WorldWideScience

Sample records for alignment-free evolutionary conservation

  1. Evolutionary conservation of alternative splicing in chicken

    OpenAIRE

    Katyal, S.; Gao, Z.; Liu, R.-Z.; R Godbout

    2007-01-01

    Alternative splicing represents a source of great diversity for regulating protein expression and function. It has been estimated that one-third to two-thirds of mammalian genes are alternatively spliced. With the sequencing of the chicken genome and analysis of transcripts expressed in chicken tissues, we are now in a position to address evolutionary conservation of alternative splicing events in chicken and mammals. Here, we compare chicken and mammalian transcript sequences of 41 alternati...

  2. Remarkable evolutionary conservation of SOX14 orthologues

    Indian Academy of Sciences (India)

    Jelena Popovic; Milena Stevanovic

    2009-04-01

    SOX proteins constitute a large family of diverse, well-conserved transcription factors present in vertebrates and invertebrates, and also implicated in control of many developmental processes. Our objectives have been to identify Sox14 gene of goat (Capra hircus), cow (Bos taurus) and rat (Rattus norvegicus), and to perform comparative analyses and mapping of SOX14 orthologues from numerous vertebrate species. PCR based approach was used to identify Sox14 of goat, cow and rat, while nucleotide and amino acid sequence alignments and mapping were performed using information currently available in public database. Comparative sequence analysis revealed remarkable identity among Sox14 orthologues and helped us to identify highly conserved motifs that represent molecular signatures of SOX14 protein that might have structural or functional significance. Further, we determined chromosomal locations of numerous predicted group B Sox genes and their neighbouring genes using currently available genome database. In conclusion, our study has not only supported the proposed model of group B Sox genes evolution in chicken and mammals, but has also revealed that additional evolutionary events split Sox B genes into different chromosomes in some mammals. Mapping data presented in this study could help in refining the understanding of the evolution of group B Sox genes in vertebrates.

  3. Efficient alignment-free DNA barcode analytics

    OpenAIRE

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-01-01

    Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient ...

  4. Strategies for measuring evolutionary conservation of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Hofacker Ivo L

    2008-02-01

    Full Text Available Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. Results We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons. Conclusion Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.

  5. An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

    OpenAIRE

    Pratas, Diogo; Silva, Raquel M; Pinho, Armando J.; Ferreira, Paulo J.S.G.

    2015-01-01

    Species evolution is indirectly registered in their genomic structure. The emergence and advances in sequencing technology provided a way to access genome information, namely to identify and study evolutionary macro-events, as well as chromosome alterations for clinical purposes. This paper describes a completely alignment-free computational method, based on a blind unsupervised approach, to detect large-scale and small-scale genomic rearrangements between pairs of DNA sequences. To illustrat...

  6. Evolutionary conservation and functional roles of ncRNA

    OpenAIRE

    Qu, Zhipeng; Adelson, David L.

    2012-01-01

    Non-coding RNAs (ncRNAs) are a class of transcribed RNA molecules without protein-coding potential. They were regarded as transcriptional noise, or the byproduct of genetic information flow from DNA to protein for a long time. However, in recent years, a number of studies have shown that ncRNAs are pervasively transcribed, and most of them show evidence of evolutionary conservation, although less conserved than protein-coding genes. More importantly, many ncRNAs have been confirmed as playing...

  7. Does the evolutionary conservation of microsatellite loci imply function?

    Energy Technology Data Exchange (ETDEWEB)

    Shriver, M.D.; Deka, R.; Ferrell, R.E. [Univ. of Pittsburgh, PA (United States)] [and others

    1994-09-01

    Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these four species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.

  8. Differences in evolutionary pressure acting within highly conserved ortholog groups

    Directory of Open Access Journals (Sweden)

    Aravind L

    2008-07-01

    Full Text Available Abstract Background 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. Results 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. Conclusion 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.

  9. Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

    Energy Technology Data Exchange (ETDEWEB)

    Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

    2003-12-31

    Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involved in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.

  10. Alignment-free comparison of genome sequences by a new numerical characterization.

    Science.gov (United States)

    Huang, Guohua; Zhou, Houqing; Li, Yongfan; Xu, Lixin

    2011-07-21

    In order to compare different genome sequences, an alignment-free method has proposed. First, we presented a new graphical representation of DNA sequences without degeneracy, which is conducive to intuitive comparison of sequences. Then, a new numerical characterization based on the representation was introduced to quantitatively depict the intrinsic nature of genome sequences, and considered as a 10-dimensional vector in the mathematical space. Alignment-free comparison of sequences was performed by computing the distances between vectors of the corresponding numerical characterizations, which define the evolutionary relationship. Two data sets of DNA sequences were constructed to assess the performance on sequence comparison. The results illustrate well validity of the method. The new numerical characterization provides a powerful tool for genome comparison. PMID:21536050

  11. Genome-based phylogeny of dsDNA viruses by a novel alignment-free method.

    Science.gov (United States)

    Gao, Yang; Luo, Liaofu

    2012-01-15

    Sequence alignment is not directly applicable to whole genome phylogeny since several events such as rearrangements make full length alignments impossible. Here, a novel alignment-free method derived from the standpoint of information theory is proposed and used to construct the whole-genome phylogeny for a population of viruses from 13 viral families comprising 218 dsDNA viruses. The method is based on information correlation (IC) and partial information correlation (PIC). We observe that (i) the IC-PIC tree segregates the population into clades, the membership of each is remarkably consistent with biologist's systematics only with little exceptions; (ii) the IC-PIC tree reveals potential evolutionary relationships among some viral families; and (iii) the IC-PIC tree predicts the taxonomic positions of certain "unclassified" viruses. Our approach provides a new way for recovering the phylogeny of viruses, and has practical applications in developing alignment-free methods for sequence classification. PMID:22100880

  12. Alignment-free sequence comparison with spaced k-mers

    OpenAIRE

    Boden, Marcus; Schöneich, Martin; Horwege, Sebastian; Lindner, Sebastian; Leimeister, Chris; Morgenstern, Burkhard

    2013-01-01

    Alignment-free methods are increasingly used for genome analysis and phylogeny reconstruction since they circumvent various difficulties of traditional approaches that rely on multiple sequence alignments. In particular, they are much faster than alignment-based methods. Most alignment-free approaches work by analyzing the k-mer composition of sequences. In this paper, we propose to use 'spaced k-mers', i.e. patterns of deterministic and 'don't care' positions instead of contiguous k-me...

  13. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder

    OpenAIRE

    Varadi, Mihaly; Guharoy, Mainak; Zsolyomi, Fruzsina; Tompa, Peter

    2015-01-01

    Background Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of th...

  14. Conservative ecological and evolutionary patterns in liverwort-fungal symbioses.

    Science.gov (United States)

    Bidartondo, Martin I; Duckett, Jeffrey G

    2010-02-01

    Liverworts, the most ancient group of land plants, form a range of intimate associations with fungi that may be analogous to the mycorrhizas of vascular plants. Most thalloid liverworts contain arbuscular mycorrhizal glomeromycete fungi similar to most vascular plants. In contrast, a range of leafy liverwort genera and one simple thalloid liverwort family (the Aneuraceae) have switched to basidiomycete fungi. These liverwort switches away from glomeromycete fungi may be expected to parallel switches undergone by vascular plants that target diverse lineages of basidiomycete fungi to form ectomycorrhizas. To test this hypothesis, we used a cultivation-independent approach to examine the basidiomycete fungi associated with liverworts in varied worldwide locations by generating fungal DNA sequence data from over 200 field collections of over 30 species. Here we show that eight leafy liverwort genera predominantly and consistently associate with members of the Sebacina vermifera species complex and that Aneuraceae thalloid liverworts associate nearly exclusively with Tulasnella species. Furthermore, within sites where multiple liverwort species co-occur, they almost never share the same fungi. Our analyses reveal a strikingly conservative ecological and evolutionary pattern of liverwort symbioses with basidiomycete fungi that is unlike that of vascular plant mycorrhizas. PMID:19812075

  15. ConPlex: a server for the evolutionary conservation analysis of protein complex structures

    OpenAIRE

    Choi, Yoon Sup; Han, Seong Kyu; Kim, Jinho; Yang, Jae-Seong; Jeon, Jouhyun; Ryu, Sung Ho; Kim, Sanguk

    2010-01-01

    Evolutionary conservation analyses are important for the identification of protein–protein interactions. For protein complex structures, sequence conservation has been applied to determine protein oligomerization states, to characterize native interfaces from non-specific crystal contacts, and to discriminate near-native structures from docking artifacts. However, a user-friendly web-based service for evolutionary conservation analysis of protein complexes has not been available. Therefore, w...

  16. Complete experimental toolbox for alignment-free quantum communication

    CERN Document Server

    D'Ambrosio, Vincenzo; Walborn, Stephen P; Aolita, Leandro; Slussarenko, Sergei; Marrucci, Lorenzo; Sciarrino, Fabio

    2012-01-01

    Quantum communication employs the counter-intuitive features of quantum physics to perform tasks that are im- possible in the classical world. It is crucial for testing the foundations of quantum theory and promises to rev- olutionize our information and communication technolo- gies. However, for two or more parties to execute even the simplest quantum transmission, they must establish, and maintain, a shared reference frame. This introduces a considerable overhead in communication resources, par- ticularly if the parties are in motion or rotating relative to each other. We experimentally demonstrate how to circumvent this problem with the efficient transmission of quantum information encoded in rotationally invariant states of single photons. By developing a complete toolbox for the efficient encoding and decoding of quantum infor- mation in such photonic qubits, we demonstrate the fea- sibility of alignment-free quantum key-distribution, and perform a proof-of-principle alignment-free entanglement distribut...

  17. Investigating evolutionary conservation of dendritic cell subset identity and functions

    Directory of Open Access Journals (Sweden)

    Thien-Phong eVu Manh

    2015-06-01

    Full Text Available Dendritic cells (DC 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

  18. ALFRED: A Practical Method for Alignment-Free Distance Computation.

    Science.gov (United States)

    Thankachan, Sharma V; Chockalingam, Sriram P; Liu, Yongchao; Apostolico, Alberto; Aluru, Srinivas

    2016-06-01

    Alignment-free approaches are gaining persistent interest in many sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, especially for large-scale sequence datasets. Besides the widely used k-mer methods, the average common substring (ACS) approach has emerged to be one of the well-known alignment-free approaches. Two recent works further generalize this ACS approach by allowing a bounded number k of mismatches in the common substrings, relying on approximation (linear time) and exact computation, respectively. Albeit having a good worst-case time complexity [Formula: see text], the exact approach is complex and unlikely to be efficient in practice. Herein, we present ALFRED, an alignment-free distance computation method, which solves the generalized common substring search problem via exact computation. Compared to the theoretical approach, our algorithm is easier to implement and more practical to use, while still providing highly competitive theoretical performances with an expected run-time of [Formula: see text]. By applying our program to phylogenetic inference as a case study, we find that our program facilitates to exactly reconstruct the topology of the reference phylogenetic tree for a set of 27 primate mitochondrial genomes, at reasonably acceptable speed. ALFRED is implemented in C++ programming language and the source code is freely available online. PMID:27138275

  19. Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

    Directory of Open Access Journals (Sweden)

    Inês Soares

    2012-01-01

    Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

  20. An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.

    Science.gov (United States)

    Pratas, Diogo; Silva, Raquel M; Pinho, Armando J; Ferreira, Paulo J S G

    2015-01-01

    Species evolution is indirectly registered in their genomic structure. The emergence and advances in sequencing technology provided a way to access genome information, namely to identify and study evolutionary macro-events, as well as chromosome alterations for clinical purposes. This paper describes a completely alignment-free computational method, based on a blind unsupervised approach, to detect large-scale and small-scale genomic rearrangements between pairs of DNA sequences. To illustrate the power and usefulness of the method we give complete chromosomal information maps for the pairs human-chimpanzee and human-orangutan. The tool by means of which these results were obtained has been made publicly available and is described in detail. PMID:25984837

  1. Complete experimental toolbox for alignment-free quantum communication

    Science.gov (United States)

    Sciarrino, Fabio

    2013-03-01

    Quantum communication employs the counter-intuitive features of quantum physics for tasks that are impossible in the classical world. It is crucial for testing the foundations of quantum theory and promises to revolutionize information and communication technologies. However, to execute even the simplest quantum transmission, one must establish, and maintain, a shared reference frame. This introduces a considerable overhead in resources, particularly if the parties are in motion or rotating relative to each other. We experimentally show how to circumvent this problem with the transmission of quantum information encoded in rotationally invariant states of single photons. Our approach exploits multiple degrees of freedom of single photons. In particular, the polarization and transverse spatial modes stand out for this purpose. Just as the circular polarization states are eigenstates of the spin angular momentum of light, the helical-wavefront Laguerre-Gaussian modes are eigenmodes of its orbital angular momentum (OAM). We implement photonic qubit invariant under rotation around the optical axis by combining the polarization with OAM properties. By developing a complete toolbox for the efficient encoding and decoding of quantum information in such photonic qubits, we demonstrate the feasibility of alignment-free quantum key-distribution, and perform proof-of-principle demonstrations of alignment-free entanglement distribution and Bell-inequality violation. The core of our toolbox is a liquid crystal device, named ``q-plate,'' that maps polarization-encoded qubits into qubits encoded in hybrid polarization-OAM states of the same photon that are invariant under arbitrary rotations around the propagation direction, and vice versa. The scheme should find applications in fundamental tests of quantum mechanics and satellite-based quantum communication. We will discuss the potential applications of this scheme to real quantum communication network. European project

  2. Dictyostelium development shows a novel pattern of evolutionary conservation.

    Science.gov (United States)

    Tian, Xiangjun; Strassmann, Joan E; Queller, David C

    2013-04-01

    von Baer's law states that early stages of animal development are the most conserved. More recent evidence supports a modified "hourglass" pattern in which an early but somewhat later stage is most conserved. Both patterns have been explained by the relative complexity of either temporal or spatial interactions; the greatest conservation and lowest evolvability occur at the time of the most complex interactions, because these cause larger effects that are harder for selection to alter. This general kind of explanation might apply universally across independent multicellular systems, as supported by the recent finding of the hourglass pattern in plants. We use RNA-seq expression data from the development of the slime mold Dictyostelium to demonstrate that it does not follow either of the two canonical patterns but instead tends to show the strongest conservation and weakest evolvability late in development. We propose that this is consistent with a version of the spatial constraints model, modified for organisms that never achieve a high degree of developmental modularity. PMID:23329689

  3. Evolutionary immune response to conserved domains in parasites and aeroallergens.

    Science.gov (United States)

    Bielory, Brett Phillip; Mainardi, Timothy; Rottem, Menachem

    2013-01-01

    The immune response based on immunoglobulin E (IgE) evolved as a defense against specific parasitic infections. In the absence of active helminthic infections, the immune system has redirected its IgE epitopes toward innocuous environmental antigens. Helminths and aeroallergens have a similar stereotypical IgE response to unique antigens that can not be explained by chance alone. This study was designed to evaluate potential homology between conserved protein domains embedded in parasitic organisms and aeroallergens. Search and retrieval systems for nucleotide and protein sequences (Entrez, BLAST, and National Center for Biotechnology Information) were searched to identify conserved domains between allergens and certain parasites. A total score was developed that correlated positively with homology between compared sequences. Over 2000 domains were examined. We found matches with a high total score (>100) that signified a strong positive correlation between sequences in allergens (n = 30) and parasites (n = 13). Multiple shared conserved domains were identified between parasites and allergens. Parasite-allergen combinations with the most significant homology (greatest total score) were Plasmodium falciparum enolase and Hev b9 (total score, 612), Schistosoma mansoni albumin and Fel d 2 (total score, 991), Ascaris lumbricoides tropomyosin and Ani s3 (total score, 531), and Wuchereria bancrofti trypsin and Blo t3 (138). Homologous conserved domains exist in specific parasites and allergens, consistent with the theory that the human IgE-eosinophil immune response to common allergens is a direct consequence of stimulation by parasitic organisms. PMID:23406942

  4. LAF: Logic Alignment Free and its application to bacterial genomes classification

    OpenAIRE

    Weitschek, Emanuel; Cunial, Fabio; Felici, Giovanni

    2015-01-01

    Alignment-free algorithms can be used to estimate the similarity of biological sequences and hence are often applied to the phylogenetic reconstruction of genomes. Most of these algorithms rely on comparing the frequency of all the distinct substrings of fixed length (k-mers) that occur in the analyzed sequences. In this paper, we present Logic Alignment Free (LAF), a method that combines alignment-free techniques and rule-based classification algorithms in order to assign biological samples ...

  5. Widespread evolutionary conservation of alternatively spliced exons in caenorhabditis

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob L; Penny, David;

    2007-01-01

    Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern in...... patterns of splicing. The functionality of the vast majority of cassette exons is underscored by various other features. We suggest that differences in conservation between lineages reflect differences in levels of functionality and further suggest that these differences are due to differences in intron...... length and the strength of consensus boundaries across lineages. Finally, we demonstrate an inverse relationship between AS and gene duplication, suggesting that the latter may be primarily responsible for the emergence of new functional transcripts in nematodes. Udgivelsesdato: 2008-Feb...

  6. Analysis of spatial chromatin organization and its evolutionary conservation

    OpenAIRE

    Kaufmann, Stefanie

    2015-01-01

    Not only the DNA's base pair composition but also its spatial structure is relevant for gene expression. This work studies the dependency of the three-dimensional genome fold on linear features and rearrangements, as well as the structural similarities in human and mouse. We show that individual inter-chromosomal contacts are not conserved, though the linear genome composition and functional properties of its organization exhibit similarities.

  7. Testing the evolutionary conservation of vocal motoneurons in vertebrates.

    Science.gov (United States)

    Albersheim-Carter, Jacob; Blubaum, Aleksandar; Ballagh, Irene H; Missaghi, Kianoush; Siuda, Edward R; McMurray, George; Bass, Andrew H; Dubuc, Réjean; Kelley, Darcy B; Schmidt, Marc F; Wilson, Richard J A; Gray, Paul A

    2016-04-01

    Medullary motoneurons drive vocalization in many vertebrate lineages including fish, amphibians, birds, and mammals. The developmental history of vocal motoneuron populations in each of these lineages remains largely unknown. The highly conserved transcription factor Paired-like Homeobox 2b (Phox2b) is presumed to be expressed in all vertebrate hindbrain branchial motoneurons, including laryngeal motoneurons essential for vocalization in humans. We used immunohistochemistry and in situ hybridization to examine Phox2b protein and mRNA expression in caudal hindbrain and rostral spinal cord motoneuron populations in seven species across five chordate classes. Phox2b was present in motoneurons dedicated to sound production in mice and frogs (bullfrog, African clawed frog), but not those in bird (zebra finch) or bony fish (midshipman, channel catfish). Overall, the pattern of caudal medullary motoneuron Phox2b expression was conserved across vertebrates and similar to expression in sea lamprey. These observations suggest that motoneurons dedicated to sound production in vertebrates are not derived from a single developmentally or evolutionarily conserved progenitor pool. PMID:26160673

  8. Evolutionary Conservation in Genes Underlying Human Psychiatric Disorders

    Directory of Open Access Journals (Sweden)

    Lisa Michelle Ogawa

    2014-05-01

    Full Text Available Many psychiatric diseases observed in humans have tenuous or absent analogs in other species. Most notable among these are schizophrenia and autism. One hypothesis has posited that these diseases have arisen as a consequence of human brain evolution, for example, that the same processes that led to advances in cognition, language, and executive function also resulted in novel diseases in humans when dysfunctional. Here, the molecular evolution of genes associated with these and other psychiatric disorders are compared among species. Genes associated with psychiatric disorders are drawn from the literature and orthologous sequences are collected from eleven primate species (human, chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, baboon, marmoset, squirrel monkey, and galago and thirty one non-primate mammalian species. Evolutionary parameters, including dN/dS, are calculated for each gene and compared between disease classes and among species, focusing on humans and primates compared to other mammals and on large-brained taxa (cetaceans, rhinoceros, walrus, bear, and elephant compared to their small-brained sister species. Evidence of differential selection in primates supports the hypothesis that schizophrenia and autism are a cost of higher brain function. Through this work a better understanding of the molecular evolution of the human brain, the pathophysiology of disease, and the genetic basis of human psychiatric disease is gained.

  9. Teaching the Toolkit: A Laboratory Series to Demonstrate the Evolutionary Conservation of Metazoan Cell Signaling Pathways

    Science.gov (United States)

    LeClair, Elizabeth E.

    2008-01-01

    A major finding of comparative genomics and developmental genetics is that metazoans share certain conserved, embryonically deployed signaling pathways that instruct cells as to their ultimate fate. Because the DNA encoding these pathways predates the evolutionary split of most animal groups, it should in principle be possible to clone…

  10. Evolutionary conservation in genes underlying human psychiatric disorders.

    Science.gov (United States)

    Ogawa, Lisa M; Vallender, Eric J

    2014-01-01

    Many psychiatric diseases observed in humans have tenuous or absent analogs in other species. Most notable among these are schizophrenia and autism. One hypothesis has posited that these diseases have arisen as a consequence of human brain evolution, for example, that the same processes that led to advances in cognition, language, and executive function also resulted in novel diseases in humans when dysfunctional. Here, the molecular evolution of the protein-coding regions of genes associated with these and other psychiatric disorders are compared among species. Genes associated with psychiatric disorders are drawn from the literature and orthologous sequences are collected from eleven primate species (human, chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, baboon, marmoset, squirrel monkey, and galago) and 34 non-primate mammalian species. Evolutionary parameters, including dN/dS, are calculated for each gene and compared between disease classes and among species, focusing on humans and primates compared to other mammals, and on large-brained taxa (cetaceans, rhinoceros, walrus, bear, and elephant) compared to their small-brained sister species. Evidence of differential selection in humans to the exclusion of non-human primates was absent, however elevated dN/dS was detected in catarrhines as a whole, as well as in cetaceans, possibly as part of a more general trend. Although this may suggest that protein changes associated with schizophrenia and autism are not a cost of the higher brain function found in humans, it may also point to insufficiencies in the study of these diseases including incomplete or inaccurate gene association lists and/or a greater role of regulatory changes or copy number variation. Through this work a better understanding of the molecular evolution of the human brain, the pathophysiology of disease, and the genetic basis of human psychiatric disease is gained. PMID:24834046

  11. Evolutionary Conserved Protein Features From Analysis of Virus Shapes

    CERN Document Server

    Bozic, Anze Losdorfer; Podgornik, Rudolf

    2013-01-01

    From the shape and size analysis of approximately 130 small icosahedral viruses we conclude that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed capsid proteins having thicknesses between 2 nm and 4 nm. To investigate whether, in addition to the conserved geometry, capsid proteins show similarities in the way they interact with one another, we examined the shapes of the capsids in detail. We classified them numerically according to their similarity to sphere and icosahedron and a set of shapes in between, all obtained from the theory of elasticity of shells. In order to make a unique and straightforward connection between an idealized, numerically calculated shape of an elastic shell and a capsid, we devised a special shape fitting procedure, the outcome of which is the idealized elastic shape fitting the capsid best. Using such a procedure we performed statistical analysis of a series of virus shapes and we f...

  12. Modeling an evolutionary conserved circadian cis-element.

    Directory of Open Access Journals (Sweden)

    Eric R Paquet

    2008-02-01

    Full Text Available Circadian oscillator networks rely on a transcriptional activator called CLOCK/CYCLE (CLK/CYC in insects and CLOCK/BMAL1 or NPAS2/BMAL1 in mammals. Identifying the targets of this heterodimeric basic-helix-loop-helix (bHLH transcription factor poses challenges and it has been difficult to decipher its specific sequence affinity beyond a canonical E-box motif, except perhaps for some flanking bases contributing weakly to the binding energy. Thus, no good computational model presently exists for predicting CLK/CYC, CLOCK/BMAL1, or NPAS2/BMAL1 targets. Here, we use a comparative genomics approach and first study the conservation properties of the best-known circadian enhancer: a 69-bp element upstream of the Drosophila melanogaster period gene. This fragment shows a signal involving the presence of two closely spaced E-box-like motifs, a configuration that we can also detect in the other four prominent CLK/CYC target genes in flies: timeless, vrille, Pdp1, and cwo. This allows for the training of a probabilistic sequence model that we test using functional genomics datasets. We find that the predicted sequences are overrepresented in promoters of genes induced in a recent study by a glucocorticoid receptor-CLK fusion protein. We then scanned the mouse genome with the fly model and found that many known CLOCK/BMAL1 targets harbor sequences matching our consensus. Moreover, the phase of predicted cyclers in liver agreed with known CLOCK/BMAL1 regulation. Taken together, we built a predictive model for CLK/CYC or CLOCK/BMAL1-bound cis-enhancers through the integration of comparative and functional genomics data. Finally, a deeper phylogenetic analysis reveals that the link between the CLOCK/BMAL1 complex and the circadian cis-element dates back to before insects and vertebrates diverged.

  13. Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.

    Science.gov (United States)

    Der Sarkissian, Clio; Ermini, Luca; Schubert, Mikkel; Yang, Melinda A; Librado, Pablo; Fumagalli, Matteo; Jónsson, Hákon; Bar-Gal, Gila Kahila; Albrechtsen, Anders; Vieira, Filipe G; Petersen, Bent; Ginolhac, Aurélien; Seguin-Orlando, Andaine; Magnussen, Kim; Fages, Antoine; Gamba, Cristina; Lorente-Galdos, Belen; Polani, Sagi; Steiner, Cynthia; Neuditschko, Markus; Jagannathan, Vidhya; Feh, Claudia; Greenblatt, Charles L; Ludwig, Arne; Abramson, Natalia I; Zimmermann, Waltraut; Schafberg, Renate; Tikhonov, Alexei; Sicheritz-Ponten, Thomas; Willerslev, Eske; Marques-Bonet, Tomas; Ryder, Oliver A; McCue, Molly; Rieder, Stefan; Leeb, Tosso; Slatkin, Montgomery; Orlando, Ludovic

    2015-10-01

    Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2-4]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878-1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations. PMID:26412128

  14. Evolutionary hierarchies of conserved blocks in 5'-noncoding sequences of dicot rbcS genes

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    Donnison Iain S

    2007-04-01

    Full Text Available Abstract Background Evolutionary processes in gene regulatory regions are major determinants of organismal evolution, but exceptionally challenging to study. We explored the possibilities of evolutionary analysis of phylogenetic footprints in 5'-noncoding sequences (NCS from 27 ribulose-1,5-bisphosphate carboxylase small subunit (rbcS genes, from three dicot families (Brassicaceae, Fabaceae and Solanaceae. Results Sequences of up to 400 bp encompassing proximal promoter and 5'-untranslated regions were analyzed. We conducted phylogenetic footprinting by several alternative methods: generalized Lempel-Ziv complexity (CLZ, multiple alignments with DIALIGN and ALIGN-M, and the MOTIF SAMPLER Gibbs sampling algorithm. These tools collectively defined 36 conserved blocks of mean length 12.8 bp. On average, 12.5 blocks were found in each 5'-NCS. The blocks occurred in arrays whose relative order was absolutely conserved, confirming the existence of 'conserved modular arrays' in promoters. Identities of half of the blocks confirmed past rbcS research, including versions of the I-box, G-box, and GT-1 sites such as Box II. Over 90% of blocks overlapped DNase-protected regions in tomato 5'-NCS. Regions characterized by low CLZ in sliding-window analyses were also frequently associated with DNase-protection. Blocks could be assigned to evolutionary hierarchies based on taxonomic distribution and estimated age. Lineage divergence dates implied that 13 blocks found in all three plant families were of Cretaceous antiquity, while other family-specific blocks were much younger. Blocks were also dated by formation of multigene families, using genome and coding sequence information. Dendrograms of evolutionary relations of the 5'-NCS were produced by several methods, including: cluster analysis using pairwise CLZ values; evolutionary trees of DIALIGN sequence alignments; and cladistic analysis of conserved blocks. Conclusion Dicot 5'-NCS contain conserved modular

  15. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Loots, G; Ovcharenko, I

    2006-08-08

    Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes entitled ECRbase that is constructed from a collection of pairwise vertebrate genome alignments produced by the ECR Browser database. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a collection of promoters in all vertebrate genomes presented in the database. The database also contains a collection of annotated transcription factor binding sites (TFBS) in all ECRs and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and two pufferfish genomes. It is freely accessible at http://ECRbase.dcode.org.

  16. Evolutionary conservation ofDmrt gene family in amphibi-ans, reptiles and birds

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Sex determining gene Mab-3 of C. elegans and doublesex of Drosophila contain a common DNA binding motif called a DM domain, both of which regulate similar aspects of sexual development. Human doublesex-related gene DMRT1 has been identified, which also contains the conserved DM-related DNA-binding domain and plays an essential role in gonadal differentiation. We present the amplification of a broad spectrum of DM domain sequences from phylogenetic diverse vertebrates (Cynops orientalis, Chrysemys scripta elegans and Coturnix coturnix) using degenerate PCR. Our results further reveal the unexpected complexity and the evolutionary conservation of the DM domain gene family.

  17. Evolutionary conservation of the WASH complex, an actin polymerization machine involved in endosomal fission

    OpenAIRE

    Derivery, Emmanuel; Gautreau, Alexis

    2010-01-01

    WASH is the Arp2/3 activating protein that is localized at the surface of endosomes, where it induces the formation of branched actin networks. This activity of WASH favors, in collaboration with dynamin, the fission of transport intermediates from endosomes, and hence regulates endosomal trafficking of several cargos. We have purified a novel stable multiprotein complex containing WASH, the WASH complex, and we examine here the evolutionary conservation of its seven subunits across diverse e...

  18. Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development.

    OpenAIRE

    2008-01-01

    It is widely accepted that evolutionary changes in conserved developmental signaling pathways play an important role in morphological evolution. However, few in silico studies were interested in tracking such changes in a signaling pathway. The Ectodysplasin (EDA) pathway provides an opportunity to fill this gap because it is involved in vertebrate skin appendage development such as scales, teeth, hair, and feathers that take an obvious part in the adaptation of species to their environment. ...

  19. Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction

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    Teppa Elin

    2012-09-01

    Full Text Available Abstract Background A large panel of methods exists that aim to identify residues with critical impact on protein function based on evolutionary signals, sequence and structure information. However, it is not clear to what extent these different methods overlap, and if any of the methods have higher predictive potential compared to others when it comes to, in particular, the identification of catalytic residues (CR in proteins. Using a large set of enzymatic protein families and measures based on different evolutionary signals, we sought to break up the different components of the information content within a multiple sequence alignment to investigate their predictive potential and degree of overlap. Results Our results demonstrate that the different methods included in the benchmark in general can be divided into three groups with a limited mutual overlap. One group containing real-value Evolutionary Trace (rvET methods and conservation, another containing mutual information (MI methods, and the last containing methods designed explicitly for the identification of specificity determining positions (SDPs: integer-value Evolutionary Trace (ivET, SDPfox, and XDET. In terms of prediction of CR, we find using a proximity score integrating structural information (as the sum of the scores of residues located within a given distance of the residue in question that only the methods from the first two groups displayed a reliable performance. Next, we investigated to what degree proximity scores for conservation, rvET and cumulative MI (cMI provide complementary information capable of improving the performance for CR identification. We found that integrating conservation with proximity scores for rvET and cMI achieved the highest performance. The proximity conservation score contained no complementary information when integrated with proximity rvET. Moreover, the signal from rvET provided only a limited gain in predictive performance when integrated with

  20. Introgression of transgenic crop alleles: Its evolutionary impacts on conserving genetic diversity of crop wild relatives

    Institute of Scientific and Technical Information of China (English)

    Bao-Rong LU

    2013-01-01

    Effective conservation of crop wild relative (CWR) species is essential for the sustainable use and genetic improvement of crop varieties,which offers greater opportunities for world food security,particularly in modem agroecosystems where CWR diversity is under severe threat.Factors such as habitat fragmentation,human disturbances,global climate change,and invasion of harmful alien species have been identified to be responsible for losses and threats to CWR diversity.However,a neglected factor,gene introgression from domesticated species through repeated outcrossing,may have a significant impact on CWR diversity.Introgression can influence genetic diversity and evolutionary processes of CWR populations through effects such as demographic swarming,genetic assimilation,and selective sweep.When largely enhancing or reducing fitness of wild plants,the introgression of crop genes will impose more significant genetic and evolutionary impacts on CWR populations,leading to undesired consequences for conserved CWR populations and species.This situation is particularly true when genetically engineered (GE) crops are deployed for commercial cultivation.It is argued that a GE crop usually contains transgenes with strong natural selection advantages,and such transgenes introgressed into CWR populations may have strong impacts on their genetic diversity and evolutionary processes,threatening their conservation.This article reviews the challenge of crop-wild gene flow,and particularly transgene introgression from GE crops,for the in situ conservation of wild relative species.The design of effective management strategies for conserving CWR species under the scenario of extensive cultivation of GE crops is also discussed.

  1. Wildlife conservation and animal temperament: causes and consequences of evolutionary change for captive, reintroduced, and wild populations

    NARCIS (Netherlands)

    McDougall, P.T.; Réale, D.; Sol, D.; Reader, S.M.

    2006-01-01

    We argue that animal temperament is an important concept for wildlife conservation science and review causes and consequences of evolutionary changes in temperament traits that may occur in captive-breeding programmes. An evolutionary perspective is valid because temperament traits are heritable, li

  2. Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

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    Bilsland Elizabeth

    2007-08-01

    Full Text Available Abstract Background The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis. Results We have used comparative genomics to identify novel uORFs in yeast with a high likelihood of having a translational regulatory role. We examined uORFs, previously shown to play a role in regulation of translation in Saccharomyces cerevisiae, for evolutionary conservation within seven Saccharomyces species. Inspection of the set of conserved uORFs yielded the following three characteristics useful for discrimination of functional from spurious uORFs: a length between 4 and 6 codons, a distance from the start of the main ORF between 50 and 150 nucleotides, and finally a lack of overlap with, and clear separation from, neighbouring uORFs. These derived rules are inherently associated with uORFs with properties similar to the GCN4 locus, and may not detect most uORFs of other types. uORFs with high scores based on these rules showed a much higher evolutionary conservation than randomly selected uORFs. In a genome-wide scan in S. cerevisiae, we found 34 conserved uORFs from 32 genes that we predict to be functional; subsequent analysis showed the majority of these to be located within transcripts. A total of 252 genes were found containing conserved uORFs with properties indicative of a functional role; all but 7 are novel. Functional content analysis of this set identified an overrepresentation of genes involved in transcriptional control and development. Conclusion Evolutionary conservation of uORFs in yeasts can be traced up to 100

  3. Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network

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    Shlomi Tomer

    2007-01-01

    Full Text Available Abstract Background Localized network patterns are assumed to represent an optimal design principle in different biological networks. A widely used method for identifying functional components in biological networks is looking for network motifs – over-represented network patterns. A number of recent studies have undermined the claim that these over-represented patterns are indicative of optimal design principles and question whether localized network patterns are indeed of functional significance. This paper examines the functional significance of regulatory network patterns via their biological annotation and evolutionary conservation. Results We enumerate all 3-node network patterns in the regulatory network of the yeast S. cerevisiae and examine the biological GO annotation and evolutionary conservation of their constituent genes. Specific 3-node patterns are found to be functionally enriched in different exogenous cellular conditions and thus may represent significant functional components. These functionally enriched patterns are composed mainly of recently evolved genes suggesting that there is no evolutionary pressure acting to preserve such functionally enriched patterns. No correlation is found between over-representation of network patterns and functional enrichment. Conclusion The findings of functional enrichment support the view that network patterns constitute an important design principle in regulatory networks. However, the wildly used method of over-representation for detecting motifs is not suitable for identifying functionally enriched patterns.

  4. Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics

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    Pesole Graziano

    2009-09-01

    Full Text Available Abstract Background The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the annotation of newly sequenced genomes. In the context of recent findings that the number non-coding transcripts in higher organisms is likely to be much higher than previously imagined, discrimination between conserved coding and non-coding sequences is a topic of considerable interest. Additionally, it should be considered desirable to discriminate between coding and non-coding conserved sequences without recourse to the use of sequence similarity searches of protein databases as such approaches exclude the identification of novel conserved proteins without characterized homologs and may be influenced by the presence in databases of sequences which are erroneously annotated as coding. Results Here we present a machine learning-based approach for the discrimination of conserved coding sequences. Our method calculates various statistics related to the evolutionary dynamics of two aligned sequences. These features are considered by a Support Vector Machine which designates the alignment coding or non-coding with an associated probability score. Conclusion We show that our approach is both sensitive and accurate with respect to comparable methods and illustrate several situations in which it may be applied, including the identification of conserved coding regions in genome sequences and the discrimination of coding from non-coding cDNA sequences.

  5. Evolutionary Conservation of 3-Iodothyronamine as an Agonist at the Trace Amine-Associated Receptor 1

    Science.gov (United States)

    Cöster, Maxi; Biebermann, Heike; Schöneberg, Torsten; Stäubert, Claudia

    2015-01-01

    Objectives The trace amine-associated receptor 1 (Taar1) is a Gs protein-coupled receptor activated by trace amines, such as β-phenylethylamine (β-PEA) and 3-iodothyronamine (T1AM). T1AM is an endogenous biogenic amine and thyroid hormone derivative that exerts several biological functions. However, the physiological relevance of T1AM acting via Taar1 is still under discussion. Therefore, we studied the structural and functional evolution of Taar1 in vertebrates to provide evidence for a conserved Taar1-mediated T1AM function. Study Design We searched public sequence databases to retrieve Taar1 sequence information from vertebrates. We cloned and functionally characterized Taar1 from selected vertebrate species using cAMP assays to determine the evolutionary conservation of T1AM action at Taar1. Results We found intact open reading frames of Taar1 in more than 100 vertebrate species, including mammals, sauropsids and amphibians. Evolutionary conservation analyses of Taar1 protein sequences revealed a high variation in amino acid residues proposed to be involved in agonist binding, especially in rodent Taar1 orthologs. Functional characterization showed that T1AM, β-PEA and p-tyramine (p-Tyr) act as agonists at all tested orthologs, but EC50 values of T1AM at rat Taar1 differed significantly when compared to all other tested vertebrate Taar1. Conclusions The high structural conservation of Taar1 throughout vertebrate evolution highlights the physiological relevance of Taar1, but species-specific differences in T1AM potency at Taar1 orthologs suggest a specialization of rat Taar1 for T1AM recognition. In contrast, β-PEA and p-Tyr potencies were rather conserved throughout all tested Taar1 orthologs. We provide evidence that the observed differences in potency are related to differences in constraint during Taar1 evolution. PMID:26601069

  6. Regulation of Notch Signaling by an Evolutionary Conserved DEAD Box RNA Helicase, Maheshvara in Drosophila melanogaster.

    Science.gov (United States)

    Surabhi, Satya; Tripathi, Bipin K; Maurya, Bhawana; Bhaskar, Pradeep K; Mukherjee, Ashim; Mutsuddi, Mousumi

    2015-11-01

    Notch signaling is an evolutionary conserved process that influences cell fate determination, cell proliferation, and cell death in a context-dependent manner. Notch signaling is fine-tuned at multiple levels and misregulation of Notch has been implicated in a variety of human diseases. We have characterized maheshvara (mahe), a novel gene in Drosophila melanogaster that encodes a putative DEAD box protein that is highly conserved across taxa and belongs to the largest group of RNA helicase. A dynamic pattern of mahe expression along with the maternal accumulation of its transcripts is seen during early stages of embryogenesis. In addition, a strong expression is also seen in the developing nervous system. Ectopic expression of mahe in a wide range of tissues during development results in a variety of defects, many of which resemble a typical Notch loss-of-function phenotype. We illustrate that ectopic expression of mahe in the wing imaginal discs leads to loss of Notch targets, Cut and Wingless. Interestingly, Notch protein levels are also lowered, whereas no obvious change is seen in the levels of Notch transcripts. In addition, mahe overexpression can significantly rescue ectopic Notch-mediated proliferation of eye tissue. Further, we illustrate that mahe genetically interacts with Notch and its cytoplasmic regulator deltex in trans-heterozygous combination. Coexpression of Deltex and Mahe at the dorso-ventral boundary results in a wing-nicking phenotype and a more pronounced loss of Notch target Cut. Taken together we report identification of a novel evolutionary conserved RNA helicase mahe, which plays a vital role in regulation of Notch signaling. PMID:26400611

  7. Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors

    Energy Technology Data Exchange (ETDEWEB)

    Alexander, Roger P [ORNL; Jouline, Igor B [ORNL

    2007-01-01

    As an important model for transmembrane signaling, methyl-accepting chemotaxis proteins (MCPs) have been extensively studied by using genetic, biochemical, and structural techniques. However, details of the molecular mechanism of signaling are still not well understood. The availability of genomic information for hundreds of species enables the identification of features in protein sequences that are conserved over long evolutionary distances and thus are critically important for function. We carried out a large-scale comparative genomic analysis of the MCP signaling and adaptation domain family and identified features that appear to be critical for receptor structure and function. Based on domain length and sequence conservation, we identified seven major MCP classes and three distinct structural regions within the cytoplasmic domain: signaling, methylation, and flexible bundle subdomains. The flexible bundle subdomain, not previously recognized in MCPs, is a conserved element that appears to be important for signal transduction. Remarkably, the N- and C-terminal helical arms of the cytoplasmic domain maintain symmetry in length and register despite dramatic variation, from 24 to 64 7-aa heptads in overall domain length. Loss of symmetry is observed in some MCPs, where it is concomitant with specific changes in the sensory module. Each major MCP class has a distinct pattern of predicted methylation sites that is well supported by experimental data. Our findings indicate that signaling and adaptation functions within the MCP cytoplasmic domain are tightly coupled, and that their coevolution has contributed to the significant diversity in chemotaxis mechanisms among different organisms.

  8. Evolutionary plasticity of habenular asymmetry with a conserved efferent connectivity pattern.

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    Aldo Villalón

    Full Text Available The vertebrate habenulae (Hb is an evolutionary conserved dorsal diencephalic nuclear complex that relays information from limbic and striatal forebrain regions to the ventral midbrain. One key feature of this bilateral nucleus is the presence of left-right differences in size, cytoarchitecture, connectivity, neurochemistry and/or gene expression. In teleosts, habenular asymmetry has been associated with preferential innervation of left-right habenular efferents into dorso-ventral domains of the midbrain interpeduncular nucleus (IPN. However, the degree of conservation of this trait and its relation to the structural asymmetries of the Hb are currently unknown. To address these questions, we performed the first systematic comparative analysis of structural and connectional asymmetries of the Hb in teleosts. We found striking inter-species variability in the overall shape and cytoarchitecture of the Hb, and in the frequency, strength and to a lesser degree, laterality of habenular volume at the population level. Directional asymmetry of the Hb was either to the left in D. rerio, E. bicolor, O. latipes, P. reticulata, B. splendens, or to the right in F. gardneri females. In contrast, asymmetry was absent in P. scalare and F. gardneri males at the population level, although in these species the Hb displayed volumetric asymmetries at the individual level. Inter-species variability was more pronounced across orders than within a single order, and coexisted with an overall conserved laterotopic representation of left-right habenular efferents into dorso-ventral domains of the IPN. These results suggest that the circuit design involving the Hb of teleosts promotes structural flexibility depending on developmental, cognitive and/or behavioural pressures, without affecting the main midbrain connectivity output, thus unveiling a key conserved role of this connectivity trait in the function of the circuit. We propose that ontogenic plasticity in habenular

  9. Developmental evolutionary biology of the vertebrate ear: conserving mechanoelectric transduction and developmental pathways in diverging morphologies

    Science.gov (United States)

    Fritzsch, B.; Beisel, K. W.; Bermingham, N. A.

    2000-01-01

    This brief overview shows that a start has been made to molecularly dissect vertebrate ear development and its evolutionary conservation to the development of the insect hearing organ. However, neither the patterning process of the ear nor the patterning process of insect sensory organs is sufficiently known at the moment to provide more than a first glimpse. Moreover, hardly anything is known about otocyst development of the cephalopod molluscs, another triploblast lineage that evolved complex 'ears'. We hope that the apparent conserved functional and cellular components present in the ciliated sensory neurons/hair cells will also be found in the genes required for vertebrate ear and insect sensory organ morphogenesis (Fig. 3). Likewise, we expect that homologous pre-patterning genes will soon be identified for the non-sensory cell development, which is more than a blocking of neuronal development through the Delta/Notch signaling system. Generation of the apparently unique ear could thus represent a multiplication of non-sensory cells by asymmetric and symmetric divisions as well as modification of existing patterning process by implementing novel developmental modules. In the final analysis, the vertebrate ear may come about by increasing the level of gene interactions in an already existing and highly conserved interactive cascade of bHLH genes. Since this was apparently achieved in all three lineages of triploblasts independently (Fig. 3), we now need to understand how much of the morphogenetic cascades are equally conserved across phyla to generate complex ears. The existing mutations in humans and mice may be able to point the direction of future research to understand the development of specific cell types and morphologies in the formation of complex arthropod, cephalopod, and vertebrate 'ears'.

  10. Patterns of evolutionary conservation of essential genes correlate with their compensability.

    Directory of Open Access Journals (Sweden)

    Tobias Bergmiller

    2012-06-01

    Full Text Available Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.

