WorldWideScience

Sample records for adaptive evolution hotspots

  1. The evolution of hotspots on Earth and Venus

    Full text: Selected hotspots on Earth and Venus, sister planet to Earth due to similarities in size, gravity and bulk composition, are analyzed. Despite those similarities, several differences, such as the lack of water, the absence of plate tectonics, and a low degree of erosion affect Venusian mantle plumes with respect to their structure and dimension, their surface manifestation and their role in the heat budget of the planet Venus. Special attention will be paid to the magmatic output over the time. (author)

  2. Xplorelab Hotspot Zuidplaspolder. Climate Adaptation in the Zuidplaspolder. Final report

    The Zuidplaspolder lies within the triangle formed by Rotterdam, Zoetermeer and Gouda and includes the lowest lying reclaimed land area in the Netherlands. The Zuidplaspolder has been designated to absorb the urban expansion demands of the Southern part of the Randstad, the prime Dutch West coast urban agglomeration. The following developments have been planned: the building of 7,000-30,000 homes, hundreds of hectares of commercial properties and greenhouses; improvements to the infrastructure; development of extra natural reserves, green zones and green zonal links; space for water storage. The Zuidplaspolder has to be developed in a sustainable way. Therefore future inhabitants and businesses should not have to suffer any negative effects from climate change. The Xplorelab of the province of Zuid- Holland has investigated which climate change impacts will effect the Zuidplas and what can be done to mitigate this. This report shows the effects and the adaptation possibilities. There are also preliminary assessments of the potential (social) costs and benefits. Examples of measures are: no construction in lowest lying areas of polder; aggregation of surfaces water management areas; expansion of peak rainwater storage space; assessment of safety margins for storm barriers; construction in harmony with the geomorphological structures; placing of compartmental dikes; building waterproof houses; connecting and strengthening natural conservation area; seasonal storage of rain water for dry periods; utilizing green areas and water as anti-'heatstress' measures Five climate resilient pilot projects have been designed, based on analyses of the effects of climate change. The total additional cost for four of them amounts to tens of millions of euros. The eventual cost to society is expected to become a benefit in the long run. The Zuidplaspolder spatial plan appears to be climate resilient but it can still be improved. Despite the net positive result, implementation of

  3. Hotspots, basalts, and the evolution of the mantle

    Anderson, D. L.

    1981-01-01

    It is noted that the trace element concentration patterns of continental and ocean island basalts and of mid-ocean ridge basalts are complementary. Estimates of the relative sizes of the source regions for these fundamentally different basalt types can be arrived at from the trace element enrichment-depletion patterns. Their combined volume occupies the greater part of the mantle above the 670 km discontinuity. It is pointed out that the source regions separated as a result of early mantle differentiation and crystal fractionation from the resulting melt. The mid-ocean ridge basalts source evolved from an eclogite cumulate that gave up its late-stage enriched fluids at various times to the shallower mantle and continental crust. The mid-ocean ridge basalts source is rich in garnet and clinopyroxene, while the continental and ocean island basalt source is a garnet peridotite that has experienced secondary enrichment. These relationships are found to be consistent with the evolution of a terrestrial magma ocean.

  4. Adaptive evolution in ecological communities.

    Martin M Turcotte

    Full Text Available Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.

  5. The Adaptive Evolution Database (TAED)

    Liberles, David A; Schreiber, David R.; Govindarajan, Sridhar; Chamberlin, Stephen G.; Steven A Benner

    2001-01-01

    Background The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes in GenBank. It can therefore support large-scale genomic surveys, of which we present here The Adaptive Evolution Database (TAED). In TAED, potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotid...

  6. The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes.

    Lesecque, Yann; Glémin, Sylvain; Lartillot, Nicolas; Mouchiroud, Dominique; Duret, Laurent

    2014-11-01

    Recombination is an essential process in eukaryotes, which increases diversity by disrupting genetic linkage between loci and ensures the proper segregation of chromosomes during meiosis. In the human genome, recombination events are clustered in hotspots, whose location is determined by the PRDM9 protein. There is evidence that the location of hotspots evolves rapidly, as a consequence of changes in PRDM9 DNA-binding domain. However, the reasons for these changes and the rate at which they occur are not known. In this study, we investigated the evolution of human hotspot loci and of PRDM9 target motifs, both in modern and archaic human lineages (Denisovan) to quantify the dynamic of hotspot turnover during the recent period of human evolution. We show that present-day human hotspots are young: they have been active only during the last 10% of the time since the divergence from chimpanzee, starting to be operating shortly before the split between Denisovans and modern humans. Surprisingly, however, our analyses indicate that Denisovan recombination hotspots did not overlap with modern human ones, despite sharing similar PRDM9 target motifs. We further show that high-affinity PRDM9 target motifs are subject to a strong self-destructive drive, known as biased gene conversion (BGC), which should lead to the loss of the majority of them in the next 3 MYR. This depletion of PRDM9 genomic targets is expected to decrease fitness, and thereby to favor new PRDM9 alleles binding different motifs. Our refined estimates of the age and life expectancy of human hotspots provide empirical evidence in support of the Red Queen hypothesis of recombination hotspots evolution. PMID:25393762

  7. The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes.

    Yann Lesecque

    2014-11-01

    Full Text Available Recombination is an essential process in eukaryotes, which increases diversity by disrupting genetic linkage between loci and ensures the proper segregation of chromosomes during meiosis. In the human genome, recombination events are clustered in hotspots, whose location is determined by the PRDM9 protein. There is evidence that the location of hotspots evolves rapidly, as a consequence of changes in PRDM9 DNA-binding domain. However, the reasons for these changes and the rate at which they occur are not known. In this study, we investigated the evolution of human hotspot loci and of PRDM9 target motifs, both in modern and archaic human lineages (Denisovan to quantify the dynamic of hotspot turnover during the recent period of human evolution. We show that present-day human hotspots are young: they have been active only during the last 10% of the time since the divergence from chimpanzee, starting to be operating shortly before the split between Denisovans and modern humans. Surprisingly, however, our analyses indicate that Denisovan recombination hotspots did not overlap with modern human ones, despite sharing similar PRDM9 target motifs. We further show that high-affinity PRDM9 target motifs are subject to a strong self-destructive drive, known as biased gene conversion (BGC, which should lead to the loss of the majority of them in the next 3 MYR. This depletion of PRDM9 genomic targets is expected to decrease fitness, and thereby to favor new PRDM9 alleles binding different motifs. Our refined estimates of the age and life expectancy of human hotspots provide empirical evidence in support of the Red Queen hypothesis of recombination hotspots evolution.

  8. An Adaptive Memory Evolution Algorithm

    Caihong Wu

    2013-01-01

    Full Text Available Memory mechanism is applied to the optimization algorithm by more study. In order to improve the algorithm of adaptive ability, introducing memory ability in evolutionary algorithm framework, an Adaptive Memory Evolution Algorithm (AMEA is proposed. The algorithm set matrix to record the exploring experiences and exploring results of the individual parent. The algorithm uses these records to guide the generation of offspring. And thus AMEA can adaptively select the dimension to mutate and exploring radius. In addition, to improve the algorithm accuracy, the algorithm raises the best opportunities by using super-variation operator. In the simulation test, compared with similar algorithms, the results show that AMEA has fast convergence speed and optimum performance of global convergence.

  9. Contact and hybrid zone hotspots and evolution of birds in the Middle East

    2007-01-01

    The Middle East is an important contact zone for a considerable number of bird taxa from the western and eastern Palearctic and from the great Saharo-Sindian jesert belt. Using WORLDMAP software, we analyzed the geographical distribution of secondary contact zones for parapatric species pairs of birds in the Middle East. We identified 56 species (29 species pairs) that make contact in the Middle East. The species pairs belong to three orders, i.e. Falconiformes, Piciformes, and Passeriformes. Almost half (46%) of these species pairs hybridize in their contact zones. Although contact zones occur over a large part of northern Middle East, spatially they were not evenly distributed. Contact zone richness was highest in the mountain ranges south of the Caspian Sea and the Caucasus. The hottest hotspots, where up to nine bird species pairs occur sympatrically, are situated in north-eastern Iran and Azerbaijan. We discuss the relevance of these hotspots for improving our understanding of the biogeography and evolution of the avifauna in the Middle East.

  10. Molecular evolution and thermal adaptation

    Chen, Peiqiu

    2011-12-01

    In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

  11. Quantifying adaptive evolution in the Drosophila immune system.

    Darren J Obbard

    2009-10-01

    Full Text Available It is estimated that a large proportion of amino acid substitutions in Drosophila have been fixed by natural selection, and as organisms are faced with an ever-changing array of pathogens and parasites to which they must adapt, we have investigated the role of parasite-mediated selection as a likely cause. To quantify the effect, and to identify which genes and pathways are most likely to be involved in the host-parasite arms race, we have re-sequenced population samples of 136 immunity and 287 position-matched non-immunity genes in two species of Drosophila. Using these data, and a new extension of the McDonald-Kreitman approach, we estimate that natural selection fixes advantageous amino acid changes in immunity genes at nearly double the rate of other genes. We find the rate of adaptive evolution in immunity genes is also more variable than other genes, with a small subset of immune genes evolving under intense selection. These genes, which are likely to represent hotspots of host-parasite coevolution, tend to share similar functions or belong to the same pathways, such as the antiviral RNAi pathway and the IMD signalling pathway. These patterns appear to be general features of immune system evolution in both species, as rates of adaptive evolution are correlated between the D. melanogaster and D. simulans lineages. In summary, our data provide quantitative estimates of the elevated rate of adaptive evolution in immune system genes relative to the rest of the genome, and they suggest that adaptation to parasites is an important force driving molecular evolution.

  12. Genome Hotspots for Nucleotide Substitutions and the Evolution of Influenza A (H1N1) Human Strains

    Civetta, Alberto; Ostapchuk, David Cecil Murphy; Nwali, Basil

    2016-01-01

    In recent years a number of studies have brought attention to the role of positive selection during the evolution of antigenic escape by influenza strains. Particularly, the identification of positively selected sites within antigenic domains of viral surface proteins has been used to suggest that the evolution of viral–host receptor binding specificity is driven by selection. Here we show that, following the 1918 outbreak, the antigenic sites of the hemagglutinin (HA) viral surface protein and the stalk region of neuraminidase became substitution hotspots. The hotspots show similar patterns of nucleotide substitution bias at synonymous and nonsynonymous sites. Such bias imposes directionality in amino acid replacements that can influence signals of selection at antigenic sites. Our results suggest that the high accumulation of substitutions within the antigenic sites of HA can explain not only cases of antigenic escape by antigenic drift but also lead to occasional episodes of viral extinction. PMID:26988249

  13. Evolution of adaptation mechanisms: Adaptation energy, stress, and oscillating death.

    Gorban, Alexander N; Tyukina, Tatiana A; Smirnova, Elena V; Pokidysheva, Lyudmila I

    2016-09-21

    In 1938, Selye proposed the notion of adaptation energy and published 'Experimental evidence supporting the conception of adaptation energy.' Adaptation of an animal to different factors appears as the spending of one resource. Adaptation energy is a hypothetical extensive quantity spent for adaptation. This term causes much debate when one takes it literally, as a physical quantity, i.e. a sort of energy. The controversial points of view impede the systematic use of the notion of adaptation energy despite experimental evidence. Nevertheless, the response to many harmful factors often has general non-specific form and we suggest that the mechanisms of physiological adaptation admit a very general and nonspecific description. We aim to demonstrate that Selye׳s adaptation energy is the cornerstone of the top-down approach to modelling of non-specific adaptation processes. We analyze Selye׳s axioms of adaptation energy together with Goldstone׳s modifications and propose a series of models for interpretation of these axioms. Adaptation energy is considered as an internal coordinate on the 'dominant path' in the model of adaptation. The phenomena of 'oscillating death' and 'oscillating remission' are predicted on the base of the dynamical models of adaptation. Natural selection plays a key role in the evolution of mechanisms of physiological adaptation. We use the fitness optimization approach to study of the distribution of resources for neutralization of harmful factors, during adaptation to a multifactor environment, and analyze the optimal strategies for different systems of factors. PMID:26801872

  14. Parallel genotypic adaptation: when evolution repeats itself

    Wood, Troy E.; Burke, John M.; Rieseberg, Loren H.

    2005-01-01

    Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic...

  15. Louisville Seamount Trail: implications for geodynamic mantle flow models and the geochemical evolution of primary hotspots

    Koppers, Anthony A.; YAMAZAKI, Toshitsugu; Geldmacher, Jörg; L. Anderson; Beier, C.; Buchs, David M.; Chen, L.; Cohen, B.; Deschamps, F.; Dorais, M; Ebuna, D.; Fitton, J.; Fulton, P M; Ganbat, E.; Gee, J. S.

    2011-01-01

    The Louisville Seamount Trail is a 4300 km long volcanic chain that has been built in the past 80 m.y. as the Pacific plate moved over a persistent mantle melting anomaly or hotspot. Because of its linear morphology and its long-lived age-progressive volcanism, Louisville is the South Pacific counterpart of the much better studied Hawaiian-Emperor Seamount Trail. Together, Louisville and Hawaii are textbook examples of two primary hotspots that have been keystones in deciphering the motion of...

  16. Adaptive genic evolution in the Drosophila genomes

    Shapiro, Joshua A; Huang, Wei; Zhang, Chenhui;

    2007-01-01

    Determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. A suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large and....... melanogaster and its close relatives were adaptive. (iv) This signature of adaptive evolution is observable only in regions of normal recombination. Hence, the low level of polymorphism observed in regions of reduced recombination may not be driven primarily by positive selection. Finally, we discuss the...... sites than expected, hinting at the action of selective sweeps. (ii) The level of polymorphism is negatively correlated with the rate of nonsynonymous divergence across loci. Thus, even under strict neutrality, the ratio of amino acid to silent nucleotide changes (A:S) between Drosophila species is...

  17. Adaptation, plant evolution, and the fossil record

    Knoll, A. H.; Niklas, K. J.

    1987-01-01

    The importance of adaptation in determining patterns of evolution has become an important focus of debate in evolutionary biology. As it pertains to paleobotany, the issue is whether or not adaptive evolution mediated by natural selection is sufficient to explain the stratigraphic distributions of taxa and character states observed in the plant fossil record. One means of addressing this question is the functional evaluation of stratigraphic series of plant organs set in the context of paleoenvironmental change and temporal patterns of floral composition within environments. For certain organ systems, quantitative estimates of biophysical performance can be made on the basis of structures preserved in the fossil record. Performance estimates for plants separated in time or space can be compared directly. Implicit in different hypotheses of the forces that shape the evolutionary record (e.g. adaptation, mass extinction, rapid environmental change, chance) are predictions about stratigraphic and paleoenvironmental trends in the efficacy of functional performance. Existing data suggest that following the evolution of a significant structural innovation, adaptation for improved functional performance can be a major determinant of evolutionary changes in plants; however, there are structural and development limits to functional improvement, and once these are reached, the structure in question may no longer figure strongly in selection until and unless a new innovation evolves. The Silurian-Devonian paleobotanical record is consistent with the hypothesis that the succession of lowland floodplain dominants preserved in the fossil record of this interval was determined principally by the repeated evolution of new taxa that rose to ecological importance because of competitive advantages conferred by improved biophysical performance. This does not seem to be equally true for Carboniferous-Jurassic dominants of swamp and lowland floodplain environments. In these cases

  18. Farming System Evolution and Adaptive Capacity: Insights for Adaptation Support

    Jami L. Dixon

    2014-02-01

    Full Text Available Studies of climate impacts on agriculture and adaptation often provide current or future assessments, ignoring the historical contexts farming systems are situated within. We investigate how historical trends have influenced farming system adaptive capacity in Uganda using data from household surveys, semi-structured interviews, focus-group discussions and observations. By comparing two farming systems, we note three major findings: (1 similar trends in farming system evolution have had differential impacts on the diversity of farming systems; (2 trends have contributed to the erosion of informal social and cultural institutions and an increasing dependence on formal institutions; and (3 trade-offs between components of adaptive capacity are made at the farm-scale, thus influencing farming system adaptive capacity. To identify the actual impacts of future climate change and variability, it is important to recognize the dynamic nature of adaptation. In practice, areas identified for further adaptation support include: shift away from one-size-fits-all approach the identification and integration of appropriate modern farming method; a greater focus on building inclusive formal and informal institutions; and a more nuanced understanding regarding the roles and decision-making processes of influential, but external, actors. More research is needed to understand farm-scale trade-offs and the resulting impacts across spatial and temporal scales.

  19. Evolution or adaptation? What do heritable adaptive changes imply?

    M. Kemal Irmak

    2014-02-01

    Full Text Available Interactions between environmental factors and epigenetic inheritance system produce a great deal of variation from one geographic region to another in human craniofacial morphology, skin color, hair form, stature and body proportions. In this system, while environmental factors produce modifications in the body, they simultaneously induce long-term epigenetic modifications in the germ cells that are inherited to offspring. This kind of heritable changes is called biological adaptation. It was previously reported that biological adaptation is limited to neural crest derivatives such as craniofacial tissues, melanocytes, and structures related to hair form, stature and body proportions. Thus, inheritance of adaptive changes is limited to a number of traits and species-to-species evolution seems unlikely. [J Exp Integr Med 2014; 4(1.000: 13-16

  20. From global to regional and back again: common climate stressors of marine ecosystems relevant for adaptation across five ocean warming hotspots.

    Popova, Ekaterina; Yool, Andrew; Byfield, Valborg; Cochrane, Kevern; Coward, Andrew C; Salim, Shyam S; Gasalla, Maria A; Henson, Stephanie A; Hobday, Alistair J; Pecl, Gretta T; Sauer, Warwick H; Roberts, Michael J

    2016-06-01

    Ocean warming 'hotspots' are regions characterized by above-average temperature increases over recent years, for which there are significant consequences for both living marine resources and the societies that depend on them. As such, they represent early warning systems for understanding the impacts of marine climate change, and test-beds for developing adaptation options for coping with those impacts. Here, we examine five hotspots off the coasts of eastern Australia, South Africa, Madagascar, India and Brazil. These particular hotspots have underpinned a large international partnership that is working towards improving community adaptation by characterizing, assessing and projecting the likely future of coastal-marine food resources through the provision and sharing of knowledge. To inform this effort, we employ a high-resolution global ocean model forced by Representative Concentration Pathway 8.5 and simulated to year 2099. In addition to the sea surface temperature, we analyse projected stratification, nutrient supply, primary production, anthropogenic CO2 -driven ocean acidification, deoxygenation and ocean circulation. Our simulation finds that the temperature-defined hotspots studied here will continue to experience warming but, with the exception of eastern Australia, may not remain the fastest warming ocean areas over the next century as the strongest warming is projected to occur in the subpolar and polar areas of the Northern Hemisphere. Additionally, we find that recent rapid change in SST is not necessarily an indicator that these areas are also hotspots of the other climatic stressors examined. However, a consistent facet of the hotspots studied here is that they are all strongly influenced by ocean circulation, which has already shown changes in the recent past and is projected to undergo further strong change into the future. In addition to the fast warming, change in local ocean circulation represents a distinct feature of present and future

  1. Recent acceleration of human adaptive evolution

    Hawks, John; Wang, Eric T; Cochran, Gregory M.; Harpending, Henry C.; Moyzis, Robert K.

    2007-01-01

    Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9-million HapMap SNP dataset, we found that selection has accelerated greatly during the last 40,000 years. We tested the null hypothesis that the observed age distribution of recent positively selected linkage blocks is consistent with a constant rate of adaptive substitution during human evolution. We show that a constant rate high enough to explain the number of recently selected variants would pred...

  2. Adapting Digital Libraries to Continual Evolution

    Barkstrom, Bruce R.; Finch, Melinda; Ferebee, Michelle; Mackey, Calvin

    2002-01-01

    In this paper, we describe five investment streams (data storage infrastructure, knowledge management, data production control, data transport and security, and personnel skill mix) that need to be balanced against short-term operating demands in order to maximize the probability of long-term viability of a digital library. Because of the rapid pace of information technology change, a digital library cannot be a static institution. Rather, it has to become a flexible organization adapted to continuous evolution of its infrastructure.

  3. Evolutionary Hotspots in the Mojave Desert

    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.

  4. From global to regional and back again: common climate stressors of marine ecosystems relevant for adaptation across five ocean warming hotspots

    Popova, E.; Yool, A.; Byfield, V.; Cochrane, K.; A. C. Coward; Salim, S. S.; Gasalla, M.A.; S. A. Henson; Hobday, A. J.; Pecl, G.; Sauer, W.; Roberts, M.

    2016-01-01

    Ocean warming “hotspots” are regions characterised by above-average temperature increases over recent years, for which there are significant consequences for both living marine resources and the societies that depend on them. As such, they represent early warning systems for understanding the impacts of marine climate change, and test-beds for developing adaptation options for coping with those impacts. Here, we examine five hotspots off the coasts of eastern Australia, South Africa, Madagasc...

  5. Viral host-adaptation:insights from evolution experiments with phages

    Hall, James Pj; Harrison, Ellie; Brockhurst, Michael A

    2013-01-01

    Phages, viral parasites of bacteria, share fundamental features of pathogenic animal and plant viruses and represent a highly tractable empirical model system to understand viral evolution and in particular viral host-adaptation. Phage adaptation to a particular host genotype often results in improved fitness by way of parallel evolution whereby independent lineages hit upon identical adaptive solutions. By contrast, phage adaptation to an evolving host population leads to the evolution of in...

  6. Epistatic adaptive evolution of human color vision.

    Shozo Yokoyama

    2014-12-01

    Full Text Available Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation. This initial step may be untangled by analyzing appropriate ancestral molecules, but it is a daunting task to recapitulate the evolution of non-additive (epistatic interactions of amino acids and function of a protein separately. To adapt to the ultraviolet (UV-free retinal environment, the short wavelength-sensitive (SWS1 visual pigment in human (human S1 switched from detecting UV to absorbing blue light during the last 90 million years. Mutagenesis experiments of the UV-sensitive pigment in the Boreoeutherian ancestor show that the blue-sensitivity was achieved by seven mutations. The experimental and quantum chemical analyses show that 4,008 of all 5,040 possible evolutionary trajectories are terminated prematurely by containing a dehydrated nonfunctional pigment. Phylogenetic analysis further suggests that human ancestors achieved the blue-sensitivity gradually and almost exclusively by epistasis. When the final stage of spectral tuning of human S1 was underway 45-30 million years ago, the middle and long wavelength-sensitive (MWS/LWS pigments appeared and so-called trichromatic color vision was established by interprotein epistasis. The adaptive evolution of human S1 differs dramatically from orthologous pigments with a major mutational effect used in achieving blue-sensitivity in a fish and several mammalian species and in regaining UV vision in birds. These observations imply that the mechanisms of epistatic interactions must be understood by studying various orthologues in different species that have adapted to various ecological and physiological environments.

  7. Adaptive CGFs Based on Grammatical Evolution

    Jian Yao

    2015-01-01

    Full Text Available Computer generated forces (CGFs play blue or red units in military simulations for personnel training and weapon systems evaluation. Traditionally, CGFs are controlled through rule-based scripts, despite the doctrine-driven behavior of CGFs being rigid and predictable. Furthermore, CGFs are often tricked by trainees or fail to adapt to new situations (e.g., changes in battle field or update in weapon systems, and, in most cases, the subject matter experts (SMEs review and redesign a large amount of CGF scripts for new scenarios or training tasks, which is both challenging and time-consuming. In an effort to overcome these limitations and move toward more true-to-life scenarios, a study using grammatical evolution (GE to generate adaptive CGFs for air combat simulations has been conducted. Expert knowledge is encoded with modular behavior trees (BTs for compatibility with the operators in genetic algorithm (GA. GE maps CGFs, represented with BTs to binary strings, and uses GA to evolve CGFs with performance feedback from the simulation. Beyond-visual-range air combat experiments between adaptive CGFs and nonadaptive baseline CGFs have been conducted to observe and study this evolutionary process. The experimental results show that the GE is an efficient framework to generate CGFs in BTs formalism and evolve CGFs via GA.

  8. Pervasive Adaptive Evolution in Primate Seminal Proteins.

    2005-09-01

    Full Text Available Seminal fluid proteins show striking effects on reproduction, involving manipulation of female behavior and physiology, mechanisms of sperm competition, and pathogen defense. Strong adaptive pressures are expected for such manifestations of sexual selection and host defense, but the extent of positive selection in seminal fluid proteins from divergent taxa is unknown. We identified adaptive evolution in primate seminal proteins using genomic resources in a tissue-specific study. We found extensive signatures of positive selection when comparing 161 human seminal fluid proteins and 2,858 prostate-expressed genes to those in chimpanzee. Seven of eight outstanding genes yielded statistically significant evidence of positive selection when analyzed in divergent primates. Functional clues were gained through divergent analysis, including several cases of species-specific loss of function in copulatory plug genes, and statistically significant spatial clustering of positively selected sites near the active site of kallikrein 2. This study reveals previously unidentified positive selection in seven primate seminal proteins, and when considered with findings in Drosophila, indicates that extensive positive selection is found in seminal fluid across divergent taxonomic groups.

  9. Influence of chance, history, and adaptation on digital evolution

    Wagenaar, Daniel A.; Adami, Christoph

    2004-01-01

    We evolved multiple clones of populations of digital organisms to study the effects of chance, history, and adaptation in evolution. We show that clones adapted to a specific environment can adapt to new environments quickly and efficiently, although their history remains a significant factor in their fitness. Adaptation is most significant (and the effects of history less so) if the old and new environments are dissimilar. For more similar environments, adaptation is slower while history is ...

  10. Adaptive Parameter Selection for Strategy Adaptation in Differential Evolution for Continuous Optimization

    Wenyin Gong; Zhihua Cai

    2012-01-01

    In order to automatically select the most suitable strategy for a specific problem without any prior knowledge, in this paper, we present an adaptive parameter selection technique for strategy adaptation in differential evolution (DE). First, a simple strategy adaptation mechanism is employed to implement the adaptive strategy selection in DE. Then, the probability- matching-based adaptive parameter selection method is proposed to select the best parameter of the strategy adaptation mechanism...

  11. Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

    Halligan, D.; Oliver, F.; Eyre-Walker, A.; Harr, B; Keightley, P

    2010-01-01

    The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast...

  12. Accelerated regulatory gene evolution in an adaptive radiation

    Barrier, Marianne; Robichaux, Robert H.; Purugganan, Michael D.

    2001-01-01

    The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive ra...

  13. Adaptive Game Level Creation through Rank-based Interactive Evolution

    Liapis, Antonios; Martínez, Héctor Pérez; Togelius, Julian;

    2013-01-01

    This paper introduces Rank-based Interactive Evolution (RIE) which is an alternative to interactive evolution driven by computational models of user preferences to generate personalized content. In RIE, the computational models are adapted to the preferences of users which, in turn, are used...... artificial agents. Results suggest that RIE is both faster and more robust than standard interactive evolution and outperforms other state-of-the-art interactive evolution approaches....

  14. Extensive X-linked adaptive evolution in central chimpanzees

    Hvilsom, Christina; Qian, Yu; Bataillon, Thomas;

    2012-01-01

    dominance of beneficial (adaptive) and deleterious mutations. Here we capture and sequence the complete exomes of 12 chimpanzees and present the largest set of protein-coding polymorphism to date. We report extensive adaptive evolution specifically targeting the X chromosome of chimpanzees with as much as...... 30% of all amino acid replacements being adaptive. Adaptive evolution is barely detectable on the autosomes except for a few striking cases of recent selective sweeps associated with immunity gene clusters. We also find much stronger purifying selection than observed in humans, and in contrast to...

  15. Adaptive differential evolution a robust approach to multimodal problem optimization

    Zhang, Jingqiao; Zhang, Jingqiao

    2009-01-01

    The fundamental theme of this book is theoretical study of differential evolution and algorithmic analysis of parameter adaptive schemes. The book offers real-world insights into a variety of large-scale complex industrial applications.

  16. Phylogenomic evidence of adaptive evolution in the ancestry of humans

    Goodman, Morris; Sterner, Kirstin N.

    2010-01-01

    In Charles Darwin’s tree model for life’s evolution, natural selection adaptively modifies newly arisen species as they branch apart from their common ancestor. In accord with this Darwinian concept, the phylogenomic approach to elucidating adaptive evolution in genes and genomes in the ancestry of modern humans requires a well supported and well sampled phylogeny that accurately places humans and other primates and mammals with respect to one another. For more than a century, first from the ...

  17. Adaptation and evolution of drug-resistant Mycobacterium tuberculosis

    I.L. Bergval

    2013-01-01

    Many studies have been conducted on drug resistance and the evolution of Mycobacterium tuberculosis. Notwithstanding, many molecular mechanisms facilitating the emergence, adaptation and spread of drug-resistant tuberculosis have yet to be discovered. This thesis reports studies of the adaptive mech

  18. Urban Evolution: The Role of Water and Adaptation

    Kaushal, S.

    2015-12-01

    The structure, function, and services of urban ecosystems evolve over time scales from seconds to centuries as Earth's population grows, infrastructure ages, and management decisions alter them. The concept of "urban evolution" was proposed in order to study changes in urban ecosystems over time. Urban evolution has exerted a major influence on Earth's water and elemental cycles from local to global scales over human history. A current understanding of urban evolution allows urban planning, management, and restoration to move beyond reactive management to predictive management. We explore two key mechanisms of urban evolution, urban selective pressure and adaptation, and their relationship to the evolution of modern water and biogeochemical cycles. Urban selective pressure is an environmental or societal driver contributing to urban adaptation. Urban adaptation is the sequential process by which an urban structure, function, or services becomes more fitted to its changing environment or human choices. We show how hydrological and biogeochemical traits evolve across successive generations of urban ecosystems via shifts in selective pressures and adaptations. We also discuss how urban evolution can be divided into distinct stages and transition periods of growth and expansion and decay and repair during the Anthropocene epoch. We explore multiple examples and drivers of urban evolution and adaptations including the role of unintended consequences and societal drivers. We also present a conceptual model for the evolution of urban waters from the Industrial Revolution to the present day emphasizing the role of urban adaptations in response to selective pressures. Finally, we conclude by proposing new concepts and questions for future research related to the urban evolution of water, material, and energy cycles.

  19. Evolution of speech-specific cognitive adaptations

    Bart ede Boer

    2015-09-01

    Full Text Available This paper briefly reviews theoretical results that shed light on what kind of cognitive adaptations we can expect to have evolved for (combinatorial speech and then reviews concrete empirical work investigating adaptations for combinatorial speech. The paper argues that an evolutionary perspective is natural when investigating cognitive adaptations related to speech and language. This is because properties of language are determined through complex interaction between biologically evolved cognitive mechanisms (possibly adapted to language and cultural (evolutionary processes. It turns out that there is as yet no strong direct evidence for cognitive traits that have undergone selection related to speech in general or combinatorial structure in particular, but there is indirect evidence that indicates selection. However, the traits that may have undergone selection are expected to be continuously variable ones, rather than the discrete ones that linguists have focused on traditionally.

  20. Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot.

    Paun, Ovidiu; Turner, Barbara; Trucchi, Emiliano; Munzinger, Jérôme; Chase, Mark W; Samuel, Rosabelle

    2016-03-01

    Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia. PMID:26430059

  1. Fitness seascapes and adaptive evolution of the influenza virus

    Lassig, Michael

    2014-03-01

    The seasonal human influenza A virus undergoes rapid genome evolution. This process is triggered by interactions with the host immune system and produces significant year-to-year sequence turnover in the population of circulating viral strains. We develop a dynamical fitness model that predicts the evolution of the viral population from one year to the next. Two factors are shown to determine the fitness of a viral strain: adaptive changes, which are under positive selection, and deleterious mutations, which affect conserved viral functions such as protein stability. Combined with the influenza strain tree, this fitness model maps the adaptive history of influenza A. We discuss the implications of our results for the statistical theory of adaptive evolution in asexual populations. Based on this and related systems, we touch upon the fundamental question of when evolution can be predicted. Joint work with Marta Luksza, Columbia University.

  2. Evolution or adaptation? What do heritable adaptive changes imply?

    M. Kemal Irmak

    2014-01-01

    Interactions between environmental factors and epigenetic inheritance system produce a great deal of variation from one geographic region to another in human craniofacial morphology, skin color, hair form, stature and body proportions. In this system, while environmental factors produce modifications in the body, they simultaneously induce long-term epigenetic modifications in the germ cells that are inherited to offspring. This kind of heritable changes is called biological adaptation. It wa...

  3. How co-evolution can enhance the adaptation power of artificial evolution: Implications for evolutionary robotics

    Nolfi, S.; Floreano, D.

    1998-01-01

    Co-evolution (i.e. the evolution of two or more competing populations with coupled fitness) has several interesting features that may potentially enhance the power of adaptation of artificial evolution. In particular, as discussed by Dawkins and Krebs [2], competing populations may reciprocally drive one another to increasing levels of complexity by producing an evolutionary “arms race”. In this paper we will investigate the role of co-evolution in the context of evolutionary robotics. In par...

  4. Adaptive Strategy Selection in Differential Evolution

    Gong, Wenyin; Fialho, Álvaro; Cai, Zhihua

    2010-01-01

    Differential evolution (DE) is a simple yet powerful evolutionary algorithm for global numerical optimization. Different strategies have been proposed for the offspring generation; but the selection of which of them should be applied is critical for the DE performance, besides being problem-dependent. In this paper, the probability matching technique is employed in DE to autonomously select the most suitable strategy while solving the problem. Four credit assignment methods, that update the k...

  5. An Adaptive Unified Differential Evolution Algorithm for Global Optimization

    Qiang, Ji; Mitchell, Chad

    2014-11-03

    In this paper, we propose a new adaptive unified differential evolution algorithm for single-objective global optimization. Instead of the multiple mutation strate- gies proposed in conventional differential evolution algorithms, this algorithm employs a single equation unifying multiple strategies into one expression. It has the virtue of mathematical simplicity and also provides users the flexibility for broader exploration of the space of mutation operators. By making all control parameters in the proposed algorithm self-adaptively evolve during the process of optimization, it frees the application users from the burden of choosing appro- priate control parameters and also improves the performance of the algorithm. In numerical tests using thirteen basic unimodal and multimodal functions, the proposed adaptive unified algorithm shows promising performance in compari- son to several conventional differential evolution algorithms.

  6. Increased tolerance towards serine obtained by adaptive laboratory evolution

    Mundhada, Hemanshu; Seoane, Jose Miguel; Koza, Anna; Herrgard, Markus; Feist, Adam; Nielsen, Alex Toftgaard

    2014-01-01

    glyA), the conversion of serine to pyruvate (encoded by sdaA, sdaB and tdcG) was also deleted. As expected, the resulting strain turned out to be susceptible to even low concentrations of serine in the media. In order to improve the tolerance of the strain towards serine, adaptive laboratory evolution...... increased. During the evolution experiment, the serine tolerance was increased substantially. Genome re-sequencing was subsequently used to analyze the genotype of a number of selected strains. These results reveal insights towards the adaptation process as well as the mechanism of serine tolerance....

  7. Ecology and Evolution of Adaptive Morphological Variation in Fish Populations

    Svanbäck, Richard

    2004-01-01

    The work in this thesis deals with the ecology and evolution of adaptive individual variation. Ecologists have long used niche theory to describe the ecology of a species as a whole, treating conspecific individuals as ecological equivalent. During recent years, research about individual variation in diet and morphology has gained interest in adaptive radiations and ecological speciation. Such variation among individual niche use may have important conservation implications as well as ecologi...

  8. Adaptive Network Dynamics and Evolution of Leadership in Collective Migration

    Pais, Darren; Leonard, Naomi Ehrich

    2013-01-01

    The evolution of leadership in migratory populations depends not only on costs and benefits of leadership investments but also on the opportunities for individuals to rely on cues from others through social interactions. We derive an analytically tractable adaptive dynamic network model of collective migration with fast timescale migration dynamics and slow timescale adaptive dynamics of individual leadership investment and social interaction. For large populations, our analysis of bifurcatio...

  9. Stable recombination hotspots in birds.

    Singhal, Sonal; Leffler, Ellen M; Sannareddy, Keerthi; Turner, Isaac; Venn, Oliver; Hooper, Daniel M; Strand, Alva I; Li, Qiye; Raney, Brian; Balakrishnan, Christopher N; Griffith, Simon C; McVean, Gil; Przeworski, Molly

    2015-11-20

    The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have recombination hotspots, which are enriched near functional genomic elements. Unlike in mice and apes, most hotspots are shared between the two species, and their conservation seems to extend over tens of millions of years. These observations suggest that in the absence of PRDM9, recombination targets functional features that both enable access to the genome and constrain its evolution. PMID:26586757

  10. Link-based formalism for time evolution of adaptive networks

    Zhou, Jie; Chen, Guanrong

    2013-01-01

    Network topology and nodal dynamics are two fundamental stones of adaptive networks. Detailed and accurate knowledge of these two ingredients is crucial for understanding the evolution and mechanism of adaptive networks. In this paper, by adopting the framework of the adaptive SIS model proposed by Gross et al. [Phys. Rev. Lett. 96, 208701 (2006)] and carefully utilizing the information of degree correlation of the network, we propose a link-based formalism for describing the system dynamics with high accuracy and subtle details. Several specific degree correlation measures are introduced to reveal the coevolution of network topology and system dynamics.

  11. Evolutionary potential and adaptation of Banksia attenuata (Proteaceae) to climate and fire regime in southwestern Australia, a global biodiversity hotspot

    He, Tianhua; D’Agui, Haylee; Lim, Sim Lin; Enright, Neal J.; Luo, Yiqi

    2016-05-01

    Substantial climate changes are evident across Australia, with declining rainfall and rising temperature in conjunction with frequent fires. Considerable species loss and range contractions have been predicted; however, our understanding of how genetic variation may promote adaptation in response to climate change remains uncertain. Here we characterized candidate genes associated with rainfall gradients, temperatures, and fire intervals through environmental association analysis. We found that overall population adaptive genetic variation was significantly affected by shortened fire intervals, whereas declining rainfall and rising temperature did not have a detectable influence. Candidate SNPs associated with rainfall and high temperature were diverse, whereas SNPs associated with specific fire intervals were mainly fixed in one allele. Gene annotation further revealed four genes with functions in stress tolerance, the regulation of stomatal opening and closure, energy use, and morphogenesis with adaptation to climate and fire intervals. B. attenuata may tolerate further changes in rainfall and temperature through evolutionary adaptations based on their adaptive genetic variation. However, the capacity to survive future climate change may be compromised by changes in the fire regime.

  12. Recombination hotspots flank the Cryptococcus mating-type locus: implications for the evolution of a fungal sex chromosome.

    Yen-Ping Hsueh

    2006-11-01

    Full Text Available Recombination increases dramatically during meiosis to promote genetic exchange and generate recombinant progeny. Interestingly, meiotic recombination is unevenly distributed throughout genomes, and, as a consequence, genetic and physical map distances do not have a simple linear relationship. Recombination hotspots and coldspots have been described in many organisms and often reflect global features of chromosome structure. In particular, recombination frequencies are often distorted within or outside sex-determining regions of the genome. Here, we report that recombination is elevated adjacent to the mating-type locus (MAT in the pathogenic basidiomycete Cryptococcus neoformans. Among fungi, C. neoformans has an unusually large MAT locus, and recombination is suppressed between the two >100-kilobase mating-type specific alleles. When genetic markers were introduced at defined physical distances from MAT, we found the meiotic recombination frequency to be approximately 20% between MAT and a flanking marker at 5, 10, 50, or 100 kilobases from the right border. As a result, the physical/genetic map ratio in the regions adjacent to MAT is distorted approximately 10- to 50-fold compared to the genome-wide average. Moreover, recombination frequently occurred on both sides of MAT and negative interference between crossovers was observed. MAT heterozygosity was not required for enhanced recombination, implying that this process is not due to a physical distortion from the two non-paired alleles and could also occur during same-sex mating. Sequence analysis revealed a correlation between high G + C content and these hotspot regions. We hypothesize that the presence of recombinational activators may have driven several key events during the assembly and reshaping of the MAT locus and may have played similar roles in the origins of both metabolic and biosynthetic gene clusters. Our findings suggest that during meiosis the MAT locus may be exchanged onto

  13. The rule of declining adaptability in microbial evolution experiments

    Alejandro eCouce

    2015-03-01

    Full Text Available One of the most recurrent observations after two decades of microbial evolution experiments regards the dynamics of fitness change. In a given environment, low-fitness genotypes are recurrently observed to adapt faster than their more fit counterparts. Since adaptation is the main macroscopic outcome of Darwinian evolution, studying its patterns of change could potentially provide insight into key issues of evolutionary theory, from fixation dynamics to the genetic architecture of organisms. Here, we re-analyze several published datasets from experimental evolution with microbes and show that, despite large differences in the origin of the data, a pattern of inverse dependence of adaptability with fitness clearly emerges. In quantitative terms, it is remarkable to observe little if any degree of idiosyncrasy across systems as diverse as virus, bacteria and yeast. The universality of this phenomenon suggests that its emergence might be understood from general principles, giving rise to the exciting prospect that evolution might be statistically predictable at the macroscopic level. We discuss this possibilities in the light of the various theories of adaptation that have been proposed and delineate future directions of research.

  14. Adaptive evolution and effective population size in wild house mice

    Phifer-Rixey, M.; Bonhomme, F.; Boursot, P.; Churchill, G. A.; Piálek, Jaroslav; Tucker, P.; Nachman, M.

    2012-01-01

    Roč. 29, č. 10 (2012), s. 2949-2955. ISSN 0737-4038 R&D Projects: GA ČR GA206/08/0640 Institutional support: RVO:68081766 Keywords : substitution * adaptation * evolution * effective population size * house mouse Subject RIV: EG - Zoology Impact factor: 10.353, year: 2012

  15. The adaptive evolution of the mammalian mitochondrial genome

    O'Brien Stephen J

    2008-03-01

    Full Text Available Abstract Background The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Results Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas. Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Conclusion Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.

  16. An Adaptive Multiobjective Differential Evolution Algorithm

    Fangqing Gu

    2013-02-01

    Full Text Available The mutation strategy and control parameter have a significant influence on the performance of differential evolution. An local and global mutation operator based subregion and external set strategies are proposed in this paper. They use the idea of direct simplexmethod of mathematical programming. It is advantageous to search the better solutions in the search space. The local mutation operator is applied to improve the local search performance of the algorithm and accelerate convergence speed. The global mutation operator is usedto exploit a wider area and jump out of the local optima. Anadaptive strategy for assigning mutation strategies and control parameters is proposed in this paper. The more successful is a mutation strategy and control parameter setting in the previous search, the more chance it will be used in the further search. Moreover, a novel crossover operator based subregion and external set strategy also is introduced. In order to demonstrate the performance of the proposed algorithm, it is compared with the MOEA/D-DE and the hybrid-NSGA-II-DE. The result indicates that the proposed algorithm is efficient.

  17. Evolution of evolvability via adaptation of mutation rates.

    Bedau, Mark A; Packard, Norman H

    2003-05-01

    We examine a simple form of the evolution of evolvability-the evolution of mutation rates-in a simple model system. The system is composed of many agents moving, reproducing, and dying in a two-dimensional resource-limited world. We first examine various macroscopic quantities (three types of genetic diversity, a measure of population fitness, and a measure of evolutionary activity) as a function of fixed mutation rates. The results suggest that (i) mutation rate is a control parameter that governs a transition between two qualitatively different phases of evolution, an ordered phase characterized by punctuated equilibria of diversity, and a disordered phase of characterized by noisy fluctuations around an equilibrium diversity, and (ii) the ability of evolution to create adaptive structure is maximized when the mutation rate is just below the transition between these two phases of evolution. We hypothesize that this transition occurs when the demands for evolutionary memory and evolutionary novelty are typically balanced. We next allow the mutation rate itself to evolve, and we observe that evolving mutation rates adapt to values at this transition. Furthermore, the mutation rates adapt up (or down) as the evolutionary demands for novelty (or memory) increase, thus supporting the balance hypothesis. PMID:12689727

  18. The two sides of complement C3d: evolution of electrostatics in a link between innate and adaptive immunity.

    Chris A Kieslich

    Full Text Available The interaction between complement fragment C3d and complement receptor 2 (CR2 is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement system and adaptive immunity, which is formed through the association of the B-cell co-receptor complex, including the C3d-CR2 interaction, is a much more recent adaptation. Human C3d and CR2 have net charges of -1 and +7 respectively, and are believed to have evolved favoring the role of electrostatics in their functions. To investigate the role of electrostatics in the function and evolution of human C3d and CR2, we have applied electrostatic similarity methods to identify regions of evolutionarily conserved electrostatic potential based on 24 homologues of complement C3d and 4 homologues of CR2. We also examine the effects of structural perturbation, as introduced through molecular dynamics and mutations, on spatial distributions of electrostatic potential to identify perturbation resistant regions, generated by so-called electrostatic "hot-spots". Distributions of electrostatic similarity based on families of perturbed structures illustrate the presence of electrostatic "hot-spots" at the two functional sites of C3d, while the surface of CR2 lacks electrostatic "hot-spots" despite its excessively positive nature. We propose that the electrostatic "hot-spots" of C3d have evolved to optimize its dual-functionality (covalently attaching to pathogen surfaces and interaction with CR2, which are both necessary for the formation B-cell co-receptor complexes. Comparison of the perturbation resistance of the electrostatic character of the homologues of C3d suggests that there was an emergence of a new role of electrostatics, and a transition in the function of C3

  19. OASes and STING: adaptive evolution in concert.

    Mozzi, Alessandra; Pontremoli, Chiara; Forni, Diego; Clerici, Mario; Pozzoli, Uberto; Bresolin, Nereo; Cagliani, Rachele; Sironi, Manuela

    2015-04-01

    OAS (2'-5'-oligoadenylate synthases) proteins and cyclic GMP-AMP synthase (cGAS, gene symbol: MB21D1) patrol the cytoplasm for the presence of foreign nucleic acids. Upon binding to double-stranded RNA or double-stranded DNA, OAS proteins and cGAS produce nucleotide second messengers to activate RNase L and STING (stimulator of interferon genes, gene symbol: TMEM173), respectively; this leads to the initiation of antiviral responses. We analyzed the evolutionary history of the MB21D1-TMEM173 and OAS-RNASEL axes in primates and bats and found evidence of widespread positive selection in both orders. In TMEM173, residue 230, a major determinant of response to natural ligands and to mimetic drugs (e.g., DMXAA), was positively selected in Primates and Chiroptera. In both orders, selection also targeted an α-helix/loop element in RNase L that modulates the enzyme preference for single-stranded RNA versus stem loops. Analysis of positively selected sites in OAS1, OAS2, and MB21D1 revealed parallel evolution, with the corresponding residues being selected in different genes. As this cannot result from gene conversion, these data suggest that selective pressure acting on OAS and MB21D1 genes is related to nucleic acid recognition and to the specific mechanism of enzyme activation, which requires a conformational change. Finally, a population genetics-phylogenetics analysis in humans, chimpanzees, and gorillas detected several positively selected sites in most genes. Data herein shed light into species-specific differences in infection susceptibility and in response to synthetic compounds, with relevance for the design of synthetic compounds as vaccine adjuvants. PMID:25752600

  20. Local adaptation and the evolution of chromosome fusions.

    Guerrero, Rafael F; Kirkpatrick, Mark

    2014-10-01

    We use forward and coalescent models of population genetics to study chromosome fusions that reduce the recombination between two locally adapted loci. Under a continent-island model, a fusion spreads and reaches a polymorphic equilibrium when it causes recombination between locally adapted alleles to be less than their selective advantage. In contrast, fusions in a two-deme model always spread; whether it reaches a polymorphic equilibrium or becomes fixed depends on the relative recombination rates of fused homozygotes and heterozygotes. Neutral divergence around fusion polymorphisms is markedly increased, showing peaks at the point of fusion and at the locally adapted loci. Local adaptation could explain the evolution of many of chromosome fusions, which are some of the most common chromosome rearrangements in nature. PMID:24964074

  1. Adaptive Network Dynamics and Evolution of Leadership in Collective Migration

    Pais, Darren

    2013-01-01

    The evolution of leadership in migratory populations depends not only on costs and benefits of leadership investments but also on the opportunities for individuals to rely on cues from others through social interactions. We derive an analytically tractable adaptive dynamic network model of collective migration with fast timescale migration dynamics and slow timescale adaptive dynamics of individual leadership investment and social interaction. For large populations, our analysis of bifurcations with respect to investment cost explains the observed hysteretic effect associated with recovery of migration in fragmented environments. Further, we show a minimum connectivity threshold above which there is evolutionary branching into leader and follower populations. For small populations, we show how the topology of the underlying social interaction network influences the emergence and location of leaders in the adaptive system. Our model and analysis can describe other adaptive network dynamics involving collective...

  2. Adaptive functional evolution of leptin in cold-adaptive pika family

    2008-01-01

    @@ Aresearch team led by Prof.ZHAO Xinquan with the CAS Northwest Institute of Plateau Biology has put forward the viewpoint for the first time that adaptive functional evolution may occur in the leptin protein of the pika (Ochotona) family, a typical coldadaptive mammal.

  3. Adaptive evolution of facial colour patterns in Neotropical primates

    Santana, Sharlene E.; Lynch Alfaro, Jessica; Alfaro, Michael E.

    2012-01-01

    The rich diversity of primate faces has interested naturalists for over a century. Researchers have long proposed that social behaviours have shaped the evolution of primate facial diversity. However, the primate face constitutes a unique structure where the diverse and potentially competing functions of communication, ecology and physiology intersect, and the major determinants of facial diversity remain poorly understood. Here, we provide the first evidence for an adaptive role of facial co...

  4. In the light of directed evolution: Pathways of adaptive protein evolution

    Bloom, Jesse D; Arnold, Frances H.

    2009-01-01

    Directed evolution is a widely-used engineering strategy for improving the stabilities or biochemical functions of proteins by repeated rounds of mutation and selection. These experiments offer empirical lessons about how proteins evolve in the face of clearly-defined laboratory selection pressures. Directed evolution has revealed that single amino acid mutations can enhance properties such as catalytic activity or stability and that adaptation can often occur through pathways consisting of s...

  5. Insights into Arbovirus Evolution and Adaptation from Experimental Studies

    Alexander T. Ciota

    2010-12-01

    Full Text Available Arthropod-borne viruses (arboviruses are maintained in nature by cycling between vertebrate hosts and haematophagous invertebrate vectors. These viruses are responsible for causing a significant public health burden throughout the world, with over 100 species having the capacity to cause human disease. Arbovirus outbreaks in previously naïve environments demonstrate the potential of these pathogens for expansion and emergence, possibly exacerbated more recently by changing climates. These recent outbreaks, together with the continued devastation caused by endemic viruses, such as Dengue virus which persists in many areas, demonstrate the need to better understand the selective pressures that shape arbovirus evolution. Specifically, a comprehensive understanding of host-virus interactions and how they shape both host-specific and virus‑specific evolutionary pressures is needed to fully evaluate the factors that govern the potential for host shifts and geographic expansions. One approach to advance our understanding of the factors influencing arbovirus evolution in nature is the use of experimental studies in the laboratory. Here, we review the contributions that laboratory passage and experimental infection studies have made to the field of arbovirus adaptation and evolution, and how these studies contribute to the overall field of arbovirus evolution. In particular, this review focuses on the areas of evolutionary constraints and mutant swarm dynamics; how experimental results compare to theoretical predictions; the importance of arbovirus ecology in shaping viral swarms; and how current knowledge should guide future questions relevant to understanding arbovirus evolution.

  6. Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots.

    Philipp J Keller

    2009-06-01

    Full Text Available Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome. Meiosis, which is thought to play a major role in handling mutations on the population level, recombines chromosomes via non-randomly distributed hot spots for meiotic recombination. In many genomes, various types of genetic elements are distributed in patterns that are currently not well understood. In particular, important (essential genes are arranged in clusters, which often cannot be explained by a functional relationship of the involved genes. Here we show by computer simulation that essential gene (EG clustering provides a fitness benefit in handling deleterious mutations in sexual populations with variable levels of inbreeding and outbreeding. We find that recessive lethal mutations enforce a selective pressure towards clustered genome architectures. Our simulations correctly predict (i the evolution of non-random distributions of meiotic crossovers, (ii the genome-wide anti-correlation of meiotic crossovers and EG clustering, (iii the evolution of EG enrichment in pericentromeric regions and (iv the associated absence of meiotic crossovers (cold centromeres. Our results furthermore predict optimal crossover rates for yeast chromosomes, which match the experimentally determined rates. Using a Saccharomyces cerevisiae conditional mutator strain, we show that haploid lethal phenotypes result predominantly from mutation of single loci and generally do not impair mating, which leads to an accumulation of mutational load following meiosis and mating. We hypothesize that purging of deleterious mutations in essential genes constitutes an important factor driving meiotic crossover. Therefore, the increased robustness of populations to deleterious mutations, which arises from clustered genome architectures, may provide a significant selective force shaping crossover distribution. Our analysis reveals a new

  7. Research of circuit evolution design based on adaptive HereBoy algorithm

    Huicong WU; Wang, Jinze; Chuncao LIU; Gao, JinJin

    2015-01-01

    Aiming at solving the convergence rate problem in the latter stage of circuit evolution design, adaptive HereBoy algorithm together with the population evolution idea of GA is adapted to study the impact of adaptive-adjust factor on the evolution of convergence rate. One circuit model which is based on the similarities between combinatorial circuit and neural network is proposed, on which the matrix encoding scheme of combinatorial circuit is discussed. Besides of this, extrint evolution is a...

