

2017-05-01

Although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. Here, we characterize the Aggregation Factor (AF) gene family, which encodes putative allorecognition factors in the demosponge Amphimedon queenslandica, and trace its evolution across 24 sponge (Porifera) species. The AF locus in Amphimedon is comprised of a cluster of five similar genes that encode Calx-beta and Von Willebrand domains and a newly defined Wreath domain, and are highly polymorphic. Further AF variance appears to be generated through individualistic patterns of RNA editing. The AF gene family varies between poriferans, with protein sequences and domains diagnostic of the AF family being present in Amphimedon and other demosponges, but absent from other sponge classes. Within the demosponges, AFs vary widely with no two species having the same AF repertoire or domain organization. The evolution of AFs suggests that their diversification occurs via high allelism, and the continual and rapid gain, loss and shuffling of domains over evolutionary time. Given the marked differences in metazoan allorecognition genes, we propose the rapid evolution of AFs in sponges provides a model for understanding the extensive diversification of self-nonself recognition systems in the animal kingdom. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

RBF neural network based PI pitch controller for a class of 5-MW wind turbines using particle swarm optimization algorithm.

PubMed

Poultangari, Iman; Shahnazi, Reza; Sheikhan, Mansour

2012-09-01

In order to control the pitch angle of blades in wind turbines, commonly the proportional and integral (PI) controller due to its simplicity and industrial usability is employed. The neural networks and evolutionary algorithms are tools that provide a suitable ground to determine the optimal PI gains. In this paper, a radial basis function (RBF) neural network based PI controller is proposed for collective pitch control (CPC) of a 5-MW wind turbine. In order to provide an optimal dataset to train the RBF neural network, particle swarm optimization (PSO) evolutionary algorithm is used. The proposed method does not need the complexities, nonlinearities and uncertainties of the system under control. The simulation results show that the proposed controller has satisfactory performance. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.

An ecoimmunological approach to study evolutionary and ancient links between coagulation, complement and Innate immunity

PubMed Central

Kasetty, Gopinath; Alyafei, Saud; Smeds, Emanuel; Salo-Ahen, Outi M. H.; Hansson, Stefan R.; Egesten, Arne; Herwald, Heiko

2018-01-01

ABSTRACT Coagulation, complement, and innate immunity are tightly interwoven and form an alliance that can be traced back to early eukaryotic evolution. Here we employed an ecoimmunological approach using Tissue Factor Pathway Inhibitor (TFPI)-1-derived peptides from the different classes of vertebrates (i.e. fish, reptile, bird, and mammals) and tested whether they can boost killing of various human bacterial pathogens in plasma. We found signs of species-specific conservation and diversification during evolution in these peptides that significantly impact their antibacterial activity. Though all peptides tested executed bactericidal activity in mammalian plasma (with the exception of rodents), no killing was observed in plasma from birds, reptiles, and fish, pointing to a crucial role for the classical pathway of the complement system. We also observed an interference of these peptides with the human intrinsic pathway of coagulation though, unlike complement activation, this mechanism appears not to be evolutionary conserved. PMID:29473457

Natural Killer T Cells: An Ecological Evolutionary Developmental Biology Perspective

PubMed Central

Kumar, Amrendra; Suryadevara, Naveenchandra; Hill, Timothy M.; Bezbradica, Jelena S.; Van Kaer, Luc; Joyce, Sebastian

2017-01-01

Type I natural killer T (NKT) cells are innate-like T lymphocytes that recognize glycolipid antigens presented by the MHC class I-like protein CD1d. Agonistic activation of NKT cells leads to rapid pro-inflammatory and immune modulatory cytokine and chemokine responses. This property of NKT cells, in conjunction with their interactions with antigen-presenting cells, controls downstream innate and adaptive immune responses against cancers and infectious diseases, as well as in several inflammatory disorders. NKT cell properties are acquired during development in the thymus and by interactions with the host microbial consortium in the gut, the nature of which can be influenced by NKT cells. This latter property, together with the role of the host microbiota in cancer therapy, necessitates a new perspective. Hence, this review provides an initial approach to understanding NKT cells from an ecological evolutionary developmental biology (eco-evo-devo) perspective. PMID:29312339

Probing the Molecular Outflows of the Coldest Known Object in the Universe: The Boomerang Nebula

NASA Astrophysics Data System (ADS)

Sahai, Raghvendra; Vlemmings, W.; Nyman, L. A.; Huggins, P.

2012-05-01

The Boomerang Nebula is the coldest known object in the Universe, and an extreme member of the class of Pre-Planetary Nebulae, objects which represent a short-lived transitional phase between the AGB and Planetary Nebula evolutionary stages. The Boomerang's estimated prodigious mass-loss rate (0.001 solar masses/year) and low-luminosity (300 Lsun) lack an explanation in terms of current paradigms for dusty mass-loss and standard evolutionary theory of intermediate-mass stars. Single-dish CO J=1-0 observations (with a 45 arcsec beam) show that the high-speed outflow in this object has cooled to a temperature significantly below the temperature of the cosmic background radiation. We report on our high-resolution ALMA mapping of the CO lines in this ultra-cold nebula to determine the origin of these extreme conditions and robustly confirm current estimates of the fundamental physical properties of its ultra-cold outflow.