  11. Integrating Traditional and Evolutionary Knowledge in Biodiversity Conservation: a Population Level Case Study

    Directory of Open Access Journals (Sweden)

    Rene Dion

    2006-12-01

    Full Text Available Despite their dual importance in the assessment of endangered/threatened species, there have been few attempts to integrate traditional ecological knowledge (TEK and evolutionary biology knowledge (EBK at the population level. We contrasted long-term aboriginal TEK with previously obtained EBK in the context of seasonal migratory habits and population biology of a salmonid fish, brook charr, (Salvelinus fontinalis inhabiting a large, remote postglacial lake. Compilation of TEK spanning four decades involved analytical workshops, semidirective interviews, and collaborative fieldwork with local aboriginal informants and fishing guides. We found that TEK complemented EBK of brook charr by providing concordant and additional information about (1 population viability; (2 breeding areas and migration patterns of divergent populations; and (3 the behavioral ecology of populations within feeding areas; all of which may ultimately affect the maintenance of population diversity. Aboriginal concerns related to human pressures on this species, not revealed by EBK, also help to focus future conservation initiatives for divergent populations and to encourage restoration of traditional fishing practices. However, relative to EBK, the relevance of TEK to salmonid biodiversity conservation was evident mainly at a smaller spatial scale, for example, that of individual rivers occupied by populations or certain lake sectors. Nevertheless, EBK was only collected over a 4-yr period, so TEK provided an essential long-term temporal window to evaluate population differences and persistence. We concluded that, despite different conceptual underpinnings, spatially and temporally varying TEK and EBK both contribute to the knowledge base required to achieve sustainability and effective biodiversity conservation planning for a given species. Such integration may be particularly relevant in many isolated regions, where intraspecific diversity can go unrecognized due to sparse

  12. An evolutionary analysis of flightin reveals a conserved motif unique and widespread in Pancrustacea.

    Science.gov (United States)

    Soto-Adames, Felipe N; Alvarez-Ortiz, Pedro; Vigoreaux, Jim O

    2014-01-01

    Flightin is a thick filament protein that in Drosophila melanogaster is uniquely expressed in the asynchronous, indirect flight muscles (IFM). Flightin is required for the structure and function of the IFM and is indispensable for flight in Drosophila. Given the importance of flight acquisition in the evolutionary history of insects, here we study the phylogeny and distribution of flightin. Flightin was identified in 69 species of hexapods in classes Collembola (springtails), Protura, Diplura, and insect orders Thysanura (silverfish), Dictyoptera (roaches), Orthoptera (grasshoppers), Pthiraptera (lice), Hemiptera (true bugs), Coleoptera (beetles), Neuroptera (green lacewing), Hymenoptera (bees, ants, and wasps), Lepidoptera (moths), and Diptera (flies and mosquitoes). Flightin was also found in 14 species of crustaceans in orders Anostraca (water flea), Cladocera (brine shrimp), Isopoda (pill bugs), Amphipoda (scuds, sideswimmers), and Decapoda (lobsters, crabs, and shrimps). Flightin was not identified in representatives of chelicerates, myriapods, or any species outside Pancrustacea (Tetraconata, sensu Dohle). Alignment of amino acid sequences revealed a conserved region of 52 amino acids, referred herein as WYR, that is bound by strictly conserved tryptophan (W) and arginine (R) and an intervening sequence with a high content of tyrosines (Y). This motif has no homologs in GenBank or PROSITE and is unique to flightin and paraflightin, a putative flightin paralog identified in decapods. A third motif of unclear affinities to pancrustacean WYR was observed in chelicerates. Phylogenetic analysis of amino acid sequences of the conserved motif suggests that paraflightin originated before the divergence of amphipods, isopods, and decapods. We conclude that flightin originated de novo in the ancestor of Pancrustacea > 500 MYA, well before the divergence of insects (~400 MYA) and the origin of flight (~325 MYA), and that its IFM-specific function in Drosophila is a more

  13. Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance.

    Directory of Open Access Journals (Sweden)

    Yuan-Yuan Li

    2006-07-01

    Full Text Available Several "head-to-head" (or "bidirectional" gene pairs have been studied in individual experiments, but genome-wide analysis of this gene organization, especially in terms of transcriptional correlation and functional association, is still insufficient. We conducted a systematic investigation of head-to-head gene organization focusing on structural features, evolutionary conservation, expression correlation and functional association. Of the present 1,262, 1,071, and 491 head-to-head pairs identified in human, mouse, and rat genomes, respectively, pairs with 1- to 400-base pair distance between transcription start sites form the majority (62.36%, 64.15%, and 55.19% for human, mouse, and rat,respectively of each dataset, and the largest group is always the one with a transcription start site distance of 101 to 200 base pairs. The phylogenetic analysis among Fugu, chicken, and human indicates a negative selection on the separation of head-to-head genes across vertebrate evolution, and thus the ancestral existence of this gene organization. The expression analysis shows that most of the human head-to-head genes are significantly correlated,and the correlation could be positive, negative, or alternative depending on the experimental conditions. Finally, head to-head genes statistically tend to perform similar functions, and gene pairs associated with the significant cofunctions seem to have stronger expression correlations. The findings indicate that the head-to-head gene organization is ancient and conserved, which subjects functionally related genes to correlated transcriptional regulation and thus provides an exquisite mechanism of transcriptional regulation based on gene organization. These results have significantly expanded the knowledge about head-to-head gene organization. Supplementary materials for this study are available at http://www.scbit.org/h2h.

  14. Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation.

    Science.gov (United States)

    Chaiboonchoe, Amphun; Ghamsari, Lila; Dohai, Bushra; Ng, Patrick; Khraiwesh, Basel; Jaiswal, Ashish; Jijakli, Kenan; Koussa, Joseph; Nelson, David R; Cai, Hong; Yang, Xinping; Chang, Roger L; Papin, Jason; Yu, Haiyuan; Balaji, Santhanam; Salehi-Ashtiani, Kourosh

    2016-07-19

    Metabolic networks, which are mathematical representations of organismal metabolism, are reconstructed to provide computational platforms to guide metabolic engineering experiments and explore fundamental questions on metabolism. Systems level analyses, such as interrogation of phylogenetic relationships within the network, can provide further guidance on the modification of metabolic circuitries. Chlamydomonas reinhardtii, a biofuel relevant green alga that has retained key genes with plant, animal, and protist affinities, serves as an ideal model organism to investigate the interplay between gene function and phylogenetic affinities at multiple organizational levels. Here, using detailed topological and functional analyses, coupled with transcriptomics studies on a metabolic network that we have reconstructed for C. reinhardtii, we show that network connectivity has a significant concordance with the co-conservation of genes; however, a distinction between topological and functional relationships is observable within the network. Dynamic and static modes of co-conservation were defined and observed in a subset of gene-pairs across the network topologically. In contrast, genes with predicted synthetic interactions, or genes involved in coupled reactions, show significant enrichment for both shorter and longer phylogenetic distances. Based on our results, we propose that the metabolic network of C. reinhardtii is assembled with an architecture to minimize phylogenetic profile distances topologically, while it includes an expansion of such distances for functionally interacting genes. This arrangement may increase the robustness of C. reinhardtii's network in dealing with varied environmental challenges that the species may face. The defined evolutionary constraints within the network, which identify important pairings of genes in metabolism, may offer guidance on synthetic biology approaches to optimize the production of desirable metabolites. PMID:27357594

  15. Clustering of reads with alignment-free measures and quality values

    OpenAIRE

    Comin, Matteo; Leoni, Andrea; Schimd, Michele

    2015-01-01

    Background The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers count...

  16. H3K36ac Is an Evolutionary Conserved Plant Histone Modification That Marks Active Genes.

    Science.gov (United States)

    Mahrez, Walid; Arellano, Minerva Susana Trejo; Moreno-Romero, Jordi; Nakamura, Miyuki; Shu, Huan; Nanni, Paolo; Köhler, Claudia; Gruissem, Wilhelm; Hennig, Lars

    2016-03-01

    In eukaryotic cells, histones are subject to a large number of posttranslational modifications whose sequential or combinatorial action affects chromatin structure and genome function. We identified acetylation at Lys-36 in histone H3 (H3K36ac) as a new chromatin modification in plants. The H3K36ac modification is evolutionary conserved in seed plants, including the gymnosperm Norway spruce (Picea abies) and the angiosperms rice (Oryza sativa), tobacco (Nicotiana tabacum), and Arabidopsis (Arabidopsis thaliana). In Arabidopsis, H3K36ac is highly enriched in euchromatin but not in heterochromatin. Genome-wide chromatin immunoprecipitation sequencing experiments revealed that H3K36ac peaks at the 5' end of genes, mainly on the two nucleosomes immediately distal to the transcription start site, independently of gene length. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for H3K36ac homeostasis. H3K36ac and H3K36me3 show negative crosstalk, which is mediated by GCN5 and the histone methyl transferase SDG8. Although H3K36ac is associated with gene activity, we did not find a linear relationship between H3K36ac and transcript levels, suggesting that H3K36ac is a binary indicator of transcription. PMID:26764380

  17. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

    Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

  18. Are Pharmaceuticals with Evolutionary Conserved Molecular Drug Targets More Potent to Cause Toxic Effects in Non-Target Organisms?

    OpenAIRE

    Sara Furuhagen; Anne Fuchs; Elin Lundström Belleza; Magnus Breitholtz; Elena Gorokhova

    2014-01-01

    The ubiquitous use of pharmaceuticals has resulted in a continuous discharge into wastewater and pharmaceuticals and their metabolites are found in the environment. Due to their design towards specific drug targets, pharmaceuticals may be therapeutically active already at low environmental concentrations. Several human drug targets are evolutionary conserved in aquatic organisms, raising concerns about effects of these pharmaceuticals in non-target organisms. In this study, we hypothesized th...

  19. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets.

    Science.gov (United States)

    Hogan, Gregory J; Brown, Patrick O; Herschlag, Daniel

    2015-11-01

    Reprogramming of a gene's expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs. We identified that RNA targets of Puf3 orthologs have been conserved over 100-500 million years of evolution in five eukaryotic lineages. Focusing on Puf proteins and their targets across 80 fungi, we constructed a parsimonious model for their evolutionary history. This model entails extensive and coordinated changes in the Puf targets as well as changes in the number of Puf genes and alterations of RNA binding specificity including that: 1) Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes predates the origin of budding yeasts and filamentous fungi and was maintained for 500 million years, throughout the evolution of budding yeast. 2) In filamentous fungi, remarkably, more than 150 of the ancestral Puf3 targets were gained by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and a sister lineage losing Puf3 as a regulator of these RNAs. The decrease in gene expression of these mRNAs upon deletion of Puf4 in filamentous fungi (N. crassa) in contrast to the increase upon Puf3 deletion in budding yeast (S. cerevisiae) suggests that the output of the RNA regulatory network is different with Puf4 in filamentous fungi than with Puf3 in budding yeast. 3) The coregulated Puf4 target set in filamentous fungi expanded to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle and other nuclear-encoded RNAs with mitochondrial function not bound by Puf3 in budding yeast, observations that provide additional evidence for substantial rewiring of post-transcriptional regulation. 4) Puf3 also expanded and diversified its targets in filamentous fungi, gaining interactions with the mRNAs encoding the mitochondrial electron transport

  20. Evolutionary Conservation of Xylan Biosynthetic Genes in Selaginella moellendorffii and Physcomitrella patens.

    Science.gov (United States)

    Haghighat, Marziyeh; Teng, Quincy; Zhong, Ruiqin; Ye, Zheng-Hua

    2016-08-01

    Xylan is a major cross-linking hemicellulose in secondary walls of vascular tissues, and the recruitment of xylan as a secondary wall component was suggested to be a pivotal event for the evolution of vascular tissues. To decipher the evolution of xylan structure and xylan biosynthetic genes, we analyzed xylan substitution patterns and characterized genes mediating methylation of glucuronic acid (GlcA) side chains in xylan of the model seedless vascular plant, Selaginella moellendorffii, and investigated GT43 genes from S. moellendorffii and the model non-vascular plant, Physcomitrella patens, for their roles in xylan biosynthesis. Using nuclear magentic resonance spectroscopy, we have demonstrated that S. moellendorffii xylan consists of β-1,4-linked xylosyl residues subsituted solely with methylated GlcA residues and that xylans from both S. moellendorffii and P. patens are acetylated at O-2 and O-3. To investigate genes responsible for GlcA methylation of xylan, we identified two DUF579 genes in the S. moellendorffii genome and showed that one of them, SmGXM, encodes a glucuronoxylan methyltransferase capable of adding the methyl group onto the GlcA side chain of xylooligomers. Furthermore, we revealed that the two GT43 genes in S. moellendorffii, SmGT43A and SmGT43B, are functional orthologs of the Arabidopsis xylan backbone biosynthetic genes IRX9 and IRX14, respectively, indicating the evolutionary conservation of the involvement of two functionally non-redundant groups of GT43 genes in xylan backbone biosynthesis between seedless and seed vascular plants. Among the five GT43 genes in P. patens, PpGT43A was found to be a functional ortholog of Arabidopsis IRX9, suggesting that the recruitment of GT43 genes in xylan backbone biosynthesis occurred when non-vascular plants appeared on land. PMID:27345025

  1. Neotropical fish-fruit interactions: eco-evolutionary dynamics and conservation.

    Science.gov (United States)

    Correa, Sandra Bibiana; Costa-Pereira, Raul; Fleming, Theodore; Goulding, Michael; Anderson, Jill T

    2015-11-01

    Frugivorous fish play a prominent role in seed dispersal and reproductive dynamics of plant communities in riparian and floodplain habitats of tropical regions worldwide. In Neotropical wetlands, many plant species have fleshy fruits and synchronize their fruiting with the flood season, when fruit-eating fish forage in forest and savannahs for periods of up to 7 months. We conducted a comprehensive analysis to examine the evolutionary origin of fish-fruit interactions, describe fruit traits associated with seed dispersal and seed predation, and assess the influence of fish size on the effectiveness of seed dispersal by fish (ichthyochory). To date, 62 studies have documented 566 species of fruits and seeds from 82 plant families in the diets of 69 Neotropical fish species. Fish interactions with flowering plants are likely to be as old as 70 million years in the Neotropics, pre-dating most modern bird-fruit and mammal-fruit interactions, and contributing to long-distance seed dispersal and possibly the radiation of early angiosperms. Ichthyochory occurs across the angiosperm phylogeny, and is more frequent among advanced eudicots. Numerous fish species are capable of dispersing small seeds, but only a limited number of species can disperse large seeds. The size of dispersed seeds and the probability of seed dispersal both increase with fish size. Large-bodied species are the most effective seed dispersal agents and remain the primary target of fishing activities in the Neotropics. Thus, conservation efforts should focus on these species to ensure continuity of plant recruitment dynamics and maintenance of plant diversity in riparian and floodplain ecosystems. PMID:25599800

  2. Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos

    OpenAIRE

    Tiancheng Liu; Lin Yu; Guohui Ding; Zhen Wang; Lei Liu; Hong Li; Yixue Li

    2015-01-01

    Evolutionary developmental biology (EVO-DEVO) tries to decode evolutionary constraints on the stages of embryonic development. Two models—the “funnel-like” model and the “hourglass” model—have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED) were undetected in previous studies. Based on single cell RNA sequencing of stages during human ...

  3. A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs

    Science.gov (United States)

    Xu, Minli; Su, Zhengchang

    2010-01-01

    Background Transcription factor binding site (TFBS) motifs can be accurately represented by position frequency matrices (PFM) or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs. In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described. Methodology/Principal Findings Here we describe a novel alignment-free method for quantifying the similarity of motifs using their PFMs by converting PFMs into k-mer vectors. The motifs could then be compared by measuring the similarity among their corresponding k-mer vectors. Conclusions/Significance We demonstrate that our method in general achieves similar performance or outperforms the existing methods for clustering motifs according to their binding preference and identifying similar motifs of transcription factors of the same family. PMID:20098703

  4. A novel alignment-free method for comparing transcription factor binding site motifs.

    Directory of Open Access Journals (Sweden)

    Minli Xu

    Full Text Available BACKGROUND: Transcription factor binding site (TFBS motifs can be accurately represented by position frequency matrices (PFM or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs. In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe a novel alignment-free method for quantifying the similarity of motifs using their PFMs by converting PFMs into k-mer vectors. The motifs could then be compared by measuring the similarity among their corresponding k-mer vectors. CONCLUSIONS/SIGNIFICANCE: We demonstrate that our method in general achieves similar performance or outperforms the existing methods for clustering motifs according to their binding preference and identifying similar motifs of transcription factors of the same family.

  5. Alignment-Free Methods for the Detection and Specificity Prediction of Adenylation Domains.

    Science.gov (United States)

    Agüero-Chapin, Guillermin; Pérez-Machado, Gisselle; Sánchez-Rodríguez, Aminael; Santos, Miguel Machado; Antunes, Agostinho

    2016-01-01

    Identifying adenylation domains (A-domains) and their substrate specificity can aid the detection of nonribosomal peptide synthetases (NRPS) at genome/proteome level and allow inferring the structure of oligopeptides with relevant biological activities. However, that is challenging task due to the high sequence diversity of A-domains (~10-40 % of amino acid identity) and their selectivity for 50 different natural/unnatural amino acids. Altogether these characteristics make their detection and the prediction of their substrate specificity a real challenge when using traditional sequence alignment methods, e.g., BLAST searches. In this chapter we describe two workflows based on alignment-free methods intended for the identification and substrate specificity prediction of A-domains. To identify A-domains we introduce a graphical-numerical method, implemented in TI2BioP version 2.0 (topological indices to biopolymers), which in a first step uses protein four-color maps to represent A-domains. In a second step, simple topological indices (TIs), called spectral moments, are derived from the graphical representations of known A-domains (positive dataset) and of unrelated but well-characterized sequences (negative set). Spectral moments are then used as input predictors for statistical classification techniques to build alignment-free models. Finally, the resulting alignment-free models can be used to explore entire proteomes for unannotated A-domains. In addition, this graphical-numerical methodology works as a sequence-search method that can be ensemble with homology-based tools to deeply explore the A-domain signature and cope with the diversity of this class (Aguero-Chapin et al., PLoS One 8(7):e65926, 2013). The second workflow for the prediction of A-domain's substrate specificity is based on alignment-free models constructed by transductive support vector machines (TSVMs) that incorporate information of uncharacterized A-domains. The construction of the models was

  6. Mitochondrial and Nuclear DNA Survey of Zootoca vivipara across the Eastern Italian Alps: Evolutionary Relationships, Historical Demography and Conservation Implications

    Science.gov (United States)

    Cornetti, Luca; Menegon, Michele; Giovine, Giovanni; Heulin, Benoit; Vernesi, Cristiano

    2014-01-01

    The European common lizard Zootoca vivipara exhibits reproductive bimodality, with populations being either viviparous or oviparous. In the central-eastern Italian Alps oviparous populations (Z. v. carniolica) and viviparous populations (Z. v. vivipara) partly overlap geographically. Studying the evolutionary relationship between these taxa presents an interesting opportunity to gain insight into the evolution of this trait. We aim to: i) test whether Z. v. carniolica, which is endangered, constitutes an ESU (Evolutionary Significant Unity); ii) infer mtDNA divergence time between the Z. v. carniolica clade and all the other Z. vivipara subspecies with the aid of an external calibration point; and iii) describe the phylogeographical and demographic scenarios in the area. To do so we sequenced about 200 individuals for mitochondrial variation; 64 of them were also analysed for three nuclear genes. Furthermore, we analysed the same nuclear markers in 17 individuals from the other oviparous subspecies Z. v. louislantzi and 11 individuals of Z. v. vivipara from widespread geographical origins. The mtDNA and nDNA loci that we examined supported the monophyly of Z. v. carniolica. The mtDNA-based estimate of divergence time between Z. v. carniolica and all the other subspecies indicated a separation at 4.5 Mya (95% CI 6.1–2.6), with about 5% of sequence divergence. Considering that Z. v. carniolica harbours higher genetic diversity, while Z. v. vivipara from central-eastern Alps shows a signature of recent population and spatial expansion, we argue that Z. v. carniolica represents a distinct evolutionary unit, with a presumably long-term evolutionary history of separation. Z. v. carniolica populations, occurring at higher latitudes and altitudes than insofar supposed, live in peat bogs, a seriously threatened habitat: taking into account also its evolutionary distinctness, specific conservation measures should be considered. PMID:24465784

  7. Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos

    Directory of Open Access Journals (Sweden)

    Tiancheng Liu

    2015-01-01

    Full Text Available Evolutionary developmental biology (EVO-DEVO tries to decode evolutionary constraints on the stages of embryonic development. Two models—the “funnel-like” model and the “hourglass” model—have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA. Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

  8. Genomic Signal Processing Methods for Computation of Alignment-Free Distances from DNA Sequences

    Science.gov (United States)

    Borrayo, Ernesto; Mendizabal-Ruiz, E. Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P.; Morales, J. Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments. PMID:25393409

  9. Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait

    Directory of Open Access Journals (Sweden)

    Shirai Leila T

    2012-02-01

    Full Text Available Abstract Background The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. Results We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eyespot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. Conclusions The evolutionary history of gene

  10. Conservation genomics reveals multiple evolutionary units within Bell’s Vireo (Vireo bellii).

    Science.gov (United States)

    Klicka, Luke B.; Kus, Barbara E.; Title, Pascal O.; Burns, Kevin J.

    2016-01-01

    The Bell’s Vireo (Vireo bellii) is a widespread North American species of bird that has declined since the mid-1960s primarily due to habitat modification. Throughout its range, Bell’s Vireo populations are regulated under varying degrees of protection; however, the species has never been characterized genetically. Therefore, the current taxonomy used to guide management decisions may misrepresent the true evolutionary history for the species. We sequenced 86 individuals for ND2 and genotyped 48 individuals for genome-wide SNPs to identify distinct lineages within Bell’s Vireo. Phylogenetic analyses uncovered two distinct clades that are separated in the arid southwestern United States, near the border of the Chihuahuan and Sonoran Deserts. These clades diverged from each other approximately 1.11–2.04 mya. The timing of diversification, geographic location, and niche modeling of the east/west divergence suggest vicariance as a mode of diversification for these two lineages. Analyses of the SNP dataset provided additional resolution and indicated the Least Bell’s Vireo populations are a distinct evolutionary lineage. Our genetic evidence, together with information from morphology and behavior, suggests that the Bell’s Vireo complex involves two species, each containing two separate subspecies. This new information has implications for the federal, state and other listing status of Bell’s Vireo throughout its range.

  11. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.

    Directory of Open Access Journals (Sweden)

    Pandurang S Kolekar

    Full Text Available Rhinoviruses (RV are increasingly being reported to cause mild to severe infections of respiratory tract in humans. RV are antigenically the most diverse species of the genus Enterovirus and family Picornaviridae. There are three species of RV (RV-A, -B and -C, with 80, 32 and 55 serotypes/types, respectively. Antigenic variation is the main limiting factor for development of a cross-protective vaccine against RV.Serotyping of Rhinoviruses is carried out using cross-neutralization assays in cell culture. However, these assays become laborious and time-consuming for the large number of strains. Alternatively, serotyping of RV is carried out by alignment-based phylogeny of both protein and nucleotide sequences of VP1. However, serotyping of RV based on alignment-based phylogeny is a multi-step process, which needs to be repeated every time a new isolate is sequenced. In view of the growing need for serotyping of RV, an alignment-free method based on "return time distribution" (RTD of amino acid residues in VP1 protein has been developed and implemented in the form of a web server titled RV-Typer. RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (k = 2 to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods. The web server is available at http://bioinfo.net.in/RV-Typer/home.html.

  12. Structural proteomics of minimal organisms: conservation ofprotein fold usage and evolutionary implications

    Energy Technology Data Exchange (ETDEWEB)

    Chandonia, John-Marc; Kim, Sung-Hou

    2006-03-15

    Background: Determining the complete repertoire of proteinstructures for all soluble, globular proteins in a single organism hasbeen one of the major goals of several structural genomics projects inrecent years. Results: We report that this goal has nearly been reachedfor several "minimal organisms"--parasites or symbionts with reducedgenomes--for which over 95 percent of the soluble, globular proteins maynow be assigned folds, overall 3-D backbone structures. We analyze thestructures of these proteins as they relate to cellular functions, andcompare conservation off old usage between functional categories. We alsocompare patterns in the conservation off olds among minimal organisms andthose observed between minimal organisms and other bacteria. Conclusion:We find that proteins performing essential cellular functions closelyrelated to transcription and translation exhibit a higher degree ofconservation in fold usage than proteins in other functional categories.Folds related to transcription and translation functional categories werealso over represented in minimal organisms compared to otherbacteria.

  13. Thyroid Hormone Regulation of Adult Intestinal Stem Cell Development: Mechanisms and Evolutionary Conservations

    OpenAIRE

    Sun, Guihong; Shi, Yun-Bo

    2012-01-01

    The adult mammalian intestine has long been used as a model to study adult stem cell function and tissue renewal as the intestinal epithelium is constantly undergoing self-renewal throughout adult life. This is accomplished through the proliferation and subsequent differentiation of the adult stem cells located in the crypt. The development of this self-renewal system is, however, poorly understood. A number of studies suggest that the formation/maturation of the adult intestine is conserved ...

  14. Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses

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    Igor R. Costa

    2014-12-01

    Full Text Available Essential amino acids (EAA consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS and betaine-homocysteine S-methyltransferase (BHMT diverged from the expected Tree of Life (ToL relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.

  15. Evolutionary Conservation of a GPCR-Independent Mechanism of Trimeric G Protein Activation

    Science.gov (United States)

    Coleman, Brantley D.; Marivin, Arthur; Parag-Sharma, Kshitij; DiGiacomo, Vincent; Kim, Seongseop; Pepper, Judy S.; Casler, Jason; Nguyen, Lien T.; Koelle, Michael R.; Garcia-Marcos, Mikel

    2016-01-01

    Trimeric G protein signaling is a fundamental mechanism of cellular communication in eukaryotes. The core of this mechanism consists of activation of G proteins by the guanine-nucleotide exchange factor (GEF) activity of G protein coupled receptors. However, the duration and amplitude of G protein-mediated signaling are controlled by a complex network of accessory proteins that appeared and diversified during evolution. Among them, nonreceptor proteins with GEF activity are the least characterized. We recently found that proteins of the ccdc88 family possess a Gα-binding and activating (GBA) motif that confers GEF activity and regulates mammalian cell behavior. A sequence similarity-based search revealed that ccdc88 genes are highly conserved across metazoa but the GBA motif is absent in most invertebrates. This prompted us to investigate whether the GBA motif is present in other nonreceptor proteins in invertebrates. An unbiased bioinformatics search in Caenorhabditis elegans identified GBAS-1 (GBA and SPK domain containing-1) as a GBA motif-containing protein with homologs only in closely related worm species. We demonstrate that GBAS-1 has GEF activity for the nematode G protein GOA-1 and that the two proteins are coexpressed in many cells of living worms. Furthermore, we show that GBAS-1 can activate mammalian Gα-subunits and provide structural insights into the evolutionarily conserved determinants of the GBA–G protein interface. These results demonstrate that the GBA motif is a functional GEF module conserved among highly divergent proteins across evolution, indicating that the GBA-Gα binding mode is strongly constrained under selective pressure to mediate receptor-independent G protein activation in metazoans. PMID:26659249

  16. A phylogenetic study of SPBP and RAI1: evolutionary conservation of chromatin binding modules.

    Directory of Open Access Journals (Sweden)

    Sagar Darvekar

    Full Text Available Our genome is assembled into and array of highly dynamic nucleosome structures allowing spatial and temporal access to DNA. The nucleosomes are subject to a wide array of post-translational modifications, altering the DNA-histone interaction and serving as docking sites for proteins exhibiting effector or "reader" modules. The nuclear proteins SPBP and RAI1 are composed of several putative "reader" modules which may have ability to recognise a set of histone modification marks. Here we have performed a phylogenetic study of their putative reader modules, the C-terminal ePHD/ADD like domain, a novel nucleosome binding region and an AT-hook motif. Interactions studies in vitro and in yeast cells suggested that despite the extraordinary long loop region in their ePHD/ADD-like chromatin binding domains, the C-terminal region of both proteins seem to adopt a cross-braced topology of zinc finger interactions similar to other structurally determined ePHD/ADD structures. Both their ePHD/ADD-like domain and their novel nucleosome binding domain are highly conserved in vertebrate evolution, and construction of a phylogenetic tree displayed two well supported clusters representing SPBP and RAI1, respectively. Their genome and domain organisation suggest that SPBP and RAI1 have occurred from a gene duplication event. The phylogenetic tree suggests that this duplication has happened early in vertebrate evolution, since only one gene was identified in insects and lancelet. Finally, experimental data confirm that the conserved novel nucleosome binding region of RAI1 has the ability to bind the nucleosome core and histones. However, an adjacent conserved AT-hook motif as identified in SPBP is not present in RAI1, and deletion of the novel nucleosome binding region of RAI1 did not significantly affect its nuclear localisation.

  17. Evolutionary Conservation of a GPCR-Independent Mechanism of Trimeric G Protein Activation.

    Science.gov (United States)

    Coleman, Brantley D; Marivin, Arthur; Parag-Sharma, Kshitij; DiGiacomo, Vincent; Kim, Seongseop; Pepper, Judy S; Casler, Jason; Nguyen, Lien T; Koelle, Michael R; Garcia-Marcos, Mikel

    2016-03-01

    Trimeric G protein signaling is a fundamental mechanism of cellular communication in eukaryotes. The core of this mechanism consists of activation of G proteins by the guanine-nucleotide exchange factor (GEF) activity of G protein coupled receptors. However, the duration and amplitude of G protein-mediated signaling are controlled by a complex network of accessory proteins that appeared and diversified during evolution. Among them, nonreceptor proteins with GEF activity are the least characterized. We recently found that proteins of the ccdc88 family possess a Gα-binding and activating (GBA) motif that confers GEF activity and regulates mammalian cell behavior. A sequence similarity-based search revealed that ccdc88 genes are highly conserved across metazoa but the GBA motif is absent in most invertebrates. This prompted us to investigate whether the GBA motif is present in other nonreceptor proteins in invertebrates. An unbiased bioinformatics search in Caenorhabditis elegans identified GBAS-1 (GBA and SPK domain containing-1) as a GBA motif-containing protein with homologs only in closely related worm species. We demonstrate that GBAS-1 has GEF activity for the nematode G protein GOA-1 and that the two proteins are coexpressed in many cells of living worms. Furthermore, we show that GBAS-1 can activate mammalian Gα-subunits and provide structural insights into the evolutionarily conserved determinants of the GBA-G protein interface. These results demonstrate that the GBA motif is a functional GEF module conserved among highly divergent proteins across evolution, indicating that the GBA-Gα binding mode is strongly constrained under selective pressure to mediate receptor-independent G protein activation in metazoans. PMID:26659249

  18. Evolutionary conservation of ten microsatellite loci in four species of Felidae.

    Science.gov (United States)

    Menotti-Raymond, M A; O'Brien, S J

    1995-01-01

    Short tandem repeat polymorphisms (STRP), or microsatellites, are widespread among vertebrate genomes and are useful in gene mapping and population studies due to a high level of length polymorphism. We describe here the isolation, characterization, and PCR amplification of 10 microsatellite loci from the domestic cat, Felis catus. The flanking primer sequences were conserved among other Felidae species, and amplification products demonstrated abundant polymorphism in puma, lion, cheetah, and domestic cat. The cheetah sample exhibited the lowest level of polymorphism for these loci among felid species. PMID:7658003

  19. Evolutionary Conservation and Diversification of the Translation Initiation Apparatus in Trypanosomatids

    Directory of Open Access Journals (Sweden)

    Alexandra Zinoviev

    2012-01-01

    Full Text Available Trypanosomatids are ancient eukaryotic parasites that migrate between insect vectors and mammalian hosts, causing a range of diseases in humans and domestic animals. Trypanosomatids feature a multitude of unusual molecular features, including polycistronic transcription and subsequent processing by trans-splicing and polyadenylation. Regulation of protein coding genes is posttranscriptional and thus, translation regulation is fundamental for activating the developmental program of gene expression. The spliced-leader RNA is attached to all mRNAs. It contains an unusual hypermethylated cap-4 structure in its 5 end. The cap-binding complex, eIF4F, has gone through evolutionary changes in accordance with the requirement to bind cap-4. The eIF4F components in trypanosomatids are highly diverged from their orthologs in higher eukaryotes, and their potential functions are discussed. The cap-binding activity in all eukaryotes is a target for regulation and plays a similar role in trypanosomatids. Recent studies revealed a novel eIF4E-interacting protein, involved in directing stage-specific and stress-induced translation pathways. Translation regulation during stress also follows unusual regulatory cues, as the increased translation of Hsp83 following heat stress is driven by a defined element in the 3 UTR, unlike higher eukaryotes. Overall, the environmental switches experienced by trypanosomatids during their life cycle seem to affect their translational machinery in unique ways.

  20. Evolutionary conservation of dual Sec translocases in the cyanelles of Cyanophora paradoxa

    Directory of Open Access Journals (Sweden)

    Löffelhardt Wolfgang

    2008-11-01

    Full Text Available Abstract Background Cyanelles, the peptidoglycan-armored plastids of glaucocystophytes, occupy a unique bridge position in between free-living cyanobacteria and chloroplasts. In some respects they side with cyanobacteria whereas other features are clearly shared with chloroplasts. The Sec translocase, an example for "conservative sorting" in the course of evolution, is found in the plasma membrane of all prokaryotes, in the thylakoid membrane of chloroplasts and in both these membrane types of cyanobacteria. Results In this paper we present evidence for a dual location of the Sec translocon in the thylakoid as well as inner envelope membranes of the cyanelles from Cyanophora paradoxa, i. e. conservative sorting sensu stricto. The prerequisite was the generation of specific antisera directed against cyanelle SecY that allowed immunodetection of the protein on SDS gels from both membrane types separated by sucrose density gradient floatation centrifugation. Immunoblotting of blue-native gels yielded positive but differential results for both the thylakoid and envelope Sec complexes, respectively. In addition, heterologous antisera directed against components of the Toc/Tic translocons and binding of a labeled precursor protein were used to discriminate between inner and outer envelope membranes. Conclusion The envelope translocase can be envisaged as a prokaryotic feature missing in higher plant chloroplasts but retained in cyanelles, likely for protein transport to the periplasm. Candidate passengers are cytochrome c6 and enzymes of peptidoglycan metabolism. The minimal set of subunits of the Toc/Tic translocase of a primitive plastid is proposed.

  1. Phylogeography of Camellia taliensis (Theaceae inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

    Directory of Open Access Journals (Sweden)

    Liu Yang

    2012-06-01

    Full Text Available Abstract Background As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. Results Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314 were almost as high as at PAL (h = 0.836; π = 0.00417. Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989, suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301 provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel’s test of nrDNA haplotypes (r = 0.234, P  Conclusions We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.

  2. Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Ermini, Luca; Schubert, Mikkel;

    2015-01-01

    short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878–1929 CE, including the Holotype. These were compared to the...... hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show......Przewalski’s horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still...

  3. Expression analysis of five zebrafish RXFP3 homologues reveals evolutionary conservation of gene expression pattern.

    Science.gov (United States)

    Donizetti, Aldo; Fiengo, Marcella; Iazzetti, Giovanni; del Gaudio, Rosanna; Di Giaimo, Rossella; Pariante, Paolo; Minucci, Sergio; Aniello, Francesco

    2015-01-01

    Relaxin peptides exert different functions in reproduction and neuroendocrine processes via interaction with two evolutionarily unrelated groups of receptors: RXFP1 and RXFP2 on one hand, RXFP3 and RXFP4 on the other hand. Evolution of receptor genes after splitting of tetrapods and teleost lineage led to a different retention rate between mammals and fish, with the latter having more gene copies compared to the former. In order to improve our knowledge on the evolution of the relaxin ligands/receptors system and have insights on their function in early stages of life, in the present paper we analyzed the expression pattern of five zebrafish RXFP3 homologue genes during embryonic development. In our analysis, we show that only two of the five genes are expressed during embryogenesis and that their transcripts are present in all the developmental stages. Spatial localization analysis of these transcripts revealed that the gene expression is restricted in specific territories starting from early pharyngula stage. Both genes are expressed in the brain but in different cell clusters and in extra-neural territories, one gene in the interrenal gland and the other in the pancreas. These two genes share expression territories with the homologue mammalian counterpart, highlighting a general conservation of gene expression regulatory processes and their putative function during evolution that are established early in vertebrate embryogenesis. PMID:25384467

  4. An evolutionary conserved early replicating segment on the sex chromosomes of man and the great apes.

    Science.gov (United States)

    Weber, B; Schempp, W; Wiesner, H

    1986-01-01

    Replication studies on prometaphase chromosomes of man, the chimpanzee, the pygmy chimpanzee, the gorilla, and the orangutan reveal great interspecific homologies between the autosomes. The early replicating X chromosomes clearly show a high degree of conservation of both the pattern and the time course of replication. An early replicating segment on the short arm of the X chromosomes of man (Xp22.3) which escapes inactivation can be found on the X chromosomes of the great apes as well. Furthermore, the most early replicating segment on the Y chromosomes of all species tested appears to be homologous to this segment on the X chromosomes. Therefore, these early replicating segments in the great apes may correspond to the pseudoautosomal segment proposed to exist in man. From further cytogenetic characterization of the Y chromosomes it is evident that structural alterations have resulted in an extreme divergence in both the euchromatic and heterochromatic parts. It is assumed, therefore, that, in contrast to the X chromosomes, the Y chromosomes have undergone a rapid evolution within the higher primates. PMID:3096642

  5. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

    Directory of Open Access Journals (Sweden)

    Ana Zafra Ruano

    2016-05-01

    Full Text Available Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.

  6. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

    Science.gov (United States)

    Zafra Ruano, Ana; Cilia, Elisa; Couceiro, José R; Ruiz Sanz, Javier; Schymkowitz, Joost; Rousseau, Frederic; Luque, Irene; Lenaerts, Tom

    2016-05-01

    Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis. PMID:27213566

  7. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors

    Science.gov (United States)

    Ruiz Sanz, Javier; Schymkowitz, Joost; Rousseau, Frederic

    2016-01-01

    Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis. PMID:27213566

  8. Are pharmaceuticals with evolutionary conserved molecular drug targets more potent to cause toxic effects in non-target organisms?

    Directory of Open Access Journals (Sweden)

    Sara Furuhagen

    Full Text Available The ubiquitous use of pharmaceuticals has resulted in a continuous discharge into wastewater and pharmaceuticals and their metabolites are found in the environment. Due to their design towards specific drug targets, pharmaceuticals may be therapeutically active already at low environmental concentrations. Several human drug targets are evolutionary conserved in aquatic organisms, raising concerns about effects of these pharmaceuticals in non-target organisms. In this study, we hypothesized that the toxicity of a pharmaceutical towards a non-target invertebrate depends on the presence of the human drug target orthologs in this species. This was tested by assessing toxicity of pharmaceuticals with (miconazole and promethazine and without (levonorgestrel identified drug target orthologs in the cladoceran Daphnia magna. The toxicity was evaluated using general toxicity endpoints at individual (immobility, reproduction and development, biochemical (RNA and DNA content and molecular (gene expression levels. The results provide evidence for higher toxicity of miconazole and promethazine, i.e. the drugs with identified drug target orthologs. At the individual level, miconazole had the lowest effect concentrations for immobility and reproduction (0.3 and 0.022 mg L-1, respectively followed by promethazine (1.6 and 0.18 mg L-1, respectively. At the biochemical level, individual RNA content was affected by miconazole and promethazine already at 0.0023 and 0.059 mg L-1, respectively. At the molecular level, gene expression for cuticle protein was significantly suppressed by exposure to both miconazole and promethazine; moreover, daphnids exposed to miconazole had significantly lower vitellogenin expression. Levonorgestrel did not have any effects on any endpoints in the concentrations tested. These results highlight the importance of considering drug target conservation in environmental risk assessments of pharmaceuticals.

  9. Geometric constraints derived from the law of conservation of volume and applied to evolutionary models for detachment folding

    Energy Technology Data Exchange (ETDEWEB)

    Dahlstrom, C.D.A. (Chevron Corp., San Francisco, CA (USA))

    1990-03-01

    This paper presents geometric arguments for modifying the conventional concept for the evolution of concentric fold trains above nonductile detachment zones. The common geometric model for concentric folding above a detachment invokes a wave train with fixed fold axes regularly spaced along the fold panel. Limb lengths from crest to trough remain constant as the limb dips increase to uplift the anticlinal crests while the synclinal troughs slide parallel to the detachment plane. The basic depth to detachment calculation, which derives from the Law of Conservation of Volume, requires that the area of uplift above regional for a concentric anticline be equal to the arithmetic product of the shortening and the depth to detachment. This imposes a geometric constraint with which a constant limb length anticline, growing by increasing limb dip above a fixed detachment plane, cannot comply unless, in the early stages, mobile material in the detachment zone flows from the synclinal troughs to the anticlinal crests and then, in the later stages, the flow direction reverses. Relatively few detachment zones contain a significant amount of mobile salt or shale. Therefore, in most concentric detachment fold trains, a basic geometric incompatibility exists between the conventional geometric model and the Law of Conservation of Volume. The conflict can be resolved by an evolutionary fold model wherein the anticlinal fold limbs are short at the inception of folding and grow longer as dips increase and the fold grows. In this model, the anticlinal axes generally are fixed and the synclinal axes active, which has structural and economic implications for the distribution of permeability and syntectonic sediments as well as for the migration and entrapment of hydrocarbons. 18 figs.

  10. Spt-Ada-Gcn5-Acetyltransferase (SAGA Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination.

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    Rakesh Srivastava

    Full Text Available The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of Arabidopsis thaliana and Oryza sativa genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated via the regulation of gene expression. The in silico expression analysis of the SAGA components in Arabidopsis and O. sativa clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA subunits in Arabidopsis. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.

  11. Conservation genetics of evolutionary lineages of the endangered mountain yellow-legged frog, Rana muscosa (Amphibia: Ranidae), in southern California

    Science.gov (United States)

    Schoville, Sean D.; Tustall, Tate S.; Vredenburg, Vance T.; Backlin, Adam R.; Gallegos, Elizabeth; Wood, Dustin A.; Fisher, Robert N.

    2011-01-01

    Severe population declines led to the listing of southern California Rana muscosa (Ranidae) as endangered in 2002. Nine small populations inhabit watersheds in three isolated mountain ranges, the San Gabriel, San Bernardino and San Jacinto. One population from the Dark Canyon tributary in the San Jacinto Mountains has been used to establish a captive breeding population at the San Diego Zoo Institute for Conservation Research. Because these populations may still be declining, it is critical to gather information on how genetic variation is structured in these populations and what historical inter-population connectivity existed between populations. Additionally, it is not clear whether these populations are rapidly losing genetic diversity due to population bottlenecks. Using mitochondrial and microsatellite data, we examine patterns of genetic variation in southern California and one of the last remaining populations of R. muscosa in the southern Sierra Nevada. We find low levels of genetic variation within each population and evidence of genetic bottlenecks. Additionally, substantial population structure is evident, suggesting a high degree of historical isolation within and between mountain ranges. Based on estimates from a multi-population isolation with migration analysis, these populations diversified during glacial episodes of the Pleistocene, with little gene flow during population divergence. Our data demonstrate that unique evolutionary lineages of R. muscosa occupy each mountain range in southern California and should be managed separately. The captive breeding program at Dark Canyon is promising, although mitigating the loss of neutral genetic diversity relative to the natural population might require additional breeding frogs.

  12. The protonation state of histidine 111 regulates the aggregation of the evolutionary most conserved region of the human prion protein.

    Science.gov (United States)

    Fonseca-Ornelas, Luis; Zweckstetter, Markus

    2016-08-01

    In a group of neurodegenerative diseases, collectively termed transmissible spongiform encephalopathies, the prion protein aggregates into β-sheet rich amyloid-like deposits. Because amyloid structure has been connected to different prion strains and cellular toxicity, it is important to obtain insight into the structural properties of prion fibrils. Using a combination of solution NMR spectroscopy, thioflavin-T fluorescence and electron microscopy we here show that within amyloid fibrils of a peptide containing residues 108-143 of the human prion protein [humPrP (108-143)]-the evolutionary most conserved part of the prion protein - residue H111 and S135 are in close spatial proximity and their interaction is critical for fibrillization. We further show that residues H111 and H140 share the same microenvironment in the unfolded, monomeric state of the peptide, but not in the fibrillar form. While protonation of H140 has little influence on fibrillization of humPrP (108-143), a positive charge at position 111 blocks the conformational change, which is necessary for amyloid formation of humPrP (108-143). Our study thus highlights the importance of protonation of histidine residues for protein aggregation and suggests point mutations to probe the structure of infectious prion particles. PMID:27184108

  13. Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

    OpenAIRE

    Liu Yang; Yang Shi-xiong; Ji Peng-zhang; Gao Li-zhi

    2012-01-01

    Abstract Background As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. Results Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the n...

  14. Planar solar concentrator featuring alignment-free total-internal-reflection collectors and an innovative compound tracker.