  8. Localizing recent adaptive evolution in the human genome

    Williamson, Scott H; Hubisz, Melissa J; Clark, Andrew G;

    2007-01-01

    Identifying genomic locations that have experienced selective sweeps is an important first step toward understanding the molecular basis of adaptive evolution. Using statistical methods that account for the confounding effects of population demography, recombination rate variation, and single......-nucleotide polymorphism ascertainment, while also providing fine-scale estimates of the position of the selected site, we analyzed a genomic dataset of 1.2 million human single-nucleotide polymorphisms genotyped in African-American, European-American, and Chinese samples. We identify 101 regions of the human genome with......, clusters of olfactory receptors, genes involved in nervous system development and function, immune system genes, and heat shock genes. We also observe consistent evidence of selective sweeps in centromeric regions. In general, we find that recent adaptation is strikingly pervasive in the human genome, with...

  9. Strategy Uniform Crossover Adaptation Evolution in a Minority Game

    杨伟松; 汪秉宏; 全宏俊; 胡进锟

    2003-01-01

    We propose a new adaptation minority game for understanding the complex dynamical behaviour characterized by agent interactions competing limited resources in many natural and social systems. Intelligent agents may modify a part of their strategies periodically, depending on the strategyperformances. In the present model, the strategies will be updated according to a uniform-crossover variation process inspired by genetic evolution algorithm in biology. The performances of the agents in our model are calculated for different parameter conditions. It has been found that the new system may evolve via the strategy uniform crossover adaptation mechanism into a frozen equilibrium state in which the performance of the system may reach the best limit, implying the strongest cooperation among agents and the most effective utilization of the social resources.

  10. Live hot, die young: transmission distortion in recombination hotspots.

    Graham Coop

    2007-03-01

    Full Text Available There is strong evidence that hotspots of meiotic recombination in humans are transient features of the genome. For example, hotspot locations are not shared between human and chimpanzee. Biased gene conversion in favor of alleles that locally disrupt hotspots is a possible explanation of the short lifespan of hotspots. We investigate the implications of such a bias on human hotspots and their evolution. Our results demonstrate that gene conversion bias is a sufficiently strong force to produce the observed lack of sharing of intense hotspots between species, although sharing may be much more common for weaker hotspots. We investigate models of how hotspots arise, and find that only models in which hotspot alleles do not initially experience drive are consistent with observations of rather hot hotspots in the human genome. Mutations acting against drive cannot successfully introduce such hotspots into the population, even if there is direct selection for higher recombination rates, such as to ensure correct segregation during meiosis. We explore the impact of hotspot alleles on patterns of haplotype variation, and show that such alleles mask their presence in population genetic data, making them difficult to detect.

  11. Adaptive evolution of the vertebrate skeletal muscle sodium channel

    Jian Lu

    2011-01-01

    Full Text Available Tetrodotoxin (TTX is a highly potent neurotoxin that blocks the action potential by selectively binding to voltage-gated sodium channels (Na v. The skeletal muscle Na v (Na v1.4 channels in most pufferfish species and certain North American garter snakes are resistant to TTX, whereas in most mammals they are TTX-sensitive. It still remains unclear as to whether the difference in this sensitivity among the various vertebrate species can be associated with adaptive evolution. In this study, we investigated the adaptive evolution of the vertebrate Na v1.4 channels. By means of the CODEML program of the PAML 4.3 package, the lineages of both garter snakes and pufferfishes were denoted to be under positive selection. The positively selected sites identified in the p-loop regions indicated their involvement in Na v1.4 channel sensitivity to TTX. Most of these sites were located in the intracellular regions of the Na v1.4 channel, thereby implying the possible association of these regions with the regulation of voltage-sensor movement.

  12. Adaptive network dynamics and evolution of leadership in collective migration

    Pais, Darren; Leonard, Naomi E.

    2014-01-01

    The evolution of leadership in migratory populations depends not only on costs and benefits of leadership investments but also on the opportunities for individuals to rely on cues from others through social interactions. We derive an analytically tractable adaptive dynamic network model of collective migration with fast timescale migration dynamics and slow timescale adaptive dynamics of individual leadership investment and social interaction. For large populations, our analysis of bifurcations with respect to investment cost explains the observed hysteretic effect associated with recovery of migration in fragmented environments. Further, we show a minimum connectivity threshold above which there is evolutionary branching into leader and follower populations. For small populations, we show how the topology of the underlying social interaction network influences the emergence and location of leaders in the adaptive system. Our model and analysis can be extended to study the dynamics of collective tracking or collective learning more generally. Thus, this work may inform the design of robotic networks where agents use decentralized strategies that balance direct environmental measurements with agent interactions.

  13. Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae

    Boehnisch Claudia

    2008-04-01

    Full Text Available Abstract Background Lysozymes are important model enzymes in biomedical research with a ubiquitous taxonomic distribution ranging from phages up to plants and animals. Their main function appears to be defence against pathogens, although some of them have also been implicated in digestion. Whereas most organisms have only few lysozyme genes, nematodes of the genus Caenorhabditis possess a surprisingly large repertoire of up to 15 genes. Results We used phylogenetic inference and sequence analysis tools to assess the evolution of lysozymes from three congeneric nematode species, Caenorhabditis elegans, C. briggsae, and C. remanei. Their lysozymes fall into three distinct clades, one belonging to the invertebrate-type and the other two to the protist-type lysozymes. Their diversification is characterised by (i ancestral gene duplications preceding species separation followed by maintenance of genes, (ii ancestral duplications followed by gene loss in some of the species, and (iii recent duplications after divergence of species. Both ancestral and recent gene duplications are associated in several cases with signatures of adaptive sequence evolution, indicating that diversifying selection contributed to lysozyme differentiation. Current data strongly suggests that genetic diversity translates into functional diversity. Conclusion Gene duplications are a major source of evolutionary innovation. Our analysis provides an evolutionary framework for understanding the diversification of lysozymes through gene duplication and subsequent differentiation. This information is expected to be of major value in future analysis of lysozyme function and in studies of the dynamics of evolution by gene duplication.

  14. Hotspots Definition Study

    In the Dutch research programme Climate changes Spatial Planning (CcSP) many scientific projects are carried out. They often take a multidisciplinary approach to the climate issue. However, more attention needed to be given to embedding the programme into practice. Therefore, the board decided to start a hotspot programme. A hotspot was defined as a pilot project in a sector, place or region in which spatial planning and climate change play an important role in the physical shape and land use of the area and where conflicts of interest are found between these and other factors. The hotspot programme started with a definition study. This report is the result of this study. The goal of the study was to identify, describe and evaluate possible hotspots. In two workshops with policy-makers from national and regional governments, consultancy firms and nature conservation organizations, a large number of potential hotspots were identified. Fifteen were selected after the workshops took place and described in detail. The selection was done using a set of conditional criteria, criteria that all had to be met. Two potential hotspots were withdrawn after the selection. Since the Board of the CcSP programme expressed its interest in financing six to seven hotspots, a prioritization was made, using prioritizing criteria. Also the potential hotspots were assessed looking at regional distribution, thematic coverage and target groups. After this assessment and an analysis of the hotspots taking some other factors into account (eg. some hotspots were very similar or one could easily be incorporated in another one) five hotspots were selected: Kampen, Biesbosch-Haringvliet, Zuidplaspolder, Delta Waters and Tilburg. Options to fill the last two places were: Grounds for Change, Noordoostpolder, Oude Vaart Valley and Arnhem/Nijmegen (KAN). For these remaining potential hotspots draft terms of reference were drawn as basis for a project proposals. These terms of reference are added to

  15. Adaptive evolution of centromere proteins in plants and animals

    Henikoff Steven

    2004-08-01

    Full Text Available Abstract Background Centromeres represent the last frontiers of plant and animal genomics. Although they perform a conserved function in chromosome segregation, centromeres are typically composed of repetitive satellite sequences that are rapidly evolving. The nucleosomes of centromeres are characterized by a special H3-like histone (CenH3, which evolves rapidly and adaptively in Drosophila and Arabidopsis. Most plant, animal and fungal centromeres also bind a large protein, centromere protein C (CENP-C, that is characterized by a single 24 amino-acid motif (CENPC motif. Results Whereas we find no evidence that mammalian CenH3 (CENP-A has been evolving adaptively, mammalian CENP-C proteins contain adaptively evolving regions that overlap with regions of DNA-binding activity. In plants we find that CENP-C proteins have complex duplicated regions, with conserved amino and carboxyl termini that are dissimilar in sequence to their counterparts in animals and fungi. Comparisons of Cenpc genes from Arabidopsis species and from grasses revealed multiple regions that are under positive selection, including duplicated exons in some grasses. In contrast to plants and animals, yeast CENP-C (Mif2p is under negative selection. Conclusions CENP-Cs in all plant and animal lineages examined have regions that are rapidly and adaptively evolving. To explain these remarkable evolutionary features for a single-copy gene that is needed at every mitosis, we propose that CENP-Cs, like some CenH3s, suppress meiotic drive of centromeres during female meiosis. This process can account for the rapid evolution and the complexity of centromeric DNA in plants and animals as compared to fungi.

  16. Comparative genomics reveals insights into avian genome evolution and adaptation

    Zhang, Guojie; Li, Cai; Li, Qiye;

    2014-01-01

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

  17. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    Fei Shi

    2011-01-01

    Full Text Available Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions.

  18. Adaptive evolution of synthetic cooperating communities improves growth performance.

    Xiaolin Zhang

    Full Text Available Symbiotic interactions between organisms are important for human health and biotechnological applications. Microbial mutualism is a widespread phenomenon and is important in maintaining natural microbial communities. Although cooperative interactions are prevalent in nature, little is known about the processes that allow their initial establishment, govern population dynamics and affect evolutionary processes. To investigate cooperative interactions between bacteria, we constructed, characterized, and adaptively evolved a synthetic community comprised of leucine and lysine Escherichia coli auxotrophs. The co-culture can grow in glucose minimal medium only if the two auxotrophs exchange essential metabolites - lysine and leucine (or its precursors. Our experiments showed that a viable co-culture using these two auxotrophs could be established and adaptively evolved to increase growth rates (by ∼3 fold and optical densities. While independently evolved co-cultures achieved similar improvements in growth, they took different evolutionary trajectories leading to different community compositions. Experiments with individual isolates from these evolved co-cultures showed that changes in both the leucine and lysine auxotrophs improved growth of the co-culture. Interestingly, while evolved isolates increased growth of co-cultures, they exhibited decreased growth in mono-culture (in the presence of leucine or lysine. A genome-scale metabolic model of the co-culture was also constructed and used to investigate the effects of amino acid (leucine or lysine release and uptake rates on growth and composition of the co-culture. When the metabolic model was constrained by the estimated leucine and lysine release rates, the model predictions agreed well with experimental growth rates and composition measurements. While this study and others have focused on cooperative interactions amongst community members, the adaptive evolution of communities with other

  19. Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals

    Machado João

    2011-11-01

    Full Text Available Abstract Background Matrix extracellular phosphoglycoprotein (MEPE belongs to a family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs that play a key role in skeleton development, particularly in mineralization, phosphate regulation and osteogenesis. MEPE associated disorders cause various physiological effects, such as loss of bone mass, tumors and disruption of renal function (hypophosphatemia. The study of this developmental gene from an evolutionary perspective could provide valuable insights on the adaptive diversification of morphological phenotypes in vertebrates. Results Here we studied the adaptive evolution of the MEPE gene in 26 Eutherian mammals and three birds. The comparative genomic analyses revealed a high degree of evolutionary conservation of some coding and non-coding regions of the MEPE gene across mammals indicating a possible regulatory or functional role likely related with mineralization and/or phosphate regulation. However, the majority of the coding region had a fast evolutionary rate, particularly within the largest exon (1467 bp. Rodentia and Scandentia had distinct substitution rates with an increased accumulation of both synonymous and non-synonymous mutations compared with other mammalian lineages. Characteristics of the gene (e.g. biochemical, evolutionary rate, and intronic conservation differed greatly among lineages of the eight mammalian orders. We identified 20 sites with significant positive selection signatures (codon and protein level outside the main regulatory motifs (dentonin and ASARM suggestive of an adaptive role. Conversely, we find three sites under selection in the signal peptide and one in the ASARM motif that were supported by at least one selection model. The MEPE protein tends to accumulate amino acids promoting disorder and potential phosphorylation targets. Conclusion MEPE shows a high number of selection signatures, revealing the crucial role of positive selection in the

  20. Fisheries-induced neutral and adaptive evolution in exploited fish populations and consequences for their adaptive potential

    Marty, Lise; Dieckmann, Ulf; Ernande, Bruno

    2015-01-01

    Fishing may induce neutral and adaptive evolution affecting life-history traits, and molecular evidence has shown that neutral genetic diversity has declined in some exploited populations. Here, we theoretically study the interplay between neutral and adaptive evolution caused by fishing. An...... individual-based eco-genetic model is devised that includes neutral and functional loci in a realistic ecological setting. In line with theoretical expectations, we find that fishing induces evolution towards slow growth, early maturation at small size and higher reproductive investment. We show, first, that...

  1. How Adaptive Learning Affects Evolution: Reviewing Theory on the Baldwin Effect

    Sznajder, B.; Sabelis, M.W.; M. Egas

    2011-01-01

    We review models of the Baldwin effect, i.e., the hypothesis that adaptive learning (i.e., learning to improve fitness) accelerates genetic evolution of the phenotype. Numerous theoretical studies scrutinized the hypothesis that a non-evolving ability of adaptive learning accelerates evolution of genetically determined behavior. However, their results are conflicting in that some studies predict an accelerating effect of learning on evolution, whereas others show a decelerating effect. We beg...

  2. How adaptive learning affects evolution: reviewing theory on the Baldwin effect

    Sznajder, B.; Sabelis, M.W.; M. Egas

    2012-01-01

    We review models of the Baldwin effect, i.e., the hypothesis that adaptive learning (i.e., learning to improve fitness) accelerates genetic evolution of the phenotype. Numerous theoretical studies scrutinized the hypothesis that a non-evolving ability of adaptive learning accelerates evolution of genetically determined behavior. However, their results are conflicting in that some studies predict an accelerating effect of learning on evolution, whereas others show a decelerating effect. We beg...

  3. Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment.

    Suenaga, Hikaru

    2015-01-01

    Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose. PMID:26441940

  4. Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment

    Hikaru eSuenaga

    2015-09-01

    Full Text Available Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and therefore enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose.

  5. MODIS Hotspot Validation over Thailand

    Veerachai Tanpipat; Prayoonyong Nuchaiya; Kiyoshi Honda

    2009-01-01

    To ensure remote sensing MODIS hotspot (also known as active fire products or hotspots) quality and precision in forest fire control and management in Thailand, an increased level of confidence is needed. Accuracy assessment of MODIS hotspots utilizing field survey data validation is described. A quantitative evaluation of MODIS hotspot products has been carried out since the 2007 forest fire season. The carefully chosen hotspots were scattered throughout the country and within the protected ...

  6. Nutrient-dependent/pheromone-controlled adaptive evolution: a model

    James Vaughn Kohl

    2013-06-01

    Full Text Available Background: The prenatal migration of gonadotropin-releasing hormone (GnRH neurosecretory neurons allows nutrients and human pheromones to alter GnRH pulsatility, which modulates the concurrent maturation of the neuroendocrine, reproductive, and central nervous systems, thus influencing the development of ingestive behavior, reproductive sexual behavior, and other behaviors. Methods: This model details how chemical ecology drives adaptive evolution via: (1 ecological niche construction, (2 social niche construction, (3 neurogenic niche construction, and (4 socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH and systems biology. Results: Nutrients are metabolized to pheromones that condition behavior in the same way that food odors condition behavior associated with food preferences. The epigenetic effects of olfactory/pheromonal input calibrate and standardize molecular mechanisms for genetically predisposed receptor-mediated changes in intracellular signaling and stochastic gene expression in GnRH neurosecretory neurons of brain tissue. For example, glucose and pheromones alter the hypothalamic secretion of GnRH and LH. A form of GnRH associated with sexual orientation in yeasts links control of the feedback loops and developmental processes required for nutrient acquisition, movement, reproduction, and the diversification of species from microbes to man. Conclusion: An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively

  7. Chromosome inversions, adaptive cassettes and the evolution of species' ranges.

    Kirkpatrick, Mark; Barrett, Brian

    2015-05-01

    A chromosome inversion can spread when it captures locally adapted alleles or when it is introduced into a species by hybridization with adapted alleles that were previously absent. We present a model that shows how both processes can cause a species range to expand. Introgression of an inversion that carries novel, locally adapted alleles is a particularly powerful mechanism for range expansion. The model supports the earlier proposal that introgression of an inversion triggered a large range expansion of a malaria mosquito. These results suggest a role for inversions as cassettes of genes that can accelerate adaptation by crossing species boundaries, rather than protecting genomes from introgression. PMID:25583098

  8. Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics

    Castoe, Todd A.; de Koning, A. P. Jason; Pollock, David D.

    2010-01-01

    Definitive identification of convergent evolution, the acquisition of the same biological trait in unrelated lineages, provides one of the most compelling sources of evidence for natural selection. Although numerous examples of convergent morphological evolution are well known (such as the independent development of wings in birds and mammals), cases of convergent evolution at the molecular-genetic level appear to be quite rare. We recently discovered a remarkable case of convergent molecular...

  9. HOTSPOT: The Snake River Scientifi c Drilling Project— Tracking the Yellowstone Hotspot Through Space and Time

    Douglas F. Williams

    2006-09-01

    Full Text Available The project “HOTSPOT: Scientifi c Drilling of the Snake River Plain” held its inaugural workshop in Twin Falls, Idaho, U.S.A. on 18–21 May 2006. This inter-disciplinary workshop, sponsored by the International Continental Scientifi c Drilling Program (ICDP, explored the major scientifi c and logistical issues central to a transect of boreholes along the hotspot track and addressing the geochemical evolution of continental lithosphere in response to interaction with deepseated mantle hotspots or plumes. A series of four to six bore holes is envisioned, each about 1.5–2.0 km deep and located along the axis of the Snake River Plain. The holes will specific ally target the origin and evolution of hotspot-related volcanism in space and time. To accomplish scientific and logistical planning, sixty scientists from six countries attended the workshop.

  10. Widespread adaptive evolution during repeated evolutionary radiations in New World lupins

    Nevado, Bruno; Atchison, Guy W.; Hughes, Colin E.; Filatov, Dmitry A.

    2016-01-01

    The evolutionary processes that drive rapid species diversification are poorly understood. In particular, it is unclear whether Darwinian adaptation or non-adaptive processes are the primary drivers of explosive species diversifications. Here we show that repeated rapid radiations within New World lupins (Lupinus, Leguminosae) were underpinned by a major increase in the frequency of adaptation acting on coding and regulatory changes genome-wide. This contrasts with far less frequent adaptation in genomes of slowly diversifying lupins and all other plant genera analysed. Furthermore, widespread shifts in optimal gene expression coincided with shifts to high rates of diversification and evolution of perenniality, a putative key adaptation trait thought to have triggered the evolutionary radiations in New World lupins. Our results reconcile long-standing debate about the relative importance of protein-coding and regulatory evolution, and represent the first unambiguous evidence for the rapid onset of lineage- and genome-wide accelerated Darwinian evolution during rapid species diversification. PMID:27498896

  11. Bacteria are different: Observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes

    Levin, Bruce R.; Bergstrom, Carl T.

    2000-01-01

    To some extent, the genetic theory of adaptive evolution in bacteria is a simple extension of that developed for sexually reproducing eukaryotes. In other, fundamental ways, the process of adaptive evolution in bacteria is quantitatively and qualitatively different from that of organisms for which recombination is an integral part of the reproduction process. In this speculative and opinionated discussion, we explore these differences. In particular, we consider (i...

  12. Characterizing Microbe-Environment Interactions Through Experimental Evolution: The Autonomous Adaptive Directed Evolution Chamber

    Ibanez, C. R.; Blaich, J.; Owyang, S.; Storrs, A.; Moffet, A.; Wong, N.; Zhou, J.; Gentry, D.

    2015-12-01

    We are developing a laboratory system for studying micro- to meso-scale interactions between microorganisms and their physicochemical environments. The Autonomous Adaptive Directed Evolution Chamber (AADEC) cultures microorganisms in controlled,small-scale geochemical environments. It observes corresponding microbial interactions to these environments and has the ability to adjust thermal, chemical, and other parameters in real time in response to these interactions. In addition to the sensed data, the system allows the generation of time-resolved ecological, genomic, etc. samples on the order of microbial generations. The AADEC currently houses cultures in liquid media and controls UVC radiation, heat exposure, and nutrient supply. In a proof-of-concept experimental evolution application, it can increase UVC radiation resistance of Escherichia coli cultures by iteratively exposing them to UVC and allowing the surviving cells to regrow. A baseline characterization generated a million fold resistance increase. This demonstration uses a single-well growth chamber prototype, but it was limited by scalability. We have expanded upon this system by implementing a microwell plate compatible fluidics system and sensor housing. This microwell plate system increases the diversity of microbial interactions seen in response to the geochemical environments generated by the system, allowing greater control over individual cultures' environments and detection of rarer events. The custom microfluidic card matches the footprint of a standard microwell plate. This card enables controllable fluid flow between wells and introduces multiple separate exposure and sensor chambers, increasing the variety of sensors compatible with the system. This gives the device control over scale and the interconnectedness of environments within the system. The increased controllability of the multiwell system provides a platform for implementing machine learning algorithms that will autonomously

  13. Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor

    Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben;

    2013-01-01

    evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae...

  14. Experiments on the role of deleterious mutations as stepping stones in adaptive evolution

    Covert, Arthur W.; Richard E Lenski; Wilke, Claus O.; Ofria, Charles

    2013-01-01

    It might seem obvious that deleterious mutations must impede evolution. However, a later mutation may interact with a deleterious predecessor, facilitating otherwise inaccessible adaptations. Although such interactions have been reported before, it is unclear whether they are rare and inconsequential or, alternatively, are important for sustaining adaptation. We studied digital organisms—computer programs that replicate and evolve—to compare adaptation in populations where deleterious mutatio...

  15. Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

    Flegr Jaroslav

    2013-01-01

    Abstract Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ. Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecol...

  16. Trichinella spiralis: the evolution of adaptation and parasitism

    Parasitism among nematodes has occurred in multiple, independent events. Deciphering processes that drive species diversity and adaptation are keys to understanding parasitism and advancing control strategies. Studies have been put forth on morphological and physiological aspects of parasitism and a...

  17. Adaptive evolution of complex innovations through stepwise metabolic niche expansion.

    Szappanos, Balázs; Fritzemeier, Jonathan; Csörgő, Bálint; Lázár, Viktória; Lu, Xiaowen; Fekete, Gergely; Bálint, Balázs; Herczeg, Róbert; Nagy, István; Notebaart, Richard A; Lercher, Martin J; Pál, Csaba; Papp, Balázs

    2016-01-01

    A central challenge in evolutionary biology concerns the mechanisms by which complex metabolic innovations requiring multiple mutations arise. Here, we propose that metabolic innovations accessible through the addition of a single reaction serve as stepping stones towards the later establishment of complex metabolic features in another environment. We demonstrate the feasibility of this hypothesis through three complementary analyses. First, using genome-scale metabolic modelling, we show that complex metabolic innovations in Escherichia coli can arise via changing nutrient conditions. Second, using phylogenetic approaches, we demonstrate that the acquisition patterns of complex metabolic pathways during the evolutionary history of bacterial genomes support the hypothesis. Third, we show how adaptation of laboratory populations of E. coli to one carbon source facilitates the later adaptation to another carbon source. Our work demonstrates how complex innovations can evolve through series of adaptive steps without the need to invoke non-adaptive processes. PMID:27197754

  18. Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits

    Martin Olivier C; Espinosa-Soto Carlos; Wagner Andreas

    2011-01-01

    Abstract Background Many important evolutionary adaptations originate in the modification of gene regulatory circuits to produce new gene activity phenotypes. How do evolving populations sift through an astronomical number of circuits to find circuits with new adaptive phenotypes? The answer may often involve phenotypic plasticity. Phenotypic plasticity allows a genotype to produce different - alternative - phenotypes after non-genetic perturbations that include gene expression noise, environ...

  19. Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits

    Espinosa-Soto, C.; Martin, O. C.; Wagner, A

    2011-01-01

    BACKGROUND: Many important evolutionary adaptations originate in the modification of gene regulatory circuits to produce new gene activity phenotypes. How do evolving populations sift through an astronomical number of circuits to find circuits with new adaptive phenotypes? The answer may often involve phenotypic plasticity. Phenotypic plasticity allows a genotype to produce different - alternative - phenotypes after non-genetic perturbations that include gene expression noise, environment...

  20. From lifetime to evolution: timescales of human gut microbiota adaptation

    Sara eQuercia; Marco eCandela; Cristina eGiuliani; Silvia eTurroni; Donata eLuiselli; Simone eRampelli; Patrizia eBrigidi; Claudio eFranceschi; Maria Giulia eBacalini; Paolo eGaragnani; Chiara ePirazzini

    2014-01-01

    Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The gut microbiota continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily varia...

  1. From lifetime to evolution: timescales of human gut microbiota adaptation

    Quercia, Sara; Candela, Marco; Giuliani, Cristina; Turroni, Silvia; Luiselli, Donata; Rampelli, Simone; Brigidi, Patrizia; Franceschi, Claudio; Bacalini, Maria Giulia; Garagnani, Paolo; Pirazzini, Chiara

    2014-01-01

    Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations i...

  2. BEHAVIOR EVOLUTION OF WEB SERVICES WITH DYNAMIC ADAPTATION

    Ginjala Srikanth Reddy; Bagam Laxmaiah

    2013-01-01

    Web services are self contained, self-describing modular application that can be published, located, and invoked across the Web‖. The Business Organization and many companies provides their services to meet new needs, technological changes and requirements of these users. So the providers and web designers to provides the needs of Adaptable Web Services that supports the existing features as well as new features also. we mean to be able to automatically adapt the business processes at run-t...

  3. The bill of evolution: trophic adaptations in anseriform birds

    Kurk, Carolina Deborah

    2008-01-01

    Adaptive radiation involves the rapid divergence of a single ancestral species into a group of species each occupying a different ecological niche. Differences between species are the result of trade-offs in the ability to exploit different environments to avoid competitive interactions. The many species of wildfowl and their diversity in feeding methods are believed to represent an example of adaptive radiation. Frequently used feeding methods are filtering small food items from water and te...

  4. Fecundity increase supports adaptive radiation hypothesis in spider web evolution

    Todd A. Blackledge; Coddington, Jonathan A.; Agnarsson, Ingi

    2009-01-01

    Identifying the mechanisms driving adaptive radiations is key to explaining the diversity of life. The extreme reliance of spiders upon silk for survival provides an exceptional system in which to link patterns of diversification to adaptive changes in silk use. Most of the world’s 41,000 species of spiders belong to two apical lineages of spiders that exhibit quite different silk ecologies, distinct from their ancestors. Orb spiders spin highly stereotyped webs that are suspended in air and ...

  5. Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

    Marvig, Rasmus Lykke; Madsen Sommer, Lea Mette; Molin, Søren;

    2015-01-01

    Little is known about how within-host evolution compares between genotypically different strains of the same pathogenic species. We sequenced the whole genomes of 474 longitudinally collected clinical isolates of Pseudomonas aeruginosa sampled from 34 children and young individuals with cystic...... fibrosis. Our analysis of 36 P. aeruginosa lineages identified convergent molecular evolution in 52 genes. This list of genes suggests a role in host adaptation for remodeling of regulatory networks and central metabolism, acquisition of antibiotic resistance and loss of extracellular virulence factors...... genes involved in host adaptation may help in predicting bacterial evolution in patients with cystic fibrosis and in the design of future intervention strategies....

  6. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    Yin-Chu Wang; Song Qin; Fei Shi

    2011-01-01

    Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is ...

  7. Data Warehouse Schema Evolution and Adaptation Framework Using Ontology

    Thenmozhi, M.; K.Vivekanandan

    2014-01-01

    Data Warehouse systems aim at integrating data from multiple heterogeneous, distributed, autonomous data sources. Due to changing business needs the data warehouse systems are never meant to be static. Changes in the data source structure or business requirements would result in the evolution of data warehouse schema structure. When data warehouse schema evolves the dependent modules such as its mappings, queries and views gets affected. The existing works on data warehouse evolution focus on...

  8. Immune genes undergo more adaptive evolution than non-immune system genes in Daphnia pulex

    McTaggart Seanna J

    2012-05-01

    Full Text Available Abstract Background Understanding which parts of the genome have been most influenced by adaptive evolution remains an unsolved puzzle. Some evidence suggests that selection has the greatest impact on regions of the genome that interact with other evolving genomes, including loci that are involved in host-parasite co-evolutionary processes. In this study, we used a population genetic approach to test this hypothesis by comparing DNA sequences of 30 putative immune system genes in the crustacean Daphnia pulex with 24 non-immune system genes. Results In support of the hypothesis, results from a multilocus extension of the McDonald-Kreitman (MK test indicate that immune system genes as a class have experienced more adaptive evolution than non-immune system genes. However, not all immune system genes show evidence of adaptive evolution. Additionally, we apply single locus MK tests and calculate population genetic parameters at all loci in order to characterize the mode of selection (directional versus balancing in the genes that show the greatest deviation from neutral evolution. Conclusions Our data are consistent with the hypothesis that immune system genes undergo more adaptive evolution than non-immune system genes, possibly as a result of host-parasite arms races. The results of these analyses highlight several candidate loci undergoing adaptive evolution that could be targeted in future studies.

  9. HOTSPOT: The Snake River Scientific Drilling Project – Tracking the Yellowstone Hotspot Through Space and Time

    Shervais, J. W.; Branney, M.J.; Geist, D.J.; Hanan, B. B.; Hughes, S; Prokopenko, A. A.; D. F. Williams

    2006-01-01

    The project “HOTSPOT: Scientifi c Drilling of the Snake River Plain” held its inaugural workshop in Twin Falls, Idaho, U.S.A. on 18–21 May 2006. This inter-disciplinary workshop, sponsored by the International Continental Scientifi c Drilling Program (ICDP), explored the major scientifi c and logistical issues central to a transect of boreholes along the hotspot track and addressing the geochemical evolution of continental lithosphere in response to interaction with deepseated mantle hotspots...

  10. Complex Adaptive Systems and the Evolution of Reciprocation

    Sigmund, K.

    1998-01-01

    Complex adaptive systems play a major role in the theory of reciprocal altruism. Starting with Axelrod's celebrated computer tournaments, a wide variety of computer simulations show that cooperation can evolve in populations of selfish agents, both with direct and indirect reciprocation.

  11. Hotspots critical care evaluation

    D. Humphris; N A Connell; Meyer, E.; Lees, A

    2006-01-01

    This report evaluates a series of critical care education interventions for nurses which took place within Southampton University Hospital Trust (SUHT) and Portsmouth Hospital Trust (PHT) in 2004 and 2005. These interventions were funded by the Hotspots project and commissioned by the Hampshire and Isle of Wight Workforce Development Directorate (WDD). As part of the ongoing commitment to incorporate evidence into practice, the WDD commissioned an independent impact evaluation of these interv...

  12. From lifetime to evolution: timescales of human gut microbiota adaptation

    Sara eQuercia

    2014-11-01

    Full Text Available Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The gut microbiota continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.

  13. From lifetime to evolution: timescales of human gut microbiota adaptation.

    Quercia, Sara; Candela, Marco; Giuliani, Cristina; Turroni, Silvia; Luiselli, Donata; Rampelli, Simone; Brigidi, Patrizia; Franceschi, Claudio; Bacalini, Maria Giulia; Garagnani, Paolo; Pirazzini, Chiara

    2014-01-01

    Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies. PMID:25408692

  14. Adaptive virulence evolution: the good old fitness-based approach.

    Alizon, Samuel; Michalakis, Yannis

    2015-05-01

    Infectious diseases could be expected to evolve towards complete avirulence to their hosts if given enough time. However, this is not the case. Often, virulence is maintained because it is linked to adaptive advantages to the parasite, a situation that is often associated with the hypothesis known as the transmission-virulence trade-off hypothesis. Here, we argue that this hypothesis has three limitations, which are related to how virulence is defined, the possibility of multiple trade-offs, and the difficulty of testing the hypothesis empirically. By adopting a fitness-based approach, where the relation between virulence and the fitness of the parasite throughout its life cycle is directly assessed, it is possible to address these limitations and to determine directly whether virulence is adaptive. PMID:25837917

  15. Adaptive evolution of centromere proteins in plants and animals

    Henikoff Steven; Bryson Terri D; Talbert Paul B

    2004-01-01

    Abstract Background Centromeres represent the last frontiers of plant and animal genomics. Although they perform a conserved function in chromosome segregation, centromeres are typically composed of repetitive satellite sequences that are rapidly evolving. The nucleosomes of centromeres are characterized by a special H3-like histone (CenH3), which evolves rapidly and adaptively in Drosophila and Arabidopsis. Most plant, animal and fungal centromeres also bind a large protein, centromere prote...

  16. Diversity and adaptive evolution of Saccharomyces wine yeast: a review

    Marsit, Souhir; Dequin, Sylvie

    2015-01-01

    Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary hi...

  17. Adaptive Evolution of the FADS Gene Cluster within Africa

    Mathias, Rasika A; Fu, Wenqing; Akey, Joshua M.; Ainsworth, Hannah C; Torgerson, Dara G.; Ruczinski, Ingo; Sergeant, Susan; Kathleen C. Barnes; Chilton, Floyd H.

    2012-01-01

    Long chain polyunsaturated fatty acids (LC-PUFAs) are essential for brain structure, development, and function, and adequate dietary quantities of LC-PUFAs are thought to have been necessary for both brain expansion and the increase in brain complexity observed during modern human evolution. Previous studies conducted in largely European populations suggest that humans have limited capacity to synthesize brain LC-PUFAs such as docosahexaenoic acid (DHA) from plant-based medium chain (MC) PUFA...

  18. Microbial community succession mechanism coupling with adaptive evolution of adsorption performance in chalcopyrite bioleaching.

    Feng, Shoushuai; Yang, Hailin; Wang, Wu

    2015-09-01

    The community succession mechanism of Acidithiobacillus sp. coupling with adaptive evolution of adsorption performance were systematically investigated. Specifically, the μmax of attached and free cells was increased and peak time was moved ahead, indicating both cell growth of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans was promoted. In the mixed strains system, the domination courses of A. thiooxidans was dramatically shortened from 22th day to 15th day, although community structure finally approached to the normal system. Compared to A. ferrooxidans, more positive effects of adaptive evolution on cell growth of A. thiooxidans were shown in either single or mixed strains system. Moreover, higher concentrations of sulfate and ferric ions indicated that both sulfur and iron metabolism was enhanced, especially of A. thiooxidans. Consistently, copper ion production was improved from 65.5 to 88.5 mg/L. This new adaptive evolution and community succession mechanism may be useful for guiding similar bioleaching processes. PMID:25978855

  19. Self-adaptive differential evolution algorithm incorporating local search for protein-ligand docking

    Differential Evolution (DE) algorithm is powerful in optimization problems over several real parameters. DE depends on strategies to generate new trial solutions and the associated parameter values for searching performance. In self-adaptive DE, the automatic learning about previous evolution was used to determine the best mutation strategy and its parameter settings. By combining the self-adaptive DE and Hooke Jeeves local search, we developed a new docking method named SADock (Strategy Adaptation Dock) with the help of AutoDock4 scoring function. As the accuracy and performance of SADock was evaluated in self-docking using the Astex diverse set, the introduced SADock showed better success ratio (89%) than the success ratio (60%) of the Lamarckian genetic algorithm (LGA) of AutoDock4. The self-adapting scheme enabled our new docking method to converge fast and to be robust through the various docking problems.

  20. Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

    Shen Tong

    2012-03-01

    Full Text Available Abstract Background Cetaceans (whales, dolphins and porpoises are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs, which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω values along most (30 out of 33 examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS, and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions This

  1. Experiments on the role of deleterious mutations as stepping stones in adaptive evolution.

    Covert, Arthur W; Lenski, Richard E; Wilke, Claus O; Ofria, Charles

    2013-08-20

    Many evolutionary studies assume that deleterious mutations necessarily impede adaptive evolution. However, a later mutation that is conditionally beneficial may interact with a deleterious predecessor before it is eliminated, thereby providing access to adaptations that might otherwise be inaccessible. It is unknown whether such sign-epistatic recoveries are inconsequential events or an important factor in evolution, owing to the difficulty of monitoring the effects and fates of all mutations during experiments with biological organisms. Here, we used digital organisms to compare the extent of adaptive evolution in populations when deleterious mutations were disallowed with control populations in which such mutations were allowed. Significantly higher fitness levels were achieved over the long term in the control populations because some of the deleterious mutations served as stepping stones across otherwise impassable fitness valleys. As a consequence, initially deleterious mutations facilitated the evolution of complex, beneficial functions. We also examined the effects of disallowing neutral mutations, of varying the mutation rate, and of sexual recombination. Populations evolving without neutral mutations were able to leverage deleterious and compensatory mutation pairs to overcome, at least partially, the absence of neutral mutations. Substantially raising or lowering the mutation rate reduced or eliminated the long-term benefit of deleterious mutations, but introducing recombination did not. Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions. PMID:23918358

  2. Evolutionary constraints on adaptive evolution during range expansion in an invasive plant

    Colautti, Robert I.; Christopher G. Eckert; Barrett, Spencer C. H.

    2010-01-01

    Biological invasions may expose populations to strong selection for local adaptation along geographical gradients in climate. However, evolution during contemporary timescales can be constrained by low standing genetic variation and genetic correlations among life-history traits. We examined limits to local adaptation associated with northern migration of the invasive wetland plant purple loosestrife (Lythrum salicaria) using a selection model incorporating a trade-off between flowering time ...

  3. Aspects of the Evolution and Adaptive Significance of Regional Endothermy in Fishes

    Sepulveda, Chugey J.A.

    2005-01-01

    This dissertation addressed questions related to the selective advantages of regional endothermy and its independent evolution among several fish groups. The chapters integrate laboratory and field physiological measurements to provide a better understanding ofthe evolution of regional endothermy and its importance as an adaptation to the pelagic environment. Studies on the swimming energetics of the eastern Pacific bonito (Sarda chiliensis) revealed that the bonito had a similar cost of tran...

  4. Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility

    Tomatis, Pablo E.; Fabiane, Stella M.; Simona, Fabio; Carloni, Paolo; Sutton, Brian J.; Vila, Alejandro J.

    2008-01-01

    Protein evolution is crucial for organismal adaptation and fitness. This process takes place by shaping a given 3-dimensional fold for its particular biochemical function within the metabolic requirements and constraints of the environment. The complex interplay between sequence, structure, functionality, and stability that gives rise to a particular phenotype has limited the identification of traits acquired through evolution. This is further complicated by the fact that mutations are pleiot...

  5. Genomic evidence of adaptive evolution in emergent Vibrio parahaemolyticus ecotypes

    Jeffrey W. Turner

    2016-07-01

    Full Text Available Abstract The ubiquitous marine bacterium Vibrio parahaemolyticus is a leading cause of illness associated with seafood consumption. The emergence of two genetically distinct ecotypes (ST3 and ST36 has led to an alarming increase in the size and frequency of disease outbreaks. We conducted a genomic comparison of 30 V. parahaemolyticus genomes that represent a diverse collection of 15 genetically distinct ecotypes, including newly sequenced representatives of ST3 and ST36, isolated from both clinical and environmental sources. A multistep evolutionary analysis showed that genes associated with sensing and responding to environmental stimuli have evolved under positive selection, identifying examples of convergent evolution between ST3 and ST36. A comparison of predicted proteomes indicated that ST3 and ST36 ecotypes laterally acquired tens of novel genes associated with a variety of functions including dormancy, homeostasis and membrane transport. Genes identified in this study play an apparent role in environmental fitness and may confer cross protection against stressors encountered in the human host. Together, these results show the evolution of stress response is an important genetic mechanism correlated with the recent emergence of the ST3 and ST36 ecotypes.

  6. The evolution of adhesiveness as a social adaptation.

    Garcia, Thomas; Doulcier, Guilhem; De Monte, Silvia

    2015-01-01

    Cellular adhesion is a key ingredient to sustain collective functions of microbial aggregates. Here, we investigate the evolutionary origins of adhesion and the emergence of groups of genealogically unrelated cells with a game-theoretical model. The considered adhesiveness trait is costly, continuous and affects both group formation and group-derived benefits. The formalism of adaptive dynamics reveals two evolutionary stable strategies, at each extreme on the axis of adhesiveness. We show that cohesive groups can evolve by small mutational steps, provided the population is already endowed with a minimum adhesiveness level. Assortment between more adhesive types, and in particular differential propensities to leave a fraction of individuals ungrouped at the end of the aggregation process, can compensate for the cost of increased adhesiveness. We also discuss the change in the social nature of more adhesive mutations along evolutionary trajectories, and find that altruism arises before directly beneficial behavior, despite being the most challenging form of cooperation. PMID:26613415

  7. Adaptive topology evolution in information-sharing social networks

    Chen, Duanbing; Lu, Linyuan; Medo, Matus; Zhang, Yi-Cheng; Zhou, Tao

    2011-01-01

    The advent of Internet and World Wide Web has led to unprecedent growth of the information available. People usually face the information overload by following a limited number of sources which best fit their interests. In order to get the picture it is important to address issues like who people do follow and how they search for better information sources. In this work we conduct an empirical analysis on different on-line social networking sites, and draw inspiration from its results to present different source selection strategies in an adaptive model for social recommendation. We show that local search rules which enhance the typical topological features of real social communities give rise to network configurations that are globally optimal. Hence these abstract rules help to create networks which are both effective in information diffusion and people friendly.

  8. Diversity and adaptive evolution of Saccharomyces wine yeast: a review.

    Marsit, Souhir; Dequin, Sylvie

    2015-11-01

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

  9. The genomic signatures of Shigella evolution, adaptation and geographical spread.

    The, Hao Chung; Thanh, Duy Pham; Holt, Kathryn E; Thomson, Nicholas R; Baker, Stephen

    2016-04-01

    Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp. PMID:26923111

  10. Geopolitical hotspots : Saudi Arabia

    This presentation reviewed the geopolitics of energy in the Middle East, with particular reference to Saudi Arabia as a potential hotspot. The author examined the question of who actually governs Saudi Arabia and the core relationship between Crown Prince Abdullah and the interior Minister, Prince Nayef. Issues regarding the country's social stability were discussed with reference to the high unemployment rate. The financial security of Saudi Arabia was also discussed with reference to the need for economic and political reform. Expectations for Saudi petroleum output were outlined along with regional spurs for energy competition and OPEC participation

  11. Adaptation to salinity in mangroves: Implication on the evolution of salt-tolerance

    LIANG Shan; ZHOU RenChao; DONG SuiSui; SHI SuHua

    2008-01-01

    A plant's adaptation to its environment is one of the most important issues in evolutionary biology. Mangroves are trees that inhabit the intertidal zones with high salinity, while salt tolerance competence of different species varies. Even congeneric species usually occupy distinct positions of intertidal zones due to differential ability of salt tolerance. Some species have different ecotypes that adapt well to littoral and terrestrial environments, respectively. These characteristics of mangroves make them ideal ecological models to study adaptation of mangroves to salinity. Here, we briefly depict adaptive traits of salt tolerance in mangroves with respect to anatomy, physiology and biochemistry, and review the major advances recently made on both the genetic and genomic levels. Results from studies on individual genes or whole genomes of mangroves have confirmed conclusions drawn from studies on anatomy, physiology and biochemistry, and have further indicated that specific patterns of gene expression might contribute to adaptive evolution of mangroves under high salinity. By integrating all information from mangroves and performing comparisons among species of mangroves and non-mangroves, we could give a general picture of adaptation of mangroves to salinity, thus providing a new avenue for further studies on a molecular basis of adaptive evolution of mangroves.

  12. Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates

    Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa;

    2014-01-01

    BACKGROUND:  Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. METHODS:  We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used ...

  13. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    Sen, Lin

    2011-06-03

    Abstract Background The chloroplast-localized ribulose-1, 5-biphosphate carboxylase\\/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. Results We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. Conclusions The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such

  14. Adaptive evolution of the FADS gene cluster within Africa.

    Rasika A Mathias

    Full Text Available Long chain polyunsaturated fatty acids (LC-PUFAs are essential for brain structure, development, and function, and adequate dietary quantities of LC-PUFAs are thought to have been necessary for both brain expansion and the increase in brain complexity observed during modern human evolution. Previous studies conducted in largely European populations suggest that humans have limited capacity to synthesize brain LC-PUFAs such as docosahexaenoic acid (DHA from plant-based medium chain (MC PUFAs due to limited desaturase activity. Population-based differences in LC-PUFA levels and their product-to-substrate ratios can, in part, be explained by polymorphisms in the fatty acid desaturase (FADS gene cluster, which have been associated with increased conversion of MC-PUFAs to LC-PUFAs. Here, we show evidence that these high efficiency converter alleles in the FADS gene cluster were likely driven to near fixation in African populations by positive selection ∼85 kya. We hypothesize that selection at FADS variants, which increase LC-PUFA synthesis from plant-based MC-PUFAs, played an important role in allowing African populations obligatorily tethered to marine sources for LC-PUFAs in isolated geographic regions, to rapidly expand throughout the African continent 60-80 kya.

  15. The elusive nature of adaptive mitochondrial DNA evolution of an Arctic lineage prone to frequent introgression

    Melo-Ferreira, Jose; Vilela, Joana; Fonseca, Miguel M.;

    2014-01-01

    Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from...... understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread...... lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may...

  16. Self-adaptive learning based discrete differential evolution algorithm for solving CJWTA problem

    Yu Xue; Yi Zhuang; Tianquan Ni; Siru Ni; Xuezhi Wen

    2014-01-01

    Cooperative jamming weapon-target assignment (CJWTA) problem is a key issue in electronic countermeasures (ECM). Some symbols which relevant to the CJWTA are defined firstly. Then, a formulation of jamming fitness is presented. Final y, a model of the CJWTA problem is constructed. In order to solve the CJWTA problem efficiently, a self-adaptive learning based discrete differential evolution (SLDDE) algorithm is proposed by introduc-ing a self-adaptive learning mechanism into the traditional discrete differential evolution algorithm. The SLDDE algorithm steers four candidate solution generation strategies simultaneously in the framework of the self-adaptive learning mechanism. Computa-tional simulations are conducted on ten test instances of CJWTA problem. The experimental results demonstrate that the proposed SLDDE algorithm not only can generate better results than only one strategy based discrete differential algorithms, but also outper-forms two algorithms which are proposed recently for the weapon-target assignment problems.

  17. Adaptive evolution of the osmoregulation-related genes in cetaceans during secondary aquatic adaptation

    Xu, Shixia; Yang, Yunxia; Zhou, Xuming; Xu, Junxiao; Zhou, Kaiya; Yang, Guang

    2013-01-01

    Background Osmoregulation was a primary challenge for cetaceans during the evolutionary transition from a terrestrial to a mainly hyperosmotic environment. Several physiological mechanisms have been suggested to maintain the water and salt balance in cetaceans, but their genetic and evolutionary bases remain poorly explored. The current study investigated the genes involved in osmoregulation in cetaceans and compared them with their counterparts in terrestrial mammals to test whether adaptive...

  18. Adaptation to Temporally Fluctuating Environments by the Evolution of Maternal Effects.

    Dey, Snigdhadip; Proulx, Stephen R; Teotónio, Henrique

    2016-02-01

    All organisms live in temporally fluctuating environments. Theory predicts that the evolution of deterministic maternal effects (i.e., anticipatory maternal effects or transgenerational phenotypic plasticity) underlies adaptation to environments that fluctuate in a predictably alternating fashion over maternal-offspring generations. In contrast, randomizing maternal effects (i.e., diversifying and conservative bet-hedging), are expected to evolve in response to unpredictably fluctuating environments. Although maternal effects are common, evidence for their adaptive significance is equivocal since they can easily evolve as a correlated response to maternal selection and may or may not increase the future fitness of offspring. Using the hermaphroditic nematode Caenorhabditis elegans, we here show that the experimental evolution of maternal glycogen provisioning underlies adaptation to a fluctuating normoxia-anoxia hatching environment by increasing embryo survival under anoxia. In strictly alternating environments, we found that hermaphrodites evolved the ability to increase embryo glycogen provisioning when they experienced normoxia and to decrease embryo glycogen provisioning when they experienced anoxia. At odds with existing theory, however, populations facing irregularly fluctuating normoxia-anoxia hatching environments failed to evolve randomizing maternal effects. Instead, adaptation in these populations may have occurred through the evolution of fitness effects that percolate over multiple generations, as they maintained considerably high expected growth rates during experimental evolution despite evolving reduced fecundity and reduced embryo survival under one or two generations of anoxia. We develop theoretical models that explain why adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that such deterministic maternal effects are more likely to contribute to adaptation than

  19. Long-term dynamics of adaptive evolution in a globally important phytoplankton species to ocean acidification.

    Schlüter, Lothar; Lohbeck, Kai T; Gröger, Joachim P; Riebesell, Ulf; Reusch, Thorsten B H

    2016-07-01

    Marine phytoplankton may adapt to ocean change, such as acidification or warming, because of their large population sizes and short generation times. Long-term adaptation to novel environments is a dynamic process, and phenotypic change can take place thousands of generations after exposure to novel conditions. We conducted a long-term evolution experiment (4 years = 2100 generations), starting with a single clone of the abundant and widespread coccolithophore Emiliania huxleyi exposed to three different CO2 levels simulating ocean acidification (OA). Growth rates as a proxy for Darwinian fitness increased only moderately under both levels of OA [+3.4% and +4.8%, respectively, at 1100 and 2200 μatm partial pressure of CO2 (Pco2)] relative to control treatments (ambient CO2, 400 μatm). Long-term adaptation to OA was complex, and initial phenotypic responses of ecologically important traits were later reverted. The biogeochemically important trait of calcification, in particular, that had initially been restored within the first year of evolution was later reduced to levels lower than the performance of nonadapted populations under OA. Calcification was not constitutively lost but returned to control treatment levels when high CO2-adapted isolates were transferred back to present-day control CO2 conditions. Selection under elevated CO2 exacerbated a general decrease of cell sizes under long-term laboratory evolution. Our results show that phytoplankton may evolve complex phenotypic plasticity that can affect biogeochemically important traits, such as calcification. Adaptive evolution may play out over longer time scales (>1 year) in an unforeseen way under future ocean conditions that cannot be predicted from initial adaptation responses. PMID:27419227

  20. Rapid evolution in response to introduced predators II: the contribution of adaptive plasticity

    Knapp Roland A

    2007-02-01

    Full Text Available Abstract Background Introductions of non-native species can significantly alter the selective environment for populations of native species, which can respond through phenotypic plasticity or genetic adaptation. We examined phenotypic and genetic responses of Daphnia populations to recent introductions of non-native fish to assess the relative roles of phenotypic plasticity versus genetic change in causing the observed patterns. The Daphnia community in alpine lakes throughout the Sierra Nevada of California (USA is ideally suited for investigation of rapid adaptive evolution because there are multiple lakes with and without introduced fish predators. We conducted common-garden experiments involving presence or absence of chemical cues produced by fish and measured morphological and life-history traits in Daphnia melanica populations collected from lakes with contrasting fish stocking histories. The experiment allowed us to assess the degree of population differentiation due to fish predation and examine the contribution of adaptive plasticity in the response to predator introduction. Results Our results show reductions in egg number and body size of D. melanica in response to introduced fish. These phenotypic changes have a genetic basis but are partly due to a direct response to chemical cues from fish via adaptive phenotypic plasticity. Body size showed the largest phenotypic change, on the order of nine phenotypic standard deviations, with approximately 11% of the change explained by adaptive plasticity. Both evolutionary and plastic changes in body size and egg number occurred but no changes in the timing of reproduction were observed. Conclusion Native Daphnia populations exposed to chemical cues produced by salmonid fish predators display adaptive plasticity for body size and fecundity. The magnitude of adaptive plasticity was insufficient to explain the total phenotypic change, so the realized change in phenotypic means in populations

  1. Structures of the Apo and FAD-Bound Forms of 2-Hydroxybiphenyl 3-monooxygenase (HbpA) Locate Activity Hotspots Identified by Using Directed Evolution

    Jensen, Chantel N.; Mielke, Tamara; Farrugia, Joseph E; Frank, Annika; Man, Henry; Hart, Sam; Turkenburg, Johan P.; Grogan, Gideon

    2015-01-01

    The FAD-dependent monooxygenase HbpA from Pseudomonas azelaica HBP1 catalyses the hydroxylation of 2-hydroxybiphenyl (2HBP) to 2,3-dihydroxybiphenyl (23DHBP). HbpA has been used extensively as a model for studying flavoprotein hydroxylases under process conditions, and has also been subjected to directed-evolution experiments that altered its catalytic properties. The structure of HbpA has been determined in its apo and FAD-complex forms to resolutions of 2.76 and 2.03 Å, respectively. Compar...