Natural Killer T Cells: An Ecological Evolutionary Developmental Biology Perspective.

PubMed

Kumar, Amrendra; Suryadevara, Naveenchandra; Hill, Timothy M; Bezbradica, Jelena S; Van Kaer, Luc; Joyce, Sebastian

2017-01-01

Type I natural killer T (NKT) cells are innate-like T lymphocytes that recognize glycolipid antigens presented by the MHC class I-like protein CD1d. Agonistic activation of NKT cells leads to rapid pro-inflammatory and immune modulatory cytokine and chemokine responses. This property of NKT cells, in conjunction with their interactions with antigen-presenting cells, controls downstream innate and adaptive immune responses against cancers and infectious diseases, as well as in several inflammatory disorders. NKT cell properties are acquired during development in the thymus and by interactions with the host microbial consortium in the gut, the nature of which can be influenced by NKT cells. This latter property, together with the role of the host microbiota in cancer therapy, necessitates a new perspective. Hence, this review provides an initial approach to understanding NKT cells from an ecological evolutionary developmental biology (eco-evo-devo) perspective.

Toward understanding the evolution of vertebrate gene regulatory networks: comparative genomics and epigenomic approaches.

PubMed

Martinez-Morales, Juan R

2016-07-01

Vertebrates, as most animal phyla, originated >500 million years ago during the Cambrian explosion, and progressively radiated into the extant classes. Inferring the evolutionary history of the group requires understanding the architecture of the developmental programs that constrain the vertebrate anatomy. Here, I review recent comparative genomic and epigenomic studies, based on ChIP-seq and chromatin accessibility, which focus on the identification of functionally equivalent cis-regulatory modules among species. This pioneer work, primarily centered in the mammalian lineage, has set the groundwork for further studies in representative vertebrate and chordate species. Mapping of active regulatory regions across lineages will shed new light on the evolutionary forces stabilizing ancestral developmental programs, as well as allowing their variation to sustain morphological adaptations on the inherited vertebrate body plan. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The cultural evolution of emergent group-level traits.

PubMed

Smaldino, Paul E

2014-06-01

Many of the most important properties of human groups - including properties that may give one group an evolutionary advantage over another - are properly defined only at the level of group organization. Yet at present, most work on the evolution of culture has focused solely on the transmission of individual-level traits. I propose a conceptual extension of the theory of cultural evolution, particularly related to the evolutionary competition between cultural groups. The key concept in this extension is the emergent group-level trait. This type of trait is characterized by the structured organization of differentiated individuals and constitutes a unit of selection that is qualitatively different from selection on groups as defined by traditional multilevel selection (MLS) theory. As a corollary, I argue that the traditional focus on cooperation as the defining feature of human societies has missed an essential feature of cooperative groups. Traditional models of cooperation assume that interacting with one cooperator is equivalent to interacting with any other. However, human groups involve differential roles, meaning that receiving aid from one individual is often preferred to receiving aid from another. In this target article, I discuss the emergence and evolution of group-level traits and the implications for the theory of cultural evolution, including ramifications for the evolution of human cooperation, technology, and cultural institutions, and for the equivalency of multilevel selection and inclusive fitness approaches.

Engineering the evolution of self-organizing behaviors in swarm robotics: a case study.

PubMed

Trianni, Vito; Nolfi, Stefano

2011-01-01

Evolutionary robotics (ER) is a powerful approach for the automatic synthesis of robot controllers, as it requires little a priori knowledge about the problem to be solved in order to obtain good solutions. This is particularly true for collective and swarm robotics, in which the desired behavior of the group is an indirect result of the control and communication rules followed by each individual. However, the experimenter must make several arbitrary choices in setting up the evolutionary process, in order to define the correct selective pressures that can lead to the desired results. In some cases, only a deep understanding of the obtained results can point to the critical aspects that constrain the system, which can be later modified in order to re-engineer the evolutionary process towards better solutions. In this article, we discuss the problem of engineering the evolutionary machinery that can lead to the desired result in the swarm robotics context. We also present a case study about self-organizing synchronization in a swarm of robots, in which some arbitrarily chosen properties of the communication system hinder the scalability of the behavior to large groups. We show that by modifying the communication system, artificial evolution can synthesize behaviors that scale properly with the group size.