    Science.gov (United States)

    Teng, Tun-Chien; Lai, Wei-Che

    2014-12-15

    This study proposed a planar solar concentrator featuring alignment-free total-internal-reflection (TIR) collectors and an innovative compound tracker. The compound tracker, combining a mechanical single-axis tracker and scrollable prism sheets, can achieve a performance on a par with dual-axis tracking while reducing the cost of the tracking system and increasing its robustness. The alignment-free TIR collectors are assembled on the waveguide without requiring alignment, so the planar concentrator is relatively easily manufactured and markedly increases the feasibility for use in large concentrators. Further, the identical TIR collector is applicable to various-sized waveguide slab without requiring modification, which facilitates flexibility regarding the size of the waveguide slab. In the simulation model, the thickness of the slab was 2 mm, and its maximal length reached 6 m. With an average angular tolerance of ±0.6°, and after considering both the Fresnel loss and the angular spread of the sun, the simulation indicates that the waveguide concentrator of a 1000-mm length provides the optical efficiencies of 62-77% at the irradiance concentrations of 387-688, and the one of a 2000-mm length provides the optical efficiencies of 52-64.5% at the irradiance concentrations of 645-1148. Alternatively, if a 100-mm horizontally staggered waveguide slab is collocated with the alignment-free TIR collectors, the optical efficiency would be greatly improved up to 91.5% at an irradiance concentration of 1098 (C(geo) = 1200X). PMID:25607496

  15. Nme gene family evolutionary history reveals pre-metazoan origins and high conservation between humans and the sea anemone, Nematostella vectensis.

    Directory of Open Access Journals (Sweden)

    Thomas Desvignes

    Full Text Available BACKGROUND: The Nme gene family is involved in multiple physiological and pathological processes such as cellular differentiation, development, metastatic dissemination, and cilia functions. Despite the known importance of Nme genes and their use as clinical markers of tumor aggressiveness, the associated cellular mechanisms remain poorly understood. Over the last 20 years, several non-vertebrate model species have been used to investigate Nme functions. However, the evolutionary history of the family remains poorly understood outside the vertebrate lineage. The aim of the study was thus to elucidate the evolutionary history of the Nme gene family in Metazoans. METHODOLOGY/PRINCIPAL FINDINGS: Using a total of 21 eukaryote species including 14 metazoans, the evolutionary history of Nme genes was reconstructed in the metazoan lineage. We demonstrated that the complexity of the Nme gene family, initially thought to be restricted to chordates, was also shared by the metazoan ancestor. We also provide evidence suggesting that the complexity of the family is mainly a eukaryotic innovation, with the exception of Nme8 that is likely to be a choanoflagellate/metazoan innovation. Highly conserved gene structure, genomic linkage, and protein domains were identified among metazoans, some features being also conserved in eukaryotes. When considering the entire Nme family, the starlet sea anemone is the studied metazoan species exhibiting the most conserved gene and protein sequence features with humans. In addition, we were able to show that most of the proteins known to interact with human NME proteins were also found in starlet sea anemone. CONCLUSION/SIGNIFICANCE: Together, our observations further support the association of Nme genes with key cellular functions that have been conserved throughout metazoan evolution. Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of

  16. USING ECO-EVOLUTIONARY INDIVIDUAL-BASED MODELS TO INVESTIGATE SPATIALLY-DEPENDENT PROCESSES IN CONSERVATION GENETICS

    Science.gov (United States)

    Eco-evolutionary population simulation models are powerful new forecasting tools for exploring management strategies for climate change and other dynamic disturbance regimes. Additionally, eco-evo individual-based models (IBMs) are useful for investigating theoretical feedbacks ...

  17. Simple Ligand–Receptor Interaction Descriptor (SILIRID for alignment-free binding site comparison

    Directory of Open Access Journals (Sweden)

    Vladimir Chupakhin

    2014-06-01

    Full Text Available We describe SILIRID (Simple Ligand–Receptor Interaction Descriptor, a novel fixed size descriptor characterizing protein–ligand interactions. SILIRID can be obtained from the binary interaction fingerprints (IFPs by summing up the bits corresponding to identical amino acids. This results in a vector of 168 integer numbers corresponding to the product of the number of entries (20 amino acids and one cofactor and 8 interaction types per amino acid (hydrophobic, aromatic face to face, aromatic edge to face, H-bond donated by the protein, H-bond donated by the ligand, ionic bond with protein cation and protein anion, and interaction with metal ion. Efficiency of SILIRID to distinguish different protein binding sites has been examined in similarity search in sc-PDB database, a druggable portion of the Protein Data Bank, using various protein–ligand complexes as queries. The performance of retrieval of structurally and evolutionary related classes of proteins was comparable to that of state-of-the-art approaches (ROC AUC ≈ 0.91. SILIRID can efficiently be used to visualize chemogenomic space covered by sc-PDB using Generative Topographic Mapping (GTM: sc-PDB SILIRID data form clusters corresponding to different protein types.

  18. Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus microplus

    Directory of Open Access Journals (Sweden)

    Tateno Yoshio

    2011-06-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are small non-coding RNAs that act as regulators of gene expression in eukaryotes modulating a large diversity of biological processes. The discovery of miRNAs has provided new opportunities to understand the biology of a number of species. The cattle tick, Rhipicephalus (Boophilus microplus, causes significant economic losses in cattle production worldwide and this drives us to further understand their biology so that effective control measures can be developed. To be able to provide new insights into the biology of cattle ticks and to expand the repertoire of tick miRNAs we utilized Illumina technology to sequence the small RNA transcriptomes derived from various life stages and selected organs of R. microplus. Results To discover and profile cattle tick miRNAs we employed two complementary approaches, one aiming to find evolutionary conserved miRNAs and another focused on the discovery of novel cattle-tick specific miRNAs. We found 51 evolutionary conserved R. microplus miRNA loci, with 36 of these previously found in the tick Ixodes scapularis. The majority of the R. microplus miRNAs are perfectly conserved throughout evolution with 11, 5 and 15 of these conserved since the Nephrozoan (640 MYA, Protostomian (620MYA and Arthropoda (540 MYA ancestor, respectively. We then employed a de novo computational screening for novel tick miRNAs using the draft genome of I. scapularis and genomic contigs of R. microplus as templates. This identified 36 novel R. microplus miRNA loci of which 12 were conserved in I. scapularis. Overall we found 87 R. microplus miRNA loci, of these 15 showed the expression of both miRNA and miRNA* sequences. R. microplus miRNAs showed a variety of expression profiles, with the evolutionary-conserved miRNAs mainly expressed in all life stages at various levels, while the expression of novel tick-specific miRNAs was mostly limited to particular life stages and/or tick organs. Conclusions

  19. Evolution of the 4-coumarate:coenzyme A ligase (4CL) gene family:Conserved evolutionary pattern and two new gene classes in gymnosperms

    Institute of Scientific and Technical Information of China (English)

    Hui GAO; Dong-Mei GUO; Wen-Juan LIU; Jin-Hua RAN; Xiao-Quan WANG

    2012-01-01

    The 4-coumarate:coenzyme A ligase (4CL) is the branch point enzyme that channels the general phenylpropanoid metabolism into specific lignin and flavonoid biosynthesis branches.Genetic engineering experiments on the 4CL gene have been carried out in many species,but the precise functions of different gene members are still unresolved.To investigate the evolutionary relationships and functional differentiation of the 4CL gene family,we made a comprehensive evolutionary analysis of this gene family from 27 species representing the major lineages of land plants.The phylogenetic analysis indicates that both vascular and seed plant 4CL genes form monophyletic groups,and that three and two 4CL classes can be recognized in gymnosperms and angiosperms,respectively.The evolutionary rate and frequency of duplication of the 4CL gene family are much more conserved than that of the CAD/SAD (cinnamyl/sinapyl alcohol dehydrogenase) gene family,which catalyzes the last step in monolignol biosynthesis.This may be due to different selective pressures on these genes whose products catalyze different steps in the biosynthesis pathway.In addition,we found two new major classes of 4CL genes in gymnosperms.

  20. LA CONSERVACIÓN BIOLÓGICA Y SU PERSPECTIVA EVOLUTIVA Biological Conservation and its Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    OLGA L MONTENEGRO

    Full Text Available Este artículo revisa tres de las principales causas de amenaza a la diversidad biológica, como son la fragmentación y pérdida del hábitat, así como la invasión de especies exóticas, principalmente en lo que compete a sus implicaciones evolutivas. Los efectos de la fragmentación y/o pérdida del hábitat pueden revisarse a la luz de la sinergia entre factores demográficos y genéticos que moldean cambios evolutivos o que llevan a las poblaciones al vórtice de la extinción. Las invasiones biológicas, aunque han generado pérdidas considerables en la diversidad biológica, ofrecen un escenario interesante para estudiar procesos evolutivos contemporáneos.This paper reviews three of the main threats to biological diversity, such as habitat fragmentation /habitat loss, and invasion of exotic species, mainly from their evolutionary implications. Effects of habitat fragmentation/habitat loss could be addressed by looking at the synergy between demographic and genetic factors that together shape evolutionary changes or otherwise bring populations to extinction vortex. Biological invasions, in spite of their strong negative effects on biological diversity, offer an interesting scenario to study contemporary evolutionary processes.

  1. An evolutionary conserved region (ECR in the human dopamine receptor D4 gene supports reporter gene expression in primary cultures derived from the rat cortex

    Directory of Open Access Journals (Sweden)

    Haddley Kate

    2011-05-01

    Full Text Available Abstract Background Detecting functional variants contributing to diversity of behaviour is crucial for dissecting genetics of complex behaviours. At a molecular level, characterisation of variation in exons has been studied as they are easily identified in the current genome annotation although the functional consequences are less well understood; however, it has been difficult to prioritise regions of non-coding DNA in which genetic variation could also have significant functional consequences. Comparison of multiple vertebrate genomes has allowed the identification of non-coding evolutionary conserved regions (ECRs, in which the degree of conservation can be comparable with exonic regions suggesting functional significance. Results We identified ECRs at the dopamine receptor D4 gene locus, an important gene for human behaviours. The most conserved non-coding ECR (D4ECR1 supported high reporter gene expression in primary cultures derived from neonate rat frontal cortex. Computer aided analysis of the sequence of the D4ECR1 indicated the potential transcription factors that could modulate its function. D4ECR1 contained multiple consensus sequences for binding the transcription factor Sp1, a factor previously implicated in DRD4 expression. Co-transfection experiments demonstrated that overexpression of Sp1 significantly decreased the activity of the D4ECR1 in vitro. Conclusion Bioinformatic analysis complemented by functional analysis of the DRD4 gene locus has identified a a strong enhancer that functions in neurons and b a transcription factor that may modulate the function of that enhancer.

  2. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

    Institute of Scientific and Technical Information of China (English)

    Guanghong Zuo; Bailin Hao

    2015-01-01

    A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/without login requirements.

  3. Bacillus thuringiensis insecticidal Cry1Aa toxin binds to a highly conserved region of aminopeptidase N in the host insect leading to its evolutionary success.

    Science.gov (United States)

    Nakanishi, K; Yaoi, K; Shimada, N; Kadotani, T; Sato, R

    1999-06-15

    Bacillus thuringiensis insecticidal protein, Cry1Aa toxin, binds to a specific receptor in insect midguts and has insecticidal activity. Therefore, the structure of the receptor molecule is probably a key factor in determining the binding affinity of the toxin and insect susceptibility. The cDNA fragment (PX frg1) encoding the Cry1Aa toxin-binding region of an aminopeptidase N (APN) or an APN family protein from diamondback moth, Plutella xylostella midgut was cloned and sequenced. A comparison between the deduced amino acid sequence of PX frg1 and other insect APN sequences shows that Cry1Aa toxin binds to a highly conserved region of APN family protein. In this paper, we propose a model to explain the mechanism that causes B. thuringiensis evolutionary success and differing insect susceptibility to Cry1Aa toxin. PMID:10366728

  4. The evolutionary conserved gene C16orf35 encodes a nucleo-cytoplasmic protein that interacts with p73

    Energy Technology Data Exchange (ETDEWEB)

    Lunardi, Andrea; Chiacchiera, Fulvio; D' Este, Elisa [Laboratorio Nazionale CIB (LNCIB), AREA Science Park, Padriciano 99, 34149 Trieste (Italy); Carotti, Marcello [Laboratorio Nazionale CIB (LNCIB), AREA Science Park, Padriciano 99, 34149 Trieste (Italy); Dipartimento di Scienze della Vita, Universita degli Studi di Trieste, Via L. Giorgieri 1, 34129 Trieste (Italy); Ferro, Marco Dal [Laboratorio Nazionale CIB (LNCIB), AREA Science Park, Padriciano 99, 34149 Trieste (Italy); Minin, Giulio Di; Sal, Giannino Del [Laboratorio Nazionale CIB (LNCIB), AREA Science Park, Padriciano 99, 34149 Trieste (Italy); Dipartimento di Scienze della Vita, Universita degli Studi di Trieste, Via L. Giorgieri 1, 34129 Trieste (Italy); Collavin, Licio, E-mail: collavin@lncib.it [Laboratorio Nazionale CIB (LNCIB), AREA Science Park, Padriciano 99, 34149 Trieste (Italy); Dipartimento di Scienze della Vita, Universita degli Studi di Trieste, Via L. Giorgieri 1, 34129 Trieste (Italy)

    2009-10-16

    C16orf35 is a highly conserved gene positioned upstream of the alpha-globins in humans and other vertebrates. The deduced protein is also highly conserved, it has no defined structural features or domains, and its function is currently unknown. Here we show that the C16orf35 protein has nuclear and cytosolic distribution, and can localize to PML nuclear bodies. The C16orf35 protein was detected in several human transformed cells lines, and studies of transient and stable overexpression indicate that increased levels of C16orf35 inhibit cell proliferation. We also find that C16orf35 interacts with human p73, and represses transcription by TAp73{gamma} but not by TAp73{alpha}. This selectivity is not due to differential interaction, since C16orf35 binds both p73 variants. Our data suggest that C16orf35 can modulate differentially the specific activities of selected p73 isoforms.

  5. GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis

    Science.gov (United States)

    Heltshe, Sonya L.; Hayden, Hillary S.; Radey, Matthew C.; Weiss, Eli J.; Damman, Christopher J.; Zisman, Timothy L.; Suskind, David L.; Miller, Samuel I.

    2016-01-01

    Background Comparative analysis of gut microbiomes in clinical studies of human diseases typically rely on identification and quantification of species or genes. In addition to exploring specific functional characteristics of the microbiome and potential significance of species diversity or expansion, microbiome similarity is also calculated to study change in response to therapies directed at altering the microbiome. Established ecological measures of similarity can be constructed from species abundances, however methods for calculating these commonly used ecological measures of similarity directly from whole genome shotgun (WGS) metagenomic sequence are lacking. Results We present an alignment-free method for calculating similarity of WGS metagenomic sequences that is analogous to the Bray–Curtis index for species, implemented by the General Utility for Testing Sequence Similarity (GUTSS) software application. This method was applied to intestinal microbiomes of healthy young children to measure developmental changes toward an adult microbiome during the first 3 years of life. We also calculate similarity of donor and recipient microbiomes to measure establishment, or engraftment, of donor microbiota in fecal microbiota transplantation (FMT) studies focused on mild to moderate Crohn's disease. We show how a relative index of similarity to donor can be calculated as a measure of change in a patient's microbiome toward that of the donor in response to FMT. Conclusion Because clinical efficacy of the transplant procedure cannot be fully evaluated without analysis methods to quantify actual FMT engraftment, we developed a method for detecting change in the gut microbiome that is independent of species identification and database bias, sensitive to changes in relative abundance of the microbial constituents, and can be formulated as an index for correlating engraftment success with clinical measures of disease. More generally, this method may be applied to clinical

  6. The endocrine system controlling sexual reproduction in animals: Part of the evolutionary ancient but well conserved immune system?

    Science.gov (United States)

    De Loof, Arnold; Schoofs, Liliane; Huybrechts, Roger

    2016-01-15

    Drastic changes in hormone titers, in particular of steroid hormones, are intuitively interpreted as necessary and beneficial for optimal functioning of animals. Peaks in progesterone- and estradiol titers that accompany the estrus cycle in female vertebrates as well as in ecdysteroids at each molt and during metamorphosis of holometabolous insects are prominent examples. A recent analysis of insect metamorphosis yielded the view that, in general, a sharp rise in sex steroid hormone titer signals that somewhere in the body some tissue(s) is undergoing programmed cell death/apoptosis. Increased steroid production is part of this process. Typical examples are ovarian follicle cells in female vertebrates and invertebrates and the prothoracic gland cells, the main production site of ecdysteroids in larval insects. A duality emerges: programmed cell death-apoptosis is deleterious at the cellular level, but it may yield beneficial effects at the organismal level. Reconciling both opposites requires reevaluating the probable evolutionary origin and role of peptidic brain hormones that direct steroid hormone synthesis. Do e.g. Luteinizing Hormone in vertebrates and Prothoracicotropic Hormone (PTTH: acting through the Torso receptor) in insects still retain an ancient role as toxins in the early immune system? Does the functional link of some neuropeptides with Ca(2+)-induced apoptosis make sense in endocrine archeology? The endocrine system as a remnant of the ancient immune system is undoubtedly counterintuitive. Yet, we will argue that such paradigm enables the logical framing of many aspects, the endocrine one inclusive of both male and female reproductive physiology. PMID:26707056

  7. Evolutionary and functional conservation of the DNA non-homologous end-joining protein, XLF/Cernunnos.

    Science.gov (United States)

    Hentges, Pierre; Ahnesorg, Peter; Pitcher, Robert S; Bruce, Chris K; Kysela, Boris; Green, Andrew J; Bianchi, Julie; Wilson, Thomas E; Jackson, Stephen P; Doherty, Aidan J

    2006-12-01

    Non-homologous end-joining is a major pathway of DNA double-strand break repair in mammalian cells, deficiency in which confers radiosensitivity and immune deficiency at the whole organism level. A core protein complex comprising the Ku70/80 heterodimer together with a complex between DNA ligase IV and XRCC4 is conserved throughout eukaryotes and assembles at double-strand breaks to mediate ligation of broken DNA ends. In Saccharomyces cerevisiae an additional NHEJ protein, Nej1p, physically interacts with the ligase IV complex and is required in vivo for ligation of DNA double-strand breaks. Recent studies with cells derived from radiosensitive and immune-deficient patients have identified the human protein, XLF (also named Cernunnos), as a crucial NHEJ protein. Here we show that XLF and Nej1p are members of the same protein superfamily and that this family has members in diverse eukaryotes. Indeed, we show that a member of this family encoded by a previously uncharacterized open-reading frame in the Schizosaccharomyces pombe genome is required for NHEJ in this organism. Furthermore, our data reveal that XLF family proteins can bind to DNA and directly interact with the ligase IV-XRCC4 complex to promote DSB ligation. We therefore conclude that XLF family proteins interact with the ligase IV-XRCC4 complex to constitute the evolutionarily conserved enzymatic core of the NHEJ machinery. PMID:17038309

  8. Exploring climate niches of ponderosa pine (Pinus ponderosa Douglas ex Lawson) haplotypes in the western United States: Implications for evolutionary history and conservation

    Science.gov (United States)

    Shinneman, Douglas; Means, Robert E.; Potter, Kevin M.; Hipkins, Valerie D.

    2016-01-01

    Ponderosa pine (Pinus ponderosa Douglas ex Lawson) occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. ponderosa) and Rocky Mountain (P. p. var. scopulorum) varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM), ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P. p. vars. ponderosa and scopulorum, respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated with

  9. Exploring Climate Niches of Ponderosa Pine (Pinus ponderosa Douglas ex Lawson) Haplotypes in the Western United States: Implications for Evolutionary History and Conservation.

    Science.gov (United States)

    Shinneman, Douglas J; Means, Robert E; Potter, Kevin M; Hipkins, Valerie D

    2016-01-01

    Ponderosa pine (Pinus ponderosa Douglas ex Lawson) occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. ponderosa) and Rocky Mountain (P. p. var. scopulorum) varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM), ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P. p. vars. ponderosa and scopulorum, respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated with discrete

  10. Exploring Climate Niches of Ponderosa Pine (Pinus ponderosa Douglas ex Lawson Haplotypes in the Western United States: Implications for Evolutionary History and Conservation.

    Directory of Open Access Journals (Sweden)

    Douglas J Shinneman

    Full Text Available Ponderosa pine (Pinus ponderosa Douglas ex Lawson occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. ponderosa and Rocky Mountain (P. p. var. scopulorum varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM, ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P. p. vars. ponderosa and scopulorum, respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated

  11. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

    Science.gov (United States)

    Salgado, Heladia; Peralta-Gil, Martin; Gama-Castro, Socorro; Santos-Zavaleta, Alberto; Muñiz-Rascado, Luis; García-Sotelo, Jair S.; Weiss, Verena; Solano-Lira, Hilda; Martínez-Flores, Irma; Medina-Rivera, Alejandra; Salgado-Osorio, Gerardo; Alquicira-Hernández, Shirley; Alquicira-Hernández, Kevin; López-Fuentes, Alejandra; Porrón-Sotelo, Liliana; Huerta, Araceli M.; Bonavides-Martínez, César; Balderas-Martínez, Yalbi I.; Pannier, Lucia; Olvera, Maricela; Labastida, Aurora; Jiménez-Jacinto, Verónica; Vega-Alvarado, Leticia; del Moral-Chávez, Victor; Hernández-Alvarez, Alfredo; Morett, Enrique; Collado-Vides, Julio

    2013-01-01

    This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available. PMID:23203884

  12. Evolutionary conservation of the presumptive neural plate markers AmphiSox1/2/3 and AmphiNeurogenin in the invertebrate chordate amphioxus

    Science.gov (United States)

    Holland, L. Z.; Schubert, M.; Holland, N. D.; Neuman, T.

    2000-01-01

    Amphioxus, as the closest living invertebrate relative of the vertebrates, can give insights into the evolutionary origin of the vertebrate body plan. Therefore, to investigate the evolution of genetic mechanisms for establishing and patterning the neuroectoderm, we cloned and determined the embryonic expression of two amphioxus transcription factors, AmphiSox1/2/3 and AmphiNeurogenin. These genes are the earliest known markers for presumptive neuroectoderm in amphioxus. By the early neurula stage, AmphiNeurogenin expression becomes restricted to two bilateral columns of segmentally arranged neural plate cells, which probably include precursors of motor neurons. This is the earliest indication of segmentation in the amphioxus nerve cord. Later, expression extends to dorsal cells in the nerve cord, which may include precursors of sensory neurons. By the midneurula, AmphiSox1/2/3 expression becomes limited to the dorsal part of the forming neural tube. These patterns resemble those of their vertebrate and Drosophila homologs. Taken together with the evolutionarily conserved expression of the dorsoventral patterning genes, BMP2/4 and chordin, in nonneural and neural ectoderm, respectively, of chordates and Drosophila, our results are consistent with the evolution of the chordate dorsal nerve cord and the insect ventral nerve cord from a longitudinal nerve cord in a common bilaterian ancestor. However, AmphiSox1/2/3 differs from its vertebrate homologs in not being expressed outside the CNS, suggesting that additional roles for this gene have evolved in connection with gene duplication in the vertebrate lineage. In contrast, expression in the midgut of AmphiNeurogenin together with the gene encoding the insulin-like peptide suggests that amphioxus may have homologs of vertebrate pancreatic islet cells, which express neurogenin3. In addition, AmphiNeurogenin, like its vertebrate and Drosophila homologs, is expressed in apparent precursors of epidermal chemosensory and

  13. Identification of a truncated splice variant of IL-18 receptor alpha in the human and rat, with evidence of wider evolutionary conservation

    Directory of Open Access Journals (Sweden)

    Chris S. Booker

    2014-09-01

    Full Text Available Interleukin-18 (IL-18 is a pro-inflammatory cytokine which stimulates activation of the nuclear factor kappa beta (NF-κB pathway via interaction with the IL-18 receptor. The receptor itself is formed from a dimer of two subunits, with the ligand-binding IL-18Rα subunit being encoded by the IL18R1 gene. A splice variant of murine IL18r1, which has been previously described, is formed by transcription of an unspliced intron (forming a ‘type II’ IL18r1 transcript and is predicted to encode a receptor with a truncated intracellular domain lacking the capacity to generate downstream signalling. In order to examine the relevance of this finding to human IL-18 function, we assessed the presence of a homologous transcript by reverse transcription-polymerase chain reaction (RT-PCR in the human and rat as another common laboratory animal. We present evidence for type II IL18R1 transcripts in both species. While the mouse and rat transcripts are predicted to encode a truncated receptor with a novel 5 amino acid C-terminal domain, the human sequence is predicted to encode a truncated protein with a novel 22 amino acid sequence bearing resemblance to the ‘Box 1’ motif of the Toll/interleukin-1 receptor (TIR domain, in a similar fashion to the inhibitory interleukin-1 receptor 2. Given that transcripts from these three species are all formed by inclusion of homologous unspliced intronic regions, an analysis of homologous introns across a wider array of 33 species with available IL18R1 gene records was performed, which suggests similar transcripts may encode truncated type II IL-18Rα subunits in other species. This splice variant may represent a conserved evolutionary mechanism for regulating IL-18 activity.

  14. Conservation = Conservation

    OpenAIRE

    Daget, Jacques; Gaigher, I.C.; Ssentongo, G.W.

    1988-01-01

    African freshwater fishes are endangered by over exploitation of live fish for aquarists and for exports, intensive fishing of species with low resilience, introduction of exotic species, pollution, general environmental modification by man. Therefore, to ensure conservation to fish species, it is necessary to increase basic knowledge in order to provide guidelines and a scientific basis for conservation measures. The three main lines for the development of a fish conservation policy are publ...

  15. Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

    Science.gov (United States)

    Robinson, J.; Snider, M.; Duke, J.; Moyer, G.R.

    2014-01-01

     The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina

  16. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover, they are...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary...

  17. Evolutionary Computing

    OpenAIRE

    Eiben, Aguston; Schoenauer, Marc

    2002-01-01

    Evolutionary computing (EC) is an exciting development in Computer Science. It amounts to building, applying and studying algorithms based on the Darwinian principles of natural selection. In this paper we briefly introduce the main concepts behind evolutionary computing. We present the main components all evolutionary algorithms (EA), sketch the differences between different types of EAs and survey application areas ranging from optimization, modeling and simulation to entertainment.

  18. Evolutionary Economics

    OpenAIRE

    Dopfer, Kurt

    2006-01-01

    The paper provides an overview of major recent contributions in evolutionary economics. It starts of demonstrating that the pioneers of this approach such as Veblen, Schumpeter, Marshall and Hayek saw the economy as continuously changing and that this kind of "realism of perception" guides essentially also contemporary evolutionary economics. The economy is viewed as an evolving system of structured knowledge governing economic operations. Theoretically, a micro-meso-macro architecture is pro...

  19. Evolutionary algorithms

    OpenAIRE

    Szöllösi, Tomáš

    2012-01-01

    The first part of this work deals with the optimization and evolutionary algorithms which are used as a tool to solve complex optimization problems. The discussed algorithms are Differential Evolution, Genetic Algorithm, Simulated Annealing and deterministic non-evolutionary algorithm Taboo Search.. Consequently the discussion is held on the issue of testing the optimization algorithms through the use of the test function gallery and comparison solution all algorithms on Travelling salesman p...

  20. Evolutionary algorithms

    OpenAIRE

    Eremeev, Anton V.

    2015-01-01

    This manuscript contains an outline of lectures course "Evolutionary Algorithms" read by the author in Omsk State University n.a. F.M.Dostoevsky. The course covers Canonic Genetic Algorithm and various other genetic algorithms as well as evolutioanry algorithms in general. Some facts, such as the Rotation Property of crossover, the Schemata Theorem, GA performance as a local search and "almost surely" convergence of evolutionary algorithms are given with complete proofs. The text is in Russian.

  1. Dissecting a Role of Evolutionary-conserved but Non-critical Disulfide Bridges in Cysteine-Rich Peptides Using ω-Conotoxin GVIA and its Selenocysteine Analogs

    OpenAIRE

    Gowd, Konkallu Hanumae; Blais, Kirk D.; Elmslie, Keith S.; Andrew M Steiner; Olivera, Baldomero M.; Bulaj, Grzegorz

    2012-01-01

    Conotoxins comprise a large group of peptidic neurotoxins that employ diverse disulfide-rich scaffolds. Each scaffold is determined by an evolutionarily conserved pattern of cysteine residues. Although many structure-activity relationship studies confirm the functional and structural importance of disulfide crosslinks, there is growing evidence that not all disulfide bridges are critical in maintaining activities of conotoxins. To answer the fundamental biological question of what the role of...

  2. Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY

    OpenAIRE

    Abhishek Kumar

    2015-01-01

    The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6), based on three independent biological features—genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes ar...

  3. The Jumonji gene family in Crassostrea gigas suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster gametogenesis and development.

    Science.gov (United States)

    Fellous, Alexandre; Favrel, Pascal; Guo, Ximing; Riviere, Guillaume

    2014-03-15

    Jumonji (Jmj) proteins are histone demethylases, which control the identity of stem cells. Jmj genes were characterized from plants to mammals where they have been implicated in the epigenetic regulation of development. Despite the Pacific oyster Crassostrea gigas representing one of the most important aquaculture resources worldwide, the molecular mechanisms governing the embryogenesis and reproduction of this lophotrochozoan species remain poorly understood. However, annotations in the C. gigas EST library suggested the presence of putative Jumonji genes, raising the question of the conservation of this family of histone demethylases in the oyster. Using Primer walking, 5'-RACE PCR and in silico analyses, we characterized nine Jumonji orthologues in the oyster, called Cg-Jmj, bearing conserved domains critical for putative histone demethylase activity. Phylogenic analyses revealed that oyster Jumonji cluster into two distinct groups: 'single-domain Jmj' and 'multi-domain Jmj', and define 8 subgroups corresponding to each cognate orthologues in metazoans. RT-qPCR investigations showed specific regulations of Cg-Jmj mRNAs during the early development and along the reproduction cycle. Furthermore, in situ and in toto hybridizations indicate that oyster Jumonji genes are transcribed mostly within the gonad in adult oysters whereas they display a ubiquitous expression during embryonic and larval development. Our study demonstrates the presence of nine Jumonji orthologues in the oyster C. gigas. Their domain conservation and their expression profile suggest an implication during reproduction and development, questioning about the epigenetic regulation by histone methylation in lophotrochozoans. PMID:24406622

  4. Liberal-Conservative Synthesis: the Experience of Creating the Concept of Evolutionary Modernization of Russia in the Second half of the 19th Century

    Directory of Open Access Journals (Sweden)

    Maxim N. Krot

    2015-06-01

    Full Text Available The article is devoted to consideration of the liberal-conservative conception of Russia formed in the second half of the 19th century by a number of Russian public figures and statesmen, the most prominent of which were B.N. Chicherin, K.D. Cavelin and A.D. Gradovsky. The author reveals the main stages of modernization of the social and political system in Russia suggested by the liberals. The author deals with the concrete projects of changes and reforms, characterizes the methods of achieving these aims. The article reveals the essence of the liberal-conservative "anticonstitutionalism" of the 60s and the first half of the 70s of the 19th century, identifies the main arguments, used by the representatives of this social thought trend for proving their opinion. One issue is considered separately: the draft of the administrative reform by K.D. Kavelin, having offered a wide reorganization of the supreme bodies of state administration and the nature of their formation in order to prepare the basis for establishing of representative government in Russia in the future. The article characterizes the situation in Russia at the turn of 1870 - 1880s, under the circumstances of which there is a gradual transition of liberal conservatives to the idea of immediate creation of representative bodies in Russia. The author analyzes in detail the following: the main arguments and motivations, having induced them to introducing the requirements as well as the projects themselves, devoted to the establishment of elected representative bodies that were supposed to be integrated into the existing government management, complementing and improving it. In the article special attention is drawn to the harmonious combination of liberal - reformational and conservative-preserving principles that, according to its authors, on the one hand, must have promoted the evolution of social and political relations in the country, have avoided their stagnation and degradation

  5. Evolutionary awareness.

    Science.gov (United States)

    Gorelik, Gregory; Shackelford, Todd K

    2014-01-01

    In this article, we advance the concept of "evolutionary awareness," a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities-which we refer to as "intergenerational extended phenotypes"-by helping us to construct a better future for ourselves, for other sentient beings, and for our environment. PMID:25300054

  6. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  7. Characterization of SoxB2 and SoxC genes in Amphi-oxus (Branchiostoma belcheri):Implications for their evolutionary conservation

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Most Sox genes directly affect cell fate determination and differentiation. In this study,we isolated two Sox genes:SoxB2 and SoxC from amphioxus (Branchiostoma belcheri),the closest living invertebrate relative of the vertebrates. Alignments of SoxB2 and SoxC protein sequences and their vertebrate homologs show high conservation of their HMG domains. Phylogenic analysis shows that amphioxus SoxB2 and SoxC fall out of the vertebrate branches,suggesting that vertebrate homologs might arise from gene duplications during evolution. The two genes possess similar spatial and temporal expression patterns during embryogenesis and in adults. They are both maternally inherited. During neurulation,they are expressed in the neural ectoderm and archenterons. In adults,they are expressed not only in the nerve cord,but also in the gut,midgut diverticulum,gill and oocytes. These results suggest that amphioxus SoxB2 and SoxC might co-function and have conserved functions in the nervous system and gonads as their vertebrate homologs.

  8. Comparative genetic structure in pines: evolutionary and conservation consequences Estructura genética comparada en pinos: consecuencias evolutivas y para la conservación

    Directory of Open Access Journals (Sweden)

    PATRICIA DELGADO

    2002-03-01

    Full Text Available Pines have been the focus of several studies that estimate population genetic parameters using both allozymes and chloroplast single sequence repeats (SSRs. Also, the genus has also been recently studied using molecular systematics so that we now have a more clear understanding of their evolutionary history. With this background we studied comparatively the genetic structure in pines. Expected heterozygosity is particularly constant with a 99 % confidence interval between 0.19 and 0.23 in species that have been studied until now using allozymes. There is a significant proportion of species (9/41 that show high population differentiation estimates (Fst = or larger than 0.15 and five of these have large and wingless seeds probably associated with low densities, bird dispersal mechanisms and resistance to water stress. These species include the North American pinyon pines. Outcrossing rates are also constant among species from both subgenus Pinus and subgenus Strobus, which probably reflects a selective limit to the amount of deleterious alleles that can be maintained in pine species and this also affects inbreeding levels. We also explored the data published using microsatellites in pines and conclude that these markers uncover a higher proportion of variation and genetic differentiation as expected and that the evolutionary models that are used to derive the population genetic structure estimators should take into account other sources of mutation (point mutations, larger insertions and or deletions and duplications to better understand the comparative applications of these molecular markersLos pinos han sido el objeto de varios estudios para estimar los parámetros genéticos de la población utilizando tanto aloenzimas como fragmentos repetidos de secuencia sencilla (RSSs de cloroplasto. Este género también ha sido estudiado recientemente utilizando sistemática molecular de tal manera que ahora tenemos un entendimiento más claro de su

  9. Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY

    Directory of Open Access Journals (Sweden)

    Abhishek Kumar

    2015-06-01

    Full Text Available The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6, based on three independent biological features—genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2 of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, details of the phylogenetic history and genomic characteristics of vertebrate serpins are revisited.

  10. Historical ecology meets conservation and evolutionary genetics: a secondary contact zone between Carabus violaceus (Coleoptera, Carabidae populations inhabiting ancient and recent woodlands in north-western Germany

    Directory of Open Access Journals (Sweden)

    Andrea Matern

    2011-05-01

    Full Text Available Only very few cases have documented that an increase in connectivity after a period of fragmentation in ecological time has had an effect on the distribution, genetic structure and morphology of stenotopic species. In this study we present an example of clinal variability in a woodland ground beetle as a result of changes in the connectivity of a landscape during the last two centuries. The study area hosts both the nominate form C. violaceus s. str. and the subspecies C. v. purpurascens, which is ranked as a distinct species by some authors. We studied 12 Carabus violaceus populations from a 30 km transect of ancient and recent forests in north-western Germany. We analyzed three polymorphic enzyme loci, classified the elytron sculpture and measured the shape of the aedeagus tip of the specimens. C. violaceus showed secondary gradients both in allozyme markers and morphometric characters in our study area. A genetic differentiation of 16% between the populations is high but lies within the range of intraspecific variability in habitat specialists of the genus Carabus. Populations had no significant deficit of heterozygotes. We found many hybrid populations in terms of morphological properties. This study highlights the conservation value of ancient woodland and the consequences of landscape connectivity and defragmentation on the genetic setting of a ground beetle. Moreover, it shows that differences in the external shape of male genitalia do not prevent gene flow within the genus Carabus. Thus, the establishment of species status should not exclusively be based on this property.

  11. First karyotypical description of two American Ciconiiform birds, Mycteria americana (Ciconiidae and Platalea ajaja (Threskiornithidae and its significance for the chromosome evolutionary and biological conservation approaches

    Directory of Open Access Journals (Sweden)

    Mercival Roberto Francisco

    2000-12-01

    Full Text Available The karyotypes of Mycteria americana (Ciconiidae and Platalea ajaja (Threskiornithidae are described. Both species have a diploid number of 2n = 72. There are slight chromosome morphology differences, which could be related to distinct chromosome evolution pathways of these two families. Besides a better understanding of the chromosome relationships among Ciconiiformes, this first chromosome characterization of M. americana and P. ajaja is an important tool for the conservation of both species.No presente trabalho foram descritos os cariótipos de Mycteria americana (Ciconiidae e Platalea ajaja (Threskiornithidae. Embora ambas as espécies tenham apresentado o número diplóide 2n = 72, foram observadas diferenças na morfologia cariotípica resultantes de processos evolutivos distintos que parecem ocorrer entre as duas famílias. Além de contribuir para um melhor entendimento da evolução cromossômica dentro da ordem Ciconiiformes, a caracterização cariotípica de M. americana e P. ajaja vem representar uma importante ferramenta para a realização de planos de manejo e conservação destas espécies.

  12. Spliceosomal introns in the 5′ untranslated region of plant BTL RING-H2 ubiquitin ligases are evolutionary conserved and required for gene expression

    Science.gov (United States)

    2013-01-01

    Background Introns located close to the 5′ end of a gene or in the 5′ untranslated region often exert positive effects on gene expression. This effect, known as intron-mediated enhancement (IME), has been observed in diverse eukaryotic organisms, including plants. The sequences involved in IME seem to be spread across the intron and function in an additive manner. The IMEter algorithm was developed to predict plant introns that may enhance gene expression. We have identified several plant members of the BTL class of E3s, which may have orthologs across eukaryotes, that contain a 5′UTR intron. The RING finger E3 ligases are key enzymes of the ubiquitination system that mediate the transfer of ubiquitin to substrates. Results In this study, we retrieved BTL sequences from several angiosperm species and found that 5′UTR introns showing a strong IMEter score were predicted, suggesting that they may be conserved by lineage. Promoter-GUS fusion lines were used to confirm the IME effect of these 5′UTR introns on gene expression. IMEter scores of BTLs were compared with the 5′UTR introns of two gene families MHX and polyubiquitin genes. Conclusions Analysis performed in two Arabidopsis BTL E3 ligases genes indicated that the 5′UTR introns were essential for gene expression in all the tissues tested. Comparison of the average 5′UTR intron size on three gene families in ten angiosperm species suggests that a prevalent size for a 5′UTR intron is in the range of 600 nucleotides, and that the overall IMEter score within a gene family is preserved across several angiosperms. Our results indicated that gene expression dependent on a 5′UTR intron is an efficient regulatory mechanism in BTL E3 ligases that has been preserved throughout plant evolution. PMID:24228887

  13. Cloning and modeling of CD8 beta in the amphibian ambystoma Mexicanum. Evolutionary conserved structures for interactions with major histocompatibility complex (MHC) class I molecules.

    Science.gov (United States)

    Fellah, Julien S; Tuffèry, Pierre; Etchebest, Catherine; Guillet, Françoise; Bleux, Christian; Charlemagne, Jacques

    2002-04-17

    Mammalian and avian T-cells exhibit a large number of well characterized surface molecules associated with their maturation degree. Very little is known in comparison with T-cell differentiation in ectothermic vertebrates. This is mainly due to the lack of probes to identify T-cell subsets. We cloned and sequenced the first ectothermic CD8 beta DNA complementary to RNA from an amphibian species, the Mexican axolotl. The CD8 beta chain was 30-36% identical with its avian and mammalian homologues. The extracellular V-like domain contained the two typically conserved cysteines and was followed by a J-like sequence containing the canonical Phe-Gly-X-Gly stretch. The connecting peptide was much longer than in other species and contained potential O-glycosylation sites. The axolotl CD8 beta and major histocompatibility complex class I molecules were modeled using human HLA-A2/CD8 alphaalpha complex as template. The backbone conformation of axolotl CD8 beta matched well with the CD8 alpha-2 subunit of the human complex but significant structural differences were located in the CDR1, CDR2 and DE loops. Both axolotl and human class I showed large negative surface potential. The interacting area of the human CD8 alpha chain and of the corresponding region of axolotl CD8 beta had positive electrostatic potential compatible with complexation with the corresponding class I molecules. The presence of a CD8 beta homologue in an amphibian species implies that it was already present in the Devonian ancestor of amphibians and mammals, i.e. more than 400 million years ago. PMID:12034498

  14. Evolutionary Psychology

    OpenAIRE

    Heylighen, Francis

    2011-01-01

    Evolutionary psychology (EP) is an approach to the study of the mind that is founded on Darwin’s theory of evolution by natural selection. It assumes that our mental abilities, emotions and preferences are adapted specifically for solving problems of survival and reproduction in humanity’s ancestral environment, and derives testable predictions from this assumption. This has important implications for our understanding of the conditions for human well-being.

  15. Evolutionary thinking

    OpenAIRE

    Hunt, Tam

    2015-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this de...

  16. Evolutionary conservation—evaluating the adaptive potential of species

    OpenAIRE

    Eizaguirre, Christophe; Baltazar-Soares, Miguel

    2014-01-01

    Despite intense efforts, biodiversity around the globe continues to decrease. To cease this phenomenon, we urgently need a better knowledge not only of the true extent of biodiversity, but also of the evolutionary potential of species to respond to environmental change. These aims are the heart of the developing field of Evolutionary conservation. Here, after describing problems associated with implementing evolutionary perspectives into management, we outline how evolutionary principles can ...

  17. Evolutionary conservation of the mature oocyte proteome

    Directory of Open Access Journals (Sweden)

    Tamar Lotan

    2014-06-01

    Significance: The current study provides the first proteomic profile of an oocyte of a cnidarian organism the starlet sea anemone N. vectensis and gives new insights on the ancient origin of an oocyte proteome template. The comparative analysis with a chordate oocyte suggests that the oocyte proteome predates the divergence of the cnidarian and bilaterian lineages. In addition, the data generated in the study will serve as a valuable resource for further developmental and evolutional studies.

  18. Evolutionary Information Theory

    OpenAIRE

    Mark Burgin

    2013-01-01

    Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we const...

  19. Evolutionary food web models in fragmented landscapes

    OpenAIRE

    Allhoff, Korinna Theresa

    2015-01-01

    Ecosystems all over the world currently experience dramatic changes in their environment. The direct consequences are increased extinction rates. Food webs, which are networks of predator-prey interactions, provide a basic understanding of ecosystems and therefore help to identify reasonable conservation strategies. In this thesis, I analyze evolutionary metacommunities, which can be modeled as evolutionary networks of networks: The outer networks represent fragmented landscapes of sever...

  20. Evolutionary principles and their practical application

    DEFF Research Database (Denmark)

    Hendry, A. P.; Kinnison, M. T.; Heino, M.;

    2011-01-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are...... also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of...

  1. Evolutionary Information Theory

    Directory of Open Access Journals (Sweden)

    Mark Burgin

    2013-04-01

    Full Text Available Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we construct and study universal evolutionary machines and automata, which form the base for evolutionary information theory. The first class of measures introduced and studied in this paper is evolutionary information size of symbolic objects relative to classes of automata or machines. In particular, it is proved that there is an invariant and optimal evolutionary information size relative to different classes of evolutionary machines. As a rule, different classes of algorithms or automata determine different information size for the same object. The more powerful classes of algorithms or automata decrease the information size of an object in comparison with the information size of an object relative to weaker4 classes of algorithms or machines. The second class of measures for evolutionary information in symbolic objects is studied by introduction of the quantity of evolutionary information about symbolic objects relative to a class of automata or machines. To give an example of applications, we briefly describe a possibility of modeling physical evolution with evolutionary machines to demonstrate applicability of evolutionary information theory to all material processes. At the end of the paper, directions for future research are suggested.

  2. Hybridization of evolutionary algorithms

    OpenAIRE

    Fister, Iztok; Mernik, Marjan; Brest, Janez

    2012-01-01

    Evolutionary algorithms are good general problem solver but suffer from a lack of domain specific knowledge. However, the problem specific knowledge can be added to evolutionary algorithms by hybridizing. Interestingly, all the elements of the evolutionary algorithms can be hybridized. In this chapter, the hybridization of the three elements of the evolutionary algorithms is discussed: the objective function, the survivor selection operator and the parameter settings. As an objective function...

  3. Incorporating evolutionary principles into environmental management and policy

    DEFF Research Database (Denmark)

    Lankau, Richard; Jørgensen, Peter Søgaard; Harris, David J.;

    2011-01-01

    As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history in...... evolutionary changes. Such evolution-based management has potential to be a highly efficient and consistent way to create greater ecological resilience to widespread, rapid, and multifaceted environmental change....... conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding...

  4. Evolutionary Rent-Seeking

    OpenAIRE

    Hehenkamp, Burkhard; Leininger, Wolfgang; Possajennikov, Alex

    2001-01-01

    Tullock’s analysis of rent-seeking is reconsidered from an evolutionary point of view. We show that evolutionarily stable behavior in a rent-seeking contest differs from efficient rent-seeking behavior in a Nash equilibrium. We explore that implications of evolutionary stability for rent-seeking behavior and relate them to the well examined Nash equilibrium behavior. A most interesting result is an overdissipation law, which holds in evolutionary equilibrium.