  2. A Convergent Differential Evolution Algorithm with Hidden Adaptation Selection for Engineering Optimization

    Zhongbo Hu

    2014-01-01

    Full Text Available Many improved differential Evolution (DE algorithms have emerged as a very competitive class of evolutionary computation more than a decade ago. However, few improved DE algorithms guarantee global convergence in theory. This paper developed a convergent DE algorithm in theory, which employs a self-adaptation scheme for the parameters and two operators, that is, uniform mutation and hidden adaptation selection (haS operators. The parameter self-adaptation and uniform mutation operator enhance the diversity of populations and guarantee ergodicity. The haS can automatically remove some inferior individuals in the process of the enhancing population diversity. The haS controls the proposed algorithm to break the loop of current generation with a small probability. The breaking probability is a hidden adaptation and proportional to the changes of the number of inferior individuals. The proposed algorithm is tested on ten engineering optimization problems taken from IEEE CEC2011.

  3. Diversity-dependent cladogenesis and trait evolution in the adaptive radiation of the auks (aves: alcidae).

    Weir, Jason T; Mursleen, Sara

    2013-02-01

    Through the course of an adaptive radiation, the evolutionary speed of cladogenesis and ecologically relevant trait evolution are expected to slow as species diversity increases, niches become occupied, and ecological opportunity declines. We develop new likelihood-based models to test diversity-dependent evolution in the auks, one of only a few families of seabirds adapted to underwater "flight," and which exhibit a large variety of bill sizes and shapes. Consistent with the expectations of adaptive radiation, we find both a decline in rates of cladogenesis (a sixfold decline) and bill shape (a 64-fold decline) evolution as diversity increased. Bill shape diverged into two clades at the basal cladogenesis event with one clade possessing mostly long, narrow bills used to forage primarily on fish, and the other with short thick bills used to forage primarily on plankton. Following this initial divergence in bill shape, size, a known correlate of both prey size and maximum diving depth, diverged rapidly within each of these clades. These results suggest that adaptive radiation in foraging traits underwent initial divergence in bill shape to occupy different food resources, followed by size differentiation to subdivide each niche along the depth axis of the water column. PMID:23356613

  4. The evolution of control and distribution of adaptive mutations in a metabolic pathway.

    Wright, Kevin M; Rausher, Mark D

    2010-02-01

    In an attempt to understand whether it should be expected that some genes tend to be used disproportionately often by natural selection, we investigated two related phenomena: the evolution of flux control among enzymes in a metabolic pathway and properties of adaptive substitutions in pathway enzymes. These two phenomena are related by the principle that adaptive substitutions should occur more frequently in enzymes with greater flux control. Predicting which enzymes will be preferentially involved in adaptive evolution thus requires an evolutionary theory of flux control. We investigated the evolution of enzyme control in metabolic pathways with two models of enzyme kinetics: metabolic control theory (MCT) and Michaelis-Menten saturation kinetics (SK). Our models generate two main predictions for pathways in which reactions are moderately to highly irreversible: (1) flux control will evolve to be highly unequal among enzymes in a pathway and (2) upstream enzymes evolve a greater control coefficient then those downstream. This results in upstream enzymes fixing the majority of beneficial mutations during adaptive evolution. Once the population has reached high fitness, the trend is reversed, with the majority of neutral/slightly deleterious mutations occurring in downstream enzymes. These patterns are the result of three factors (the first of these is unique to the MCT simulations while the other two seem to be general properties of the metabolic pathways): (1) the majority of randomly selected, starting combinations of enzyme kinetic rates generate pathways that possess greater control for the upstream enzymes compared to downstream enzymes; (2) selection against large pools of intermediate substrates tends to prevent majority control by downstream enzymes; and (3) equivalent mutations in enzyme kinetic rates have the greatest effect on flux for enzymes with high levels of flux control, and these enzymes will accumulate adaptive substitutions, strengthening their

  5. Genomics of adaptation during experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa.

    Alex Wong

    2012-09-01

    Full Text Available Adaptation is likely to be an important determinant of the success of many pathogens, for example when colonizing a new host species, when challenged by antibiotic treatment, or in governing the establishment and progress of long-term chronic infection. Yet, the genomic basis of adaptation is poorly understood in general, and for pathogens in particular. We investigated the genetics of adaptation to cystic fibrosis-like culture conditions in the presence and absence of fluoroquinolone antibiotics using the opportunistic pathogen Pseudomonas aeruginosa. Whole-genome sequencing of experimentally evolved isolates revealed parallel evolution at a handful of known antibiotic resistance genes. While the level of antibiotic resistance was largely determined by these known resistance genes, the costs of resistance were instead attributable to a number of mutations that were specific to individual experimental isolates. Notably, stereotypical quinolone resistance mutations in DNA gyrase often co-occurred with other mutations that, together, conferred high levels of resistance but no consistent cost of resistance. This result may explain why these mutations are so prevalent in clinical quinolone-resistant isolates. In addition, genes involved in cyclic-di-GMP signalling were repeatedly mutated in populations evolved in viscous culture media, suggesting a shared mechanism of adaptation to this CF-like growth environment. Experimental evolutionary approaches to understanding pathogen adaptation should provide an important complement to studies of the evolution of clinical isolates.

  6. Self-Adaptive Surrogate-Assisted Covariance Matrix Adaptation Evolution Strategy

    Loshchilov, Ilya; Sebag, Michèle

    2012-01-01

    This paper presents a novel mechanism to adapt surrogate-assisted population-based algorithms. This mechanism is applied to ACM-ES, a recently proposed surrogate-assisted variant of CMA-ES. The resulting algorithm, saACM-ES, adjusts online the lifelength of the current surrogate model (the number of CMA-ES generations before learning a new surrogate) and the surrogate hyper-parameters. Both heuristics significantly improve the quality of the surrogate model, yielding a significant speed-up of saACM-ES compared to the ACM-ES and CMA-ES baselines. The empirical validation of saACM-ES on the BBOB-2012 noiseless testbed demonstrates the efficiency and the scalability w.r.t the problem dimension and the population size of the proposed approach, that reaches new best results on some of the benchmark problems.

  7. [Episodes of adaptive evolution of mitochondrial genome in Asiatic salamanders (Amphibia, Caudata, Hynobiidae)].

    Maliarchuk, B A; Derenko, M V; Denisova, G A

    2014-02-01

    To elucidate the effect of natural selection on the evolution of mitochondrial DNA (mtDNA) in Asiatic salamanders of the family Hynobiidae, nucleotide sequences of 12 protein-coding genes were analyzed. Using a mixed effects model of evolution, it was found that, in spite of the pronounced effect of negative selection on the mtDNA evolution in Hynobiidae (which is typical for the animals in general), two phylogenetic clusters, the West Asian one, represented by the genera Ranodon and Paradactylodon, and North Eurasian one, represented by the genus Salamandrella, were formed under the influence of episodic positive selection. Analysis of protein sequences encoded by the mitochondrial genome also supported the influence of positive selection on the evolution of Hynobiidae at some stages of their cladogenesis. It is suggested that the signatures of adaptive evolution detected in the mtDNA of Hynobiidae were determined by the complex and long-lasting history of their formation, accompanied by adaptation to the changing environment. PMID:25711027

  8. Venus: Mantle convection, hotspots, and tectonics

    The putative paradigm that planets of the same size and mass have the same tectonic style led to the adaptation of the mechanisms of terrestrial plate tectonics as the a priori model of the way Venus should behave. Data acquired over the last decade by Pioneer Venus, Venera, and ground-based radar have modified this view sharply and have illuminated the lack of detailed understanding of the plate tectonic mechanism. For reference, terrestrial mechanisms are briefly reviewed. Venusian lithospheric divergence, hotspot model, and horizontal deformation theories are proposed and examined

  9. Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes

    ZHANG Wenjuan; ZHANG Yuan; ZHONG Yang

    2006-01-01

    Nonsynonymous-synonymous substitution rate ratio (dN/dS) is an important measure for evaluating selective pressure based on the protein-coding sequences. Maximum likelihood (ML) method with codon-substitution models is a powerful statistic tool for detecting amino acid sites under positive selection and adaptive evolution. We analyzed the hepatitis C virus (HCV) envelope protein-coding sequences from 18 general geno/ subtypes worldwide, and found 4 amino acid sites under positive selection. Since these sites are located in different immune epitopes, it is reasonable to anticipate that our study would have potential values in biomedicine. It also suggests that the ML method is an effective way to detect adaptive evolution in virus proteins with relatively high genetic diversity.

  10. Tolerance and adaptive evolution of triacylglycerol-producing Rhodococcus opacus to lignocellulose-derived inhibitors

    Kurosawa, Kazuhiko; Laser, Josephine; Sinskey, Anthony J.

    2015-01-01

    First published by BioMed Central Kurosawa, Kazuhiko ; Laser, Josephine ; Sinskey Anthony J : Tolerance and adaptive evolution of triacylglycerol-producing Rhodococcus opacus to lignocellulose-derived inhibitors. - In: Biotechnoloy for Biofuels. - ISSN 1754-6834 (online). - 8 (2015), art. 76. - doi:10.1186/s13068-015-0258-3. Background: Lignocellulosic biomass has been investigated as a renewable non-food source for production of biofuels. A significant technical challenge to using lign...

  11. An Adaptive Hybrid Algorithm Based on Particle Swarm Optimization and Differential Evolution for Global Optimization

    Xiaobing Yu; Jie Cao; Haiyan Shan; Li Zhu; Jun Guo

    2014-01-01

    Particle swarm optimization (PSO) and differential evolution (DE) are both efficient and powerful population-based stochastic search techniques for solving optimization problems, which have been widely applied in many scientific and engineering fields. Unfortunately, both of them can easily fly into local optima and lack the ability of jumping out of local optima. A novel adaptive hybrid algorithm based on PSO and DE (HPSO-DE) is formulated by developing a balanced parameter between PSO and D...

  12. Directed evolution on the cold adapted properties of TAB5 alkaline phosphatase

    Koutsioulis, D.; Wang, E.; Tzanodaskalaki, M; Nikiforaki, D.; Deli, A; Feller, Georges; Heikinheimo, P.; Bouriotis, V

    2008-01-01

    Psychrophilic alkaline phosphatase (AP) from the Antarctic strain TAB5 was subjected to directed evolution in order to identify the key residues steering the enzyme's cold-adapted activity and stability. A round of random mutagenesis and further recombination yielded three thermostable and six thermolabile variants of the TAB5 AP. All of the isolated variants were characterised by their residual activity after heat treatment, Michaelis-Menten kinetics, activation energy and microcalorimetric ...

  13. Mathematical study of stochastic models of evolution belonging to the ecological theory of adaptive dynamics

    Champagnat, Nicolas

    2004-01-01

    This thesis is interested in the probabilistic study ofecological models belonging to the recent theory of "adaptive dynamics". After having presented and generalized the scope and biological heuristics of these models, we obtain a microscopic justification of a jump process modelizing evolution from a measure-valued interacting particle system describing the population dynamics at the individual level. This is a time scale separation result based on two asymptotics: rare mutations and large ...

  14. Parameter extraction of different fuel cell models with transferred adaptive differential evolution

    To improve the design and control of FC (fuel cell) models, it is important to extract their unknown parameters. Generally, the parameter extraction problems of FC models can be transformed as nonlinear and multi-variable optimization problems. To extract the parameters of different FC models exactly and fast, in this paper, we propose a transferred adaptive DE (differential evolution) framework, in which the successful parameters of the adaptive DE solving previous problems are properly transferred to solve new optimization problems in the similar problem-domains. Based on this framework, an improved adaptive DE method (TRADE, in short) is presented as an illustration. To verify the performance of our proposal, TRADE is used to extract the unknown parameters of two types of fuel cell models, i.e., PEMFC (proton exchange membrane fuel cell) and SOFC (solid oxide fuel cell). The results of TRADE are also compared with those of other state-of-the-art EAs (evolutionary algorithms). Even though the modification is very simple, the results indicate that TRADE can extract the parameters of both PEMFC and SOFC models exactly and fast. Moreover, the V–I characteristics obtained by TRADE agree well with the simulated and experimental data in all cases for both types of fuel cell models. Also, it improves the performance of the original adaptive DE significantly in terms of both the quality of final solutions and the convergence speed in all cases. Additionally, TRADE is able to provide better results compared with other EAs. - Highlights: • A framework of transferred adaptive differential evolution is proposed. • Based on the framework, an improved differential evolution (TRADE) is presented. • TRADE obtains very promising results to extract the parameters of PEMFC and SOFC models

  15. Evolution and Adaptation of Wild Emmer Wheat Populations to Biotic and Abiotic Stresses.

    Huang, Lin; Raats, Dina; Sela, Hanan; Klymiuk, Valentina; Lidzbarsky, Gabriel; Feng, Lihua; Krugman, Tamar; Fahima, Tzion

    2016-08-01

    The genetic bottlenecks associated with plant domestication and subsequent selection in man-made agroecosystems have limited the genetic diversity of modern crops and increased their vulnerability to environmental stresses. Wild emmer wheat, the tetraploid progenitor of domesticated wheat, distributed along a wide range of ecogeographical conditions in the Fertile Crescent, has valuable "left behind" adaptive diversity to multiple diseases and environmental stresses. The biotic and abiotic stress responses are conferred by series of genes and quantitative trait loci (QTLs) that control complex resistance pathways. The study of genetic diversity, genomic organization, expression profiles, protein structure and function of biotic and abiotic stress-resistance genes, and QTLs could shed light on the evolutionary history and adaptation mechanisms of wild emmer populations for their natural habitats. The continuous evolution and adaptation of wild emmer to the changing environment provide novel solutions that can contribute to safeguarding food for the rapidly growing human population. PMID:27296141

  16. Evolution and Adaptation in Pseudomonas aeruginosa Biofilms Driven by Mismatch Repair System-Deficient Mutators

    Luján, Adela M.; Maciá, María D.; Yang, Liang;

    2011-01-01

    , which are rarely eradicated despite intensive antibiotic therapy. Current knowledge indicates that three major adaptive strategies, biofilm development, phenotypic diversification, and mutator phenotypes [driven by a defective mismatch repair system (MRS)], play important roles in P. aeruginosa chronic...... infections, but the relationship between these strategies is still poorly understood. We have used the flow-cell biofilm model system to investigate the impact of the mutS associated mutator phenotype on development, dynamics, diversification and adaptation of P. aeruginosa biofilms. Through competition...... diversification, evidenced by biofilm architecture features and by a wider range and proportion of morphotypic colony variants, respectively. Additionally, morphotypic variants generated in mutator biofilms showed increased competitiveness, providing further evidence for mutator-driven adaptive evolution in the...

  17. Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation

    Jobson, Richard W.; Nielsen, Rasmus; Laakkonen, Liisa; Wikström, Mårten; Albert, Victor A.

    2004-01-01

    Much recent attention in the study of adaptation of organismal form has centered on developmental regulation. As such, the highly conserved respiratory machinery of eukaryotic cells might seem an unlikely target for selection supporting novel morphologies. We demonstrate that a dramatic molecular evolutionary rate increase in subunit I of cytochrome c oxidase (COX) from an active-trapping lineage of carnivorous plants is caused by positive Darwinian selection. Bladderworts (Utricularia) trap plankton when water-immersed, negatively pressured suction bladders are triggered. The resetting of traps involves active ion transport, requiring considerable energy expenditure. As judged from the quaternary structure of bovine COX, the most profound adaptive substitutions are two contiguous cysteines absent in ≈99.9% of databased COX I sequences from Eukaryota, Archaea, and Bacteria. This motif lies directly at the docking point of COX I helix 3 and cytochrome c, and modeling of bovine COX I suggests the possibility of an unprecedented helix-terminating disulfide bridge that could alter COX/cytochrome c dissociation kinetics. Thus, the key adaptation in Utricularia likely lies in molecular energetic changes that buttressed the mechanisms responsible for the bladderworts' radical morphological evolution. Along with evidence for COX evolution underlying expansion of the anthropoid neocortex, our findings underscore that important morphological and physiological innovations must often be accompanied by specific adaptations in proteins with basic cellular functions. PMID:15596720

  18. Adaptation and evolution in marine environments. Vol. 2. The impacts of global change on biodiversity

    Verde, Cinzia; Di Prisco, Guido (eds.) [CNR, Napoli (Italy). Inst. of Protein Biochemistry

    2013-02-01

    Offers a regionally focussed approach. Describes research on adaptive evolution. State-of-the-art content. The second volume of ''Adaptation and Evolution in Marine Environments - The Impacts of Global Change on Biodiversity'' from the series ''From Pole to Pole'' integrates the marine biology contribution of the first tome to the IPY 2007-2009, presenting overviews of organisms (from bacteria and ciliates to higher vertebrates) thriving on polar continental shelves, slopes and deep sea. The speed and extent of warming in the Arctic and in regions of Antarctica (the Peninsula, at the present) are greater than elsewhere. Changes impact several parameters, in particular the extent of sea ice; organisms, ecosystems and communities that became finely adapted to increasing cold in the course of millions of years are now becoming vulnerable, and biodiversity is threatened. Investigating evolutionary adaptations helps to foresee the impact of changes in temperate areas, highlighting the invaluable contribution of polar marine research to present and future outcomes of the IPY in the Earth system scenario.

  19. Gene duplication and adaptive evolution of digestive proteases in Drosophila arizonae female reproductive tracts.

    Erin S Kelleher

    2007-08-01

    Full Text Available It frequently has been postulated that intersexual coevolution between the male ejaculate and the female reproductive tract is a driving force in the rapid evolution of reproductive proteins. The dearth of research on female tracts, however, presents a major obstacle to empirical tests of this hypothesis. Here, we employ a comparative EST approach to identify 241 candidate female reproductive proteins in Drosophila arizonae, a repleta group species in which physiological ejaculate-female coevolution has been documented. Thirty-one of these proteins exhibit elevated amino acid substitution rates, making them candidates for molecular coevolution with the male ejaculate. Strikingly, we also discovered 12 unique digestive proteases whose expression is specific to the D. arizonae lower female reproductive tract. These enzymes belong to classes most commonly found in the gastrointestinal tracts of a diverse array of organisms. We show that these proteases are associated with recent, lineage-specific gene duplications in the Drosophila repleta species group, and exhibit strong signatures of positive selection. Observation of adaptive evolution in several female reproductive tract proteins indicates they are active players in the evolution of reproductive tract interactions. Additionally, pervasive gene duplication, adaptive evolution, and rapid acquisition of a novel digestive function by the female reproductive tract points to a novel coevolutionary mechanism of ejaculate-female interaction.

  20. Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

    Carolina M. Voloch

    2014-11-01

    Full Text Available Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G, RNA-dependent RNA polymerase (L and polymerase (P genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.

  1. Within-host co-evolution of chronic viruses and the adaptive immune system

    Nourmohammad, Armita

    We normally think of evolution occurring in a population of organisms, in response to their external environment. Rapid evolution of cellular populations also occurs within our bodies, as the adaptive immune system works to eliminate infection. Some pathogens, such as HIV, are able to persist in a host for extended periods of time, during which they also evolve to evade the immune response. In this talk I will introduce an analytical framework for the rapid co-evolution of B-cell and viral populations, based on the molecular interactions between them. Since the co-evolution of antibodies and viruses is perpetually out of equilibrium, I will show how to quantify the amount of adaptation in each of the two populations by analysis of their co-evolutionary history. I will discuss the consequences of competition between lineages of antibodies, and characterize the fate of a given lineage dependent on the state of the antibody and viral populations. In particular, I will discuss the conditions for emergence of highly potent broadly neutralizing antibodies, which are now recognized as critical for designing an effective vaccine against HIV.

  2. Evolution of regulatory networks towards adaptability and stability in a changing environment.

    Lee, Deok-Sun

    2014-11-01

    Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that sparse and heterogeneous connectivity patterns emerge, which show qualitative agreement with real transcriptional regulatory networks and metabolic networks. The characteristic scaling behavior of stability reflects the balance between robustness and flexibility. The scaling of fluctuation in the perturbation spread shows a dynamic crossover, which is analyzed by investigating separately the stochasticity of internal dynamics and the network structure differences depending on the evolution pathways. Our study delineates how the ambivalent pressure of evolution shapes biological networks, which can be helpful for studying general complex systems interacting with environments. PMID:25493848

  3. Evolution of regulatory networks towards adaptability and stability in a changing environment

    Lee, Deok-Sun

    2014-11-01

    Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that sparse and heterogeneous connectivity patterns emerge, which show qualitative agreement with real transcriptional regulatory networks and metabolic networks. The characteristic scaling behavior of stability reflects the balance between robustness and flexibility. The scaling of fluctuation in the perturbation spread shows a dynamic crossover, which is analyzed by investigating separately the stochasticity of internal dynamics and the network structure differences depending on the evolution pathways. Our study delineates how the ambivalent pressure of evolution shapes biological networks, which can be helpful for studying general complex systems interacting with environments.

  4. Functional evolution of leptin of Ochotona curzoniae in adaptive thermogenesis driven by cold environmental stress.

    Jie Yang

    Full Text Available BACKGROUND: Environmental stress can accelerate the directional selection and evolutionary rate of specific stress-response proteins to bring about new or altered functions, enhancing an organism's fitness to challenging environments. Plateau pika (Ochotona curzoniae, an endemic and keystone species on Qinghai-Tibetan Plateau, is a high hypoxia and low temperature tolerant mammal with high resting metabolic rate and non-shivering thermogenesis to cope in this harsh plateau environment. Leptin is a key hormone related to how these animals regulate energy homeostasis. Previous molecular evolutionary analysis helped to generate the hypothesis that adaptive evolution of plateau pika leptin may be driven by cold stress. METHODOLOGY/PRINCIPAL FINDINGS: To test the hypothesis, recombinant pika leptin was first purified. The thermogenic characteristics of C57BL/6J mice injected with pika leptin under warm (23±1°C and cold (5±1°C acclimation is investigated. Expression levels of genes regulating adaptive thermogenesis in brown adipose tissue and the hypothalamus are compared between pika leptin and human leptin treatment, suggesting that pika leptin has adaptively and functionally evolved. Our results show that pika leptin regulates energy homeostasis via reduced food intake and increased energy expenditure under both warm and cold conditions. Compared with human leptin, pika leptin demonstrates a superior induced capacity for adaptive thermogenesis, which is reflected in a more enhanced β-oxidation, mitochondrial biogenesis and heat production. Moreover, leptin treatment combined with cold stimulation has a significant synergistic effect on adaptive thermogenesis, more so than is observed with a single cold exposure or single leptin treatment. CONCLUSIONS/SIGNIFICANCE: These findings support the hypothesis that cold stress has driven the functional evolution of plateau pika leptin as an ecological adaptation to the Qinghai-Tibetan Plateau.

  5. MODIS Hotspot Validation over Thailand

    Veerachai Tanpipat

    2009-11-01

    Full Text Available To ensure remote sensing MODIS hotspot (also known as active fire products or hotspots quality and precision in forest fire control and management in Thailand, an increased level of confidence is needed. Accuracy assessment of MODIS hotspots utilizing field survey data validation is described. A quantitative evaluation of MODIS hotspot products has been carried out since the 2007 forest fire season. The carefully chosen hotspots were scattered throughout the country and within the protected areas of the National Parks and Wildlife Sanctuaries. Three areas were selected as test sites for validation guidelines. Both ground and aerial field surveys were also conducted in this study by the Forest Fire Control Division, National Park, Wildlife and Plant Conversation Department, Ministry of Natural Resources and Environment, Thailand. High accuracy of 91.84 %, 95.60% and 97.53% for the 2007, 2008 and 2009 fire seasons were observed, resulting in increased confidence in the use of MODIS hotspots for forest fire control and management in Thailand.

  6. Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1 in cetaceans

    Montgomery Stephen H

    2011-04-01

    Full Text Available Abstract Background Representatives of Cetacea have the greatest absolute brain size among animals, and the largest relative brain size aside from humans. Despite this, genes implicated in the evolution of large brain size in primates have yet to be surveyed in cetaceans. Results We sequenced ~1240 basepairs of the brain development gene microcephalin (MCPH1 in 38 cetacean species. Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution using site and branch models of molecular evolution. We also tested the hypothesis that selection on MCPH1 was correlated with brain size in cetaceans using a continuous regression analysis that accounted for phylogenetic history. Our analyses revealed widespread signals of adaptive evolution in the MCPH1 of Cetacea and in other subclades of Mammalia, however, there was not a significant positive association between ω and brain size within Cetacea. Conclusion In conjunction with a recent study of Primates, we find no evidence to support an association between MCPH1 evolution and the evolution of brain size in highly encephalized mammalian species. Our finding of significant positive selection in MCPH1 may be linked to other functions of the gene.

  7. Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

    Klemm, Elizabeth J; Gkrania-Klotsas, Effrossyni; Hadfield, James; Forbester, Jessica L; Harris, Simon R; Hale, Christine; Heath, Jennifer N; Wileman, Thomas; Clare, Simon; Kane, Leanne; Goulding, David; Otto, Thomas D; Kay, Sally; Doffinger, Rainer; Cooke, Fiona J; Carmichael, Andrew; Lever, Andrew M L; Parkhill, Julian; MacLennan, Calman A; Kumararatne, Dinakantha; Dougan, Gordon; Kingsley, Robert A

    2016-01-01

    Host adaptation is a key factor contributing to the emergence of new bacterial, viral and parasitic pathogens. Many pathogens are considered promiscuous because they cause disease across a range of host species, while others are host-adapted, infecting particular hosts(1). Host adaptation can potentially progress to host restriction, where the pathogen is strictly limited to a single host species and is frequently associated with more severe symptoms. Host-adapted and host-restricted bacterial clades evolve from within a broader host-promiscuous species and sometimes target different niches within their specialist hosts, such as adapting from a mucosal to a systemic lifestyle. Genome degradation, marked by gene inactivation and deletion, is a key feature of host adaptation, although the triggers initiating genome degradation are not well understood. Here, we show that a chronic systemic non-typhoidal Salmonella infection in an immunocompromised human patient resulted in genome degradation targeting genes that are expendable for a systemic lifestyle. We present a genome-based investigation of a recurrent blood-borne Salmonella enterica serotype Enteritidis (S. Enteritidis) infection covering 15 years in an interleukin-12 β1 receptor-deficient individual that developed into an asymptomatic chronic infection. The infecting S. Enteritidis harboured a mutation in the mismatch repair gene mutS that accelerated the genomic mutation rate. Phylogenetic analysis and phenotyping of multiple patient isolates provides evidence for a remarkable level of within-host evolution that parallels genome changes present in successful host-restricted bacterial pathogens but never before observed on this timescale. Our analysis identifies common pathways of host adaptation and demonstrates the role that immunocompromised individuals can play in this process. PMID:27572160

  8. Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes

    Shaohua eFan

    2014-06-01

    Full Text Available African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile tilapia (Oreochromis niloticus, a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the tilapia genome as the reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs, short insertions and deletions (indels, inversions and deletions. In total, around 18.8, 17.7, 17.0 and 17.0 million SNPs, 2.3, 2.2, 1.4 and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710 and 2634 deletions were inferred to have evolved in the N. brichardi, A. burtoni, P. nyererei and M. zebra respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes.

  9. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota.

    Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A; McHardy, Alice C; Embley, T Martin; Prosser, James I; Macqueen, Daniel J

    2015-07-28

    The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400-700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum. PMID:26170282

  10. Niche evolution and adaptive radiation: Testing the order of trait divergence

    Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.

    2006-01-01

    In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in

  11. Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling

    Vrugt, Jasper A [Los Alamos National Laboratory; Hyman, James M [Los Alamos National Laboratory; Robinson, Bruce A [Los Alamos National Laboratory; Higdon, Dave [Los Alamos National Laboratory; Ter Braak, Cajo J F [NETHERLANDS; Diks, Cees G H [UNIV OF AMSTERDAM

    2008-01-01

    Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.

  12. Simulation of Old Urban Residential Area Evolution Based on Complex Adaptive System

    YANG Fan; WANG Xiao-ming; HUA Hong

    2009-01-01

    On the basis of complex adaptive system theory,this paper proposed an agent-based model of old urban residential area,in which,residents and providers are the two adaptive agents.The behaviors of residents and providers in this model are trained with back propagation and simulated with Swarm software based on environment-rules-agents interaction.This model simulates the evolution of old urban residential area and analyzes the relations between the evolution and urban management with the background of Chaozhou city.As a result,the following are obtained:(1) Simulation without government intervention indicates the trend of housing ageing,environmental deterioration,economic depression,and social filtering-down in old urban residential area.If the development of old urban residential area is under control of developers in market,whose desire is profit maximization,and factors such as social justice,historic and culture value will be ignored.(2) If the government carries out some policies and measures which will perfectly serve their original aims,simulation reveals that old urban residential area could be adapted to environment and keep sustainable development.This conclusion emphasizes that government must act as initiator and program maker for guiding residents and other providers directly in the development of old urban residential area.

  13. Online evolution for a self-adapting robotic navigation system using evolvable hardware.

    Keymeulen, D; Iwata, M; Kuniyoshi, Y; Higuchi, T

    1998-01-01

    Great interest has been shown in the application of the principles of artificial life to physically embedded systems such as mobile robots, computer networks, home devices able continuously and autonomously to adapt their behavior to changes of the environments. At the same time researchers have been working on the development of evolvable hardware, and new integrated circuits that are able to adapt their hardware autonomously and in real time in a changing environment. This article describes the navigation task for a real mobile robot and its implementation on evolvable hardware. The robot must track a colored ball, while avoiding obstacles in an environment that is unknown and dynamic. Although a model-free evolution method is not feasible for real-world applications due to the sheer number of possible interactions with the environment, we show that a model-based evolution can reduce these interactions by two orders of magnitude, even when some of the robot's sensors are blinded, thus allowing us to apply evolutionary processes online to obtain a self-adaptive tracking system in the real world, when the implementation is accelerated by the utilization of evolvable hardware. PMID:10352238

  14. Tectonics, climate, and the rise and demise of continental aquatic species richness hotspots.

    Neubauer, Thomas A; Harzhauser, Mathias; Georgopoulou, Elisavet; Kroh, Andreas; Mandic, Oleg

    2015-09-15

    Continental aquatic species richness hotspots are unevenly distributed across the planet. In present-day Europe, only two centers of biodiversity exist (Lake Ohrid on the Balkans and the Caspian Sea). During the Neogene, a wide variety of hotspots developed in a series of long-lived lakes. The mechanisms underlying the presence of richness hotspots in different geological periods have not been properly examined thus far. Based on Miocene to Recent gastropod distributions, we show that the existence and evolution of such hotspots in inland-water systems are tightly linked to the geodynamic history of the European continent. Both past and present hotspots are related to the formation and persistence of long-lived lake systems in geological basins or to isolation of existing inland basins and embayments from the marine realm. The faunal evolution within hotspots highly depends on warm climates and surface area. During the Quaternary icehouse climate and extensive glaciations, limnic biodiversity sustained a severe decline across the continent and most former hotspots disappeared. The Recent gastropod distribution is mainly a geologically young pattern formed after the Last Glacial Maximum (19 ky) and subsequent formation of postglacial lakes. The major hotspots today are related to long-lived lakes in preglacially formed, permanently subsiding geological basins. PMID:26305934

  15. Hotspots and the evolution of the mantle

    Anderson, D. L.

    1979-01-01

    Trace element patterns show that continental and ocean island basalts are complementary to mid-ocean ridge basalts (MORB). The relative sizes of the two source regions can be estimated from enrichment/depletion patterns. Their combined volume, computed from estimates of whole mantle abundances, occupies the entire upper mantle. The source regions appear to be the result of an early differentiation of the mantle. The MORB source evolved from the melt fraction which lost its late stage enriched fluids to the overlying plume source. The MORB source is primarily garnet and clinopyroxene, consistent with it being an eclogite cumulate.

  16. Co-evolution of Hormone Metabolism and Signaling Networks Expands Plant Adaptive Plasticity.

    Weng, Jing-Ke; Ye, Mingli; Li, Bin; Noel, Joseph P

    2016-08-11

    Classically, hormones elicit specific cellular responses by activating dedicated receptors. Nevertheless, the biosynthesis and turnover of many of these hormone molecules also produce chemically related metabolites. These molecules may also possess hormonal activities; therefore, one or more may contribute to the adaptive plasticity of signaling outcomes in host organisms. Here, we show that a catabolite of the plant hormone abscisic acid (ABA), namely phaseic acid (PA), likely emerged in seed plants as a signaling molecule that fine-tunes plant physiology, environmental adaptation, and development. This trait was facilitated by both the emergence-selection of a PA reductase that modulates PA concentrations and by the functional diversification of the ABA receptor family to perceive and respond to PA. Our results suggest that PA serves as a hormone in seed plants through activation of a subset of ABA receptors. This study demonstrates that the co-evolution of hormone metabolism and signaling networks can expand organismal resilience. PMID:27518563

  17. Evolution and adaptation in Pseudomonas aeruginosa biofilms driven by mismatch repair system-deficient mutators.

    Adela M Luján

    Full Text Available Pseudomonas aeruginosa is an important opportunistic pathogen causing chronic airway infections, especially in cystic fibrosis (CF patients. The majority of the CF patients acquire P. aeruginosa during early childhood, and most of them develop chronic infections resulting in severe lung disease, which are rarely eradicated despite intensive antibiotic therapy. Current knowledge indicates that three major adaptive strategies, biofilm development, phenotypic diversification, and mutator phenotypes [driven by a defective mismatch repair system (MRS], play important roles in P. aeruginosa chronic infections, but the relationship between these strategies is still poorly understood. We have used the flow-cell biofilm model system to investigate the impact of the mutS associated mutator phenotype on development, dynamics, diversification and adaptation of P. aeruginosa biofilms. Through competition experiments we demonstrate for the first time that P. aeruginosa MRS-deficient mutators had enhanced adaptability over wild-type strains when grown in structured biofilms but not as planktonic cells. This advantage was associated with enhanced micro-colony development and increased rates of phenotypic diversification, evidenced by biofilm architecture features and by a wider range and proportion of morphotypic colony variants, respectively. Additionally, morphotypic variants generated in mutator biofilms showed increased competitiveness, providing further evidence for mutator-driven adaptive evolution in the biofilm mode of growth. This work helps to understand the basis for the specific high proportion and role of mutators in chronic infections, where P. aeruginosa develops in biofilm communities.

  18. Adaptive Plasmid Evolution Results in Host-Range Expansion of a Broad-Host-Range Plasmid

    De Gelder, Leen; Williams, Julia J.; Ponciano, José M; Sota, Masahiro; Eva M. Top

    2008-01-01

    Little is known about the range of hosts in which broad-host-range (BHR) plasmids can persist in the absence of selection for plasmid-encoded traits, and whether this “long-term host range” can evolve over time. Previously, the BHR multidrug resistance plasmid pB10 was shown to be highly unstable in Stenotrophomonas maltophilia P21 and Pseudomonas putida H2. To investigate whether this plasmid can adapt to such unfavorable hosts, we performed evolution experiments wherein pB10 was maintained ...

  19. HANDOVER ADAPTATION FOR DYNAMIC LOAD BALANCING IN 3GPP LONG TERM EVOLUTION SYSTEMS

    Nasri, Ridha; Altman, Zwi

    2007-01-01

    The long-Term Evolution (LTE) of the 3GPP (3rd Generation Partnership Project) radio access network is in early stage of specification. Self-tuning and self-optimisation algorithms are currently studied with the aim of enriching the LTE standard. This paper investigates auto-tuning of LTE mobility algorithm. The auto-tuning is carried out by adapting handover parameters of each base station according to its radio load and the load of its adjacent cells. The auto-tuning alleviates cell congest...

  20. Explaining the evolution of European Union foreign climate policy: A case of bounded adaptiveness

    Simon Schunz

    2012-01-01

    Ever since the inception of the United Nations climate regime in the early 1990s, the European Union has aspired to play a leading part in the global combat against climate change. Based on an analysis of how the Union has developed its foreign climate policy to fulfil this role over the past two decades, the paper sets out to identify the driving factors behind this evolution. It demonstrates that the EU’s development in this area was co-determined by adaptations to shifting international ...

  1. Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs

    Patarnello, Tomaso; Cozzi, Bruno; Negrisolo, Enrico

    2016-01-01

    The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers. PMID:27336480

  2. Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs.

    Montelli, Stefano; Peruffo, Antonella; Patarnello, Tomaso; Cozzi, Bruno; Negrisolo, Enrico

    2016-01-01

    The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers. PMID:27336480

  3. Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

    Flegr Jaroslav

    2013-01-01

    Full Text Available Abstract Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ. Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III, genetic revolution model of Mayr (class IV or the frozen plasticity theory of Flegr (class V, suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation – while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III or elastic (class IV and V on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation. The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories. Reviewers This article was reviewed by Claus Wilke, Pierre Pantarotti and David Penny (nominated by Anthony Poole.

  4. An adaptive left–right eigenvector evolution algorithm for vibration isolation control

    The purpose of this research is to investigate the feasibility of utilizing an adaptive left and right eigenvector evolution (ALREE) algorithm for active vibration isolation. As depicted in the previous paper presented by Wu and Wang (2008 Smart Mater. Struct. 17 015048), the structural vibration behavior depends on both the disturbance rejection capability and mode shape distributions, which correspond to the left and right eigenvector distributions of the system, respectively. In this paper, a novel adaptive evolution algorithm is developed for finding the optimal combination of left–right eigenvectors of the vibration isolator, which is an improvement over the simultaneous left–right eigenvector assignment (SLREA) method proposed by Wu and Wang (2008 Smart Mater. Struct. 17 015048). The isolation performance index used in the proposed algorithm is defined by combining the orthogonality index of left eigenvectors and the modal energy ratio index of right eigenvectors. Through the proposed ALREE algorithm, both the left and right eigenvectors evolve such that the isolation performance index decreases, and therefore one can find the optimal combination of left–right eigenvectors of the closed-loop system for vibration isolation purposes. The optimal combination of left–right eigenvectors is then synthesized to determine the feedback gain matrix of the closed-loop system. The result of the active isolation control shows that the proposed method can be utilized to improve the vibration isolation performance compared with the previous approaches

  5. Reflected Adaptive Differential Evolution with Two External Archives for Large-Scale Global Optimization

    Rashida Adeeb Khanum

    2016-02-01

    Full Text Available JADE is an adaptive scheme of nature inspired algorithm, Differential Evolution (DE. It performed considerably improved on a set of well-studied benchmark test problems. In this paper, we evaluate the performance of new JADE with two external archives to deal with unconstrained continuous large-scale global optimization problems labeled as Reflected Adaptive Differential Evolution with Two External Archives (RJADE/TA. The only archive of JADE stores failed solutions. In contrast, the proposed second archive stores superior solutions at regular intervals of the optimization process to avoid premature convergence towards local optima. The superior solutions which are sent to the archive are reflected by new potential solutions. At the end of the search process, the best solution is selected from the second archive and the current population. The performance of RJADE/TA algorithm is then extensively evaluated on two test beds. At first on 28 latest benchmark functions constructed for the 2013 Congress on Evolutionary Computation special session. Secondly on ten benchmark problems from CEC2010 Special Session and Competition on Large-Scale Global Optimization. Experimental results demonstrated a very competitive perfor-mance of the algorithm.

  6. Adaptive evolution of the myo6 gene in old world fruit bats (family: pteropodidae).

    Shen, Bin; Han, Xiuqun; Jones, Gareth; Rossiter, Stephen J; Zhang, Shuyi

    2013-01-01

    Myosin VI (encoded by the Myo6 gene) is highly expressed in the inner and outer hair cells of the ear, retina, and polarized epithelial cells such as kidney proximal tubule cells and intestinal enterocytes. The Myo6 gene is thought to be involved in a wide range of physiological functions such as hearing, vision, and clathrin-mediated endocytosis. Bats (Chiroptera) represent one of the most fascinating mammal groups for molecular evolutionary studies of the Myo6 gene. A diversity of specialized adaptations occur among different bat lineages, such as echolocation and associated high-frequency hearing in laryngeal echolocating bats, large eyes and a strong dependence on vision in Old World fruit bats (Pteropodidae), and specialized high-carbohydrate but low-nitrogen diets in both Old World and New World fruit bats (Phyllostomidae). To investigate what role(s) the Myo6 gene might fulfill in bats, we sequenced the coding region of the Myo6 gene in 15 bat species and used molecular evolutionary analyses to detect evidence of positive selection in different bat lineages. We also conducted real-time PCR assays to explore the expression levels of Myo6 in a range of tissues from three representative bat species. Molecular evolutionary analyses revealed that the Myo6 gene, which was widely considered as a hearing gene, has undergone adaptive evolution in the Old World fruit bats which lack laryngeal echolocation and associated high-frequency hearing. Real-time PCR showed the highest expression level of the Myo6 gene in the kidney among ten tissues examined in three bat species, indicating an important role for this gene in kidney function. We suggest that Myo6 has undergone adaptive evolution in Old World fruit bats in relation to receptor-mediated endocytosis for the preservation of protein and essential nutrients. PMID:23620821

  7. Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.

    A Faddeeva

    Full Text Available Collembola (springtails represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor.We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade.Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response, ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development.We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land.

  8. Cold adaptation of a mesophilic cellulase, EG III from Trichoderma reesei, by directed evolution

    XIAO; Zhizhuang(肖志壮); WANG; Pan(王攀); QU; Yinbo(曲音波); GAO; Peiji(高培基); WANG; Tianhong(汪天虹)

    2002-01-01

    Cold-active enzymes have received little research attention although they are very useful in industries. Since the structure bases of cold adaptation of enzymes are still unclear, it is also very difficult to obtain cold-adapted enzymes for industrial applications using routine protein engineering methods. In this work, we employed directed evolution method to randomly mutate a mesophilic cellulase, endoglucanase III (EG III) from Trichoderma reesei, and obtained a cold- adapted mutant, designated as w-3. DNA sequence analysis indicates that w-3 is a truncated form of native EG III with a deletion of 25 consecutive amino acids at C-terminus. Further examination of enzymatic kinetics and thermal stability shows that mutant w-3 has a higher Kcat value and becomes more thermolabile than its parent. In addition, activation energies of w-3 and wild type EG III calculated from Arrhenius equation are 13.3 kJ@mol-1 and 26.2 kJ@mol-1, respectively. Therefore, the increased specific activity of w-3 at lower temperatures could result from increased Kcat value and decreased activation energy.

  9. Rapid adaptive evolution of colour vision in the threespine stickleback radiation.

    Rennison, Diana J; Owens, Gregory L; Heckman, Nancy; Schluter, Dolph; Veen, Thor

    2016-05-11

    Vision is a sensory modality of fundamental importance for many animals, aiding in foraging, detection of predators and mate choice. Adaptation to local ambient light conditions is thought to be commonplace, and a match between spectral sensitivity and light spectrum is predicted. We use opsin gene expression to test for local adaptation and matching of spectral sensitivity in multiple independent lake populations of threespine stickleback populations derived since the last ice age from an ancestral marine form. We show that sensitivity across the visual spectrum is shifted repeatedly towards longer wavelengths in freshwater compared with the ancestral marine form. Laboratory rearing suggests that this shift is largely genetically based. Using a new metric, we found that the magnitude of shift in spectral sensitivity in each population corresponds strongly to the transition in the availability of different wavelengths of light between the marine and lake environments. We also found evidence of local adaptation by sympatric benthic and limnetic ecotypes to different light environments within lakes. Our findings indicate rapid parallel evolution of the visual system to altered light conditions. The changes have not, however, yielded a close matching of spectrum-wide sensitivity to wavelength availability, for reasons we discuss. PMID:27147098

  10. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

    Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Heimberg, Alysha M; Jansen, Hans J; McCleary, Ryan J R; Kerkkamp, Harald M E; Vos, Rutger A; Guerreiro, Isabel; Calvete, Juan J; Wüster, Wolfgang; Woods, Anthony E; Logan, Jessica M; Harrison, Robert A; Castoe, Todd A; de Koning, A P Jason; Pollock, David D; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S; Ribeiro, José M C; Arntzen, Jan W; van den Thillart, Guido E E J M; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P; Spaink, Herman P; Duboule, Denis; McGlinn, Edwina; Kini, R Manjunatha; Richardson, Michael K

    2013-12-17

    Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection. PMID:24297900

  11. The evolution model of Uppsala in light of the complex adaptive systems approach

    Rennaly Alves da Silva

    2013-11-01

    Full Text Available The behavioral approach to the internationalization of companies explains that the movements toward external markets occur in accordance with the increasing commitment of resources to mitigate the effects of uncertainty and reduce the perception of risk. Evidence indicates that the theories and practices developed in the domestic market may not be able to explain the reality of companies that operate in international markets. Thus, the Paradigm of Complexity presents itself as a comprehensive alternative to realize the relationships within organizations and markets. Accordingly, the aim of this theoretical paper is to analyze the evolution of the Uppsala Model between years 1975 and 2010 with the understanding of the companies in the process of internationalization as Complex Adaptive Systems, in accordance with the Model Kelly and Allison (1998. Four propositions are presented that show the links between the approaches. The most surprising is the perception that the conceptual evolution of the Uppsala Model seems to accompany the evolution of complexity levels, presented in Model Kelly and Allison.

  12. Biosensor-driven adaptive laboratory evolution of l-valine production in Corynebacterium glutamicum.

    Mahr, Regina; Gätgens, Cornelia; Gätgens, Jochem; Polen, Tino; Kalinowski, Jörn; Frunzke, Julia

    2015-11-01

    Adaptive laboratory evolution has proven a valuable strategy for metabolic engineering. Here, we established an experimental evolution approach for improving microbial metabolite production by imposing an artificial selective pressure on the fluorescent output of a biosensor using fluorescence-activated cell sorting. Cells showing the highest fluorescent output were iteratively isolated and (re-)cultivated. The L-valine producer Corynebacterium glutamicum ΔaceE was equipped with an L-valine-responsive sensor based on the transcriptional regulator Lrp of C. glutamicum. Evolved strains featured a significantly higher growth rate, increased L-valine titers (~25%) and a 3-4-fold reduction of by-product formation. Genome sequencing resulted in the identification of a loss-of-function mutation (UreD-E188*) in the gene ureD (urease accessory protein), which was shown to increase L-valine production by up to 100%. Furthermore, decreased L-alanine formation was attributed to a mutation in the global regulator GlxR. These results emphasize biosensor-driven evolution as a straightforward approach to improve growth and productivity of microbial production strains. PMID:26453945

  13. Trade-offs and evolution of thermal adaptation in the Irish potato famine pathogen Phytophthora infestans.

    Yang, Li-Na; Zhu, Wen; Wu, E-Jiao; Yang, Ce; Thrall, Peter H; Burdon, Jeremy J; Jin, Li-Ping; Shang, Li-Ping; Zhan, Jiasui

    2016-08-01

    Temperature is one of the most important environmental parameters with crucial impacts on nearly all biological processes. Due to anthropogenic activity, average air temperatures are expected to increase by a few degrees in coming decades, accompanied by an increased occurrence of extreme temperature events. Such global trends are likely to have various major impacts on human society through their influence on natural ecosystems, food production and biotic interactions, including diseases. In this study, we used a combination of statistical genetics, experimental evolution and common garden experiments to investigate the evolutionary potential for thermal adaptation in the potato late blight pathogen, Phytophthora infestans, and infer its likely response to changing temperatures. We found a trade-off associated with thermal adaptation to heterogeneous environments in P. infestans, with the degree of the trade-off peaking approximately at the pathogen's optimum growth temperature. A genetic trade-off in thermal adaptation was also evidenced by the negative association between a strain's growth rate and its thermal range for growth, and warm climates selecting for a low pathogen growth rate. We also found a mirror effect of phenotypic plasticity and genetic adaptation on growth rate. At below the optimum, phenotypic plasticity enhances pathogen's growth rate but nature selects for slower growing genotypes when temperature increases. At above the optimum, phenotypic plasticity reduces pathogen's growth rate but natural selection favours for faster growing genotypes when temperature increases further. We conclude from these findings that the growth rate of P. infestans will only be marginally affected by global warming. PMID:27288627

  14. Multifunctional adaptive NS1 mutations are selected upon human influenza virus evolution in the mouse.

    Nicole E Forbes

    Full Text Available The role of the NS1 protein in modulating influenza A virulence and host range was assessed by adapting A/Hong Kong/1/1968 (H3N2 (HK-wt to increased virulence in the mouse. Sequencing the NS genome segment of mouse-adapted variants revealed 11 mutations in the NS1 gene and 4 in the overlapping NEP gene. Using the HK-wt virus and reverse genetics to incorporate mutant NS gene segments, we demonstrated that all NS1 mutations were adaptive and enhanced virus replication (up to 100 fold in mouse cells and/or lungs. All but one NS1 mutant was associated with increased virulence measured by survival and weight loss in the mouse. Ten of twelve NS1 mutants significantly enhanced IFN-β antagonism to reduce the level of IFN β production relative to HK-wt in infected mouse lungs at 1 day post infection, where 9 mutants induced viral yields in the lung that were equivalent to or significantly greater than HK-wt (up to 16 fold increase. Eight of 12 NS1 mutants had reduced or lost the ability to bind the 30 kDa cleavage and polyadenylation specificity factor (CPSF30 thus demonstrating a lack of correlation with reduced IFN β production. Mutant NS1 genes resulted in increased viral mRNA transcription (10 of 12 mutants, and protein production (6 of 12 mutants in mouse cells. Increased transcription activity was demonstrated in the influenza mini-genome assay for 7 of 11 NS1 mutants. Although we have shown gain-of-function properties for all mutant NS genes, the contribution of the NEP mutations to phenotypic changes remains to be assessed. This study demonstrates that NS1 is a multifunctional virulence factor subject to adaptive evolution.

  15. Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test

    Berlin Sofia; Smith Nick GC

    2005-01-01

    Abstract Background Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive ...

  16. Fiddling in biodiversity hotspots while deserts burn? Collapse of the Sahara's megafauna

    Durant, S. M.; Woodroffe, R.; Belbachir, F.; Cornforth, W. A.; Jacobson, A.; Pettorelli, N.; Purchase, G.; Wacher, T.; De Ornellas, P.; Ransom, C.; Baillie, J.; Bashir, S.; Newby, J.; Abáigar, T.; M. Cano

    2014-01-01

    Biodiversity hotspots understandably attract considerable conservation attention. However, deserts are rarely viewed as conservation priority areas, due to their relatively low productivity, yet these systems are home to unique species, adapted to harsh and highly variable environments. While global attention has been focused on hotspots, the world's largest tropical desert, the Sahara, has suffered a catastrophic decline in megafauna. Of 14 large vertebrates that have historically occurred i...

  17. Design Of Multivariable Fractional Order Pid Controller Using Covariance Matrix Adaptation Evolution Strategy

    Sivananaithaperumal Sudalaiandi

    2014-06-01

    Full Text Available This paper presents an automatic tuning of multivariable Fractional-Order Proportional, Integral and Derivative controller (FO-PID parameters using Covariance Matrix Adaptation Evolution Strategy (CMAES algorithm. Decoupled multivariable FO-PI and FO-PID controller structures are considered. Oustaloup integer order approximation is used for the fractional integrals and derivatives. For validation, two Multi-Input Multi- Output (MIMO distillation columns described byWood and Berry and Ogunnaike and Ray are considered for the design of multivariable FO-PID controller. Optimal FO-PID controller is designed by minimizing Integral Absolute Error (IAE as objective function. The results of previously reported PI/PID controller are considered for comparison purposes. Simulation results reveal that the performance of FOPI and FO-PID controller is better than integer order PI/PID controller in terms of IAE. Also, CMAES algorithm is suitable for the design of FO-PI / FO-PID controller.

  18. Explaining the evolution of European Union foreign climate policy: A case of bounded adaptiveness

    Simon Schunz

    2012-02-01

    Full Text Available Ever since the inception of the United Nations climate regime in the early 1990s, the European Union has aspired to play a leading part in the global combat against climate change. Based on an analysis of how the Union has developed its foreign climate policy to fulfil this role over the past two decades, the paper sets out to identify the driving factors behind this evolution. It demonstrates that the EU’s development in this area was co-determined by adaptations to shifting international dynamics strongly bounded by purely domestic concerns. Providing a concise understanding and explanation of how the Union designs its foreign policy with regard to one emblematic issue of its international activity, the contribution provides insights into the remarkably rapid, but not always effective maturation of this unique actor’s involvement in global politics.