Computability, Gödel's incompleteness theorem, and an inherent limit on the predictability of evolution

PubMed Central

Day, Troy

2012-01-01

The process of evolutionary diversification unfolds in a vast genotypic space of potential outcomes. During the past century, there have been remarkable advances in the development of theory for this diversification, and the theory's success rests, in part, on the scope of its applicability. A great deal of this theory focuses on a relatively small subset of the space of potential genotypes, chosen largely based on historical or contemporary patterns, and then predicts the evolutionary dynamics within this pre-defined set. To what extent can such an approach be pushed to a broader perspective that accounts for the potential open-endedness of evolutionary diversification? There have been a number of significant theoretical developments along these lines but the question of how far such theory can be pushed has not been addressed. Here a theorem is proven demonstrating that, because of the digital nature of inheritance, there are inherent limits on the kinds of questions that can be answered using such an approach. In particular, even in extremely simple evolutionary systems, a complete theory accounting for the potential open-endedness of evolution is unattainable unless evolution is progressive. The theorem is closely related to Gödel's incompleteness theorem, and to the halting problem from computability theory. PMID:21849390

Evolutionary institutionalism.

PubMed

Fürstenberg, Dr Kai

Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

Deciphering the evolutionary history of open and closed mitosis.

PubMed

Sazer, Shelley; Lynch, Michael; Needleman, Daniel

2014-11-17

The origin of the nucleus at the prokaryote-to-eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the 'closed' mitosis of some yeasts, but loses its integrity in the 'open' mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and documenting patterns of mitotic nuclear variation within and among species and mapping them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

The utility of rat jejunal permeability for biopharmaceutics classification system.

PubMed

Zakeri-Milani, Parvin; Valizadeh, Hadi; Tajerzadeh, Hosnieh; Islambulchilar, Ziba

2009-12-01

The biopharmaceutical classification system has been developed to provide a scientific approach for classifying drug compounds based on their dose/solubility ratio and human intestinal permeability. Therefore in this study a new classification is presented, which is based on a correlation between rat and human intestinal permeability values. In situ technique in rat jejunum was used to determine the effective intestinal permeability of tested drugs. Then three dimensionless parameters--dose number, absorption number, and dissolution number (D(o), A(n), and D(n))--were calculated for each drug. Four classes of drugs were defined, that is, class I, D(0) < 0.5, P(eff(rat)) > 5.09 x 10(-5) cm/s; class II, D(o) > 1, P(eff(rat)) > 5.09 x 10( -5) cm/s; class III, D(0) < 0.5, P(eff(rat)) < 4.2 x 10(-5) cm/s; and class IV, D(o) > 1, P(eff(rat)) < 4.2 x 10(-5) cm/s. A region of borderline drugs (0.5 < D(o) < 1, 4.2 x 10(-5) < P(eff(rat)) < 5.09 x 10(-5) cm/s) was also defined. According to obtained results and proposed classification for drugs, it is concluded that drugs could be categorized correctly based on dose number and their intestinal permeability values in rat model using single-pass intestinal perfusion technique. This classification enables us to remark defined characteristics for intestinal absorption of all four classes using suitable cutoff points for both dose number and rat effective intestinal permeability values.

Young stellar population and ongoing star formation in the H II complex Sh2-252

NASA Astrophysics Data System (ADS)

Jose, Jessy; Pandey, A. K.; Samal, M. R.; Ojha, D. K.; Ogura, K.; Kim, J. S.; Kobayashi, N.; Goyal, A.; Chauhan, N.; Eswaraiah, C.

2013-07-01

In this paper, an extensive survey of the star-forming complex Sh2-252 has been undertaken with an aim to explore its hidden young stellar population as well as to understand the structure and star formation history for the first time. This complex is composed of five prominent embedded clusters associated with the subregions A, C, E, NGC 2175s and Teu 136. We used Two Micron All Sky Survey-near-infrared and Spitzer-Infrared Array Camera, Multiband Imaging Photometer for Spitzer photometry to identify and classify the young stellar objects (YSOs) by their infrared (IR) excess emission. Using the IR colour-colour criteria, we identified 577 YSOs, of which, 163 are Class I, 400 are Class II and 14 are transition disc YSOs, suggesting a moderately rich number of YSOs in this complex. Spatial distribution of the candidate YSOs shows that they are mostly clustered around the subregions in the western half of the complex, suggesting enhanced star formation activity towards its west. Using the spectral energy distribution and optical colour-magnitude diagram-based age analyses, we derived probable evolutionary status of the subregions of Sh2-252. Our analysis shows that the region A is the youngest (˜0.5 Myr), the regions B, C and E are of similar evolutionary stage (˜1-2 Myr) and the clusters NGC 2175s and Teu 136 are slightly evolved (˜2-3 Myr). Morphology of the region in the 1.1 mm map shows a semicircular shaped molecular shell composed of several clumps and YSOs bordering the western ionization front of Sh2-252. Our analyses suggest that next generation star formation is currently under way along this border and that possibly fragmentation of the matter collected during the expansion of the H II region as one of the major processes is responsible for such stars. We observed the densest concentration of YSOs (mostly Class I, ˜0.5 Myr) at the western outskirts of the complex, within a molecular clump associated with water and methanol masers and we suggest that it is indeed a site of cluster formation at a very early evolutionary stage, sandwiched between the two relatively evolved CH II regions A and B.