  5. Overview: Evolutionary Algorithms

    OpenAIRE

    Bartz-Beielstein, Thomas (Dr.); Mersmann, Olaf

    2014-01-01

    Evolutionary algorithm (EA) is an umbrella term used to describe population-based stochastic direct search algorithms that in some sense mimic natural evolution. Prominent representatives of such algorithms are genetic algorithms, evolution strategies, evolutionary programming, and genetic programming. On the basis of the evolutionary cycle, similarities and differences between these algorithms are described. We briefly discuss how EAs can be adapted to work well in case of multiple objective...

  6. Overview: Evolutionary Algorithms

    OpenAIRE

    Bartz-Beielstein, Thomas (Dr.); Branke, Jürgen; Mehnen, Jörn; Mersmann, Olaf

    2015-01-01

    Evolutionary algorithm (EA) is an umbrella term used to describe population-based stochastic direct search algorithms that in some sense mimic natural evolution. Prominent representatives of such algorithms are genetic algorithms, evolution strategies, evolutionary programming, and genetic programming. On the basis of the evolutionary cycle, similarities and differences between these algorithms are described. We briefly discuss how EAs can be adapted to work well in case of multiple objective...

  7. Evolutionary Algorithm Definition

    Directory of Open Access Journals (Sweden)

    Nada M.A. AL-Salami

    2009-01-01

    Full Text Available Problem statement: Most resent evolutionary algorithms work under weak theoretical basis and thus, they are computationally expensive. Approach: This study discussed the use of new evolutionary algorithm for automatic programming, based on theoretical definitions of program behaviors. Evolutionary process adapted fixed and self-organized input-output specification of the problem, to evolve good finite state machine that efficiently satisfies these specifications. Results: The proposed algorithm enhanced evolutionary process by simultaneously solving multi-parts from the same problem. Conclusion: The probability that the algorithm will converge to the optimal solution was highly enhanced when decomposing the main problem into multi-part.

  8. Evolutionary humanoid robotics

    CERN Document Server

    Eaton, Malachy

    2015-01-01

    This book examines how two distinct strands of research on autonomous robots, evolutionary robotics and humanoid robot research, are converging. The book will be valuable for researchers and postgraduate students working in the areas of evolutionary robotics and bio-inspired computing.

  9. Evolutionary Justification of Plagiarism

    OpenAIRE

    Karpov, Alexander

    2016-01-01

    This paper provides evolutionary game theoretic model of plagiarism. The paper finds the relationship between author effort, publication value, and the frequency of plagiarism. There are two types of equilibria. Plagiarist-free equilibria are neutrally stable. The only evolutionary stable state is characterized by a positive share of plagiarists.

  10. Polymorphic Evolutionary Games.

    Science.gov (United States)

    Fishman, Michael A

    2016-06-01

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. PMID:27016340

  11. Evolutionary history of the mammalian synaptonemal complex.

    Science.gov (United States)

    Fraune, Johanna; Brochier-Armanet, Céline; Alsheimer, Manfred; Volff, Jean-Nicolas; Schücker, Katharina; Benavente, Ricardo

    2016-06-01

    The synaptonemal complex (SC), a key structure of meiosis that assembles during prophase I, has been initially described 60 years ago. Since then, the structure has been described in many sexually reproducing organisms. However, the SC protein components were characterized in only few model organisms. Surprisingly, they lacked an apparent evolutionary relationship despite the conserved structural organization of the SC. For better understanding of this obvious discrepancy, the evolutionary history of the SC and its individual components has been investigated in Metazoa in detail. The results are consistent with the notion of a single origin of the metazoan SC and provide evidence for a dynamic evolutionary history of the SC components. In this mini review, we recapitulate and discuss new insights into metazoan SC evolution. PMID:26968413

  12. Towards an evolutionary model of transcription networks.

    Directory of Open Access Journals (Sweden)

    Dan Xie

    2011-06-01

    Full Text Available DNA evolution models made invaluable contributions to comparative genomics, although it seemed formidable to include non-genomic features into these models. In order to build an evolutionary model of transcription networks (TNs, we had to forfeit the substitution model used in DNA evolution and to start from modeling the evolution of the regulatory relationships. We present a quantitative evolutionary model of TNs, subjecting the phylogenetic distance and the evolutionary changes of cis-regulatory sequence, gene expression and network structure to one probabilistic framework. Using the genome sequences and gene expression data from multiple species, this model can predict regulatory relationships between a transcription factor (TF and its target genes in all species, and thus identify TN re-wiring events. Applying this model to analyze the pre-implantation development of three mammalian species, we identified the conserved and re-wired components of the TNs downstream to a set of TFs including Oct4, Gata3/4/6, cMyc and nMyc. Evolutionary events on the DNA sequence that led to turnover of TF binding sites were identified, including a birth of an Oct4 binding site by a 2nt deletion. In contrast to recent reports of large interspecies differences of TF binding sites and gene expression patterns, the interspecies difference in TF-target relationship is much smaller. The data showed increasing conservation levels from genomic sequences to TF-DNA interaction, gene expression, TN, and finally to morphology, suggesting that evolutionary changes are larger at molecular levels and smaller at functional levels. The data also showed that evolutionarily older TFs are more likely to have conserved target genes, whereas younger TFs tend to have larger re-wiring rates.

  13. Evolutionary tree reconstruction

    Science.gov (United States)

    Cheeseman, Peter; Kanefsky, Bob

    1990-01-01

    It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed.

  14. Do species conservation assessments capture genetic diversity?

    Directory of Open Access Journals (Sweden)

    Malin C. Rivers

    2014-12-01

    Our results support the view that current threat thresholds of the IUCN Red List criteria reflect genetic diversity, and hence evolutionary potential; although the genetic diversity distinction between threatened categories was less evident. Thus, by supplementing conventional conservation assessments with genetic data, new insights into the biological robustness of IUCN Red List assessments for targeted conservation initiatives can be achieved.

  15. When development matters: From evolutionary psychology to evolutionary developmental psychology

    OpenAIRE

    Hernández Blasi, Carlos; Bjorklund, David F.; Gardiner, Amy K.

    2008-01-01

    This article presents evolutionary developmental psychology (EDP) as an emerging field of evolutionary psychology (EP). In describing the core tenets of both approaches and the differences between them, we emphasize the important roles that evolution and development have in understanding human behaviour. We suggest that developmental psychologists should pay more attention to evolutionary issues and, conversely, evolutionary psychologists should take development seriously ...

  16. Adaptive Evolutionary Clustering

    OpenAIRE

    Xu, Kevin S.; Kliger, Mark; Hero III, Alfred O.

    2011-01-01

    In many practical applications of clustering, the objects to be clustered evolve over time, and a clustering result is desired at each time step. In such applications, evolutionary clustering typically outperforms traditional static clustering by producing clustering results that reflect long-term trends while being robust to short-term variations. Several evolutionary clustering algorithms have recently been proposed, often by adding a temporal smoothness penalty to the cost function of a st...

  17. Evolutionary Theorizing in Economics

    OpenAIRE

    Richard R. Nelson; Winter, Sidney G.

    2002-01-01

    This paper reviews the case for an evolutionary approach to problems of economic analysis, ranging from the details of individual firm behavior in the short run through industrial dynamics to the historical evolution of institutions and technologies. We draw upon a substantial body of recent research contributions. We characterize micro behavior as governed by skills and routines that are shaped by learning and selection. We then consider major areas of application of evolutionary thinking, i...

  18. Music and evolutionary computation

    OpenAIRE

    Reis, Cecília; Marques, Viriato M.; Machado, J. A. Tenreiro

    2011-01-01

    This paper presents a brief history of the western music: from its genesis to serialism and the Darmstadt school. Also some mathematical aspects of music are then presented and confronted with music as a form of art. The question is, are these two distinct aspects compatible? Can computers be of real help in automatic composition? The more appealing algorithmic approach is evolutionary computation as it offers creativity potential. Therefore, the Evolutionary Algorithms are then introduced an...

  19. Applications of Evolutionary Computation

    OpenAIRE

    Squillero, Giovanni

    2015-01-01

    This book constitutes the refereed conference proceedings of the 18th International Conference on the Applications of Evolutionary Computation, EvoApplications 2015, held in Copenhagen, Spain, in April 2015, colocated with the Evo* 2015 events EuroGP, EvoCOP, and EvoMUSART. The 72 revised full papers presented were carefully reviewed and selected from 125 submissions. EvoApplications 2015 consisted of the following 13 tracks: EvoBIO (evolutionary computation, machine learning and data mining ...

  20. Proteomics in evolutionary ecology.

    Science.gov (United States)

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  1. Teaching evolutionary biology

    Directory of Open Access Journals (Sweden)

    Tidon Rosana

    2004-01-01

    Full Text Available Evolutionary Biology integrates several disciplines of Biology in a complex and interactive manner, where a deep understanding of the subject demands knowledge in diverse areas. Since this knowledge is often inaccessible to the majority of specialized professionals, including the teachers, we present some reflections in order to stimulate discussions aimed at the improvement of the conditions of education in this area. We examine the profile of evolutionary teaching in Brazil, based on questionnaires distributed to teachers in Secondary Education in the Federal District, on data provided by the "National Institute for Educational Studies and Research", and on information collected from teachers working in various regions of this country. Issues related to biological misconceptions, curriculum and didactic material are discussed, and some proposals are presented with the objective of aiding discussions aimed at the improvement of the teaching of evolutionary biology.

  2. Human nutrition: evolutionary perspectives.

    Science.gov (United States)

    Barnicot, N A

    2005-01-01

    In recent decades, much new evidence relating to the ape forerunners of modern humans has come to hand and diet appears to be an important factor. At some stage, there must have been a transition from a largely vegetarian ape diet to a modern human hunting economy providing significant amounts of meat. On an even longer evolutionary time scale the change was more complex. The mechanisms of evolutionary change are now better understood than they were in Darwin's time, thanks largely to great advances in genetics, both experimental and theoretical. It is virtually certain that diet, as a major component of the human environment, must have exerted evolutionary effects, but researchers still have little good evidence. PMID:17393680

  3. Total Integrative Evolutionary Communication

    DEFF Research Database (Denmark)

    Nedergaard Thomsen, Ole; Brier, Søren

    2014-01-01

    and, on the other, Peircean biosemiotics. According to Cybersemiotics, language is primarily a creative process of total integrative evolutionary communication. It comprises three evolutionary stages: (1) biological reflexive languaging (the reflexive foundation of social coordination), (2......). In this inclusive hierarchy language games subsume the other stages, and thus human evolutionary communication is primarily a symbolic-conventional practice. It is intertwined with the practice of living, that is, with different life forms, including other forms of semiotic behavior. Together they form a coherent...... biological and socio-cultural practice. The basic “molecule” of the cybersemiotic model of human communication is a dyad between two linguistic cyborgs, alias natural language users. Single human communicators are thus “atoms”. They are hybrids between nature and nurture, manipulating all sorts...

  4. Evolutionary Computation:ao Overview

    Institute of Scientific and Technical Information of China (English)

    HeZhenya; WeiChengjian

    1997-01-01

    Evolutionary computation is a field of simulating evolution on a computer.Both aspects of it ,the problem solving aspect and the aspect of modeling natural evolution,are important.Simulating evolution on a computer results in stochastic optimization techniques that can outperform classical methods of optimization when applied to difficult real-world problems.There are currently four main avenues of research in simulated evolution:genetic algorithms,evolutionary programming,evolution strategies,and genetic programming.This paper presents a brief overview of thd field on evolutionary computation,including some theoretical issues,adaptive mechanisms,improvements,constrained optimizqtion,constrained satisfaction,evolutionary neural networks,evolutionary fuzzy systems,hardware evolution,evolutionary robotics,parallel evolutionary computation,and co-evolutionary models.The applications of evolutionary computation for optimizing system and intelligent information processing in telecommunications are also introduced.

  5. Evolutionary Statistical Procedures

    CERN Document Server

    Baragona, Roberto; Poli, Irene

    2011-01-01

    This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

  6. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  7. Evolutionary Theories of Detection

    Energy Technology Data Exchange (ETDEWEB)

    Fitch, J P

    2005-04-29

    Current, mid-term and long range technologies for detection of pathogens and toxins are briefly described in the context of performance metrics and operational scenarios. Predictive (evolutionary) and speculative (revolutionary) assessments are given with trade-offs identified, where possible, among competing performance goals.

  8. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    Part E, Evolutionary Computation, edited by Professors Frank Neumann, Carsten Witt, Peter Merz, Carlos A. Coello Coello, Oliver Schütze, Thomas Bartz-Beielstein, Jörn Mehnen, and Günther Raidl, concerns the third fundamental element of what is traditionally being considered to be the core of Comp...

  9. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    Ellen Clarke

    2014-04-01

    An `evolutionary transition in individuality’ or `major transition’ is a transformation in the hierarchical level at which natural selection operates on a population. In this article I give an abstract (i.e. level-neutral and substrate-neutral) articulation of the transition process in order to precisely understand how such processes can happen, especially how they can get started.

  10. Recent Advances in Evolutionary Computation

    Institute of Scientific and Technical Information of China (English)

    Xin Yao; Yong Xu

    2006-01-01

    Evolutionary computation has experienced a tremendous growth in the last decade in both theoretical analyses and industrial applications. Its scope has evolved beyond its original meaning of "biological evolution" toward a wide variety of nature inspired computational algorithms and techniques, including evolutionary, neural, ecological, social and economical computation, etc., in a unified framework. Many research topics in evolutionary computation nowadays are not necessarily "evolutionary". This paper provides an overview of some recent advances in evolutionary computation that have been made in CERCIA at the University of Birmingham, UK. It covers a wide range of topics in optimization, learning and design using evolutionary approaches and techniques, and theoretical results in the computational time complexity of evolutionary algorithms. Some issues related to future development of evolutionary computation are also discussed.

  11. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    OpenAIRE

    Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

    2012-01-01

    Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more oppo...

  12. Protein interface classification by evolutionary analysis

    Directory of Open Access Journals (Sweden)

    Duarte Jose M

    2012-12-01

    Full Text Available Abstract Background Distinguishing biologically relevant interfaces from lattice contacts in protein crystals is a fundamental problem in structural biology. Despite efforts towards the computational prediction of interface character, many issues are still unresolved. Results We present here a protein-protein interface classifier that relies on evolutionary data to detect the biological character of interfaces. The classifier uses a simple geometric measure, number of core residues, and two evolutionary indicators based on the sequence entropy of homolog sequences. Both aim at detecting differential selection pressure between interface core and rim or rest of surface. The core residues, defined as fully buried residues (>95% burial, appear to be fundamental determinants of biological interfaces: their number is in itself a powerful discriminator of interface character and together with the evolutionary measures it is able to clearly distinguish evolved biological contacts from crystal ones. We demonstrate that this definition of core residues leads to distinctively better results than earlier definitions from the literature. The stringent selection and quality filtering of structural and sequence data was key to the success of the method. Most importantly we demonstrate that a more conservative selection of homolog sequences - with relatively high sequence identities to the query - is able to produce a clearer signal than previous attempts. Conclusions An evolutionary approach like the one presented here is key to the advancement of the field, which so far was missing an effective method exploiting the evolutionary character of protein interfaces. Its coverage and performance will only improve over time thanks to the incessant growth of sequence databases. Currently our method reaches an accuracy of 89% in classifying interfaces of the Ponstingl 2003 datasets and it lends itself to a variety of useful applications in structural biology and

  13. Conservation Value

    OpenAIRE

    Tisdell, Clement A.

    2010-01-01

    This paper outlines the significance of the concept of conservation value and discusses ways in which it is determined paying attention to views stemming from utilitarian ethics and from deontological ethics. The importance of user costs in relation to economic decisions about the conservation and use of natural resources is emphasised. Particular attention is given to competing views about the importance of conserving natural resources in order to achieve economic sustainability. This then l...

  14. Evolutionary impacts of fishing: overfishing's ‘Darwinian debt’

    OpenAIRE

    Pandolfi, John M.

    2009-01-01

    Human harvesting of fish results in far greater mortality than natural causes, with enormous potential to affect the phenotypic traits of fish populations, even after exploitation stops. Central to understanding these effects is the untangling of the genetic versus environmental components of phenotypic response. Evolutionary consequences of harvesting must be incorporated into conservation and management strategies.

  15. Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

    Science.gov (United States)

    Jack, Benjamin R.; Meyer, Austin G.; Echave, Julian; Wilke, Claus O.

    2016-01-01

    Functional residues in proteins tend to be highly conserved over evolutionary time. However, to what extent functional sites impose evolutionary constraints on nearby or even more distant residues is not known. Here, we report pervasive conservation gradients toward catalytic residues in a dataset of 524 distinct enzymes: evolutionary conservation decreases approximately linearly with increasing distance to the nearest catalytic residue in the protein structure. This trend encompasses, on average, 80% of the residues in any enzyme, and it is independent of known structural constraints on protein evolution such as residue packing or solvent accessibility. Further, the trend exists in both monomeric and multimeric enzymes and irrespective of enzyme size and/or location of the active site in the enzyme structure. By contrast, sites in protein–protein interfaces, unlike catalytic residues, are only weakly conserved and induce only minor rate gradients. In aggregate, these observations show that functional sites, and in particular catalytic residues, induce long-range evolutionary constraints in enzymes. PMID:27138088

  16. Evolutionary computation in stochastic environments

    OpenAIRE

    Schmidt, Christian

    2007-01-01

    This book develops efficient methods for the application of Evolutionary Algorithms on stochastic problems. To achieve this, procedures for statistical selection are systematically analyzed with respect to different measures and significantly improved. It is shown how to adapt one of the best procedures for the needs of Evolutionary Algorithms and Evolutionary operators for efficient implementation in stochastic environments are identified.

  17. Canonical transformations and Hamiltonian evolutionary systems

    International Nuclear Information System (INIS)

    In many Lagrangian field theories, one has a Poisson bracket defined on the space of local functionals. We find necessary and sufficient conditions for a transformation on the space of local functionals to be canonical in three different cases. These three cases depend on the specific dimensions of the vector bundle of the theory and the associated Hamiltonian differential operator. We also show how a canonical transformation transforms a Hamiltonian evolutionary system and its conservation laws. Finally, we illustrate these ideas with three examples.

  18. Evolutionary status of Entamoeba

    Institute of Scientific and Technical Information of China (English)

    DONG Jiuhong; WEN Jianfan; XIN Dedong; LU Siqi

    2004-01-01

    In addition to its medical importance as parasitic pathogen, Entamoeba has aroused people's interest in its evolutionary status for a long time. Lacking mitochondrion and other intracellular organelles common to typical eukaryotes, Entamoeba and several other amitochondrial protozoans have been recognized as ancient pre-mitochondriate eukaryotes and named "archezoa", the most primitive extant eukaryotes. It was suggested that they might be living fossils that remained in a primitive stage of evolution before acquisition of organelles, lying close to the transition between prokaryotes and eukaryotes. However, recent studies revealed that Entamoeba contained an organelle, "crypton" or "mitosome", which was regarded as specialized or reductive mitochondrion. Relative molecular phylogenetic analyses also indicated the existence or the probable existence of mitochondrion in Entamoeba. Our phylogenetic analysis based on DNA topoisomerase II strongly suggested its divergence after some mitchondriate eukaryotes. Here, all these recent researches are reviewed and the evolutionary status of Entamoeba is discussed.

  19. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  20. Evolutionary Design in Embryogeny

    Science.gov (United States)

    Ashlock, Daniel

    In biology texts embryogeny is defined as "the development or production of an embryo." An embryo is a living creature in its first stage of life, from the fertilized egg cell through the initial development of its morphology and its chemical networks. The study of embryogeny is part of developmental biology [1, 2]. The reader may wonder why a book on evolutionary design should have a section on embryogeny. Computational embryogeny is the study of representations for evolutionary computation that mimic biological embryogeny. These representations contain analogs to the complex biological processes that steer a single cell to become a rose, a mouse, or a man. The advantage of using embryogenic representations is their richness of expression. A small seed of information can be expanded, through a developmental process, into a complex and potentially useful object. This richness of expression comes at a substantial price: the developmental process is sufficiently complex to be unpredictable.

  1. Role of exterior and evolutionary skew-symmetric differential forms in mathematical physics

    OpenAIRE

    Petrova, L. I.

    2005-01-01

    A role of skew-symmetric differential forms in mathematical physics relates to the fact that they reflect the properties of conservation laws. The closed exterior forms correspond to the conservation laws for physical fields, whereas the evolutionary forms correspond to the conservation laws for material media. Skew-symmetric differential forms can describe a conjugacy of any objects (that correspond to the conservation laws). The closed exterior forms describe conjugated objects. And the evo...

  2. Evolutionary economics and psychology

    OpenAIRE

    Witt, Ulrich

    2006-01-01

    Evolutionary economics is a paradigm for explaining the transformation of the economy. To achieve its goal, it needs being founded on a proper theory of economic behavior. The paper discusses these foundations. It is argued that the historical malleability of economic behavior is based on the interactions between innate behavior dispositions and adaptation mechanisms on the one hand and the limited, and always selective, cognitive and observational learning that contributes to an ever more ex...

  3. Learning in evolutionary environments

    OpenAIRE

    Dosi, Giovanni; Marengo, Luigi; Fagiolo, Giogio

    2001-01-01

    The purpose of this work is to present a sort of short selective guide to an enormous and diverse literature on learning processes in economics. We argue that learning is an ubiquitous characteristic of most economic and social systems but it acquires even greater importance in explicitly evolutionary environments where: a) heterogeneous agents systematically display various forms of "bounded rationality"; b) there is a persistent appearance of novelties, both as exogenous shocks and as the r...

  4. Evolutionary game design

    CERN Document Server

    Browne, Cameron

    2011-01-01

    The book describes the world's first successful experiment in fully automated board game design. Evolutionary methods were used to derive new rule sets within a custom game description language, and self-play trials used to estimate each derived game's potential to interest human players. The end result is a number of new and interesting games, one of which has proved popular and gone on to be commercially published.

  5. Evolutionary genomics of Entamoeba

    OpenAIRE

    Weedall, Gareth D.; Hall, Neil

    2011-01-01

    Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population ...

  6. Evolutionary health psychology

    OpenAIRE

    Dickins, Thomas E.

    2006-01-01

    For the last decade and a half the discipline of Evolutionary Psychology (EP) has been developing with great success. The first collection of significant papers was published in 1992 (Barkow et al.) and recently a landmark handbook has been produced summing the progress so far, as well as setting an agenda for future study (Buss, 2005). Unlike other areas within Psychology, EP extends its interest to all behaviours, rightly seeing them as part of an evolved phenotype, and health has not escap...

  7. Introduction to Evolutionary Algorithms

    CERN Document Server

    Yu, Xinjie

    2010-01-01

    Evolutionary algorithms (EAs) are becoming increasingly attractive for researchers from various disciplines, such as operations research, computer science, industrial engineering, electrical engineering, social science, economics, etc. This book presents an insightful, comprehensive, and up-to-date treatment of EAs, such as genetic algorithms, differential evolution, evolution strategy, constraint optimization, multimodal optimization, multiobjective optimization, combinatorial optimization, evolvable hardware, estimation of distribution algorithms, ant colony optimization, particle swarm opti

  8. Asymmetric Evolutionary Games.

    Science.gov (United States)

    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. PMID:26308326

  9. Evolutionary Hotspots in the Mojave Desert

    Directory of Open Access Journals (Sweden)

    Sharyn B. Marks

    2013-04-01

    Full Text Available Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

  10. Reshaping conservation

    DEFF Research Database (Denmark)

    Funder, Mikkel; Danielsen, Finn; Ngaga, Yonika;

    2013-01-01

    members strengthen the monitoring practices to their advantage, and to some extent move them beyond the reach of government agencies and conservation and development practitioners. This has led to outcomes that are of greater social and strategic value to communities than the original 'planned' benefits......, although the monitoring scheme has also to some extent become dominated by local 'conservation elites' who negotiate the terrain between the state and other community members. Our findings suggest that we need to move beyond simplistic assumptions of community strategies and incentives in participatory...... conservation and allow for more adaptive and politically explicit governance spaces in protected area management....

  11. Priorities for global felid conservation.

    Science.gov (United States)

    Dickman, Amy J; Hinks, Amy E; Macdonald, Ewan A; Burnham, Dawn; Macdonald, David W

    2015-06-01

    Conservation resources are limited, necessitating prioritization of species and locations for action. Most prioritization approaches are based solely on biologically relevant characteristics of taxa or areas and ignore geopolitical realities. Doing so risks a poor return on conservation investment due to nonbiological factors, such as economic or political instability. We considered felids, a taxon which attracts intense conservation attention, to demonstrate a new approach that incorporates both intrinsic species traits and geopolitical characteristics of countries. We developed conservation priority scores for wild felids based on their International Union for Conservation of Nature status, body mass, habitat, range within protected area, evolutionary distinctiveness, and conservation umbrella potential. We used published data on governance, economics and welfare, human population pressures, and conservation policy to assign conservation-likelihood scores to 142 felid-hosting countries. We identified 71 countries as high priorities (above median) for felid conservation. These countries collectively encompassed all 36 felid species and supported an average of 96% of each species' range. Of these countries, 60.6% had below-average conservation-likelihood scores, which indicated these countries are relatively risky conservation investments. Governance was the most common factor limiting conservation likelihood. It was the major contributor to below-median likelihood scores for 62.5% of the 32 felid species occurring in lower-likelihood countries. Governance was followed by economics for which scores were below median for 25% of these species. An average of 58% of species' ranges occurred in 43 higher-priority lower-likelihood countries. Human population pressure was second to governance as a limiting factor when accounting for percentage of species' ranges in each country. As conservation likelihood decreases, it will be increasingly important to identify relevant

  12. 基于整合蛋白质进化保守性的伪氨基酸组成成分预测蛋白质亚细胞定位%USING PSEUDO AMINO ACID COMPOSITION TO PREDICT PROTEIN SUBCELLULAR LOCALIZATION:APPROACHED BY INCORPORATING EVOLUTIONARY CONSERVATION INFORMATION

    Institute of Scientific and Technical Information of China (English)

    李利珍; 董自梅

    2009-01-01

    Information of the subcellular locations of proteins is important because it can provide useful insights about their functions.as well as how and in what kind of cellular environments they interact with each other and with other molecules.Knowledge of the localization of proteins within cellular compartments Call help understand the intricate pathways that regulate biological processes at the cellular level.Facing the explosion of newly generated protein sequences in the post genomic era,developing an automated method for fast and reliably annotating their subcellular locations is becoming more and more important.Here,a novel approach was developed by incorporating protein evolutionary conservation information.Based on the concept of Chou's pseudo amino acid composition (PseAAC) and per residue conservation score calculated with an improved evolutionary conservation algorithm, each protein can be represented as a feature vector created with multi-scale energy (MSE).In addition,the protein Can be represented as other feature vectors based on amino acid composition (AAC),weighted auto-correlation function and Moment descriptor methods.Then,the feature vectors of all protein sequences are further input into multi-class support vector machines to predict 12 kinds of subcellular locations.Finally,the results of four kinds of feature classifiers were fused through a product rule system.Compared with the results reported by the previous investigators,higher Success rates were obtained in both jackknife cross-validation test and independent dataset test,suggesting that introducing protein evolutionary information and the concept of fusing multi-features classifiers ale quite encouraging and promising,and may become a useful tool in complementing the existing methods.%蛋白质亚细胞定位信息对于确定蛋白质功能非常重要,它可以提供蛋白质在什么细胞环境下相互作用或与其它分子作用的信息,另外,如果知道蛋白质在细胞中的

  13. Conservative ecological and evolutionary patterns in liverwort–fungal symbioses

    OpenAIRE

    Bidartondo, Martin I.; Duckett, Jeffrey G.

    2009-01-01

    Liverworts, the most ancient group of land plants, form a range of intimate associations with fungi that may be analogous to the mycorrhizas of vascular plants. Most thalloid liverworts contain arbuscular mycorrhizal glomeromycete fungi similar to most vascular plants. In contrast, a range of leafy liverwort genera and one simple thalloid liverwort family (the Aneuraceae) have switched to basidiomycete fungi. These liverwort switches away from glomeromycete fungi may be expected to parallel s...

  14. Evolutionary conservation of species' roles in food webs

    OpenAIRE

    Stouffer, D. B.; Sales-Pardo, M.; Sirer, M. I.; Bascompte, J.

    2012-01-01

    Studies of ecological networks (the web of interactions between species in a community) demonstrate an intricate link between a community’s structure and its long-term viability. It remains unclear, however, how much a community’s persistence depends on the identities of the species present, or how much the role played by each species varies as a function of the community in which it is found. We measured species’ roles by studying how species are embedded within the overall network and th...

  15. Evolutionary conservation in genes underlying human psychiatric disorders

    OpenAIRE

    Eric Joseph Vallender

    2014-01-01

    Many psychiatric diseases observed in humans have tenuous or absent analogs in other species. Most notable among these are schizophrenia and autism. One hypothesis has posited that these diseases have arisen as a consequence of human brain evolution, for example, that the same processes that led to advances in cognition, language, and executive function also resulted in novel diseases in humans when dysfunctional. Here, the molecular evolution of the protein-coding regions of genes associated...

  16. Evolutionary divergence of chloroplast FAD synthetase proteins

    Directory of Open Access Journals (Sweden)

    Arilla-Luna Sonia

    2010-10-01

    Full Text Available Abstract Background Flavin adenine dinucleotide synthetases (FADSs - a group of bifunctional enzymes that carry out the dual functions of riboflavin phosphorylation to produce flavin mononucleotide (FMN and its subsequent adenylation to generate FAD in most prokaryotes - were studied in plants in terms of sequence, structure and evolutionary history. Results Using a variety of bioinformatics methods we have found that FADS enzymes localized to the chloroplasts, which we term as plant-like FADS proteins, are distributed across a variety of green plant lineages and constitute a divergent protein family clearly of cyanobacterial origin. The C-terminal module of these enzymes does not contain the typical riboflavin kinase active site sequence, while the N-terminal module is broadly conserved. These results agree with a previous work reported by Sandoval et al. in 2008. Furthermore, our observations and preliminary experimental results indicate that the C-terminus of plant-like FADS proteins may contain a catalytic activity, but different to that of their prokaryotic counterparts. In fact, homology models predict that plant-specific conserved residues constitute a distinct active site in the C-terminus. Conclusions A structure-based sequence alignment and an in-depth evolutionary survey of FADS proteins, thought to be crucial in plant metabolism, are reported, which will be essential for the correct annotation of plant genomes and further structural and functional studies. This work is a contribution to our understanding of the evolutionary history of plant-like FADS enzymes, which constitute a new family of FADS proteins whose C-terminal module might be involved in a distinct catalytic activity.

  17. Evolutionary Psychology: The Academic Debate

    OpenAIRE

    Suplizio, Jean

    2005-01-01

    This dissertation examines the academic debate that surrounds the new field called "Evolutionary Psychology." Evolutionary psychology has emerged as the most popular successor theory to human sociobiology. Its proponents search for evolved psychological mechanisms and emphasize universal features of the human mind. My thesis is that in order to flourish evolutionary psychologists must engage other researchers on equal terms -- something they have not been doing. To show this, I examine the...

  18. Theoretical Aspects of Evolutionary Algorithms

    OpenAIRE

    Wegener, Ingo

    2001-01-01

    Randomized search heuristics like simulated annealing and evolutionary algorithms are applied successfully in many different situations. However, the theory on these algorithms is still in its infancy. Here it is discussed how and why such a theory should be developed. Afterwards, some fundamental results on evolutionary algorithms are presented in order to show how theoretical results on randomized search heuristics can be proved and how they contribute to the understanding of evolutionary a...

  19. Evolutionary algorithms in multiobjective problems

    OpenAIRE

    Syomkin, A. M.; Zmitrovich, A. I.

    2003-01-01

    Many real-world problems involve two types of difficulties: 1) multiple, conflicting objectives and 2) a highly complex search space. Efficient evolutionary strategies have been developed to deal with both types of difficulties. Evolutionary algorithms possess several characteristics such as parallelism and robustness that make them preferable to classical optimization methods. In this work 1 conducted comparative studies among the well-known evolutionary algorithms based on NP-hard 0-1 multi...

  20. Binary Evolutionary Models

    CERN Document Server

    Han, Z

    2008-01-01

    In this talk, we present the general principles of binary evolution and give two examples. The first example is the formation of subdwarf B stars (sdBs) and their application to the long-standing problem of ultraviolet excess (also known as UV-upturn) in elliptical galaxies. The second is for the progenitors of type Ia supernovae (SNe Ia). We discuss the main binary interactions, i.e., stable Roche lobe overflow (RLOF) and common envelope (CE) evolution, and show evolutionary channels leading to the formation of various binary-related objects. In the first example, we show that the binary model of sdB stars of Han et al. (2002, 2003) can reproduce field sdB stars and their counterparts, extreme horizontal branch (EHB) stars, in globular clusters. By applying the binary model to the study of evolutionary population synthesis, we have obtained an ``a priori'' model for the UV-upturn of elliptical galaxies and showed that the UV-upturn is most likely resulted from binary interactions. This has major implications...

  1. Distributed Evolutionary Computation using REST

    CERN Document Server

    Castillo, P A; Mora, A M; Laredo, J L J; Romero, G; Rivas, V M; Merelo, J J

    2011-01-01

    This paper analises distributed evolutionary computation based on the Representational State Transfer (REST) protocol, which overlays a farming model on evolutionary computation. An approach to evolutionary distributed optimisation of multilayer perceptrons (MLP) using REST and language Perl has been done. In these experiments, a master-slave based evolutionary algorithm (EA) has been implemented, where slave processes evaluate the costly fitness function (training a MLP to solve a classification problem). Obtained results show that the parallel version of the developed programs obtains similar or better results using much less time than the sequential version, obtaining a good speedup.

  2. On the evolutionary stage of the interacting binary AU Mon

    CERN Document Server

    Mennickent, R E

    2014-01-01

    We present a study of the evolutionary stage of the interacting binary and Double Periodic Variable AU Monocerotis. A multi-parametric Chi2 minimization is made between the observed parameters and those predicted by the grid of non-conservative and conservative evolutionary models by Van Rensbergen et al., finding the model that best represents the current stellar and system parameters. According to this model, the system started with initial masses 4 M_sun and 3.6 M_sun and orbital period 3.0 days, 196 million years ago, and at present undergoes a Case-B mass-exchange episode. This evolutionary stage is consistent with the reported existence of a circumprimary accretion disk. However, the implied high mass transfer rate contrasts with the absence of significant orbital period change if the mass exchange is conservative. We show that this can occur if the system has recently entered in a non-conservative stage of mass transfer and the efficiency of mass and angular momentum loss satisfy certain conditions.

  3. Targeted gene flow for conservation.

    Science.gov (United States)

    Kelly, Ella; Phillips, Ben L

    2016-04-01

    Anthropogenic threats often impose strong selection on affected populations, causing rapid evolutionary responses. Unfortunately, these adaptive responses are rarely harnessed for conservation. We suggest that conservation managers pay close attention to adaptive processes and geographic variation, with an eye to using them for conservation goals. Translocating pre-adapted individuals into recipient populations is currently considered a potentially important management tool in the face of climate change. Targeted gene flow, which involves moving individuals with favorable traits to areas where these traits would have a conservation benefit, could have a much broader application in conservation. Across a species' range there may be long-standing geographic variation in traits or variation may have rapidly developed in response to a threatening process. Targeted gene flow could be used to promote natural resistance to threats to increase species resilience. We suggest that targeted gene flow is a currently underappreciated strategy in conservation that has applications ranging from the management of invasive species and their impacts to controlling the impact and virulence of pathogens. PMID:26332195

  4. Spore: Spawning Evolutionary Misconceptions?

    Science.gov (United States)

    Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.

    2010-10-01

    The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.

  5. Complexity in Evolutionary Processes

    International Nuclear Information System (INIS)

    Darwin's principle of evolution by natural selection is readily casted into a mathematical formalism. Molecular biology revealed the mechanism of mutation and provides the basis for a kinetic theory of evolution that models correct reproduction and mutation as parallel chemical reaction channels. A result of the kinetic theory is the existence of a phase transition in evolution occurring at a critical mutation rate, which represents a localization threshold for the population in sequence space. Occurrence and nature of such phase transitions depend critically on fitness landscapes. The fitness landscape being tantamount to a mapping from sequence or genotype space into phenotype space is identified as the true source of complexity in evolution. Modeling evolution as a stochastic process is discussed and neutrality with respect to selection is shown to provide a major challenge for understanding evolutionary processes (author)

  6. Two Aspects of Evolutionary Algorithms

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In this paper we discuss the paradigm of evolutionary algorithms (Eas). We argue about the need for new heuristics in real-world problem solving, discussing reasons why some problems are difficult tosolve. After introducing the main concepts of evolutionary algorithms, we concentrate on two issues:(1)self-adaptation of the parameters of EA, and (2) handling constraints.

  7. Open Issues in Evolutionary Robotics.

    Science.gov (United States)

    Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

    2016-01-01

    One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots. PMID:26581015

  8. Evolutionary transitions in bacterial symbiosis

    OpenAIRE

    Sachs, Joel L.; Skophammer, Ryan G.; Regus, John U.

    2011-01-01

    Diverse bacterial lineages form beneficial infections with eukaryotic hosts. The origins, evolution, and breakdown of these mutualisms represent important evolutionary transitions. To examine these key events, we synthesize data from diverse interactions between bacteria and eukaryote hosts. Five evolutionary transitions are investigated, including the origins of bacterial associations with eukaryotes, the origins and subsequent stable maintenance of bacterial mutualism with hosts, the captur...

  9. Topics of Evolutionary Computation 2001

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem......This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem...

  10. Evolutionary Design of Boolean Functions

    Institute of Scientific and Technical Information of China (English)

    WANG Zhang-yi; ZHANG Huan-guo; QIN Zhong-ping; MENG Qing-shu

    2005-01-01

    We use evolutionary computing to synthesize Boolean functions randomly. By using specific crossover and mutation operator in evolving process and modifying search space and fitness function, we get some high non-linearity functions which have other good cryptography characteristics such as autocorrelation etc. Comparing to other heuristic search techniques, evolutionary computing approach is more effective because of global search strategy and implicit parallelism.

  11. Chaos Synthesis by Evolutionary Algorithms

    Czech Academy of Sciences Publication Activity Database

    Zelinka, I.; Chen, G.; Čelikovský, Sergej

    Berlin : Springer-Verlag, 2010 - (Zelinka, I.; Čelikovský, S.; Richter, H.; Chen, G.), s. 345-382 ISBN 978-3-642-10706-1. - (Studies in Computational Intelligence. 267) Institutional research plan: CEZ:AV0Z10750506 Keywords : chaos synthesis * evolutionary algorithms * self organizingmigrating * evolutionary computing Subject RIV: BC - Control Systems Theory

  12. Hybrid zone and its genetic analysis: implication for conservation

    Institute of Scientific and Technical Information of China (English)

    ZHENGDong; LIUXue-dong; MAJian-zhang

    2003-01-01

    Hybrid zone is a very critical concept within the evolutionary biology, because it would offer us a better insight to understand the evolutionary role of gene flow and hybridization based on the cline model. This minireview presents an expatia-tion of history perspectives and research developments upon basic concepts including hybrid zones, hybridization, hybrid and its the genetic cline model. Moreover, by figuring out the existing problem around the hybrids within conservative theory and prac-tices, it suggests that the theory of hybrid zone be introduced into conservation biology and it would be provide a broader and more open theoretical background for conservative research and practices.

  13. Evolutionary Explanations of Eating Disorders

    Directory of Open Access Journals (Sweden)

    Igor Kardum

    2008-12-01

    Full Text Available This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evolutionary explanations of anorexia nervosa are presented together with their main weaknesses. Evolutionary explanations of eating disorders based on the reproductive suppression hypothesis and its variants derived from kin selection theory and the model of parental manipulation were elaborated. The sexual competition hypothesis of eating disorder, adapted to flee famine hypothesis as well as explanation based on the concept of social attention holding power and the need to belonging were also explained. The importance of evolutionary theory in modern conceptualization and research of eating disorders is emphasized.

  14. Individual-based modeling of ecological and evolutionary processes

    Science.gov (United States)

    DeAngelis, Donald L.; Mooij, Wolf M.

    2005-01-01

    Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.

  15. [Conservation Units.

    Science.gov (United States)

    Texas Education Agency, Austin.

    Each of the six instructional units deals with one aspect of conservation: forests, water, rangeland, minerals (petroleum), and soil. The area of the elementary school curriculum with which each correlates is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the…

  16. Creative conservation

    NARCIS (Netherlands)

    Bentham, Roelof J.

    1968-01-01

    The increasing exploitation of our natural resources, the unlimited occupation of ever more new areas, and the intensification of land-use, make it necessary for us to expand the concept of conservation. But we also need to reconsider that concept itself. For the changing conditions in the present-d

  17. Generalising Conservativity

    OpenAIRE

    Zuber, Richard

    2010-01-01

    A constraint on functions from sets and relations to sets is studied. This constraint is a generalisation of the constraint of conservativity known from the study of generalised quantifiers in natural languages. It is suggested that this generalised constraint constitutes a semantic universal

  18. Dynamic Conservation of Forest Genetic Resources in 33 European Countries

    OpenAIRE

    2013-01-01

    Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across Europe (33 countries). On the basis of information available in the European Information System on FGR (EUFGIS Portal), species distribution maps, and environmental stratification of the continent, we ...

  19. Evolutionary History of Trihelix Family and Their Functional Diversification

    OpenAIRE

    Qin, Yao; Ma, Xin; Yu, Guanghui; Wang, Qi; Wang, Liang; Kong, Lingrang; Kim, Wook; Wang, Hong Wei

    2014-01-01

    In this study, we carried out an evolutionary, transcriptional, and functional analyses of the trihelix transcription factor family. A total of 319 trihelix members, identified from 11 land plant species, were classified into five clades. The results of phylogeny indicate the binding domains of GT1 and GT2 diverged early in the existence of land plants. Genomic localization revealed that the trihelix family members were highly conserved among cereal species, even though some homeologs generat...

  20. Evolutionary Reconstruction and Population Genetics Analysis of Aurora Kinases

    OpenAIRE

    Balu Kamaraj; Ambuj Kumar; Rituraj Purohit

    2013-01-01

    BACKGROUND: Aurora kinases belong to the highly conserved kinase family and play a vital role in cell cycle regulation. The structure and function of these kinases are inter-related and sometimes they also act as substitutes in case of knockdown of other aurora kinases. METHOD: In this work we carried out the evolutionary reconstruction and population genetic studies of aurora kinase proteins. Substitution saturation test, CAI (Codon adaptation index), gene expression and RSCU (Relative synon...

  1. Quantifying evolutionary constraints on B cell affinity maturation

    OpenAIRE

    McCoy, Connor O.; Bedford, Trevor; Minin, Vladimir N.; Bradley, Philip; Robins, Harlan; Frederick A. Matsen IV

    2014-01-01

    The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B cell sequence data, and then apply them to a very deep short-read data set of B cell receptors. We find that the substitution process is conserved acros...

  2. Quantifying evolutionary constraints on B-cell affinity maturation

    OpenAIRE

    McCoy, Connor O.; Bedford, Trevor; Minin, Vladimir N.; Bradley, Philip; Robins, Harlan; Frederick A Matsen

    2015-01-01

    The antibody repertoire of each individual is continuously updated by the evolutionary process of B-cell receptor (BCR) mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B-cell sequence data, and then apply them to a very deep short-read dataset of BCRs. We find that the substitution process is conserved across indiv...

  3. Sequence Analysis and Evolutionary Studies of Reelin Proteins

    OpenAIRE

    Malini Manoharan; Sayyed Auwn Muhammad; Ramanathan Sowdhamini

    2015-01-01

    The reelin gene is conserved across many vertebrate species, including humans. The protein product of this gene plays several important roles in early brain development and regulation of neural network plasticity of a matured brain structure. With an extended structure of 3461 amino acid sequences, consisting of eight reelin repeats, the human reelin sequence stands out as an exceptional model for evolutionary studies. In this study, sequence analysis of the human reelin and its homologues an...

  4. Evolutionary Constraints of Phosphorylation in Eukaryotes, Prokaryotes, and Mitochondria*

    OpenAIRE

    Gnad, Florian; Forner, Francesca; Zielinska, Dorota F.; Birney, Ewan; Gunawardena, Jeremy; Mann, Matthias

    2010-01-01

    High accuracy mass spectrometry has proven to be a powerful technology for the large scale identification of serine/threonine/tyrosine phosphorylation in the living cell. However, despite many described phosphoproteomes, there has been no comparative study of the extent of phosphorylation and its evolutionary conservation in all domains of life. Here we analyze the results of phosphoproteomics studies performed with the same technology in a diverse set of organisms. For the most ancient organ...