  19. Micro-Foundations of Organizational Adaptation : A Field Study in the Evolution of Product Development Capabilities in a Design Firm

    Salvato, Carlo

    2006-01-01

    The aim of this dissertation is to improve knowledge of how organizations adapt to their dynamic environments, by developing a detailed understanding of the configuration and evolution of organizational replicators. Among open questions in the literature on organizational adaptation, I have explored the following: How can the structure of organizational replicators and the nature of their components be realistically described? How do different organizational replicators interact with each oth...

  20. The ALICE-HMPID Detector Control System: Its evolution towards an expert and adaptive system

    De Cataldo, G.; Franco, A.; Pastore, C.; Sgura, I.; Volpe, G.

    2011-05-01

    The High Momentum Particle IDentification (HMPID) detector is a proximity focusing Ring Imaging Cherenkov (RICH) for charged hadron identification. The HMPID is based on liquid C 6F 14 as the radiator medium and on a 10 m 2 CsI coated, pad segmented photocathode of MWPCs for UV Cherenkov photon detection. To ensure full remote control, the HMPID is equipped with a detector control system (DCS) responding to industrial standards for robustness and reliability. It has been implemented using PVSS as Slow Control And Data Acquisition (SCADA) environment, Programmable Logic Controller as control devices and Finite State Machines for modular and automatic command execution. In the perspective of reducing human presence at the experiment site, this paper focuses on DCS evolution towards an expert and adaptive control system, providing, respectively, automatic error recovery and stable detector performance. HAL9000, the first prototype of the HMPID expert system, is then presented. Finally an analysis of the possible application of the adaptive features is provided.

  1. Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant.

    Junjie Tao

    Full Text Available Limestone Karst areas possess high levels of biodiversity and endemism. Primulina is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome PHYE from available transcriptome resources of Primulina and amplified partial sequences of PHYE from the genomic DNA of 74 Primulina species. Then, we used maximum-likelihood approaches to explore molecular evolution of PHYE in this Karst cave plant. The results showed that PHYE was dominated by purifying selection in both data sets, and two sites were identified as potentially under positive selection. Furthermore, the ω ratio varies greatly among different functional domains of PHYE and among different species lineages. These results suggest that potential positive selection in PHYE might have played an important role in the adaption of Primulina to heterogeneous light environments in Karst regions, and different species lineages might have been subjected to different selective pressures.

  2. Adaptive Evolution of cry Genes in Bacillus thuringiensis:Implications for Their Specificity Determination

    2007-01-01

    The cry gene family, produced during the late exponential phase of growth in Bacillus thuringiensis, is a large, still-growing family of homologous genes, in which each gene encodes a protein with strong specific activity against only one or a few insect species. Extensive studies are mostly focusing on the structural and functional relationships of Cry proteins, and have revealed several residues or domains that are important for the target recognition and receptor attachment. In this study,we have employed a maximum likelihood method to detect evidence of adaptive evolution in Cry proteins, and have identified 24 positively selected residues, which are all located in Domain Ⅱ or Ⅲ. Combined with known data from mutagenesis studies, the majority of these residues, at the molecular level, contribute much to the insect specificity determination. We postulate that the potential pressures driving the diversification of Cry proteins may be in an attempt to adapt for the "arm race" between δ-endotoxins and the targeted insects, or to enlarge their target spectra, hence result in the functional divergence. The sites identified to be under positive selection would provide targets for further structural and functional analyses on Cry proteins.

  3. Adaptive evolution of defense ability leads to diversification of prey species.

    Zu, Jian; Wang, Jinliang; Du, Jianqiang

    2014-06-01

    In this paper, by using the adaptive dynamics approach, we investigate how the adaptive evolution of defense ability promotes the diversity of prey species in an initial one-prey-two-predator community. We assume that the prey species can evolve to a safer strategy such that it can reduce the predation risk, but a prey with a high defense ability for one predator may have a low defense ability for the other and vice versa. First, by using the method of critical function analysis, we find that if the trade-off is convex in the vicinity of the evolutionarily singular strategy, then this singular strategy is a continuously stable strategy. However, if the trade-off is weakly concave near the singular strategy and the competition between the two predators is relatively weak, then the singular strategy may be an evolutionary branching point. Second, we find that after the branching has occurred in the prey strategy, if the trade-off curve is globally concave, then the prey species might eventually evolve into two specialists, each caught by only one predator species. However, if the trade-off curve is convex-concave-convex, the prey species might eventually branch into two partial specialists, each being caught by both of the two predators and they can stably coexist on the much longer evolutionary timescale. PMID:24770878

  4. Adaptations to sexual selection and sexual conflict: insights from experimental evolution and artificial selection.

    Edward, Dominic A; Fricke, Claudia; Chapman, Tracey

    2010-08-27

    Artificial selection and experimental evolution document natural selection under controlled conditions. Collectively, these techniques are continuing to provide fresh and important insights into the genetic basis of evolutionary change, and are now being employed to investigate mating behaviour. Here, we focus on how selection techniques can reveal the genetic basis of post-mating adaptations to sexual selection and sexual conflict. Alteration of the operational sex ratio of adult Drosophila over just a few tens of generations can lead to altered ejaculate allocation patterns and the evolution of resistance in females to the costly effects of elevated mating rates. We provide new data to show how male responses to the presence of rivals can evolve. For several traits, the way in which males responded to rivals was opposite in lines selected for male-biased, as opposed to female-biased, adult sex ratio. This shows that the manipulation of the relative intensity of intra- and inter-sexual selection can lead to replicable and repeatable effects on mating systems, and reveals the potential for significant contemporary evolutionary change. Such studies, with important safeguards, have potential utility for understanding sexual selection and sexual conflict across many taxa. We discuss how artificial selection studies combined with genomics will continue to deepen our knowledge of the evolutionary principles first laid down by Darwin 150 years ago. PMID:20643744

  5. Optimization of reactor network design problem using Jumping Gene Adaptation of Differential Evolution

    Gujarathi, Ashish M.; Purohit, S.; Srikanth, B.

    2015-06-01

    Detailed working principle of jumping gene adaptation of differential evolution (DE-JGa) is presented. The performance of the DE-JGa algorithm is compared with the performance of differential evolution (DE) and modified DE (MDE) by applying these algorithms on industrial problems. In this study Reactor network design (RND) problem is solved using DE, MDE, and DE-JGa algorithms: These industrial processes are highly nonlinear and complex with reference to optimal operating conditions with many equality and inequality constraints. Extensive computational comparisons have been made for all the chemical engineering problems considered. The results obtained in the present study show that DE-JGa algorithm outperforms the other algorithms (DE and MDE). Several comparisons are made among the algorithms with regard to the number of function evaluations (NFE)/CPU- time required to find the global optimum. The standard deviation and the variance values obtained using DE-JGa, DE and MDE algorithms also show that the DE-JGa algorithm gives consistent set of results for the majority of the test problems and the industrial real world problems.

  6. Adaptive evolution of simian immunodeficiency viruses isolated from two conventional progressor macaques with neuroaids

    Foley, Brian T [Los Alamos National Laboratory; Korber, Bette T [Los Alamos National Laboratory

    2008-01-01

    Simian immunodeficiency virus infection of macaques may result in neuroAIDS, a feature more commonly observed in macaques with rapid progressive disease than in those with conventional disease. This is the first report of two conventional progressors (H631 and H636) with encephalitis in rhesus macaques inoculated with a derivative of SIVsmES43-3. Phylogenetic analyses of viruses isolated from the cerebral spinal fluid (CSF) and plasma from both animals demonstrated tissue compartmentalization. Additionally, virus from the central nervous system (CNS) was able to infect primary macaque monocyte-derived macrophages more efficiently than virus from plasma. Conversely, virus isolated from plasma was able to replicate better in peripheral blood mononuclear cells than virus from CNS. We speculate that these viruses were under different selective pressures in their separate compartments. Furthermore, these viruses appear to have undergone adaptive evolution to preferentially replicate in their respective cell targets. Analysis of the number of potential N-linked glycosylation sites (PNGS) in gp160 showed that there was a statistically significant loss of PNGS in viruses isolated from CNS in both macaques compared to SIVsmE543-3. Moreover, virus isolated from the brain in H631, had statistically significant loss of PNGS compared to virus isolated from CSF and plasma of the same animal. It is possible that the brain isolate may have adapted to decrease the number of PNGS given that humoral immune selection pressure is less likely to be encountered in the brain. These viruses provide a relevant model to study the adaptations required for SIV to induce encephalitis.

  7. Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails

    Koene Joris M

    2005-03-01

    Full Text Available Abstract Background Evolutionary conflicts of interest between the sexes often lead to co-evolutionary arms races consisting of repeated arisal of traits advantageous for one sex but harmful to the other sex, and counter-adaptations by the latter. In hermaphrodites, these antagonistic interactions are at least an equally important driving force. Here, we investigate the evolution of one of the most striking examples of sexual conflict in hermaphrodites, the so-called shooting of love-darts in land snails. Stabbing this calcareous dart through the partner's skin ultimately increases paternity. This trait is obviously beneficial for the shooter, but it manipulates sperm storage in the receiver. Hence, an arms race between the love-dart and the spermatophore receiving organs may be expected. Results We performed a detailed phylogenetic analysis of 28S ribosomal RNA gene sequences from dart-possessing land snail species. Both the Shimodaira-Hasegawa test and Bayesian posterior probabilities rejected a monophyletic origin of most reproductive structures, including the love-dart, indicating that most traits arose repeatedly. Based on the inferred phylogenetic trees, we calculated phylogenetically independent contrasts for the different reproductive traits. Subsequent principal component and correlation analyses demonstrated that these contrasts covary, meaning that correlated evolution of these traits occurred. Conclusion Our study represents the first comprehensive comparative analysis of reproductive organ characteristics in simultaneous hermaphrodites. Moreover, it strongly suggests that co-evolutionary arms races can result from sexual conflict in these organisms and play a key role in the evolution of hermaphroditic mating systems.

  8. Adaptive Evolution of Genes Duplicated from the Drosophila pseudoobscura neo-X Chromosome

    Meisel, Richard P.; Hilldorfer, Benedict B.; Koch, Jessica L.; Lockton, Steven; Schaeffer, Stephen W.

    2010-01-01

    Drosophila X chromosomes are disproportionate sources of duplicated genes, and these duplications are usually the result of retrotransposition of X-linked genes to the autosomes. The excess duplication is thought to be driven by natural selection for two reasons: X chromosomes are inactivated during spermatogenesis, and the derived copies of retroposed duplications tend to be testis expressed. Therefore, autosomal derived copies of retroposed genes provide a mechanism for their X-linked paralogs to “escape” X inactivation. Once these duplications have fixed, they may then be selected for male-specific functions. Throughout the evolution of the Drosophila genus, autosomes have fused with X chromosomes along multiple lineages giving rise to neo-X chromosomes. There has also been excess duplication from the two independent neo-X chromosomes that have been examined—one that occurred prior to the common ancestor of the willistoni species group and another that occurred along the lineage leading to Drosophila pseudoobscura. To determine what role natural selection plays in the evolution of genes duplicated from the D. pseudoobscura neo-X chromosome, we analyzed DNA sequence divergence between paralogs, polymorphism within each copy, and the expression profiles of these duplicated genes. We found that the derived copies of all duplicated genes have elevated nonsynonymous polymorphism, suggesting that they are under relaxed selective constraints. The derived copies also tend to have testis- or male-biased expression profiles regardless of their chromosome of origin. Genes duplicated from the neo-X chromosome appear to be under less constraints than those duplicated from other chromosome arms. We also find more evidence for historical adaptive evolution in genes duplicated from the neo-X chromosome, suggesting that they are under a unique selection regime in which elevated nonsynonymous polymorphism provides a large reservoir of functional variants, some of which are

  9. The contribution of ancestry, chance, and past and ongoing selection to adaptive evolution

    Amitabh Joshi; Robinson B. Castillo; Laurence D. Mueller

    2003-12-01

    often not be due to differently shaped fitness functions, but rather due to differences in how the fitness function maps onto the actual distribution of phenotypes in a given population. We discuss these results in the light of previous work on reverse evolution, and the role of ancestry, chance, and past and ongoing selection in adaptive evolution.

  10. Adaptive evolution of Desulfovibrio alaskensis G20 for developing resistance to perchlorate

    Mehta-Kolte, M. G.; Youngblut, M.; Redford, S.; Gregoire, P.; Carlson, H. K.; Coates, J. D.

    2015-12-01

    resistance to perchlorate and suggest that adaptive evolution is a valuable tool to understand potential responses of microorganism to any environmental perturbations imposed during oil production.

  11. Experimental Evolution under Fluctuating Thermal Conditions Does Not Reproduce Patterns of Adaptive Clinal Differentiation in Drosophila melanogaster.

    Kellermann, Vanessa; Hoffmann, Ary A; Kristensen, Torsten Nygaard; Moghadam, Neda Nasiri; Loeschcke, Volker

    2015-11-01

    Experimental evolution can be a useful tool for testing the impact of environmental factors on adaptive changes in populations, and this approach is being increasingly used to understand the potential for evolutionary responses in populations under changing climates. However, selective factors will often be more complex in natural populations than in laboratory environments and produce different patterns of adaptive differentiation. Here we test the ability of laboratory experimental evolution under different temperature cycles to reproduce well-known patterns of clinal variation in Drosophila melanogaster. Six fluctuating thermal regimes mimicking the natural temperature conditions along the east coast of Australia were initiated. Contrary to expectations, on the basis of field patterns there was no evidence for adaptation to thermal regimes as reflected by changes in cold and heat resistance after 1-3 years of laboratory natural selection. While laboratory evolution led to changes in starvation resistance, development time, and body size, patterns were not consistent with those seen in natural populations. These findings highlight the complexity of factors affecting trait evolution in natural populations and indicate that caution is required when inferring likely evolutionary responses from the outcome of experimental evolution studies. PMID:26655772

  12. Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms.

    Minjun Yang

    Full Text Available Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC. Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and niche adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.

  13. Evolution of motion uncertainty in rectal cancer: implications for adaptive radiotherapy

    Kleijnen, Jean-Paul J. E.; van Asselen, Bram; Burbach, Johannes P. M.; Intven, Martijn; Philippens, Marielle E. P.; Reerink, Onne; Lagendijk, Jan J. W.; Raaymakers, Bas W.

    2016-01-01

    Reduction of motion uncertainty by applying adaptive radiotherapy strategies depends largely on the temporal behavior of this motion. To fully optimize adaptive strategies, insight into target motion is needed. The purpose of this study was to analyze stability and evolution in time of motion uncertainty of both the gross tumor volume (GTV) and clinical target volume (CTV) for patients with rectal cancer. We scanned 16 patients daily during one week, on a 1.5 T MRI scanner in treatment position, prior to each radiotherapy fraction. Single slice sagittal cine MRIs were made at the beginning, middle, and end of each scan session, for one minute at 2 Hz temporal resolution. GTV and CTV motion were determined by registering a delineated reference frame to time-points later in time. The 95th percentile of observed motion (dist95%) was taken as a measure of motion. The stability of motion in time was evaluated within each cine-MRI separately. The evolution of motion was investigated between the reference frame and the cine-MRIs of a single scan session and between the reference frame and the cine-MRIs of several days later in the course of treatment. This observed motion was then converted into a PTV-margin estimate. Within a one minute cine-MRI scan, motion was found to be stable and small. Independent of the time-point within the scan session, the average dist95% remains below 3.6 mm and 2.3 mm for CTV and GTV, respectively 90% of the time. We found similar motion over time intervals from 18 min to 4 days. When reducing the time interval from 18 min to 1 min, a large reduction in motion uncertainty is observed. A reduction in motion uncertainty, and thus the PTV-margin estimate, of 71% and 75% for CTV and tumor was observed, respectively. Time intervals of 15 and 30 s yield no further reduction in motion uncertainty compared to a 1 min time interval.

  14. DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size

    Piontkivska Helen

    2005-02-01

    Full Text Available Abstract Background Birds have smaller average genome sizes than other tetrapod classes, and it has been proposed that a relatively low frequency of repeating DNA is one factor in reduction of avian genome sizes. Results DNA repeat arrays in the sequenced portion of the chicken (Gallus gallus autosomes were quantified and compared with those in human autosomes. In the chicken 10.3% of the genome was occupied by DNA repeats, in contrast to 44.9% in human. In the chicken, the percentage of a chromosome occupied by repeats was positively correlated with chromosome length, but even the largest chicken chromosomes had repeat densities much lower than those in human, indicating that avoidance of repeats in the chicken is not confined to minichromosomes. When 294 simple sequence repeat types shared between chicken and human genomes were compared, mean repeat array length and maximum repeat array length were significantly lower in the chicken than in human. Conclusions The fact that the chicken simple sequence repeat arrays were consistently smaller than arrays of the same type in human is evidence that the reduction in repeat array length in the chicken has involved numerous independent evolutionary events. This implies that reduction of DNA repeats in birds is the result of adaptive evolution. Reduction of DNA repeats on minichromosomes may be an adaptation to permit chiasma formation and alignment of small chromosomes. However, the fact that repeat array lengths are consistently reduced on the largest chicken chromosomes supports the hypothesis that other selective factors are at work, presumably related to the reduction of cell size and consequent advantages for the energetic demands of flight.

  15. Adaptive evolution of a derived radius morphology in manakins (Aves, Pipridae) to support acrobatic display behavior.

    Friscia, Anthony; Sanin, Gloria D; Lindsay, Willow R; Day, Lainy B; Schlinger, Barney A; Tan, Josh; Fuxjager, Matthew J

    2016-06-01

    The morphology of the avian skeleton is often studied in the context of adaptations for powered flight. The effects of other evolutionary forces, such as sexual selection, on avian skeletal design are unclear, even though birds produce diverse behaviors that undoubtedly require a variety of osteological modifications. Here, we investigate this issue in a family of passerine birds called manakins (Pipridae), which have evolved physically unusual and elaborate courtship displays. We report that, in species within the genus Manacus, the shaft of the radius is heavily flattened and shows substantial solidification. Past work anecdotally notes this morphology and attributes it to the species' ability to hit their wings together above their heads to produce loud mechanical sonations. Our results show that this feature is unique to Manacus compared to the other species in our study, including a variety of taxa that produce other sonations through alternate wing mechanisms. At the same time, our data reveal striking similarities across species in total radius volume and solidification. Together, this suggests that supposedly adaptive alterations in radial morphology occur within a conserved framework of a set radius volume and solidness, which in turn is likely determined by natural selection. Further allometric analyses imply that the radius is less constrained by body size and the structural demands that underlie powered flight, compared to other forelimb bones that are mostly unmodified across taxa. These results are consistent with the idea that the radius is more susceptible to selective modification by sexual selection. Overall, this study provides some of the first insight into the osteological evolution of passerine birds, as well as the way in which opposing selective forces can shape skeletal design in these species. J. Morphol. 277:766-775, 2016. © 2016 Wiley Periodicals, Inc. PMID:27027525

  16. Adaptive evolution of the Hox gene family for development in bats and dolphins.

    Lu Liang

    Full Text Available Bats and cetaceans (i.e., whales, dolphins, porpoises are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii and cetaceans (represented by Tursiops truncatus for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation.

  17. Adaptive evolution of foraging-related trait in intraguild predation system.

    Wang, Xin; Fan, Meng; Hao, Lina

    2016-04-01

    This paper considers a tri-trophic food chain in which the top predator (intraguild predator) also feeds on the basal resource. We refer to the model as intraguild predation. We analyze its dynamics from an evolutionary perspective. The attack rate or foraging effort of the middle species (intraguild prey) for the basal resources is assumed to be evolvable and is also assumed to be traded off with the vulnerability to being attacked by the top predator. We focus on the analysis of the evolutionary dynamics of the attack rate using the adaptive dynamics approximation of mutation limited evolution. In particular, the critical function analysis is applied. This study reveals that the evolutionary dynamics of the intraguild predation system is completely characterized by the concavity of the trade-off function and admits trichotomous dynamic scenarios: (1) when the trade-off function is more concave than the critical function, an evolutionary singular strategy exists and is a repeller; (2) when the trade-off function is less concave than the critical function, the evolutionary singular strategy is convergence stable and turns into an evolutionary branching point, in which case the monomorphic intraguild prey will split into two different types; (3) when the trade-off function is convex, the evolutionary singular strategy turns into a continuous stable strategy and is uninvadable. Our theoretical analysis suggests that the adaptive foraging behavior may strongly influence the community stability. Consequently, it may promote the diversity of intraguild prey and the persistence of the system on the evolutionary timescale, which highlight a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. This modeling approach provides a venue for research on indirect effects from an evolutionary perspective. PMID:26845664

  18. Adaptive evolution of the Hox gene family for development in bats and dolphins.

    Liang, Lu; Shen, Yong-Yi; Pan, Xiao-Wei; Zhou, Tai-Cheng; Yang, Chao; Irwin, David M; Zhang, Ya-Ping

    2013-01-01

    Bats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation. PMID:23825528

  19. Evolution of Heat Sensors Drove Shifts in Thermosensation between Xenopus Species Adapted to Different Thermal Niches.

    Saito, Shigeru; Ohkita, Masashi; Saito, Claire T; Takahashi, Kenji; Tominaga, Makoto; Ohta, Toshio

    2016-05-20

    Temperature is one of the most critical environmental factors affecting survival, and thus species that inhabit different thermal niches have evolved thermal sensitivities suitable for their respective habitats. During the process of shifting thermal niches, various types of genes expressed in diverse tissues, including those of the peripheral to central nervous systems, are potentially involved in the evolutionary changes in thermosensation. To elucidate the molecular mechanisms behind the evolution of thermosensation, thermal responses were compared between two species of clawed frogs (Xenopus laevis and Xenopus tropicalis) adapted to different thermal environments. X. laevis was much more sensitive to heat stimulation than X. tropicalis at the behavioral and neural levels. The activity and sensitivity of the heat-sensing TRPA1 channel were higher in X. laevis compared with those of X. tropicalis The thermal responses of another heat-sensing channel, TRPV1, also differed between the two Xenopus species. The species differences in Xenopus TRPV1 heat responses were largely determined by three amino acid substitutions located in the first three ankyrin repeat domains, known to be involved in the regulation of rat TRPV1 activity. In addition, Xenopus TRPV1 exhibited drastic species differences in sensitivity to capsaicin, contained in chili peppers, between the two Xenopus species. Another single amino acid substitution within Xenopus TRPV1 is responsible for this species difference, which likely alters the neural and behavioral responses to capsaicin. These combined subtle amino acid substitutions in peripheral thermal sensors potentially serve as a driving force for the evolution of thermal and chemical sensation. PMID:27022021

  20. Evolution and adaptation of the pandemic A/H1N1 2009 influenza virus

    Ducatez MF

    2011-07-01

    Full Text Available Mariette F Ducatez, Thomas P Fabrizio, Richard J WebbyDepartment of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USAAbstract: The emergence of the 2009 H1N1 pandemic influenza virus [A(H1N1pdm09] has provided the public health community with many challenges, but also the scientific community with an opportunity to monitor closely its evolution through the processes of drift and shift. To date, and despite having circulated in humans for nearly two years, little antigenic variation has been observed in the A(H1N1pdm09 viruses. However, as the A(H1N1pdm09 virus continues to circulate and the immunologic pressure within the human population increases, future antigenic change is almost a certainty. Several coinfections of A(H1N1pdm09 and seasonal A(H1N1 or A(H3N2 viruses have been observed, but no reassortant viruses have been described in humans, suggesting a lack of fitness of reassortant viruses or a lack of opportunities for interaction of different viral lineages. In contrast, multiple reassortment events have been detected in swine populations between A(H1N1 pdm09 and other endemic swine viruses. Somewhat surprisingly, many of the well characterized influenza virus virulence markers appear to have limited impact on the phenotype of the A(H1N1pdm09 viruses when they have been introduced into mutant viruses in laboratory settings. As such, it is unclear what the evolutionary path of the pandemic virus will be, but the monitoring of any changes in the circulating viruses will remain a global public and animal health priority.Keywords: influenza, pandemic, evolution, adaptation

  1. Two goose-type lysozymes in Mytilus galloprovincialis: possible function diversification and adaptive evolution.

    Qing Wang

    Full Text Available Two goose-type lysozymes (designated as MGgLYZ1 and MGgLYZ2 were identified from the mussel Mytilus galloprovincialis. MGgLYZ1 mRNA was widely expressed in the examined tissues and responded sensitively to bacterial challenge in hemocytes, while MGgLYZ2 mRNA was predominately expressed and performed its functions in hepatopancreas. However, immunolocalization analysis showed that both these lysozymes were expressed in all examined tissues with the exception of adductor muscle. Recombinant MGgLYZ1 and MGgLYZ2 could inhibit the growth of several Gram-positive and Gram-negative bacteria, and they both showed the highest activity against Pseudomonas putida with the minimum inhibitory concentration (MIC of 0.95-1.91 µM and 1.20-2.40 µM, respectively. Protein sequences analysis revealed that MGgLYZ2 had lower isoelectric point and less protease cutting sites than MGgLYZ1. Recombinant MGgLYZ2 exhibited relative high activity at acidic pH of 4-5, while MGgLYZ1 have an optimum pH of 6. These results indicated MGgLYZ2 adapted to acidic environment and perhaps play an important role in digestion. Genomic structure analysis suggested that both MGgLYZ1 and MGgLYZ2 genes are composed of six exons with same length and five introns, indicating these genes were conserved and might originate from gene duplication during the evolution. Selection pressure analysis showed that MGgLYZ1 was under nearly neutral selection while MGgLYZ2 evolved under positive selection pressure with three positively selected amino acid residues (Y(102, L(200 and S(202 detected in the mature peptide. All these findings suggested MGgLYZ2 perhaps served as a digestive lysozyme under positive selection pressure during the evolution while MGgLYZ1 was mainly involved in innate immune responses.

  2. Decongestion of urban areas with hotspot-pricing

    Solé-Ribalta, Albert; Arenas, Alex

    2016-01-01

    The rapid growth of population in urban areas is jeopardizing the mobility and air quality worldwide. One of the most notable problems arising is that of traffic congestion which in turn affects air pollution. With the advent of technologies able to sense real-time data about cities, and its public distribution for analysis, we are in place to forecast scenarios valuable to ameliorate and control congestion. Here, we propose a local congestion pricing scheme, hotspot-pricing, that surcharges vehicles traversing congested junctions. The proposed tax is computed from the estimation of the evolution of congestion at local level, and the expected response of users to the tax (elasticity). Results on cities' road networks, considering real-traffic data, show that the proposed hotspot-pricing scheme would be more effective than current mechanisms to decongest urban areas, and paves the way towards sustainable congestion in urban areas.

  3. Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster

    Jakobek Judy L

    2007-07-01

    Full Text Available Abstract Background The biosynthesis of aflatoxin (AF involves over 20 enzymatic reactions in a complex polyketide pathway that converts acetate and malonate to the intermediates sterigmatocystin (ST and O-methylsterigmatocystin (OMST, the respective penultimate and ultimate precursors of AF. Although these precursors are chemically and structurally very similar, their accumulation differs at the species level for Aspergilli. Notable examples are A. nidulans that synthesizes only ST, A. flavus that makes predominantly AF, and A. parasiticus that generally produces either AF or OMST. Whether these differences are important in the evolutionary/ecological processes of species adaptation and diversification is unknown. Equally unknown are the specific genomic mechanisms responsible for ordering and clustering of genes in the AF pathway of Aspergillus. Results To elucidate the mechanisms that have driven formation of these clusters, we performed systematic searches of aflatoxin cluster homologs across five Aspergillus genomes. We found a high level of gene duplication and identified seven modules consisting of highly correlated gene pairs (aflA/aflB, aflR/aflS, aflX/aflY, aflF/aflE, aflT/aflQ, aflC/aflW, and aflG/aflL. With the exception of A. nomius, contrasts of mean Ka/Ks values across all cluster genes showed significant differences in selective pressure between section Flavi and non-section Flavi species. A. nomius mean Ka/Ks values were more similar to partial clusters in A. fumigatus and A. terreus. Overall, mean Ka/Ks values were significantly higher for section Flavi than for non-section Flavi species. Conclusion Our results implicate several genomic mechanisms in the evolution of ST, OMST and AF cluster genes. Gene modules may arise from duplications of a single gene, whereby the function of the pre-duplication gene is retained in the copy (aflF/aflE or the copies may partition the ancestral function (aflA/aflB. In some gene modules, the

  4. Adaptive evolution of Schizochytrium sp. by continuous high oxygen stimulations to enhance docosahexaenoic acid synthesis.

    Sun, Xiao-Man; Ren, Lu-Jing; Ji, Xiao-Jun; Chen, Sheng-Lan; Guo, Dong-Sheng; Huang, He

    2016-07-01

    Adaptive laboratory evolution (ALE) is an effective method in changing the strain characteristics. Here, ALE with high oxygen as a selection pressure was applied to improve the production capacity of Schizochytrium sp. Results showed that cell dry weight (CDW) of endpoint strain was 32.4% higher than that of starting strain. But slight lipid accumulation impairment was observed. These major performance changes were accompanied with enhanced isocitrate dehydrogenase enzyme activity and reduced ATP:citrate lyase enzyme activity. And a serious decrease of 62.6% in SDHA 140rpm→170rpm was observed in the endpoint strain. To further study the docosahexaenoic acid (DHA) production ability of evolved strain, fed-batch strategy was applied and 84.34g/L of cell dry weight and 26.40g/L of DHA yield were observed. In addition, endpoint strain produced greatly less squalene than starting strain. This work demonstrated that ALE may be a promising tool in modifying microalga strains. PMID:27030957

  5. Adaptive evolution of threonine deaminase in plant defense against insect herbivores

    Gonzales-Vigil, Eliana; Bianchetti, Christopher M.; Phillips, Jr., George N.; Howe, Gregg A. (MSU); (UW)

    2011-11-07

    Gene duplication is a major source of plant chemical diversity that mediates plant-herbivore interactions. There is little direct evidence, however, that novel chemical traits arising from gene duplication reduce herbivory. Higher plants use threonine deaminase (TD) to catalyze the dehydration of threonine (Thr) to {alpha}-ketobutyrate and ammonia as the committed step in the biosynthesis of isoleucine (Ile). Cultivated tomato and related Solanum species contain a duplicated TD paralog (TD2) that is coexpressed with a suite of genes involved in herbivore resistance. Analysis of TD2-deficient tomato lines showed that TD2 has a defensive function related to Thr catabolism in the gut of lepidopteran herbivores. During herbivory, the regulatory domain of TD2 is removed by proteolysis to generate a truncated protein (pTD2) that efficiently degrades Thr without being inhibited by Ile. We show that this proteolytic activation step occurs in the gut of lepidopteran but not coleopteran herbivores, and is catalyzed by a chymotrypsin-like protease of insect origin. Analysis of purified recombinant enzymes showed that TD2 is remarkably more resistant to proteolysis and high temperature than the ancestral TD1 isoform. The crystal structure of pTD2 provided evidence that electrostatic interactions constitute a stabilizing feature associated with adaptation of TD2 to the extreme environment of the lepidopteran gut. These findings demonstrate a role for gene duplication in the evolution of a plant defense that targets and co-opts herbivore digestive physiology.

  6. Adaptive evolution of tight junction protein claudin-14 in echolocating whales.

    Xu, Huihui; Liu, Yang; He, Guimei; Rossiter, Stephen J; Zhang, Shuyi

    2013-11-10

    Toothed whales and bats have independently evolved specialized ultrasonic hearing for echolocation. Recent findings have suggested that several genes including Prestin, Tmc1, Pjvk and KCNQ4 appear to have undergone molecular adaptations associated with the evolution of this ultrasonic hearing in mammals. Here we studied the hearing gene Cldn14, which encodes the claudin-14 protein and is a member of tight junction proteins that functions in the organ of Corti in the inner ear to maintain a cationic gradient between endolymph and perilymph. Particular mutations in human claudin-14 give rise to non-syndromic deafness, suggesting an essential role in hearing. Our results uncovered two bursts of positive selection, one in the ancestral branch of all toothed whales and a second in the branch leading to the delphinid, phocoenid and ziphiid whales. These two branches are the same as those previously reported to show positive selection in the Prestin gene. Furthermore, as with Prestin, the estimated hearing frequencies of whales significantly correlate with numbers of branch-wise non-synonymous substitutions in Cldn14, but not with synonymous changes. However, in contrast to Prestin, we found no evidence of positive selection in bats. Our findings from Cldn14, and comparisons with Prestin, strongly implicate multiple loci in the acquisition of echolocation in cetaceans, but also highlight possible differences in the evolutionary route to echolocation taken by whales and bats. PMID:23965379

  7. Metabolic engineering and adaptive evolution for efficient production of D-lactic acid in Saccharomyces cerevisiae.

    Baek, Seung-Ho; Kwon, Eunice Y; Kim, Yong Hwan; Hahn, Ji-Sook

    2016-03-01

    There is an increasing demand for microbial production of lactic acid (LA) as a monomer of biodegradable poly lactic acid (PLA). Both optical isomers, D-LA and L-LA, are required to produce stereocomplex PLA with improved properties. In this study, we developed Saccharomyces cerevisiae strains for efficient production of D-LA. D-LA production was achieved by expressing highly stereospecific D-lactate dehydrogenase gene (ldhA, LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 in S. cerevisiae lacking natural LA production activity. D-LA consumption after glucose depletion was inhibited by deleting DLD1 encoding D-lactate dehydrogenase and JEN1 encoding monocarboxylate transporter. In addition, ethanol production was reduced by deleting PDC1 and ADH1 genes encoding major pyruvate decarboxylase and alcohol dehydrogenase, respectively, and glycerol production was eliminated by deleting GPD1 and GPD2 genes encoding glycerol-3-phosphate dehydrogenase. LA tolerance of the engineered D-LA-producing strain was enhanced by adaptive evolution and overexpression of HAA1 encoding a transcriptional activator involved in weak acid stress response, resulting in effective D-LA production up to 48.9 g/L without neutralization. In a flask fed-batch fermentation under neutralizing condition, our evolved strain produced 112.0 g/L D-LA with a yield of 0.80 g/g glucose and a productivity of 2.2 g/(L · h). PMID:26596574

  8. Strain improvement of Chlorella sp. for phenol biodegradation by adaptive laboratory evolution.

    Wang, Libo; Xue, Chuizhao; Wang, Liang; Zhao, Quanyu; Wei, Wei; Sun, Yuhan

    2016-04-01

    Microalgae are highly efficient photosynthesis cell factories for CO2 capture, biofuel productions and wastewater treatment. Phenol is a typical environmental contaminant. Microalgae normally have a low tolerance for, and a low degradation rate to, high concentration of phenol. Adaptive laboratory evolution was performed for phenolic wastewater treatment by Chlorella sp. The resulting strain was obtained after 31 cycles (about 95d) under 500mg/L phenol as environmental stress. It could grow under 500mg/L and 700mg/L phenol without significant inhibition. The maximal biomass concentrations of the resulting strain at day 8 were 3.40g/L under 500mg/L phenol and 2.70g/L under 700mg/L phenol, respectively. They were more than two times of those of the original strain. In addition, 500mg/L phenol was fully removed by the resulting strain in 7d when the initial cell density was 0.6g/L. PMID:26803904

  9. Evolution of cooperation in the spatial public goods game with adaptive reputation assortment

    Chen, Mei-huan; Wang, Li; Sun, Shi-wen; Wang, Juan; Xia, Cheng-yi

    2016-01-01

    We present a new spatial public goods game model, which takes the individual reputation and behavior diversity into account at the same time, to investigate the evolution of cooperation. Initially, each player x will be endowed with an integer Rx between 1 and Rmax to characterize his reputation value, which will be adaptively varied according to the strategy action at each time step. Then, the agents play the game and the system proceeds in accordance with a Fermi-like rule, in which a multiplicative factor (wy) to denote the individual difference to perform the strategy transfer will be placed before the traditional Fermi probability. For influential participants, wy is set to be 1.0, but be a smaller value w (0 reputation threshold (RC), and the greater the threshold, the higher the fraction of cooperators. The origin of promotion of cooperation will be attributed to the fact that the larger reputation threshold renders the higher heterogeneity in the fraction of two types of players and strategy spreading capability. Our work is conducive to a better understanding of the emergence of cooperation within many real-world systems.

  10. Shared human-chimpanzee pattern of perinatal femoral shaft morphology and its implications for the evolution of hominin locomotor adaptations.

    Naoki Morimoto

    Full Text Available BACKGROUND: Acquisition of bipedality is a hallmark of human evolution. How bipedality evolved from great ape-like locomotor behaviors, however, is still highly debated. This is mainly because it is difficult to infer locomotor function, and even more so locomotor kinematics, from fossil hominin long bones. Structure-function relationships are complex, as long bone morphology reflects phyletic history, developmental programs, and loading history during an individual's lifetime. Here we discriminate between these factors by investigating the morphology of long bones in fetal and neonate great apes and humans, before the onset of locomotion. METHODOLOGY/PRINCIPAL FINDINGS: Comparative morphometric analysis of the femoral diaphysis indicates that its morphology reflects phyletic relationships between hominoid taxa to a greater extent than taxon-specific locomotor adaptations. Diaphyseal morphology in humans and chimpanzees exhibits several shared-derived features, despite substantial differences in locomotor adaptations. Orangutan and gorilla morphologies are largely similar, and likely represent the primitive hominoid state. CONCLUSIONS/SIGNIFICANCE: These findings are compatible with two possible evolutionary scenarios. Diaphyseal morphology may reflect retained adaptive traits of ancestral taxa, hence human-chimpanzee shared-derived features may be indicative of the locomotor behavior of our last common ancestor. Alternatively, diaphyseal morphology might reflect evolution by genetic drift (neutral evolution rather than selection, and might thus be more informative about phyletic relationships between taxa than about locomotor adaptations. Both scenarios are consistent with the hypothesis that knuckle-walking in chimpanzees and gorillas resulted from convergent evolution, and that the evolution of human bipedality is unrelated to extant great ape locomotor specializations.

  11. Within-host evolution of Pseudomonas aeruginosa reveals adaptation toward iron acquisition from hemoglobin

    Marvig, Rasmus Lykke; Pedersen, Søren Damkiær; Khademi, Seyed Mohammad Hossein;

    2014-01-01

    adaptive evolution in two distinct lineages (DK1 and PA clone C). Furthermore, in all three lineages, phuR promoter mutations coincided with the loss of pyoverdine production, suggesting that within-host adaptation toward heme utilization is triggered by the loss of pyoverdine production. Targeting heme...... of other iron-scavenging mechanisms and/or an increase in the availability of hemoglobin at the site of infection. This information is relevant to the design of novel CF therapeutics and the development of models of chronic CF infections....

  12. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses

    Caspeta, Luis; Nielsen, Jens

    2015-01-01

    adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses...... proteins showed that the lethal temperature for yeast is around 49°C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number...

  13. Capturing Hotspots For Constrained Indoor Movement

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua

    2013-01-01

    Finding the hotspots in large indoor spaces is very important for getting overloaded locations, security, crowd management, indoor navigation and guidance. The tracking data coming from indoor tracking are huge in volume and not readily available for finding hotspots. This paper presents a graph...

  14. HotSpot Software Configuration Management Plan

    Walker, H; Homann, S G

    2009-03-12

    This Software Configuration Management Plan (SCMP) describes the software configuration management procedures used to ensure that the HotSpot dispersion model meets the requirements of its user base, which includes: (1) Users of the PC version of HotSpot for consequence assessment, hazard assessment and safety analysis calculations; and (2) Users of the NARAC Web and iClient software tools, which allow users to run HotSpot for consequence assessment modeling These users and sponsors of the HotSpot software and the organizations they represent constitute the intended audience for this document. This plan is intended to meet Critical Recommendations 1 and 3 from the Software Evaluation of HotSpot and DOE Safety Software Toolbox Recommendation for inclusion of HotSpot in the Department of Energy (DOE) Safety Software Toolbox. HotSpot software is maintained for the Department of Energy Office of Emergency Operations by the National Atmospheric Release Advisory Center (NARAC) at Lawrence Livermore National Laboratory (LLNL). An overview of HotSpot and NARAC are provided.

  15. Microbial hotspots and hot moments in soil

    Kuzyakov, Yakov; Blagodatskaya, Evgenia

    2015-04-01

    Soils are the most heterogeneous parts of the biosphere, with an extremely high differentiation of properties and processes within nano- to macroscales. The spatial and temporal heterogeneity of input of labile organics by plants creates microbial hotspots over short periods of time - the hot moments. We define microbial hotspots as small soil volumes with much faster process rates and much more intensive interactions compared to the average soil conditions. Such hotspots are found in the rhizosphere, detritusphere, biopores (including drilosphere) and on aggregate surfaces, but hotspots are frequently of mixed origin. Hot moments are short-term events or sequences of events inducing accelerated process rates as compared to the averaged rates. Thus, hotspots and hot moments are defined by dynamic characteristics, i.e. by process rates. For this hotspot concept we extensively reviewed and examined the localization and size of hotspots, spatial distribution and visualization approaches, transport of labile C to and from hotspots, lifetime and process intensities, with a special focus on process rates and microbial activities. The fraction of active microorganisms in hotspots is 2-20 times higher than in the bulk soil, and their specific activities (i.e. respiration, microbial growth, mineralization potential, enzyme activities, RNA/DNA ratio) may also be much higher. The duration of hot moments in the rhizosphere is limited and is controlled by the length of the input of labile organics. It can last a few hours up to a few days. In the detritusphere, however, the duration of hot moments is regulated by the output - by decomposition rates of litter - and lasts for weeks and months. Hot moments induce succession in microbial communities and intense intra- and interspecific competition affecting C use efficiency, microbial growth and turnover. The faster turnover and lower C use efficiency in hotspots counterbalances the high C inputs, leading to the absence of strong

  16. Adapt

    Bargatze, L. F.

    2015-12-01

    Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

  17. Regulatory modulation of the T-box gene Tbx5 links development, evolution, and adaptation of the sternum

    Bickley, Sorrel R. B.; Logan, Malcolm P. O.

    2014-01-01

    The fin-to-limb transition and acquisition of sterna were critical steps in the evolution of tetrapods, but despite the importance of the sternum in enabling quadrupedal locomotion and avian flight, the mechanisms controlling acquisition and evolutionary adaptation of sterna are not understood. Furthermore, the mechanisms that underlie sternum development and sternal defects are not known. We describe T-box transcription factor gene Tbx5 function in sternum formation, how disruption of TBX5 c...

  18. Evolution of genes related to temperature adaptation in Drosophila melanogaster as revealed by QTL and population genetics analyses

    WILCHES, RICARDO

    2014-01-01

    The fixation of beneficial variants leaves genomic footprints characterized by a reduction of genetic variation at linked neutral sites and strong, localized allele frequency differentiation among subpopulations. In contrast, for phenotypic evolution the effect of adaptation on the genes controlling the trait is little understood. Theoretical work on polygenic selection suggests that fixations of beneficial alleles (causing selective sweeps) are less likely than small-to-moderate allele frequ...

  19. Experimental Evolution of a Bacteriophage Virus Reveals the Trajectory of Adaptation across a Fecundity/Longevity Trade-Off

    Heineman, Richard H.; Brown, Sam P.

    2012-01-01

    Life history theory attempts to account for how organisms lead their lives, balancing the conflicting demands of reproduction and survival. Here, we track the genomic and phenotypic evolution of the bacteriophage virus T7 across a postulated fecundity/longevity constraint. We adapted T7 to a challenging survival environment (6M urea). Our evolved strain displayed a significant improvement in propagule survival, coupled with a significant loss of fecundity (reduced growth rate on host cells). ...

  20. Modularity, adaptability and evolution in the AUTOPIA architecture for control of autonomous vehicles. Updating Mechatronics of Automatic Cars

    Pérez Rastelli, Joshué; González, Carlos; Milanés, Vicente; Onieva, Enrique; Godoy, Jorge; Pedro, Teresa de

    2009-01-01

    International audience Computer systems to carry out control algorithms on autonomous vehicles have been developed in recent years. However, the advances in peripheral devices allow connecting the actuator controllers to the control system by means of standard communication links (USB, CAN, Ethernet ... ).The goal is to permit the use of standard computers. In this paper, we present the evolution of AUTOPIA architecture and its modularity and adaptability to move the old system based on IS...

  1. Evolution of highly pathogenic avian influenza H5N1 viruses in Egypt indicating progressive adaptation.

    Arafa, A; Suarez, D; Kholosy, S G; Hassan, M K; Nasef, S; Selim, A; Dauphin, G; Kim, M; Yilma, J; Swayne, D; Aly, M M

    2012-10-01

    Highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype was first diagnosed in poultry in Egypt in 2006, and since then the disease became enzootic in poultry throughout the country, affecting the poultry industry and village poultry as well as infecting humans. Vaccination has been used as a part of the control strategy to help to control the disease. Epidemiological data with sequence analysis of H5N1 viruses is important to link the mechanism of virus evolution in Egypt. This study describes the evolutionary pattern of Egyptian H5N1 viruses based on molecular characterization for the isolates collected from commercial poultry farms and village poultry from 2006 to 2011. Genetic analysis of the hemagglutinin (HA) gene was done by sequencing of the full-length H5 gene. The epidemiological pattern of disease outbreaks in Egyptian poultry farms seems to be seasonal with no specific geographic distribution across the country. The molecular epidemiological data revealed that there are two major groups of viruses: the classic group of subclade 2.2.1 and a variant group of 2.2.1.1. The classic group is prevailing mainly in village poultry and had fewer mutations compared to the originally introduced virus in 2006. Since 2009, this group has started to be transmitted back to commercial sectors. The variant group emerged by late 2007, was prevalent mainly in vaccinated commercial poultry, mutated continuously at a higher rate until 2010, and started to decline in 2011. Genetic analysis of the neuraminidase (NA) gene and the other six internal genes indicates a grouping of the Egyptian viruses similar to that obtained using the HA gene, with no obvious reassortments. The results of this study indicate that HPAI-H5N1 viruses are progressively evolving and adapting in Egypt and continue to acquire new mutations every season. PMID:22760662

  2. Interacting proteins on human spermatozoa: adaptive evolution of the binding of semenogelin I to EPPIN.

    Erick J R Silva

    Full Text Available Semenogelin I (SEMG1 is found in human semen coagulum and on the surface of spermatozoa bound to EPPIN. The physiological significance of the SEMG1/EPPIN interaction on the surface of spermatozoa is its capacity to modulate sperm progressive motility. The present study investigates the hypothesis that the interacting surface of SEMG1 and EPPIN co-evolved within the Hominoidea time scale, as a result of adaptive pressures applied by their roles in sperm protection and reproductive fitness. Our results indicate that some amino acid residues of SEMG1 and EPPIN possess a remarkable deficiency of variation among hominoid primates. We observe a distinct residue change unique to humans within the EPPIN sequence containing a SEMG1 interacting surface, namely His92. In addition, Bayes Empirical Bayes analysis for positive selection indicates that the SEMG1 Cys239 residue underwent positive selection in humans, probably as a consequence of its role in increasing the binding affinity of these interacting proteins. We confirm the critical role of Cys239 residue for SEMG1 binding to EPPIN and inhibition of sperm motility by showing that recombinant SEMG1 mutants in which Cys239 residue was changed to glycine, aspartic acid, histidine, serine or arginine have reduced capacity to interact to EPPIN and to inhibit human sperm motility in vitro. In conclusion, our results indicate that EPPIN and SEMG1 rapidly co-evolved in primates due to their critical role in the modulation of sperm motility in the semen coagulum, providing unique insights into the molecular co-evolution of sperm surface interacting proteins.

  3. Adaptive evolution of a generalist parasitoid: implications for the effectiveness of biological control agents

    Zepeda-Paulo, Francisca A; Ortiz-Martínez, Sebastián A; Figueroa, Christian C.; Lavandero, Blas

    2013-01-01

    The use of alternative hosts imposes divergent selection pressures on parasitoid populations. In response to selective pressures, these populations may follow different evolutionary trajectories. Divergent natural selection could promote local host adaptation in populations, translating into direct benefits for biological control, thereby increasing their effectiveness on the target host. Alternatively, adaptive phenotypic plasticity could be favored over local adaptation in temporal and spat...

  4. A pivot mutation impedes reverse evolution across an adaptive landscape for drug resistance in Plasmodium vivax

    Ogbunugafor, C. Brandon; Hartl, Daniel

    2016-01-01

    Background: The study of reverse evolution from resistant to susceptible phenotypes can reveal constraints on biological evolution, a topic for which evolutionary theory has relatively few general principles. The public health catastrophe of antimicrobial resistance in malaria has brought these constraints on evolution into a practical realm, with one proposed solution: withdrawing anti-malarial medication use in high resistance settings, built on the assumption that reverse evolution occurs ...

  5. Exploring the correlations between sequence evolution rate and phenotypic divergence across the Mammalian tree provides insights into adaptive evolution

    Jan Janecka; Bhanu Chowdhary; William Murphy

    2012-11-01

    Sequence evolution behaves in a relatively consistent manner, leading to one of the fundamental paradigms in biology, the existence of a `molecular clock’. The molecular clock can be distilled to the concept of accumulation of substitutions, through time yielding a stable rate from which we can estimate lineage divergence. Over the last 50 years, evolutionary biologists have obtained an in-depth understanding of this clock’s nuances. It has been fine-tuned by taking into account the vast heterogeneity in rates across lineages and genes, leading to `relaxed’ molecular clock methods for timetree reconstruction. Sequence rate varies with life history traits including body size, generation time and metabolic rate, and we review recent studies on this topic. However, few studies have explicitly examined correlates between molecular evolution and morphological evolution. The patterns observed across diverse lineages suggest that rates of molecular and morphological evolution are largely decoupled. We discuss how identifying the molecular mechanisms behind rapid functional radiations are central to understanding evolution. The vast functional divergence within mammalian lineages that have relatively `slow’ sequence evolution refutes the hypotheses that pulses in diversification yielding major phenotypic change are the result of steady accumulation of substitutions. Patterns rather suggest phenotypic divergence is likely caused by regulatory alterations mediated through mechanisms such as insertions/deletions in functional regions. These can rapidly arise and sweep to fixation faster than predicted from a lineage’s sequence neutral substitution rate, enabling species to leapfrog between phenotypic `islands’. We suggest research directions that could illuminate mechanisms behind the functional diversity we see today.

  6. Comprehensive Transcriptome Analysis of Six Catfish Species from an Altitude Gradient Reveals Adaptive Evolution in Tibetan Fishes

    Xiuhui Ma

    2016-01-01

    Full Text Available Glyptosternoid fishes (Siluriformes, one of the three broad fish lineages (the two other are schizothoracines and Triplophysa, have a limited distribution in the rivers in the Tibetan Plateau and peripheral regions. To investigate the genetic mechanisms underlying adaptation to the Tibetan Plateau in several fish species from gradient altitudes, a total of 20,659,183–37,166,756 sequence reads from six species of catfish were generated by Illumina sequencing, resulting in six assemblies. Analysis of the 1,656 orthologs among the six assembled catfish unigene sets provided consistent evidence for genome-wide accelerated evolution in the three glyptosternoid lineages living at high altitudes. A large number of genes refer to functional categories related to hypoxia and energy metabolism exhibited rapid evolution in the glyptosternoid lineages relative to yellowhead catfish living in plains areas. Genes showing signatures of rapid evolution and positive selection in the glyptosternoid lineages were also enriched in functions associated with energy metabolism and hypoxia. Our analyses provide novel insights into highland adaptation in fishes and can serve as a foundation for future studies aiming to identify candidate genes underlying the genetic basis of adaptation in Tibetan fishes.

  7. Which Beak Fits the Bill? An Activity Examining Adaptation, Natural Selection and Evolution

    Darling, Randi

    2014-01-01

    Evolution is a unifying concept within biology. In fact, Dobzhansky, a noted evolutionary biologist, argued, "Nothing in biology makes sense except in the light of evolution" (Dobzhansky, 1973). However, often students have misconceptions about evolution. There are a number of available activities where students use tools (representing…

  8. Distribution of recombination hotspots in the human genome--a comparison of computer simulations with real data.

    Dorota Mackiewicz

    Full Text Available Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar.

  9. Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution.