14 CFR 93.350 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... AND GENERAL OPERATING RULES SPECIAL AIR TRAFFIC RULES New York Class B Airspace Hudson River and East... Exclusion, as defined in paragraph (d) of this section, from one end to the other. (c) New York Class B... the LGA VOR/DME 6-mile arc to the north tip of Roosevelt Island. (d) New York Class B airspace Hudson...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2012 CFR

2012-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2010 CFR

2010-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2014 CFR

2014-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2011 CFR

2011-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

49 CFR 216.15 - Special notice for repairs-track class.

Code of Federal Regulations, 2013 CFR

2013-10-01

... requirements for the class at which the track is being operated, as defined in the Track Safety Standards (49 CFR part 213), he notifies the railroad in writing that the track is being lowered in class and that... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION SPECIAL NOTICE AND EMERGENCY ORDER PROCEDURES: RAILROAD TRACK...

Risk Classification and Risk-based Safety and Mission Assurance

NASA Technical Reports Server (NTRS)

Leitner, Jesse A.

2014-01-01

Recent activities to revamp and emphasize the need to streamline processes and activities for Class D missions across the agency have led to various interpretations of Class D, including the lumping of a variety of low-cost projects into Class D. Sometimes terms such as Class D minus are used. In this presentation, mission risk classifications will be traced to official requirements and definitions as a measure to ensure that projects and programs align with the guidance and requirements that are commensurate for their defined risk posture. As part of this, the full suite of risk classifications, formal and informal will be defined, followed by an introduction to the new GPR 8705.4 that is currently under review.GPR 8705.4 lays out guidance for the mission success activities performed at the Classes A-D for NPR 7120.5 projects as well as for projects not under NPR 7120.5. Furthermore, the trends in stepping from Class A into higher risk posture classifications will be discussed. The talk will conclude with a discussion about risk-based safety and mission assuranceat GSFC.

Ligand Recognition by A-Class Eph Receptors: Crystal Structures of the EphA2 Ligand-Binding Domain and the EphA2/ephrin-A1 Complex

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

Himanen, J.; Goldgur, Y; Miao, H

2009-01-01

Ephrin (Eph) receptor tyrosine kinases fall into two subclasses (A and B) according to preferences for their ephrin ligands. All published structural studies of Eph receptor/ephrin complexes involve B-class receptors. Here, we present the crystal structures of an A-class complex between EphA2 and ephrin-A1 and of unbound EphA2. Although these structures are similar overall to their B-class counterparts, they reveal important differences that define subclass specificity. The structures suggest that the A-class Eph receptor/ephrin interactions involve smaller rearrangements in the interacting partners, better described by a 'lock-and-key'-type binding mechanism, in contrast to the 'induced fit' mechanism defining the B-class molecules.more » This model is supported by structure-based mutagenesis and by differential requirements for ligand oligomerization by the two subclasses in cell-based Eph receptor activation assays. Finally, the structure of the unligated receptor reveals a homodimer assembly that might represent EphA2-specific homotypic cell adhesion interactions.« less

Logical definability and asymptotic growth in optimization and counting problems

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

Compton, K.

1994-12-31

There has recently been a great deal of interest in the relationship between logical definability and NP-optimization problems. Let MS{sub n} (resp. MP{sub n}) be the class of problems to compute, for given a finite structure A, the maximum number of tuples {bar x} in A satisfying a {Sigma}{sub n} (resp. II{sub n}) formula {psi}({bar x}, {bar S}) as {bar S} ranges over predicates on A. Kolaitis and Thakur showed that the classes MS{sub n} and MP{sub n} collapse to a hierarchy of four levels. Papadimitriou and Yannakakis previously showed that problems in the two lowest levels MS{sub 0} andmore » MS{sub 1} (which they called Max Snp and Max Np) are approximable to within a contrast factor in polynomial time. Similarly, Saluja, Subrahmanyam, and Thakur defined SS{sub n} (resp. SP{sub n}) to be the class of problems to compute, for given a finite structure A, the number of tuples ({bar T}, {bar S}) satisfying a given {Sigma}{sub n} (resp. II{sub n}) formula {psi}({bar T}, {bar c}) in A. They showed that the classes SS{sub n} and SP{sub n} collapse to a hierarchy of five levels and that problems in the two lowest levels SS{sub 0} and SS{sub 1} have a fully polynomial time randomized approximation scheme. We define extended classes MSF{sub n}, MPF{sub n} SSF{sub n}, and SPF{sub n} by allowing formulae to contain predicates definable in a logic known as least fixpoint logic. The resulting hierarchies classes collapse to the same number of levels and problems in the bottom levels can be approximated as before, but now some problems descend from the highest levels in the original hierarchies to the lowest levels in the new hierarchies. We introduce a method characterizing rates of growth of average solution sizes thereby showing a number of important problems do not belong MSF{sub 1} and SSF{sub 1}. This method is related to limit laws for logics and the probabilistic method from combinatorics.« less

Inter-class competition in stage-structured populations: effects of adult density on life-history traits of adult and juvenile common lizards.