  5. Modeling tumor evolutionary dynamics

    Directory of Open Access Journals (Sweden)

    Beatriz eStransky

    2013-02-01

    Full Text Available Tumorigenesis can be seen as an evolutionary process, in which the transformation of a normal cell into a tumor cell involves a number of limiting genetic and epigenetic events, occurring in a series of discrete stages. However, not all mutations in a cell are directly involved in cancer development and it is likely that most of them (passenger mutations do not contribute in any way to tumorigenesis. Moreover, the process of tumor evolution is punctuated by selection of advantageous (driver mutations and clonal expansions. Regarding these driver mutations, it is uncertain how many limiting events are required and / or sufficient to promote a tumorigenic process or what are the values associated with the adaptive advantage of different driver mutations. In spite of the availability of high-quality cancer data, several assumptions about the mechanistic process of cancer initiation and development remain largely untested, both mathematically and statistically. Here we review the development of mathematical/computational models where some assumptions were tested and discuss the impact of these models to the field of tumor biology.

  6. Evolutionary tracks for Betelgeuse

    CERN Document Server

    Dolan, Michelle M; Lam, Doan Duc; Lan, Nguyen Quynh; Herczeg, Gregory J; Dearborn, David S P

    2014-01-01

    We have constructed a series of non-rotating quasi-hydrostatic evolutionary models for the M2 Iab supergiant Betelgeuse ($\\alpha~Orionis$). Our models are constrained by multiple values for the observed temperature, luminosity, surface composition and mass loss for this star, along with the parallax distance and high resolution imagery that determines its radius. We have then applied our best-fit models to analyze the observed variations in surface luminosity and the size of detected surface bright spots as the result of up-flowing convective material from regions of high temperature in a surface convective zone. We also attempt to explain the intermittently observed periodic variability in a simple radial linear adiabatic pulsation model. Based upon the best fit to all observed data, we suggest a best progenitor mass estimate of $ 20 ^{+5}_{-3} M_\\odot$ and a current lifetime of $8.0 - 8.5$ Myr based upon the observed ejected mass while on the giant branch.

  7. Industrial Applications of Evolutionary Algorithms

    CERN Document Server

    Sanchez, Ernesto; Tonda, Alberto

    2012-01-01

    This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

  8. Evolutionary model with Turing machines

    Science.gov (United States)

    Feverati, Giovanni; Musso, Fabio

    2008-06-01

    The development of a large noncoding fraction in eukaryotic DNA and the phenomenon of the code bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code growth) the evolution of a complex code cannot be attained without maintaining a large inactive fraction. To test this hypothesis we performed computer simulations of an evolutionary toy model for Turing machines, studying the relations among fitness and coding versus noncoding ratio while varying mutation and code growth rates. The results suggest that, in our model, having a large reservoir of noncoding states constitutes a great (long term) evolutionary advantage.

  9. Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes.

    Science.gov (United States)

    Kohli, Gurjeet S; John, Uwe; Van Dolah, Frances M; Murray, Shauna A

    2016-08-01

    Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success. PMID:26784357

  10. Insights from life history theory for an explicit treatment of trade-offs in conservation biology.

    Science.gov (United States)

    Charpentier, Anne

    2015-06-01

    As economic and social contexts become more embedded within biodiversity conservation, it becomes obvious that resources are a limiting factor in conservation. This recognition is leading conservation scientists and practitioners to increasingly frame conservation decisions as trade-offs between conflicting societal objectives. However, this framing is all too often done in an intuitive way, rather than by addressing trade-offs explicitly. In contrast, the concept of trade-off is a keystone in evolutionary biology, where it has been investigated extensively. I argue that insights from evolutionary theory can provide methodological and theoretical support to evaluating and quantifying trade-offs in biodiversity conservation. I reviewed the diverse ways in which trade-offs have emerged within the context of conservation and how advances from evolutionary theory can help avoid the main pitfalls of an implicit approach. When studying both evolutionary trade-offs (e.g., reproduction vs. survival) and conservation trade-offs (e.g., biodiversity conservation vs. agriculture), it is crucial to correctly identify the limiting resource, hold constant the amount of this resource when comparing different scenarios, and choose appropriate metrics to quantify the extent to which the objectives have been achieved. Insights from studies in evolutionary theory also reveal how an inadequate selection of conservation solutions may result from considering suboptimal rather than optional solutions when examining whether a trade-off exits between 2 objectives. Furthermore, the shape of a trade-off curve (i.e., whether the relationship between 2 objectives follows a concave, convex, or linear form) is known to affect crucially the definition of optimal solutions in evolutionary biology and very likely affects decisions in biodiversity conservation planning too. This interface between evolutionary biology and biodiversity conservation can therefore provide methodological guidance to

  11. Evolutionary computation for reinforcement learning

    NARCIS (Netherlands)

    S. Whiteson

    2012-01-01

    Algorithms for evolutionary computation, which simulate the process of natural selection to solve optimization problems, are an effective tool for discovering high-performing reinforcement-learning policies. Because they can automatically find good representations, handle continuous action spaces, a

  12. Evolutionary Processes and Mental Deficiency

    Science.gov (United States)

    Spitz, Herman H.

    1973-01-01

    The author hypothesizes that central nervous system damage of deficiency associated with mental retardation affects primarily those cortical processes which developed at a late stage in man's evolutionary history. (Author)

  13. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  14. Lifetime learning in evolutionary robotics

    OpenAIRE

    Ruud, Else-Line Malene

    2015-01-01

    Inspired by animals ability to learn and adapt to changes in their environment during life, hybrid evolutionary algorithms which include local optimization between generations have been developed and successfully applied in a number of research areas. Despite the possible benefits this kind of algorithm could have in the field of evolutionary robotics, very little research has been done on this topic. This thesis explores the effects of learning used in cooperation with a genetic algorithm t...

  15. Coevolution Evolutionary Algorithm: A Survey

    OpenAIRE

    Jeniefer Kavetha. M

    2013-01-01

    Evolutionary Computing techniques have become one of the most powerful tools for solving optimization problems and isbased on the mechanisms of natural selection and genetics. In Evolutionary Algorithm, Co-evolution is a natural choice for learning in problem domains where one agent’s behaviour is directly related to the behaviour of other agents. Co-evolution provides a framework to implement search heuristics that are more elaborate than those driving the exploration of the state space in c...

  16. Counterpunishment revisited: an evolutionary approach

    OpenAIRE

    Wolff, Irenaeus

    2009-01-01

    Evolutionary game theory has shown that in environments characterised by a social-dilemma situation punishment may be an adaptive behaviour. Experimental evidence closely corresponds to this finding but yields contradictory results on the cooperation-enhancing effect of punishment if players are allowed to retaliate against their punishers. The present study sets out to examine the question of whether cooperation will still be part of an evolutionary stable strategy if we allow for counterpun...

  17. Freud: the first evolutionary psychologist?

    Science.gov (United States)

    LeCroy, D

    2000-04-01

    An evolutionary perspective on attachment theory and psychoanalytic theory brings these two fields together in interesting ways. Application of the evolutionary principle of parent-offspring conflict to attachment theory suggests that attachment styles represent context-sensitive, evolved (adaptive) behaviors. In addition, an emphasis on offspring counter-strategies to adult reproductive strategies leads to consideration of attachment styles as overt manifestations of psychodynamic mediating processes, including the defense mechanisms of repression and reaction formation. PMID:10818628

  18. Evolutionary Explanations of Eating Disorders

    OpenAIRE

    Igor Kardum; Asmir Gračanin; Jasna Hudek-Knežević

    2008-01-01

    This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evoluti...

  19. How competition affects evolutionary rescue

    OpenAIRE

    Osmond, Matthew Miles; de Mazancourt, Claire

    2013-01-01

    Populations facing novel environments can persist by adapting. In nature, the ability to adapt and persist will depend on interactions between coexisting individuals. Here we use an adaptive dynamic model to assess how the potential for evolutionary rescue is affected by intra- and interspecific competition. Intraspecific competition (negative density-dependence) lowers abundance, which decreases the supply rate of beneficial mutations, hindering evolutionary rescue. On the other hand, inters...

  20. Evolutionary economics and regional policy

    OpenAIRE

    Lambooy, Jan G.; Boschma, Ron

    2001-01-01

    The principal objective of this paper is to formulate some possible links between evolutionary economics and regional policy, a topic that has not (yet) been covered by the literature. We firstly give a brief overview of some issues of regional policy, conceived as a strategy to influence the spatial matrix of economic development. Then, we outline what we take to be the essential arguments and components of evolutionary economics. More in particular, we focus attention on the economic founda...

  1. Behaviour Trees for Evolutionary Robotics

    OpenAIRE

    Scheper, Kirk Y. W.; Tijmons, Sjoerd; de Visser, Coen C.; de Croon, Guido C. H. E.

    2014-01-01

    Evolutionary Robotics allows robots with limited sensors and processing to tackle complex tasks by means of sensory-motor coordination. In this paper we show the first application of the Behaviour Tree framework to a real robotic platform using the Evolutionary Robotics methodology. This framework is used to improve the intelligibility of the emergent robotic behaviour as compared to the traditional Neural Network formulation. As a result, the behaviour is easier to comprehend and manually ad...

  2. Evolutionary computation for trading systems

    OpenAIRE

    Kaucic, Massimiliano

    2008-01-01

    Evolutionary computations, also called evolutionary algorithms, consist of several heuristics, which are able to solve optimization tasks by imitating some aspects of natural evolution. They may use different levels of abstraction, but they are always working on populations of possible solutions for a given task. The basic idea is that if only those individuals of a population which meet a certain selection criteria reproduce, while the remaining individuals die, the population wi...

  3. Evolutionary Algorithms and Dynamic Programming

    OpenAIRE

    Doerr, Benjamin; Eremeev, Anton; Neumann, Frank; Theile, Madeleine; Thyssen, Christian

    2013-01-01

    Recently, it has been proven that evolutionary algorithms produce good results for a wide range of combinatorial optimization problems. Some of the considered problems are tackled by evolutionary algorithms that use a representation which enables them to construct solutions in a dynamic programming fashion. We take a general approach and relate the construction of such algorithms to the development of algorithms using dynamic programming techniques. Thereby, we give general guidelines on how ...

  4. Evolutionary Algorithms in Astronautic Applications

    OpenAIRE

    Maiwald, Volker

    2010-01-01

    Evolutionary algorithms (EA) are a computation tool that utilizes biological principles found in the evolution theory. One major difference to other optimization methods is the fact that a large group of solutions is evaluated, not a single one. Combination of various solutions from such a group, called population, allows improvement of the solutions. Overall several terms in usage in the field of evolutionary algorithms have their origin in genetics or biology, especially the ...

  5. Evolutionary Algorithms for Reinforcement Learning

    OpenAIRE

    Grefenstette, J. J.; Moriarty, D. E.; Schultz, A.C.

    2011-01-01

    There are two distinct approaches to solving reinforcement learning problems, namely, searching in value function space and searching in policy space. Temporal difference methods and evolutionary algorithms are well-known examples of these approaches. Kaelbling, Littman and Moore recently provided an informative survey of temporal difference methods. This article focuses on the application of evolutionary algorithms to the reinforcement learning problem, emphasizing alternative policy represe...

  6. Evolutionary paths of streptococcal and staphylococcal superantigens

    Directory of Open Access Journals (Sweden)

    Okumura Kayo

    2012-08-01

    Full Text Available Abstract Background Streptococcus pyogenes (GAS harbors several superantigens (SAgs in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of S. dysgalactiae subsp. equisimilis (SDSE, the closest relative of GAS. Although speG is the only SAg gene of SDSE, speG was present in only 50% of clinical SDSE strains and smez in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs. Results We compared the sequences of the 12–60 kb speG regions of nine SDSE strains, five speG+ and four speG–. We found that the synteny of this region was highly conserved, whether or not the speG gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that speG is the direct descendant of a common ancestor of streptococcal SAgs, whereas smez was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that speG was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking smez was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, selW, and a staphylococcal SAg -like gene, ssl, in the core genomes of all Staphylococcus aureus strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by speG, selW and ssl suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant. Conclusions Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and

  7. Do Psychological Sex Differences Reflect Evolutionary Bisexual Partitioning?

    Science.gov (United States)

    Trofimova, Irina

    2015-01-01

    This article analyzes sex differences in communicative and exploratory abilities and mental disabilities from the rarely discussed perspective of sex differences in the shape of phenotypic distributions. The article reviews the most consistent findings related to such differences and compares them with the evolutionary theory of sex (ETS). The ETS considers sexual dimorphism as a functional specialization of a species into 2 partitions: variational and conservational. The analysis suggests that male superiority in risk and sensation seeking and physical abilities; higher rates of psychopathy, dyslexia, and autism; and higher birth and accidental death rates reflects the systemic variational function of the male sex. Female superiority in verbal abilities, lawfulness, socialization, empathy, and agreeableness is presented as a reflection of the systemic conservational function of the female sex. From this perspective psychological sex differences in communicative and exploratory abilities might not just be an accidental result of sexual selection or labor distribution in early humans. It might reflect a global functional differentiation tendency within a species to expand its phenotypic diversity and at the same time to conserve beneficial features in the species' behavior. The article also offers an addition to the ETS by suggesting that the male sex (variable partition) plays an evolutionary role in pruning of the redundant excesses in a species' bank of beneficial characteristics despite resistance from the conservational partition. PMID:26721176

  8. The major synthetic evolutionary transitions

    Science.gov (United States)

    Solé, Ricard

    2016-01-01

    Evolution is marked by well-defined events involving profound innovations that are known as ‘major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These ‘synthetic’ transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431528

  9. Evolutionary genetics of maternal effects.

    Science.gov (United States)

    Wolf, Jason B; Wade, Michael J

    2016-04-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single-locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype-phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype-phenotype relationship frequency dependent, resulting in the appearance of negative frequency-dependent selection, while additive MGEs contribute a component of parent-of-origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be "available" to the evolving population. PMID:26969266

  10. Structural symmetry in evolutionary games.

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-10-01

    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

  11. The major synthetic evolutionary transitions.

    Science.gov (United States)

    Solé, Ricard

    2016-08-19

    Evolution is marked by well-defined events involving profound innovations that are known as 'major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These 'synthetic' transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined.This article is part of the themed issue 'The major synthetic evolutionary transitions'. PMID:27431528

  12. Neuronal boost to evolutionary dynamics

    Science.gov (United States)

    de Vladar, Harold P.; Szathmáry, Eörs

    2015-01-01

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

  13. Prediction of conserved regulatory elements in promoter regions of the cattle genome

    Science.gov (United States)

    Cross-species DNA sequence comparison is the primary approach to discover regulatory elements by identifying highly conserved sequences due to evolutionary constraints. Previously, we reported that a systematic approach, combining position-specific weight matrixes (JASPAR) and phylogenetic footprint...

  14. Systematic identification of conserved regulatory elements in upstream promoter regions of the cattle genome

    Science.gov (United States)

    Cross-species DNA sequence comparison is the primary approach to discover regulatory elements by identifying highly conserved sequences due to evolutionary constraints. Previously, we reported that a systematic approach, combining position-specific weight matrixes (JASPAR) and phylogenetic footprint...

  15. Complicated evolutionary patterns of microRNAs in vertebrates

    Institute of Scientific and Technical Information of China (English)

    WANG XiaoWo; ZHANG XueGong; LI YanDa

    2008-01-01

    MicroRNAs (miRNAs) are a class of~22 nt long endogenous non-coding RNAs that play important regulatory roles in diverse organisms. Up to now, little is known about the evolutionary properties of these crucial regulators. Most miRNAs were thought to be phylogenetically conserved, but recently, a number of poorly-conserved miRNAs have been reported and miRNA innovation is shown to be an ongoing process. In this work, through the characterization of an miRNA super family, we studied the evolutionary patterns of miRNAs in vertebrates. Recently generated miRNAs seem to evolve rapidly during a certain period following their emergence. Multiple lineage-specific expansions were observed. Homolgous premiRNAs may produce mature products from the opposite stem arms following tandem duplications, which may have important contribution to miRNA innovation. Our observations of miRNAs' complicated evolutionary patterns support the notion that these key regulatory molecules may play very active roles in evolution.

  16. Evolutionary and Functional Relationships in the Truncated Hemoglobin Family.

    Science.gov (United States)

    Bustamante, Juan P; Radusky, Leandro; Boechi, Leonardo; Estrin, Darío A; Ten Have, Arjen; Martí, Marcelo A

    2016-01-01

    Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends. PMID:26788940

  17. Complete experimental toolbox for alignment-free quantum communication

    OpenAIRE

    D'Ambrosio V.; Nagali E.; Walborn S.P.; Aolita L.; Slussarenko S.; Marrucci L.; Sciarrino F.

    2012-01-01

    Quantum communication employs the counter-intuitive features of quantum physics to perform tasks that are im- possible in the classical world. It is crucial for testing the foundations of quantum theory and promises to rev- olutionize our information and communication technolo- gies. However, for two or more parties to execute even the simplest quantum transmission, they must establish, and maintain, a shared reference frame. This introduces a considerable overhead in communication resources,...

  18. Evolutionary optimization of optical antennas

    CERN Document Server

    Feichtner, Thorsten; Kiunke, Markus; Hecht, Bert

    2012-01-01

    The design of nano-antennas is so far mainly inspired by radio-frequency technology. However, material properties and experimental settings need to be reconsidered at optical frequencies, which entails the need for alternative optimal antenna designs. Here a checkerboard-type, initially random array of gold cubes is subjected to evolutionary optimization. To illustrate the power of the approach we demonstrate that by optimizing the near-field intensity enhancement the evolutionary algorithm finds a new antenna geometry, essentially a split-ring/two-wire antenna hybrid which surpasses by far the performance of a conventional gap antenna by shifting the n=1 split-ring resonance into the optical regime.

  19. The evolutionary psychology of hunger.

    Science.gov (United States)

    Al-Shawaf, Laith

    2016-10-01

    An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses. PMID:27328100

  20. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

  1. Micro Evolutionary Processes and Adaptation

    Institute of Scientific and Technical Information of China (English)

    SHADMANOV; R; K; RUBAN; I; N; VOROPAEVA; N; L; SHADMANOVA; A; R

    2008-01-01

    It would be well to note that in the absence of clear data about the formation of adaptation systems,or mechanisms of their occurrence,all that is recognized is the realization of the micro evolutionary processes.There is no well-defined connection between information exchange and formation of

  2. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

    Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

  3. Evolutionary studies of the Gnetales

    OpenAIRE

    Hou, Chen

    2016-01-01

    The Gnetales consist of three distinct genera, Ephedra, Gnetum and Welwitschia with considerable divergence among them regarding morphological, ecological and molecular characters. A longstanding debate of the similarity between the Gnetales and angiosperms and the unresolved seed plant phylogeny intrigues plant scientists to further investigate the evolutionary history of the Gnetales. The presented projects deal with interdisciplinary questions on proteomics, chloroplast genomes, phylogenet...

  4. The Challange of Evolutionary Learning.

    Science.gov (United States)

    Banathy, Bela H.

    Emerging educational needs in the interdependent world of the Information Age are explored. The current global human predicament in the historical context of the evolution of human systems is examined. A description is given of a systems view of the current evolutionary stage and the new educational needs of the Information Age that can be derived…

  5. Evolutionary Psychology and Intelligence Research

    Science.gov (United States)

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative…

  6. Evolutionary Perspective in Child Growth

    Directory of Open Access Journals (Sweden)

    Ze’ev Hochberg

    2011-07-01

    Full Text Available Hereditary, environmental, and stochastic factors determine a child’s growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment.

  7. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

    OpenAIRE

    Gómez-Marín, Carlos; Tena, Juan J.; Acemel, Rafael D.; López-Mayorga, Macarena; Naranjo, Silvia; de la Calle-Mustienes, Elisa; Maeso, Ignacio; Beccari, Leonardo; Aneas, Ivy; Vielmas, Erika; Bovolenta, Paola; Nobrega, Marcelo A.; Carvajal, Jaime; Gómez-Skarmeta, José Luis

    2015-01-01

    Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply ev...

  8. Eco-evolutionary feedbacks during experimental range expansions.

    Science.gov (United States)

    Fronhofer, Emanuel A; Altermatt, Florian

    2015-01-01

    Understanding biological range expansions and invasions is of great ecological and economical interest. Importantly, spatial dynamics can be deeply affected by rapid evolution depending on the ecological context. Using experimental evolution in replicated microcosm landscapes and numerical analyses we show experimentally that the ecological process of range expansions leads to the evolution of increased dispersal. This evolutionary change counter-intuitively feeds back on (macro-)ecological patterns affecting the spatial distribution of population densities. While existing theory suggests that densities decrease from range cores to range margins due to K-selection, we show the reverse to be true when competition is considered explicitly including resource dynamics. We suggest that a dispersal-foraging trade-off, leading to more 'prudent' foraging at range margins, is the driving mechanism behind the macroecological pattern reported. In conclusion, rapid multi-trait evolution and eco-evolutionary feedbacks are highly relevant for understanding macroecological patterns and designing appropriate conservation strategies. PMID:25902302

  9. Animal models and conserved processes

    Directory of Open Access Journals (Sweden)

    Greek Ray

    2012-09-01

    Full Text Available Abstract Background The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation? Methods We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes. Results Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes. Conclusion We conclude that even the presence of conserved processes is

  10. An Evolutionary Framework for 3-SAT Problems

    OpenAIRE

    Borgulya, István

    2003-01-01

    In this paper we present a new evolutionary framework for 3-SAT. This method can be divided into three stages, where each stage is an evolutionary algorithm. The first stage improves the quality of the initial population. The second stage improves the speed of the algorithm periodically generating new solutions. The 3rd stage is a hybrid evolutionary algorithm, which improves the solutions with a local search. The key points of our algorithm are the evolutionary framework and the mutation ope...

  11. From computers to cultivation: reconceptualizing evolutionary psychology

    OpenAIRE

    Louise eBarrett; Thomas ePollet; Gert eStulp

    2014-01-01

    Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behaviour, and the rigour with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated...

  12. From computers to cultivation: reconceptualizing evolutionary psychology

    OpenAIRE

    Barrett, Louise; Pollet, Thomas V.; Stulp, Gert

    2014-01-01

    Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that, as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behavior, and the rigor with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated....

  13. Evolutionary Optimization in an Algorithmic Setting

    OpenAIRE

    Burgin, Mark; Eberbach, Eugene

    2006-01-01

    Evolutionary processes proved very useful for solving optimization problems. In this work, we build a formalization of the notion of cooperation and competition of multiple systems working toward a common optimization goal of the population using evolutionary computation techniques. It is justified that evolutionary algorithms are more expressive than conventional recursive algorithms. Three subclasses of evolutionary algorithms are proposed here: bounded finite, unbounded finite and infinite...

  14. OPTIMISED RANDOM MUTATIONS FOR EVOLUTIONARY ALGORITHMS

    OpenAIRE

    Sean McGerty; Frank Moisiadis

    2014-01-01

    To demonstrate our approaches we will use Sudoku puzzles, which are an excellent test bed for evolutionary algorithms. The puzzles are accessible enough for people to enjoy. However the more complex puzzles require thousands of iterations before an evolutionary algorithm finds a solution. If we were attempting to compare evolutionary algorithms we could count their iterations to solution as an indicator of relative efficiency. Evolutionary algorithms however include a process of r...

  15. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.

    Science.gov (United States)

    Gnad, Florian; Forner, Francesca; Zielinska, Dorota F; Birney, Ewan; Gunawardena, Jeremy; Mann, Matthias

    2010-12-01

    High accuracy mass spectrometry has proven to be a powerful technology for the large scale identification of serine/threonine/tyrosine phosphorylation in the living cell. However, despite many described phosphoproteomes, there has been no comparative study of the extent of phosphorylation and its evolutionary conservation in all domains of life. Here we analyze the results of phosphoproteomics studies performed with the same technology in a diverse set of organisms. For the most ancient organisms, the prokaryotes, only a few hundred proteins have been found to be phosphorylated. Applying the same technology to eukaryotic species resulted in the detection of thousands of phosphorylation events. Evolutionary analysis shows that prokaryotic phosphoproteins are preferentially conserved in all living organisms, whereas-site specific phosphorylation is not. Eukaryotic phosphosites are generally more conserved than their non-phosphorylated counterparts (with similar structural constraints) throughout the eukaryotic domain. Yeast and Caenorhabditis elegans are two exceptions, indicating that the majority of phosphorylation events evolved after the divergence of higher eukaryotes from yeast and reflecting the unusually large number of nematode-specific kinases. Mitochondria present an interesting intermediate link between the prokaryotic and eukaryotic domains. Applying the same technology to this organelle yielded 174 phosphorylation sites mapped to 74 proteins. Thus, the mitochondrial phosphoproteome is similarly sparse as the prokaryotic phosphoproteomes. As expected from the endosymbiotic theory, phosphorylated as well as non-phosphorylated mitochondrial proteins are significantly conserved in prokaryotes. However, mitochondrial phosphorylation sites are not conserved throughout prokaryotes, consistent with the notion that serine/threonine phosphorylation in prokaryotes occurred relatively recently in evolution. Thus, the phosphoproteome reflects major events in the

  16. Conservation Lands and Preserves, Private - Conservation Wells

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — The conservation well layer identifies the permitted surface location of oil and gas conservation wells that have not been plugged. These include active, regulatory...

  17. The citation field of evolutionary economics

    NARCIS (Netherlands)

    Dolfsma, Wilfred; Leydesdorff, Loet

    2010-01-01

    Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal tha

  18. On the Analysis of Evolutionary Algorithms

    OpenAIRE

    Jansen, Thomas; Wegener, Ingo

    2001-01-01

    There is a lot of experimental evidence that crossover is, for some functions, an essential operator of evolutionary algorithms. Nevertheless, it was an open problem to prove for some function that an evolutionary algorithm using crossover is essentially more efficient than evolutionary algorithms without crossover. In this paper, such an example is presented and its properties are proved.

  19. Schroedinger operators and evolutionary strategies

    International Nuclear Information System (INIS)

    First we introduce a simple model for the description of evolutionary algorithms, which is based on 2nd order partial differential equations for the distribution function of the individuals. Then we turn to the properties of Boltzmann's and Darwin's strategy. the next chapter is dedicated to the mathematical properties of Schroedinger operators. Both statements on the spectral density and their reproducibility during the simulation are summarized. The remaining of this chapter are dedicated to the analysis of the kernel as well as the dependence of the Schroedinger operator on the potential. As conclusion from the results of this chapter we obtain the classification of the strategies in dependence of the fitness. We obtain the classification of the evolutionary strategies, which are described by a 2nd order partial differential equation, in relation to their solution behaviour. Thereafter we are employed with the variation of the mutation distribution

  20. Evolutionary model of stock markets

    Science.gov (United States)

    Kaldasch, Joachim

    2014-12-01

    The paper presents an evolutionary economic model for the price evolution of stocks. Treating a stock market as a self-organized system governed by a fast purchase process and slow variations of demand and supply the model suggests that the short term price distribution has the form a logistic (Laplace) distribution. The long term return can be described by Laplace-Gaussian mixture distributions. The long term mean price evolution is governed by a Walrus equation, which can be transformed into a replicator equation. This allows quantifying the evolutionary price competition between stocks. The theory suggests that stock prices scaled by the price over all stocks can be used to investigate long-term trends in a Fisher-Pry plot. The price competition that follows from the model is illustrated by examining the empirical long-term price trends of two stocks.

  1. The evolutionary origins of hierarchy

    OpenAIRE

    Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff

    2015-01-01

    Hierarchical organization -- the recursive composition of sub-modules -- is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been s...

  2. Lesbian tomboys and "evolutionary butch".

    Science.gov (United States)

    Zevy, Lee

    2004-01-01

    ABSTRACT Lesbian tomboy development occurs within a psychosexual experiential field on a continuum from childhood gender dissonance to evolutionary butch in adulthood. Through the process of integrating gender development, sexual orientation, and identity development, tomboy lesbians learn how to maintain a sense of self and organize desire within a complicated familial/socio/cultural/context. Traversing these complications usually brings adolescent and adult lesbians into therapy where they need clinicians who understand this unique course of development. PMID:24820882

  3. Evolutionary Bits'n'Spikes

    OpenAIRE

    D. Floreano; Schoeni, N.; Caprari, G.; Blynel, J.; Standish, R. K.; Beadau, M. A.; Abbass, H. A.

    2002-01-01

    We describe a model and implementation of evolutionary spiking neurons for embedded microcontrollers with few bytes of memory and very low power consumption. The approach is tested with an autonomous microrobot of less than 1 in^3 that evolves the ability to move in a small maze without human intervention and external computers. Considering the very large diffusion, small size, and low cost of embedded microcontrollers, the approach described here could find its way in several intelligent dev...

  4. Evolutionary potential games on lattices

    OpenAIRE

    Szabo, Gyorgy; Borsos, Istvan

    2015-01-01

    Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition h...

  5. Mutualism, Parasitism, and Evolutionary Adaptation

    OpenAIRE

    Watson, Richard A.; Reil, Torsten; Pollack, Jordan B.

    2000-01-01

    Our investigations concern the role of symbiosis as an enabling mechanism in evolutionary adaptation. Previous work has illustrated how the formation of mutualist groups can guide genetic variation so as to enable the evolution of ultimately independent organisms that would otherwise be unobtainable. The new experiments reported here show that this effect applies not just in genetically related organisms but may also occur from symbiosis between distinct species. In addition, a new detail is ...

  6. Evolutionary robotics – A review

    Indian Academy of Sciences (India)

    Dilip Kumar Pratihar

    2003-12-01

    In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system. Several methods have been tried by various investigators to solve this problem. This paper provides a survey on some of these important studies carried out in the recent past.

  7. Evolutionary biology and life histories

    OpenAIRE

    Brown, C R; Thomson, D. L.

    2004-01-01

    The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demogr...

  8. The evolutionary portrait of metazoan NAD salvage.

    Directory of Open Access Journals (Sweden)

    João Carneiro

    Full Text Available Nicotinamide Adenine Dinucleotide (NAD levels are essential for cellular homeostasis and survival. Main sources of intracellular NAD are the salvage pathways from nicotinamide, where Nicotinamide phosphoribosyltransferases (NAMPTs and Nicotinamidases (PNCs have a key role. NAMPTs and PNCs are important in aging, infection and disease conditions such as diabetes and cancer. These enzymes have been considered redundant since either one or the other exists in each individual genome. The co-occurrence of NAMPT and PNC was only recently detected in invertebrates though no structural or functional characterization exists for them. Here, using expression and evolutionary analysis combined with homology modeling and protein-ligand docking, we show that both genes are expressed simultaneously in key species of major invertebrate branches and emphasize sequence and structural conservation patterns in metazoan NAMPT and PNC homologues. The results anticipate that NAMPTs and PNCs are simultaneously active, raising the possibility that NAD salvage pathways are not redundant as both are maintained to fulfill the requirement for NAD production in some species.

  9. Evolutionary stability of sex chromosomes in snakes.

    Science.gov (United States)

    Rovatsos, Michail; Vukić, Jasna; Lymberakis, Petros; Kratochvíl, Lukáš

    2015-12-22

    Amniote vertebrates possess various mechanisms of sex determination, but their variability is not equally distributed. The large evolutionary stability of sex chromosomes in viviparous mammals and birds was believed to be connected with their endothermy. However, some ectotherm lineages seem to be comparably conserved in sex determination, but previously there was a lack of molecular evidence to confirm this. Here, we document a stability of sex chromosomes in advanced snakes based on the testing of Z-specificity of genes using quantitative PCR (qPCR) across 37 snake species (our qPCR technique is suitable for molecular sexing in potentially all advanced snakes). We discovered that at least part of sex chromosomes is homologous across all families of caenophidian snakes (Acrochordidae, Xenodermatidae, Pareatidae, Viperidae, Homalopsidae, Colubridae, Elapidae and Lamprophiidae). The emergence of differentiated sex chromosomes can be dated back to about 60 Ma and preceded the extensive diversification of advanced snakes, the group with more than 3000 species. The Z-specific genes of caenophidian snakes are (pseudo)autosomal in the members of the snake families Pythonidae, Xenopeltidae, Boidae, Erycidae and Sanziniidae, as well as in outgroups with differentiated sex chromosomes such as monitor lizards, iguanas and chameleons. Along with iguanas, advanced snakes are therefore another example of ectothermic amniotes with a long-term stability of sex chromosomes comparable with endotherms. PMID:26702042

  10. On evolutionary spatial heterogeneous games

    Science.gov (United States)

    Fort, H.

    2008-03-01

    How cooperation between self-interested individuals evolve is a crucial problem, both in biology and in social sciences, that is far from being well understood. Evolutionary game theory is a useful approach to this issue. The simplest model to take into account the spatial dimension in evolutionary games is in terms of cellular automata with just a one-parameter payoff matrix. Here, the effects of spatial heterogeneities of the environment and/or asymmetries in the interactions among the individuals are analysed through different extensions of this model. Instead of using the same universal payoff matrix, bimatrix games in which each cell at site ( i, j) has its own different ‘temptation to defect’ parameter T(i,j) are considered. First, the case in which these individual payoffs are constant in time is studied. Second, an evolving evolutionary spatial game such that T=T(i,j;t), i.e. besides depending on the position evolves (by natural selection), is used to explore the combination of spatial heterogeneity and natural selection of payoff matrices.

  11. Testing evolutionary convergence on Europa

    International Nuclear Information System (INIS)

    A major objective in solar system exploration is the insertion of appropriate biology-oriented experiments in future missions. We discuss various reasons for suggesting that this type of research be considered a high priority for feasibility studies and, subsequently, for technological development of appropriate melters and submersibles. Based on numerous examples, we argue in favour of the assumption that Darwin's theory is valid for the evolution of life anywhere in the universe. We have suggested how to obtain preliminary insights into the question of the distribution of life in the universe. Universal evolution of intelligent behaviour is at the end of an evolutionary pathway, in which evolution of ion channels in the membrane of microorganisms occurs in its early stages. Further, we have argued that a preliminary test of this conjecture is feasible with experiments on the Europan surface or ocean, involving evolutionary biosignatures (ion channels). This aspect of the exploration for life in the solar system should be viewed as a complement to the astronomical approach for the search of evidence of the later stages of the evolutionary pathways towards intelligent behaviour. (author)

  12. Evolutionary reconstruction and population genetics analysis of aurora kinases.

    Directory of Open Access Journals (Sweden)

    Balu Kamaraj

    Full Text Available BACKGROUND: Aurora kinases belong to the highly conserved kinase family and play a vital role in cell cycle regulation. The structure and function of these kinases are inter-related and sometimes they also act as substitutes in case of knockdown of other aurora kinases. METHOD: In this work we carried out the evolutionary reconstruction and population genetic studies of aurora kinase proteins. Substitution saturation test, CAI (Codon adaptation index, gene expression and RSCU (Relative synonymous codon usage values were computed for all the three aurora kinases. Linear regression method was used to check the dependency of gene expression on their CAI values. RESULTS: The results suggested that aurora-B and aurora-C has shown convergence in their evolutionary pathway. Moreover, the aurora-A I57V mutation showed high penetrance in human population and exist at very high frequency (84.4% when compared to the native residue (15.6%. The mutation showed notable range of functional gain and seemed to be promising for the evolution of aurora-A function. Mutant allele might also become a challenging prospect for understanding the pattern of evolution followed by cell cycle kinases. CONCLUSION: The overall result suggested that the aurora-A is currently under the evolutionary transition and to determine the functional significance of the mutation further investigation are required.

  13. Evolutionary Origin of the Proepicardium

    Directory of Open Access Journals (Sweden)

    Elena Cano

    2013-05-01

    Full Text Available The embryonic epicardium and the cardiac mesenchyme derived from it are critical to heart development. The embryonic epicardium arises from an extracardiac progenitor tissue called the proepicardium, a proliferation of coelomic cells located at the limit between the liver and the sinus venosus. A proepicardium has not been described in invertebrates, and the evolutionary origin of this structure in vertebrates is unknown. We herein suggest that the proepicardium might be regarded as an evolutionary derivative from an ancient pronephric external glomerulus that has lost its excretory role. In fact, we previously described that the epicardium arises by cell migration from the primordia of the right pronephric external glomerulus in a representative of the most primitive vertebrate lineage, the lamprey Petromyzon marinus. In this review, we emphasize the striking similarities between the gene expression profiles of the proepicardium and the developing kidneys, as well as the parallelisms in the signaling mechanisms involved in both cases. We show some preliminary evidence about the existence of an inhibitory mechanism blocking glomerular differentiation in the proepicardium. We speculate as to the possibility that this developmental link between heart and kidney can be revealing a phylogenetically deeper association, supported by the existence of a heart-kidney complex in Hemichordates. Finally, we suggest that primitive hematopoiesis could be related with this heart-kidney complex, thus accounting for the current anatomical association of the hematopoietic stem cells with an aorta-gonad-mesonephros area. In summary, we think that our hypothesis can provide new perspectives on the evolutionary origin of the vertebrate heart.

  14. ChIP-seq Identification of Weakly Conserved Heart Enhancers

    Energy Technology Data Exchange (ETDEWEB)

    Blow, Matthew J.; McCulley, David J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Bristow, James; Ren, Bing; Black, Brian L.; Rubin, Edward M.; Visel, Axel; Pennacchio, Len A.

    2010-07-01

    Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type.

  15. 7 CFR 12.23 - Conservation plans and conservation systems.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 1 2010-01-01 2010-01-01 false Conservation plans and conservation systems. 12.23... CONSERVATION Highly Erodible Land Conservation § 12.23 Conservation plans and conservation systems. (a) Use of field office technical guide. A conservation plan or conservation system developed for the purposes...

  16. A comprehensive classification and evolutionary analysis of plant homeobox genes.

    Science.gov (United States)

    Mukherjee, Krishanu; Brocchieri, Luciano; Bürglin, Thomas R

    2009-12-01

    The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also characterized by conserved intron-exon structure and by unique codomain architectures. We identified many new genes belonging to previously defined classes (HD-ZIP I to IV, BEL, KNOX, PLINC, WOX). Other newly identified genes allowed us to characterize PHD, DDT, NDX, and LD genes as members of four new evolutionary classes and to define two additional classes, which we named SAWADEE and PINTOX. Our comprehensive analysis allowed us to identify several newly characterized conserved motifs, including novel zinc finger motifs in SAWADEE and DDT. Members of the BEL and KNOX classes were found in Chlorobionta (green plants) and in Rhodophyta. We found representatives of the DDT, WOX, and PINTOX classes only in green plants, including unicellular green algae, moss, and vascular plants. All 14 homeobox gene classes were represented in flowering plants, Selaginella, and moss, suggesting that they had already differentiated in the last common ancestor of moss and vascular plants. PMID:19734295

  17. Steps Towards an Evolutionary Physics

    CERN Document Server

    Tiezzi, E

    2006-01-01

    If thermodynamics is to physics as logic is to philosophy, recent theoretical advancements lend new coherence to the marvel and dynamism of life on Earth. Enzo Tiezzi's "Steps Towards an Evolutionary Physics" is a primer and guide, to those who would to stand on the shoulders of giants to attain this view: Heisenberg, Planck, Bateson, Varela, and Prigogine as well as notable contemporary scientists. The adventure of such a free and enquiring spirit thrives not so much on answers as on new questions. The book offers a new gestalt on the uncertainty principle and concept of probability. A wide r

  18. Evolutionary Optimization The UGP Toolkit

    CERN Document Server

    Sanchez, Ernesto; Squillero, Giovanni

    2011-01-01

    This book describes an award-winning evolutionary algorithm that outperformed experts and conventional heuristics in solving several industrial problems. It presents a discussion of the theoretical and practical aspects that enabled I GP (MicroGP) to autonomously find the optimal solution of hard problems, handling highly structured data, such as full-fledged assembly programs, with functions and interrupt handlers. For a practitioner, I GP is simply a versatile optimizer to tackle most problems with limited setup effort. The book is valuable for all who require heuristic problem-solving metho

  19. Micro Evolutionary Processes and Adaptation

    Institute of Scientific and Technical Information of China (English)

    SHADMANOV R K; RUBAN I N; VOROPAEVA N L; SHADMANOVA A R

    2008-01-01

    @@ It would be well to note that in the absence of clear data about the formation of adaptation systems,or mechanisms of their occurrence,all that is recognized is the realization of the micro evolutionary processes.There is no well-defined connection between information exchange and formation of adaptation systems.Obviously,it occurs because mechanisms and systems reacting to any external actions are not considered from the point of view of "coexistence" of dynamic and static processes and structures.

  20. Metabolism at Evolutionary Optimal States

    Directory of Open Access Journals (Sweden)

    Iraes Rabbers

    2015-06-01

    Full Text Available Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies, adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of enzymes, and by rewiring metabolism. The trade-offs that can occur during such optimizations then indicate fundamental limits to evolutionary innovations and bioengineering. In this paper, we review several theoretical and experimental findings about mechanisms for metabolic optimization.

  1. Evolutionary robotics: model or design?

    OpenAIRE

    Trianni, Vito

    2014-01-01

    In this paper, I review recent work in evolutionary robotics (ER), and discuss the perspectives and future directions of the field. First, I propose to draw a crisp distinction between studies that exploit ER as a design methodology on the one hand, and studies that instead use ER as a modeling tool to better understand phenomena observed in biology. Such a distinction is not always that obvious in the literature, however. It is my conviction that ER would profit from an explicit commitment t...

  2. Evolutionary Constraints to Viroid Evolution

    Directory of Open Access Journals (Sweden)

    Santiago F. Elena

    2009-09-01

    Full Text Available We suggest that viroids are trapped into adaptive peaks as the result of adaptive constraints. The first one is imposed by the necessity to fold into packed structures to escape from RNA silencing. This creates antagonistic epistases, which make future adaptive trajectories contingent upon the first mutation and slow down the rate of adaptation. This second constraint can only be surpassed by increasing genetic redundancy or by recombination. Eigen’s paradox imposes a limit to the increase in genome complexity in the absence of mechanisms reducing mutation rate. Therefore, recombination appears as the only possible route to evolutionary innovation in viroids.

  3. Multidimensional extended spatial evolutionary games.

    Science.gov (United States)

    Krześlak, Michał; Świerniak, Andrzej

    2016-02-01

    The goal of this paper is to study the classical hawk-dove model using mixed spatial evolutionary games (MSEG). In these games, played on a lattice, an additional spatial layer is introduced for dependence on more complex parameters and simulation of changes in the environment. Furthermore, diverse polymorphic equilibrium points dependent on cell reproduction, model parameters, and their simulation are discussed. Our analysis demonstrates the sensitivity properties of MSEGs and possibilities for further development. We discuss applications of MSEGs, particularly algorithms for modelling cell interactions during the development of tumours. PMID:26318169

  4. Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system.

    Science.gov (United States)

    Mordhorst, Bethany R; Wilson, Miranda L; Conant, Gavin C

    2016-01-01

    In this review, we discuss the way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems. In the first part of the review, we contrast the rapid evolution seen in some reproductive genes with the generally conservative nature of development. We discuss directional selection and coevolution as potential drivers of rapid evolution in sperm and egg proteins. Such rapid change is very different from the highly conservative nature of later embryo development. However, it is not unique, as some regions of the sex chromosomes also show elevated rates of evolutionary change. To explain these contradictory trends, we argue that it is not reproductive functions per se that induce rapid evolution. Rather, it is the fact that biotic interactions, such as speciation events and sexual conflict, have no evolutionary endpoint and hence can drive continuous evolutionary changes. Returning to the question of sex chromosome evolution, we discuss the way that recent advances in evolutionary genomics and systems biology and, in particular, the development of a theory of gene balance provide a better understanding of the evolutionary patterns seen on these chromosomes. We end the review with a discussion of a surprising and incompletely understood phenomenon observed in early embryos: namely the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide. We argue that evolutionary insights, from both yeasts and tumor cells, help to explain the Warburg effect, and that new metabolic modeling approaches are useful in assessing the potential sources of the effect. PMID:26254045

  5. Evolutionary genomics of LysM genes in land plants

    Directory of Open Access Journals (Sweden)

    Stacey Gary

    2009-08-01

    Full Text Available Abstract Background The ubiquitous LysM motif recognizes peptidoglycan, chitooligosaccharides (chitin and, presumably, other structurally-related oligosaccharides. LysM-containing proteins were first shown to be involved in bacterial cell wall degradation and, more recently, were implicated in perceiving chitin (one of the established pathogen-associated molecular patterns and lipo-chitin (nodulation factors in flowering plants. However, the majority of LysM genes in plants remain functionally uncharacterized and the evolutionary history of complex LysM genes remains elusive. Results We show that LysM-containing proteins display a wide range of complex domain architectures. However, only a simple core architecture is conserved across kingdoms. Each individual kingdom appears to have evolved a distinct array of domain architectures. We show that early plant lineages acquired four characteristic architectures and progressively lost several primitive architectures. We report plant LysM phylogenies and associated gene, protein and genomic features, and infer the relative timing of duplications of LYK genes. Conclusion We report a domain architecture catalogue of LysM proteins across all kingdoms. The unique pattern of LysM protein domain architectures indicates the presence of distinctive evolutionary paths in individual kingdoms. We describe a comparative and evolutionary genomics study of LysM genes in plant kingdom. One of the two groups of tandemly arrayed plant LYK genes likely resulted from an ancient genome duplication followed by local genomic rearrangement, while the origin of the other groups of tandemly arrayed LYK genes remains obscure. Given the fact that no animal LysM motif-containing genes have been functionally characterized, this study provides clues to functional characterization of plant LysM genes and is also informative with regard to evolutionary and functional studies of animal LysM genes.