    Sharma, Poonam; Gupta, Sushim Kumar; Rolain, Jean-Marc

    2014-03-01

    Cystic fibrosis (CF) airways harbor a wide variety of new and/or emerging multidrug resistant bacteria which impose a heavy burden on patients. These bacteria live in close proximity with one another, which increases the frequency of lateral gene transfer. The exchange and movement of mobile genetic elements and genomic islands facilitate the spread of genes between genetically diverse bacteria, which seem to be advantageous to the bacterium as it allows adaptation to the new niches of the CF lungs. Niche adaptation is one of the major evolutionary forces shaping bacterial genome composition and in CF the chronic strains adapt and become less virulent. The purpose of this review is to shed light on CF bacterial genome alterations. Next-generation sequencing technology is an exciting tool that may help us to decipher the genome architecture and the evolution of bacteria colonizing CF lungs. PMID:24502835

  10. A Differential Evolution Based Adaptive Neural Network Pitch Controller for a Doubly Fed Wind Turbine Generator System

    A.H.M.A. Rahim

    2013-12-01

    Full Text Available Extraction of maximum energy from wind and transferring it to the grid with high efficiency are challenging problems. To this end, this study proposes a smart pitch controller for a wind turbine-doubly fed induction generator system using a Differential Evolution (DE based adaptive neural network. The nominal weights for the back-propagation neural network controller are obtained from input-output training data generated by DE optimization method. These weights are then adaptively updated in time domain depending on the variation of the system outputs. The adaptive control strategy has been tested through simulation of complete system dynamics comprising of the turbine-generator system and its various components. It has been observed that the DE based smart pitch controller is able to achieve efficient energy transfer to the grid and at the same time provide a good damping profile. Locally collected wind data was used in the testing phase.

  11. hotspot: software to support sperm-typing for investigating recombination hotspots

    Dutheil, Julien Y.; Klötzl, Fabian; Haubold, Bernhard

    2016-01-01

    Motivation: In many organisms, including humans, recombination clusters within recombination hotspots. The standard method for de novo detection of recombinants at hotspots is sperm typing. This relies on allele-specific PCR at single nucleotide polymorphisms. Designing allele-specific primers by hand is time-consuming. We have therefore written a package to support hotspot detection and analysis. Results: hotspot consists of four programs: asp looks up SNPs and designs allele-specific primers; aso constructs allele-specific oligos for mapping recombinants; xov implements a maximum-likelihood method for estimating the crossover rate; six, finally, simulates typing data. Availability and Implementation: hotspot is written in C. Sources are freely available under the GNU General Public License from http://github.com/evolbioinf/hotspot/ Contact: haubold@evolbio.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153632

  12. Coral Reef Watch, Hotspots, 50 km

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA Coral Reef Watch provides Coral Bleaching hotspot maps derived from NOAA's Polar Operational Environmental Satellites (POES). This data provides global area...

  13. Duplication and Adaptive Evolution of a Key Centromeric Protein in Mimulus, a Genus with Female Meiotic Drive.

    Finseth, Findley R; Dong, Yuzhu; Saunders, Arpiar; Fishman, Lila

    2015-10-01

    The fundamental asymmetry of female meiosis creates an arena for genetic elements to compete for inclusion in the egg, promoting the selfish evolution of centromere variants that maximize their transmission to the future egg. Such "female meiotic drive" has been hypothesized to explain the paradoxically complex and rapidly evolving nature of centromeric DNA and proteins. Although theoretically widespread, few cases of active drive have been observed, thereby limiting the opportunities to directly assess the impact of centromeric drive on molecular variation at centromeres and binding proteins. Here, we characterize the molecular evolutionary patterns of CENH3, the centromere-defining histone variant, in Mimulus monkeyflowers, a genus with one of the few known cases of active centromere-associated female meiotic drive. First, we identify a novel duplication of CENH3 in diploid Mimulus, including in lineages with actively driving centromeres. Second, we demonstrate long-term adaptive evolution at several sites in the N-terminus of CENH3, a region with some meiosis-specific functions that putatively interacts with centromeric DNA. Finally, we infer that the paralogs evolve under different selective regimes; some sites in the N-terminus evolve under positive selection in the pro-orthologs or only one paralog (CENH3_B) and the paralogs exhibit significantly different patterns of polymorphism within populations. Our finding of long-term, adaptive evolution at CENH3 in the context of centromere-associated meiotic drive supports an antagonistic, coevolutionary battle for evolutionary dominance between centromeric DNA and binding proteins. PMID:26104011

  14. Capturing Hotspots For Constrained Indoor Movement

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua

    2013-01-01

    Finding the hotspots in large indoor spaces is very important for getting overloaded locations, security, crowd management, indoor navigation and guidance. The tracking data coming from indoor tracking are huge in volume and not readily available for finding hotspots. This paper presents a graph-based model for constrained indoor movement that can map the tracking records into mapping records which represent the entry and exit times of an object in a particular location. Then it discusses the...

  15. 国际健康素养研究演进路径、研究热点与前沿可视化分析%The Visualization Analysis of Evolution Pathway, Research Hotspots and Research Fronts of International Health Literacy

    姚强; 刘小利; 杜建; 张士靖

    2011-01-01

    The aim of this paper is to reveal the evolution in the latest 30 years, research hotspots and research fronts of Health Literacy. We retrieved the whole documents data by topic word "health literacy" from 1990 to 2010 in SCI, SSCI. Documents are visualized through a number of co-citation maps. which filtered the critical node documents in the evolution of health literacy research by knowledge visualization tool, CiteSpace. We also applied its function of document-noun phrase network ,keywords clusting and burst detecting to analyse the research hotspots and research fronts. 11 critical node documents perfectly showed the evolution pathway of health literacy research, 2 clear clusters and 19 burst terms indicated the research hotspots and research fronts. Health literacy and mental health literacy are two domain research fields of health literacy. Such subjects or fields as connotation of health literacy, health materials' readability, rapid assessment of literacy levels, health education,emergency and chronic disease or infections represented by AIDS are research fronts and development trends in future.%文章目的在于梳理30多年来健康素养领域研究的演进路径,揭示研究热点与研究前沿.为此,将1 990一201 o年s CI、sscI数据库中收录的主题为"健康素养"的论文数据作为研究对象,应用citespace知识可视化软件绘制文献共被引网络图谱,析出健康素养演进过程中的关键节点文献;并应用其文献共引一名词短语混合网络图谱、关键词聚类和膨胀词探测功能分析了研究热点与研究前沿.11篇关键节点文献很好地展示了健康素养领域研完的演进路径,2个明显的聚类以及19个突现词表征了研究热点与研究前沿.文章认为健康素养和精神健康素养是目前两个主流研究领域.健康素养内涵、健康材料的可读性、快速测评工具和方法、健康教育、突发性事件以及以艾滋病为代表的慢性病与传

  16. High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots

    Pitt Joel PW

    2008-01-01

    Full Text Available Abstract Background Microsatellites are highly abundant in eukaryotic genomes but their function and evolution are not yet well understood. Their elevated mutation rate makes them ideal markers of genetic difference, but high levels of unexplained heterogeneity in mutation rates among microsatellites at different genomic locations need to be elucidated in order to improve the power and accuracy of the many types of study that use them as genetic markers. Recombination could contribute to this heterogeneity, since while replication errors are thought to be the predominant mechanism for microsatellite mutation, meiotic recombination is involved in some mutation events. There is also evidence suggesting that microsatellites could function as recombination signals. The yeast S. cerevisiae is a useful model organism with which to further explore the link between microsatellites and recombination, since it is very amenable to genetic study, and meiotic recombination hotspots have been mapped throughout its entire genome. Results We examined in detail the relationship between microsatellites and hotspots of meiotic double-strand breaks, the precursors of meiotic recombination, throughout the S. cerevisiae genome. We included all tandem repeats with motif length (repeat period between one and six base pairs. Long, short and two-copy arrays were considered separately. We found that long, mono-, di- and trinucleotide microsatellites are around twice as frequent in hot than non-hot intergenic regions. The associations are weak or absent for repeats with less than six copies, and also for microsatellites with 4–6 base pair motifs, but high-copy arrays with motif length greater than three are relatively very rare throughout the genome. We present evidence that the association between high-copy, short-motif microsatellites and recombination hotspots is not driven by effects on microsatellite distribution of other factors previously linked to both

  17. Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate‐induced range shifts

    Hargreaves, Anna; Bailey, Susan; Laird, Robert

    2015-01-01

    contracting range limits is facilitated by two processes that potentially enable edge populations to experience and adjust to the effects of climate deterioration before they cause extinction: (i) climate-induced fitness declines towards range limits and (ii) local adaptation to a shifting climate gradient......Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low-latitude/low-elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution at......, increased kin selection in smaller populations, and an emergent fitness asymmetry that favoured dispersal in low-quality habitat. However, this initial dispersal advantage at low-fitness RLs did not facilitate climate tracking, as it was outweighed by an increased probability of extinction. Locally adapted...

  18. Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature.

    Bradbury, Ian R; Hubert, Sophie; Higgins, Brent; Borza, Tudor; Bowman, Sharen; Paterson, Ian G; Snelgrove, Paul V R; Morris, Corey J; Gregory, Robert S; Hardie, David C; Hutchings, Jeffrey A; Ruzzante, Daniel E; Taggart, Chris T; Bentzen, Paul

    2010-12-22

    Despite the enormous economic and ecological importance of marine organisms, the spatial scales of adaptation and biocomplexity remain largely unknown. Yet, the preservation of local stocks that possess adaptive diversity is critical to the long-term maintenance of productive stable fisheries and ecosystems. Here, we document genomic evidence of range-wide adaptive differentiation in a broadcast spawning marine fish, Atlantic cod (Gadus morhua), using a genome survey of single nucleotide polymorphisms. Of 1641 gene-associated polymorphisms examined, 70 (4.2%) tested positive for signatures of selection using a Bayesian approach. We identify a subset of these loci (n=40) for which allele frequencies show parallel temperature-associated clines (p<0.001, r2=0.89) in the eastern and western north Atlantic. Temperature associations were robust to the statistical removal of geographic distance or latitude effects, and contrasted 'neutral' loci, which displayed no temperature association. Allele frequencies at temperature-associated loci were significantly correlated, spanned three linkage groups and several were successfully annotated supporting the involvement of multiple independent genes. Our results are consistent with the evolution and/or selective sweep of multiple genes in response to ocean temperature, and support the possibility of a new conservation paradigm for non-model marine organisms based on genomic approaches to resolving functional and adaptive diversity. PMID:20591865

  19. Experimental evolution of a bacteriophage virus reveals the trajectory of adaptation across a fecundity/longevity trade-off.

    Richard H Heineman

    Full Text Available Life history theory attempts to account for how organisms lead their lives, balancing the conflicting demands of reproduction and survival. Here, we track the genomic and phenotypic evolution of the bacteriophage virus T7 across a postulated fecundity/longevity constraint. We adapted T7 to a challenging survival environment (6M urea. Our evolved strain displayed a significant improvement in propagule survival, coupled with a significant loss of fecundity (reduced growth rate on host cells. However, the increased resistance to urea did not generalise to increased resistance against temperature stress, highlighting that propagule durability is environment dependent. Previous comparative studies predicted that changes in propagule resistance would be mediated by changes in capsid proteins or gene deletions. In contrast, we found that point mutations in internal core protein genes (6.7 and 16 were responsible for the increased urea resistance of our evolved strain. Prior to the emergence of the 6.7 and 16 mutations, a distinct set of 5-point mutations peaked at over 20% prevalence before attenuating, suggestive of negative epistatic interactions during adaptation. Our results illustrate that parasites can adapt to specific transmission environments, and that this adaptation can impose costs on the subsequent ability to exploit host cells, potentially constraining durable parasites to lower virulence.

  20. Adaptive Evolution in the Glucose Transporter 4 Gene Slc2a4 in Old World Fruit Bats (Family: Pteropodidae)

    Shen, Bin; Han, Xiuqun; Zhang, Junpeng; Rossiter, Stephen J.; Zhang, Shuyi

    2012-01-01

    Frugivorous and nectarivorous bats are able to ingest large quantities of sugar in a short time span while avoiding the potentially adverse side-effects of elevated blood glucose. The glucose transporter 4 protein (GLUT4) encoded by the Slc2a4 gene plays a critical role in transmembrane skeletal muscle glucose uptake and thus glucose homeostasis. To test whether the Slc2a4 gene has undergone adaptive evolution in bats with carbohydrate-rich diets in relation to their insect-eating sister taxa...

  1. Evolution of opercle shape in cichlid fishes from Lake Tanganyika - adaptive trait interactions in extant and extinct species flocks.

    Wilson, Laura A B; Colombo, Marco; Sánchez-Villagra, Marcelo R; Salzburger, Walter

    2015-01-01

    Phenotype-environment correlations and the evolution of trait interactions in adaptive radiations have been widely studied to gain insight into the dynamics underpinning rapid species diversification. In this study we explore the phenotype-environment correlation and evolution of operculum shape in cichlid fishes using an outline-based geometric morphometric approach combined with stable isotope indicators of macrohabitat and trophic niche. We then apply our method to a sample of extinct saurichthyid fishes, a highly diverse and near globally distributed group of actinopterygians occurring throughout the Triassic, to assess the utility of extant data to inform our understanding of ecomorphological evolution in extinct species flocks. A series of comparative methods were used to analyze shape data for 54 extant species of cichlids (N = 416), and 6 extinct species of saurichthyids (N = 44). Results provide evidence for a relationship between operculum shape and feeding ecology, a concentration in shape evolution towards present along with evidence for convergence in form, and significant correlation between the major axes of shape change and measures of gut length and body elongation. The operculum is one of few features that can be compared in extant and extinct groups, enabling reconstruction of phenotype-environment interactions and modes of evolutionary diversification in deep time. PMID:26584885

  2. Adaptive gains through repeated gene loss: parallel evolution of cyanogenesis polymorphisms in the genus Trifolium (Fabaceae)

    Olsen, Kenneth M.; Kooyers, Nicholas J.; Small, Linda L.

    2014-01-01

    Variation in cyanogenesis (hydrogen cyanide release following tissue damage) was first noted in populations of white clover more than a century ago, and subsequent decades of research have established this system as a classic example of an adaptive chemical defence polymorphism. Here, we document polymorphisms for cyanogenic components in several relatives of white clover, and we determine the molecular basis of this trans-specific adaptive variation. One hundred and thirty-nine plants, repre...

  3. Adaptive Evolution of the Venom-Targeted vWF Protein in Opossums that Eat Pitvipers

    Sharon A Jansa; Voss, Robert S.

    2011-01-01

    The rapid evolution of venom toxin genes is often explained as the result of a biochemical arms race between venomous animals and their prey. However, it is not clear that an arms race analogy is appropriate in this context because there is no published evidence for rapid evolution in genes that might confer toxin resistance among routinely envenomed species. Here we report such evidence from an unusual predator-prey relationship between opossums (Marsupialia: Didelphidae) and pitvipers (Serp...

  4. Science and technology libraries in evolution: adaptation and synergy for survival and success

    Nieuwenhuysen, Paul

    2004-01-01

    A brief overview is presented of some challenges that science and technology libraries have to face, caused by the evolution from classical libraries towards more electronic and digital libraries. This is a consequence of the fast evolution in information and communication technology (ICT) that has lead to more applications of ICT, not only to manage classical libraries, but also to create, distribute and access information resources in digital format through computer networks.

  5. First Results from HOTSPOT: The Snake River Plain Scientific Drilling Project, Idaho, U.S.A.

    John W. Shervais

    2013-03-01

    Full Text Available HOTSPOT is an international collaborative effort to understand the volcanic history of the Snake River Plain (SRP. The SRP overlies a thermal anomaly, the Yellowstone-Snake River hotspot, that is thought to represent a deep-seated mantle plume under North America. Theprimary goal of this project is to document the volcanic and stratigraphic history of the SRP, which represents the surface expression of this hotspot, and to understand how it affected the evolution of continental crust and mantle. An additional goal is to evaluate the geothermal potential of southern Idaho.Project HOTSPOT has completed three drill holes. (1 The Kimama site is located along the central volcanic axis of the SRP; our goal here was to sample a long-term record of basaltic volcanism in the wake of the SRP hotspot. (2 The Kimberly site is located near the margin of the plain; our goal here was to sample a record of high-temperaturerhyolite volcanism associated with the underlying plume. This site was chosen to form a nominally continuous record of volcanism when paired with the Kimama site. (3 The Mountain Home site is located in the western plain; our goal here was to sample the Pliocene-Pleistocene transition in lake sediments at this site and to sample older basalts that underlie the sediments.We report here on our initial results for each site, and on some of the geophysical logging studies carried out as part of this project.

  6. The Evolution of Olfactory Gene Families in Drosophila and the Genomic Basis of chemical-Ecological Adaptation in Drosophila suzukii

    Ramasamy, Sukanya; Ometto, Lino; Crava, Cristina M.; Revadi, Santosh; Kaur, Rupinder; Horner, David S.; Pisani, Davide; Dekker, Teun; Anfora, Gianfranco; Rota-Stabelli, Omar

    2016-01-01

    How the evolution of olfactory genes correlates with adaption to new ecological niches is still a debated topic. We explored this issue in Drosophila suzukii, an emerging model that reproduces on fresh fruit rather than in fermenting substrates like most other Drosophila. We first annotated the repertoire of odorant receptors (ORs), odorant binding proteins (OBPs), and antennal ionotropic receptors (aIRs) in the genomes of two strains of D. suzukii and of its close relative Drosophila biarmipes. We then analyzed these genes on the phylogeny of 14 Drosophila species: whereas ORs and OBPs are characterized by higher turnover rates in some lineages including D. suzukii, aIRs are conserved throughout the genus. Drosophila suzukii is further characterized by a non-random distribution of OR turnover on the gene phylogeny, consistent with a change in selective pressures. In D. suzukii, we found duplications and signs of positive selection in ORs with affinity for short-chain esters, and loss of function of ORs with affinity for volatiles produced during fermentation. These receptors—Or85a and Or22a—are characterized by divergent alleles in the European and American genomes, and we hypothesize that they may have been replaced by some of the duplicated ORs in corresponding neurons, a hypothesis reciprocally confirmed by electrophysiological recordings. Our study quantifies the evolution of olfactory genes in Drosophila and reveals an array of genomic events that can be associated with the ecological adaptations of D. suzukii. PMID:27435796

  7. Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain.

    Ji, Boyang; Zhang, Sheng-Da; Arnoux, Pascal; Rouy, Zoe; Alberto, François; Philippe, Nadège; Murat, Dorothée; Zhang, Wei-Jia; Rioux, Jean-Baptiste; Ginet, Nicolas; Sabaty, Monique; Mangenot, Sophie; Pradel, Nathalie; Tian, Jiesheng; Yang, Jing; Zhang, Lichen; Zhang, Wenyan; Pan, Hongmiao; Henrissat, Bernard; Coutinho, Pedro M; Li, Ying; Xiao, Tian; Médigue, Claudine; Barbe, Valérie; Pignol, David; Talla, Emmanuel; Wu, Long-Fei

    2014-02-01

    Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane-bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH-2. The high number of repeats and transposable elements account for the differences in QH-2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH-2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium-quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH-2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH-2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH-2 neither has TonB and TonB-dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH-2 to marine sediments in comparison with its closely related freshwater counterparts. PMID:23841906

  8. Adaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago

    Ronfort Joëlle

    2007-11-01

    Full Text Available Abstract Background The NODULATION RECEPTOR KINASE (NORK gene encodes a Leucine-Rich Repeat (LRR-containing receptor-like protein and controls the infection by symbiotic rhizobia and endomycorrhizal fungi in Legumes. The occurrence of numerous amino acid changes driven by directional selection has been reported in this gene, using a limited number of messenger RNA sequences, but the functional reason of these changes remains obscure. The Medicago genus, where changes in rhizobial associations have been previously examined, is a good model to test whether the evolution of NORK is influenced by rhizobial interactions. Results We sequenced a region of 3610 nucleotides (encoding a 392 amino acid-long region of the NORK protein in 32 Medicago species. We confirm that positive selection in NORK has occurred within the Medicago genus and find that the amino acid positions targeted by selection occur in sites outside of solvent-exposed regions in LRRs, and other sites in the N-terminal region of the protein. We tested if branches of the Medicago phylogeny where changes of rhizobial symbionts occurred displayed accelerated rates of amino acid substitutions. Only one branch out of five tested, leading to M. noeana, displays such a pattern. Among other branches, the most likely for having undergone positive selection is not associated with documented shift of rhizobial specificity. Conclusion Adaptive changes in the sequence of the NORK receptor have involved the LRRs, but targeted different sites than in most previous studies of LRR proteins evolution. The fact that positive selection in NORK tends not to be associated to changes in rhizobial specificity indicates that this gene was probably not involved in evolving rhizobial preferences. Other explanations (e.g. coevolutionary arms race must be tested to explain the adaptive evolution of NORK.

  9. The evolution of an annual life cycle in killifish: adaptation to ephemeral aquatic environments through embryonic diapause.

    Furness, Andrew I

    2016-08-01

    An annual life cycle is characterized by growth, maturity, and reproduction condensed into a single, short season favourable to development, with production of embryos (seeds, cysts, or eggs) capable of surviving harsh conditions which juveniles or adults cannot tolerate. More typically associated with plants in desert environments, or temperate-zone insects exposed to freezing winters, the evolution of an annual life cycle in vertebrates is fairly novel. Killifish, small sexually dimorphic fishes in the Order Cyprinodontiformes, have adapted to seasonally ephemeral water bodies across much of Africa and South America through the independent evolution of an annual life history. These annual killifish produce hardy desiccation-resistant eggs that undergo diapause (developmental arrest) and remain buried in the soil for long periods when fish have perished due to the drying of their habitat. Killifish are found in aquatic habitats that span a continuum from permanent and stable to seasonal and variable, thus providing a useful system in which to piece together the evolutionary history of this life cycle using natural comparative variation. I first review adaptations for life in ephemeral aquatic environments in killifish, with particular emphasis on the evolution of embryonic diapause. I then bring together available evidence from a variety of approaches and provide a scenario for how this annual life cycle evolved. There are a number of features within Aplocheiloidei killifish including their inhabitation of marginal or edge aquatic habitat, their small size and rapid attainment of maturity, and egg properties that make them particularly well suited to the colonization of ephemeral waters. PMID:25969869

  10. Recovery of Phenotypes Obtained by Adaptive Evolution through Inverse Metabolic Engineering

    Hong, Kuk-Ki; Nielsen, Jens

    2012-01-01

    In a previous study, system level analysis of adaptively evolved yeast mutants showing improved galactose utilization revealed relevant mutations. The governing mutations were suggested to be in the Ras/PKA signaling pathway and ergosterol metabolism. Here, site-directed mutants having one of the...

  11. Evolution of fitness trade-offs in locally adapted populations of Pseudomonas fluorescens

    Schick, Alana; Bailey, Susan; Kassen, Rees

    2015-01-01

    characterize the genetic causes of trade-offs generating local adaptation in populations of Pseudomonas fluorescens that had previously been evolved for specialization on three different carbon resources. We measured the fitness effects of mutations that arose during selection in that environment...

  12. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle.

    Chen, Songlin; Zhang, Guojie; Shao, Changwei; Huang, Quanfei; Liu, Geng; Zhang, Pei; Song, Wentao; An, Na; Chalopin, Domitille; Volff, Jean-Nicolas; Hong, Yunhan; Li, Qiye; Sha, Zhenxia; Zhou, Heling; Xie, Mingshu; Yu, Qiulin; Liu, Yang; Xiang, Hui; Wang, Na; Wu, Kui; Yang, Changgeng; Zhou, Qian; Liao, Xiaolin; Yang, Linfeng; Hu, Qiaomu; Zhang, Jilin; Meng, Liang; Jin, Lijun; Tian, Yongsheng; Lian, Jinmin; Yang, Jingfeng; Miao, Guidong; Liu, Shanshan; Liang, Zhuo; Yan, Fang; Li, Yangzhen; Sun, Bin; Zhang, Hong; Zhang, Jing; Zhu, Ying; Du, Min; Zhao, Yongwei; Schartl, Manfred; Tang, Qisheng; Wang, Jun

    2014-03-01

    Genetic sex determination by W and Z chromosomes has developed independently in different groups of organisms. To better understand the evolution of sex chromosomes and the plasticity of sex-determination mechanisms, we sequenced the whole genomes of a male (ZZ) and a female (ZW) half-smooth tongue sole (Cynoglossus semilaevis). In addition to insights into adaptation to a benthic lifestyle, we find that the sex chromosomes of these fish are derived from the same ancestral vertebrate protochromosome as the avian W and Z chromosomes. Notably, the same gene on the Z chromosome, dmrt1, which is the male-determining gene in birds, showed convergent evolution of features that are compatible with a similar function in tongue sole. Comparison of the relatively young tongue sole sex chromosomes with those of mammals and birds identified events that occurred during the early phase of sex-chromosome evolution. Pertinent to the current debate about heterogametic sex-chromosome decay, we find that massive gene loss occurred in the wake of sex-chromosome 'birth'. PMID:24487278

  13. Evolution of spatio-temporal drought characteristics: validation, projections and effect of adaptation scenarios

    J.-P. Vidal

    2012-02-01

    Full Text Available Drought events develop in both space and time and they are therefore best described through summary joint spatio-temporal characteristics, like mean duration, mean affected area and total magnitude. This paper addresses the issue of future projections of such characteristics of drought events over France through three main research questions: (1 are downscaled climate projections able to reproduce spatio-temporal characteristics of meteorological and agricultural droughts in France over a present-day period? (2 How such characteristics will evolve over the 21st century? (3 How to use standardized drought indices to represent theoretical adaptation scenarios? These questions are addressed using the Isba land surface model, downscaled climate projections from the ARPEGE General Circulation Model under three emissions scenarios, as well as results from a previously performed 50-yr multilevel and multiscale drought reanalysis over France. Spatio-temporal characteristics of meteorological and agricultural drought events are computed using the Standardized Precipitation Index and the Standardized Soil Wetness Index, respectively, and for time scales of 3 and 12 months. Results first show that the distributions of joint spatio-temporal characteristics of observed events are well reproduced by the downscaled hydroclimate projections over a present-day period. All spatio-temporal characteristics of drought events are then found to dramatically increase over the 21st century, with stronger changes for agricultural droughts. Two theoretical adaptation scenarios are eventually built based on hypotheses of adaptation to evolving climate and hydrological normals, either retrospective or prospective, and by taking advantage of the statistical properties of the standardized drought indices. The perceived spatio-temporal characteristics of drought events derived from these theoretical adaptation scenarios show much reduced changes, but they call for more

  14. Evolution of spatio-temporal drought characteristics: validation, projections and effect of adaptation scenarios

    J.-P. Vidal

    2012-08-01

    Full Text Available Drought events develop in both space and time and they are therefore best described through summary joint spatio-temporal characteristics, such as mean duration, mean affected area and total magnitude. This paper addresses the issue of future projections of such characteristics of drought events over France through three main research questions: (1 Are downscaled climate projections able to simulate spatio-temporal characteristics of meteorological and agricultural droughts in France over a present-day period? (2 How such characteristics will evolve over the 21st century? (3 How to use standardized drought indices to represent theoretical adaptation scenarios? These questions are addressed using the Isba land surface model, downscaled climate projections from the ARPEGE General Circulation Model under three emissions scenarios, as well as results from a previously performed 50-yr multilevel and multiscale drought reanalysis over France. Spatio-temporal characteristics of meteorological and agricultural drought events are computed using the Standardized Precipitation Index and the Standardized Soil Wetness Index, respectively, and for time scales of 3 and 12 months. Results first show that the distributions of joint spatio-temporal characteristics of observed events are well simulated by the downscaled hydroclimate projections over a present-day period. All spatio-temporal characteristics of drought events are then found to dramatically increase over the 21st century, with stronger changes for agricultural droughts. Two theoretical adaptation scenarios are eventually built based on hypotheses of adaptation to evolving climate and hydrological normals, either retrospective or prospective. The perceived spatio-temporal characteristics of drought events derived from these theoretical adaptation scenarios show much reduced changes, but they call for more realistic scenarios at both the catchment and national scale in order to accurately assess the

  15. Ancient and recent adaptive evolution of primate non-homologous end joining genes.

    Ann Demogines

    2010-10-01

    Full Text Available In human cells, DNA double-strand breaks are repaired primarily by the non-homologous end joining (NHEJ pathway. Given their critical nature, we expected NHEJ proteins to be evolutionarily conserved, with relatively little sequence change over time. Here, we report that while critical domains of these proteins are conserved as expected, the sequence of NHEJ proteins has also been shaped by recurrent positive selection, leading to rapid sequence evolution in other protein domains. In order to characterize the molecular evolution of the human NHEJ pathway, we generated large simian primate sequence datasets for NHEJ genes. Codon-based models of gene evolution yielded statistical support for the recurrent positive selection of five NHEJ genes during primate evolution: XRCC4, NBS1, Artemis, POLλ, and CtIP. Analysis of human polymorphism data using the composite of multiple signals (CMS test revealed that XRCC4 has also been subjected to positive selection in modern humans. Crystal structures are available for XRCC4, Nbs1, and Polλ; and residues under positive selection fall exclusively on the surfaces of these proteins. Despite the positive selection of such residues, biochemical experiments with variants of one positively selected site in Nbs1 confirm that functions necessary for DNA repair and checkpoint signaling have been conserved. However, many viruses interact with the proteins of the NHEJ pathway as part of their infectious lifecycle. We propose that an ongoing evolutionary arms race between viruses and NHEJ genes may be driving the surprisingly rapid evolution of these critical genes.

  16. Putting 'Local' Back into Public Wifi Hotspots

    Korn, Matthias; Klokmose, Clemens Nylandsted

    2012-01-01

    Public Wifi hotspots in cafes and public places are based on wireless local area network technology (WLAN). In contrast to the common understanding of connecting directly to the internet when connecting to a Wifi hotspot, we are proposing to bring the original notion of connecting to a local...... network back to the fore. By hooking into the act of a user connecting to a local network, we see a design space emerge that allows us to spur various (off- and on-line) activities in a hyperlocal context. We propose to (re-)explore this notion of the locality of networks in the age of the ubiquitous Wifi...

  17. Has Human Evolution Stopped?

    Templeton, Alan R.

    2010-01-01

    It has been argued that human evolution has stopped because humans now adapt to their environment via cultural evolution and not biological evolution. However, all organisms adapt to their environment, and humans are no exception. Culture defines much of the human environment, so cultural evolution has actually led to adaptive evolution in humans. Examples are given to illustrate the rapid pace of adaptive evolution in response to cultural innovations. These adaptive responses have important ...

  18. Evolution of ITER Tritium Confinement strategy and adaptation to Cadarache site conditions and French regulatory requirements

    The ITER Nuclear Buildings include the Tokamak, Tritium and Diagnostic Buildings (Tokamak Complex) and the Hot Cell and Low Level Radioactive Waste Buildings (Hot Cell Complex). The Tritium Confinement strategy of the Nuclear Buildings comprises key features of the atmosphere and vent detritiation systems and the heating, ventilation and air conditioning systems. The designs developed during the ITER EDA (engineering design activities) for these systems need to be adapted to the specific conditions of the Cadarache site and modified to conform with the regulatory requirements applicable to installations nucleaires de base (INB) - basic nuclear installations - in France. The highest priority for such adaptation has been identified as the Tritium Confinement of the Tokamak Complex and the progress in development of a robust, coherent design concept compliant with French practice is described in the paper

  19. Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution.

    Kersting, Anna R; Bornberg-Bauer, Erich; Moore, Andrew D; Grath, Sonja

    2012-01-01

    Plant genomes are generally very large, mostly paleopolyploid, and have numerous gene duplicates and complex genomic features such as repeats and transposable elements. Many of these features have been hypothesized to enable plants, which cannot easily escape environmental challenges, to rapidly adapt. Another mechanism, which has recently been well described as a major facilitator of rapid adaptation in bacteria, animals, and fungi but not yet for plants, is modular rearrangement of protein-coding genes. Due to the high precision of profile-based methods, rearrangements can be well captured at the protein level by characterizing the emergence, loss, and rearrangements of protein domains, their structural, functional, and evolutionary building blocks. Here, we study the dynamics of domain rearrangements and explore their adaptive benefit in 27 plant and 3 algal genomes. We use a phylogenomic approach by which we can explain the formation of 88% of all arrangements by single-step events, such as fusion, fission, and terminal loss of domains. We find many domains are lost along every lineage, but at least 500 domains are novel, that is, they are unique to green plants and emerged more or less recently. These novel domains duplicate and rearrange more readily within their genomes than ancient domains and are overproportionally involved in stress response and developmental innovations. Novel domains more often affect regulatory proteins and show a higher degree of structural disorder than ancient domains. Whereas a relatively large and well-conserved core set of single-domain proteins exists, long multi-domain arrangements tend to be species-specific. We find that duplicated genes are more often involved in rearrangements. Although fission events typically impact metabolic proteins, fusion events often create new signaling proteins essential for environmental sensing. Taken together, the high volatility of single domains and complex arrangements in plant genomes

  20. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba

    CARRETERO PAULET, LORENZO; Chang, T-H; Librado Sanz, Pablo; Ibarra Laclette, E.; Herrera Estrella, L.; Rozas Liras, Julio A.; Albert, V.A.

    2015-01-01

    The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compa...

  1. Genome-Wide Analysis of Adaptive Molecular Evolution in the Carnivorous Plant Utricularia gibba

    Carretero-Paulet, Lorenzo; Chang, Tien-Hao; Librado, Pablo; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Rozas, Julio; Albert, Victor A.

    2015-01-01

    The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compa...

  2. Rapid evolution in response to introduced predators II: the contribution of adaptive plasticity

    Knapp Roland A; Bakelar Jeremy W; Latta Leigh C; Pfrender Michael E

    2007-01-01

    Abstract Background Introductions of non-native species can significantly alter the selective environment for populations of native species, which can respond through phenotypic plasticity or genetic adaptation. We examined phenotypic and genetic responses of Daphnia populations to recent introductions of non-native fish to assess the relative roles of phenotypic plasticity versus genetic change in causing the observed patterns. The Daphnia community in alpine lakes throughout the Sierra Neva...

  3. Long-Term Experimental Evolution in Escherichia Coli. VI. Environmental Constraints on Adaptation and Divergence

    Travisano, M.

    1997-01-01

    The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the f...

  4. Seismic communication in a blind subterranean mammal: a major somatosensory mechanism in adaptive evolution underground.

    Nevo, E.; Heth, G; Pratt, H

    1991-01-01

    Seismic communication, through low-frequency and patterned substrate-borne vibrations that are generated by head thumping, and which travel long distances underground, is important in the nonvisual communication of subterranean mole rats of the Spalax ehrenbergi superspecies (2n = 52, 54, 58, and 60) in Israel. This importance pertains both intraspecifically in adaptation and interspecifically in speciation. Neurophysiologic, behavioral, and anatomic findings in this study suggest that the me...

  5. Sex-specific adaptation drives early sex chromosome evolution in Drosophila.

    Zhou, Qi; Bachtrog, Doris

    2012-07-20

    Most species' sex chromosomes are derived from ancient autosomes and show few signatures of their origins. We studied the sex chromosomes of Drosophila miranda, where a neo-Y chromosome originated only approximately 1 million years ago. Whole-genome and transcriptome analysis reveals massive degeneration of the neo-Y, that male-beneficial genes on the neo-Y are more likely to undergo accelerated protein evolution, and that neo-Y genes evolve biased expression toward male-specific tissues--the shrinking gene content of the neo-Y becomes masculinized. In contrast, although older X chromosomes show a paucity of genes expressed in male tissues, neo-X genes highly expressed in male-specific tissues undergo increased rates of protein evolution if haploid in males. Thus, the response to sex-specific selection can shift at different stages of X differentiation, resulting in masculinization or demasculinization of the X-chromosomal gene content. PMID:22822149

  6. The evolution of Rare Pride: using evaluation to drive adaptive management in a biodiversity conservation organization.

    Jenks, Brett; Vaughan, Peter W; Butler, Paul J

    2010-05-01

    Rare Pride is a social marketing program that stimulates human behavior change in order to promote biodiversity conservation in critically threatened regions in developing countries. A series of formal evaluation studies, networking strategies, and evaluative inquiries have driven a 20-year process of adaptive management that has resulted in extensive programmatic changes within Pride. This paper describes the types of evaluation that Rare used to drive adaptive management and the changes it caused in Pride's theory-of-change and programmatic structure. We argue that (a) qualitative data gathered from partners and staff through structured interviews is most effective at identifying problems with current programs and procedures, (b) networking with other organizations is the most effective strategy for learning of new management strategies, and (c) quantitative data gathered through surveys is effective at measuring program impact and quality. Adaptive management has allowed Rare to increase its Pride program from implementing about two campaigns per year in 2001 to more than 40 per year in 2009 while improving program quality and maintaining program impact. PMID:19733908

  7. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution.

    Zhang, Guo-Qiang; Xu, Qing; Bian, Chao; Tsai, Wen-Chieh; Yeh, Chuan-Ming; Liu, Ke-Wei; Yoshida, Kouki; Zhang, Liang-Sheng; Chang, Song-Bin; Chen, Fei; Shi, Yu; Su, Yong-Yu; Zhang, Yong-Qiang; Chen, Li-Jun; Yin, Yayi; Lin, Min; Huang, Huixia; Deng, Hua; Wang, Zhi-Wen; Zhu, Shi-Lin; Zhao, Xiang; Deng, Cao; Niu, Shan-Ce; Huang, Jie; Wang, Meina; Liu, Guo-Hui; Yang, Hai-Jun; Xiao, Xin-Ju; Hsiao, Yu-Yun; Wu, Wan-Lin; Chen, You-Yi; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Luo, Yi-Bo; Van de Peer, Yves; Liu, Zhong-Jian

    2016-01-01

    Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae. PMID:26754549

  8. The Gene Tbx5 Links Development, Evolution and Adaptation of the Sternum in Terrestrial Vertebrates

    Bickley, S. R. B.

    2013-01-01

    The transition from fins to limbs during the colonisation of land was a key innovation in vertebrate evolution. Changes in the limb and shoulder girdle during this event have been investigated extensively, but little attention has been given to the acquisition of the sternum, a feature considered characteristic of virtually all terrestrial vertebrates, and which is mandatory for tetrapod locomotion. The sternum is a thin flat bone lying at the ventral midline of the thorax that provides a cru...

  9. The evolution of the human pelvis: changing adaptations to bipedalism, obstetrics and thermoregulation

    Gruss, Laura Tobias; Schmitt, Daniel

    2015-01-01

    The fossil record of the human pelvis reveals the selective priorities acting on hominin anatomy at different points in our evolutionary history, during which mechanical requirements for locomotion, childbirth and thermoregulation often conflicted. In our earliest upright ancestors, fundamental alterations of the pelvis compared with non-human primates facilitated bipedal walking. Further changes early in hominin evolution produced a platypelloid birth canal in a pelvis that was wide overall,...

  10. Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition

    Voogdt, Carlos G.P.; Bouwman, Lieneke I.; Kik, Marja J. L.; Wagenaar, Jaap A.; van Putten, Jos P. M.

    2016-01-01

    Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein arc...

  11. Has the microbiota played a critical role in the evolution of the adaptive immune system?

    Lee, Yun Kyung; Mazmanian, Sarkis K.

    2010-01-01

    Although microbes have been classically viewed as pathogens, it is now well established that the majority of host-bacterial interactions are symbiotic. During development and into adulthood, gut bacteria shape the tissues, cells and molecular profile of our gastrointestinal immune system. This partnership, forged over many millennia of co-evolution, is based on a molecular exchange involving bacterial signals that are recognized by host receptors to mediate beneficial outcomes for both microb...

  12. Ancient and Recent Adaptive Evolution of Primate Non-Homologous End Joining Genes

    Ann Demogines; Alysia M East; Ji-Hoon Lee; Grossman, Sharon R.; Sabeti, Pardis C.; Paull, Tanya T.; Sawyer, Sara L.

    2010-01-01

    In human cells, DNA double-strand breaks are repaired primarily by the non-homologous end joining (NHEJ) pathway. Given their critical nature, we expected NHEJ proteins to be evolutionarily conserved, with relatively little sequence change over time. Here, we report that while critical domains of these proteins are conserved as expected, the sequence of NHEJ proteins has also been shaped by recurrent positive selection, leading to rapid sequence evolution in other protein domains. In order to...

  13. The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

    Morris, J. Jeffrey; Lenski, Richard E.; Zinser, Erik R

    2012-01-01

    ABSTRACT Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and “Candidatus Pelagibacter,” and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We prese...

  14. Human and non-human primate genomes share hotspots of positive selection.

    David Enard

    2010-02-01

    Full Text Available Among primates, genome-wide analysis of recent positive selection is currently limited to the human species because it requires extensive sampling of genotypic data from many individuals. The extent to which genes positively selected in human also present adaptive changes in other primates therefore remains unknown. This question is important because a gene that has been positively selected independently in the human and in other primate lineages may be less likely to be involved in human specific phenotypic changes such as dietary habits or cognitive abilities. To answer this question, we analysed heterozygous Single Nucleotide Polymorphisms (SNPs in the genomes of single human, chimpanzee, orangutan, and macaque individuals using a new method aiming to identify selective sweeps genome-wide. We found an unexpectedly high number of orthologous genes exhibiting signatures of a selective sweep simultaneously in several primate species, suggesting the presence of hotspots of positive selection. A similar significant excess is evident when comparing genes positively selected during recent human evolution with genes subjected to positive selection in their coding sequence in other primate lineages and identified using a different test. These findings are further supported by comparing several published human genome scans for positive selection with our findings in non-human primate genomes. We thus provide extensive evidence that the co-occurrence of positive selection in humans and in other primates at the same genetic loci can be measured with only four species, an indication that it may be a widespread phenomenon. The identification of positive selection in humans alongside other primates is a powerful tool to outline those genes that were selected uniquely during recent human evolution.

  15. Human and non-human primate genomes share hotspots of positive selection.

    Enard, David; Depaulis, Frantz; Roest Crollius, Hugues

    2010-02-01

    Among primates, genome-wide analysis of recent positive selection is currently limited to the human species because it requires extensive sampling of genotypic data from many individuals. The extent to which genes positively selected in human also present adaptive changes in other primates therefore remains unknown. This question is important because a gene that has been positively selected independently in the human and in other primate lineages may be less likely to be involved in human specific phenotypic changes such as dietary habits or cognitive abilities. To answer this question, we analysed heterozygous Single Nucleotide Polymorphisms (SNPs) in the genomes of single human, chimpanzee, orangutan, and macaque individuals using a new method aiming to identify selective sweeps genome-wide. We found an unexpectedly high number of orthologous genes exhibiting signatures of a selective sweep simultaneously in several primate species, suggesting the presence of hotspots of positive selection. A similar significant excess is evident when comparing genes positively selected during recent human evolution with genes subjected to positive selection in their coding sequence in other primate lineages and identified using a different test. These findings are further supported by comparing several published human genome scans for positive selection with our findings in non-human primate genomes. We thus provide extensive evidence that the co-occurrence of positive selection in humans and in other primates at the same genetic loci can be measured with only four species, an indication that it may be a widespread phenomenon. The identification of positive selection in humans alongside other primates is a powerful tool to outline those genes that were selected uniquely during recent human evolution. PMID:20140238

  16. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans.

    Shmuel Sattath

    Full Text Available In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot, and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3% that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis

  17. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba.

    Carretero-Paulet, Lorenzo; Chang, Tien-Hao; Librado, Pablo; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Rozas, Julio; Albert, Victor A

    2015-02-01

    The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan. PMID:25577200

  18. The Emergence of Motives in Liminal Hotspots

    Nissen, Morten; Sørensen, Kathrine Solgaard

    2016-01-01

    (probably to no avail) dismissed for not taking account of the deep theoretical problems. This article suggests instead to re-articulate them with the conceptual repertoire of liminal hotspots, which directs attention to the emergent nature of activities and collectives, and thus motives. This is done as...

  19. Creating Hotspots for the Knowledge Economy

    Van de Klundert, M.; Van Winden, W.

    2012-01-01

    The emerging knowledge economy alters the expectations for contemporary work environments. Everywhere, we see the development of campuses and other types of “knowledge hotspots”. In this article, the authors discuss the emergence of these hotspots, and provide a number of examples. They identify a n

  20. Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose

    Gao, Guangliang; Zhao, Xianzhi; Li, Qin; He, Chuan; Zhao, Wenjing; Liu, Shuyun; Ding, Jinmei; Ye, Weixing; Wang, Jun; Chen, Ye; Wang, Haiwei; Li, Jing; Luo, Yi; Su, Jian; Huang, Yong; Liu, Zuohua; Dai, Ronghua; Shi, Yixiang; Meng, He; Wang, Qigui

    2016-01-01

    The goose is an economically important waterfowl that exhibits unique characteristics and abilities, such as liver fat deposition and fibre digestion. Here, we report de novo whole-genome assemblies for the goose and swan goose and describe the evolutionary relationships among 7 bird species, including domestic and wild geese, which diverged approximately 3.4~6.3 million years ago (Mya). In contrast to chickens as a proximal species, the expanded and rapidly evolving genes found in the goose genome are mainly involved in metabolism, including energy, amino acid and carbohydrate metabolism. Further integrated analysis of the host genome and gut metagenome indicated that the most widely shared functional enrichment of genes occurs for functions such as glycolysis/gluconeogenesis, starch and sucrose metabolism, propanoate metabolism and the citrate cycle. We speculate that the unique physiological abilities of geese benefit from the adaptive evolution of the host genome and symbiotic interactions with gut microbes. PMID:27608918

  1. Life in the Fast Lane: The Evolution of an Adaptive Vehicle Control System

    Jochem, Todd; Pomerleau, Dean

    1996-01-01

    Giving robots the ability to operate in the real world has been, and continues to be, one of the most difficult tasks in AI research. Since 1987, researchers at Carnegie Mellon University have been investigating one such task. Their research has been focused on using adaptive, vision-based systems to increase the driving performance of the Navlab line of on-road mobile robots. This research has led to the development of a neural network system that can learn to drive on many road types simply...

  2. The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss.

    Morris, J Jeffrey; Lenski, Richard E; Zinser, Erik R

    2012-01-01

    Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and "Candidatus Pelagibacter," and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependencies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism's limiting resources, provided the gene's function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates "beneficiaries" of reduced genomic content that are dependent on leaky "helpers," and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world. PMID:22448042

  3. Introgressive Hybridization and the Evolution of Lake-Adapted Catostomid Fishes.

    Dowling, Thomas E; Markle, Douglas F; Tranah, Greg J; Carson, Evan W; Wagman, David W; May, Bernard P

    2016-01-01

    Hybridization has been identified as a significant factor in the evolution of plants as groups of interbreeding species retain their phenotypic integrity despite gene exchange among forms. Recent studies have identified similar interactions in animals; however, the role of hybridization in the evolution of animals has been contested. Here we examine patterns of gene flow among four species of catostomid fishes from the Klamath and Rogue rivers using molecular and morphological traits. Catostomus rimiculus from the Rogue and Klamath basins represent a monophyletic group for nuclear and morphological traits; however, the Klamath form shares mtDNA lineages with other Klamath Basin species (C. snyderi, Chasmistes brevirostris, Deltistes luxatus). Within other Klamath Basin taxa, D. luxatus was largely fixed for alternate nuclear alleles relative to C. rimiculus, while Ch. brevirostris and C. snyderi exhibited a mixture of these alleles. Deltistes luxatus was the only Klamath Basin species that exhibited consistent covariation of nuclear and mitochondrial traits and was the primary source of mismatched mtDNA in Ch. brevirostris and C. snyderi, suggesting asymmetrical introgression into the latter species. In Upper Klamath Lake, D. luxatus spawning was more likely to overlap spatially and temporally with C. snyderi and Ch. brevirostris than either of those two with each other. The latter two species could not be distinguished with any molecular markers but were morphologically diagnosable in Upper Klamath Lake, where they were largely spatially and temporally segregated during spawning. We examine parallel evolution and syngameon hypotheses and conclude that observed patterns are most easily explained by introgressive hybridization among Klamath Basin catostomids. PMID:26959681

  4. The unusual Samoan hotspot: A "hotspot highway" juxtaposed with a trench

    Jackson, M. G.; Konter, J. G.; Koppers, A. A.

    2011-12-01

    Oceanic hotspots are fed by (relatively) stationary, upwelling mantle plumes that melt beneath mobile tectonic plates. This mechanism results in the generation of a linear chain of volcanoes exhibiting a clear age progression: the islands and seamounts should be increasingly older with increasing distance from the inferred location of the mantle plume. Located in the southwest Pacific, the Cook-Austral volcanic islands and seamounts were long thought to lack a clear age progression, and it has been argued that the Cook-Austral volcanic chain is an example of a hotspot not fed by a mantle plume. However, work by Chauvel et al (1997) showed that the Cook-Austral volcanoes have been generated by three distinct, co-linear mantle plumes spaced by ~1000 km, resulting in 3 overlapping hotspot tracks. Critically, the volcanoes generated by each hotspot exhibit a clear age progression that emerges from its respective plume. Using plate motion models, the reconstructed tracks of the three Cook-Austral hotspots backtrack through the region of the Pacific plate now occupied by the Samoan hotspot between 10 and 40 Ma (Konter et al., 2008). Owing to the unusual number of hotspots (Samoa is the fourth) that have been hosted in the region, we refer to this corridor of the Pacific plate as the "hotspot highway." The Samoan hotspot is burning through and thus crosscutting the trails of the older Cook-Austral hotspots. Consistent with this hypothesis, Jackson et al. (2010) reported volcanic features from the Cook-Austral hotspots in the Samoan region, including three seamounts and one atoll with geochemical affinities to the Cook-Austral hotspot. The Pacific lithosphere was likely "preconditioned" (metasomatized) by the three Cook-Australs hotspots before the arrival of the Samoan plume into the region, yet geochemical signatures associated with the Cook-Austral hotspot pedigrees are not evident in Samoan shield lavas. However, Samoan rejuvenated lavas exhibit a clear EMI (enriched

  5. Expansion of quasispecies diversity but no evidence for adaptive evolution of SHIV during rapid serial transfers among seronegative macaques

    Four successive, rapid serial passages of the nonpathogenic, CCR5-tropic simian-human immunodeficiency virus SHIVSF162 in rhesus macaques resulted in an increase in acute plasma viremia with each passage and the emergence of a pathogenic isolate SHIVSF162P3 in one of the passage three transfer animals (macaque T353). To explore the mechanism(s) underlying increased virulence of SHIVSF162 upon in vivo passage, the evolution of the HIV-1 envelope gene was characterized in plasma and PBMC samples obtained from animals before (week 1) and after (week 3) the time of virus transfer. We found no evidence in support of adaptive evolution of the HIV gp120 during rapid serial passage; however, the animals which later received passage virus had more diverse quasispecies. SHIVSF162P3-like gp120 sequences were first detected in macaque T353 at week 6, after seroconversion. These sequence changes increased in frequency and number at later time points. The first sequence change conferred neutralization escape but not an increase in viral infectivity that could account for the apparent increase in replicative capacity of the later passage viruses. Collectively, our data argue against any host-specific adaptation of the HIV-1 envelope gp120 as the basis for the generation of more aggressive SHIV variants during rapid serial transfers in seronegative macaques, and support the model of quasispecies diversity as a predictor of pathogenesis. Envelope sequence changes accumulate principally in response to immune pressure exerted by the host, generating viral variants that can persist in the presence of a strong host immune response

  6. How to Survive the Anthropocene: Adaptive Atheism and the Evolution of Homo deiparensis

    F. LeRon Shults

    2015-06-01

    Full Text Available Why is it so easy to ignore the ecological and economic crises of the Anthropocene? This article unveils some of the religious biases whose covert operation facilitates the repression or rejection of warnings about the consequences of extreme climate change and excessive capitalist consumption. The evolved defaults that are most relevant for our purposes here have to do with mental credulity toward religious content (beliefs about supernatural agents and with social congruity in religious contexts (behaviors shaped by supernatural rituals. Learning how to contest these phylogenetically inherited and culturally fortified biases may be a necessary condition for adapting to and altering our current natural and social environments in ways that will enhance the chances for the survival (and flourishing of Homo sapiens and other sentient species. I outline a conceptual framework, derived from empirical findings and theoretical developments in the bio-cultural sciences of religion, which can help clarify why and how gods are imaginatively conceived and nurtured by ritually engaged believers. Finally, I discuss the role that “adaptive atheism” might play in responding to the crises of the Anthropocene.

  7. Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli.

    Selwyn Quan

    2012-01-01

    Full Text Available Adaptation to novel environments is often associated with changes in gene regulation. Nevertheless, few studies have been able both to identify the genetic basis of changes in regulation and to demonstrate why these changes are beneficial. To this end, we have focused on understanding both how and why the lactose utilization network has evolved in replicate populations of Escherichia coli. We found that lac operon regulation became strikingly variable, including changes in the mode of environmental response (bimodal, graded, and constitutive, sensitivity to inducer concentration, and maximum expression level. In addition, some classes of regulatory change were enriched in specific selective environments. Sequencing of evolved clones, combined with reconstruction of individual mutations in the ancestral background, identified mutations within the lac operon that recapitulate many of the evolved regulatory changes. These mutations conferred fitness benefits in environments containing lactose, indicating that the regulatory changes are adaptive. The same mutations conferred different fitness effects when present in an evolved clone, indicating that interactions between the lac operon and other evolved mutations also contribute to fitness. Similarly, changes in lac regulation not explained by lac operon mutations also point to important interactions with other evolved mutations. Together these results underline how dynamic regulatory interactions can be, in this case evolving through mutations both within and external to the canonical lactose utilization network.