PubMed

San-Jose, Luis M; Peñalver-Alcázar, Miguel; Huyghe, Katleen; Breedveld, Merel C; Fitze, Patrick S

2016-12-01

Ecological and evolutionary processes in natural populations are largely influenced by the population's stage-structure. Commonly, different classes have different competitive abilities, e.g., due to differences in body size, suggesting that inter-class competition may be important and largely asymmetric. However, experimental evidence states that inter-class competition, which is important, is rare and restricted to marine fish. Here, we manipulated the adult density in six semi-natural populations of the European common lizard, Zootoca vivipara, while holding juvenile density constant. Adult density affected juveniles, but not adults, in line with inter-class competition. High adult density led to lower juvenile survival and growth before hibernation. In contrast, juvenile survival after hibernation was higher in populations with high adult density, pointing to relaxed inter-class competition. As a result, annual survival was not affected by adult density, showing that differences in pre- and post-hibernation survival balanced each other out. The intensity of inter-class competition affected reproduction, performance, and body size in juveniles. Path analyses unravelled direct treatment effects on early growth (pre-hibernation) and no direct treatment effects on the parameters measured after hibernation. This points to allometry of treatment-induced differences in early growth, and it suggests that inter-class competition mainly affects the early growth of the competitively inferior class and thereby their future performance and reproduction. These results are in contrast with previous findings and, together with results in marine fish, suggest that the strength and direction of density dependence may depend on the degree of inter-class competition, and thus on the availability of resources used by the competing classes.

Disentangling the benefits of sex.

PubMed

Roze, Denis

2012-01-01

Understanding the evolutionary advantage of sexual reproduction remains one of the most fundamental questions in evolutionary biology. Most of the current hypotheses rely on the fact that sex increases genetic variation, thereby enhancing the efficiency of natural selection; an important body of theoretical work has defined the conditions under which sex can be favoured through this effect. Over the last decade, experimental evolution in model organisms has provided evidence that sex indeed allows faster rates of adaptation. A new study on facultatively sexual rotifers shows that increased rates of sex can be favoured during adaptation to new environmental conditions and explores the cause of this effect. The results provide support for the idea that the benefits of increasing genetic variation may compensate for the short-term costs of sexual reproduction.

Functional Rarity: The Ecology of Outliers.

PubMed

Violle, Cyrille; Thuiller, Wilfried; Mouquet, Nicolas; Munoz, François; Kraft, Nathan J B; Cadotte, Marc W; Livingstone, Stuart W; Mouillot, David

2017-05-01

Rarity has been a central topic for conservation and evolutionary biologists aiming to determine the species characteristics that cause extinction risk. More recently, beyond the rarity of species, the rarity of functions or functional traits, called functional rarity, has gained momentum in helping to understand the impact of biodiversity decline on ecosystem functioning. However, a conceptual framework for defining and quantifying functional rarity is still lacking. We introduce 12 different forms of functional rarity along gradients of species scarcity and trait distinctiveness. We then highlight the potential key role of functional rarity in the long-term and large-scale maintenance of ecosystem processes, as well as the necessary linkage between functional and evolutionary rarity. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Evolution of Cartography Graduate Programs and the Development of New Graduate Programs in Cartography: An Assessment of Models.

ERIC Educational Resources Information Center

Steinke, Theodore R.

This paper traces the historical development of cartography graduate programs, establishes an evolutionary model, and evaluates the model to determine if it has some utility today for the development of programs capable of producing highly skilled cartographers. Cartography is defined to include traditional cartography, computer cartography,…

Continuous "in vitro" Evolution of a Ribozyme Ligase: A Model Experiment for the Evolution of a Biomolecule

ERIC Educational Resources Information Center

Ledbetter, Michael P.; Hwang, Tony W.; Stovall, Gwendolyn M.; Ellington, Andrew D.

2013-01-01

Evolution is a defining criterion of life and is central to understanding biological systems. However, the timescale of evolutionary shifts in phenotype limits most classroom evolution experiments to simple probability simulations. "In vitro" directed evolution (IVDE) frequently serves as a model system for the study of Darwinian…

National heritage areas: examining organizational development and the role of the National Park Service as federal partner

Treesearch

Susan Martin-Williams; Steven Selin

2007-01-01

Understanding the organizational development of National Heritage Areas (NHAs) and defining the National Park Service's (NPS) role within individual NHAs guided this qualitative study. Information gained during telephone interviews led to the development of an a priori model of the evolutionary stages of NHAs' organizational development and...

Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis

USDA-ARS?s Scientific Manuscript database

The correct identification of the source population of an invasive species is a prerequisite for defining and testing different hypotheses concerning the environmental and evolutionary factors responsible for biological invasions. The native area of invasive species may be large, barely known and/or...