  6. Improving DNA Computing Using Evolutionary Techniques

    Directory of Open Access Journals (Sweden)

    Godar J. Ibrahim

    2016-03-01

    Full Text Available the field of DNA Computing has attracted many biologists and computer scientists as it has a biological interface, small size and substantial parallelism. DNA computing depends on DNA molecules’ biochemical reactions which they can randomly anneal and they might accidentally cause improper or unattractive computations. This will inspire opportunities to use evolutionary computation via DNA. Evolutionary Computation emphasizes on probabilistic search and optimization methods which are mimicking the organic evolution models. The research work aims at offering a simulated evolutionary DNA computing model which incorporates DNA computing with an evolutionary algorithm. This evolutionary approach provides the likelihood for increasing dimensionality through replacing the typical filtering method by an evolutionary one. Thus, via iteratively increasing and recombination a population of strands, eliminating incorrect solutions from the population, and choosing the best solutions via gel electrophoresis, an optimal or near-optimal solution can be evolved rather than extracted from the initial population.

  7. Conservation Actions Based on Red Lists Do Not Capture the Functional and Phylogenetic Diversity of Birds in Brazil

    OpenAIRE

    Hidasi-Neto, José; Loyola, Rafael Dias; Cianciaruso, Marcus Vinicius

    2013-01-01

    Red Lists of threatened species play a critical role in conservation science and practice. However, policy-making based on Red Lists ignores ecological and evolutionary consequences of losing biodiversity because these lists focus on species alone. To decide if relying on Red Lists alone can help to conserve communities’ functional (FD) and phylogenetic (PD) diversity, it is useful to evaluate whether Red List categories represent species with diverse ecological traits and evolutionary histor...

  8. The emerging empirics of evolutionary economic geography

    OpenAIRE

    Boschma, RA; Frenken, K Koen

    2010-01-01

    Following last decade’s programmatic papers on Evolutionary Economic Geography, we report on recent empirical advances and how this empirical work can be positioned vis-à-vis other strands of research in economic geography. First, we review studies on the path dependent nature of clustering, and how the evolutionary perspective relates to that of New Economic Geography. Second, we discuss research on agglomeration externalities in Regional Science, and how Evolutionary Economic Geography cont...

  9. EVOLUTIONARY THEORY AND THE MARKET COMPETITION

    OpenAIRE

    Nicoleta SIRGHI

    2014-01-01

    Evolutionary theory study of processes that transform economy for firms, institutions, industries, employment, production, trade and growth within, through the actions of diverse agents from experience and interactions, using evolutionary methodology. Evolutionary theory analyses the unleashing of a process of technological and institutional innovation by generating and testing a diversity of ideas which discover and accumulate more survival value for the costs incurred than competing alterna...

  10. The Citation Field of Evolutionary Economics

    OpenAIRE

    Dolfsma, Wilfred; Leydesdorff, Loet

    2010-01-01

    Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal that is indispensable in the exchange of expert knowledge on topics and using approaches that relate naturally with it. Analyzing citation data for the relevant academic field for the Journal of Evolu...

  11. Evolutionary robotics: what, why, and where to

    OpenAIRE

    Doncieux, Stephane; Bredeche, Nicolas; Mouret, Jean-Baptiste; Eiben, Agoston E. (Gusz)

    2015-01-01

    Evolutionary robotics applies the selection, variation, and heredity principles of natural evolution to the design of robots with embodied intelligence. It can be considered as a subfield of robotics that aims to create more robust and adaptive robots. A pivotal feature of the evolutionary approach is that it considers the whole robot at once, and enables the exploitation of robot features in a holistic manner. Evolutionary robotics can also be seen as an innovative approach to the study of e...

  12. Regional systems of innovation: an evolutionary perspective

    OpenAIRE

    Cooke, P.; M G Uranga; G Etxebarria

    1998-01-01

    The authors develop the concept of regional systems of innovation and relate it to preexisting research on national systems of innovation. They argue that work conducted in the 'new regional science' field is complementary to systems of innovation approaches. They seek to link new regional work to evolutionary economics, and argue for the development of evolutionary regional science. Common elements of interest to evolutionary innovation research and new regional science are important in unde...

  13. DC operating point analysis using evolutionary computing

    OpenAIRE

    Crutchley, DA; Zwolinski, M.

    2004-01-01

    This paper discusses and evaluates a new approach to operating point analysis based on evolutionary computing (EC). EC can find multiple solutions to a problem by using a parallel search through a population. At the operating point(s) of a circuit the overall error has a minimum value. Therefore, we use an Evolutionary Algorithm (EA) to search the solution space to find these minima. Various evolutionary algorithms are described. Several such algorithms have been implemented in a full circuit...

  14. Comparison Study Of Multiobjective Evolutionary Algorithms

    OpenAIRE

    Syomkin, A. M.

    2004-01-01

    Many real-world problems involve two types of difficulties: 1) multiple, conflicting objectives and 2) a highly complex search space. Efficient evolutionary strategies have been developed to deal with both difficulties. Evolutionary algorithms possess several characteristics such as parallelism and robustness that make them preferable to classical optimization methods. In the presented paper I conducted comparison studies among the well-known evolutionary algorithms based on NP-hard 0-1 multi...

  15. Evolutionary Algorithms for the Unit Commitment Problem

    OpenAIRE

    UYAR, A. Şima; Türkay, Belgin

    2008-01-01

    This paper compares three evolutionary computation techniques, namely Steady-State Genetic Algorithms, Evolutionary Strategies and Differential Evolution for the Unit Commitment Problem. The comparison is based on a set of experiments conducted on benchmark datasets as well as on real-world data obtained from the Turkish Interconnected Power System. The results of two state-of-the-art evolutionary approaches, namely a Generational Genetic Algorithm and a Memetic Algorithm for the same...

  16. Behavior Trees for Evolutionary Robotics.

    Science.gov (United States)

    Scheper, Kirk Y W; Tijmons, Sjoerd; de Visser, Cornelis C; de Croon, Guido C H E

    2016-01-01

    Evolutionary Robotics allows robots with limited sensors and processing to tackle complex tasks by means of sensory-motor coordination. In this article we show the first application of the Behavior Tree framework on a real robotic platform using the evolutionary robotics methodology. This framework is used to improve the intelligibility of the emergent robotic behavior over that of the traditional neural network formulation. As a result, the behavior is easier to comprehend and manually adapt when crossing the reality gap from simulation to reality. This functionality is shown by performing real-world flight tests with the 20-g DelFly Explorer flapping wing micro air vehicle equipped with a 4-g onboard stereo vision system. The experiments show that the DelFly can fully autonomously search for and fly through a window with only its onboard sensors and processing. The success rate of the optimized behavior in simulation is 88%, and the corresponding real-world performance is 54% after user adaptation. Although this leaves room for improvement, it is higher than the 46% success rate from a tuned user-defined controller. PMID:26606468

  17. Evolutionary potential games on lattices

    Science.gov (United States)

    Szabó, György; Borsos, István

    2016-04-01

    Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the "equilibrium state" by adding non-potential components representing games of cyclic dominance.

  18. Evolutionary development of tensegrity structures.

    Science.gov (United States)

    Lobo, Daniel; Vico, Francisco J

    2010-09-01

    Contributions from the emerging fields of molecular genetics and evo-devo (evolutionary developmental biology) are greatly benefiting the field of evolutionary computation, initiating a promise of renewal in the traditional methodology. While direct encoding has constituted a dominant paradigm, indirect ways to encode the solutions have been reported, yet little attention has been paid to the benefits of the proposed methods to real problems. In this work, we study the biological properties that emerge by means of using indirect encodings in the context of form-finding problems. A novel indirect encoding model for artificial development has been defined and applied to an engineering structural-design problem, specifically to the discovery of tensegrity structures. This model has been compared with a direct encoding scheme. While the direct encoding performs similarly well to the proposed method, indirect-based results typically outperform the direct-based results in aspects not directly linked to the nature of the problem itself, but to the emergence of properties found in biological organisms, like organicity, generalization capacity, or modularity aspects which are highly valuable in engineering. PMID:20619314

  19. Evolutionary epistemology a multiparadigm program

    CERN Document Server

    Pinxten, Rik

    1987-01-01

    This volume has its already distant origin in an inter­national conference on Evolutionary Epistemology the editors organized at the University of Ghent in November 1984. This conference aimed to follow up the endeavor started at the ERISS (Epistemologically Relevant Internalist Sociology of Science) conference organized by Don Campbell and Alex Rosen­ berg at Cazenovia Lake, New York, in June 1981, whilst in­ jecting the gist of certain current continental intellectual developments into a debate whose focus, we thought, was in danger of being narrowed too much, considering the still underdeveloped state of affairs in the field. Broadly speaking, evolutionary epistemology today con­ sists of two interrelated, yet qualitatively distinct inves­ tigative efforts. Both are drawing on Darwinian concepts, which may explain why many people have failed to discriminate them. One is the study of the evolution of the cognitive apparatus of living organisms, which is first and foremost the province of biologists and...

  20. The Evolutionary Puzzle of Suicide

    Directory of Open Access Journals (Sweden)

    Henri-Jean Aubin

    2013-12-01

    Full Text Available Mechanisms of self-destruction are difficult to reconcile with evolution’s first rule of thumb: survive and reproduce. However, evolutionary success ultimately depends on inclusive fitness. The altruistic suicide hypothesis posits that the presence of low reproductive potential and burdensomeness toward kin can increase the inclusive fitness payoff of self-removal. The bargaining hypothesis assumes that suicide attempts could function as an honest signal of need. The payoff may be positive if the suicidal person has a low reproductive potential. The parasite manipulation hypothesis is founded on the rodent—Toxoplasma gondii host-parasite model, in which the parasite induces a “suicidal” feline attraction that allows the parasite to complete its life cycle. Interestingly, latent infection by T. gondii has been shown to cause behavioral alterations in humans, including increased suicide attempts. Finally, we discuss how suicide risk factors can be understood as nonadaptive byproducts of evolved mechanisms that malfunction. Although most of the mechanisms proposed in this article are largely speculative, the hypotheses that we raise accept self-destructive behavior within the framework of evolutionary theory.

  1. Evolutionary Autonomous Health Monitoring System (EAHMS) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — For supporting NASA's Robotics, Tele-Robotics and Autonomous Systems Roadmap, we are proposing the "Evolutionary Autonomous Health Monitoring System" (EAHMS) for...

  2. Behavioural biology: an effective and relevant conservation tool.

    Science.gov (United States)

    Buchholz, Richard

    2007-08-01

    'Conservation behaviour' is a young discipline that investigates how proximate and ultimate aspects of the behaviour of an animal can be of value in preventing the loss of biodiversity. Rumours of its demise are unfounded. Conservation behaviour is quickly building a capacity to positively influence environmental decision making. The theoretical framework used by animal behaviourists is uniquely valuable to elucidating integrative solutions to human-wildlife conflicts, efforts to reintroduce endangered species and reducing the deleterious effects of ecotourism. Conservation behaviourists must join with other scientists under the multidisciplinary umbrella of conservation biology without giving up on their focus: the mechanisms, development, function and evolutionary history of individual differences in behaviour. Conservation behaviour is an increasingly relevant tool in the preservation of nature. PMID:17590477

  3. Fast evolutionary genetic differentiation during experimental colonizations

    Indian Academy of Sciences (India)

    Josiane Santos; Marta Pascual; Pedro Simões; Inês Fragata; Michael R. Rose; Margarida Matos

    2013-08-01

    Founder effects during colonization of a novel environment are expected to change the genetic composition of populations, leading to differentiation between the colonizer population and its source population. Another expected outcome is differentiation among populations derived from repeated independent colonizations starting from the same source. We have previously detected significant founder effects affecting rate of laboratory adaptation among Drosophila subobscura laboratory populations derived from the wild. We also showed that during the first generations in the laboratory, considerable genetic differentiation occurs between foundations. The present study deepens that analysis, taking into account the natural sampling hierarchy of six foundations, derived from different locations, different years and from two samples in one of the years. We show that striking stochastic effects occur in the first two generations of laboratory culture, effects that produce immediate differentiation between foundations, independent of the source of origin and despite similarity among all founders. This divergence is probably due to powerful genetic sampling effects during the first few generations of culture in the novel laboratory environment, as a result of a significant drop in $N_{\\text{e}}$. Changes in demography as well as high variance in reproductive success in the novel environment may contribute to the low values of $N_{\\text{e}}$. This study shows that estimates of genetic differentiation between natural populations may be accurate when based on the initial samples collected in the wild, though considerable genetic differentiation may occur in the very first generations of evolution in a new, confined environment. Rapid and significant evolutionary changes can thus occur during the early generations of a founding event, both in the wild and under domestication, effects of interest for both scientific and conservation purposes.

  4. Scalable computing for evolutionary genomics.

    Science.gov (United States)

    Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert

    2012-01-01

    Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project

  5. Markov Networks in Evolutionary Computation

    CERN Document Server

    Shakya, Siddhartha

    2012-01-01

    Markov networks and other probabilistic graphical modes have recently received an upsurge in attention from Evolutionary computation community, particularly in the area of Estimation of distribution algorithms (EDAs).  EDAs have arisen as one of the most successful experiences in the application of machine learning methods in optimization, mainly due to their efficiency to solve complex real-world optimization problems and their suitability for theoretical analysis. This book focuses on the different steps involved in the conception, implementation and application of EDAs that use Markov networks, and undirected models in general. It can serve as a general introduction to EDAs but covers also an important current void in the study of these algorithms by explaining the specificities and benefits of modeling optimization problems by means of undirected probabilistic models. All major developments to date in the progressive introduction of Markov networks based EDAs are reviewed in the book. Hot current researc...

  6. Evolutionary Subnetworks in Complex Systems

    CERN Document Server

    Li, Menghui; Lai, Choy-Heng

    2009-01-01

    Links in a practical network may have different functions, which makes the original network a combination of some functional subnetworks. Here, by a model of coupled oscillators, we investigate how such functional subnetworks are evolved and developed according to the network structure and dynamics. In particular, we study the case of evolutionary clustered networks in which the function of each link (either attractive or repulsive coupling) is updated by the local dynamics. It is found that, during the process of system evolution, the network is gradually stabilized into a particular form in which the attractive (repulsive) subnetwork consists only the intralinks (interlinks). Based on the properties of subnetwork evolution, we also propose a new algorithm for network partition which is distinguished by the convenient operation and fast computing speed.

  7. Evolutionary advantages of adaptive rewarding

    CERN Document Server

    Szolnoki, Attila

    2012-01-01

    Our wellbeing depends as much on our personal success, as it does on the success of our society. The realization of this fact makes cooperation a very much needed trait. Experiments have shown that rewards can elevate our readiness to cooperate, but since giving a reward inevitably entails paying a cost for it, the emergence and stability of such behavior remain elusive. Here we show that allowing for the act of rewarding to self-organize in dependence on the success of cooperation creates several evolutionary advantages that instill new ways through which collaborative efforts are promoted. Ranging from indirect territorial battle to the spontaneous emergence and destruction of coexistence, phase diagrams and the underlying spatial patterns reveal fascinatingly reach social dynamics that explains why this costly behavior has evolved and persevered. Comparisons with adaptive punishment, however, uncover an Achilles heel of adaptive rewarding that is due to over-aggression, which in turn hinders optimal utiliz...

  8. Evolutionary Games and Social Conventions

    DEFF Research Database (Denmark)

    Hansen, Pelle Guldborg

    2007-01-01

    which any theory of convention must revolve. In response, the so-called evolutionary turn has developed. While retaining the broad framework, in which games are described in terms of strategies and payoffs, this marks a transition from the classical assumptions of perfect rationality and common......Some thirty years ago Lewis published his Convention: A Philosophical Study (Lewis, 2002). This laid the foundation for a game-theoretic approach to social conventions, but became more famously known for its seminal analysis of common knowledge; the concept receiving its canonical analysis in...... Aumann (1976) and which, together with the assumptions of perfect rationality, came to be defining of classical game theory. However, classical game theory is currently undergoing severe crisis as a tool for exploring social phenomena; a crisis emerging from the problem of equilibrium selection around...

  9. Evolutionary origin of cardiac malformations.

    Science.gov (United States)

    Taussig, H B

    1988-10-01

    The author has proposed in previous publications that isolated cardiac malformations have an evolutionary origin. This is partly supported by the fact that isolated cardiac malformations found in humans occur also in other placental mammals as well as in birds. External gross examination of the heart in just over 5,000 birds was carried out during a 3 year period. Anomalies included one instance of duplicate hearts, two specimens in which no heart could be identified and in a fourth, a yellow-rumped warbler, the heart lay in the neck outside of the thoracic cavity. Published reports of similar occurrences of an ectopically placed heart concern birds, cattle and humans. The fact that various species of both placental mammals and birds show evidence of heritability for heart defects, and that these species cannot interbreed, combined with the fact that birds and mammals have many similar malformations, points to either a common external causative factor or a common origin. Genes that code the malformed heart must be transmitted with that part of the genetic makeup common to all birds and mammals. Malformations caused by teratogens produce widespread organ injury to a potentially normal embryo whereas the evolutionary malformation is an organ-specific anomaly in an otherwise normal mammal or bird and occurs in widely separated species. The implications of this theory are important for parents of children with an isolated congenital heart defect who may have ingested one or another drug or chemical or have been exposed to toxins or infectious agents before or after conception of the affected offspring. PMID:3047192

  10. Evolutionary primacy of sodium bioenergetics

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2008-04-01

    Full Text Available Abstract Background The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the F-type (found in most bacteria and eukaryotic mitochondria and chloroplasts and V-type (found in archaea, some bacteria, and eukaryotic vacuoles ATPases can translocate either protons or sodium ions. The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments. Results We combine structural and phylogenetic analyses to clarify the evolutionary relation between the proton- and sodium-translocating ATPases. A comparison of the structures of the membrane-embedded oligomeric proteolipid rings of sodium-dependent F- and V-ATPases reveals nearly identical sets of amino acids involved in sodium binding. We show that the sodium-dependent ATPases are scattered among proton-dependent ATPases in both the F- and the V-branches of the phylogenetic tree. Conclusion Barring convergent emergence of the same set of ligands in several lineages, these findings indicate that the use of sodium gradient for ATP synthesis is the ancestral modality of membrane bioenergetics. Thus, a primitive, sodium-impermeable but proton-permeable cell membrane that harboured a set of sodium-transporting enzymes appears to have been the evolutionary predecessor of the more structurally demanding proton-tight membranes. The use of proton as the coupling ion appears to be a later innovation that emerged on several independent occasions. Reviewers This article was reviewed by J. Peter Gogarten, Martijn A. Huynen, and Igor B. Zhulin. For the full reviews, please go to the Reviewers' comments section.

  11. Paradoxes in Biodiversity Conservation

    OpenAIRE

    David Pearce

    2005-01-01

    Biodiversity is important for human wellbeing, but it is declining. Measures to conserve biodiversity are essential but may be a waste of effort if several paradoxes are not addressed. The highest levels of diversity are in nations least able to practise effective conservation. The flow of funds to international biodiversity conservation appears trivial when compared to the scale of biodiversity loss. International agreements may not actually protect or conserve more than what would have been...

  12. Evolutionary design assistants for architecture

    Directory of Open Access Journals (Sweden)

    N. Onur Sönmez

    2015-04-01

    Full Text Available In its parallel pursuit of an increased competitivity for design offices and more pleasurable and easier workflows for designers, artificial design intelligence is a technical, intellectual, and political challenge. While human-machine cooperation has become commonplace through Computer Aided Design (CAD tools, a more improved collaboration and better support appear possible only through an endeavor into a kind of artificial design intelligence, which is more sensitive to the human perception of affairs.Considered as part of the broader Computational Design studies, the research program of this quest can be called Artificial / Autonomous / Automated Design (AD. The current available level of Artificial Intelligence (AI for design is limited and a viable aim for current AD would be to develop design assistants that are capable of producing drafts for various design tasks. Thus, the overall aim of this thesis is the development of approaches, techniques, and tools towards artificial design assistants that offer a capability for generating drafts for sub-tasks within design processes. The main technology explored for this aim is Evolutionary Computation (EC, and the target design domain is architecture. The two connected research questions of the study concern, first, the investigation of the ways to develop an architectural design assistant, and secondly, the utilization of EC for the development of such assistants.While developing approaches, techniques, and computational tools for such an assistant, the study also carries out a broad theoretical investigation into the main problems, challenges, and requirements towards such assistants on a rather overall level. Therefore, the research is shaped as a parallel investigation of three main threads interwoven along several levels, moving from a more general level to specific applications. The three research threads comprise, first, theoretical discussions and speculations with regard to both existing

  13. Conservation Action Handbook.

    Science.gov (United States)

    National Rifle Association, Washington, DC.

    Conservation problems are identified, with some suggestions for action. General areas covered are: Wildlife Conservation, Soil Conservation, Clean Water, Air Pollution Action, and Outdoor Recreation Action. Appendices list private organizations or agencies concerned with natural resource use and/or management, congressional committees considering…

  14. Stochastic Conservation Laws?

    CERN Document Server

    Sidharth, B G

    1998-01-01

    We examine conservation laws, typically the conservation of linear momentum, in the light of a recent successful formulation of fermions as Kerr-Newman type Black Holes, which are created fluctuationally from a background Zero Point Field. We conclude that these conservation laws are to be taken in the spirit of thermodynamic laws.

  15. Conservation in Physics.

    Science.gov (United States)

    Finkel, Edward

    1991-01-01

    Discussed is the physical concept of conservation as it is framed within the laws of conservation of mass, of momentum, and of energy. The derivation of Ohm's Law as a generalization of the relationship between the observed measurements of voltage and current serves as the exemplar of how conservation theories are formed. (JJK)

  16. Information Geometry and Evolutionary Game Theory

    CERN Document Server

    Harper, Marc

    2009-01-01

    The Shahshahani geometry of evolutionary game theory is realized as the information geometry of the simplex, deriving from the Fisher information metric of the manifold of categorical probability distributions. Some essential concepts in evolutionary game theory are realized information-theoretically. Results are extended to the Lotka-Volterra equation and to multiple population systems.

  17. Handbook of differential equations evolutionary equations

    CERN Document Server

    Dafermos, CM

    2008-01-01

    The material collected in this volume discusses the present as well as expected future directions of development of the field with particular emphasis on applications. The seven survey articles present different topics in Evolutionary PDE's, written by leading experts.- Review of new results in the area- Continuation of previous volumes in the handbook series covering Evolutionary PDEs- Written by leading experts

  18. On the Evolutionary Stability of Bargaining Inefficiency

    DEFF Research Database (Denmark)

    Poulsen, Anders

    This paper investigates whether 'tough' bargaining behavior, which gives rise to inefficiency, can be evolutionary stable. We show that in a two-stage Nash Demand Game tough behavior survives. Indeed, almost all the surplus may be wasted. We also study the Ultimatum Game. Here evolutionary...

  19. Algorithmic Mechanism Design of Evolutionary Computation.

    Science.gov (United States)

    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. PMID:26257777

  20. On Economic Applications of Evolutionary Game Theory

    OpenAIRE

    Daniel Friedman

    2010-01-01

    Evolutionary games have considerable unrealized potential for modeling substantive economic issues. They promise richer predictions than orthodox game models but often require more extensive specifications. This paper exposits the specification of evolutionary game models and classifies the possible asymptotic behavior for one and two dimensional models.

  1. Oversimplifying Evolutionary Psychology Leads to Explanatory Gaps

    Science.gov (United States)

    Tate, Chuck; Ledbetter, Jay N.

    2010-01-01

    Comments on Evolutionary psychology: Controversies, questions, prospects, and limitations by Confer et al. They argued that SST cannot explain the existence of either homosexuality or suicide within the human species. We contend that a sufficiently nuanced evolutionary position has no difficulties explaining either phenomenon. Also in this…

  2. 08051 Executive Summary -- Theory of Evolutionary Algorithms

    OpenAIRE

    Arnold, Dirk V.; Auger, Anne; Rowe, Jonathan E.; Witt, Carsten

    2008-01-01

    The 2008 Dagstuhl Seminar "Theory of Evolutionary Algorithms" was the fifth in a firmly established series of biannual events. In the week from Jan. 27, 2008 to Feb. 1, 2008, 47 researchers from nine countries discussed their recent work and trends in evolutionary computation.

  3. Generalized Evolutionary Algorithm based on Tsallis Statistics

    OpenAIRE

    Dukkipati, Ambedkar; Murty, M. Narasimha; Bhatnagar, Shalabh

    2004-01-01

    Generalized evolutionary algorithm based on Tsallis canonical distribution is proposed. The algorithm uses Tsallis generalized canonical distribution to weigh the configurations for `selection' instead of Gibbs-Boltzmann distribution. Our simulation results show that for an appropriate choice of non-extensive index that is offered by Tsallis statistics, evolutionary algorithms based on this generalization outperform algorithms based on Gibbs-Boltzmann distribution.

  4. The Citation Field of Evolutionary Economics

    CERN Document Server

    Dolfsma, Wilfred

    2010-01-01

    Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal that is indispensable in the exchange of expert knowledge on topics and using approaches that relate naturally with it. Analyzing citation data for the relevant academic field for the Journal of Evolutionary Economics, we use insights from scientometrics and social network analysis to find that, indeed, the JEE is a central player in this interdisciplinary field aiming mostly at understanding technological and regional dynamics. It does not, however, link firmly with the natural sciences (including biology) nor to management sciences, entrepreneurship, and organization studies. Another journal that could be perceived to have evolutionary acumen, the Journal of Economic Issues, does relate to heterodox economics journa...

  5. Evolutionary Psychiatry and Nosology: Prospects and Limitations

    Directory of Open Access Journals (Sweden)

    Luc Faucher

    2012-11-01

    Full Text Available In this paper, I explain why evolutionary psychiatry is not where the next revolution in psychiatry will come from. I will proceed as follows. Firstly, I will review some of the problems commonly attributed to current nosologies, more specifically to the DSM. One of these problems is the lack of a clear and consensual definition of mental disorder; I will then examine specific attempts to spell out such a definition that use the evolutionary framework. One definition that deserves particular attention (for a number of reasons that I will mention later, is one put forward by Jerome Wakefield. Despite my sympathy for his position, I must indicate a few reasons why I think his attempt might not be able to resolve the problems related to current nosologies. I suggest that it might be wiser for an evolutionary psychiatrist to adopt the more integrative framework of “treatable conditions” (Cosmides and Tooby, 1999. As it is thought that an evolutionary approach can contribute to transforming the way we look at mental disorders, I will provide the reader with a brief sketch of the basic tenets of evolutionary psychology. The picture of the architecture of the human mind that emerges from evolutionary psychology is thought by some to be the crucial backdrop to identifying specific mental disorders and distinguishing them from normal conditions. I will also provide two examples of how evolutionary thinking is supposed to change our thinking about some disorders. Using the case of depression, I will then show what kind of problems evolutionary explanations of particular psychopathologies encounter. In conclusion, I will evaluate where evolutionary thinking leaves us in regard to what I identify as the main problems of our current nosologies. I’ll then argue that the prospects of evolutionary psychiatry are not good.

  6. Exactly conservative integrators

    Energy Technology Data Exchange (ETDEWEB)

    Shadwick, B.A.; Bowman, J.C.; Morrison, P.J.

    1995-07-19

    Traditional numerical discretizations of conservative systems generically yield an artificial secular drift of any nonlinear invariants. In this work we present an explicit nontraditional algorithm that exactly conserves invariants. We illustrate the general method by applying it to the Three-Wave truncation of the Euler equations, the Volterra-Lotka predator-prey model, and the Kepler problem. We discuss our method in the context of symplectic (phase space conserving) integration methods as well as nonsymplectic conservative methods. We comment on the application of our method to general conservative systems.

  7. Exactly conservation integrators

    Energy Technology Data Exchange (ETDEWEB)

    Shadwick, B.A.; Bowman, J.C.; Morrison, P.J. [Univ. of Texas, Austin, TX (United States)

    1999-03-01

    Traditional explicit numerical discretizations of conservative systems generically predict artificial secular drifts of any nonlinear invariants. In this work the authors present a general approach for developing explicit nontraditional algorithms that conserve such invariants exactly. They illustrate the method by applying it to the three-wave truncation of the Euler equations, the Lotka-Volterra predator-prey model, and the Kepler problem. The ideas are discussed in the context of symplectic (phase-space-conserving) integration methods as well as nonsymplectic conservative methods. They comment on the application of the method to general conservative systems.

  8. Inflated impact factors? The true impact of evolutionary papers in non-evolutionary journals.

    Science.gov (United States)

    Postma, Erik

    2007-01-01

    Amongst the numerous problems associated with the use of impact factors as a measure of quality are the systematic differences in impact factors that exist among scientific fields. While in theory this can be circumvented by limiting comparisons to journals within the same field, for a diverse and multidisciplinary field like evolutionary biology, in which the majority of papers are published in journals that publish both evolutionary and non-evolutionary papers, this is impossible. However, a journal's overall impact factor may well be a poor predictor for the impact of its evolutionary papers. The extremely high impact factors of some multidisciplinary journals, for example, are by many believed to be driven mostly by publications from other fields. Despite plenty of speculation, however, we know as yet very little about the true impact of evolutionary papers in journals not specifically classified as evolutionary. Here I present, for a wide range of journals, an analysis of the number of evolutionary papers they publish and their average impact. I show that there are large differences in impact among evolutionary and non-evolutionary papers within journals; while the impact of evolutionary papers published in multidisciplinary journals is substantially overestimated by their overall impact factor, the impact of evolutionary papers in many of the more specialized, non-evolutionary journals is significantly underestimated. This suggests that, for evolutionary biologists, publishing in high-impact multidisciplinary journals should not receive as much weight as it does now, while evolutionary papers in more narrowly defined journals are currently undervalued. Importantly, however, their ranking remains largely unaffected. While journal impact factors may thus indeed provide a meaningful qualitative measure of impact, a fair quantitative comparison requires a more sophisticated journal classification system, together with multiple field-specific impact statistics per

  9. Inflated impact factors? The true impact of evolutionary papers in non-evolutionary journals.

    Directory of Open Access Journals (Sweden)

    Erik Postma

    Full Text Available Amongst the numerous problems associated with the use of impact factors as a measure of quality are the systematic differences in impact factors that exist among scientific fields. While in theory this can be circumvented by limiting comparisons to journals within the same field, for a diverse and multidisciplinary field like evolutionary biology, in which the majority of papers are published in journals that publish both evolutionary and non-evolutionary papers, this is impossible. However, a journal's overall impact factor may well be a poor predictor for the impact of its evolutionary papers. The extremely high impact factors of some multidisciplinary journals, for example, are by many believed to be driven mostly by publications from other fields. Despite plenty of speculation, however, we know as yet very little about the true impact of evolutionary papers in journals not specifically classified as evolutionary. Here I present, for a wide range of journals, an analysis of the number of evolutionary papers they publish and their average impact. I show that there are large differences in impact among evolutionary and non-evolutionary papers within journals; while the impact of evolutionary papers published in multidisciplinary journals is substantially overestimated by their overall impact factor, the impact of evolutionary papers in many of the more specialized, non-evolutionary journals is significantly underestimated. This suggests that, for evolutionary biologists, publishing in high-impact multidisciplinary journals should not receive as much weight as it does now, while evolutionary papers in more narrowly defined journals are currently undervalued. Importantly, however, their ranking remains largely unaffected. While journal impact factors may thus indeed provide a meaningful qualitative measure of impact, a fair quantitative comparison requires a more sophisticated journal classification system, together with multiple field

  10. Exploring the long-term variability and evolutionary stage of the interacting binary DQ Velorum

    CERN Document Server

    Barría, D; Graczyk, D; Kołaczkowski, Z

    2014-01-01

    To progress in the comprehension of the double periodic variable (DPV) phenomenon, we analyse a series of optical spectra of the DPV system DQ Velorum during much of its long-term cycle. In addition, we investigate the evolutionary history of DQ Vel using theoretical evolutionary models to obtain the best representation for the current observed stellar and orbital parameters of the binary. We investigate the evolution of DQ Vel through theoretical evolutionary models to estimate the age and the mass transfer rate which are compared with those of its twin V393 Scorpii. Donor subtracted spectra covering around 60% of the long-term cycle, allow us to investigate time-modulated spectral variations of the gainer star plus the disc. We compare the observed stellar parameters of the system with a grid of theoretical evolutionary tracks computed under a conservative and a non-conservative evolution regime. We have found that the EW of Balmer and helium lines in the donor subtracted spectra are modulated with the long...

  11. Phylogeny meets ecotoxicology: evolutionary patterns of sensitivity to a common insecticide

    OpenAIRE

    Hammond, John I.; Jones, Devin K; Stephens, Patrick R.; Relyea, Rick A.

    2012-01-01

    Pesticides commonly occur in aquatic systems and pose a substantial challenge to the conservation of many taxa. Ecotoxicology has traditionally met this challenge by focusing on short-term, single-species tests and conducting risk assessments based on the most sensitive species tested. Rarely have ecotoxicology data been examined from an evolutionary perspective, and to our knowledge, there has never been a phylogenetic analysis of sensitivity, despite the fact that doing so would provide ins...

  12. Probing the evolutionary history of epigenetic mechanisms: what can we learn from marine diatoms

    OpenAIRE

    Achal Rastogi; Xin Lin; Bérangère Lombard; Damarys Loew; Leïla Tirichine

    2015-01-01

    Recent progress made on epigenetic studies revealed the conservation of epigenetic features in deep diverse branching species including Stramenopiles, plants and animals. This suggests their fundamental role in shaping species genomes across different evolutionary time scales. Diatoms are a highly successful and diverse group of phytoplankton with a fossil record of about 190 million years ago. They are distantly related from other super-groups of Eukaryotes and have retained some of the epig...

  13. Dynamic Waste Management (DWM):Towards an evolutionary decision-making approach

    OpenAIRE

    Rojo, Gabriel; Glaus, Mathias; Hausler, Robert; Laforest, Valérie; Bourgois, Jacques

    2013-01-01

    To guarantee sustainable and dynamic waste management, the dynamic waste management approach (DWM) suggests an evolutionary new approach that maintains a constant flow towards the most favourable waste treatment processes (facilities) within a system. To that end, DWM is based on the law of conservation of energy, which allows the balancing of a network, while considering the constraints of incoming (h1) and outgoing (h2) loads, as well as the distribution network (ΔH) characteristics. The de...

  14. Evolutionary insights into duffy gene in mammalian taxa with comparative genetic analysis

    OpenAIRE

    Gauri Awasthi; Aditya P. Dash

    2009-01-01

    Background & objectives: Evolutionary analyses of genes conserved across taxa are keys tounderstand the complexity of gene and genome variation. Since malaria is a highly infectioushuman disease and its susceptibility in human is genetically controlled, characterization andevolutionary analyses of such genes are of prime importance to understand genetic mechanisms ofdisease susceptibility. In the present study we have characterized and performed comparativegenomic analyses of the human Duffy ...

  15. A novel stability criterion for interval time-delay chaotic systems via the evolutionary programming approach

    International Nuclear Information System (INIS)

    This paper investigates a novel stability criterion for interval time-delay chaotic systems via the evolutionary programming (EP) approach. First a delay-dependent criterion is derived for ensuring the stability of degenerate time-delay systems, and then by solving eigenvalue location optimization problems, which will be defined later, the robust stability of interval time-delay systems can be guaranteed. An example is given to verify our method that yields less conservative results than those appeared in the literature

  16. EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization

    OpenAIRE

    Rackham, Owen J. L.; Shihab, Hashem A; Johnson, Michael R.; Petretto, Enrico

    2014-01-01

    Methods to interpret personal genome sequences are increasingly required. Here, we report a novel framework (EvoTol) to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation of protein sequences and can incorporate tissue-specific gene expression data. We apply this framework to the analysis of whole-exome sequence data in epilepsy and congenital heart disease, and demon...

  17. Evolutionary genomics of animal personality.

    Science.gov (United States)

    van Oers, Kees; Mueller, Jakob C

    2010-12-27

    Research on animal personality can be approached from both a phenotypic and a genetic perspective. While using a phenotypic approach one can measure present selection on personality traits and their combinations. However, this approach cannot reconstruct the historical trajectory that was taken by evolution. Therefore, it is essential for our understanding of the causes and consequences of personality diversity to link phenotypic variation in personality traits with polymorphisms in genomic regions that code for this trait variation. Identifying genes or genome regions that underlie personality traits will open exciting possibilities to study natural selection at the molecular level, gene-gene and gene-environment interactions, pleiotropic effects and how gene expression shapes personality phenotypes. In this paper, we will discuss how genome information revealed by already established approaches and some more recent techniques such as high-throughput sequencing of genomic regions in a large number of individuals can be used to infer micro-evolutionary processes, historical selection and finally the maintenance of personality trait variation. We will do this by reviewing recent advances in molecular genetics of animal personality, but will also use advanced human personality studies as case studies of how molecular information may be used in animal personality research in the near future. PMID:21078651

  18. The Evolutionary Origins of Hierarchy.

    Science.gov (United States)

    Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff

    2016-06-01

    Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics. PMID:27280881

  19. Evolutionary advantages of adaptive rewarding

    International Nuclear Information System (INIS)

    Our well-being depends on both our personal success and the success of our society. The realization of this fact makes cooperation an essential trait. Experiments have shown that rewards can elevate our readiness to cooperate, but since giving a reward inevitably entails paying a cost for it, the emergence and stability of such behavior remains elusive. Here we show that allowing for the act of rewarding to self-organize in dependence on the success of cooperation creates several evolutionary advantages that instill new ways through which collaborative efforts are promoted. Ranging from indirect territorial battle to the spontaneous emergence and destruction of coexistence, phase diagrams and the underlying spatial patterns reveal fascinatingly rich social dynamics that explain why this costly behavior has evolved and persevered. Comparisons with adaptive punishment, however, uncover an Achilles heel of adaptive rewarding, coming from over-aggression, which in turn hinders optimal utilization of network reciprocity. This may explain why, despite its success, rewarding is not as firmly embedded into our societal organization as punishment. (paper)

  20. Evolutionary dynamics of group fairness.

    Science.gov (United States)

    Santos, Fernando P; Santos, Francisco C; Paiva, Ana; Pacheco, Jorge M

    2015-08-01

    The emergence and impact of fairness is commonly studied in the context of 2-person games, notably the Ultimatum Game. Often, however, humans face problems of collective action involving more than two individuals where fairness is known to play a very important role, and whose dynamics cannot be inferred from what is known from 2-person games. Here, we propose a generalization of the Ultimatum Game for an arbitrary number of players--the Multiplayer Ultimatum Game. Proposals are made to a group of responders who must individually reject or accept the proposal. If the total number of individual acceptances stands below a given threshold, the offer will be rejected; otherwise, the offer will be accepted, and equally shared by all responders. We investigate the evolution of fairness in populations of individuals by means of evolutionary game theory, providing both analytical insights and results from numerical simulations. We show how imposing stringent consensuses significantly increases the value of the proposals, leading to fairer outcomes and more tolerant players. Furthermore, we show how stochastic effects--such as imitation errors and/or errors when assessing the fitness of others--may further enhance the overall success in reaching fair collective action. PMID:25936348

  1. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.

    Science.gov (United States)

    Gómez-Marín, Carlos; Tena, Juan J; Acemel, Rafael D; López-Mayorga, Macarena; Naranjo, Silvia; de la Calle-Mustienes, Elisa; Maeso, Ignacio; Beccari, Leonardo; Aneas, Ivy; Vielmas, Erika; Bovolenta, Paola; Nobrega, Marcelo A; Carvajal, Jaime; Gómez-Skarmeta, José Luis

    2015-06-16

    Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution. PMID:26034287

  2. The Exercise–Affect–Adherence Pathway: An Evolutionary Perspective

    Science.gov (United States)

    Lee, Harold H.; Emerson, Jessica A.; Williams, David M.

    2016-01-01

    The low rates of regular exercise and overall physical activity (PA) in the general population represent a significant public health challenge. Previous research suggests that, for many people, exercise leads to a negative affective response and, in turn, reduced likelihood of future exercise. The purpose of this paper is to examine this exercise–affect–adherence relationship from an evolutionary perspective. Specifically, we argue that low rates of physical exercise in the general population are a function of the evolved human tendency to avoid unnecessary physical exertion. This innate tendency evolved because it allowed our evolutionary ancestors to conserve energy for physical activities that had immediate adaptive utility such as pursuing prey, escaping predators, and engaging in social and reproductive behaviors. The commonly observed negative affective response to exercise is an evolved proximate psychological mechanism through which humans avoid unnecessary energy expenditure. The fact that the human tendencies toward negative affective response to and avoidance of unnecessary physical activities are innate does not mean that they are unchangeable. Indeed, it is only because of human-engineered changes in our environmental conditions (i.e., it is no longer necessary for us to work for our food) that our predisposition to avoid unnecessary physical exertion has become a liability. Thus, it is well within our capabilities to reengineer our environments to once again make PA necessary or, at least, to serve an immediate functional purpose. We propose a two-pronged approach to PA promotion based on this evolutionary functional perspective: first, to promote exercise and other physical activities that are perceived to have an immediate purpose, and second, to instill greater perceived purpose for a wider range of physical activities. We posit that these strategies are more likely to result in more positive (or less negative) affective responses to exercise

  3. Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes

    Indian Academy of Sciences (India)

    Zhao Jun Shao; Eric Rivals; Na Zhao; Sovan Lek; Jianbo Chang; Patrick Berrebi

    2011-08-01

    The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align phylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121–96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69–10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types.

  4. Phylodiversity to inform conservation policy: An Australian example.

    Science.gov (United States)

    Laity, Tania; Laffan, Shawn W; González-Orozco, Carlos E; Faith, Daniel P; Rosauer, Dan F; Byrne, Margaret; Miller, Joseph T; Crayn, Darren; Costion, Craig; Moritz, Craig C; Newport, Karl

    2015-11-15

    Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylodiversity measures provide important additional information about biodiversity that can improve conservation policy and outcomes. As a biodiverse nation with a strong legislative and policy framework, Australia provides an opportunity to use phylogenetic information to inform conservation decision-making. We explored the application of phylodiversity measures across Australia with a focus on two highly biodiverse regions, the south west of Western Australia (SWWA) and the South East Queensland bioregion (SEQ). We analysed seven diverse groups of organisms spanning five separate phyla on the evolutionary tree of life, the plant genera Acacia and Daviesia, mammals, hylid frogs, myobatrachid frogs, passerine birds, and camaenid land snails. We measured species richness, weighted species endemism (WE) and two phylodiversity measures, phylogenetic diversity (PD) and phylogenetic endemism (PE), as well as their respective complementarity scores (a measure of gains and losses) at 20 km resolution. Higher PD was identified within SEQ for all fauna groups, whereas more PD was found in SWWA for both plant groups. PD and PD complementarity were strongly correlated with species richness and species complementarity for most groups but less so for plants. PD and PE were found to complement traditional species-based measures for all groups studied: PD and PE follow similar spatial patterns to richness and WE, but highlighted different areas that would not be identified by conventional species-based biodiversity analyses alone. The application of phylodiversity measures, particularly the novel weighted complementary measures considered here, in conservation can enhance protection of the evolutionary history that contributes to present day biodiversity values of areas. Phylogenetic measures in conservation

  5. Spatial pattern of invasion and the evolutionary responses of native plant species.

    Science.gov (United States)

    Stotz, Gisela C; Gianoli, Ernesto; Cahill, James F

    2016-09-01

    Invasive plant species can have a strong negative impact on the resident native species, likely imposing new selective pressures on them. Altered selective pressures may result in evolutionary changes in some native species, reducing competitive exclusion and allowing for coexistence with the invader. Native genotypes that are able to coexist with strong invaders may represent a valuable resource for management efforts. A better understanding of the conditions under which native species are more, or less, likely to adapt to an invader is necessary to incorporate these eco-evolutionary dynamics into management strategies. We propose that the spatial structure of invasion, in particular the size and isolation of invaded patches, is one factor which can influence the evolutionary responses of native species through modifying gene flow and the strength of selection. We present a conceptual model in which large, dense, and well-connected patches result in a greater likelihood of native species adaptation. We also identify characteristics of the interacting species that may influence the evolutionary response of native species to invasion and outline potential management implications. Identifying areas of rapid evolutionary change may offer one additional tool to managers in their effort to conserve biodiversity in the face of invasion. PMID:27606003

  6. Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.

    Science.gov (United States)

    Wang, Jun; Tao, Feng; Marowsky, Nicholas C; Fan, Chuanzhu

    2016-09-01

    Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883

  7. Evolutionary relationships of wild hominids recapitulated by gut microbial communities.

    Directory of Open Access Journals (Sweden)

    Howard Ochman

    Full Text Available Multiple factors over the lifetime of an individual, including diet, geography, and physiologic state, will influence the microbial communities within the primate gut. To determine the source of variation in the composition of the microbiota within and among species, we investigated the distal gut microbial communities harbored by great apes, as present in fecal samples recovered within their native ranges. We found that the branching order of host-species phylogenies based on the composition of these microbial communities is completely congruent with the known relationships of the hosts. Although the gut is initially and continuously seeded by bacteria that are acquired from external sources, we establish that over evolutionary timescales, the composition of the gut microbiota among great ape species is phylogenetically conserved and has diverged in a manner consistent with vertical inheritance.