  8. Patterns of genome evolution that have accompanied host adaptation in Salmonella.

    Langridge, Gemma C; Fookes, Maria; Connor, Thomas R; Feltwell, Theresa; Feasey, Nicholas; Parsons, Bryony N; Seth-Smith, Helena M B; Barquist, Lars; Stedman, Anna; Humphrey, Tom; Wigley, Paul; Peters, Sarah E; Maskell, Duncan J; Corander, Jukka; Chabalgoity, Jose A; Barrow, Paul; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R

    2015-01-20

    Many bacterial pathogens are specialized, infecting one or few hosts, and this is often associated with more acute disease presentation. Specific genomes show markers of this specialization, which often reflect a balance between gene acquisition and functional gene loss. Within Salmonella enterica subspecies enterica, a single lineage exists that includes human and animal pathogens adapted to cause infection in different hosts, including S. enterica serovar Enteritidis (multiple hosts), S. Gallinarum (birds), and S. Dublin (cattle). This provides an excellent evolutionary context in which differences between these pathogen genomes can be related to host range. Genome sequences were obtained from ∼ 60 isolates selected to represent the known diversity of this lineage. Examination and comparison of the clades within the phylogeny of this lineage revealed signs of host restriction as well as evolutionary events that mark a path to host generalism. We have identified the nature and order of events for both evolutionary trajectories. The impact of functional gene loss was predicted based upon position within metabolic pathways and confirmed with phenotyping assays. The structure of S. Enteritidis is more complex than previously known, as a second clade of S. Enteritidis was revealed that is distinct from those commonly seen to cause disease in humans or animals, and that is more closely related to S. Gallinarum. Isolates from this second clade were tested in a chick model of infection and exhibited a reduced colonization phenotype, which we postulate represents an intermediate stage in pathogen-host adaptation. PMID:25535353

  9. The Evolution of Two-Component Systems in Bacteria RevealsDifferent Strategies for Niche Adaptation

    Alm, Eric; Huang, Katherine; Arkin, Adam

    2006-09-13

    Two-component systems including histidine protein kinasesrepresent the primary signal transduction paradigm in prokaryoticorganisms. To understand how these systems adapt to allow organisms todetect niche-specific signals, we analyzed the phylogenetic distributionof nearly 5000 histidine protein kinases from 207 sequenced prokaryoticgenomes. We found that many genomes carry a large repertoire of recentlyevolved signaling genes, which may reflect selective pressure to adapt tonew environmental conditions. Both lineage-specific gene family expansionand horizontal gene transfer play major roles in the introduction of newhistidine kinases into genomes; however, there are differences in howthese two evolutionary forces act. Genes imported via horizontal transferare more likely to retain their original functionality as inferred from asimilar complement of signaling domains, while gene family expansionaccompanied by domain shuffling appears to be a major source of novelgenetic diversity. Family expansion is the dominantsource of newhistidine kinase genes in the genomes most enriched in signalingproteins, and detailed analysis reveals that divergence in domainstructure and changes in expression patterns are hallmarks of recentexpansions. Finally, while these two modes of gene acquisition arewidespread across bacterial taxa, there are clear species-specificpreferences for which mode is used.

  10. HOTSPOT Health Physics codes for the PC

    The HOTSPOT Health Physics codes were created to provide Health Physics personnel with a fast, field-portable calculation tool for evaluating accidents involving radioactive materials. HOTSPOT codes are a first-order approximation of the radiation effects associated with the atmospheric release of radioactive materials. HOTSPOT programs are reasonably accurate for a timely initial assessment. More importantly, HOTSPOT codes produce a consistent output for the same input assumptions and minimize the probability of errors associated with reading a graph incorrectly or scaling a universal nomogram during an emergency. The HOTSPOT codes are designed for short-term (less than 24 hours) release durations. Users requiring radiological release consequences for release scenarios over a longer time period, e.g., annual windrose data, are directed to such long-term models as CAPP88-PC (Parks, 1992). Users requiring more sophisticated modeling capabilities, e.g., complex terrain; multi-location real-time wind field data; etc., are directed to such capabilities as the Department of Energy's ARAC computer codes (Sullivan, 1993). Four general programs -- Plume, Explosion, Fire, and Resuspension -- calculate a downwind assessment following the release of radioactive material resulting from a continuous or puff release, explosive release, fuel fire, or an area contamination event. Other programs deal with the release of plutonium, uranium, and tritium to expedite an initial assessment of accidents involving nuclear weapons. Additional programs estimate the dose commitment from the inhalation of any one of the radionuclides listed in the database of radionuclides; calibrate a radiation survey instrument for ground-survey measurements; and screen plutonium uptake in the lung (see FIDLER Calibration and LUNG Screening sections)

  11. Adaptive co-evolution of strategies and network leading to optimal cooperation level in spatial prisoner's dilemma game

    We study evolutionary prisoner's dilemma game on adaptive networks where a population of players co-evolves with their interaction networks. During the co-evolution process, interacted players with opposite strategies either rewire the link between them with probability p or update their strategies with probability 1 – p depending on their payoffs. Numerical simulation shows that the final network is either split into some disconnected communities whose players share the same strategy within each community or forms a single connected network in which all nodes are in the same strategy. Interestingly, the density of cooperators in the final state can be maximised in an intermediate range of p via the competition between time scale of the network dynamics and that of the node dynamics. Finally, the mean-field analysis helps to understand the results of numerical simulation. Our results may provide some insight into understanding the emergence of cooperation in the real situation where the individuals' behaviour and their relationship adaptively co-evolve. (general)

  12. Adaptive response to DNA-damaging agents in natural Saccharomyces cerevisiae populations from "Evolution Canyon", Mt. Carmel, Israel.

    Gabriel A Lidzbarsky

    Full Text Available BACKGROUND: Natural populations of most organisms, especially unicellular microorganisms, are constantly exposed to harsh environmental factors which affect their growth. UV radiation is one of the most important physical parameters which influences yeast growth in nature. Here we used 46 natural strains of Saccharomyces cerevisiae isolated from several natural populations at the "Evolution Canyon" microsite (Nahal Oren, Mt. Carmel, Israel. The opposing slopes of this canyon share the same geology, soil, and macroclimate, but they differ in microclimatic conditions. The interslope differences in solar radiation (200%-800% more on the "African" slope caused the development of two distinct biomes. The south-facing slope is sunnier and has xeric, savannoid "African" environment while the north-facing slope is represented by temperate, "European" forested environment. Here we studied the phenotypic response of the S. cerevisiae strains to UVA and UVC radiations and to methyl methanesulfonate (MMS in order to evaluate the interslope effect on the strains' ability to withstand DNA-damaging agents. METHODOLOGY/PRINCIPAL FINDINGS: We exposed our strains to the different DNA-damaging agents and measured survival by counting colony forming units. The strains from the "African" slope were more resilient to both UVA and MMS than the strains from the "European" slope. In contrast, we found that there was almost no difference between strains (with similar ploidy from the opposite slopes, in their sensitivity to UVC radiation. These results suggest that the "African" strains are more adapted to higher solar radiation than the "European" strains. We also found that the tetraploids strains were more tolerant to all DNA-damaging agents than their neighboring diploid strains, which suggest that high ploidy level might be a mechanism of adaptation to high solar radiation. CONCLUSIONS/SIGNIFICANCE: Our results and the results of parallel studies with several other

  13. Setal morphology and cirral setation of thoracican barnacle cirri: adaptations and implications for thoracican evolution

    Chan, B.K.K.; Garm, A.; Høeg, Jens Thorvald

    2008-01-01

    volcano. Of the pedunculates, I. cumingi has the least complex setation pattern consisting of only serrulate types. This is consistent with its very simplified feeding mode and an apparent inability to discriminate between food items. Octolasmis warwickii is slightly more modified, while both P. polymerus...... and C. mitella have a more diversified setation. The balanomorphan species exhibit by far the most complex cirral setation. This is consistent with the several types of suspension feeding seen in these species, their ability to identify and sort captured food items and even to perform microfiltration...... in the mantle cavity using the setae on their three pairs of maxillipeds. Our results indicate that in thoracican barnacles, adaptations in feeding behaviour are associated with changes in the setation pattern of the cirri. In addition, the setal types and their distribution on the cirri are...

  14. CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems

    Shah, Shiraz Ali; Garrett, Roger Antony

    2011-01-01

    CRISPR/Cas and CRISPR/Cmr immune machineries of archaea and bacteria provide an adaptive and effective defence mechanism directed specifically against viruses and plasmids. Present data suggest that both CRISPR/Cas and Cmr modules can behave like integral genetic elements. They tend to be located...... in the more variable regions of chromosomes and are displaced by genome shuffling mechanisms including transposition. CRISPR loci may be broken up and dispersed in chromosomes by transposons with the potential for creating genetic novelty. Both CRISPR/Cas and Cmr modules appear to exchange readily...... the significant barriers imposed by their differing conjugative, transcriptional and translational mechanisms. There are parallels between the CRISPR crRNAs and eukaryal siRNAs, most notably to germ cell piRNAs which are directed, with the help of effector proteins, to silence or destroy transposons...

  15. Adaptative evolution of metallothionein 3 in the Cd/Zn hyperaccumulator Thlaspi caerulescens

    Roosens, N.H.; Bernard, C.; Verbruggen, N. [Lab. de Physiologie et Genetique Moleculaire des Plantes, Univ. Libre de Bruxelles, Brussels (Belgium); Leplae, R. [Service de Conformation des Macromolecules Biologiques et Bioinformatique, Univ. Libre de Bruxelles, Brussels (Belgium)

    2005-04-01

    A functional screening in yeast allowed to identify various cDNAs from the Cd/Zn hyper-accumulator Thlaspi caerulescens. TcMT3 displayed high identity with its closest homologue in Arabidopsis thaliana but variation in its Cys residues. Functional analysis in yeast supported a higher binding capacity for Cu, but not for Cd or Zn, of TcMT3 compared to AtMT3. Expression analysis in plants indicated that metallothionein 3 (MT3) like all the other T. caerulescens genes from the screen studied is overexpressed in all studied populations of T. caerulescens compared to A. thaliana. TcMT3 was induced by Cu, but not by Cd. Moreover significant variation in expression within T. caerulescens populations that have contrasting tolerance and accumulation capacities indicated a possible local adaptation of MT3. (orig.)

  16. Sequestration of plant-derived glycosides by leaf beetles: A model system for evolution and adaptation

    Wilhelm Boland

    2015-12-01

    Full Text Available Leaf beetles have developed an impressive repertoire of toxins and repellents to defend themselves against predators. Upon attack, the larvae discharge small droplets from glandular reservoirs on their back. The reservoirs are “bioreactors” performing the late reactions of the toxin-production from plant-derived or de novo synthesised glucosides. The import of the glucosides into the bioreactor relies on a complex transport system. Physiological studies revealed a functional network of transporters guiding the glucosides through the larval body into the defensive system. The first of the involved transporters has been identified and characterised concerning selectivity, tissue distribution, and regulation. The development of a well-tuned transport system, perfectly adjusted to the compounds provided by the food plants, provides the functional basis for the leaf beetle defenses and their local adaptation to their host plants.

  17. Evolution and adaptation of marine annelids in interstitial and cave habitats

    Martinez Garcia, Alejandro

    The origin of anchialine and marine cave fauna is still a highly debated topic in Evolutionary Biology. Restricted and disjunct distribution and uncertain affinities of some marine cave endemic lineages have favored their interpretation as living fossils, surviving the extinction of their coastal...... relatives in cave subterranean ecological refugia. Active colonization and ecological speciation to particular cave niches has been alternatively suggested, but the evaluation of that scenario is obscured by the dominance of crustaceans in anchialine habitats, ecologically similar out and inside caves. The...... main goal of this thesis is to explore the evolutionary processes behind colonization and adaptation to submarine cave ecosystems in the Atlantic Ocean using annelids as a model, mainly when they involved ancestrally interstitial forms. In order to do that, we studied selected lineages of annelids with...

  18. Groundwater nitrate concentration evolution under climate change and agricultural adaptation scenarios: Prince Edward Island, Canada

    D. Paradis

    2015-08-01

    Full Text Available Nitrate (N-NO3 concentration in groundwater, the sole source of potable water in Prince Edward Island (PEI, Canada, currently exceeds the 10 mg L−1 (N-NO3 health threshold for drinking water in 6 % of domestic wells. Increasing climatic and socio-economic pressures on PEI agriculture may further deteriorate groundwater quality. This study assesses how groundwater nitrate concentrations could evolve due to the forecasted climate change and its related potential changes in agricultural practices. For this purpose, a tridimensional numerical groundwater flow and mass transport model was developed for the aquifer system of the entire Island (5660 km2. A number of different groundwater flow and mass transport simulations were made to evaluate the potential impact of the projected climate change and agricultural adaptation. According to the simulations for year 2050, N-NO3 concentration would increase due to two main causes: (1 the progressive attainment of steady-state conditions related to present-day nitrogen loadings, and (2 the increase in nitrogen loadings due to changes in agricultural practices provoked by future climatic conditions. The combined effects of equilibration with loadings, climate and agricultural adaptation would lead to a 25 to 32 % increase in N-NO3 concentration over the Island aquifer system. Climate change alone (practices maintained at their current level would contribute only 0 to 6 % to that increase according to the various climate scenarios. Moreover, simulated trends in groundwater N-NO3 concentration suggest that an increased number of domestic wells (more than doubling would exceed the nitrate drinking water criteria. This study underlines the need to develop and apply better agricultural management practices to ensure sustainability of long-term groundwater resources. The simulations also show that observable benefits from positive changes in agricultural practices would be delayed in time due to the slow dynamics

  19. Groundwater nitrate concentration evolution under climate change and agricultural adaptation scenarios: Prince Edward Island, Canada

    Paradis, D.; Vigneault, H.; Lefebvre, R.; Savard, M. M.; Ballard, J.-M.; Qian, B.

    2015-08-01

    Nitrate (N-NO3) concentration in groundwater, the sole source of potable water in Prince Edward Island (PEI, Canada), currently exceeds the 10 mg L-1 (N-NO3) health threshold for drinking water in 6 % of domestic wells. Increasing climatic and socio-economic pressures on PEI agriculture may further deteriorate groundwater quality. This study assesses how groundwater nitrate concentrations could evolve due to the forecasted climate change and its related potential changes in agricultural practices. For this purpose, a tridimensional numerical groundwater flow and mass transport model was developed for the aquifer system of the entire Island (5660 km2). A number of different groundwater flow and mass transport simulations were made to evaluate the potential impact of the projected climate change and agricultural adaptation. According to the simulations for year 2050, N-NO3 concentration would increase due to two main causes: (1) the progressive attainment of steady-state conditions related to present-day nitrogen loadings, and (2) the increase in nitrogen loadings due to changes in agricultural practices provoked by future climatic conditions. The combined effects of equilibration with loadings, climate and agricultural adaptation would lead to a 25 to 32 % increase in N-NO3 concentration over the Island aquifer system. Climate change alone (practices maintained at their current level) would contribute only 0 to 6 % to that increase according to the various climate scenarios. Moreover, simulated trends in groundwater N-NO3 concentration suggest that an increased number of domestic wells (more than doubling) would exceed the nitrate drinking water criteria. This study underlines the need to develop and apply better agricultural management practices to ensure sustainability of long-term groundwater resources. The simulations also show that observable benefits from positive changes in agricultural practices would be delayed in time due to the slow dynamics of nitrate

  20. Groundwater nitrate concentration evolution under climate change and agricultural adaptation scenarios: Prince Edward Island, Canada

    Paradis, Daniel; Vigneault, Harold; Lefebvre, René; Savard, Martine M.; Ballard, Jean-Marc; Qian, Budong

    2016-03-01

    Nitrate (N-NO3) concentration in groundwater, the sole source of potable water in Prince Edward Island (PEI, Canada), currently exceeds the 10 mg L-1 (N-NO3) health threshold for drinking water in 6 % of domestic wells. Increasing climatic and socio-economic pressures on PEI agriculture may further deteriorate groundwater quality. This study assesses how groundwater nitrate concentration could evolve due to the forecasted climate change and its related potential changes in agricultural practices. For this purpose, a tridimensional numerical groundwater flow and mass transport model was developed for the aquifer system of the entire Island (5660 km2). A number of different groundwater flow and mass transport simulations were made to evaluate the potential impact of the projected climate change and agricultural adaptation. According to the simulations for year 2050, N-NO3 concentration would increase due to two main causes: (1) the progressive attainment of steady-state conditions related to present-day nitrogen loadings, and (2) the increase in nitrogen loadings due to changes in agricultural practices provoked by future climatic conditions. The combined effects of equilibration with loadings, climate and agricultural adaptation would lead to a 25 to 32 % increase in N-NO3 concentration over the Island aquifer system. The change in groundwater recharge regime induced by climate change (with current agricultural practices) would only contribute 0 to 6 % of that increase for the various climate scenarios. Moreover, simulated trends in groundwater N-NO3 concentration suggest that an increased number of domestic wells (more than doubling) would exceed the nitrate drinking water criteria. This study underlines the need to develop and apply better agricultural management practices to ensure sustainability of long-term groundwater resources. The simulations also show that observable benefits from positive changes in agricultural practices would be delayed in time due to

  1. Evolution and adaptation of Pseudomonas aeruginosa in cystic fibrosis airways

    Madsen Sommer, Lea Mette

    laboratory experiments, with a high degree of control and rigour. But to truly understand evolution and the complex mechanisms it deploys, it is necessary to combine the laboratory learnings with investigations of natural systems. –Though, this can be tricky. Because of the heterogeneity and constant change...... studies in the CF model system and general evolutionary theories, many of which have been developed from observations of other organisms.This comparison has initially been sought by showing the plausibility of using comprehensive collections of longitudinally sampled single isolates, for their use in...... patients (Study 3), and 35 P. aeruginosa isolates from 12 primary ciliary dyskinesia (PCD) patients (Study 4), we were able to find genetic and phenotypic links across countries and diseases.All three studies (not including the metagenome study) had common clonal lineages and clear overlaps of genetic...

  2. The adaptive evolution of virulence: a review of theoretical predictions and empirical tests.

    Cressler, Clayton E; McLEOD, David V; Rozins, Carly; VAN DEN Hoogen, Josée; Day, Troy

    2016-06-01

    Why is it that some parasites cause high levels of host damage (i.e. virulence) whereas others are relatively benign? There are now numerous reviews of virulence evolution in the literature but it is nevertheless still difficult to find a comprehensive treatment of the theory and data on the subject that is easily accessible to non-specialists. Here we attempt to do so by distilling the vast theoretical literature on the topic into a set of relatively few robust predictions. We then provide a comprehensive assessment of the available empirical literature that tests these predictions. Our results show that there have been some notable successes in integrating theory and data but also that theory and empiricism in this field do not 'speak' to each other very well. We offer a few suggestions for how the connection between the two might be improved. PMID:26302775

  3. From climate change predictions to actions ? conserving vulnerable animal groups in hotspots at a regional scale.

    Carvalho, Silvia Benoliel; Brito, José Carlos; Crespo, Eduardo J.; Possingham, Hugh

    2010-01-01

    Abstract Current climate change is a major threat to biodiversity. Species unable to adapt or move will face local or global extinction and this is more likely to happen to species with narrow climatic and habitat requirements and limited dispersal abilities, such as amphibians and reptiles. Biodiversity losses are likely to be greatest in global biodiversity hotspots where climate change is fast, such as the Iberian Peninsula. Here we assess the impact of climate change on 37 ende...

  4. Evolution of ITER tritium confinement strategy and adaptation to Cadrache site conditions and French regulatory requirements

    The ITER Nuclear Buildings include the Tokamak, Tritium and Diagnostic Buildings (Tokamak Complex) and the Hot Cell and Low Level Radioactive Waste Buildings. The Tritium Confinement Strategy of the Nuclear Buildings comprises key features of the Atmosphere and Vent Detritiation Systems (ADS/VDS) and the Heating, Ventilation and Air Conditioning (HVAC) Systems. The designs developed during the ITER EDA (Engineering Design Activities) for these systems need to be adapted to the specific conditions of the Cadarache site and modified to conform with the regulatory requirements applicable to Installations Nucleaires de Base (INB) - Basic Nuclear Installations - in France. The highest priority for such adaptation has been identified as the Tritium Confinement of the Tokamak Complex and the progress in development of a robust, coherent design concept compliant with French practice is described in the paper. The Tokamak Complex HVAC concept for generic conditions was developed for operational cost minimisation under more extreme climatic conditions (primarily temperature) than those valid for Cadarache, and incorporated recirculation of a large fraction of the air flow through the HVAC systems to achieve this objective. Due to the impracticality of precluding the spread of contamination from areas of higher activity to less contaminated areas, this concept has been abandoned in favour of a once-through configuration, which requires a complete redesign, with revised air change rates, module sizes, layout, redundancy provisions and other features. The ADS/VDS concept developed for the generic design of the ITER Tokamak Complex is undergoing a radical revision in which the system architecture, module sizing and basic process are being optimised for the Cadarache conditions. Investigation is being launched into the implementation of a wet stripper concept to replace the molecular sieve (MS) beds incorporated in the generic design, where concerns have been raised over low

  5. Upscaling nitrogen removal capacity from local hotspots to low stream orders’ drainage basins

    Peiffer, Stefan; de Dreuzy, Jean-Raynald; Krause, Stefan; Hannah, David M; Fleckenstein, Jan H.; Sebilo, Mathieu; Bishop, Kevin; Hubert-Moy, Laurence

    2015-01-01

    Denitrification is the main process removing nitrate in river drainage basins and buffer input from agricultural land and limits aquatic ecosystem pollution. However, the identification of denitrification hotspots (for example, riparian zones), their role in a landscape context and the evolution of their overall removal capacity at the drainage basin scale are still challenging. The main approaches used (that is, mass balance method, denitrification proxies, and potential wetted areas) suf...

  6. Adaptive melanin response of the soil fungus Aspergillus niger to UV radiation stress at "Evolution Canyon", Mount Carmel, Israel.

    Natarajan Singaravelan

    Full Text Available BACKGROUND: Adaptation is an evolutionary process in which traits in a population are tailored by natural selection to better meet the challenges presented by the local environment. The major discussion relating to natural selection concerns the portraying of the cause and effect relationship between a presumably adaptive trait and selection agents generating it. Therefore, it is necessary to identify trait(s that evolve in direct response to selection, enhancing the organism's fitness. "Evolution Canyon" (EC in Israel mirrors a microcosmic evolutionary system across life and is ideal to study natural selection and local adaptation under sharply, microclimatically divergent environments. The south-facing, tropical, sunny and xeric "African" slope (AS receives 200%-800% higher solar radiation than the north-facing, temperate, shady and mesic "European" slope (ES, 200 meters apart. Thus, solar ultraviolet radiation (UVR is a major selection agent in EC influencing the organism-environment interaction. Melanin is a trait postulated to have evolved for UV-screening in microorganisms. Here we investigate the cause and effect relationship between differential UVR on the opposing slopes of EC and the conidial melanin concentration of the filamentous soil fungus Aspergillus niger. We test the working hypothesis that the AS strains exhibit higher melanin content than strains from the ES resulting in higher UV resistance. METHODOLOGY/PRINCIPAL FINDINGS: We measured conidial melanin concentration of 80 strains from the EC using a spectrophotometer. The results indicated that mean conidial melanin concentration of AS strains were threefold higher than ES strains and the former resisted UVA irradiation better than the latter. Comparisons of melanin in the conidia of A. niger strains from sunny and shady microniches on the predominantly sunny AS and predominantly shady ES indicated that shady conditions on the AS have no influence on the selection on melanin

  7. Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation.

    Sarah A Palmer

    Full Text Available BACKGROUND: Archaeobotanical samples of barley (Hordeum vulgare L. found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years. METHODOLOGY AND FINDINGS: We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure. CONCLUSIONS: The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.

  8. Adaptive evolution of the chrysanthemyl diphosphate synthase gene involved in irregular monoterpene metabolism

    Liu Ping-Li

    2012-11-01

    Full Text Available Abstract Background Chrysanthemyl diphosphate synthase (CDS is a key enzyme in biosynthetic pathways producing pyrethrins and irregular monoterpenes. These compounds are confined to plants of the tribe Anthemideae of the Asteraceae, and play an important role in defending the plants against herbivorous insects. It has been proposed that the CDS genes arose from duplication of the farnesyl diphosphate synthase (FDS gene and have different function from FDSs. However, the duplication time toward the origin of CDS and the evolutionary force behind the functional divergence of the CDS gene are still unknown. Results Two duplication events were detected in the evolutionary history of the FDS gene family in the Asteraceae, and the second duplication led to the origin of CDS. CDS occurred after the divergence of the tribe Mutisieae from other tribes of Asteraceae but before the birth of the Anthemideae tribe. After its origin, CDS accumulated four mutations in sites homologous to the substrate-binding and catalysis sites of FDS. Of these, two sites were involved in the binding of the nucleophilic substrate isopentenyl diphosphate in FDS. Maximum likelihood analyses showed that some sites in CDS were under positive selection and were scattered throughout primary sequences, whereas in the three-dimensional structure model they clustered in the large central cavity. Conclusion Positive selection associated with gene duplication played a major role in the evolution of CDS.

  9. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas

    Worden, Alexandra Z.; Lee, Jae-Hyeok; Mock, Thomas; Rouze, Pierre; Simmons, Melinda P.; Aerts, Andrea L.; Allen, Andrew E.; Cuvelier, Marie L.; Derelle, Evelyne; Everett, Meredieht V.; Foulon, Elodie; Grimwood, Jane; Gundlach, Heidrun; Henrissat, Bernard; Napoli, Carolyn; McDonald, Sarah M.; Parker, Micaela S.; Rombauts, Stephane; Salamov, Asaf; von Dassow, Peter; Badger, Jonathan G,; Coutinho, Pedro M.; Demir, Elif; Dubchak, Inna; Gentemann, Chelle; Eikrem, Wenche; Gready, Jill E.; John, Uwe; Lanier, William; Lindquist, Erika A.; Lucas, Susan; Mayer, Kluas F. X.; Moreau, Herve; Not, Fabrice; Otillar, Robert; Panaud, Olivier; Pangilinan, Jasmyn; Paulsen, Ian; Piegu, Benoit; Poliakov, Aaron; Robbens, Steven; Schmutz, Jeremy; Roulza, Eve; Wyss, Tania; Zelensky, Alexander; Zhou, Kemin; Armbrust, E. Virginia; Bhattacharya, Debashish; Goodenough, Ursula W.; Van de Peer, Yves; Grigoriev, Igor V.

    2009-10-14

    Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90percent of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

  10. Comparative phylogeography of oceanic archipelagos: Hotspots for inferences of evolutionary process

    Shaw, Kerry L.; Gillespie, Rosemary G.

    2016-01-01

    Remote island archipelagos offer superb opportunities to study the evolution of community assembly because of their relatively young and simple communities where speciation contributes to the origin and evolution of community structure. There is great potential for common phylogeographic patterns among remote archipelagos that originate through hotspot volcanism, particularly when the islands formed are spatially isolated and linearly arranged. The progression rule is characterized by a phylogeographic concordance between island age and lineage age in a species radiation. Progression is most likely to arise when a species radiation begins on an older island before the emergence of younger islands of a hotspot archipelago. In the simplest form of progression, colonization of younger islands as they emerge and offer appropriate habitat, is coincident with cladogenesis. In this paper, we review recent discoveries of the progression rule on seven hotspot archipelagos. We then discuss advantages that progression offers to the study of community assembly, and insights that community dynamics may offer toward understanding the evolution of progression. We describe results from two compelling cases of progression where the mosaic genome may offer insights into contrasting demographic histories that shed light on mechanisms of speciation and progression on remote archipelagos. PMID:27432948

  11. Hormones and phenotypic plasticity: Implications for the evolution of integrated adaptive phenotypes

    Sean C.LEMA; Jun KITANO

    2013-01-01

    It is generally accepted that taxa exhibit genetic variation in phenotypic plasticity,but many questions remain unanswered about how divergent plastic responses evolve under dissimilar ecological conditions.Hormones are signaling molecules that act as proximate mediators of phenotype expression by regulating a variety of cellular,physiological,and behavioral responses.Hormones not only change cellular and physiological states but also influence gene expression directly or indirectly,thereby linking environmental conditions to phenotypic development.Studying how hormonal pathways respond to environmental variation and how those responses differ between individuals,populations,and species can expand our understanding of the evolution of phenotypic plasticity.Here,we explore the ways that the study of hormone signaling is providing new insights into the underlying proximate bases for individual,population or species variation in plasticity.Using several studies as exemplars,we examine how a 'norm of reaction' approach can be used in investigations of hormone-mediated plasticity to inform the following:1) how environmental cues affect the component hormones,receptors and enzymes that comprise any endocrine signaling pathway,2) how genetic and epigenetic variation in endocrine-associated genes can generate variation in plasticity among these diverse components,and 3) how phenotypes mediated by the same hormone can be coupled and decoupled via independent plastic responses of signaling components across target tissues.Future studies that apply approaches such as reaction norms and network modeling to questions concerning how hormones link environmental stimuli to ecologically-relevant phenotypic responses should help unravel how phenotypic plasticity evolves.

  12. Managing Heterogeneous Wireless Environments via Hotspot Servers

    Simunic, Tajana; Qadeer, Wajahat; De Micheli, Giovanni

    2005-01-01

    Wireless communication today supports heterogeneous wireless devices with a number of different wireless network interfaces (WNICs). A large fraction of communication is infrastructure based, so the wireless access points and hotspot servers have become more ubiquitous. Battery lifetime is still a critical issue, with WNICs typically consuming a large fraction of the overall power budget in a mobile device. In this work we present a new technique for managing power consumption and QoS ...

  13. Predator diversity hotspots in the blue ocean

    Worm, Boris; Lotze, Heike K.; Myers, Ransom A.

    2003-01-01

    Concentrations of biodiversity, or hotspots, represent conservation priorities in terrestrial ecosystems but remain largely unexplored in marine habitats. In the open ocean, many large predators such as tunas, sharks, billfishes, and sea turtles are of current conservation concern because of their vulnerability to overfishing and ecosystem role. Here we use scientific-observer records from pelagic longline fisheries in the Atlantic and Pacific Oceans to show that ocean...

  14. Hotspot Mainport Schiphol : midterm review report

    Döpp, S.; Brink, van den, R.B.A.; Hartogensis, O. K.; Jacobs, A; Homan, C.; Sondij, J.

    2012-01-01

    The focus of Knowledge for Climate (KfC) research in Hotspot Schiphol Mainport is to optimize the contribution of meteorological services to a sustainable operation and reliable operation of Schiphol airport. Three research projects have been carried out in the first tranche of the Knowledge for Climate programme on climate change and local critical weather conditions at Mainport Schiphol. Two projects (IMPACT and WindVisions) will be continued in the second tranche of the programme, in the K...

  15. SENTIMENT ANALYSIS FOR ONLINE FORUMS HOTSPOT DETECTION

    K. Nirmala Devi

    2012-01-01

    Full Text Available The user generated content on the web grows rapidly in this emergent information age. The evolutionary changes in technology make use of such information to capture only the user’s essence and finally the useful information are exposed to information seekers. Most of the existing research on text information processing, focuses in the factual domain rather than the opinion domain. Text mining plays a vital role in online forum opinion mining. But opinion mining from online forum is much more difficult than pure text process due to their semi structured characteristics. In this paper we detect online hotspot forums by computing sentiment analysis for text data available in each forum. This approach analyzes the forum text data and computes value for each piece of text. The proposed approach combines K-means clustering and Support Vector Machine (SVM classification algorithm that can be used to group the forums into two clusters forming hotspot forums and non-hotspot forums within the current time span. The experiment helps to identify that K-means and SVM together achieve highly consistent results. The prediction result of SVM is also compared with other classifiers such as Naïve Bayes, Decision tree and among them SVM performs the best.

  16. Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species.

    Allison, Andrew B; Kohler, Dennis J; Ortega, Alicia; Hoover, Elizabeth A; Grove, Daniel M; Holmes, Edward C; Parrish, Colin R

    2014-11-01

    Canine parvovirus (CPV) emerged as a new pandemic pathogen of dogs in the 1970s and is closely related to feline panleukopenia virus (FPV), a parvovirus of cats and related carnivores. Although both viruses have wide host ranges, analysis of viral sequences recovered from different wild carnivore species, as shown here, demonstrated that>95% were derived from CPV-like viruses, suggesting that CPV is dominant in sylvatic cycles. Many viral sequences showed host-specific mutations in their capsid proteins, which were often close to sites known to control binding to the transferrin receptor (TfR), the host receptor for these carnivore parvoviruses, and which exhibited frequent parallel evolution. To further examine the process of host adaptation, we passaged parvoviruses with alternative backgrounds in cells from different carnivore hosts. Specific mutations were selected in several viruses and these differed depending on both the background of the virus and the host cells in which they were passaged. Strikingly, these in vitro mutations recapitulated many specific changes seen in viruses from natural populations, strongly suggesting they are host adaptive, and which were shown to result in fitness advantages over their parental virus. Comparison of the sequences of the transferrin receptors of the different carnivore species demonstrated that many mutations occurred in and around the apical domain where the virus binds, indicating that viral variants were likely selected through their fit to receptor structures. Some of the viruses accumulated high levels of variation upon passage in alternative hosts, while others could infect multiple different hosts with no or only a few additional mutations. Overall, these studies demonstrate that the evolutionary history of a virus, including how long it has been circulating and in which hosts, as well as its phylogenetic background, has a profound effect on determining viral host range. PMID:25375184

  17. Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria

    Ying eZhang

    2014-03-01

    Full Text Available The rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. Using the class Epsilonproteobacteria as a case study, we investigated the composition, flexibility, and function of its pan-genomes. Models were constructed to extrapolate the expansion of pan-genomes at three different taxonomic levels. The results show that, for Epsilonproteobacteria the seemingly large genome variations among strains of the same species are less noticeable when compared with groups at higher taxonomic ranks, indicating that genome stability is imposed by the potential existence of taxonomic boundaries. The analyses of pan-genomes has also defined a set of universally conserved core genes, based on which a phylogenetic tree was constructed to confirm that thermophilic species from deep-sea hydrothermal vents represent the most ancient lineages of Epsilonproteobacteria. Moreover, by comparing the flexible genome of a chemoautotrophic deep-sea vent species to 1 genomes of species belonging to the same genus, but inhabiting different environments, and 2 genomes of other vent species, but belonging to different genera, we were able to delineate the relative importance of lineage-specific versus niche-specific genes. This result not only emphasizes the overall importance of phylogenetic proximity in shaping the variable part of the genome, but also highlights the adaptive functions of niche-specific genes. Overall, by modeling the expansion of pan-genomes and analyzing core and flexible genes, this study provides snapshots on how the complex processes of gene acquisition, conservation, and removal affect the evolution of different species, and contribute to the metabolic diversity and versatility of Epsilonproteobacteria.

  18. TH-A-BRF-02: BEST IN PHYSICS (JOINT IMAGING-THERAPY) - Modeling Tumor Evolution for Adaptive Radiation Therapy

    Liu, Y; Lee, CG [University of Toronto, Toronto, ON (Canada); Chan, TCY [University of Toronto, Toronto, ON (Canada); Techna Institute for the Advancement of Technology for Health, Toronto, ON (Canada); Cho, YB; Islam, MK [University of Toronto, Toronto, ON (Canada); Princess Margaret Hospital, Toronto, ON (Canada); Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) (Canada)

    2014-06-15

    Purpose: To develop mathematical models of tumor geometry changes under radiotherapy that may support future adaptive paradigms. Methods: A total of 29 cervical patients were scanned using MRI, once for planning and weekly thereafter for treatment monitoring. Using the tumor volumes contoured by a radiologist, three mathematical models were investigated based on the assumption of a stochastic process of tumor evolution. The “weekly MRI” model predicts tumor geometry for the following week from the last two consecutive MRI scans, based on the voxel transition probability. The other two models use only the first pair of consecutive MRI scans, and the transition probabilities were estimated via tumor type classified from the entire data set. The classification is based on either measuring the tumor volume (the “weekly volume” model), or implementing an auxiliary “Markov chain” model. These models were compared to a constant volume approach that represents the current clinical practice, using various model parameters; e.g., the threshold probability β converts the probability map into a tumor shape (larger threshold implies smaller tumor). Model performance was measured using volume conformity index (VCI), i.e., the union of the actual target and modeled target volume squared divided by product of these two volumes. Results: The “weekly MRI” model outperforms the constant volume model by 26% on average, and by 103% for the worst 10% of cases in terms of VCI under a wide range of β. The “weekly volume” and “Markov chain” models outperform the constant volume model by 20% and 16% on average, respectively. They also perform better than the “weekly MRI” model when β is large. Conclusion: It has been demonstrated that mathematical models can be developed to predict tumor geometry changes for cervical cancer undergoing radiotherapy. The models can potentially support adaptive radiotherapy paradigm by reducing normal tissue dose. This research

  19. The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity

    Kieslich, Chris A.; Morikis, Dimitrios

    2012-01-01

    The interaction between complement fragment C3d and complement receptor 2 (CR2) is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement system and adaptive immunity, which is formed through the association of the B-cell co-receptor complex, including the C3d-CR2 interaction, is a much more recent adaptation. Human C3d and CR2 have net charges of −1 and +7 respectively, and are believed to have evolved favoring the role of electrostatics in their functions. To investigate the role of electrostatics in the function and evolution of human C3d and CR2, we have applied electrostatic similarity methods to identify regions of evolutionarily conserved electrostatic potential based on 24 homologues of complement C3d and 4 homologues of CR2. We also examine the effects of structural perturbation, as introduced through molecular dynamics and mutations, on spatial distributions of electrostatic potential to identify perturbation resistant regions, generated by so-called electrostatic “hot-spots”. Distributions of electrostatic similarity based on families of perturbed structures illustrate the presence of electrostatic “hot-spots” at the two functional sites of C3d, while the surface of CR2 lacks electrostatic “hot-spots” despite its excessively positive nature. We propose that the electrostatic “hot-spots” of C3d have evolved to optimize its dual-functionality (covalently attaching to pathogen surfaces and interaction with CR2), which are both necessary for the formation B-cell co-receptor complexes. Comparison of the perturbation resistance of the electrostatic character of the homologues of C3d suggests that there was an emergence of a new role of electrostatics, and a transition in the function of C3

  20. TH-A-BRF-02: BEST IN PHYSICS (JOINT IMAGING-THERAPY) - Modeling Tumor Evolution for Adaptive Radiation Therapy

    Purpose: To develop mathematical models of tumor geometry changes under radiotherapy that may support future adaptive paradigms. Methods: A total of 29 cervical patients were scanned using MRI, once for planning and weekly thereafter for treatment monitoring. Using the tumor volumes contoured by a radiologist, three mathematical models were investigated based on the assumption of a stochastic process of tumor evolution. The “weekly MRI” model predicts tumor geometry for the following week from the last two consecutive MRI scans, based on the voxel transition probability. The other two models use only the first pair of consecutive MRI scans, and the transition probabilities were estimated via tumor type classified from the entire data set. The classification is based on either measuring the tumor volume (the “weekly volume” model), or implementing an auxiliary “Markov chain” model. These models were compared to a constant volume approach that represents the current clinical practice, using various model parameters; e.g., the threshold probability β converts the probability map into a tumor shape (larger threshold implies smaller tumor). Model performance was measured using volume conformity index (VCI), i.e., the union of the actual target and modeled target volume squared divided by product of these two volumes. Results: The “weekly MRI” model outperforms the constant volume model by 26% on average, and by 103% for the worst 10% of cases in terms of VCI under a wide range of β. The “weekly volume” and “Markov chain” models outperform the constant volume model by 20% and 16% on average, respectively. They also perform better than the “weekly MRI” model when β is large. Conclusion: It has been demonstrated that mathematical models can be developed to predict tumor geometry changes for cervical cancer undergoing radiotherapy. The models can potentially support adaptive radiotherapy paradigm by reducing normal tissue dose. This research

  1. The geography of sex-specific selection, local adaptation, and sexual dimorphism.

    Connallon, Tim

    2015-09-01

    Local adaptation and sexual dimorphism are iconic evolutionary scenarios of intraspecific adaptive differentiation in the face of gene flow. Although theory has traditionally considered local adaptation and sexual dimorphism as conceptually distinct processes, emerging data suggest that they often act concurrently during evolutionary diversification. Here, I merge theories of local adaptation in space and sex-specific adaptation over time, and show that their confluence yields several new predictions about the roles of context-specific selection, migration, and genetic correlations, in adaptive diversification. I specifically revisit two influential predictions from classical studies of clinal adaptation and sexual dimorphism: (1) that local adaptation should decrease with distance from the species' range center and (2) that opposing directional selection between the sexes (sexual antagonism) should inevitably accompany the evolution of sexual dimorphism. I show that both predictions can break down under clinally varying selection. First, the geography of local adaptation can be sexually dimorphic, with locations of relatively high local adaptation differing profoundly between the sexes. Second, the intensity of sexual antagonism varies across the species' range, with subpopulations near the range center representing hotspots for antagonistic selection. The results highlight the context-dependent roles of migration versus sexual conflict as primary constraints to adaptive diversification. PMID:26194274

  2. Exploring equivalence domain in nonlinear inverse problems using Covariance Matrix Adaption Evolution Strategy (CMAES) and random sampling

    Grayver, Alexander V.; Kuvshinov, Alexey V.

    2016-05-01

    This paper presents a methodology to sample equivalence domain (ED) in nonlinear partial differential equation (PDE)-constrained inverse problems. For this purpose, we first applied state-of-the-art stochastic optimization algorithm called Covariance Matrix Adaptation Evolution Strategy (CMAES) to identify low-misfit regions of the model space. These regions were then randomly sampled to create an ensemble of equivalent models and quantify uncertainty. CMAES is aimed at exploring model space globally and is robust on very ill-conditioned problems. We show that the number of iterations required to converge grows at a moderate rate with respect to number of unknowns and the algorithm is embarrassingly parallel. We formulated the problem by using the generalized Gaussian distribution. This enabled us to seamlessly use arbitrary norms for residual and regularization terms. We show that various regularization norms facilitate studying different classes of equivalent solutions. We further show how performance of the standard Metropolis-Hastings Markov chain Monte Carlo algorithm can be substantially improved by using information CMAES provides. This methodology was tested by using individual and joint inversions of magneotelluric, controlled-source electromagnetic (EM) and global EM induction data.

  3. Exploring equivalence domain in non-linear inverse problems using Covariance Matrix Adaption Evolution Strategy (CMAES) and random sampling

    Grayver, Alexander V.; Kuvshinov, Alexey V.

    2016-02-01

    This paper presents a methodology to sample equivalence domain (ED) in non-linear PDE-constrained inverse problems. For this purpose, we first applied state-of-the-art stochastic optimization algorithm called Covariance Matrix Adaptation Evolution Strategy (CMAES) to identify low misfit regions of the model space. These regions were then randomly sampled to create an ensemble of equivalent models and quantify uncertainty. CMAES is aimed at exploring model space globally and is robust on very ill-conditioned problems. We show that the number of iterations required to converge grows at a moderate rate with respect to number of unknowns and the algorithm is embarrassingly parallel. We formulated the problem by using the generalized Gaussian distribution. This enabled us to seamlessly use arbitrary norms for residual and regularization terms. We show that various regularization norms facilitate studying different classes of equivalent solutions. We further show how performance of the standard Metropolis-Hastings Markov chain Monte Carlo (MCMC) algorithm can be substantially improved by using information CMAES provides. This methodology was tested by using individual and joint inversions of Magneotelluric, Controlled-source Electromagnetic (EM) and Global EM induction data.

  4. Photo-Oxidative Stress-Driven Mutagenesis and Adaptive Evolution on the Marine Diatom Phaeodactylum tricornutum for Enhanced Carotenoid Accumulation

    Zhiqian Yi

    2015-09-01

    Full Text Available Marine diatoms have recently gained much attention as they are expected to be a promising resource for sustainable production of bioactive compounds such as carotenoids and biofuels as a future clean energy solution. To develop photosynthetic cell factories, it is important to improve diatoms for value-added products. In this study, we utilized UVC radiation to induce mutations in the marine diatom Phaeodactylum tricornutum and screened strains with enhanced accumulation of neutral lipids and carotenoids. Adaptive laboratory evolution (ALE was also used in parallel to develop altered phenotypic and biological functions in P. tricornutum and it was reported for the first time that ALE was successfully applied on diatoms for the enhancement of growth performance and productivity of value-added carotenoids to date. Liquid chromatography-mass spectrometry (LC-MS was utilized to study the composition of major pigments in the wild type P. tricornutum, UV mutants and ALE strains. UVC radiated strains exhibited higher accumulation of fucoxanthin as well as neutral lipids compared to their wild type counterpart. In addition to UV mutagenesis, P. tricornutum strains developed by ALE also yielded enhanced biomass production and fucoxanthin accumulation under combined red and blue light. In short, both UV mutagenesis and ALE appeared as an effective approach to developing desired phenotypes in the marine diatoms via electromagnetic radiation-induced oxidative stress.

  5. Photo-Oxidative Stress-Driven Mutagenesis and Adaptive Evolution on the Marine Diatom Phaeodactylum tricornutum for Enhanced Carotenoid Accumulation.

    Yi, Zhiqian; Xu, Maonian; Magnusdottir, Manuela; Zhang, Yuetuan; Brynjolfsson, Sigurdur; Fu, Weiqi

    2015-10-01

    Marine diatoms have recently gained much attention as they are expected to be a promising resource for sustainable production of bioactive compounds such as carotenoids and biofuels as a future clean energy solution. To develop photosynthetic cell factories, it is important to improve diatoms for value-added products. In this study, we utilized UVC radiation to induce mutations in the marine diatom Phaeodactylum tricornutum and screened strains with enhanced accumulation of neutral lipids and carotenoids. Adaptive laboratory evolution (ALE) was also used in parallel to develop altered phenotypic and biological functions in P. tricornutum and it was reported for the first time that ALE was successfully applied on diatoms for the enhancement of growth performance and productivity of value-added carotenoids to date. Liquid chromatography-mass spectrometry (LC-MS) was utilized to study the composition of major pigments in the wild type P. tricornutum, UV mutants and ALE strains. UVC radiated strains exhibited higher accumulation of fucoxanthin as well as neutral lipids compared to their wild type counterpart. In addition to UV mutagenesis, P. tricornutum strains developed by ALE also yielded enhanced biomass production and fucoxanthin accumulation under combined red and blue light. In short, both UV mutagenesis and ALE appeared as an effective approach to developing desired phenotypes in the marine diatoms via electromagnetic radiation-induced oxidative stress. PMID:26426027

  6. An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile

    Shen, Yu; Chen, Xiao; Peng, Bingyin; Chen, Liyuan; Hou, Jin; Bao, Xiaoming [Shandong Univ., Jinan (China). State Key Lab. of Microbial Technology

    2012-11-15

    Factors related to ethanol production from xylose in engineered Saccharomyces cerevisiae that contain an exogenous initial metabolic pathway are still to be elucidated. In the present study, a strain that expresses the xylose isomerase gene of Piromyces sp. Pi-xylA and overexpresses XKS1, RPE1, RKI1, TAL1, and TKL1, with deleted GRE3 and COX4 genes was constructed. The xylose utilization capacity of the respiratory deficiency strain was poor but improved via adaptive evolution in xylose. The {mu}{sub max} of the evolved strain in 20 gl{sup -1} xylose is 0.11 {+-} 0.00 h{sup -1}, and the evolved strain consumed 17.83 gl{sup -1} xylose within 72 h, with an ethanol yield of 0.43 gg{sup -1} total consumed sugars during glucose-xylose cofermentation. Global transcriptional changes and effect of several specific genes were studied. The result revealed that the increased xylose isomerase activity, the upregulation of enzymes involved in glycolysis and glutamate synthesis, and the downregulation of trehalose and glycogen synthesis, may have contributed to the improved xylose utilization of the strain. Furthermore, the deletion of PHO13 decreased the xylose growth in the respiration deficiency strain although deleting PHO13 can improve the xylose metabolism in other strains. (orig.)

  7. pSum-SaDE: A Modified p-Median Problem and Self-Adaptive Differential Evolution Algorithm for Text Summarization

    Rasim M. Alguliev

    2011-01-01

    Full Text Available Extractive multidocument summarization is modeled as a modified p-median problem. The problem is formulated with taking into account four basic requirements, namely, relevance, information coverage, diversity, and length limit that should satisfy summaries. To solve the optimization problem a self-adaptive differential evolution algorithm is created. Differential evolution has been proven to be an efficient and robust algorithm for many real optimization problems. However, it still may converge toward local optimum solutions, need to manually adjust the parameters, and finding the best values for the control parameters is a consuming task. In the paper is proposed a self-adaptive scaling factor in original DE to increase the exploration and exploitation ability. This paper has found that self-adaptive differential evolution can efficiently find the best solution in comparison with the canonical differential evolution. We implemented our model on multi-document summarization task. Experiments have shown that the proposed model is competitive on the DUC2006 dataset.

  8. Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.

    Holloway, AK; Bruneau, BG; Sukonnik, T; Rubenstein, JL; Pollard, KS

    2016-01-01

    Mammals have evolved remarkably different sensory, reproductive, metabolic, and skeletal systems. To explore the genetic basis for these differences, we developed a comparative genomics approach to scan whole-genome multiple sequence alignments to identify regions that evolved rapidly in an ancestral lineage but are conserved within extant species. This pattern suggests that ancestral changes in function were maintained in descendants. After applying this test to therian mammals, we identifie...

  9. Genetics of diversification: a hotspot locus for pigmentation evolution

    Silva, Carolina Martins Peralta Lopes da

    2015-01-01

    Tese de mestrado em Biologia Evolutiva e do Desenvolvimento, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2015 Um dos grandes desafios da biologia evolutiva é caracterizar os loci e as mutações que contribuem para a variabilidade fenotípica de características adaptativas. Existem exemplos clássicos que demonstram a base genética de determinadas características em que o seu papel adaptativo é conhecido, nomeadamente as manchas nas asas da mosca da fruta, os espinh...

  10. Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome

    Kuenne Carsten

    2013-01-01

    Full Text Available Abstract Background Listeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of such microbes. The diversity of this species has not been exhaustively explored yet, as previous efforts have focused on analyses of serotypes primarily implicated in human listeriosis. We conducted complete genome sequencing of 11 strains employing 454 GS FLX technology, thereby achieving full coverage of all serotypes including the first complete strains of serotypes 1/2b, 3c, 3b, 4c, 4d, and 4e. These were comparatively analyzed in conjunction with publicly available data and assessed for pathogenicity in the Galleria mellonella insect model. Results The species pan-genome of L. monocytogenes is highly stable but open, suggesting an ability to adapt to new niches by generating or including new genetic information. The majority of gene-scale differences represented by the accessory genome resulted from nine hyper variable hotspots, a similar number of different prophages, three transposons (Tn916, Tn554, IS3-like, and two mobilizable islands. Only a subset of strains showed CRISPR/Cas bacteriophage resistance systems of different subtypes, suggesting a supplementary function in maintenance of chromosomal stability. Multiple phylogenetic branches of the genus Listeria imply long common histories of strains of each lineage as revealed by a SNP-based core genome tree highlighting the impact of small mutations for the evolution of species L. monocytogenes. Frequent loss or truncation of genes described to be vital for virulence or pathogenicity was confirmed as a recurring pattern, especially for strains belonging to lineages III and II. New candidate genes implicated in virulence function were predicted based on functional domains and phylogenetic distribution. A comparative analysis of small regulatory RNA candidates

  11. Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals.

    Lynch, Vincent J.; Roth, Jutta J; Takahashi, Kazuhiko; Dunn, Casey W.; Nonaka, Daisuke F.; Stopper, Geffrey F.; Wagner, Günter P.

    2004-01-01

    The evolution of morphological characters is mediated by the evolution of developmental genes. Evolutionary changes can either affect cis-regulatory elements, leading to differences in their temporal and spatial regulation, or affect the coding region. Although there is ample evidence for the importance of cis-regulatory evolution, it has only recently been shown that transcription factors do not remain functionally equivalent during evolution. These results suggest that the evolution of tran...