Computational complexity of ecological and evolutionary spatial dynamics

PubMed Central

Ibsen-Jensen, Rasmus; Chatterjee, Krishnendu; Nowak, Martin A.

2015-01-01

There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP). PMID:26644569

Probing binding hot spots at protein-RNA recognition sites.

PubMed

Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

2016-01-29

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Extra-Zodiacal-Cloud Astronomy via Solar Electric Propulsion

NASA Technical Reports Server (NTRS)

Benson, Scott W.; Falck, Robert D.; Oleson, Steven R.; Greenhouse, Matthew A.; Kruk, Jeffrey W.; Gardner, Jonathan P.; Thronson, Harley A.; Vaughn, Frank J.; Fixsen, Dale J.

2011-01-01

Solar electric propulsion (SEP) is often considered as primary propulsion for robotic planetary missions, providing the opportunity to deliver more payload mass to difficult, high-delta-velocity destinations. However, SEP application to astrophysics has not been well studied. This research identifies and assesses a new application of SEP as primary propulsion for low-cost high-performance robotic astrophysics missions. The performance of an optical/infrared space observatory in Earth orbit or at the Sun-Earth L2 point (SEL2) is limited by background emission from the Zodiacal dust cloud that has a disk morphology along the ecliptic plane. By delivering an observatory to a inclined heliocentric orbit, most of this background emission can be avoided, resulting in a very substantial increase in science performance. This advantage enabled by SEP allows a small-aperture telescope to rival the performance of much larger telescopes located at SEL2. In this paper, we describe a novel mission architecture in which SEP technology is used to enable unprecedented telescope sensitivity performance per unit collecting area. This extra-zodiacal mission architecture will enable a new class of high-performance, short-development time, Explorer missions whose sensitivity and survey speed can rival flagship-class SEL2 facilities, thus providing new programmatic flexibility for NASA's astronomy mission portfolio. A mission concept study was conducted to evaluate this application of SEP. Trajectory analyses determined that a 700 kg-class science payload could be delivered in just over 2 years to a 2 AU mission orbit inclined 15 to the ecliptic using a 13 kW-class NASA's Evolutionary Xenon Thruster (NEXT) SEP system. A mission architecture trade resulted in a SEP stage architecture, in which the science spacecraft separates from the stage after delivery to the mission orbit. The SEP stage and science spacecraft concepts were defined in collaborative engineering environment studies. The SEP stage architecture approach offers benefits beyond a single astrophysics mission. A variety of low-cost astrophysics missions could employ a standard SEP stage to achieve substantial science benefit. This paper describes the results of this study in detail, including trajectory analysis, spacecraft concept definition, description of telescope/instrument benefits, and application of the resulting SEP stage to other missions. In addition, the benefits of cooperative development and use of the SEP stage, in conjunction with a SEP flight demonstration mission currently in definition at NASA, are considered.

NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

PubMed

Vos, Rutger A; Balhoff, James P; Caravas, Jason A; Holder, Mark T; Lapp, Hilmar; Maddison, Wayne P; Midford, Peter E; Priyam, Anurag; Sukumaran, Jeet; Xia, Xuhua; Stoltzfus, Arlin

2012-07-01

In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

PubMed Central

Vos, Rutger A.; Balhoff, James P.; Caravas, Jason A.; Holder, Mark T.; Lapp, Hilmar; Maddison, Wayne P.; Midford, Peter E.; Priyam, Anurag; Sukumaran, Jeet; Xia, Xuhua; Stoltzfus, Arlin

2012-01-01

Abstract In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML. PMID:22357728

The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms

PubMed Central

2012-01-01

Background The entire evolutionary history of life can be studied using myriad sequences generated by genomic research. This includes the appearance of the first cells and of superkingdoms Archaea, Bacteria, and Eukarya. However, the use of molecular sequence information for deep phylogenetic analyses is limited by mutational saturation, differential evolutionary rates, lack of sequence site independence, and other biological and technical constraints. In contrast, protein structures are evolutionary modules that are highly conserved and diverse enough to enable deep historical exploration. Results Here we build phylogenies that describe the evolution of proteins and proteomes. These phylogenetic trees are derived from a genomic census of protein domains defined at the fold family (FF) level of structural classification. Phylogenomic trees of FF structures were reconstructed from genomic abundance levels of 2,397 FFs in 420 proteomes of free-living organisms. These trees defined timelines of domain appearance, with time spanning from the origin of proteins to the present. Timelines are divided into five different evolutionary phases according to patterns of sharing of FFs among superkingdoms: (1) a primordial protein world, (2) reductive evolution and the rise of Archaea, (3) the rise of Bacteria from the common ancestor of Bacteria and Eukarya and early development of the three superkingdoms, (4) the rise of Eukarya and widespread organismal diversification, and (5) eukaryal diversification. The relative ancestry of the FFs shows that reductive evolution by domain loss is dominant in the first three phases and is responsible for both the diversification of life from a universal cellular ancestor and the appearance of superkingdoms. On the other hand, domain gains are predominant in the last two phases and are responsible for organismal diversification, especially in Bacteria and Eukarya. Conclusions The evolution of functions that are associated with corresponding FFs along the timeline reveals that primordial metabolic domains evolved earlier than informational domains involved in translation and transcription, supporting the metabolism-first hypothesis rather than the RNA world scenario. In addition, phylogenomic trees of proteomes reconstructed from FFs appearing in each of the five phases of the protein world show that trees reconstructed from ancient domain structures were consistently rooted in archaeal lineages, supporting the proposal that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. PMID:22284070

Enhanced equivalence class formation by the delay and relational functions of meaningful stimuli.