  8. Evolutionary perspectives of telomerase RNA structure and function.

    Science.gov (United States)

    Podlevsky, Joshua D; Chen, Julian J-L

    2016-08-01

    Telomerase is the eukaryotic solution to the 'end-replication problem' of linear chromosomes by synthesising the highly repetitive DNA constituent of telomeres, the nucleoprotein cap that protects chromosome termini. Functioning as a ribonucleoprotein (RNP) enzyme, telomerase is minimally composed of the highly conserved catalytic telomerase reverse transcriptase (TERT) and essential telomerase RNA (TR) component. Beyond merely providing the template for telomeric DNA synthesis, TR is an innate telomerase component and directly facilitates enzymatic function. TR accomplishes this by having evolved structural elements for stable assembly with the TERT protein and the regulation of the telomerase catalytic cycle. Despite its prominence and prevalence, TR has profoundly diverged in length, sequence, and biogenesis pathway among distinct evolutionary lineages. This diversity has generated numerous structural and mechanistic solutions for ensuring proper RNP formation and high fidelity telomeric DNA synthesis. Telomerase provides unique insights into RNA and protein coevolution within RNP enzymes. PMID:27359343

  9. Econometric modelling of conservation

    International Nuclear Information System (INIS)

    The issue of energy conservation in general, and conservation in the natural gas markets in particular, has recently had a much lower profile than in the past, when energy prices were significantly higher and energy costs composed a much larger proportion of industrial operating costs than today. The recent downward trend in energy prices has diverted attention away from this issue. In the face of expected significant real price increases, increasing pressure from environmental groups, and directives on the part of regulator authorities, conservation is once again becoming a topic of consideration in the energy industry. From the point of view of gas demand forecasting, conservation has received too little attention. The intentions of this paper are to establish the need for forecasting conservation in the natural gas utility sector, and to construct a model of industrial demand which incorporates conservation and is appropriate for use as a forecasting tool

  10. Conservation: Toward firmer ground

    Science.gov (United States)

    1975-01-01

    The following aspects of energy conservation were discussed: conservation history and goals, conservation modes, conservation accounting-criteria, and a method to overcome obstacles. The conservation modes tested fall into one of the following categories: reduced energy consumption, increased efficiency of energy utilization, or substitution of one or more forms of energy for another which is in shorter supply or in some sense thought to be of more value. The conservation accounting criteria include net energy reduction, economic, and technical criteria. A method to overcome obstacles includes (approaches such as: direct personal impact (life style, income, security, aspiration), an element of crisis, large scale involvement of environmental, safety, and health issues, connections to big government, big business, big politics, involvement of known and speculative science and technology, appeal to moral and ethical standards, the transient nature of opportunities to correct the system.

  11. Financing Biodiversity Conservation

    OpenAIRE

    Ricardo Bayón; J. Steven Lovink; Wouter J. Veening

    2000-01-01

    Financing the conservation and sustainable use of biodiversity has been called one of the greatest challenges. At the heart of this challenge lies the low financial and political value which is often assigned to biodiversity and the resulting lack of financial mechanisms for conservation and sustainable use. This report provides an overview of existing and experimental financing mechanisms that can be used to encourage the conservation and sustainable use of biodiversity. To help to better un...

  12. Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements

    OpenAIRE

    Darling, Aaron C.E.; Mau, Bob; Blattner, Frederick R.; Perna, Nicole T.

    2004-01-01

    As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under considera...

  13. Robust optimization : formulation, kriging and evolutionary approaches

    OpenAIRE

    Le Riche, Rodolphe

    2014-01-01

    This is a two hours class on robust optimization. It starts with motivations and formulations for robust optimization, and then focuses on approaches based 1) on kriging 2) on evolutionary computation as complementary alternatives.

  14. Evolutionary origins of leadership and followership.

    Science.gov (United States)

    Van Vugt, Mark

    2006-01-01

    Drawing upon evolutionary logic, leadership is reconceptualized in terms of the outcome of strategic interactions among individuals who are following different, yet complementary, decision rules to solve recurrent coordination problems. This article uses the vast psychological literature on leadership as a database to test several evolutionary hypotheses about the origins of leadership and followership in humans. As expected, leadership correlates with initiative taking, trait measures of intelligence, specific task competencies, and several indicators of generosity. The review finds no link between leadership and dominance. The evolutionary analysis accounts for reliable age, health, and sex differences in leadership emergence. In general, evolutionary theory provides a useful, integrative framework for studying leader-follower relationships and generates various novel research hypotheses. PMID:17201593

  15. A Hybrid Chaotic Quantum Evolutionary Algorithm

    DEFF Research Database (Denmark)

    Cai, Y.; Zhang, M.; Cai, H.

    2010-01-01

    A hybrid chaotic quantum evolutionary algorithm is proposed to reduce amount of computation, speed up convergence and restrain premature phenomena of quantum evolutionary algorithm. The proposed algorithm adopts the chaotic initialization method to generate initial population which will form...... a perfect distribution in feasible solution space in advantage of randomicity and non-repetitive ergodicity of chaos, the simple quantum rotation gate to update non-optimal individuals of population to reduce amount of computation, and the hybrid chaotic search strategy to speed up its convergence...... and enhance the global search ability. A large number of tests show that the proposed algorithm has higher convergence speed and better optimizing ability than quantum evolutionary algorithm, real-coded quantum evolutionary algorithm and hybrid quantum genetic algorithm. Tests also show that when chaos...

  16. Still doing evolutionary algorithms with Perl

    CERN Document Server

    Guervos, Juan J Merelo

    2009-01-01

    Algorithm::Evolutionary (A::E from now on) was introduced in 2002, after a talk in YAPC::EU in Munich. 7 years later, A::E is in its 0.67 version (past its "number of the beast" 0.666), and has been used extensively, to the point of being the foundation of much of the (computer) science being done by our research group (and, admittedly, not many others). All is not done, however; now A::E is being integrated with POE so that evolutionary algorithms (EAs) can be combined with all kinds of servers and used in client, servers, and anything in between. In this companion to the talk I will explain what evolutionary algorithms are, what they are being used for, how to do them with Perl (using these or other fine modules found in CPAN) and what evolutionary algorithms can do for Perl at large.

  17. Evolutionary Topology Optimization for Heat Conduction Fields

    Institute of Scientific and Technical Information of China (English)

    LI Jiachun; YE Bangyan; TANG Yong; GUAN Qiming; YANG Xudong

    2006-01-01

    An effective evolutionary method for solving the structural topology design problems of heat conductive fields is presented in this paper. The topology optimization model based on minimizing the heat transport potential capacity dissipation of heat conductive field is then established and the corresponding sensitivity of objective function is derived to determine which elements would be removed of the heat conductive field for having the increment of the objective heat transport potential capacity dissipation minimized. A Filtering technique is employed in sensitivity field to eliminate numerical instabilities in the evolutionary procedure. Numerical examples are presented to demonstrate the validity and the engineering applicability of the evolutionary method by contrast with SIMP method, meanwhile we can come to a conclusion that higher speed of convergence and clearer optimal topology distribution without intermediate elements can be attained by using evolutionary strategy, with the results laying a reliable foundation for the subsequent shape and size optimizations in thermal engineering.

  18. Scheduling Earth Observing Satellites with Evolutionary Algorithms

    Science.gov (United States)

    Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

    2003-01-01

    We hypothesize that evolutionary algorithms can effectively schedule coordinated fleets of Earth observing satellites. The constraints are complex and the bottlenecks are not well understood, a condition where evolutionary algorithms are often effective. This is, in part, because evolutionary algorithms require only that one can represent solutions, modify solutions, and evaluate solution fitness. To test the hypothesis we have developed a representative set of problems, produced optimization software (in Java) to solve them, and run experiments comparing techniques. This paper presents initial results of a comparison of several evolutionary and other optimization techniques; namely the genetic algorithm, simulated annealing, squeaky wheel optimization, and stochastic hill climbing. We also compare separate satellite vs. integrated scheduling of a two satellite constellation. While the results are not definitive, tests to date suggest that simulated annealing is the best search technique and integrated scheduling is superior.

  19. The evolutionary genetics of canalization.

    Science.gov (United States)

    Flatt, Thomas

    2005-09-01

    Evolutionary genetics has recently made enormous progress in understanding how genetic variation maps into phenotypic variation. However why some traits are phenotypically invariant despite apparent genetic and environmental changes has remained a major puzzle. In the 1940s, Conrad Hal Waddington coined the concept and term "canalization" to describe the robustness of phenotypes to perturbation; a similar concept was proposed by Waddington's contemporary Ivan Ivanovich Schmalhausen. This paper reviews what has been learned about canalization since Waddington. Canalization implies that a genotype's phenotype remains relatively invariant when individuals of a particular genotype are exposed to different environments (environmental canalization) or when individuals of the same single- or multilocus genotype differ in their genetic background (genetic canalization). Consequently, genetic canalization can be viewed as a particular kind of epistasis, and environmental canalization and phenotypic plasticity are two aspects of the same phenomenon. Canalization results in the accumulation of phenotypically cryptic genetic variation, which can be released after a "decanalizing" event. Thus, canalized genotypes maintain a cryptic potential for expressing particular phenotypes, which are only uncovered under particular decanalizing environmental or genetic conditions. Selection may then act on this newly released genetic variation. The accumulation of cryptic genetic variation by canalization may therefore increase evolvability at the population level by leading to phenotypic diversification under decanalizing conditions. On the other hand, under canalizing conditions, a major part of the segregating genetic variation may remain phenotypically cryptic; canalization may therefore, at least temporarily, constrain phenotypic evolution. Mechanistically, canalization can be understood in terms of transmission patterns, such as epistasis, pleiotropy, and genotype by environment

  20. Evolutionary biology and life histories

    Directory of Open Access Journals (Sweden)

    Brown, C. R.

    2004-06-01

    Full Text Available The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demographic rates, such as survival, fecundity, and age of first breeding, and biologists from both fields have a vested interest in good analytical machinery for the estimation and analysis of these demographic rates. In the EURING conferences, we have been striving since the mid 1980s to promote a quantitative understanding of demographic rates through interdisciplinary collaboration between ecologists and statisticians. From the ecological side, the principal impetus has come from population biology, and in particular from wildlife biology, but the importance of good quantitative insights into demographic processes has long been recognized by a number of evolutionary biologists (e.g., Nichols & Kendall, 1995; Clobert, 1995; Cooch et al., 2002. In organizing this session, we have aimed to create a forum for those committed to gaining the best possible understanding of evolutionary processes through the application of modern quantitative methods for the collection and interpretation of data on marked animal populations. Here we present a short overview of the material presented in the session on evolutionary biology and life histories. In a plenary talk, Brown & Brown (2004 explored how mark–recapture methods have allowed a better understanding of the evolution of group–living and alternative reproductive tactics in colonial cliff swallows (Petrochelidon pyrrhonota. By estimating the number of transient birds passing through colonies of different sizes, they

  1. Wolbachia versus dengue: Evolutionary forecasts.

    Science.gov (United States)

    Bull, James J; Turelli, Michael

    2013-01-01

    A novel form of biological control is being applied to the dengue virus. The agent is the maternally transmitted bacterium Wolbachia, naturally absent from the main dengue vector, the mosquito Aedes aegypti. Three Wolbachia-based control strategies have been proposed. One is suppression of mosquito populations by large-scale releases of males incompatible with native females; this intervention requires ongoing releases. The other interventions transform wild mosquito populations with Wolbachia that spread via the frequency-dependent fitness advantage of Wolbachia-infected females; those interventions potentially require just a single, local release for area-wide disease control. One of these latter strategies uses Wolbachia that shortens mosquito life, indirectly preventing viral maturation/transmission. The other strategy uses Wolbachia that block viral transmission. All interventions can be undermined by viral, bacterial or mosquito evolution; viral virulence in humans may also evolve. We examine existing theory, experiments and comparative evidence to motivate predictions about evolutionary outcomes. (i) The life-shortening strategy seems the most likely to be thwarted by evolution. (ii) Mosquito suppression has a reasonable chance of working locally, at least in the short term, but long-term success over large areas is challenging. (iii) Dengue blocking faces strong selection for viral resistance but may well persist indefinitely at some level. Virulence evolution is not mathematically predictable, but comparative data provide no precedent for Wolbachia increasing dengue virulence. On balance, our analysis suggests that the considerable possible benefits of these technologies outweigh the known negatives, but the actual risk is largely unknown. PMID:24481199

  2. Evolutionary Design of Controlled Structures

    Science.gov (United States)

    Masters, Brett P.; Crawley, Edward F.

    1997-01-01

    Basic physical concepts of structural delay and transmissibility are provided for simple rod and beam structures. Investigations show the sensitivity of these concepts to differing controlled-structures variables, and to rational system modeling effects. An evolutionary controls/structures design method is developed. The basis of the method is an accurate model formulation for dynamic compensator optimization and Genetic Algorithm based updating of sensor/actuator placement and structural attributes. One and three dimensional examples from the literature are used to validate the method. Frequency domain interpretation of these controlled structure systems provide physical insight as to how the objective is optimized and consequently what is important in the objective. Several disturbance rejection type controls-structures systems are optimized for a stellar interferometer spacecraft application. The interferometric designs include closed loop tracking optics. Designs are generated for differing structural aspect ratios, differing disturbance attributes, and differing sensor selections. Physical limitations in achieving performance are given in terms of average system transfer function gains and system phase loss. A spacecraft-like optical interferometry system is investigated experimentally over several different optimized controlled structures configurations. Configurations represent common and not-so-common approaches to mitigating pathlength errors induced by disturbances of two different spectra. Results show that an optimized controlled structure for low frequency broadband disturbances achieves modest performance gains over a mass equivalent regular structure, while an optimized structure for high frequency narrow band disturbances is four times better in terms of root-mean-square pathlength. These results are predictable given the nature of the physical system and the optimization design variables. Fundamental limits on controlled performance are discussed

  3. Evolutionary fingerprints in genome-scale networks

    OpenAIRE

    Schütte, Moritz

    2012-01-01

    Mathematical modeling of biological phenomena has experienced increasing interest since new high-throughput technologies give access to growing amounts of molecular data. These modeling approaches are especially able to test hypotheses which are not yet experimentally accessible or guide an experimental setup. One particular attempt investigates the evolutionary dynamics responsible for today's composition of organisms. Computer simulations either propose an evolutionary mechanism and thus re...

  4. An evolutionary advantage for extravagant honesty

    OpenAIRE

    Bullock, Seth

    2011-01-01

    A game-theoretic model of handicap signalling over a pair of signalling channels is introduced in order to determine when one channel has an evolutionary advantage over the other. The stability conditions for honest handicap signalling are presented for a single channel and are shown to conform with the results of prior handicap signalling models. Evolutionary simulations are then used to show that, for a two-channel system in which honest signalling is possible on both channels, the channel ...

  5. The evolutionary neuroscience of tool making

    OpenAIRE

    Stout, D.; Chaminade, T.

    2007-01-01

    The appearance of the first intentionally modified stone tools over 2.5 million years ago marked a watershed in human evolutionary history, expanding the human adaptive niche and initiating a trend of technological elaboration that continues to the present day. However, the cognitive foundations of this behavioral revolution remain controversial, as do its implications for the nature and evolution of modern human technological abilities. Here we shed new light on the neural and evolutionary f...

  6. Epigenetic catalysis in an evolutionary context

    OpenAIRE

    Wallace, Dr. Rodrick

    2009-01-01

    Recent work by Ciliberti et al. finds the spinglass model of regulatory gene networks adapted from neural network studies to have a single giant connected component in a metanetwork space of interaction matrices, permitting only gradual evolutionary transition, in conflict with empirical studies of development in sea urchin species that found evidence for punctuated equilibrium evolutionary transition. Shifting perspective from the highly parallel matrix space to the grammar/syntax of the tim...

  7. Improving DNA Computing Using Evolutionary Techniques

    OpenAIRE

    Godar J. Ibrahim; Tarik A. Rashid; Ahmed T. Sadiq

    2016-01-01

    the field of DNA Computing has attracted many biologists and computer scientists as it has a biological interface, small size and substantial parallelism. DNA computing depends on DNA molecules’ biochemical reactions which they can randomly anneal and they might accidentally cause improper or unattractive computations. This will inspire opportunities to use evolutionary computation via DNA. Evolutionary Computation emphasizes on probabilistic search and optimization methods which are mimickin...

  8. Surrogate model selection for evolutionary multiobjective optimization

    Czech Academy of Sciences Publication Activity Database

    Pilát, M.; Neruda, Roman

    Piscataway : IEEE CS, 2013, s. 1860-1867. ISBN 978-1-4799-0453-2. [CEC 2013. IEEE Congress on Evolutionary Computation. Cancún (MX), 20.06.2013-23.06.2013] R&D Projects: GA ČR GAP202/11/1368 Grant ostatní: GA UK(CZ) 345511 Institutional support: RVO:67985807 Keywords : multiobjective optimization * evolutionary algorithm * meta-model * model selection Subject RIV: IN - Informatics, Computer Science

  9. Evolutionary Emotion Theory in Second Language Education

    OpenAIRE

    Stern, Joseph

    2014-01-01

    After a long period of neglect, research into emotion has accelerated over the past several decades, producing many findings and theories that could be useful in educational practice. This study focuses on the most recent research into ultimate explanations of affect, which evolutionary psychology, unlike the schools of thought that currently predominate in educational theory, can provide. This study seeks to provide context for an evolutionary view of affect through a survey of emotion th...

  10. The Evolutionary Robustness of Forgiveness and Cooperation

    CERN Document Server

    Bó, Pedro Dal

    2012-01-01

    We study the evolutionary robustness of strategies in infinitely repeated prisoners' dilemma games in which players make mistakes with a small probability and are patient. The evolutionary process we consider is given by the replicator dynamics. We show that there are strategies with a uniformly large basin of attraction independently of the size of the population. Moreover, we show that those strategies forgive defections and, assuming that they are symmetric, they cooperate.

  11. The evolutionary position of turtles revised

    OpenAIRE

    Zardoya, Rafael; Meyer, Axel

    2001-01-01

    Consensus on the evolutionary position of turtles within the amniote phylogeny has eluded evolutionary biologists for more than a century. This phylogenetic problem has remained unsolved partly because turtles have such a unique morphology that only few characters can be used to link them with any other group of amniotes. Among the many alternative hypotheses that have been postulated to explain the origin and phylogenetic relationships of turtles, a general agreement among paleontologists em...

  12. Global Optimization with Hybrid Evolutionary Computation

    OpenAIRE

    Bashir, Hassan Abdullahi

    2014-01-01

    An investigation has been made into hybrid systems which include stochastic and deterministic optimization. This thesis aims to provide new and relevant insights into the design of the nature-inspired hybrid optimization paradigms. It combines evolutionary and gradient-based methods. These hybrid evolutionary methods yield improved performance when applied to complex global optimization tasks and recent research has shown many of such hybridization policies.The thesis has three broad contribu...

  13. R. A. Fisher and Evolutionary Theory

    OpenAIRE

    Karlin, Samuel

    1992-01-01

    R. A. Fisher, apart from his fundamental contributions to statistical science, fostered many developments of theoretical evolutionary science. In commemoration of Fisher's birth centenary (1991), this paper highlights several of Fisher's interests in evolutionary processes. These include the "Fundamental Theorem of Natural Selection," studies on the phenomenon of an even sex ratio in natural populations, the "runaway process" of sexual selection and models of polygenic inheritance. Some histo...

  14. Toward an Evolutionary Theory of Production

    OpenAIRE

    Winter, Sidney G.

    2002-01-01

    Production theory in the neoclassical tradition is strong on Abstract generality. Its high level of Abstraction tends to impede understanding of technological change, partly because its perspective on production differs so much from those of engineers, managers and technologists. A more grounded approach is needed for evolutionary economics, since evolutionary thinking sees questions of production as tightly and reciprocally connected with questions of coordination, incentives, and organizati...

  15. An evolutionary basis for pollination ecology

    OpenAIRE

    Willemstein, S.C.

    1987-01-01

    In the introduction and chapter 2 the incentives and way of reasoning are given for the description of an evolutionary basis of pollination ecology. Starting from the until recently rather anecdotical character of the study of pollination ecology as a whole, and in the absence of large-scale correlations of flowerecologically important character states with angiosperm and insect phylogeny (in the sense of Hennig, 1966), an attempt is made to derive directed evolutionary lines (transformation ...

  16. The evolutionary biology of child health

    OpenAIRE

    Crespi, Bernard

    2011-01-01

    I apply evolutionary perspectives and conceptual tools to analyse central issues underlying child health, with emphases on the roles of human-specific adaptations and genomic conflicts in physical growth and development. Evidence from comparative primatology, anthropology, physiology and human disorders indicates that child health risks have evolved in the context of evolutionary changes, along the human lineage, affecting the timing, growth-differentiation phenotypes and adaptive significanc...

  17. Stellar evolutionary models: uncertainties and systematics

    OpenAIRE

    Cassisi, S.

    2005-01-01

    In this last decade, our knowledge of evolutionary and structural properties of stars of different mass and chemical composition is significantly improved. This result has been achieved as a consequence of our improved capability in understanding and describing the physical behavior of stellar matter in the different thermal regimes characteristic of the different stellar mass ranges and/or evolutionary stages. This notwithstanding, current generation of stellar models is still affected by si...

  18. Hybrid evolutionary algorithms to solve scheduling problems

    OpenAIRE

    Minetti, Gabriela F.; Salto, Carolina; Bermúdez, Carlos; Fernandez, Natalia; Alfonso, Hugo; Gallard, Raúl Hector

    2002-01-01

    The choice of a search algorithm can play a vital role in the success of a scheduling application. Evolutionary algorithms (EAs) can be used to solve this kind of combinatorial optimization problems. Compared to conventional heuristics (CH) and local search techniques (LS), EAs are not well suited for fine-tuninf those structures, which are very close to optimal solutions. Therefore, in complex problems, it is essential to build hybrid evolutionary algorithms (HEA) by incorporating CH and/or ...

  19. Ecology and Evolutionary Biology of Arabidopsis

    OpenAIRE

    Pigliucci, Massimo

    2002-01-01

    Arabidopsis thaliana is now widely used as a model system in molecular and developmental biology, as well as in physiology and cell biology. However, ecologists and evolutionary biologists have turned their attention to the mouse ear cress only much more recently and almost reluctantly. The reason for this is the perception that A. thaliana is not particularly interesting ecologically and that it represents an oddity from an evolutionary standpoint. While there is some truth in both these att...

  20. An Evolutionary Account of Technological Development

    OpenAIRE

    Faghihian, Mehrdad

    2015-01-01

    If 'nothing in biology makes sense except in the light of evolution' (Theodosius Dobzhansky, 1973) , then, does nothing in technology make sense except in the light of evolution? This study will seek to construct an evolutionary account of technological development. To this end, it will consider and analyse a variety of theoretical proposals. In this thesis I will survey existing evolutionary accounts found in socio-cultural and engineering sciences, and will evaluate how these theories ...

  1. Evolutionary Music Composition: A Quantitative Approach

    OpenAIRE

    Jensen, Johannes Høydahl

    2011-01-01

    Artificial Evolution has shown great potential in the musical domain. One task in which Evolutionary techniques have shown special promise is in the automatic creation or composition of music. However, a major challenge faced when constructing evolutionary music composition systems is finding a suitable fitness function.Several approaches to fitness have been tried. The most common is interactive evaluation. However, major efficiency challenges with such an approach have inspired the search f...

  2. Derivation of evolutionary payoffs from observable behavior

    OpenAIRE

    Feigel, Alexander; Englander, Avraham; Engel, Assaf

    2008-01-01

    Interpretation of animal behavior, especially as cooperative or selfish, is a challenge for evolutionary theory. Strategy of a competition should follow from corresponding Darwinian payoffs for the available behavioral options. The payoffs and decision making processes, however, are difficult to observe and quantify. Here we present a general method for the derivation of evolutionary payoffs from observable statistics of interactions. The method is applied to combat of male bowl and doily spi...

  3. BEAST: Bayesian evolutionary analysis by sampling trees

    OpenAIRE

    Drummond Alexei J; Rambaut Andrew

    2007-01-01

    Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based m...

  4. BEAST: Bayesian evolutionary analysis by sampling trees

    OpenAIRE

    Drummond, Alexei J.; Rambaut, Andrew

    2007-01-01

    Background: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models su...

  5. Evolutionary Ecology Models of Weed Life History

    OpenAIRE

    Dekker, Jack

    2014-01-01

    The limitations of demographic models as well as the opportunities of evolutionary models are reviewed. Flaws associated with demographic models include the confounding effects of plant architecture, representation of heterogeneous individuals in populations, and changes in deme membership confounding covariance structure. Trait-based evolutionary models include FoxPatch which represents weedy Setaria spp. seed behavior with explicit life history process prediction rules and algorithms.

  6. Evolutionary freezing in a competitive population

    OpenAIRE

    Johnson, N F; Leonard, D. J. T.; Hui, P. M.; T. S. Lo(Dept. of Chemical Physics, The Weizmann Institute of Science, Rehovot, Israel)

    1999-01-01

    We show that evolution in a population of adaptive agents, repeatedly competing for a limited resource, can come to an abrupt halt. This transition from evolutionary to non-evolutionary behavior arises as the global resource level is changed, and is reminiscent of a phase transition to a frozen state. Its origin lies in the inductive decision-making of the agents, the limited global information that they possess and the dynamical feedback inherent in the system.

  7. Evolutionary Minority Games: the benefits of imitation

    OpenAIRE

    Metzler, Richard; Horn, Christian

    2002-01-01

    In the original Evolutionary Minority Game, a segregation into two populations with opposing preferences is observed under many circumstances. We show that this segregation becomes more pronounced and more robust if the dynamics are changed slightly, such that strategies with above-average fitness become more frequent. Similar effects occur also for a generalization of the EMG to more than two choices, and for evolutionary dynamics of a different stochastic strategy for the Minority Game.

  8. Stochastic evolutionary dynamics of direct reciprocity

    OpenAIRE

    Lorens A. Imhof; Nowak, Martin A.

    2009-01-01

    Evolutionary game theory is the study of frequency-dependent selection. The success of an individual depends on the frequencies of strategies that are used in the population. We propose a new model for studying evolutionary dynamics in games with a continuous strategy space. The population size is finite. All members of the population use the same strategy. A mutant strategy is chosen from some distribution over the strategy space. The fixation probability of the mutant strategy in the reside...

  9. The evolutionary emergence of pandemic influenza

    OpenAIRE

    Day, Troy; André, Jean-Baptiste; Park, Andrew

    2006-01-01

    Pandemic influenza remains a serious public health threat and the processes involved in the evolutionary emergence of pandemic influenza strains remain incompletely understood. Here, we develop a stochastic model for the evolutionary emergence of pandemic influenza, and use it to address three main questions. (i) What is the minimum annual number of avian influenza virus infections required in humans to explain the historical rate of pandemic emergence? (ii) Are such avian influenza infection...

  10. Assessment of student conceptions of evolutionary trees

    Science.gov (United States)

    Blacquiere, Luke

    Biologists use evolutionary trees to depict hypotheses about the relationships among taxa. Trees possess lines that represent lineages, internal nodes that represent where lineages become evolutionarily isolated from one another and terminal nodes that represent the taxa under consideration. Interpreting a tree (i.e., "tree-thinking") is an important skill for biologists yet many students struggle when reading evolutionary trees. Common documented misconceptions include using morphological similarity, internal node counting or terminal node proximity, instead of identifying the internal node that represents a most recent common ancestor (MRCA), to determine relationships among taxa. I developed an instrument to assess whether students were using common ancestry or another, non-scientific, strategy to determine relationships among taxa. The study is the first to explicitly test hypotheses about how students approach reading evolutionary trees. To test the hypotheses an instrument was developed. The instrument is the first reliable and valid assessment testing student understanding of how to use most recent common ancestor to interpret evolutionary relationships in tree diagrams. Instructors can use the instrument as a diagnostic tool enabling them to help students learn this challenging concept. This study shows that, contrary to the assertion that students hold misconceptions about evolutionary trees made in the literature, students do not consistently use erroneous strategies when interpreting trees. This study suggests that a constructivist perspective of cognitive structure describes students' conception of evolutionary trees more closely than a misconception perspective.

  11. Evolutionary cell biology: two origins, one objective.

    Science.gov (United States)

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

    2014-12-01

    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

  12. Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate.

    Science.gov (United States)

    Brown, Rafe M; Weghorst, Jennifer A; Olson, Karen V; Duya, Mariano R M; Barley, Anthony J; Duya, Melizar V; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A; Dominy, Nathaniel J; Ong, Perry S; Moritz, Gillian L; Luczon, Adrian; Diesmos, Mae Lowe L; Diesmos, Arvin C; Siler, Cameron D

    2014-01-01

    Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier. PMID:25136854

  13. Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.

    Science.gov (United States)

    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

  14. On exactly conservative integrators

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, J.C. [Max-Planck-Inst. fuer Plasmaphysik, Garching (Germany); Shadwick, B.A. [Univ. of California, Berkeley, CA (United States). Dept. of Physics; Morrison, P.J. [Texas Univ., Austin, TX (United States). Inst. for Fusion Studies

    1997-06-01

    Traditional explicit numerical discretizations of conservative systems generically predict artificial secular drifts of nonlinear invariants. These algorithms are based on polynomial functions of the time step. The authors discuss a general approach for developing explicit algorithms that conserve such invariants exactly. They illustrate the method by applying it to the truncated two-dimensional Euler equations.

  15. Biodiversity Conservation in Asia

    OpenAIRE

    Dale Squires

    2014-01-01

    Asian's remarkable economic growth brought many benefits but also fuelled threats to its ecosystems and biodiversity. Economic growth brings biodiversity threats but also conservation opportunities. Continued biodiversity loss is inevitable, but the types, areas and rates of biodiversity loss are not. Prioritising biodiversity conservation, tempered by what is tractable, remains a high priority. Policy and market distortions and failures significantly underprice biodiversity, undermine ecosys...

  16. Creative Soil Conservation

    Science.gov (United States)

    Smith, Martha

    2010-01-01

    Take plant lessons outdoors with this engaging and inquiry-based activity in which third-grade students learn how to apply soil conservation methods to growing plants. They also collect data and draw conclusions about the effectiveness of their method of soil conservation. An added benefit to this activity is that the third-grade students played…

  17. Conservation in transportation

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-05-30

    A nationwide examination was made of grassroots energy conservation programs related to transportation. Information compiled from civic groups, trade associations, and corporations is included on driver awareness/mass transit; travel; and ride sharing. It is concluded that a willingness by the public to cooperate in transportation energy conservation exists and should be exploited. (LCL)

  18. Introducing Conservation of Momentum

    Science.gov (United States)

    Brunt, Marjorie; Brunt, Geoff

    2013-01-01

    The teaching of the principle of conservation of linear momentum is considered (ages 15 + ). From the principle, the momenta of two masses in an isolated system are considered. Sketch graphs of the momenta make Newton's laws appear obvious. Examples using different collision conditions are considered. Conservation of momentum is considered…

  19. Evolutionary Economics, Endogenous Growth Models, and Resource-Advantage Theory

    OpenAIRE

    Shelby D. Hunt

    1997-01-01

    The gap between evolutionary and neoclassical economics remains large. This article proposed that the gap can be narrowed by evolutionary economies developing process theories that can provide evolutionary theoretical foundations for formal models in the neoclassical equilibrium tradition. This article argues that a process of competitions labeled "resource-advantage theory," can provide an evolutionary, theoretical foundation for formal models of endogenous economic growth.

  20. Paradigms for parasite conservation.

    Science.gov (United States)

    Dougherty, Eric R; Carlson, Colin J; Bueno, Veronica M; Burgio, Kevin R; Cizauskas, Carrie A; Clements, Christopher F; Seidel, Dana P; Harris, Nyeema C

    2016-08-01

    Parasitic species, which depend directly on host species for their survival, represent a major regulatory force in ecosystems and a significant component of Earth's biodiversity. Yet the negative impacts of parasites observed at the host level have motivated a conservation paradigm of eradication, moving us farther from attainment of taxonomically unbiased conservation goals. Despite a growing body of literature highlighting the importance of parasite-inclusive conservation, most parasite species remain understudied, underfunded, and underappreciated. We argue the protection of parasitic biodiversity requires a paradigm shift in the perception and valuation of their role as consumer species, similar to that of apex predators in the mid-20th century. Beyond recognizing parasites as vital trophic regulators, existing tools available to conservation practitioners should explicitly account for the unique threats facing dependent species. We built upon concepts from epidemiology and economics (e.g., host-density threshold and cost-benefit analysis) to devise novel metrics of margin of error and minimum investment for parasite conservation. We define margin of error as the risk of accidental host extinction from misestimating equilibrium population sizes and predicted oscillations, while minimum investment represents the cost associated with conserving the additional hosts required to maintain viable parasite populations. This framework will aid in the identification of readily conserved parasites that present minimal health risks. To establish parasite conservation, we propose an extension of population viability analysis for host-parasite assemblages to assess extinction risk. In the direst cases, ex situ breeding programs for parasites should be evaluated to maximize success without undermining host protection. Though parasitic species pose a considerable conservation challenge, adaptations to conservation tools will help protect parasite biodiversity in the face of

  1. MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel

    Energy Technology Data Exchange (ETDEWEB)

    Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.; Iyer, VenkyN.; Eisen, Michael B.

    2004-10-28

    We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

  2. Linkage disequilibrium of evolutionarily conserved regions in the human genome

    Directory of Open Access Journals (Sweden)

    Johnson Todd A

    2006-12-01

    Full Text Available Abstract Background The strong linkage disequilibrium (LD recently found in genic or exonic regions of the human genome demonstrated that LD can be increased by evolutionary mechanisms that select for functionally important loci. This suggests that LD might be stronger in regions conserved among species than in non-conserved regions, since regions exposed to natural selection tend to be conserved. To assess this hypothesis, we used genome-wide polymorphism data from the HapMap project and investigated LD within DNA sequences conserved between the human and mouse genomes. Results Unexpectedly, we observed that LD was significantly weaker in conserved regions than in non-conserved regions. To investigate why, we examined sequence features that may distort the relationship between LD and conserved regions. We found that interspersed repeats, and not other sequence features, were associated with the weak LD tendency in conserved regions. To appropriately understand the relationship between LD and conserved regions, we removed the effect of repetitive elements and found that the high degree of sequence conservation was strongly associated with strong LD in coding regions but not with that in non-coding regions. Conclusion Our work demonstrates that the degree of sequence conservation does not simply increase LD as predicted by the hypothesis. Rather, it implies that purifying selection changes the polymorphic patterns of coding sequences but has little influence on the patterns of functional units such as regulatory elements present in non-coding regions, since the former are generally restricted by the constraint of maintaining a functional protein product across multiple exons while the latter may exist more as individually isolated units.

  3. Transmissible cancers in an evolutionary context.

    Science.gov (United States)

    Ujvari, Beata; Papenfuss, Anthony T; Belov, Katherine

    2016-07-01

    Cancer is an evolutionary and ecological process in which complex interactions between tumour cells and their environment share many similarities with organismal evolution. Tumour cells with highest adaptive potential have a selective advantage over less fit cells. Naturally occurring transmissible cancers provide an ideal model system for investigating the evolutionary arms race between cancer cells and their surrounding micro-environment and macro-environment. However, the evolutionary landscapes in which contagious cancers reside have not been subjected to comprehensive investigation. Here, we provide a multifocal analysis of transmissible tumour progression and discuss the selection forces that shape it. We demonstrate that transmissible cancers adapt to both their micro-environment and macro-environment, and evolutionary theories applied to organisms are also relevant to these unique diseases. The three naturally occurring transmissible cancers, canine transmissible venereal tumour (CTVT) and Tasmanian devil facial tumour disease (DFTD) and the recently discovered clam leukaemia, exhibit different evolutionary phases: (i) CTVT, the oldest naturally occurring cell line is remarkably stable; (ii) DFTD exhibits the signs of stepwise cancer evolution; and (iii) clam leukaemia shows genetic instability. While all three contagious cancers carry the signature of ongoing and fairly recent adaptations to selective forces, CTVT appears to have reached an evolutionary stalemate with its host, while DFTD and the clam leukaemia appear to be still at a more dynamic phase of their evolution. Parallel investigation of contagious cancer genomes and transcriptomes and of their micro-environment and macro-environment could shed light on the selective forces shaping tumour development at different time points: during the progressive phase and at the endpoint. A greater understanding of transmissible cancers from an evolutionary ecology perspective will provide novel avenues for

  4. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Irimia, Manuel; Mørk, Søren;

    2007-01-01

    Alternative splicing (AS) is an important contributor to proteome diversity and is regarded as an explanatory factor for the relatively low number of human genes compared with less complex animals. To assess the evolutionary conservation of AS and its developmental regulation, we have investigated...... the qualitative and quantitative expression of 21 orthologous alternative splice events through the development of 2 nematode species separated by 85-110 Myr of evolutionary time. We demonstrate that most of these alternative splice events present in Caenorhabditis elegans are conserved in...... the regulatory mechanisms controlling AS are to a large extent conserved during the evolution of Caenorhabditis. This strong conservation indicates that both major and minor splice forms have important functional roles and that the relative quantities in which they are expressed are crucial. Our...

  5. Evolutionary Image Transition Based on Theoretical Insights of Random Processes

    OpenAIRE

    Neumann, Aneta; Alexander, Bradley; Neumann, Frank

    2016-01-01

    Evolutionary algorithms have been widely studied from a theoretical perspective. In particular, the area of runtime analysis has contributed significantly to a theoretical understanding and provided insights into the working behaviour of these algorithms. We study how these insights into evolutionary processes can be used for evolutionary art. We introduce the notion of evolutionary image transition which transfers a given starting image into a target image through an evolutionary process. Co...

  6. Eco-evolutionary experience in novel species interactions.

    Science.gov (United States)

    Saul, Wolf-Christian; Jeschke, Jonathan M

    2015-03-01

    A better understanding of how ecological novelty influences interactions in new combinations of species is key for predicting interaction outcomes, and can help focus conservation and management efforts on preventing the introduction of novel organisms or species (including invasive species, GMOs, synthetic organisms, resurrected species and emerging pathogens) that seem particularly 'risky' for resident species. Here, we consider the implications of different degrees of eco-evolutionary experience of interacting resident and non-resident species, define four qualitative risk categories for estimating the probability of successful establishment and impact of novel species and discuss how the effects of novelty change over time. Focusing then on novel predator-prey interactions, we argue that novelty entails density-dependent advantages for non-resident species, with their largest effects often being at low prey densities. This is illustrated by a comparison of predator functional responses and prey predation risk curves between novel species and ecologically similar resident species, and raises important issues for the conservation of endangered resident prey species. PMID:25626585

  7. Conservation by design.

    Science.gov (United States)

    Root-Bernstein, Meredith; Ladle, Richard J

    2010-10-01

    Conservation researchers are increasingly aware of the need to conduct interdisciplinary research and to engage nonscientists in practical applications of conservation biology. But so far, industrial designers have been left out of such collaboration and outreach efforts. Conservation of wildlife often depends on products such as nest boxes, feeders, barriers, and corridors, all of which have a designed component that is frequently overlooked. Furthermore, many products are adopted without testing on short or long time scales. We argue that the design of products for conservation, and hence their functionality, effectiveness, and value, can be improved through collaboration with industrial designers. We see four key benefits that can arise from interactions with industrial designers: improvement of product quality and value, innovation and improvement in functionality of products, harmonization of conservation products with local values, and development of a psychological biomimesis approach to design. The role of industrial designers in conservation projects would be to improve factors such as product durability, affordability, functionality, and aesthetic appeal to local people. Designers can also help to create multiple product options whose success can be tested in the field. We propose that collaborations with industrial designers can contribute to the development of improvements to existing products and innovations in the practice of animal conservation. PMID:20408866

  8. Building for energy conservation

    Energy Technology Data Exchange (ETDEWEB)

    O' Callaghan, P.W.

    1978-01-01

    The need to conserve energy, how energy may be saved, and thermal energy conservation in buildings are discussed in the introductory chapter. Heat gains and losses, fluid flow, convective heat transfer, and radiative heat transfer are covered in chapter 2, fundamentals. Thermal comfort, climate, heat losses from buildings, heat gains to buildings, thermal network analysis, energy thrift, secondary effects, waste heat recovery, and altenative energy sources are subjects covered in chapters 3 to 11. The final chapter, prospectus for the future, covers discussions on areas where energy should be saved, total energy, energy management, energy accounting, and practicing energy conservation. (MCW)

  9. Transport and conservation laws

    OpenAIRE

    Zotos, X.; F. Naef; Prelovsek, P.

    1996-01-01

    We study the lowest order conservation laws in one-dimensional (1D) integrable quantum many-body models (IQM) as the Heisenberg spin 1/2 chain, the Hubbard and t-J model. We show that the energy current is closely related to the first conservation law in these models and therefore the thermal transport coefficients are anomalous. Using an inequality on the time decay of current correlations we show how the existence of conserved quantities implies a finite charge stiffness (weight of the zero...

  10. Evolutionary accounts of human behavioural diversity.

    Science.gov (United States)

    Brown, Gillian R; Dickins, Thomas E; Sear, Rebecca; Laland, Kevin N

    2011-02-12

    Human beings persist in an extraordinary range of ecological settings, in the process exhibiting enormous behavioural diversity, both within and between populations. People vary in their social, mating and parental behaviour and have diverse and elaborate beliefs, traditions, norms and institutions. The aim of this theme issue is to ask whether, and how, evolutionary theory can help us to understand this diversity. In this introductory article, we provide a background to the debate surrounding how best to understand behavioural diversity using evolutionary models of human behaviour. In particular, we examine how diversity has been viewed by the main subdisciplines within the human evolutionary behavioural sciences, focusing in particular on the human behavioural ecology, evolutionary psychology and cultural evolution approaches. In addition to differences in focus and methodology, these subdisciplines have traditionally varied in the emphasis placed on human universals, ecological factors and socially learned behaviour, and on how they have addressed the issue of genetic variation. We reaffirm that evolutionary theory provides an essential framework for understanding behavioural diversity within and between human populations, but argue that greater integration between the subfields is critical to developing a satisfactory understanding of diversity. PMID:21199836

  11. Genomics in the light of evolutionary transitions.

    Science.gov (United States)

    Durand, Pierre M; Michod, Richard E

    2010-06-01

    Molecular biology has entrenched the gene as the basic hereditary unit and genomes are often considered little more than collections of genes. However, new concepts and genomic data have emerged, which suggest that the genome has a unique place in the hierarchy of life. Despite this, a framework for the genome as a major evolutionary transition has not been fully developed. Instead, genome origin and evolution are frequently considered as a series of neutral or nonadaptive events. In this article, we argue for a Darwinian multilevel selection interpretation for the origin of the genome. We base our arguments on the multilevel selection theory of hypercycles of cooperative interacting genes and predictions that gene-level trade-offs in viability and reproduction can help drive evolutionary transitions. We consider genomic data involving mobile genetic elements as a test case of our view. A new concept of the genome as a discrete evolutionary unit emerges and the gene-genome juncture is positioned as a major evolutionary transition in individuality. This framework offers a fresh perspective on the origin of macromolecular life and sets the scene for a new, emerging line of inquiry--the evolutionary ecology of the genome. PMID:19930450

  12. Evolutionary testing using an extended Chaining Approach.

    Science.gov (United States)

    McMinn, P; Holcombe, M

    2006-01-01

    Fitness functions derived from certain types of white-box test goals can be inadequate for evolutionary software test data generation (Evolutionary Testing), due to a lack of search guidance to the required test data. Often this is because the fitness function does not take into account data dependencies within the program under test, and the fact that certain program statements may need to have been executed prior to the target structure in order for it to be feasible. This paper proposes a solution to this problem by hybridizing Evolutionary Testing with an extended Chaining Approach. The Chaining Approach is a method which identifies statements on which the target structure is data dependent, and incrementally develops chains of dependencies in an event sequence. By incorporating this facility into Evolutionary Testing, and by performing a test data search for each generated event sequence, the search can be directed into potentially promising, unexplored areas of the test object's input domain. Results presented in the paper show that test data can be found for a number of test goals with this hybrid approach that could not be found by using the original Evolutionary Testing approach alone. One such test goal is drawn from code found in the publicly available libpng library. PMID:16536890

  13. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

    OpenAIRE

    Irimia, Manuel; Tena, Juan J.; Alexis, Maria S.; Fernandez-Miñan, Ana; Maeso, Ignacio; Bogdanović, Ozren; de la Calle-Mustienes, Elisa; Roy, Scott W; Gómez-Skarmeta, José L.; Fraser, Hunter B.

    2012-01-01

    The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene order is largely scrambled over evolutionary time. Only a handful of exceptional examples are known, typically involving deeply conserved clusters of tandemly duplicated genes (e.g., Hox genes and histones). Here we report the first systematic survey of microsynteny conservation across metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs of unrelated genes that have remained tight...

  14. The sequence, structure and evolutionary features of HOTAIR in mammals

    Directory of Open Access Journals (Sweden)

    Zhu Hao

    2011-04-01

    Full Text Available Abstract Background An increasing number of long noncoding RNAs (lncRNAs have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer. Results To identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and

  15. Metro Conservation Corridors

    Data.gov (United States)

    Minnesota Department of Natural Resources — The Metro Conservation Corridors (MeCC) grow out of the natural resource analysis work done by the DNR in the late '90's, documented in the Metro Greenprint...

  16. Reasons to Conserve Nature.

    Science.gov (United States)

    Pearson, Richard G

    2016-05-01

    Is it sufficient to base arguments for conservation on the intrinsic value of nature, regardless of the services and economic benefits that biodiversity provides for humans? This question underlies much recent debate that has been at times acrimonious and has led to calls for a more inclusive approach to conservation. Yet melding different ideologies within a unified conceptual framework has proven difficult. Here I describe an approach that recognizes the importance of the level of biological organization and spatial extent in determining the strength of alternative arguments for why we should conserve nature. I argue that the framework helps reconcile contrasting viewpoints and brings clarity to when different conservation management approaches (for instance, regulation versus monetary valuation) are most appropriate. PMID:26936225

  17. Landscape Conservation Cooperatives

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Landscape Conservation Cooperatives (LCCs) are public-private partnerships composed of states, tribes, federal agencies, non-governmental organizations,...