  12. Molecular architecture of transcription factor hotspots in early adipogenesis.

    Siersbæk, Rasmus; Baek, Songjoon; Rabiee, Atefeh; Nielsen, Ronni; Traynor, Sofie; Clark, Nicholas; Sandelin, Albin; Jensen, Ole N; Sung, Myong-Hee; Hager, Gordon L; Mandrup, Susanne

    2014-06-12

    Transcription factors have recently been shown to colocalize in hotspot regions of the genome, which are further clustered into super-enhancers. However, the detailed molecular organization of transcription factors at hotspot regions is poorly defined. Here, we have used digital genomic footprinting to precisely define factor localization at a genome-wide level during the early phase of 3T3-L1 adipocyte differentiation, which allows us to obtain detailed molecular insight into how transcription factors target hotspots. We demonstrate the formation of ATF-C/EBP heterodimers at a composite motif on chromatin, and we suggest that this may be a general mechanism for integrating external signals on chromatin. Furthermore, we find evidence of extensive recruitment of transcription factors to hotspots through alternative mechanisms not involving their known motifs and demonstrate that these alternative binding events are functionally important for hotspot formation and activity. Taken together, these findings provide a framework for understanding transcription factor cooperativity in hotspots. PMID:24857666

  13. Investigating Avian Influenza Infection Hotspots in Old-World Shorebirds

    Gaidet, Nicolas; El Mamy, Ahmed B. Ould; Cappelle, Julien; Caron, Alexandre; Graeme S. Cumming; Grosbois, Vladimir; Gil, Patricia; Hammoumi, Saliha; Servan de Almeida, Renata; Fereidouni, Sasan R.; Cattoli, Giovanni; Abolnik, Celia; Mundava, Josphine; Fofana, Bouba; Ndlovu, Mduduzi

    2012-01-01

    Heterogeneity in the transmission rates of pathogens across hosts or environments may produce disease hotspots, which are defined as specific sites, times or species associations in which the infection rate is consistently elevated. Hotspots for avian influenza virus (AIV) in wild birds are largely unstudied and poorly understood. A striking feature is the existence of a unique but consistent AIV hotspot in shorebirds (Charadriiformes) associated with a single species at a specific location a...

  14. Analisis Jenis-jenis Sistem Keamanan Jaringan Wireless Hotspot

    Amri, Syaiful

    2015-01-01

    Hotspot adalah suatu kata yang tidak asing lagi didengarkan pada era modern seperti saat sekarang ini, karena banyaknya tempat-tempat yang telah dilengkapi oleh fasilitas seperti hotspot dimana hal ini memiliki kelebihan dari segi mobilitas, karena gerak seseorang tidak lagi dibatasi kabel untuk dapat mengakses internet sehingga kebutuhan akan informasi dan komunikasi dapat dipenuhi kapan pun dan dimana pun selama masih berada dalam jangkauan sinyal pada jaringan wireless Hotspot tersebut. Se...

  15. Molecular architecture of transcription factor hotspots in early adipogenesis

    Siersbæk, Rasmus; Baek, Songjoon; Rabiee, Atefeh; Nielsen, Ronni; Traynor, Sofie; Clarke, Nicholas; Sandelin, Albin Gustav; Jensen, Ole N.; Sung, Myong-Hee; Hager, Gordon L.; Mandrup, Susanne

    2014-01-01

    Transcription factors have recently been shown to colocalize in hotspot regions of the genome, which are further clustered into super-enhancers. However, the detailed molecular organization of transcription factors at hotspot regions is poorly defined. Here, we have used digital genomic footprint......Transcription factors have recently been shown to colocalize in hotspot regions of the genome, which are further clustered into super-enhancers. However, the detailed molecular organization of transcription factors at hotspot regions is poorly defined. Here, we have used digital genomic...

  16. Practical splitting methods for the adaptive integration of nonlinear evolution equations. Part I: Construction of optimized schemes and pairs of schemes

    Auzinger, Winfried

    2016-07-28

    We present a number of new contributions to the topic of constructing efficient higher-order splitting methods for the numerical integration of evolution equations. Particular schemes are constructed via setup and solution of polynomial systems for the splitting coefficients. To this end we use and modify a recent approach for generating these systems for a large class of splittings. In particular, various types of pairs of schemes intended for use in adaptive integrators are constructed.

  17. Probability Matching-based Adaptive Strategy Selection vs. Uniform Strategy Selection within Differential Evolution: An Empirical Comparison on the BBOB-2010 Noiseless Testbed

    Fialho, Álvaro; Gong, Wenyin; Cai, Zhihua

    2010-01-01

    Different strategies can be used for the generation of new candidate solutions on the Differential Evolution algorithm. However, the definition of which of them should be applied to the problem at hand is not trivial, besides being a sensitive choice with relation to the algorithm performance. In this paper, we use the BBOB-2010 noiseless benchmarking suite to further empirically validate the Probability Matching-based Adaptive Strategy Selection (PMAdapSS-DE), a method proposed to automatica...

  18. Testing biological hypotheses with embodied robots: adaptations, accidents, and by-products in the evolution of vertebrates

    Sonia F Roberts

    2014-11-01

    Full Text Available Evolutionary robotics allows biologists to test hypotheses about extinct animals. We modeled some of the first vertebrates, jawless fishes, in order to study the evolution of the trait after which vertebrates are named: vertebrae. We tested the hypothesis that vertebrae are an adaptation for enhanced feeding and fleeing performance. We created a population of autonomous embodied robots, Preyro, in which the number of vertebrae, N, were free to evolve. In addition, two other traits, the span of the caudal fin, b, and the predator detection threshold, ζ, a proxy for the lateral line sensory system, were also allowed to evolve. These three traits were chosen because they evolved early in vertebrates, are all potentially important in feeding and fleeing, and vary in form among species. Preyro took on individual identities in a given generation as defined by the population’s six diploid genotypes, Gi. Each Gi was a 3-tuple, with each element an integer specifying N, b, and, ζ. The small size of the population allowed for genetic drift to operate in concert with random mutation and mating; the presence of these mechanisms of chance provided an opportunity for N to evolve by accident. The presence of three evolvable traits provided an opportunity for direct selection on b and/or ζ to evolve N as a by-product linked trait correlation. In selection trials, different Gi embodied in Preyro attempted to feed at a light source and then flee to avoid a predator robot in pursuit. The fitness of each Gi was calculated from five different types of performance: speed, acceleration, distance to the light, distance to the predator, and the number of predator escapes initiated. In each generation, we measured the selection differential, the selection gradient, the strength of chance, and the indirect correlation selection gradient. These metrics allowed us to understand the relative contributions of the three mechanisms: direct selection, chance, and indirect

  19. Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals.

    Zielezinski, Andrzej; Karlowski, Wojciech M

    2015-01-01

    The GW182 proteins are a key component of the miRNA-dependent post-transcriptional silencing pathway in animals. They function as scaffold proteins to mediate the interaction of Argonaute (AGO)-containing complexes with cytoplasmic poly(A)-binding proteins (PABP) and PAN2-PAN3 and CCR4-NOT deadenylases. The AGO-GW182 complexes mediate silencing of the target mRNA through induction of translational repression and/or mRNA degradation. Although the GW182 proteins are a subject of extensive experimental research in the recent years, very little is known about their origin and evolution. Here, based on complex functional annotation and phylogenetic analyses, we reveal 448 members of the GW182 protein family from the earliest animals to humans. Our results indicate that a single-copy GW182/TNRC6C progenitor gene arose with the emergence of multicellularity and it multiplied in the last common ancestor of vertebrates in 2 rounds of whole genome duplication (WGD) resulting in 3 genes. Before the divergence of vertebrates, both the AGO- and CCR4-NOT-binding regions of GW182s showed significant acceleration in the accumulation of amino acid changes, suggesting functional adaptation toward higher specificity to the molecules of the silencing complex. We conclude that the silencing ability of the GW182 proteins improves with higher position in the taxonomic classification and increasing complexity of the organism. The first reconstruction of the molecular journey of GW182 proteins from the ancestral metazoan protein to the current mammalian configuration provides new insight into development of the miRNA-dependent post-transcriptional silencing pathway in animals. PMID:26106978

  20. Upscaling methane emission hotspots in boreal peatlands

    F. Cresto Aleina

    2015-10-01

    Full Text Available Upscaling the properties and the effects of small-scale surface heterogeneities to larger scales is a challenging issue in land surface modeling. We developed a novel approach to upscale local methane emissions in a boreal peatland from the micro-topographic scale to the landscape-scale. We based this new parameterization on the analysis of the water table pattern generated by the Hummock–Hollow model, a micro-topography resolving model for peatland hydrology. We introduce this parameterization of methane hotspots in a global model-like version of the Hummock–Hollow model, that underestimates methane emissions. We tested the robustness of the parameterization by simulating methane emissions for the next century forcing the model with three different RCP scenarios. The Hotspot parameterization, despite being calibrated for the 1976–2005 climatology, mimics the output of the micro-topography resolving model for all the simulated scenarios. The new approach bridges the scale gap of methane emissions between this version of the model and the configuration explicitly resolving micro-topography.

  1. Multisectoral Climate Impact Hotspots in a Warming World

    Piontek, Franziska; Mueller, Christoph; Pugh, Thomas A. M.; Clark, Douglas B.; Deryng, Delphine; Elliott, Joshua; deJesusColonGonzalez, Felipe; Floerke, Martina; Folberth, Christian; Franssen, Wietse; Frieler, Katja; Friend, Andrew D.; Gosling, Simon N.; Hemming, Deborah; Khabarov, Nikolay; Kim, Hyungjun; Lomas, Mark R.; Masaki, Yoshimitsu; Mengel, Matthias; Morse, Andrew; Neumann, Kathleen; Nishina, Kazuya; Ostberg, Sebastian; Pavlick, Ryan; Ruane, Alex C.

    2014-01-01

    The impacts of global climate change on different aspects of humanity's diverse life-support systems are complex and often difficult to predict. To facilitate policy decisions on mitigation and adaptation strategies, it is necessary to understand, quantify, and synthesize these climate-change impacts, taking into account their uncertainties. Crucial to these decisions is an understanding of how impacts in different sectors overlap, as overlapping impacts increase exposure, lead to interactions of impacts, and are likely to raise adaptation pressure. As a first step we develop herein a framework to study coinciding impacts and identify regional exposure hotspots. This framework can then be used as a starting point for regional case studies on vulnerability and multifaceted adaptation strategies. We consider impacts related to water, agriculture, ecosystems, and malaria at different levels of global warming. Multisectoral overlap starts to be seen robustly at a mean global warming of 3 degC above the 1980-2010 mean, with 11% of the world population subject to severe impacts in at least two of the four impact sectors at 4 degC. Despite these general conclusions, we find that uncertainty arising from the impact models is considerable, and larger than that from the climate models. In a low probability-high impact worst-case assessment, almost the whole inhabited world is at risk for multisectoral pressures. Hence, there is a pressing need for an increased research effort to develop a more comprehensive understanding of impacts, as well as for the development of policy measures under existing uncertainty.

  2. Biodiversity and paleobiogeography of the European freshwater Neogene: trends, hotspots and faunal turnovers

    Neubauer, Thomas A.; Harzhauser, Mathias; Georgopoulou, Elisavet; Andreas, Kroh; Mandic, Oleg

    2015-04-01

    We present an outline of a paleobiogeographic framework for the European fresh- and brackish-water systems during the Neogene. Data basis is a presence-absence matrix of lacustrine gastropods from over 2,700 localities. Cluster analyses were separately carried out on the datasets of the four time slices Early Miocene, Middle Miocene, Late Miocene, and Pliocene. Based on the results of the cluster analyses, the degree of endemicity, and geographical coherence, we classified the lake systems of the four time intervals into biogeographic units. The increasing degree of provincialism throughout the Neogene supported more detailed breakdowns in younger intervals. This pattern reflects the ongoing continentalization of Europe linked to the Alpidic Orogenesis. Additionally, the retreat of the Paratethys Sea and its isolation from the Mediterranean promoted the evolution of endemic faunas in surrounding lacustrine systems. Direct descendants such as long-lived Lake Pannon, Lake Dacia or Lake Slavonia persisted over several millions of years and promoted the evolution of highly diverse and endemic faunas. Because of their extensive duration they crucially influenced family-level composition, differences of the relative species richnesses per biogeographic unit, and rising rate of endemicity. We show that the biogeographic classification as well as the existence of biodiversity hotspots are tightly linked to the formation and evolution of long-lived lacustrine environments and thus to Europe's geodynamic history. Heat maps are provided to visualize the shifting distributions of hotspots through time. The only physiographic factor that can be shown to be correlated with species richness is the size of a lake. Other factors such as latitude, longitude or temporal duration show weak relationships. Correlation of biodiversity trends to climatic parameters such as temperature and precipitation are feasible only for selected periods. Climate is considered to have only minor

  3. Photothermal probing of plasmonic hotspots with nanomechanical resonator

    Schmid, Silvan; Wu, Kaiyu; Rindzevicius, Tomas;

    2014-01-01

    Plasmonic nanostructures (hotspots) are key components e.g. in plasmon-enhanced spectroscopy, plasmonic solar cells, or as nano heat sources. The characterization of single hotspots is still challenging due to a lack of experimental tools. We present the direct photothermal probing and mapping of...

  4. Photothermal probing of plasmonic hotspots with nanomechanical resonator

    Schmid, Silvan; Wu, Kaiyu; Rindzevicius, Tomas; Boisen, Anja

    Plasmonic nanostructures (hotspots) are key components e.g. in plasmon-enhanced spectroscopy, plasmonic solar cells, or as nano heat sources. The characterization of single hotspots is still challenging due to a lack of experimental tools. We present the direct photothermal probing and mapping of...... nanoslit array....

  5. Characteristics of suicide hotspots on the Belgian railway network.

    Debbaut, Kevin; Krysinska, Karolina; Andriessen, Karl

    2014-01-01

    In 2004, railway suicide accounted for 5.3% of all suicides in Belgium. In 2008, Infrabel (Manager of the Belgian Railway Infrastructure) introduced a railway suicide prevention programme, including identification of suicide hotspots, i.e., areas of the railway network with an elevated incidence of suicide. The study presents an analysis of 43 suicide hotspots based on Infrabel data collected during field visits and semi-structured interviews conducted in mental health facilities in the vicinity of the hotspots. Three major characteristics of the hotspots were accessibility, anonymity, and vicinity of a mental health institution. The interviews identified several risk and protective factors for railway suicide, including the training of staff, introduction of a suicide prevention policy, and the role of the media. In conclusion, a comprehensive railway suicide prevention programme should continuously safeguard and monitor hotspots, and should be embedded in a comprehensive suicide prevention programme in the community. PMID:24020492

  6. Key Biodiversity Areas identification in Japan Hotspot

    Y. Natori

    2012-08-01

    Full Text Available Priority sites within Japan Hotspot were identified using Key Biodiversity Area (KBA criteria, based on vulnerability and irreplaceability. The identification process considered 217 trigger species from mammals, birds, reptiles, amphibians, freshwater and brackish water fishes and odonates, and focused on identifying gaps in Japan’s protected-area system. We identified 228 sites as KBAs and 50 rivers as candidate KBAs. Collectively, KBAs occupy 18% of the land, about half is not protected. Sites selected include natural and semi-natural environments, and appropriate form of protection is site-dependent. Twenty percent of Japanese terrestrial area is already protected, although to varying degrees, but additional 8% should also receive protection or proper management to strengthen the conservation of biodiversity in Japan.

  7. Regional Climate Change Hotspots over Africa

    Anber, U.; Zakey, A.; Abd El Wahab, M.

    2009-04-01

    Regional Climate Change Index (RCCI), is developed based on regional mean precipitation change, mean surface air temperature change, and change in precipitation and temperature interannual variability. The RCCI is a comparative index designed to identify the most responsive regions to climate change, or Hot- Spots. The RCCI is calculated for Seven land regions over North Africa and Arabian region from the latest set of climate change projections by 14 global climates for the A1B, A2 and B1 IPCC emission scenarios. The concept of climate change can be approaches from the viewpoint of vulnerability or from that of climate response. In the former case a Hot-Spot can be defined as a region for which potential climate change impacts on the environment or different activity sectors can be particularly pronounced. In the other case, a Hot-Spot can be defined as a region whose climate is especially responsive to global change. In particular, the characterization of climate change response-based Hot-Spot can provide key information to identify and investigate climate change Hot-Spots based on results from multi-model ensemble of climate change simulations performed by modeling groups from around the world as contributions to the Fourth Assessment Report of Intergovernmental Panel on Climate Change (IPCC). A Regional Climate Change Index (RCCI) is defined based on four variables: change in regional mean surface air temperature relative to the global average temperature change ( or Regional Warming Amplification Factor, RWAF ), change in mean regional precipitation (P % , of present day value ), change in regional surface air temperature interannual variability (T % ,of present day value), change in regional precipitation interannual variability (P % ,of present day value ). In the definition of the RCCI it is important to include quantities other than mean change because often mean changes are not the only important factors for specific impacts. We thus also include inter

  8. The building of a biodiversity hotspot across a land-bridge in the Mediterranean.

    Molina-Venegas, Rafael; Aparicio, Abelardo; Lavergne, Sébastien; Arroyo, Juan

    2015-08-22

    Many of the macroevolutionary processes that have shaped present-day phylogenetic patterns were caused by geological events such as plate tectonics and temporary land-bridges. The study of spatial patterns of phylogenetic diversity can provide insights into these past events. Here we focus on a western Mediterranean biodiversity hotspot located in the southern Iberian Peninsula and northwest Africa, two regions that are separated by the Strait of Gibraltar. We explore the spatial structure of the phylogenetic relationships within and across large-scale plant assemblages. Significant turnover in terminal lineages tends to occur between landmasses, whereas turnover in deep lineages tends to occur within landmasses. Plant assemblages in the western ecoregions of this hotspot tend to be phylogenetically overdispersed but are phylogenetically clustered on its eastern margins. We discuss our results in the light of potential scenarios of niche evolution (or conservatism) and lineage diversification. The significant turnover between landmasses suggests a common scenario of allopatric speciation that could have been facilitated by the intermittent joining of the two continents. This may have constituted an important stimulus for diversification and the emergence of this western Mediterranean biodiversity hotspot. PMID:26246551

  9. Upscaling methane emission hotspots in boreal peatlands

    Cresto Aleina, Fabio; Runkle, Benjamin R. K.; Bruecher, Tim; Kleinen, Thomas; Brovkin, Victor

    2016-04-01

    Small-scale surface heterogeneities can influence land-atmosphere fluxes and therefore carbon, water and energy budgets on a larger scale. This effect is of particular relevance for high-latitude ecosystems, because of the great amount of carbon stored in their soils. Upscaling such small-scale surface heterogeneities and their effects to larger scales is a challenging issue in land surface modeling. We developed a novel approach to upscale local methane emissions in a boreal peatland from the micro-topographic scale to the landscape-scale. We based this parameterization on the analysis of the water table pattern generated by the Hummock-Hollow model (Cresto Aleina et al., 2015), a micro-topography resolving model for peatland hydrology and methane emissions. By computing the water table at the micro-topographic scale, the Hummock-Hollow model is able to describe the effects of micro-topography on hydrology and methane emissions in a typical boreal peatland. We introduce the new parameterization of methane hotspots in a global model-like version of the Hummock-Hollow model. This latter version underestimates methane emissions because of the lack of representation of micro-topographic controls on peatland hydrology. We tested the robustness of the parameterization by simulating methane emissions for the present day and for the next century, forcing the model with three different RCP scenarios. The Hotspot parameterization, despite being calibrated for the 1976-2005 climatology, mimics the output of the micro-topography resolving model for all the simulated scenarios. The new approach bridges the scale gap of methane emissions between this version of the model and the configuration explicitly resolving micro-topography.

  10. Hotspots of land use change in Europe

    Kuemmerle, Tobias; Levers, Christian; Erb, Karlheinz; Estel, Stephan; Jepsen, Martin R.; Müller, Daniel; Plutzar, Christoph; Stürck, Julia; Verkerk, Pieter J.; Verburg, Peter H.; Reenberg, Anette

    2016-06-01

    Assessing changes in the extent and management intensity of land use is crucial to understanding land-system dynamics and their environmental and social outcomes. Yet, changes in the spatial patterns of land management intensity, and thus how they might relate to changes in the extent of land uses, remains unclear for many world regions. We compiled and analyzed high-resolution, spatially-explicit land-use change indicators capturing changes in both the extent and management intensity of cropland, grazing land, forests, and urban areas for all of Europe for the period 1990–2006. Based on these indicators, we identified hotspots of change and explored the spatial concordance of area versus intensity changes. We found a clear East–West divide with regard to agriculture, with stronger cropland declines and lower management intensity in the East compared to the West. Yet, these patterns were not uniform and diverging patterns of intensification in areas highly suitable for farming, and disintensification and cropland contraction in more marginal areas emerged. Despite the moderate overall rates of change, many regions in Europe fell into at least one land-use change hotspot during 1990–2006, often related to a spatial reorganization of land use (i.e., co-occurring area decline and intensification or co-occurring area increase and disintensification). Our analyses highlighted the diverse spatial patterns and heterogeneity of land-use changes in Europe, and the importance of jointly considering changes in the extent and management intensity of land use, as well as feedbacks among land-use sectors. Given this spatial differentiation of land-use change, and thus its environmental impacts, spatially-explicit assessments of land-use dynamics are important for context-specific, regionalized land-use policy making.

  11. Methane Hotspots in the Los Angeles Megacity

    Hopkins, F. M.; Randerson, J. T.; Bush, S.; Ehleringer, J. R.; Lai, C.; Kort, E. A.; Blake, D. R.

    2013-12-01

    Airborne observations show that Los Angeles (LA) is a large source of methane to the atmosphere, yet the sources of excess methane from the urban area are poorly constrained. We used a mobile laboratory, a Ford Transit van equipped with cavity ring down spectrometers (Picarro, Inc.), to measure greenhouse gases (CH4, CO2, and CO) mole fractions in LA. On-road surveys across the LA Basin were conducted seasonally to determine patterns of CH4 enrichment in space and over time, with a focus on quantifying methane leaks from known sources. We found fugitive leaks and elevated CH4 concentrations throughout the LA Basin. Some were associated with known sources, such as landfills, wastewater treatment, and oil and gas infrastructure, while others had an unknown origin. Urban CH4 enrichment varied over the course of the year, largely due to seasonal changes in meteorological conditions. Nevertheless, our mobile surveys revealed CH4 hotspots (>200 ppb elevated with respect to background levels) that persisted among seasons. High CH4 concentrations were most easily predicted by proximity to methane sources, particularly near the coast, while elevated CH4 levels were more evenly dispersed in inland areas. CH4 hotspots had a disproportionate impact on excess methane relative to the area they accounted for, typically providing more than a quarter of excess methane measured on a transect. These data improve estimates of the relative roles of specific leaks and emission sectors to LA's excess methane. Depending on the cost of reducing these CH4 leaks, a focus on CH4 emissions may prove an effective way to reduce LA's greenhouse gas emissions in the near term.

  12. Future hotspots of terrestrial mammal loss.

    Visconti, Piero; Pressey, Robert L; Giorgini, Daniele; Maiorano, Luigi; Bakkenes, Michel; Boitani, Luigi; Alkemade, Rob; Falcucci, Alessandra; Chiozza, Federica; Rondinini, Carlo

    2011-09-27

    Current levels of endangerment and historical trends of species and habitats are the main criteria used to direct conservation efforts globally. Estimates of future declines, which might indicate different priorities than past declines, have been limited by the lack of appropriate data and models. Given that much of conservation is about anticipating and responding to future threats, our inability to look forward at a global scale has been a major constraint on effective action. Here, we assess the geography and extent of projected future changes in suitable habitat for terrestrial mammals within their present ranges. We used a global earth-system model, IMAGE, coupled with fine-scale habitat suitability models and parametrized according to four global scenarios of human development. We identified the most affected countries by 2050 for each scenario, assuming that no additional conservation actions other than those described in the scenarios take place. We found that, with some exceptions, most of the countries with the largest predicted losses of suitable habitat for mammals are in Africa and the Americas. African and North American countries were also predicted to host the most species with large proportional global declines. Most of the countries we identified as future hotspots of terrestrial mammal loss have little or no overlap with the present global conservation priorities, thus confirming the need for forward-looking analyses in conservation priority setting. The expected growth in human populations and consumption in hotspots of future mammal loss mean that local conservation actions such as protected areas might not be sufficient to mitigate losses. Other policies, directed towards the root causes of biodiversity loss, are required, both in Africa and other parts of the world. PMID:21844048

  13. Hot-Spot Avoidance With Multi-Pathing Over Infiniband: An MPI Perspective

    Vishnu, A; Koop, M; Moody, A; Mamidala, A R; Narravula, S; Panda, D K

    2007-03-06

    Large scale InfiniBand clusters are becoming increasingly popular, as reflected by the TOP 500 Supercomputer rankings. At the same time, fat tree has become a popular interconnection topology for these clusters, since it allows multiple paths to be available in between a pair of nodes. However, even with fat tree, hot-spots may occur in the network depending upon the route configuration between end nodes and communication pattern(s) in the application. To make matters worse, the deterministic routing nature of InfiniBand limits the application from effective use of multiple paths transparently and avoid the hot-spots in the network. Simulation based studies for switches and adapters to implement congestion control have been proposed in the literature. However, these studies have focused on providing congestion control for the communication path, and not on utilizing multiple paths in the network for hot-spot avoidance. In this paper, we design an MPI functionality, which provides hot-spot avoidance for different communications, without a priori knowledge of the pattern. We leverage LMC (LID Mask Count) mechanism of InfiniBand to create multiple paths in the network and present the design issues (scheduling policies, selecting number of paths, scalability aspects) of our design. We implement our design and evaluate it with Pallas collective communication and MPI applications. On an InfiniBand cluster with 48 processes, collective operations like MPI All-to-all Personalized and MPI Reduce Scatter show an improvement of 27% and 19% respectively. Our evaluation with MPI applications like NAS Parallel Benchmarks and PSTSWM on 64 processes shows significant improvement in execution time with this functionality.

  14. Pre-adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolates.

    Friman, V-P; Soanes-Brown, D; Sierocinski, P; Molin, S; Johansen, H K; Merabishvili, M; Pirnay, J-P; De Vos, D; Buckling, A

    2016-01-01

    Recent years have seen renewed interest in phage therapy--the use of viruses to specifically kill disease-causing bacteria--because of the alarming rise in antibiotic resistance. However, a major limitation of phage therapy is the ease at with bacteria can evolve resistance to phages. Here, we determined whether in vitro experimental coevolution can increase the efficiency of phage therapy by limiting the resistance evolution of intermittent and chronic cystic fibrosis Pseudomonas aeruginosa lung isolates to four different phages. We first pre-adapted all phage strains against all bacterial strains and then compared the efficacy of pre-adapted and nonadapted phages against ancestral bacterial strains. We found that evolved phages were more efficient in reducing bacterial densities than ancestral phages. This was primarily because only 50% of bacterial strains were able to evolve resistance to evolved phages, whereas all bacteria were able to evolve some level of resistance to ancestral phages. Although the rate of resistance evolution did not differ between intermittent and chronic isolates, it incurred a relatively higher growth cost for chronic isolates when measured in the absence of phages. This is likely to explain why evolved phages were more effective in reducing the densities of chronic isolates. Our data show that pathogen genotypes respond differently to phage pre-adaptation, and as a result, phage therapies might need to be individually adjusted for different patients. PMID:26476097

  15. Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity.

    Ramiro, Ricardo S; Costa, Henrique; Gordo, Isabel

    2016-09-01

    Small-colony variants (SCVs) are commonly observed in evolution experiments and clinical isolates, being associated with antibiotic resistance and persistent infections. We recently observed the repeated emergence of Escherichia coli SCVs during adaptation to the interaction with macrophages. To identify the genetic targets underlying the emergence of this clinically relevant morphotype, we performed whole-genome sequencing of independently evolved SCV clones. We uncovered novel mutational targets, not previously associated with SCVs (e.g. cydA, pepP) and observed widespread functional parallelism. All SCV clones had mutations in genes related to the electron-transport chain. As SCVs emerged during adaptation to macrophages, and often show increased antibiotic resistance, we measured SCV fitness inside macrophages and measured their antibiotic resistance profiles. SCVs had a fitness advantage inside macrophages and showed increased aminoglycoside resistance in vitro, but had collateral sensitivity to other antibiotics (e.g. tetracycline). Importantly, we observed similar results in vivo. SCVs had a fitness advantage upon colonization of the mouse gut, which could be tuned by antibiotic treatment: kanamycin (aminoglycoside) increased SCV fitness, but tetracycline strongly reduced it. Our results highlight the power of using experimental evolution as the basis for identifying the causes and consequences of adaptation during host-microbe interactions. PMID:27606007

  16. Modelling Hotspots for Invasive Alien Plants in India.

    Dibyendu Adhikari

    Full Text Available Identification of invasion hotspots that support multiple invasive alien species (IAS is a pre-requisite for control and management of invasion. However, till recently it remained a methodological challenge to precisely determine such invasive hotspots. We identified the hotspots of alien species invasion in India through Ecological Niche Modelling (ENM using species occurrence data from the Global Biodiversity Information Facility (GBIF. The predicted area of invasion for selected species were classified into 4 categories based on number of model agreements for a region i.e. high, medium, low and very low. About 49% of the total geographical area of India was predicted to be prone to invasion at moderate to high levels of climatic suitability. The intersection of anthropogenic biomes and ecoregions with the regions of 'high' climatic suitability was classified as hotspot of alien plant invasion. Nineteen of 47 ecoregions of India, harboured such hotspots. Most ecologically sensitive regions of India, including the 'biodiversity hotspots' and coastal regions coincide with invasion hotspots, indicating their vulnerability to alien plant invasion. Besides demonstrating the usefulness of ENM and open source data for IAS management, the present study provides a knowledge base for guiding the formulation of an effective policy and management strategy for controlling the invasive alien species.

  17. Modelling Hotspots for Invasive Alien Plants in India.

    Adhikari, Dibyendu; Tiwary, Raghuvar; Barik, Saroj Kanta

    2015-01-01

    Identification of invasion hotspots that support multiple invasive alien species (IAS) is a pre-requisite for control and management of invasion. However, till recently it remained a methodological challenge to precisely determine such invasive hotspots. We identified the hotspots of alien species invasion in India through Ecological Niche Modelling (ENM) using species occurrence data from the Global Biodiversity Information Facility (GBIF). The predicted area of invasion for selected species were classified into 4 categories based on number of model agreements for a region i.e. high, medium, low and very low. About 49% of the total geographical area of India was predicted to be prone to invasion at moderate to high levels of climatic suitability. The intersection of anthropogenic biomes and ecoregions with the regions of 'high' climatic suitability was classified as hotspot of alien plant invasion. Nineteen of 47 ecoregions of India, harboured such hotspots. Most ecologically sensitive regions of India, including the 'biodiversity hotspots' and coastal regions coincide with invasion hotspots, indicating their vulnerability to alien plant invasion. Besides demonstrating the usefulness of ENM and open source data for IAS management, the present study provides a knowledge base for guiding the formulation of an effective policy and management strategy for controlling the invasive alien species. PMID:26230513

  18. 国际MIS学科领域研究热点及演化路径分析*--基于10本国际权威期刊2004~2013年间的样本分析%Study of Research Hotspots and Evolution Path in International Management Information System Research Field-Based on 10 InternationalAuthoritative Journals between 2004~2013

    张敏; 朱明星; 沈雪乐

    2015-01-01

    This study collected published papers from 10 international authoritative journals within the time span of 2004-2013. Firstly, we used co-word analysis method to construct similarity matrix of high frequency keywords. Then the research hotspots were recognized based on the method of VOSviewer clustering technique. Time-topics bi-dimension networks were constructed to analyze hotspots' evolu-tion path. The results show that, knowledge sharing and knowledge management, electronic market and customer behavior, decision ana-lyzing and market forecasting, enterprise performance and risk management, system development and knowledge mining, enterprise com-petition and supply chain management were the 6 most significant research directions in the past 10 years. In the future, the new research tendency will focus on the combination of MIS and Economics, Communication, and Psychology. In addition, the research of MIS appli-cation in business and service industry will be furthered.%以10本MIS领域国际权威期刊在2004-2013年间的载文信息为数据样本,首先利用共词分析法生成高频关键词的相似矩阵,并利用VOSviewer聚类技术识别MIS研究的主题群及研究热点,之后通过构建时间-主题二维网络图对研究热点的演化路径进行了梳理。结果显示:近十年来国际MIS领域的研究热点包括知识共享与知识管理、电子商务市场与用户行为、决策分析与市场预测、企业绩效与风险管理、系统开发与知识挖掘以及企业竞争与供应链管理6个层面。 MIS学科未来的发展趋势主要集中在与经济学、传播学和心理学等学科的融合不断增强,以及与商业、服务业的交叉不断深化上。

  19. Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles

    Greenwold, Matthew J.; Bao, Weier; Jarvis, Erich D.;

    2014-01-01

    BACKGROUND: Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We have studied the molecular evolution of these gene families in the genomes of...... adaptation of birds into multiple ecological niches.......BACKGROUND: Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We have studied the molecular evolution of these gene families in the genomes of...... 48 phylogenetically diverse birds and their expression in the scales and feathers of the chicken. RESULTS: We found that the total number of α-keratins is lower in birds than mammals and non-avian reptiles, yet two α-keratin genes (KRT42 and KRT75) have expanded in birds. The β-keratins, however...

  20. Evolutionary genomics and adaptive evolution of the hedgehog gene family (Shh, Ihh and Dhh) in vertebrates

    Pereira, Joana; Johnson, Warren E.; O'Brien, Stephen J.;

    2014-01-01

    . In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an...... extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within...

  1. Central Indian Ridge and Reunion Hotspot in Rodrigues Area : Another Type of Ridge - Hotspot Interaction ?

    DYMENT, J.; HEMOND, C.; GUILLOU, H.; MAIA, M.; BRIAIS, A.; GENTE, P.

    2001-12-01

    The Rodrigues Ridge is an E-W volcanic structure which extends at 19° S from the Mascarene Plateau (59° 30'E) to 100 km East of Rodrigues Island (64° 30'E). It is neither parallel to seafloor spreading flow-lines nor to the "absolute" motion of Africa in the hotspot reference frame. 39Ar-40Ar dating of dredged samples has shown that the whole ridge formed at 8-10 Ma, suggesting a rather rapid emplacement between the former position of the Reunion hotspot and the nearest segment of the CIR at 10-8 Ma. This rules out the hypothesis that the Rodrigues Ridge was progressively built near the CIR axis, at the end of a "channeled" asthenospheric flow originating from Reunion hotspot. Sr, Nd and Pb isotopes show gradual fading of the Reunion hotspot influence with increasing distance from the Mascarene Plateau. Signs for a more recent activity are the Rodrigues Island, dated about 1 Ma, and a set of recently discovered en-echelon volcanic ridges, the Three Magi and Gasitao Ridges. They extend the Rodrigues Ridge up to the CIR axis. These ridges display a clear sigmoid shape and align along an E-W direction at 19° 40'S. Another parallel, less prominent volcanic alignment is observed about 30 km north, at 19° 25'S. K-Ar dating (Cassignol method) provides ages of 0.4 and 1.8 Ma for the easternmost Gasitao Ridge. This second age is slightly younger than that of the underlying crust given by the magnetic anomalies. Isotopic compositions are intermediate between those measured on Rodrigues Ridge and the CIR axis. The lack of conjugate bathymetric feature and the age measured on the Gasitao Ridge demonstrate that it was built off axis, in the close vicinity of the CIR. The sigmoid morphology and en-echelon alignment of Three Magi and Gasitao Ridges suggest that they correspond to tension cracks filled by magmas resulting from decompression melting of underlying mantle. Repetition of such magmatic events results in increasing volume as ridges get older, in agreement with the

  2. The Manihiki Plateau—a key to missing hotspot tracks?

    Pietsch, R.; Uenzelmann-Neben, G.

    2016-08-01

    A Neogene magmatic reactivation of the Manihiki Plateau, a large igneous province (LIP) in the central Pacific, is studied using seismic reflection data. Igneous diapirs have been identified exclusively within a narrow WNW-ESE striking corridor in the southern High Plateau (HP), which is parallel to the Neogene Pacific Plate motion and overlaps with an extrapolation of the Society Islands Hotspot (SIH) path. The igneous diapirs are characterized by a narrow width (>5 km), penetration of the Neogene sediments, and they become progressively younger towards the East (23-10 Ma). The magmatic source appears to be of small lateral extent, which leads to the conclusion that the diapirs represent Neogene hotspot volcanism within a LIP, and thus may be an older, previously unknown extension of the SIH track (>4.5 Ma). Comparing hotspot volcanism within oceanic and continental lithosphere, we further conclude that hotspot volcanism within LIP crust has similarities to tectonically faulted continental crust.

  3. Detection prospects of the TA hotspot by space observatories

    Semikoz, D; Zotov, M

    2016-01-01

    In the present-day cosmic ray data, the strongest indication of anisotropy of the ultra-high energy cosmic rays (UHECRs) is the 20-degree hotspot observed by the Telescope Array with the statistical significance of 3.4{\\sigma}. In this work, we study the possibility of detection of such a spot by space-based all-sky observatories. We show that if the detected luminosity of the hotspot is attributed to a physical effect and not a statistical fluctuation, the KLYPVE and JEM-EUSO experiments would need to collect ~300 events with E>57 EeV in order to detect the hotspot at the 5{\\sigma} confidence level with the 68% probability. We also study the dependence of the detection prospects on the hotspot luminosity.

  4. Effect of dissolved inorganic carbon on oxygen evolution and uptake by Chlamydomonas reinhardtii suspensions adapted to ambient and CO2-enriched air.

    Sültemeyer, D F; Klug, K; Fock, H P

    1987-01-01

    Mass spectrometric measurements of (16)O2 and (18)O2 isotopes were used to compare the rates of gross O2 evolution (E0), O2 uptake (U0) and net O2 evolution (NET) in relation to different concentrations of dissolved inorganic carbon (DIC) by Chlamydomonas reinhardtii cells grown in air (air-grown), in air enriched with 5% CO2 (CO2-grown) and by cells grown in 5% CO2 and then adapted to air for 6h (air-adapted).At a photon fluence rate (PFR) saturating for photosynthesis (700 μmol photons m(-2) s(-1)), pH=7.0 and 28°C, U0 equalled E0 at the DIC compensation point which was 10μM DIC for CO2-grown and zero for air-grown cells. Both E0 and U0 were strongly dependent on DIC and reached DIC saturation at 480 μM and 70 μM for CO2-grown and air-grown algae respectively. U0 increased from DIC compensation to DIC saturation. The U0 values were about 40 (CO2-grown), 165 (air-adapted) and 60 μmol O2 mg Chl(-1) h(-1) (air-grown). Above DIC compensation the U0/E0 ratios of air-adapted and air-grown algae were always higher than those of CO2-grown cells. These differences in O2 exchange between CO2- and air-grown algae seem to be inducable since air-adapted algae respond similarly to air-grown cells.For all algae, the rates of dark respiratory O2 uptake measured 5 min after darkening were considerably lower than the rates of O2 uptake just before darkening. The contribution of dark respiration, photorespiration and the Mehler reaction to U0 is discussed and the energy requirement of the inducable CO2/HCO3 (-) concentrating mechanism present in air-adapted and air-grown C. reinhardtii cells is considered. PMID:24435578

  5. Future of Endemic Flora of Biodiversity Hotspots in India

    Chitale, Vishwas Sudhir; Behera, Mukund Dev; Roy, Partha Sarthi

    2014-01-01

    India is one of the 12 mega biodiversity countries of the world, which represents 11% of world's flora in about 2.4% of global land mass. Approximately 28% of the total Indian flora and 33% of angiosperms occurring in India are endemic. Higher human population density in biodiversity hotspots in India puts undue pressure on these sensitive eco-regions. In the present study, we predict the future distribution of 637 endemic plant species from three biodiversity hotspots in India; Himalaya, Wes...

  6. Investigating avian influenza infection hotspots in old-world shorebirds.

    Nicolas Gaidet

    Full Text Available Heterogeneity in the transmission rates of pathogens across hosts or environments may produce disease hotspots, which are defined as specific sites, times or species associations in which the infection rate is consistently elevated. Hotspots for avian influenza virus (AIV in wild birds are largely unstudied and poorly understood. A striking feature is the existence of a unique but consistent AIV hotspot in shorebirds (Charadriiformes associated with a single species at a specific location and time (ruddy turnstone Arenaria interpres at Delaware Bay, USA, in May. This unique case, though a valuable reference, limits our capacity to explore and understand the general properties of AIV hotspots in shorebirds. Unfortunately, relatively few shorebirds have been sampled outside Delaware Bay and they belong to only a few shorebird families; there also has been a lack of consistent oropharyngeal sampling as a complement to cloacal sampling. In this study we looked for AIV hotspots associated with other shorebird species and/or with some of the larger congregation sites of shorebirds in the old world. We assembled and analysed a regionally extensive dataset of AIV prevalence from 69 shorebird species sampled in 25 countries across Africa and Western Eurasia. Despite this diverse and extensive coverage we did not detect any new shorebird AIV hotspots. Neither large shorebird congregation sites nor the ruddy turnstone were consistently associated with AIV hotspots. We did, however, find a low but widespread circulation of AIV in shorebirds that contrast with the absence of AIV previously reported in shorebirds in Europe. A very high AIV antibody prevalence coupled to a low infection rate was found in both first-year and adult birds of two migratory sandpiper species, suggesting the potential existence of an AIV hotspot along their migratory flyway that is yet to be discovered.

  7. Fish-derived nutrient hotspots shape coral reef benthic communities.

    Shantz, Andrew A; Ladd, Mark C; Schrack, Elizabeth; Burkepile, Deron E

    2015-12-01

    Animal-derived nutrients play an important role in structuring nutrient regimes within and between ecosystems. When animals undergo repetitive, aggregating behavior through time, they can create nutrient hotspots where rates of biogeochemical activity are higher than those found in the surrounding environment. In turn, these hotspots can influence ecosystem processes and community structure. We examined the potential for reef fishes from the family Haemulidae (grunts) to create nutrient hotspots and the potential impact of these hotspots on reef communities. To do so, we tracked the schooling locations of diurnally migrating grunts, which shelter at reef sites during the day but forage off reef each night, and measured the impact of these fish schools on benthic communities. We found that grunt schools showed a high degree of site fidelity, repeatedly returning to the same coral heads. These aggregations created nutrient hotspots around coral heads where nitrogen and phosphorus delivery was roughly 10 and 7 times the respective rates of delivery to structurally similar sites that lacked schools of these fishes. In turn, grazing rates of herbivorous fishes at grunt-derived hotspots were approximately 3 times those of sites where grunts were rare. These differences in nutrient delivery and grazing led to distinct benthic communities with higher cover of crustose coralline algae and less total algal abundance at grunt aggregation sites. Importantly, coral growth was roughly 1.5 times greater at grunt hotspots, likely due to the important nutrient subsidy. Our results suggest that schooling reef fish and their nutrient subsidies play an important role in mediating community structure on coral reefs and that overfishing may have important negative consequences on ecosystem functions. As such, management strategies must consider mesopredatory fishes in addition to current protection often offered to herbivores and top-tier predators. Furthermore, our results suggest that

  8. Mobile and Residential INEA Wi-Fi Hotspot Network

    Musznicki, Bartosz; Kowalik, Karol; Kołodziejski, Piotr; Grzybek, Eugeniusz

    2016-01-01

    Since 2012 INEA has been developing and expanding the network of IEEE 802.11 compliant Wi-Fi hotspots (access points) located across the Greater Poland region. This network consists of 330 mobile (vehicular) access points carried by public buses and trams and over 20,000 fixed residential hotspots distributed throughout the homes of INEA customers to provide Internet access via the "community Wi-Fi" service. Therefore, this paper is aimed at sharing the insights gathered by INEA throughout 4 ...

  9. A review on biological adaptation: with applications in engineering science

    LiMin Luo; WenJun Zhang

    2014-01-01

    Biological adaptation refers to that organisms change themselves at morphological, physiological, behavioral and molecular level to better survive in a changing environment. It includes phenotype adaptation and molecular adaptation. Biological adaptation is a driving force of evolution. Biological adaptation was described from Darwinian theory of evolution to the theory of molecular evolution in present paper. Adaptive control and adaptive filtering were briefly described also.

  10. Online Forums Hotspot Prediction Based on Sentiment Analysis

    V. Murali Bhaskarn

    2012-01-01

    Full Text Available Problem statement: Online forums hotspot prediction is one of the significant research areas in web mining, which can help people make proper decision in daily life. Online forums, news reports and blogs, are containing large volume of public opinion information. Rapid growth of network arouses much attention on public opinion, it is important to analyse the public opinion in time and understands the trends of their opinion correctly. Approach: The sentiment analysis and text mining are important key elements for forecasting the hotspots in online forums. Most of the traditional text mining work on static data sets, while the online hotspot forecasts works on the web information dynamically and timely. The earlier work on text information processing focuses in the factual domain rather than opinion domain. Due to the semi structured or unstructured characteristics of online public opinion, we introduce traditional Vector Space Model (VSM to express them and then use K-means to perform hotspot detection, then we use J48 classifier to perform hotspot forecast. Results: The experimentation is conducted by Rapid Miner tool and performance of proposed method J48 is compared with other method, such as Naive Bayes. The consistency between K-means and J48 is validated using three metrics. They are accuracy, sensitivity and specificity. Conclusion: The experiment helps to identify that K-means and J48 together to predict forums hotspot. The results that have been obtained using J48 present a noticeable consistency with the results achieved by K-means clustering.

  11. Molecular Architecture of Transcription Factor Hotspots in Early Adipogenesis

    Rasmus Siersbæk

    2014-06-01

    Full Text Available Transcription factors have recently been shown to colocalize in hotspot regions of the genome, which are further clustered into super-enhancers. However, the detailed molecular organization of transcription factors at hotspot regions is poorly defined. Here, we have used digital genomic footprinting to precisely define factor localization at a genome-wide level during the early phase of 3T3-L1 adipocyte differentiation, which allows us to obtain detailed molecular insight into how transcription factors target hotspots. We demonstrate the formation of ATF-C/EBP heterodimers at a composite motif on chromatin, and we suggest that this may be a general mechanism for integrating external signals on chromatin. Furthermore, we find evidence of extensive recruitment of transcription factors to hotspots through alternative mechanisms not involving their known motifs and demonstrate that these alternative binding events are functionally important for hotspot formation and activity. Taken together, these findings provide a framework for understanding transcription factor cooperativity in hotspots.

  12. Is genetic evolution predictable?

    Stern, David L; Orgogozo, Virginie

    2009-02-01

    Ever since the integration of Mendelian genetics into evolutionary biology in the early 20th century, evolutionary geneticists have for the most part treated genes and mutations as generic entities. However, recent observations indicate that all genes are not equal in the eyes of evolution. Evolutionarily relevant mutations tend to accumulate in hotspot genes and at specific positions within genes. Genetic evolution is constrained by gene function, the structure of genetic networks, and population biology. The genetic basis of evolution may be predictable to some extent, and further understanding of this predictability requires incorporation of the specific functions and characteristics of genes into evolutionary theory. PMID:19197055

  13. HOTSPOT, Field Evaluation of Radiation Release from Nuclear Accident

    1 - Description of program or function: The HOTSPOT Health Physics codes were created to provide Health Physics personnel with a fast, field-portable calculational tool for evaluating accidents involving radioactive materials. HOTSPOT codes are a first-order approximation of the radiation effects associated with the atmospheric release of radioactive materials. HOTSPOT programs are reasonably accurate for a timely initial assessment. More importantly, HOTSPOT codes produce a consistent output for the same input assumptions and minimize the probability of errors associated with reading a graph incorrectly or scaling a universal nomogram during an emergency. Four general programs, PLUME, EXPLOSION, FIRE, and RESUSPENSION, calculate a downwind assessment following the release of radioactive material resulting from a continuous or puff release, explosive release, fuel fire, or an area contamination event. Other programs deal with the release of plutonium, uranium, and tritium to expedite an initial assessment of accidents involving nuclear weapons. Additional programs estimate the dose commitment from inhalation of any one of the radionuclides listed in the database of radionuclides, calibrate a radiation survey instrument for ground survey measurements, and screening of plutonium uptake in the lung. The HOTSPOT codes are fast, portable, easy to use, and fully documented. HOTSPOT supports color high resolution monitors and printers for concentration plots and contours. The codes have been extensively used by the DOS community since 1985. Version 8 allows users to add their own custom radionuclide library and to create custom radionuclide mixtures. It also includes wet deposition to approximate the enhanced plume depletion and ground deposition due to the effects of rain. Additional release geometry options for TRITIUM RELEASE and GENERAL PLUME were added, as well as several other enhancements and improvements. See info (f1) from the main HOTSPOT menu for additional

  14. The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity

    Kieslich, Chris A.; Dimitrios Morikis

    2012-01-01

    The interaction between complement fragment C3d and complement receptor 2 (CR2) is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement system and adaptive immunity, which is formed through the association of the B-cell co-receptor compl...

  15. Reduction of ethanol yield and improvement of glycerol formation by adaptive evolution of the wine yeast Saccharomyces cerevisiae under hyperosmotic conditions.

    Tilloy, Valentin; Ortiz-Julien, Anne; Dequin, Sylvie

    2014-04-01

    There is a strong demand from the wine industry for methodologies to reduce the alcohol content of wine without compromising wine's sensory characteristics. We assessed the potential of adaptive laboratory evolution strategies under hyperosmotic stress for generation of Saccharomyces cerevisiae wine yeast strains with enhanced glycerol and reduced ethanol yields. Experimental evolution on KCl resulted, after 200 generations, in strains that had higher glycerol and lower ethanol production than the ancestral strain. This major metabolic shift was accompanied by reduced fermentative capacities, suggesting a trade-off between high glycerol production and fermentation rate. Several evolved strains retaining good fermentation performance were selected. These strains produced more succinate and 2,3-butanediol than the ancestral strain and did not accumulate undesirable organoleptic compounds, such as acetate, acetaldehyde, or acetoin. They survived better under osmotic stress and glucose starvation conditions than the ancestral strain, suggesting that the forces that drove the redirection of carbon fluxes involved a combination of osmotic and salt stresses and carbon limitation. To further decrease the ethanol yield, a breeding strategy was used, generating intrastrain hybrids that produced more glycerol than the evolved strain. Pilot-scale fermentation on Syrah using evolved and hybrid strains produced wine with 0.6% (vol/vol) and 1.3% (vol/vol) less ethanol, more glycerol and 2,3-butanediol, and less acetate than the ancestral strain. This work demonstrates that the combination of adaptive evolution and breeding is a valuable alternative to rational design for remodeling the yeast metabolic network. PMID:24532067

  16. A simple mathematical model of gradual Darwinian evolution: Emergence of a Gaussian trait distribution in adaptation along a fitness gradient

    Biktashev, Vadim N.

    2011-01-01

    We consider a simple mathematical model of gradual Darwinian evolution in continuous time and continuous trait space, due to intraspecific competition for common resource in an asexually reproducing population in constant environment, while far from evolutionary stable equilibrium. The model admits exact analytical solution. In particular, Gaussian distribution of the trait emerges from generic initial conditions.

  17. The ectodysplasin pathway: from diseases to adaptations.

    Sadier, Alexa; Viriot, Laurent; Pantalacci, Sophie; Laudet, Vincent

    2014-01-01

    The ectodysplasin (EDA) pathway, which is active during the development of ectodermal organs, including teeth, hairs, feathers, and mammary glands, and which is crucial for fine-tuning the developmental network controlling the number, size, and density of these structures, was discovered by studying human patients affected by anhidrotic/hypohidrotic ectodermal dysplasia. It comprises three main gene products: EDA, a ligand that belongs to the tumor necrosis factor (TNF)-α family, EDAR, a receptor related to the TNFα receptors, and EDARADD, a specific adaptor. This core pathway relies on downstream NF-κB pathway activation to regulate target genes. The pathway has recently been found to be associated with specific adaptations in natural populations: the magnitude of armor plates in sticklebacks and the hair structure in Asian human populations. Thus, despite its role in human disease, the EDA pathway is a 'hopeful pathway' that could allow adaptive changes in ectodermal appendages which, as specialized interfaces with the environment, are considered hot-spots of morphological evolution. PMID:24070496

  18. The Genome Sequence of the psychrophilic archaeon, Methanococcoides burtonii: the Role of Genome Evolution in Cold-adaptation

    Allen, Michelle A.; Lauro, Federico M.; Williams, Timothy J.; Burg, Dominic; Siddiqui, Khawar S.; De Francisci, David; Chong, Kevin W.Y.; Pilak, Oliver; Chew, Hwee H.; De Maere, Matthew Z.; Ting, Lily; Katrib, Marilyn; Ng, Charmaine; Sowers, Kevin R.; Galperin, Michael Y.; Anderson, Iain J.; Ivanova, Natalia; Dalin, Eileen; Martinez, Michelle; Lapidus, Alla; Hauser, Loren; Land, Miriam; Thomas, Torsten; Cavicchioli, Ricardo

    2009-04-01

    Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five tiered Evidence Rating system that ranked annotations from Evidence Rating (ER) 1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall/membrane/envelope biogenesis COG genes are over-represented. Likewise, signal transduction (COG category T) genes are over-represented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two over-represented COG categories appear to have been acquired from {var_epsilon}- and {delta}-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have

  19. Functional Adaptation of a Plant Receptor- Kinase Paved the Way for the Evolution of Intracellular Root Symbioses with Bacteria

    Markmann, Katharina; Giczey, Gábor; Parniske, Martin

    2008-01-01

    Author Summary As an adaptation to nutrient limitations in terrestrial ecosystems, most plants form Arbuscular Mycorrhiza (AM), which is a symbiotic relationship between phosphate-delivering fungi and plant roots that dates back to the earliest land plants. More recently, a small group including the legumes and close relatives has evolved the ability to accommodate nitrogen-fixing bacteria intracellularly. The resulting symbiosis is manifested by the formation of specialized root organs, the ...