PubMed

Arntzen, Erik; Nartey, Richard K; Fields, Lanny

2015-05-01

Undergraduates in six groups of 10 attempted to form three 3-node 5-member equivalence classes (A → B → C → D → E) under the simultaneous protocol. In five of six groups, all stimuli were abstract shapes; in the PIC group, C stimuli were pictures with the remainder being abstract shapes. Before class formation, participants in the Identity-S and Identity-D groups were given preliminary training to form identity conditional discriminations with the C stimuli using simultaneous and 6 s delayed matching-to-sample procedures, respectively. In the Arbitrary-S and Arbitrary-D groups, before class formation, arbitrary conditional discriminations were formed between C and X stimuli using simultaneous and 6 s delayed matching-to-sample procedures, respectively. With no preliminary training, classes in the PIC and ABS groups were formed by 80% and 0% of participants, respectively. After preliminary training, class formation (yield) increased with delay, regardless of relational type. For each of the two delays, yield was slightly greater after forming arbitrary- instead of identity-relations. Yield was greatest, however, when a class contained a meaningful stimulus (PIC). During failed class formation, probes produced experimenter-defined relations, participant-defined relations, and unsystematic responding; delay, but not the relation type in preliminary training influenced relational and indeterminate responding. These results suggest how meaningful stimuli enhance equivalence class formation. © Society for the Experimental Analysis of Behavior.

How do older adult drivers self-regulate? Characteristics of self-regulation classes defined by latent class analysis.

PubMed

Bergen, Gwen; West, Bethany A; Luo, Feijun; Bird, Donna C; Freund, Katherine; Fortinsky, Richard H; Staplin, Loren

2017-06-01

Motor-vehicle crashes were the second leading cause of injury death for adults aged 65-84years in 2014. Some older drivers choose to self-regulate their driving to maintain mobility while reducing driving risk, yet the process remains poorly understood. Data from 729 older adults (aged ≥60years) who joined an older adult ride service program between April 1, 2010 and November 8, 2013 were analyzed to define and describe classes of driving self-regulation. Latent class analysis was employed to characterize older adult driving self-regulation classes using driving frequency and avoidance of seven driving situations. Logistic regression was used to explore associations between characteristics affecting mobility and self-regulation class. Three classes were identified (low, medium, and high self-regulation). High self-regulating participants reported the highest proportion of always avoiding seven risky driving situations and the lowest driving frequency followed by medium and low self-regulators. Those who were female, aged 80years or older, visually impaired, assistive device users, and those with special health needs were more likely to be high self-regulating compared with low self-regulating. Avoidance of certain driving situations and weekly driving frequency are valid indicators for describing driving self-regulation classes in older adults. Understanding the unique characteristics and mobility limitations of each class can guide optimal transportation strategies for older adults. Published by Elsevier Ltd.

The evolution of trypanosomatid taxonomy.

PubMed

Kaufer, Alexa; Ellis, John; Stark, Damien; Barratt, Joel

2017-06-08

Trypanosomatids are protozoan parasites of the class Kinetoplastida predominately restricted to invertebrate hosts (i.e. possess a monoxenous life-cycle). However, several genera are pathogenic to humans, animals and plants, and have an invertebrate vector that facilitates their transmission (i.e. possess a dixenous life-cycle). Phytomonas is one dixenous genus that includes several plant pathogens transmitted by phytophagous insects. Trypanosoma and Leishmania are dixenous genera that infect vertebrates, including humans, and are transmitted by hematophagous invertebrates. Traditionally, monoxenous trypanosomatids such as Leptomonas were distinguished from morphologically similar dixenous species based on their restriction to an invertebrate host. Nonetheless, this criterion is somewhat flawed as exemplified by Leptomonas seymouri which reportedly infects vertebrates opportunistically. Similarly, Novymonas and Zelonia are presumably monoxenous genera yet sit comfortably in the dixenous clade occupied by Leishmania. The isolation of Leishmania macropodum from a biting midge (Forcipomyia spp.) rather than a phlebotomine sand fly calls into question the exclusivity of the Leishmania-sand fly relationship, and its suitability for defining the Leishmania genus. It is now accepted that classic genus-defining characteristics based on parasite morphology and host range are insufficient to form the sole basis of trypanosomatid taxonomy as this has led to several instances of paraphyly. While improvements have been made, resolution of evolutionary relationships within the Trypanosomatidae is confounded by our incomplete knowledge of its true diversity. The known trypanosomatids probably represent a fraction of those that exist and isolation of new species will help resolve relationships in this group with greater accuracy. This review incites a dialogue on how our understanding of the relationships between certain trypanosomatids has shifted, and discusses new knowledge that informs the present taxonomy of these important parasites.