  18. Hearing Conservation Team

    Data.gov (United States)

    Federal Laboratory Consortium — The Hearing Conservation Team focuses on ways to identify the early stages of noise-induced damage to the human ear. Our current research involves the evaluation of...

  19. Evolutionary Computation Algorithms for Cryptanalysis: A Study

    CERN Document Server

    Garg, Poonam

    2010-01-01

    The cryptanalysis of various cipher problems can be formulated as NP-Hard combinatorial problem. Solving such problems requires time and/or memory requirement which increases with the size of the problem. Techniques for solving combinatorial problems fall into two broad groups - exact algorithms and Evolutionary Computation algorithms. An exact algorithms guarantees that the optimal solution to the problem will be found. The exact algorithms like branch and bound, simplex method, brute force etc methodology is very inefficient for solving combinatorial problem because of their prohibitive complexity (time and memory requirement). The Evolutionary Computation algorithms are employed in an attempt to find an adequate solution to the problem. A Evolutionary Computation algorithm - Genetic algorithm, simulated annealing and tabu search were developed to provide a robust and efficient methodology for cryptanalysis. The aim of these techniques to find sufficient "good" solution efficiently with the characteristics ...

  20. An evolutionary model with Turing machines

    CERN Document Server

    Feverati, Giovanni

    2007-01-01

    The development of a large non-coding fraction in eukaryotic DNA and the phenomenon of the code-bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code growth) the evolution of a complex code can't be attained without maintaining a large inactive fraction. To test this hypothesis we performed computer simulations of an evolutionary toy model for Turing machines, studying the relations among fitness and coding/non-coding ratio while varying mutation and code growth rates. The results suggest that, in our model, having a large reservoir of non-coding states constitutes a great (long term) evolutionary advantage.

  1. Evolutionary Population Synthesis for Single Stellar Populations

    Institute of Scientific and Technical Information of China (English)

    张奉辉; 韩占文; 李立芳; Jarrod R.Hurley

    2002-01-01

    Using the evolutionary population synthesis technique, we present the latest integrated colours for instantaneous burst single stellar populations (SSPs) of different metallicities and we investigate their colour evolution. Unlike previous research, we adopt the stellar evolutionary models that employ, amongst other things, recent opacities and a revised equation of state (EOS), and include evolutionary processes such as convective overshooting, thermal pulses and dredge-up. The models are used in the convenient form of analytical fitting functions. In addition, we use the BaSeL model for the library of stellar spectra. This model provides an extensive low-resolution theoretical flux distribution and UB VRIJHKLM colours, which have been calibrated empirically or semi-empirically, for a wide range of stellar parameters.

  2. Evolutionary tracks of massive stars during formation

    CERN Document Server

    Smith, Michael D

    2013-01-01

    A model for massive stars is constructed by piecing together evolutionary algorithms for the protostellar structure, the environment, the inflow and the radiation feedback. We investigate specified accretion histories of constant, decelerating and accelerating forms and consider both hot and cold accretion, identified with spherical free-fall and disk accretion, respectively. Diagnostic tools for the interpretation of the phases of massive star formation and testing the evolutionary models are then developed. Evolutionary tracks able to fit Herschel Space Telescope data require the generated stars to be three to four times less massive than in previous interpretations, thus being consistent with clump star formation efficiencies of $10 -- 15\\%$. However, for these cold Hershel clumps, the bolometric temperature is not a good diagnostic to differentiate between accretion models. We also find that neither spherical nor disk accretion can explain the high radio luminosities of many protostars. Nevertheless, we d...

  3. Organisations’ evolutionary dynamics: a group dynamics approach

    Directory of Open Access Journals (Sweden)

    Germán Eduardo Vargas

    2010-04-01

    Full Text Available Colombian entrepreneurs’ straggling, reactionary and inertial orientation has been inconsistently lustified by the availability of internal and leveraged resources, a concept intensifying deficient technological capacity. Company activity (seen as being a socioeconomic unit has been integrally orientated within an evolutionary framework by company identity and cohesion as well as adaptation and evolutionary mechanisms. The present document uses a group dynamics’ model to illustrate how knowledge-based strategic orientation and integration for innovation have become an imperative for development, from slight leverage, distinguishing between two evolutionary company forms: traditional economic (inertial, as they introduce sporadic incremental improvements and modern companies (dynamic and radical innovators. Revealing conclusions obtained from such model may be used for intervening in and modernising company activity.

  4. Monochromaticity in neutral evolutionary network models.

    Science.gov (United States)

    Halu, Arda; Bianconi, Ginestra

    2012-12-01

    Recent studies on epistatic networks of model organisms have unveiled a certain type of modular property called monochromaticity in which the networks are clustered into functional modules that interact with each other through the same type of epistasis. Here, we propose and study three epistatic network models that are inspired by the duplication-divergence mechanism to gain insight into the evolutionary basis of monochromaticity and to test if it can be explained as the outcome of a neutral evolutionary hypothesis. We show that the epistatic networks formed by these stochastic evolutionary models have monochromaticity conflict distributions that are centered close to zero and are statistically significantly different from their randomized counterparts. In particular, the last model we propose yields a strictly monochromatic solution. Our results agree with the monochromaticity findings in real organisms and point toward the possible role of a neutral mechanism in the evolution of this phenomenon. PMID:23367998

  5. Aerodynamic Shape Optimization using an Evolutionary Algorithm

    Science.gov (United States)

    Holst, Terry L.; Pulliam, Thomas H.; Kwak, Dochan (Technical Monitor)

    2003-01-01

    A method for aerodynamic shape optimization based on an evolutionary algorithm approach is presented and demonstrated. Results are presented for a number of model problems to access the effect of algorithm parameters on convergence efficiency and reliability. A transonic viscous airfoil optimization problem, both single and two-objective variations, is used as the basis for a preliminary comparison with an adjoint-gradient optimizer. The evolutionary algorithm is coupled with a transonic full potential flow solver and is used to optimize the inviscid flow about transonic wings including multi-objective and multi-discipline solutions that lead to the generation of pareto fronts. The results indicate that the evolutionary algorithm approach is easy to implement, flexible in application and extremely reliable.

  6. From computers to cultivation: reconceptualizing evolutionary psychology

    Directory of Open Access Journals (Sweden)

    Louise eBarrett

    2014-08-01

    Full Text Available Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behaviour, and the rigour with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated. While the framing of the current research topic places the brain-as-computer metaphor in opposition to evolutionary psychology, the most prominent school of thought in this field (born out of cognitive psychology, and often known as the Santa Barbara school is entirely wedded to the computational theory of mind as an explanatory framework. Its unique aspect is to argue that the mind consists of a large number of functionally specialized (i.e., domain-specific computational mechanisms, or modules (the massive modularity hypothesis. Far from offering an alternative to, or an improvement on, the current perspective, we argue that evolutionary psychology is a mainstream computational theory, and that its arguments for domain-specificity often rest on shaky premises. We then go on to suggest that the various forms of e-cognition (i.e., embodied, embedded, enactive represent a true alternative to standard computational approaches, with an emphasis on cognitive integration or the extended mind hypothesis in particular. We feel this offers the most promise for human psychology because it incorporates the social and historical processes that are crucial to human ‘mind-making’ within an evolutionarily-informed framework. In addition to linking to other research areas in psychology, this approach is more likely to form productive links to other disciplines within the social sciences, not least by encouraging a healthy pluralism in approach.

  7. Comparative phylogeography and population genetics within Buteo lineatus reveals evidence of distinct evolutionary lineages

    Science.gov (United States)

    Hull, J.M.; Strobel, Bradley N.; Boal, C.W.; Hull, A.C.; Dykstra, C.R.; Irish, A.M.; Fish, A.M.; Ernest, H.B.

    2008-01-01

    Traditional subspecies classifications may suggest phylogenetic relationships that are discordant with evolutionary history and mislead evolutionary inference. To more accurately describe evolutionary relationships and inform conservation efforts, we investigated the genetic relationships and demographic histories of Buteo lineatus subspecies in eastern and western North America using 21 nuclear microsatellite loci and 375-base pairs of mitochondrial control region sequence. Frequency based analyses of mitochondrial sequence data support significant population distinction between eastern (B. l. lineatus/alleni/texanus) and western (B. l. elegans) subspecies of B. lineatus. This distinction was further supported by frequency and Bayesian analyses of the microsatellite data. We found evidence of differing demographic histories between regions; among eastern sites, mitochondrial data suggested that rapid population expansion occurred following the end of the last glacial maximum, with B. l. texanus population expansion preceding that of B. l. lineatus/alleni. No evidence of post-glacial population expansion was detected among western samples (B. l. elegans). Rather, microsatellite data suggest that the western population has experienced a recent bottleneck, presumably associated with extensive anthropogenic habitat loss during the 19th and 20th centuries. Our data indicate that eastern and western populations of B. lineatus are genetically distinct lineages, have experienced very different demographic histories, and suggest management as separate conservation units may be warranted. ?? 2008 Elsevier Inc. All rights reserved.

  8. The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

    Science.gov (United States)

    Gui, Songtao; Wu, Zhihua; Zhang, Hongyuan; Zheng, Yinzhen; Zhu, Zhixuan; Liang, Dequan; Ding, Yi

    2016-01-01

    Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified, and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing, and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots. PMID:27444405

  9. Conservation Kickstart- Catalyzing Conservation Initiatives Worldwide

    Science.gov (United States)

    Treinish, G.

    2014-12-01

    Adventurers and Scientists for Conservation (ASC) is a nonprofit organization that collects environmental data to catalyze conservation initiatives worldwide. Adventure athletes have the skills and motivation to reach the most remote corners of the world. ASC utilizes those skills to provide the scientific community with data while providing the outdoor community with purpose beyond the personal high of reaching a summit or rowing across an ocean. We carefully select projects, choosing partnerships that will maximize the impact of ASC volunteers. Each project must have a clear path to a tangible conservation outcome and demonstrate a clear need for our brand of volunteers. We partner with government agencies, universities, and independant reseachers to kickstart data collection efforts around the world. Last year, through a partnership with the Olympic National Forest, 20 volunteers from the Seattle area set up and monitored camera traps in an effort to survey for costal Pacific marten. Our work led to the species' listing as "critically imperiled" with NatureServe. A partnership with the inaugural Great Pacific Race, engaging trans-Pacific rowing teams, searched for microplastics in the Pacific Ocean as part of our ongoing microplastics campaign. In a multi-year partnership with the American Prairie Reserve (APR), ASC volunteer crews live and work on the Reserve collecting wildlife data year round. The data we obtain directly informs the Reserve's wildlife management decisions. On this project, our crews have safely and effectively navigated temperature extremes from -30 degrees to 100+ degrees while traveling in a remote location. We are currently scouting projects in the Okavango Delta of Botswana and the rainforest of Suriname where we will be able to cover large amounts of area in a short periord of time. ASC is at the crossroads of the adventure and coservation science communities. Our approach of answering specific questions by using highly skilled and

  10. Lamarck and the adaptive conservation of life

    Directory of Open Access Journals (Sweden)

    Galera, Andrés

    2009-12-01

    Full Text Available This paper studies Lamarck’s evolutionary thought through four analytic elements. Firstly, Lamarckian construction of a founding evolutionary archetype. Secondly, the interpretation of nature as a material system where the organic change represents a continuous process aimed at the adaptative conservation of life. Thirdly, the definition of a genealogical process on the origin of species which identifies the natural method. Fourthly, the redefinition of the concept of species applying the arguments of temporary relativity and individual instability.

    En este artículo se estudia el ideario evolucionista lamarckiano desarrollando cuatro elementos analíticos. Primero, la elaboración de un arquetipo evolutivo fundacional. Segundo, la interpretación de la naturaleza como un sistema material donde el cambio orgánico da sentido a un proceso continuo dirigido a la conservación de la vida. Tercero, la definición de un principio genealógico sobre el origen de las especies que identifica el método natural. Cuarto, la reformulación del concepto de especie utilizando los argumentos de relatividad temporal e inestabilidad individual.

  11. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  12. Human Resource Ecosystem and its evolutionary rules

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The Paper,based on the concept and the elements of human resource ecosystem(HR Ecosystem),studies the function and structure of HR Ecosystem,introduces the entropy theory to define the content of entropy of HR Ecosystem,constructs the corresponding distinctive model to distinguish the direction of the evolution of HR Ecosystem and the evolutionary entropy model, and applies the models to demonstrate the evolutionary rules of HR Ecosystem.The study shows that the entropy theory can be well applied to the analysis on HR Ecosystem and that it opens up a new field in the research of human resource management and provides a new effective technical method.

  13. Evolutionary strategy for achieving autonomous navigation

    Science.gov (United States)

    Gage, Douglas W.

    1999-01-01

    An approach is presented for the evolutionary development of supervised autonomous navigation capabilities for small 'backpackable' ground robots, in the context of a DARPA- sponsored program to provide robotic support to small units of dismounted warfighters. This development approach relies on the implementation of a baseline visual serving navigation capability, including tools to support operator oversight and override, which is then enhanced with semantically referenced commands and a mission scripting structure. As current and future machine perception techniques are able to automatically designate visual serving goal points, this approach should provide a natural evolutionary pathway to higher levels of autonomous operation and reduced requirements for operator intervention.

  14. Still doing evolutionary algorithms with Perl

    OpenAIRE

    Guervos, Juan J. Merelo

    2009-01-01

    Algorithm::Evolutionary (A::E from now on) was introduced in 2002, after a talk in YAPC::EU in Munich. 7 years later, A::E is in its 0.67 version (past its "number of the beast" 0.666), and has been used extensively, to the point of being the foundation of much of the (computer) science being done by our research group (and, admittedly, not many others). All is not done, however; now A::E is being integrated with POE so that evolutionary algorithms (EAs) can be combined with all kinds of serv...

  15. Comparative and evolutionary insights into CD4 gene across mammalian and avian taxa.

    Science.gov (United States)

    Khan, Naazneen

    2015-12-01

    The present day genetic architecture of a species bears much significance to its closely related species which is due to species-specific differences, shaped by different evolutionary forces across time scale. With the availability of whole genome sequence of several closely related species, it is now possible to infer evolutionary patterns of genes and genomes in specific lineages. To this respect, CD4 gene, primarily responsible for defensive mechanism in human, is conserved across a few taxa, and thus, comparative genomic studies could be useful for better understanding of host-pathogen biology. Comparative and evolutionary analyses were performed in eleven taxa (10 mammalian and avian) with different statistical algorithms. Phylogenetic inferences revealed recent divergence of human and chimpanzee, and pig was found to be diverged from rest of the taxa significantly. Additionally, gene length, microsatellites, and secondary structures were observed across taxa. The genetic architecture of CD4 gene and its evolutionary history in different mammalian taxa provide crucial evidence in support of the fact that this gene might have been evolving at a similar rate to other human immune system genes. Future population-based study and structural modeling would unravel the differential ability to interact with HIV virus and influence immune system in humans. PMID:26767121

  16. Exploring the evolutionary rate differences between human disease and non-disease genes.

    Science.gov (United States)

    Chakraborty, Sandip; Panda, Arup; Ghosh, Tapash Chandra

    2016-07-01

    Comparisons of evolutionary features between human disease and non-disease genes have a wide implication to understand the genetic basis of human disease genes. However, it has not yet been resolved whether disease genes evolve at slower or faster rate than the non-disease genes. To resolve this controversy, here we integrated human disease genes from several databases and compared their protein evolutionary rates with non-disease genes in both housekeeping and tissue-specific group. We noticed that in tissue specific group, disease genes evolve significantly at a slower rate than non-disease genes. However, we found no significant difference in evolutionary rates between disease and non-disease genes in housekeeping group. Tissue specific disease genes have a higher protein complex number, elevated gene expression level and are also associated with conserve biological processes. Finally, our regression analysis suggested that protein complex number followed by protein multifunctionality independently modulates the evolutionary rate of human disease genes. PMID:26562439

  17. Conservation of Hox gene clusters in the self-fertilizing fish Kryptolebias marmoratus (Cyprinodontiformes; Rivulidae).

    Science.gov (United States)

    Kim, B-M; Lee, B-Y; Lee, J-H; Rhee, J-S; Lee, J-S

    2016-03-01

    In this study, whole Hox gene clusters in the self-fertilizing mangrove killifish Kryptolebias marmoratus (Cyprinodontiformes; Rivulidae), a unique hermaphroditic vertebrate in which both sex organs are functional at the same time, were identified from whole genome and transcriptome sequences. The aim was to increase the understanding of the evolutionary status of conservation of this Hox gene cluster across fish species. PMID:26822496

  18. Conserved sex chromosomes across adaptively radiated Anolis lizards.

    Science.gov (United States)

    Rovatsos, Michail; Altmanová, Marie; Pokorná, Martina; Kratochvíl, Lukáš

    2014-07-01

    Vertebrates possess diverse sex-determining systems, which differ in evolutionary stability among particular groups. It has been suggested that poikilotherms possess more frequent turnovers of sex chromosomes than homoiotherms, whose effective thermoregulation can prevent the emergence of the sex reversals induced by environmental temperature. Squamate reptiles used to be regarded as a group with an extensive variability in sex determination; however, we document how the rather old radiation of lizards from the genus Anolis, known for exceptional ecomorphological variability, was connected with stability in sex chromosomes. We found that 18 tested species, representing most of the phylogenetic diversity of the genus, share the gene content of their X chromosomes. Furthermore, we discovered homologous sex chromosomes in species of two genera (Sceloporus and Petrosaurus) from the family Phrynosomatidae, serving here as an outgroup to Anolis. We can conclude that the origin of sex chromosomes within iguanas largely predates the Anolis radiation and that the sex chromosomes of iguanas remained conserved for a significant part of their evolutionary history. Next to therian mammals and birds, Anolis lizards therefore represent another adaptively radiated amniote clade with conserved sex chromosomes. We argue that the evolutionary stability of sex-determining systems may reflect an advanced stage of differentiation of sex chromosomes rather than thermoregulation strategy. PMID:24433436

  19. An intertwined evolutionary history of methanogenic archaea and sulfate reduction.

    Directory of Open Access Journals (Sweden)

    Dwi Susanti

    Full Text Available Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F(420-dependent sulfite reductase (Fsr where N- and C-terminal halves (Fsr-N and Fsr-C are homologs of F(420H(2 dehydrogenase and dissimilatory sulfite reductase (Dsr, respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP, both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest, carrying a coupled siroheme-[Fe(4-S(4] cluster and sulfite-binding Arg/Lys residues; Group III (most complex, with group I features, a Dsr-type peripheral [Fe(4-S(4] cluster and an additional [Fe(4-S(4] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe(4-S(4] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F(420H(2 dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago biologically produced sulfide deposit.

  20. Evolutionary history of the iroquois/Irx genes in metazoans

    Directory of Open Access Journals (Sweden)

    Ikmi Aissam

    2009-04-01

    Full Text Available Abstract Background The iroquois (iro/Irx genes encode transcriptional regulators that belong to the TALE superclass of homeodomain proteins and have key functions during development in both vertebrates and insects. The Irx genes occur in one or two genomic clusters containing three genes each within the Drosophila and several vertebrate genomes, respectively. The similar genomic organization in Drosophila and vertebrates is widely considered as a result of convergent evolution, due to independent tandem gene duplications. In this study, we investigate the evolutionary history of the Irx genes at the scale of the whole metazoan kingdom. Results We identified in silico the putative full complement of Irx genes in the sequenced genomes of 36 different species representative of the main metazoan lineages, including non bilaterian species, several arthropods, non vertebrate chordates, and a basal vertebrate, the sea lamprey. We performed extensive phylogenetic analyses of the identified Irx genes and defined their genomic organizations. We found that, in most species, there are several Irx genes, these genes form two to four gene clusters, and the Irx genes are physically linked to a structurally and functionally unrelated gene known as CG10632 in Drosophila. Conclusion Three main conclusions can be drawn from our study. First, an Irx cluster composed of two genes, araucan/caupolican and mirror, is ancestral to the crustaceans+insects clade and has been strongly conserved in this clade. Second, three Irx genes were probably present in the last common ancestor of vertebrates and the duplication that has given rise to the six genes organized into two clusters found in most vertebrates, likely occurred in the gnathostome lineage after its separation from sea lampreys. Third, the clustered organization of the Irx genes in various evolutionary lineages may represent an exceptional case of convergent evolution or may point to the existence of an Irx gene

  1. The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic

    Directory of Open Access Journals (Sweden)

    Silberman Jeffrey D

    2006-11-01

    Full Text Available Abstract Background Glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. The glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. However, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and sometimes involve lateral gene transfer events. We have conducted an expressed sequence tag (EST survey of the anaerobic flagellate Trimastix pyriformis to investigate the nature of the evolutionary origins of the glycolytic enzymes in this relatively unstudied organism. Results We have found genes in the Trimastix EST data that encode enzymes potentially catalyzing nine of the ten steps of the glycolytic conversion of glucose to pyruvate. Furthermore, we have found two different enzymes that in principle could catalyze the conversion of phosphoenol pyruvate (PEP to pyruvate (or the reverse reaction as part of the last step in glycolysis. Our phylogenetic analyses of all of these enzymes revealed at least four cases where the relationship of the Trimastix genes to homologs from other species is at odds with accepted organismal relationships. Although lateral gene transfer events likely account for these anomalies, with the data at hand we were not able to establish with confidence the bacterial donor lineage that gave rise to the respective Trimastix enzymes. Conclusion A number of the glycolytic enzymes of Trimastix have been transferred laterally from bacteria instead of being inherited from the last common eukaryotic ancestor. Thus, despite widespread conservation of the glycolytic biochemical pathway across eukaryote diversity, in a number of protist lineages the enzymatic components of the pathway have been replaced by lateral gene transfer from disparate evolutionary sources. It remains unclear if these replacements result from selectively advantageous properties of the introduced enzymes or if they are neutral

  2. Hydrology and Conservation Ecology

    Science.gov (United States)

    Narayanan, M.

    2006-12-01

    Responses to change in the behavior of ecological systems are largely governed by interactions at different levels. Research is essential and is to be necessarily designed to gain insights into various interactions at the community level. Sustainable resource management is only possible if conservation of biodiversity can be accomplished by properly using the knowledge discovered. It is well known that the United States Department of Agriculture provides technical information, resources, and data necessary to assist the researchers in addressing their conservation needs. Conservation aims to protect, preserve and conserve the earth's natural resources. These include, but not limited to the conservation of soil, water, minerals, air, plants and all living beings. The United States Department of Agriculture also encourages farmers and ranchers to voluntarily address threats to soil and water. Protection of wetlands and wildlife habitat has been on the radar screen of conservation experts for a very long time. The main objective has always been to help farmers and landowners conform and comply with federal and state environmental laws. During the implementation phase, farmers should be encouraged to make beneficial, cost-effective changes to methods of irrigation systems. In some cases, the hydrologic regime of the project area can be thought of as principally an issue of river flow regimes for floodplain forests. In this presentation, the author tries to focus on the impact of hydrology and conservation ecology on global warming. He also discusses the impact of hydrology and conservation ecology global air concerns such as greenhouse gas concentrations in the atmosphere. References: Chow, V. T, D. R. Maidment, and L. W. Mays. 1988. Applied Hydrology. McGraw-Hill, Inc. U.S. Soil Conservation Service. Technical Release 55: Urban Hydrology for Small Watersheds. USDA (U.S. Department of Agriculture). June 1986. Lehner, B. and P. Döll (2004). Development and validation

  3. The Data Conservancy

    Science.gov (United States)

    Choudhury, S.; Duerr, R. E.

    2009-12-01

    NSF's Sustainable Digital Data Preservation and Access Network Partners program is an ambitious attempt to integrate a wide variety of expertise and infrastructure into a network for providing "reliable digital preservation, access, integration, and analysis capabilities for science." One of the first two DataNet award recipients, the Data Conservancy, is itself a network of widely diverse partners led by the libraries at the Johns Hopkins University. The Data Conservancy is built on existing exemplar scientific projects, communities, and virtual organizations that have deep engagement with their user communities, and extensive experience with large-scale distributed system development. Data Conservancy members embrace a shared vision that data curation is not an end, but rather a means to collect, organize, validate, and preserve data needed to address the grand research challenges that face society. Data Conservancy members holdings encompass the entire range of earth, life, and space science data. New to the Data Conservancy is the concept that University libraries will be part of the distributed network of data centers and that data science will become a path in the library and information science curricula. As noted by Winston Tabb (JHU Dean of Libraries) "Data Centers are the new library stacks."

  4. Creative Conservation Communication

    Science.gov (United States)

    Houston, Jason

    2015-04-01

    I am a fellow with the International League of Conservation photographers (iLCP) and have been focused on photographing conservation dynamics at the intersection of social and environmental issues for a decade. Subjects have included traditional concerns such as deforestation, water conservation, endangered species, and fisheries. However, I rarely make photographs of the traditional nature, wildlife, landscapes, or environmental atrocities that most people think of when they think about environmentalism. Instead, I photograph people and how they live on the planet, as I believe passionately that without also considering social and cultural concerns, we will not be able to effectively and sustainably do conservation work or achieve positive environmental change. My presentation will share recent photography projects on forest conservation in Indonesian Borneo and fisheries management in Central America where I used a 'stakeholder profile-based' process to broadly survey the complexity of the issues while also making personal connections for these projects' diverse audiences. Through these case studies I will explore the opportunities and challenges of combining the authenticity, accuracy, and scientific validity of journalistic and documentary work with the emotional impact of the conventions of art and storytelling.

  5. Evolutionary Biology: Its Value to Society

    Science.gov (United States)

    Carson, Hampton L.

    1972-01-01

    Cites examples of the contribution of basic research in evolutionary biology to the solution of problems facing society (1) by dispelling myths about human origins, the nature of the individual, and the nature of race (2) by providing basic data concerning the effects of overpopulation, the production of improved sources of food, resistance of…

  6. Evolutionary minority game with heterogeneous strategy distribution

    OpenAIRE

    Lo, T. S.; Lim, S W; Hui, P. M.; Johnson, N. F.

    2000-01-01

    We present detailed numerical results for a modified form of the so-called Minority Game, which provides a simplified model of a competitive market. Each agent has a limited set of strategies, and competes to be in a minority. An evolutionary rule for strategy modification is included to mimic simple learning. The results can be understood by considering crowd formation within the population.

  7. On the Evolutionary Bases of Consumer Reinforcement

    Science.gov (United States)

    Nicholson, Michael; Xiao, Sarah Hong

    2010-01-01

    This article locates consumer behavior analysis within the modern neo-Darwinian synthesis, seeking to establish an interface between the ultimate-level theorizing of human evolutionary psychology and the proximate level of inquiry typically favored by operant learning theorists. Following an initial overview of the central tenets of neo-Darwinism,…

  8. Evolutionary optimization of production materials workflow processes

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter;

    2014-01-01

    We present an evolutionary optimisation technique for stochastic production processes, which is able to find improved production materials workflow processes with respect to arbitrary combinations of numerical quantities associated with the production process. Working from a core fragment of the ...... where a baked goods company seeks to improve production time while simultaneously minimising the cost and use of resources....

  9. Boosted Neural Networks in Evolutionary Computation

    Czech Academy of Sciences Publication Activity Database

    Holeňa, Martin; Linke, D.; Steinfeldt, N.

    Bangkok : King Mongkut's University of Technology Thonburi, 2009. s. 225-226. [ICONIP 2009. International Conference on Neural Information Processing /16./. 01.12.2009-05.12.2009, Bangkok] Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary algorithms * empirical objective functions * surrogate modelling * surrogate modelling * artificial neural networks * boosting Subject RIV: IN - Informatics, Computer Science

  10. College Students' Misconceptions about Evolutionary Trees

    Science.gov (United States)

    Meir, Eli; Perry, Judy; Herron, Jon C.; Kingsolver, Joel

    2007-01-01

    Evolution is at the center of the biological sciences and is therefore a required topic for virtually every college biology student. Over the past year, the authors have been building a new simulation software package called EvoBeaker to teach college-level evolutionary biology through simulated experiments. They have built both micro and…

  11. Using Human Evolution to Teach Evolutionary Theory

    Science.gov (United States)

    Besterman, Hugo; La Velle, Linda Baggott

    2007-01-01

    This paper discusses some traditional approaches to the teaching of evolutionary theory at pre-university level, criticising in particular some of the more commonly used models and exemplars. Curricular demands are described and an alternative approach is suggested, using the emerging story of human evolution. Recent discoveries help to illustrate…

  12. Evolutionary theory and the naturalist fallacy

    DEFF Research Database (Denmark)

    Grodal, Torben Kragh

    2008-01-01

    that great work of art are also automatically fitness-enhancing in the present day environment, at that there are simple correllations between whether a work of art has a high aesthetic value and whether it is fitness-enhancing or not.  Keywords :  Evolutionary aesthetics, film theory, literary theory...

  13. Reconstructing the evolutionary history of natural languages

    Energy Technology Data Exchange (ETDEWEB)

    Warnow, T.; Ringe, D.; Taylor, A. [Univ. of Pennsylvania, Philadelphia, PA (United States)

    1996-12-31

    In this paper we present a new methodology for determining the evolutionary history of related languages. Our methodology uses linguistic information encoded as qualitative characters, and provides much greater precision than previous methods. Our analysis of Indo-European (IE) languages resolves questions that have troubled scholars for over a century.

  14. 2004 Structural, Function and Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  15. A Clustal Alignment Improver Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene; Fogel, Gary B.; Krink, Thimo

    2002-01-01

    Multiple sequence alignment (MSA) is a crucial task in bioinformatics. In this paper we extended previous work with evolutionary algorithms (EA) by using MSA solutions obtained from the wellknown Clustal V algorithm as a candidate solution seed of the initial EA population. Our results clearly sh...

  16. Indigenous Knowledge, Ecology, and Evolutionary Biology

    OpenAIRE

    E. N. Anderson

    2011-01-01

    Review of Indigenous Knowledge, Ecology, and Evolutionary Biology. Raymond Pierotti. 2011. Routledge (Taylor & Francis Group), New York.  Pp. Xv + 264, Bibliography, index.  ISBN13: 978-0-415-87924-8 (hbk), 978-0-203-84711-4 (ebk).

  17. Teaching about Adaptation: Why Evolutionary History Matters

    Science.gov (United States)

    Kampourakis, Kostas

    2013-01-01

    Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to…

  18. Gypsy dragon: An evolutionary approach to narratives

    OpenAIRE

    Čvorović Jelena

    2007-01-01

    This paper will attempt to explain Serbian Gypsy oral narratives by applying concepts drawn from evolutionary psychology. The Gypsy story will illustrate how various narrative characteristics are used by Gypsies to employ social knowledge on local surroundings to better serve fitness solutions.

  19. Evolutionary Psychology: Controversies, Questions, Prospects, and Limitations

    Science.gov (United States)

    Confer, Jaime C.; Easton, Judith A.; Fleischman, Diana S.; Goetz, Cari D.; Lewis, David M. G.; Perilloux, Carin; Buss, David M.

    2010-01-01

    Evolutionary psychology has emerged over the past 15 years as a major theoretical perspective, generating an increasing volume of empirical studies and assuming a larger presence within psychological science. At the same time, it has generated critiques and remains controversial among some psychologists. Some of the controversy stems from…

  20. On evolutionary ray-projection dynamics

    NARCIS (Netherlands)

    Joosten, Reinoud; Roorda, Berend

    2011-01-01

    We introduce the ray-projection dynamics in evolutionary game theory by employing a ray projection of the relative fitness (vector) function, i.e., a projection unto the unit simplex along a ray through the origin. Ray-projection dynamics are weakly compatible in the terminology of Friedman (Econome

  1. Haplogroups as Evolutionary Markers of Cognitive Ability

    Science.gov (United States)

    Rindermann, Heiner; Woodley, Michael A.; Stratford, James

    2012-01-01

    Studies investigating evolutionary theories on the origins of national differences in intelligence have been criticized on the basis that both national cognitive ability measures and supposedly evolutionarily informative proxies (such as latitude and climate) are confounded with general developmental status. In this study 14 Y chromosomal…

  2. Evolutionary testing of object-oriented software

    NARCIS (Netherlands)

    L.S. Silva; M. van Someren

    2010-01-01

    It is estimated that 80% of software development cost is spent on detecting and fixing defects. To tackle this issue, a number of tools and testing techniques have been developed to improve the existing testing framework. Although techniques such as static analysis, random testing and evolutionary t

  3. BEAST: Bayesian evolutionary analysis by sampling trees

    Directory of Open Access Journals (Sweden)

    Drummond Alexei J

    2007-11-01

    Full Text Available Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

  4. Indoor Thermal Comfort, an Evolutionary Biology Perspective

    Energy Technology Data Exchange (ETDEWEB)

    Stoops, John L.

    2006-04-15

    As is becoming increasingly clear, the human species evolvedin the East African savannah. Details of the precise evolutionary chainremain unresolved however it appears that the process lasted severalmillion years, culminating with the emergence of modern Homo sapiensroughly 200,000 years ago. Following that final evolutionary developmentmodern Homo sapiens relatively quickly populated the entire world.Clearly modern Homo sapiens is a successful, resourceful and adaptablespecies. In the developed societies, modern humans live an existence farremoved from our evolutionary ancestors. As we have learned over the lastcentury, this "new" lifestyle can often result in unintendedconsequences. Clearly, our modern access to food, shelter, transportationand healthcare has resulted in greatly expanded expected lifespan butthis new lifestyle can also result in the emergence of different kinds ofdiseases and health problems. The environment in modern buildings haslittle resemblance to the environment of the savannah. We strive tocreate environments with little temperature, air movement and lightvariation. Building occupants often express great dissatisfaction withthese modern created environments and a significant fraction even developsomething akin to allergies to specific buildings (sick buildingsyndrome). Are the indoor environments we are creating fundamentallyunhealthy -- when examined from an evolutionary perspective?

  5. Evolutionary optimization of cooperative heterogeneous teams

    Science.gov (United States)

    Soule, Terence; Heckendorn, Robert B.

    2007-04-01

    There is considerable interest in developing teams of autonomous, unmanned vehicles that can function in hostile environments without endangering human lives. However, heterogeneous teams, teams of units with specialized roles and/or specialized capabilities, have received relatively little attention. Specialized roles and capabilities can significantly increase team effectiveness and efficiency. Unfortunately, developing effective cooperation mechanisms is much more difficult in heterogeneous teams. Units with specialized roles or capabilities require specialized software that take into account the role and capabilities of both itself and its neighbors. Evolutionary algorithms, algorithms modeled on the principles of natural selection, have a proven track record in generating successful teams for a wide variety of problem domains. Using classification problems as a prototype, we have shown that typical evolutionary algorithms either generate highly effective teams members that cooperate poorly or poorly performing individuals that cooperate well. To overcome these weaknesses we have developed a novel class of evolutionary algorithms. In this paper we apply these algorithms to the problem of controlling simulated, heterogeneous teams of "scouts" and "investigators". Our test problem requires producing a map of an area and to further investigate "areas of interest". We compare several evolutionary algorithms for their ability to generate individually effective members and high levels of cooperation.

  6. Evolutionary Computation Applications in Current Bioinformatics

    OpenAIRE

    Wang, Bing; Zhang, Xiang

    2010-01-01

    This chapter provides an overview of some bioinformatics tasks and the relevance of the evolutionary computation methods, especially GAs. There are two advantages of GA-based approaches. One is that GAs are easier to run in parallel than single trajectory search procedures, and therefore allow groups of processors to be utilized for a search. The other is

  7. Static and evolutionary quantum public goods games

    Science.gov (United States)

    Liao, Zeyang; Qin, Gan; Hu, Lingzhi; Li, Songjian; Xu, Nanyang; Du, Jiangfeng

    2008-05-01

    We apply the continuous-variable quantization scheme to quantize public goods game and find that new pure strategy Nash equilibria emerge in the static case. Furthermore, in the evolutionary public goods game, entanglement can also contribute to the persistence of cooperation under various population structures without altruism, voluntary participation, and punishment.

  8. Molecular selection in a unified evolutionary sequence

    Science.gov (United States)

    Fox, S. W.

    1986-01-01

    With guidance from experiments and observations that indicate internally limited phenomena, an outline of unified evolutionary sequence is inferred. Such unification is not visible for a context of random matrix and random mutation. The sequence proceeds from Big Bang through prebiotic matter, protocells, through the evolving cell via molecular and natural selection, to mind, behavior, and society.

  9. Evolutionary Algorithms for Boolean Queries Optimization

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Snášel, Václav; Neruda, Roman; Owais, S.S.J.; Krömer, P.

    2006-01-01

    Roč. 3, č. 1 (2006), s. 15-20. ISSN 1790-0832 R&D Projects: GA AV ČR 1ET100300414 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary algorithms * genetic algorithms * information retrieval * Boolean query Subject RIV: BA - General Mathematics

  10. An evolutionary basis for pollination ecology

    NARCIS (Netherlands)

    Willemstein, S.C.

    1987-01-01

    In the introduction and chapter 2 the incentives and way of reasoning are given for the description of an evolutionary basis of pollination ecology. Starting from the until recently rather anecdotical character of the study of pollination ecology as a whole, and in the absence of large-scale correla

  11. Testing for Independence between Evolutionary Processes.

    Science.gov (United States)

    Behdenna, Abdelkader; Pothier, Joël; Abby, Sophie S; Lambert, Amaury; Achaz, Guillaume

    2016-09-01

    Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens. PMID:27208890

  12. Evolutionary Stability in the Traveler's Dilemma

    Science.gov (United States)

    Barker, Andrew T.

    2009-01-01

    The traveler's dilemma is a generalization of the prisoner's dilemma which shows clearly a paradox of game theory. In the traveler's dilemma, the strategy chosen by analysis and theory seems obviously wrong intuitively. Here we develop a measure of evolutionary stability and show that the evolutionarily stable equilibrium is in some sense not very…

  13. Knowledge Guided Evolutionary Algorithms in Financial Investing

    Science.gov (United States)

    Wimmer, Hayden

    2013-01-01

    A large body of literature exists on evolutionary computing, genetic algorithms, decision trees, codified knowledge, and knowledge management systems; however, the intersection of these computing topics has not been widely researched. Moving through the set of all possible solutions--or traversing the search space--at random exhibits no control…

  14. Diversity-Based Adaptive Evolutionary Algorithms

    OpenAIRE

    Jr., Maury Meirelles Gouvêa; Araújo, Aluizio Fausto Ribeiro

    2010-01-01

    This paper presented a survey about diversity-based evolutionary algorithms. Two sets of models were presented, one to minimize the diversity loss and another to control the population diversity based on a desired diversity range or level. The problem of the inappropriate level of diversity with respect to the environment and its dynamic can be

  15. QDist—Quartet Distance Between Evolutionary Trees

    DEFF Research Database (Denmark)

    Mailund; Pedersen, Christian N. Storm

    2004-01-01

    QDist is a program for computing the quartet distance between two unrooted evolutionary trees, i.e. the number of quartet topology differences between the two trees, where a quartet topology is the topological subtree induced by four species. The implementation is based on an algorithm with running...

  16. The evolutionary advantage of diploid sex

    OpenAIRE

    Sousa, A.O.; de Oliveira, S. Moss; Martins, J. S. Sa

    2002-01-01

    We modify the Penna Model for biological aging, which is based on the mutation-accumulation theory, in order to verify if there would be any evolutionary advantage of triploid over diploid organisms. We show that this is not the case, and that usual sex is always better than that involving three individuals.

  17. Probing the evolutionary history of epigenetic mechanisms: what can we learn from marine diatoms

    Directory of Open Access Journals (Sweden)

    Achal Rastogi

    2015-07-01

    Full Text Available Recent progress made on epigenetic studies revealed the conservation of epigenetic features in deep diverse branching species including Stramenopiles, plants and animals. This suggests their fundamental role in shaping species genomes across different evolutionary time scales. Diatoms are a highly successful and diverse group of phytoplankton with a fossil record of about 190 million years ago. They are distantly related from other super-groups of Eukaryotes and have retained some of the epigenetic features found in mammals and plants suggesting their ancient origin. Phaeodactylum tricornutum and Thalassiosira pseudonana, pennate and centric diatoms, respectively, emerged as model species to address questions on the evolution of epigenetic phenomena such as what has been lost, retained or has evolved in contemporary species. In the present work, we will discuss how the study of non-model or emerging model organisms, such as diatoms, helps understand the evolutionary history of epigenetic mechanisms with a particular focus on DNA methylation and histone modifications.

  18. In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer

    Energy Technology Data Exchange (ETDEWEB)

    Poulin, Francis; Nobrega, Marcelo A.; Plajzer-Frick, Ingrid; Holt, Amy; Afzal, Veena; Rubin, Edward M.; Pennacchio, Len

    2004-10-01

    Genomic sequence comparisons between human, mouse and pufferfish (Takifugu rubripes (Fugu))have revealed a set of extremely conserved noncoding sequences. While this high degree of sequence conservation suggests severe evolutionary constraint and predicts a lack of tolerance to change in order to retain in vivo functionality, such elements have been minimally explored experimentally. In this study, we describe the in-depth characterization of an ancient conserved enhancer, Dc2 located near the dachshund gene, which displays a human-Fugu identity of 84 percent over 424 basepairs (bp). In addition to this large overall conservation, we find that Dc2 is characterized by the presence of a large block of sequence (144 bp) that is completely identical between human, mouse, chicken, zebrafish and Fugu. Through the testing of reporter vector constructs in transgenic mice, we observed that the 424 bp Dc2 conserved element is necessary and sufficient for brain tissue enhancer activity. In vivo analyses also revealed that the 144 bp 100 percent conserved sequence is necessary, but not sufficient, to replicate Dc2 enhancer function. However, the introduction of two separate 16 bp insertions into the highly conserved enhancer core did not cause any detectable modification of its in vivo activity. Our observations indicate that the 144 bp 100 percent conserved element is tolerant of change at least at the resolution of this transgenic mouse assay and suggest that purifying selection on Dc2 sequence might not be as strong as we predicted or that some unknown property also constrains this highly conserved enhancer sequence.

  19. CASSIOPE: An expert system for conserved regions searches

    Directory of Open Access Journals (Sweden)

    Grusea Simona

    2009-09-01

    Full Text Available Abstract Background Understanding genome evolution provides insight into biological mechanisms. For many years comparative genomics and analysis of conserved chromosomal regions have helped to unravel the mechanisms involved in genome evolution and their implications for the study of biological systems. Detection of conserved regions (descending from a common ancestor not only helps clarify genome evolution but also makes it possible to identify quantitative trait loci (QTLs and investigate gene function. The identification and comparison of conserved regions on a genome scale is computationally intensive, making process automation essential. Three key requirements are necessary: consideration of phylogeny to identify orthologs between multiple species, frequent updating of the annotation and panel of compared genomes and computation of statistical tests to assess the significance of identified conserved gene clusters. Results We developed a modular system superimposed on a multi-agent framework, called CASSIOPE (Clever Agent System for Synteny Inheritance and Other Phenomena in Evolution. CASSIOPE automatically identifies statistically significant conserved regions between multiple genomes based on automated phylogenies and statistical testing. Conserved regions were searched for in 19 species and 1,561 hits were found. To our knowledge, CASSIOPE is the first system to date that integrates evolutionary biology-based concepts and fulfills all three key requirements stated above. All results are available at http://194.57.197.245/cassiopeWeb/displayCluster?clusterId=1 Conclusion CASSIOPE makes it possible to study conserved regions from a chosen query genetic region and to infer conserved gene clusters based on phylogenies and statistical tests assessing the significance of these conserved regions. Source code is freely available, please contact: Pierre.pontarotti@univ-provence.fr

  20. Evolutionary Optimization of a Quadrifilar Helical Antenna

    Science.gov (United States)

    Lohn, Jason D.; Kraus, William F.; Linden, Derek S.; Clancy, Daniel (Technical Monitor)

    2002-01-01

    Automated antenna synthesis via evolutionary design has recently garnered much attention in the research literature. Evolutionary algorithms show promise because, among search algorithms, they are able to effectively search large, unknown design spaces. NASA's Mars Odyssey spacecraft is due to reach final Martian orbit insertion in January, 2002. Onboard the spacecraft is a quadrifilar helical antenna that provides telecommunications in the UHF band with landed assets, such as robotic rovers. Each helix is driven by the same signal which is phase-delayed in 90 deg increments. A small ground plane is provided at the base. It is designed to operate in the frequency band of 400-438 MHz. Based on encouraging previous results in automated antenna design using evolutionary search, we wanted to see whether such techniques could improve upon Mars Odyssey antenna design. Specifically, a co-evolutionary genetic algorithm is applied to optimize the gain and size of the quadrifilar helical antenna. The optimization was performed in-situ in the presence of a neighboring spacecraft structure. On the spacecraft, a large aluminum fuel tank is adjacent to the antenna. Since this fuel tank can dramatically affect the antenna's performance, we leave it to the evolutionary process to see if it can exploit the fuel tank's properties advantageously. Optimizing in the presence of surrounding structures would be quite difficult for human antenna designers, and thus the actual antenna was designed for free space (with a small ground plane). In fact, when flying on the spacecraft, surrounding structures that are moveable (e.g., solar panels) may be moved during the mission in order to improve the antenna's performance.