Host age modulates parasite infectivity, virulence and reproduction.

PubMed

Izhar, Rony; Ben-Ami, Frida

2015-07-01

Host age is one of the most striking differences among hosts within most populations, but there is very little data on how age-dependent effects impact ecological and evolutionary dynamics of both the host and the parasite. Here, we examined the influence of host age (juveniles, young and old adults) at parasite exposure on host susceptibility, fecundity and survival as well as parasite transmission, using two clones of the water flea Daphnia magna and two clones of its bacterial parasite Pasteuria ramosa. Younger D. magna were more susceptible to infection than older ones, regardless of host or parasite clone. Also, younger-infected D. magna became castrated faster than older hosts, but host and parasite clone effects contributed to this trait as well. Furthermore, the early-infected D. magna produced considerably more parasite transmission stages than late-infected ones, while host age at exposure did not affect virulence as it is defined in models (host mortality). When virulence is defined more broadly as the negative effects of infection on host fitness, by integrating the parasitic effects on host fecundity and mortality, then host age at exposure seems to slide along a negative relationship between host and parasite fitness. Thus, the virulence-transmission trade-off differs strongly among age classes, which in turn affects predictions of optimal virulence. Age-dependent effects on host susceptibility, virulence and parasite transmission could pose an important challenge for experimental and theoretical studies of infectious disease dynamics and disease ecology. Our results present a call for a more explicit stage-structured theory for disease, which will incorporate age-dependent epidemiological parameters. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Four classes of interactions for evolutionary games.

PubMed

Szabó, György; Bodó, Kinga S; Allen, Benjamin; Nowak, Martin A

2015-08-01

The symmetric four-strategy games are decomposed into a linear combination of 16 basis games represented by orthogonal matrices. Among these basis games four classes can be distinguished as it is already found for the three-strategy games. The games with self-dependent (cross-dependent) payoffs are characterized by matrices consisting of uniform rows (columns). Six of 16 basis games describe coordination-type interactions among the strategy pairs and three basis games span the parameter space of the cyclic components that are analogous to the rock-paper-scissors games. In the absence of cyclic components the game is a potential game and the potential matrix is evaluated. The main features of the four classes of games are discussed separately and we illustrate some characteristic strategy distributions on a square lattice in the low noise limit if logit rule controls the strategy evolution. Analysis of the general properties indicates similar types of interactions at larger number of strategies for the symmetric matrix games.

HLA-G in human reproduction: aspects of genetics, function and pregnancy complications.

PubMed

Hviid, Thomas Vauvert F

2006-01-01

The non-classical human leukocyte antigen (HLA) class Ib genes, HLA-E, -G and -F, are located on chromosome 6 in the human major histocompatibility complex (MHC). HLA class Ib antigens resemble the HLA class Ia antigens in many ways, but several major differences have been described. This review will, in particular, discuss HLA-G and its role in human reproduction and in the human MHC. HLA-G seems to be important in the modulation of the maternal immune system during pregnancy and thereby the maternal acceptance of the semiallogenic fetus. Recent findings regarding aspects of HLA-G polymorphism, the possible significance of this polymorphism in respect to HLA-G function and certain complications of pregnancy (such as pre-eclampsia and recurrent spontaneous abortions (RSA)) are discussed together with possible importance to IVF. Finally, aspects of a possible role of HLA-G in organ transplantation and in inflammatory or autoimmune disease, and of HLA-G in an evolutionary context, are also briefly examined.

Hydrodynamic models for novae with ejecta rich in oxygen, neon and magnesium

NASA Technical Reports Server (NTRS)

Starrfield, S.; Sparks, W. M.; Truran, J. W.

1985-01-01

The characteristics of a new class of novae are identified and explained. This class consists of those objects that have been observed to eject material rich in oxygen, neon, magnesium, and aluminum at high velocities. We propose that for this class of novae the outburst is occurring not on a carbon-oxygen white dwarf but on an oxygen-neon-magnesium white dwarf which has evolved from a star which had a main sequence mass of approx. 8 solar masses to approx. 12 solar masses. An outburst was simulated by evolving 1.25 solar mass white dwarfs accreting hydrogen rich material at various rates. The effective enrichment of the envelope by ONeMg material from the core is simulated by enhancing oxygen in the accreted layers. The resulting evolutionary sequences can eject the entire accreted envelope plus core material at high velocities. They can also become super-Eddington at maximum bolometric luminosity. The expected frequency of such events (approx. 1/4) is in good agreement with the observed numbers of these novae.