  20. Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula.

    Sazzini, Marco; Gnecchi Ruscone, Guido Alberto; Giuliani, Cristina; Sarno, Stefania; Quagliariello, Andrea; De Fanti, Sara; Boattini, Alessio; Gentilini, Davide; Fiorito, Giovanni; Catanoso, Mariagrazia; Boiardi, Luigi; Croci, Stefania; Macchioni, Pierluigi; Mantovani, Vilma; Di Blasio, Anna Maria; Matullo, Giuseppe; Salvarani, Carlo; Franceschi, Claudio; Pettener, Davide; Garagnani, Paolo; Luiselli, Donata

    2016-01-01

    The Italian peninsula has long represented a natural hub for human migrations across the Mediterranean area, being involved in several prehistoric and historical population movements. Coupled with a patchy environmental landscape entailing different ecological/cultural selective pressures, this might have produced peculiar patterns of population structure and local adaptations responsible for heterogeneous genomic background of present-day Italians. To disentangle this complex scenario, genome-wide data from 780 Italian individuals were generated and set into the context of European/Mediterranean genomic diversity by comparison with genotypes from 50 populations. To maximize possibility of pinpointing functional genomic regions that have played adaptive roles during Italian natural history, our survey included also ~250,000 exomic markers and ~20,000 coding/regulatory variants with well-established clinical relevance. This enabled fine-grained dissection of Italian population structure through the identification of clusters of genetically homogeneous provinces and of genomic regions underlying their local adaptations. Description of such patterns disclosed crucial implications for understanding differential susceptibility to some inflammatory/autoimmune disorders, coronary artery disease and type 2 diabetes of diverse Italian subpopulations, suggesting the evolutionary causes that made some of them particularly exposed to the metabolic and immune challenges imposed by dietary and lifestyle shifts that involved western societies in the last centuries. PMID:27582244

  1. Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula

    Sazzini, Marco; Gnecchi Ruscone, Guido Alberto; Giuliani, Cristina; Sarno, Stefania; Quagliariello, Andrea; De Fanti, Sara; Boattini, Alessio; Gentilini, Davide; Fiorito, Giovanni; Catanoso, Mariagrazia; Boiardi, Luigi; Croci, Stefania; Macchioni, Pierluigi; Mantovani, Vilma; Di Blasio, Anna Maria; Matullo, Giuseppe; Salvarani, Carlo; Franceschi, Claudio; Pettener, Davide; Garagnani, Paolo; Luiselli, Donata

    2016-01-01

    The Italian peninsula has long represented a natural hub for human migrations across the Mediterranean area, being involved in several prehistoric and historical population movements. Coupled with a patchy environmental landscape entailing different ecological/cultural selective pressures, this might have produced peculiar patterns of population structure and local adaptations responsible for heterogeneous genomic background of present-day Italians. To disentangle this complex scenario, genome-wide data from 780 Italian individuals were generated and set into the context of European/Mediterranean genomic diversity by comparison with genotypes from 50 populations. To maximize possibility of pinpointing functional genomic regions that have played adaptive roles during Italian natural history, our survey included also ~250,000 exomic markers and ~20,000 coding/regulatory variants with well-established clinical relevance. This enabled fine-grained dissection of Italian population structure through the identification of clusters of genetically homogeneous provinces and of genomic regions underlying their local adaptations. Description of such patterns disclosed crucial implications for understanding differential susceptibility to some inflammatory/autoimmune disorders, coronary artery disease and type 2 diabetes of diverse Italian subpopulations, suggesting the evolutionary causes that made some of them particularly exposed to the metabolic and immune challenges imposed by dietary and lifestyle shifts that involved western societies in the last centuries. PMID:27582244

  2. Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta.

    Faddeeva-Vakhrusheva, Anna; Derks, Martijn F L; Anvar, Seyed Yahya; Agamennone, Valeria; Suring, Wouter; Smit, Sandra; van Straalen, Nico M; Roelofs, Dick

    2016-01-01

    Collembola (springtails) are detritivorous hexapods that inhabit the soil and its litter layer. The ecology of the springtail Orchesella cincta is extensively studied in the context of adaptation to anthropogenically disturbed areas. Here, we present a draft genome of an O. cincta reference strain with an estimated size of 286.8 Mbp, containing 20,249 genes. In total, 446 gene families are expanded and 1,169 gene families evolved specific to this lineage. Besides these gene families involved in general biological processes, we observe gene clusters participating in xenobiotic biotransformation. Furthermore, we identified 253 cases of horizontal gene transfer (HGT). Although the largest percentage of them originated from bacteria (37.5%), we observe an unusually high percentage (30.4%) of such genes of fungal origin. The majority of foreign genes are involved in carbohydrate metabolism and cellulose degradation. Moreover, some foreign genes (e.g., bacillopeptidases) expanded after HGT. We hypothesize that horizontally transferred genes could be advantageous for food processing in a soil environment that is full of decaying organic material. Finally, we identified several lineage-specific genes, expanded gene families, and horizontally transferred genes, associated with altered gene expression as a consequence of genetic adaptation to metal stress. This suggests that these genome features may be preadaptations allowing natural selection to act on. In conclusion, this genome study provides a solid foundation for further analysis of evolutionary mechanisms of adaptation to environmental stressors. PMID:27289101

  3. Plastic fantastic: phenotypic plasticity, evolution, and adaptation of marine picoplankton in response to elevated pCO2

    Schaum, Charlotte Elisa Luise

    2014-01-01

    Small but mighty phytoplankton can be used as excellent model organisms to answer questions that are of importance to marine biologists and researchers in experimental evolution alike. For example, marine biologists are interested in finding out, how, in a changing ocean, the phytoplankton foundation of the ocean ecosystem is going to change - can we use short-term data to extrapolate to longer timescales? What are the physiological consequences of selection in stable and fluct...

  4. Identifying Interactions that Determine Fragment Binding at Protein Hotspots.

    Radoux, Chris J; Olsson, Tjelvar S G; Pitt, Will R; Groom, Colin R; Blundell, Tom L

    2016-05-12

    Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project. PMID:27043011

  5. HIV protein sequence hotspots for crosstalk with host hub proteins.

    Mahdi Sarmady

    Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

  6. Distribution, congruence, and hotspots of higher plants in China

    Zhao, Lina; Li, Jinya; Liu, Huiyuan; Qin, Haining

    2016-01-01

    Identifying biodiversity hotspots has become a central issue in setting up priority protection areas, especially as financial resources for biological diversity conservation are limited. Taking China’s Higher Plants Red List (CHPRL), including Bryophytes, Ferns, Gymnosperms, Angiosperms, as the data source, we analyzed the geographic patterns of species richness, endemism, and endangerment via data processing at a fine grid-scale with an average edge length of 30 km based on three aspects of richness information: species richness, endemic species richness, and threatened species richness. We sought to test the accuracy of hotspots used in identifying conservation priorities with regard to higher plants. Next, we tested the congruence of the three aspects and made a comparison of the similarities and differences between the hotspots described in this paper and those in previous studies. We found that over 90% of threatened species in China are concentrated. While a high spatial congruence is observed among the three measures, there is a low congruence between two different sets of hotspots. Our results suggest that biodiversity information should be considered when identifying biological hotspots. Other factors, such as scales, should be included as well to develop biodiversity conservation plans in accordance with the region’s specific conditions.

  7. Constraining nitrogen cycling hotspots in contaminated aquifers

    Wells, Naomi; Knoeller, Kay

    2014-05-01

    Accurate assessments of the fate of inorganic nitrogen (N) in groundwater are needed in order to mitigate the threat that ammonium (NH4+) and nitrate (NO3-) pose to water quality and the long-term health of down-gradient ecosystems. However, such assessments are currently limited by difficulties in measuring the biological attenuation (via either denitrification or anaerobic ammonia oxidation (anammox)) of these reactive species in-situ. Based on the knowledge that both of these processes can create unique fractionation patterns in the residual N pools, the objective of this research was to build a template for identifying and quantifying N removal hotspots within complex aquifers using isofluxes. The variations in concentration and isotopic abundance of multiple dissolved inorganic N species (δ15N of NH4+, and δ15N and δ18O of NO2- and NO3-) were measured in 100 wells across two contaminated megasites in Western Europe. The sampling locations were selected span the NH4+ (the dominant N form in both sites) concentration gradient (0 to 900 mg NH4+-N l-1) over depth and distance, which coincided with gradients in co-contaminants BTEX and sulphate of 0 to 5 mg l-1 4 to 11000 mg l-1, respectively. Although NO2- is a key component of both anaerobic and aerobic ammonium oxidation, it is rarely detected in groundwater. Yet, by analysing for it on-site, we found that NO2- concentrations reached up to 0.7 mg NO2-N l-1 and had a highly sensitive isotopic composition (mean of -5 ±23o (δ15N) and +11 ±12o (δ18O)). The largest NO2- concentrations coincided with those of NH4+ levels, meaning that attenuation fluxes could be partitioned between anammox and denitrification using simple isotope mass balance calculations based on Rayleigh type isotope fractionation and established nitrate (δ15N and δ18O) isotope dynamics during denitrification. The constraints on N attenuation within these complex hydrological and chemical setting created by overlaying isoflux maps for each

  8. Evolution of acoustic communication in crickets: phylogeny of Eneopterinae reveals an adaptive radiation involving high-frequency calling (Orthoptera, Grylloidea, Eneopteridae

    Robillard Tony

    2004-01-01

    Full Text Available Evolution of dominant frequencies in songs of Eneopterinae crickets was studied with respect to phylogeny. Two characters are optimized on the tree: the first describes the frequency resulting from the vibration of the harp (Fda, and the second is due to the vibration of other tegminal areas (Fdb. Fda was found to be relatively stable through the subfamily. Its low ancestral state is replaced by a high Fda only once, resulting in high-frequency calling in [Cardiodactylus (Lebinthus-Agnotecous]. A high Fdb component is added to the low ancestral Fda in Eneoptera guyanensis, resulting in frequency modulation. The onset of high Fd in this first subclade is accompanied by a high cladogenesis rate, which supports a hypothesis of adaptive radiation for high frequencies. The effectiveness of high-frequency calling is discussed in relation to the species behavior ecology.

  9. Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

    LaCroix, Ryan A.; Sandberg, Troy E.; O'Brien, Edward J.;

    2015-01-01

    Adaptive laboratory evolution (ALE) has emerged as an effective tool for scientific discovery and addressing biotechnological needs. Much of ALE's utility is derived from reproducibly obtained fitness increases. Identifying causal genetic changes and their combinatorial effects is challenging and...... exponential growth, fitness increases up to 1.6-fold were obtained compared to the wild type. These increases are comparable to previously reported maximum growth rates in similar conditions but were obtained over a shorter time frame. Across the eight replicate ALE experiments performed, causal mutations...... were identified using three approaches: identifying mutations in the same gene/region across replicate experiments, sequencing strains before and after computationally determined fitness jumps, and allelic replacement coupled with targeted ALE of reconstructed strains. Three genetic regions were most...

  10. Adaptation of the Institutions to the Social demands: The evolution of the regulator's role in the radioactive waste management

    Institutions involved in the long-term management of radioactive waste are facing a rapidly evolving environment stemming from the ongoing societal changes. As in many other environmental areas, a demand for higher public participation in the decision making process leads to a need for analysing its implications and reviewing the role of the different stakeholders in order to respond to the new social challenges. This article offers a general overview on the institutions adaptation needs, and trends and, in particular, on the evolving role of the safety regulatory authorities, mainly based on the lessons learnt within the Forum on Stakeholder Confidence (FSC). (Author) 19 refs

  11. Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

    Sandberg, Troy E.; Pedersen, Margit; LaCroix, Ryan A.;

    2014-01-01

    conditions allowed selection based on exponential-phase growth rate, yielding strains that uniformly converged toward a similar phenotype along distinct genetic paths. Adapted strains possessed as few as 6 and as many as 55 mutations, and of the 144 genes that mutated in total, 14 arose independently across...... general feature of ALE experiments. The widespread evolved expression shifts were enabled by a comparatively scant number of regulatory mutations, providing a net fitness benefit but causing suboptimal expression levels for certain genes, such as those governing flagellar formation, which then became...

  12. A new ensemble algorithm of differential evolution and backtracking search optimization algorithm with adaptive control parameter for function optimization

    Sukanta Nama

    2016-04-01

    Full Text Available Differential evolution (DE is an effective and powerful approach and it has been widely used in different environments. However, the performance of DE is sensitive to the choice of control parameters. Thus, to obtain optimal performance, time-consuming parameter tuning is necessary. Backtracking Search Optimization Algorithm (BSA is a new evolutionary algorithm (EA for solving real-valued numerical optimization problems. An ensemble algorithm called E-BSADE is proposed which incorporates concepts from DE and BSA. The performance of E-BSADE is evaluated on several benchmark functions and is compared with basic DE, BSA and conventional DE mutation strategy.

  13. Animal evolution and atmospheric pO2: is there a link between gradual animal adaptation to terrain elevation due to Ural orogeny and survival of subsequent hypoxic periods?

    Kurbel, Sven

    2014-01-01

    Considering evolution of terrestrial animals as something happening only on flat continental plains seems wrong. Many mountains have arisen and disappeared over the geologic time scale, so in all periods some areas of high altitude existed, with reduced oxygen pressure (pO2) and increased aridity. During orogeny, animal species of the raising terrain can slowly adapt to reduced oxygen levels. This review proposes that animal evolution was often driven by atmospheric oxygen availability. Trans...

  14. Per arborem ad astra: morphological adaptations to exploiting the woody habitat in the early evolution of Hymenoptera.

    Vilhelmsen, Lars; Turrisi, Giuseppe Fabrizio

    2011-01-01

    We survey morphological features of larval and adult wasps that undergo their entire larval development inside wood and interpret them in view of the lifestyle. The evolution of some of the characters is explored by mapping them on a recently published phylogeny of Hymenoptera. Based on this phylogeny, it is reasonable to assume that wood-living wasps evolved from a xylophagous/mycetophagous stage as displayed by woodwasps to a carnivorous/parasitoid lifestyle, preying on woodboring insect larvae. The latter mode of life is probably ancestral to the Apocrita which comprise the majority of the order; they share this lifestyle with their sister group, the Orussidae. However, most apocritan wasps have radiated into other habitats, the Orussidae and Stephanidae apparently being the only taxa that have retained the ancestral lifestyle of carnivorous wasps. Other apocritan lineages associated with wood (e.g., Aulacidae, Megalyridae, basal Cynipoidea and some Ichneumonoidea and Chalcidoidea) possibly entered this habitat secondarily and independently acquired morphological traits associated with it. The woody habitat was occupied by Hymenoptera during a crucial stage in their evolution where the transition from the phytophagous to carnivorous lifestyle took place. The anatomy of both larva and adults was extensively transformed in the process. PMID:20951828

  15. Macroscopic hotspots identification: A Bayesian spatio-temporal interaction approach.

    Dong, Ni; Huang, Helai; Lee, Jaeyoung; Gao, Mingyun; Abdel-Aty, Mohamed

    2016-07-01

    This study proposes a Bayesian spatio-temporal interaction approach for hotspot identification by applying the full Bayesian (FB) technique in the context of macroscopic safety analysis. Compared with the emerging Bayesian spatial and temporal approach, the Bayesian spatio-temporal interaction model contributes to a detailed understanding of differential trends through analyzing and mapping probabilities of area-specific crash trends as differing from the mean trend and highlights specific locations where crash occurrence is deteriorating or improving over time. With traffic analysis zones (TAZs) crash data collected in Florida, an empirical analysis was conducted to evaluate the following three approaches for hotspot identification: FB ranking using a Poisson-lognormal (PLN) model, FB ranking using a Bayesian spatial and temporal (B-ST) model and FB ranking using a Bayesian spatio-temporal interaction (B-ST-I) model. The results show that (a) the models accounting for space-time effects perform better in safety ranking than does the PLN model, and (b) the FB approach using the B-ST-I model significantly outperforms the B-ST approach in correctly identifying hotspots by explicitly accounting for the space-time variation in addition to the stable spatial/temporal patterns of crash occurrence. In practice, the B-ST-I approach plays key roles in addressing two issues: (a) how the identified hotspots have evolved over time and (b) the identification of areas that, whilst not yet hotspots, show a tendency to become hotspots. Finally, it can provide guidance to policy decision makers to efficiently improve zonal-level safety. PMID:27110645

  16. Molecular evolution of hepatitis A virus in a human diploid cell line

    Cai-Hua Tang; Jiang-Sen Mao; Shao-Ai Chai; Yong Chen; Fang-Cheng Zhuang

    2007-01-01

    AIM: To investigate the hotspots, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells.METHODS: Wild type hepatitis A virus H2w was serially propagated in KMB17 cells until passage 30, and the full-length genomes of H2w and its six chosen progenies were determined by directly sequencing RT-PCR products amplified from viral genomic RNA. Alignment comparison of sequences from H2w with its six progenies and phylogenetic analysis of the whole VP1 region from H2w, progenies of H2w, and other cell culture adapted hepatitis A virus were then carried out to obtain data on the molecular evolution of hepatitis A virus in the process of consecutive passage in KMB17 cells.RESULTS: Most of the mutations occurred by passage 5 and several hotspots related to adaptation of the virus during cell growth were observed. After that stage, few additional mutations occurred through the remaining duration of passage in KMB17 cells except for mutation in the virulence determinants, which occurred in the vicinity of passage 15. The phylogenetic analysis of the whole VP1 region suggested that the progenies of H2w evolved closely to other cell culture adapted hepatitis A virus, i.e. MBB, L-A-1, other than its progenitor H2w.CONCLUSION: Hepatitis A virus served as a useful model for studying molecular evolution of viruses in a given environment. The information obtained in this study may provide assistance in cultivating the next generation of a seed virus for live hepatitis A vaccine production.

  17. Some Hotspots Concerned with Smart Grid

    Wang

    2010-01-01

    The smart grid has been such a hot topic recently. In this paper the hot topics in this field, such as the definition and features of smart grid, key technical problems to be addressed such as new system components, new types of transducers and measurement technologies, advanced interfaces, event-driven fast-simulated decision-making and coordination, and adaptive control, etc., and difficulties are analyzed and discussed.

  18. Reconstruction of the most recent common ancestor sequences of SARS-Cov S gene and detection of adaptive evolution in the spike protein

    ZHANG Yuan; ZHENG Nan; HAO Pei; ZHONG Yang

    2004-01-01

    @@ The genome organization and expression strategy of severe acute respiratory syndrome coronavirus (SARSCoV) have been described extensivelyl1- 10]. As a structural glycoprotein on the virion surface, the spike protein is responsible for binding to host cellular receptors and for the fusion between the viral envelope and the cellular membrane. It also induces neutralizing antibodies in the host and mediates cellular immunity[11]. Previous studies suggested that amino acid replacements in the spike protein could dramatically alter the pathogenesis and virulence of some coronaviruses[11]. It is therefore reasonable to test the hypothesis that radical amino acid replacements in the spike protein, favored by environmental selective pressure during the process of SARS-CoV interspecific transmission[10], might make this pathogen adapt to a new host. In this study, we investigated a total of 108complete sequences of the SARS-CoV S gene from GenBank (until March 23, 2004). After omission of those records containing frame-shift mutations or low quality sequences, e.g. ZJ01, and selection of one sequence for identical records, an alignment of 42 sequences was obtained using the program Clustal-X[13]. Then, we reconstructed the most recent common ancestor (MRCA) sequences of the SARS-CoV S gene and detected the adaptive evolution in the spike protein.

  19. Enhanced Acid Tolerance in Bifidobacterium longum by Adaptive Evolution: Comparison of the Genes between the Acid-Resistant Variant and Wild-Type Strain.

    Jiang, Yunyun; Ren, Fazheng; Liu, Songling; Zhao, Liang; Guo, Huiyuan; Hou, Caiyun

    2016-03-28

    Acid stress can affect the viability of probiotics, especially Bifidobacterium. This study aimed to improve the acid tolerance of Bifidobacterium longum BBMN68 using adaptive evolution. The stress response, and genomic differences of the parental strain and the variant strain were compared by acid stress. The highest acid-resistant mutant strain (BBMN68m) was isolated from more than 100 asexual lines, which were adaptive to the acid stress for 10(th), 20(th), 30(th), 40(th), and 50(th) repeats, respectively. The variant strain showed a significant increase in acid tolerance under conditions of pH 2.5 for 2 h (from 7.92 to 4.44 log CFU/ml) compared with the wildtype strain (WT, from 7.87 to 0 log CFU/ml). The surface of the variant strain was also smoother. Comparative whole-genome analysis showed that the galactosyl transferase D gene (cpsD, bbmn68_1012), a key gene involved in exopolysaccharide (EPS) synthesis, was altered by two nucleotides in the mutant, causing alteration in amino acids, pI (from 8.94 to 9.19), and predicted protein structure. Meanwhile, cpsD expression and EPS production were also reduced in the variant strain (p < 0.05) compared with WT, and the exogenous WT-EPS in the variant strain reduced its acid-resistant ability. These results suggested EPS was related to acid responses of BBMN68. PMID:26608165

  20. A comparison of the Covariance Matrix Adaptation Evolution Strategy and the Levenberg-Marquardt method for solving multidimensional inverse transport problems

    The Covariance Matrix Adaptation Evolution Strategy (CMA-ES), a powerful optimization algorithm that mimics the process of evolution in nature, is applied to the inverse transport problems of interface location identification, source composition identification, and material mass density identification (both separately and combined) in cylindrical radioactive source/shield systems. The energies of discrete gamma-ray lines emitted by the source are assumed to be known, while the uncollided line fluxes are assumed to be measured at points external to the system. CMA-ES is compared to the Levenberg-Marquardt method, a standard gradient-based optimization algorithm, on numerical test cases using both simulated data that is perfectly consistent with the optimization process and with realistic data simulated by Monte Carlo. Numerical results indicate that the Levenberg-Marquardt method is more adept at problems with few unknowns (i.e. ≤3), but as the number of unknowns increases, CMA-ES becomes the superior strategy. Results also indicate that a parallel version of CMA-ES would be more robust than, and have competitive run times with, the Levenberg-Marquardt method for many inverse transport problems.

  1. Electric and magnetic hotspots in dielectric nanowire dimers.

    Mirzaei, Ali; Miroshnichenko, Andrey E

    2015-04-14

    We study the formation of the electric and magnetic near-field hotspots in dielectric cylindrical dimers. We compare dielectric and metallic dimers by using experimental data for all materials and consider both TM and TE polarizations of light. We demonstrate that dielectric dimers allow us to simultaneously achieve pure magnetic and electric near-field hotspots for both polarizations in contrast to plasmonic structures. This offers new approaches for near-field engineering such as sensing, control of spontaneous emission, and enhanced Raman scattering. PMID:25773044

  2. Energy efficient hotspot-targeted embedded liquid cooling of electronics

    Highlights: • We present a novel concept for hotspot-targeted, energy efficient ELC for electronic chips. • Microchannel throttling zones distribute flow optimally without any external control. • Design is optimized for highly non-uniform multicore chip heat flux maps. • Optimized design minimizes chip temperature non-uniformity. • This is achieved with pumping power consumption less than 1% of total chip power. - Abstract: Large data centers today already account for nearly 1.31% of total electricity consumption with cooling responsible for roughly 33% of that energy consumption. This energy intensive cooling problem is exacerbated by the presence of hotspots in multicore microprocessors due to excess coolant flow requirement for thermal management. Here we present a novel liquid-cooling concept, for targeted, energy efficient cooling of hotspots through passively optimized microchannel structures etched into the backside of a chip (embedded liquid cooling or ELC architecture). We adopt an experimentally validated and computationally efficient modeling approach to predict the performance of our hotspot-targeted ELC design. The design is optimized for exemplar non-uniform chip power maps using Response Surface Methodology (RSM). For industrially acceptable limits of approximately 0.4 bar (40 kPa) on pressure drop and one percent of total chip power on pumping power, the optimized designs are computationally evaluated against a base, standard ELC design with uniform channel widths and uniform flow distribution. For an average steady-state heat flux of 150 W/cm2 in core areas (hotspots) and 20 W/cm2 over remaining chip area (background), the optimized design reduces the maximum chip temperature non-uniformity by 61% to 3.7 °C. For a higher average, steady-state hotspot heat flux of 300 W/cm2, the maximum temperature non-uniformity is reduced by 54% to 8.7 °C. It is shown that the base design requires a prohibitively high level of pumping power (about 2000

  3. The complex evolutionary history of seeing red: molecular phylogeny and the evolution of an adaptive visual system in deep-sea dragonfishes (Stomiiformes: Stomiidae).

    Kenaley, Christopher P; Devaney, Shannon C; Fjeran, Taylor T

    2014-04-01

    The vast majority of deep-sea fishes have retinas composed of only rod cells sensitive to only shortwave blue light, approximately 480-490 nm. A group of deep-sea dragonfishes, the loosejaws (family Stomiidae), possesses far-red emitting photophores and rhodopsins sensitive to long-wave emissions greater than 650 nm. In this study, the rhodopsin diversity within the Stomiidae is surveyed based on an analysis of rod opsin-coding sequences from representatives of 23 of the 28 genera. Using phylogenetic inference, fossil-calibrated estimates of divergence times, and a comparative approach scanning the stomiid phylogeny for shared genotypes and substitution histories, we explore the evolution and timing of spectral tuning in the family. Our results challenge both the monophyly of the family Stomiidae and the loosejaws. Despite paraphyly of the loosejaws, we infer for the first time that far-red visual systems have a single evolutionary origin within the family and that this shift in phenotype occurred at approximately 15.4 Ma. In addition, we found strong evidence that at approximately 11.2 Ma the most recent common ancestor of two dragonfish genera reverted to a primitive shortwave visual system during its evolution from a far-red sensitive dragonfish. According to branch-site tests for adaptive evolution, we hypothesize that positive selection may be driving spectral tuning in the Stomiidae. These results indicate that the evolutionary history of visual systems in deep-sea species is complex and a more thorough understanding of this system requires an integrative comparative approach. PMID:24274363

  4. Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum.

    Sarah Green

    Full Text Available A recently emerging bleeding canker disease, caused by Pseudomonas syringae pathovar aesculi (Pae, is threatening European horse chestnut in northwest Europe. Very little is known about the origin and biology of this new disease. We used the nucleotide sequences of seven commonly used marker genes to investigate the phylogeny of three strains isolated recently from bleeding stem cankers on European horse chestnut in Britain (E-Pae. On the basis of these sequences alone, the E-Pae strains were identical to the Pae type-strain (I-Pae, isolated from leaf spots on Indian horse chestnut in India in 1969. The phylogenetic analyses also showed that Pae belongs to a distinct clade of P. syringae pathovars adapted to woody hosts. We generated genome-wide Illumina sequence data from the three E-Pae strains and one strain of I-Pae. Comparative genomic analyses revealed pathovar-specific genomic regions in Pae potentially implicated in virulence on a tree host, including genes for the catabolism of plant-derived aromatic compounds and enterobactin synthesis. Several gene clusters displayed intra-pathovar variation, including those encoding type IV secretion, a novel fatty acid biosynthesis pathway and a sucrose uptake pathway. Rates of single nucleotide polymorphisms in the four Pae genomes indicate that the three E-Pae strains diverged from each other much more recently than they diverged from I-Pae. The very low genetic diversity among the three geographically distinct E-Pae strains suggests that they originate from a single, recent introduction into Britain, thus highlighting the serious environmental risks posed by the spread of an exotic plant pathogenic bacterium to a new geographic location. The genomic regions in Pae that are absent from other P. syringae pathovars that infect herbaceous hosts may represent candidate genetic adaptations to infection of the woody parts of the tree.

  5. Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum.

    Green, Sarah; Studholme, David J; Laue, Bridget E; Dorati, Federico; Lovell, Helen; Arnold, Dawn; Cottrell, Joan E; Bridgett, Stephen; Blaxter, Mark; Huitema, Edgar; Thwaites, Richard; Sharp, Paul M; Jackson, Robert W; Kamoun, Sophien

    2010-01-01

    A recently emerging bleeding canker disease, caused by Pseudomonas syringae pathovar aesculi (Pae), is threatening European horse chestnut in northwest Europe. Very little is known about the origin and biology of this new disease. We used the nucleotide sequences of seven commonly used marker genes to investigate the phylogeny of three strains isolated recently from bleeding stem cankers on European horse chestnut in Britain (E-Pae). On the basis of these sequences alone, the E-Pae strains were identical to the Pae type-strain (I-Pae), isolated from leaf spots on Indian horse chestnut in India in 1969. The phylogenetic analyses also showed that Pae belongs to a distinct clade of P. syringae pathovars adapted to woody hosts. We generated genome-wide Illumina sequence data from the three E-Pae strains and one strain of I-Pae. Comparative genomic analyses revealed pathovar-specific genomic regions in Pae potentially implicated in virulence on a tree host, including genes for the catabolism of plant-derived aromatic compounds and enterobactin synthesis. Several gene clusters displayed intra-pathovar variation, including those encoding type IV secretion, a novel fatty acid biosynthesis pathway and a sucrose uptake pathway. Rates of single nucleotide polymorphisms in the four Pae genomes indicate that the three E-Pae strains diverged from each other much more recently than they diverged from I-Pae. The very low genetic diversity among the three geographically distinct E-Pae strains suggests that they originate from a single, recent introduction into Britain, thus highlighting the serious environmental risks posed by the spread of an exotic plant pathogenic bacterium to a new geographic location. The genomic regions in Pae that are absent from other P. syringae pathovars that infect herbaceous hosts may represent candidate genetic adaptations to infection of the woody parts of the tree. PMID:20419105

  6. Evolution of complex life cycles in trophically transmitted helminths. II. How do life-history stages adapt to their hosts?

    Parker, G A; Ball, M A; Chubb, J C

    2015-02-01

    We review how trophically transmitted helminths adapt to the special problems associated with successive hosts in complex cycles. In intermediate hosts, larvae typically show growth arrest at larval maturity (GALM). Theoretical models indicate that optimization of size at GALM requires larval mortality rate to increase with time between infection and GALM: low larval growth or paratenicity (no growth) arises from unfavourable growth and mortality rates in the intermediate host and low transmission rates to the definitive host. Reverse conditions favour high GALM size or continuous growth. Some support is found for these predictions. Intermediate host manipulation involves predation suppression (which decreases host vulnerability before the larva can establish in its next host) and predation enhancement (which increases host vulnerability after the larva can establish in its next host). Switches between suppression and enhancement suggest adaptive manipulation. Manipulation conflicts can occur between larvae of different ages/species a host individual. Larvae must usually develop to GALM before becoming infective to the next host, possibly due to trade-offs, e.g. between growth/survival in the present host and infection ability for the next host. In definitive hosts, if mortality rate is constant, optimal growth before switching to reproduction is set by the growth/morality rate ratio. Rarely, no growth occurs in definitive hosts, predicted (with empirical support) when larval size on infection exceeds growth/mortality rate. Tissue migration patterns and residence sites may be explained by variations in growth/mortality rates between host gut and soma, migration costs and benefits of releasing eggs in the gut. PMID:25645609

  7. Perception Evolution Network Based on Cognition Deepening Model-Adapting to the Emergence of New Sensory Receptor.

    Xing, Youlu; Shen, Furao; Zhao, Jinxi

    2016-03-01

    The proposed perception evolution network (PEN) is a biologically inspired neural network model for unsupervised learning and online incremental learning. It is able to automatically learn suitable prototypes from learning data in an incremental way, and it does not require the predefined prototype number or the predefined similarity threshold. Meanwhile, being more advanced than the existing unsupervised neural network model, PEN permits the emergence of a new dimension of perception in the perception field of the network. When a new dimension of perception is introduced, PEN is able to integrate the new dimensional sensory inputs with the learned prototypes, i.e., the prototypes are mapped to a high-dimensional space, which consists of both the original dimension and the new dimension of the sensory inputs. In the experiment, artificial data and real-world data are used to test the proposed PEN, and the results show that PEN can work effectively. PMID:25935048

  8. Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup

    Yu, Xiao-Jing; Zheng, Hong-Kun; Wang, Jun;

    2006-01-01

    Comparative genetic analysis between human and chimpanzee may detect genetic divergences responsible for human-specific characteristics. Previous studies have identified a series of genes that potentially underwent Darwinian positive selection during human evolution. However, without a closely...... related species as outgroup, it is difficult to identify human-lineage-specific changes, which is critical in delineating the biological uniqueness of humans. In this study, we conducted phylogeny-based analyses of 2633 human brain-expressed genes using rhesus macaque as the outgroup. We identified 47...... candidate genes showing strong evidence of positive selection in the human lineage. Genes with maximal expression in the brain showed a higher evolutionary rate in human than in chimpanzee. We observed that many immune-defense-related genes were under strong positive selection, and this trend was more...

  9. Experimental Investigations of current sheet and hotspots in pinch phase in a low energy Plasma Focus

    A low energy Mather type plasma focus device 4 KJ(140 KA, t/4 ∼ 2μs) has been developed and characterized for Hydrogen and Argon gas mixtures. The evolution of the sheet current and the presence of hot-spots in the pinch phase has been studied. A novel, non invasive diagnostic procedure to study the current sheet has been developed. As a result of these studies, a mean velocity value corresponding to 6.2 cm/μs was obtained. An array of filtered p-i-n diodes (BPX-65) located side and end-on is used in conjunction with a multipinhole and slit-wire X-ray camera. X-ray images were recorded on Ilford HP5 film using a modified Nikonos underwater camera for vacuum tightness. Similar filter combinations were used with the p-i-n diodes and the pinhole slit-wire camera. Axial electron beams were measured with a beam-target scintillator detector. Characteristic positions (6 to 13 mm of the anode), sizes (120 μm) and temperatures (300 eV) of hot-spots formed in the pinched column, were measured. Typical measured durations for the high temperature phase were of the order of 10 ns (au)

  10. Efficient Assessment of Social Hotspots in the Supply Chains of 100 Product Categories Using the Social Hotspots Database

    Catherine Benoît Norris

    2014-10-01

    Full Text Available Data collection, or the inventory step, is often the most labor-intensive phase of any Life Cycle Assessment (LCA study. The S-LCA Guidelines and numerous authors have recommended generic assessment in this first phase of an S-LCA. In an effort to identify the social hotspots in the supply chains of 100 product categories during just a few months’ time, adopting a streamlined approach was essential. The Social Hotspots Database system was developed by New Earth over 5 years. It includes a Global Input Output (IO model derived from the Global Trade Analysis Project, a Worker Hours Model constructed using annual wage payments and wage rates by country and sector, and Social Theme Tables covering 22 themes within five Social Impact Categories—Labor Rights and Decent Work, Health and Safety, Human Rights, Governance and Community Impacts. The data tables identify social risks for over 100 indicators. Both the ranking of worker hour intensity and the risk levels across multiple social themes for the Country Specific Sectors (CSS within a product category supply chain are used to calculate Social Hotspots Indexes (SHI using an additive weighting method. The CSS with the highest SHI are highlighted as social hotspots within the supply chain of the product in question. This system was tested in seven case studies in 2011. In order to further limit the number of hotspots, a set of prioritization rules was applied. This paper will review the method implemented to study the social hotspots of the 100 product categories and provide one detailed example. Limitations of the approach and recommended research avenues will be outlined.

  11. Geologic evidence of hotspot activity of Venus - Predictions for Magellan

    Stofan, Ellen R.; Saunders, R. Stephen

    1990-01-01

    A number of distinctive types of geologic features have been identified on Venus that are interpreted to be related to thermal plumes including domal rises, coronae, and major composite shield volcanoes. The basic characteristics of these features as well as their distribution are documented. The three types of features have related morphologies and are interpreted to represent a continuum of features formed by mantle plumes at scales from 100s to over 1000 km. The Artemis structure, located in Aphrodite Terra, is proposed to be a large corona. If crustal spreading processes are operating on Venus, hotspot features should form chains on the surface as seen in terrestrial ocean basins. On the basis of current data on hotspot-related feature distribution on Venus, no clear evidence exists for hotspot chains. The complete distribution of hotspot features in Magellan data will be used to understand better the relationship between interior processes and surface features, as well as to provide a test for the crustal spreading hypothesis.

  12. European hotspots as evidenced by the Palearctic distribution of songbirds

    R. Sluys; M. Aliabadian; C.S. Roselaar

    2011-01-01

    A database has been created of digitized equal area distribution maps of 2,401 phylogenetic species of songbirds endemic to the Palearctic Region. Geographic distribution of species richness delineated several hotspot regions in the Palearctic, mostly located in mountainous areas. The index of range

  13. Convergent evolution of ecomorphological adaptations in geographically isolated Bay gobies (Teleostei: Gobionellidae) of the temperate North Pacific.

    Ellingson, Ryan A; Swift, Camm C; Findley, Lloyd T; Jacobs, David K

    2014-01-01

    North Pacific Bay gobies (Teleostei: Gobioidei: Gobionellidae) inhabit bays, beaches, coastal lagoons, and estuaries of temperate Asia and North America, but are absent from the boreal northernmost Pacific. Previously, morphological characters conventionally subdivided the clade into two groups - an elongate-bodied, infaunal-inhabiting "Astrabe" group, and a deeper-bodied, non-infaunal "Chasmichthys" group - each with a disjunct East-West (amphi-) Pacific distribution. Here we use mitochondrial and multi-locus nuclear DNA sequence data to show that several morphological characters previously used to delimit these two groups have in fact arisen independently on both sides of the Pacific, revealing convergence of ecologically adaptive characters within a geographically divided clade. Basal divergence of the resultant tree coincides with a dramatic global cooling event at the Eocene/Oligocene transition, without evidence of subsequent trans-Pacific migration. A novel approach to partitioning sequence data by relative rate, as opposed to traditional gene/codon position partitioning, was used to help distinguish phylogenetic signal from noise on a per-site basis. Resulting improvements in topology and nodal support, along with decreased computational effort, suggest that this partitioning strategy may be useful for future studies in phylogenetics and phylogenomics. PMID:24148989

  14. A striking parallel between cardiolipin fatty acid composition and phylogenetic belonging in marine bivalves: a possible adaptative evolution?

    Kraffe, E; Grall, J; Le Duff, M; Soudant, P; Marty, Y

    2008-10-01

    Thirty-five species of marine mollusk bivalves were analyzed for their fatty acid (FA) composition of cardiolipin (Ptd(2)Gro). All species showed a Ptd(2)Gro with strong selectivity for only a few polyunsaturated fatty acids, but three characteristic FA profiles emerged, with clear parallels to bivalve phylogeny. A first group of 12 species belonging to the Eupteriomorphia subgroup (Filibranchia) was characterized by a Ptd(2)Gro almost exclusively composed of 22:6n-3, whereas in the four Filibranchia Pteriomorph species analyzed, this FA was combined with substantial proportions of 18:2n-6 and 18:3n-3. Finally, a third group of 20 species, all belonging to the Heterodonta subclass, possessed Ptd(2)Gro containing predominantly both 22:6n-3 and 20:5n-3. Polyunsaturated FA moieties and arrangements in the Ptd(2)Gro of some marine species investigated in other classes of the mollusk phylum (Gastropoda, Polyplacophora) were found to be different. The present results suggest that the specific Ptd(2)Gro FA compositions in bivalves are likely to be controlled and conserved in species of the same phylogenetic group. Functional significances of the evolution of this mitochondrial lipid structure in bivalves are discussed. PMID:18716818

  15. The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires.

    Ceapa, Corina; Davids, Mark; Ritari, Jarmo; Lambert, Jolanda; Wels, Michiel; Douillard, François P; Smokvina, Tamara; de Vos, Willem M; Knol, Jan; Kleerebezem, Michiel

    2016-01-01

    Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification. PMID:27358423

  16. Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

    Stukenbrock, Eva H.; Jørgensen, Frank G.; Zala, Marcello; Hansen, Troels T.; McDonald, Bruce A.; Schierup, Mikkel H.

    2010-01-01

    The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000–12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was accompanied by structural

  17. Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola.

    Eva H Stukenbrock

    Full Text Available The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000-12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was

  18. Adaptive noise

    Viney, Mark; Reece, Sarah E.

    2013-01-01

    In biology, noise implies error and disorder and is therefore something which organisms may seek to minimize and mitigate against. We argue that such noise can be adaptive. Recent studies have shown that gene expression can be noisy, noise can be genetically controlled, genes and gene networks vary in how noisy they are and noise generates phenotypic differences among genetically identical cells. Such phenotypic differences can have fitness benefits, suggesting that evolution can shape noise ...

  19. Short Inverted Repeats Are Hotspots for Genetic Instability: Relevance to Cancer Genomes

    Steve Lu

    2015-03-01

    Full Text Available Analyses of chromosomal aberrations in human genetic disorders have revealed that inverted repeat sequences (IRs often co-localize with endogenous chromosomal instability and breakage hotspots. Approximately 80% of all IRs in the human genome are short (<100 bp, yet the mutagenic potential of such short cruciform-forming sequences has not been characterized. Here, we find that short IRs are enriched at translocation breakpoints in human cancer and stimulate the formation of DNA double-strand breaks (DSBs and deletions in mammalian and yeast cells. We provide evidence for replication-related mechanisms of IR-induced genetic instability and a novel XPF cleavage-based mechanism independent of DNA replication. These discoveries implicate short IRs as endogenous sources of DNA breakage involved in disease etiology and suggest that these repeats represent a feature of genome plasticity that may contribute to the evolution of the human genome by providing a means for diversity within the population.

  20. Spatial Distribution of Volcanic Hotspots and Paterae on Io: Implications for Tidal Heating Models and Magmatic Pathways

    Hamilton, C. W.; Beggan, C. D.; Lopes, R.; Williams, D. A.; Radenbaugh, J.

    2011-01-01

    Io, the innermost of Jupiter's Galilean satellites, is the most volcanically active body in the Solar. System. Io's global mean heat flow is approximately 2 W/square m, which is approximately 20 times larger than on Earth. High surface temperatures concentrate within "hotspots" and, to date, 172 Ionian hotspots have been identified by spacecraft and Earth-based telescopes. The Laplace resonance between Io, Europa, and Ganymede maintains these satellites in noncircular orbits and causes displacement of their tidal bulges as the overhead position of Jupiter changes for each moon. Gravitational interactions between Jupiter and Io dominate the orbital evolution of the Laplacian system and generate enormous heat within to as tidal energy is dissipated. If this energy were transferred out of Io at the same rate as it is generated, then the associated surface heat flux would be 2.24 +/- 0.45 W/square m. This estimate is in good agreement with observed global heat flow, but to better constrain tidal dissipation mechanisms and infer how thermal energy is transferred to Io's surface, it is critical to closely examine the spatial distribution of volcanic features. End-member tidal dissipation models either consider that heating occurs completely in the mantle, or completely in the asthenosphere. Mixed models typically favor one-third mantle and two-thirds asthenosphere heating. Recent models also consider the effects of mantle-asthenosphere boundary permeability and asthenospheric instabilities. Deep-mantle heating models predict maximum surface heat flux near the poles, whereas asthenosphere heating models predict maxima near the equator-particularly in the Sub-Jovian and Anti-Jovian hemispheres, with smaller maxima occurring at orbit tangent longitudes. Previous studies have examined the global distribution of Ionian hotspots and patera (i.e., irregular or complex craters with scalloped edges that are generally interpreted to be volcanic calderas), but in this study, we

  1. Evolution of surface-based deformable image registration for adaptive radiotherapy of non-small cell lung cancer (NSCLC)

    To evaluate the performance of surface-based deformable image registration (DR) for adaptive radiotherapy of non-small cell lung cancer (NSCLC). Based on 13 patients with locally advanced NSCLC, CT images acquired at treatment planning, midway and the end of the radio- (n = 1) or radiochemotherapy (n = 12) course were used for evaluation of DR. All CT images were manually [gross tumor volume (GTV)] and automatically [organs-at-risk (OAR) lung, spinal cord, vertebral spine, trachea, aorta, outline] segmented. Contours were transformed into 3D meshes using the Pinnacle treatment planning system and corresponding mesh points defined control points for DR with interpolation within the structures. Using these deformation maps, follow-up CT images were transformed into the planning images and compared with the original planning CT images. A progressive tumor shrinkage was observed with median GTV volumes of 170 cm3 (range 42 cm3 - 353 cm3), 124 cm3 (19 cm3 - 325 cm3) and 100 cm3 (10 cm3 - 270 cm3) at treatment planning, mid-way and at the end of treatment. Without DR, correlation coefficients (CC) were 0.76 ± 0.11 and 0.74 ± 0.10 for comparison of the planning CT and the CT images acquired mid-way and at the end of treatment, respectively; DR significantly improved the CC to 0.88 ± 0.03 and 0.86 ± 0.05 (p = 0.001), respectively. With manual landmark registration as reference, DR reduced uncertainties on the GTV surface from 11.8 mm ± 5.1 mm to 2.9 mm ± 1.2 mm. Regarding the carina and intrapulmonary vessel bifurcations, DR reduced uncertainties by about 40% with residual errors of 4 mm to 6 mm on average. Severe deformation artefacts were observed in patients with resolving atelectasis and pleural effusion, in one patient, where the tumor was located around large bronchi and separate segmentation of the GTV and OARs was not possible, and in one patient, where no clear shrinkage but more a decay of the tumor was observed. The surface-based DR performed accurately

  2. Uncertainty based modeling of rainfall-runoff: Combined differential evolution adaptive Metropolis (DREAM) and K-means clustering

    Zahmatkesh, Zahra; Karamouz, Mohammad; Nazif, Sara

    2015-09-01

    Simulation of rainfall-runoff process in urban areas is of great importance considering the consequences and damages of extreme runoff events and floods. The first issue in flood hazard analysis is rainfall simulation. Large scale climate signals have been proved to be effective in rainfall simulation and prediction. In this study, an integrated scheme is developed for rainfall-runoff modeling considering different sources of uncertainty. This scheme includes three main steps of rainfall forecasting, rainfall-runoff simulation and future runoff prediction. In the first step, data driven models are developed and used to forecast rainfall using large scale climate signals as rainfall predictors. Due to high effect of different sources of uncertainty on the output of hydrologic models, in the second step uncertainty associated with input data, model parameters and model structure is incorporated in rainfall-runoff modeling and simulation. Three rainfall-runoff simulation models are developed for consideration of model conceptual (structural) uncertainty in real time runoff forecasting. To analyze the uncertainty of the model structure, streamflows generated by alternative rainfall-runoff models are combined, through developing a weighting method based on K-means clustering. Model parameters and input uncertainty are investigated using an adaptive Markov Chain Monte Carlo method. Finally, calibrated rainfall-runoff models are driven using the forecasted rainfall to predict future runoff for the watershed. The proposed scheme is employed in the case study of the Bronx River watershed, New York City. Results of uncertainty analysis of rainfall-runoff modeling reveal that simultaneous estimation of model parameters and input uncertainty significantly changes the probability distribution of the model parameters. It is also observed that by combining the outputs of the hydrological models using the proposed clustering scheme, the accuracy of runoff simulation in the

  3. Adaptive Coordinate Descent

    Loshchilov, Ilya; Schoenauer, Marc; Sebag, Michèle

    2011-01-01

    Independence from the coordinate system is one source of efficiency and robustness for the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). The recently proposed Adaptive Encoding (AE) procedure generalizes CMA-ES adaptive mechanism, and can be used together with any optimization algorithm. Adaptive Encoding gradually builds a transformation of the coordinate system such that the new coordinates are as decorrelated as possible with respect to the objective function. But any optimizat...

  4. 植物白花授粉的类型及其适应性进化%Categories and Adaptive Evolution of Plant Self - pollination

    杨期和; 杨和生; 李姣清

    2011-01-01

    综述了植物自花授粉的方式和类型,分析了白花授粉的生态适应性、可能的进化趋势及其影响因素.白花授粉是指两性花中雌雄蕊之间的授粉,通常也包括同株异花间的授粉.植物按授粉方式可分为自花授粉植物、异花授粉植物和常异花授粉植物3类.在自然界很少有绝对白花授粉的植物,都存在一定频率的异交,根据其自交发生的时间,可将自交分为3种方式:优先自交、竞争自交乖滞后自交.自交进化的假说主要集中在两个方面,即繁殖保障和自动选择优势,并已得到广泛的数据支持.分子生物学和生态学相结合的研究方法将进一步揭示植物自花授粉的形成与进化机制.%In this paper, the ways and categories are overviewed, and ecological adaptation and possible evolution- ary trends of plant self - pollination and their influencing factors are also analyzed. The self - pollination refers to the pollination between the pistil and stamen of the same bisexuanl flower, often including the pollination between different flowers in the same strain. Plants can be divided into 3 categories : self - pollinated plant, cross - pollina- ted plant, and often cross - pollinated plants according to pollinating ways. There is rarely absolute self - pollinated plants and is always a certain frequency of out - crossing in nature, so according to the time that the self - pollina- tion occurred, the selfing modes can be divided into three kinds : prior - selfing, competing selfing and delayed sel- ring. The self- evolution hypothesis focus on two aspects: reproduction assurance and automatic" selective advan- tage, and have been widely supported by ogy will further reveal the formation and data. The research methods of combination of molecular biology and ecol- evolution mechanism of plant self -pollination.

  5. An Effective Hybrid Self-Adapting Differential Evolution Algorithm for the Joint Replenishment and Location-Inventory Problem in a Three-Level Supply Chain

    Lin Wang

    2013-01-01

    Full Text Available The integration with different decisions in the supply chain is a trend, since it can avoid the suboptimal decisions. In this paper, we provide an effective intelligent algorithm for a modified joint replenishment and location-inventory problem (JR-LIP. The problem of the JR-LIP is to determine the reasonable number and location of distribution centers (DCs, the assignment policy of customers, and the replenishment policy of DCs such that the overall cost is minimized. However, due to the JR-LIP’s difficult mathematical properties, simple and effective solutions for this NP-hard problem have eluded researchers. To find an effective approach for the JR-LIP, a hybrid self-adapting differential evolution algorithm (HSDE is designed. To verify the effectiveness of the HSDE, two intelligent algorithms that have been proven to be effective algorithms for the similar problems named genetic algorithm (GA and hybrid DE (HDE are chosen to compare with it. Comparative results of benchmark functions and randomly generated JR-LIPs show that HSDE outperforms GA and HDE. Moreover, a sensitive analysis of cost parameters reveals the useful managerial insight. All comparative results show that HSDE is more stable and robust in handling this complex problem especially for the large-scale problem.

  6. Activation of glycerol metabolism in Xanthomonas campestris by adaptive evolution to produce a high-transparency and low-viscosity xanthan gum from glycerol.

    Wang, Zichao; Wu, Jianrong; Zhu, Li; Zhan, Xiaobei

    2016-07-01

    Many studies have focused on using crude glycerol from biodiesel to obtain valuable products, but few of these studies have focused on obtaining polysaccharides. A mutant strain of Xanthomonas campestris CCTCC M2015714 that could use glycerol to produce high-transparency and low-viscosity xanthan gum was obtained by adaptive evolution, and the yield of xanthan gum reached 11.0g/L. We found that transcriptional levels of genes related to glycerol metabolism (glpF, glpK, glpD, and fbp) in the mutant strain were all higher than those from the parent strain. Using 5g/L sucrose or glucose as starter substrate, cell growth time decreased from 36h to 24h and xanthan gum yield increased. Moreover, the mutant strain can tolerate high titer glycerol, and its activity was not affected by the impurities in crude glycerol. All these results proved that crude glycerol from biodiesel industries can be used for xanthan gum production. PMID:27030959

  7. Differential Adaptations of Methicillin-Resistant Staphylococcus aureus to Serial In Vitro Passage in Daptomycin: Evolution of Daptomycin Resistance and Role of Membrane Carotenoid Content and Fluidity

    Nagendra N. Mishra

    2012-01-01

    Full Text Available Previous studies showed serial 20 d in vitro passage of MRSA strain MW2 in sublethal daptomycin (DAP resulted in diverse perturbations in both cell membrane (CM and cell wall (CW characteristics, including increased CM rigidity; increased CW thickness; “gain-in-function” single nucleotide polymorphisms (SNPs in the mprF locus (i.e., increased synthesis and translocation of lysyl-phosphatidylglycerol (L-PG; progressive accumulation of SNPs in yyc and rpo locus genes; reduced carotenoid production; cross-resistance to innate host defense peptides. The current study was designed to characterize the reproducibility of these phenotypic and genotypic modifications following in vitro serial passages of the same parental strain. After a second 20d serial in vitro passage of parental MW2, emergence of DAP-R was associated with evolution of several phenotypes closely mirroring previous passage outcomes. However, in contrast to the initial serial passage strain set, we observed (i only modest increase in L-PG synthesis and no increase in L-PG outer CM translocation; (ii significantly increased carotenoid synthesis (P<0.05; (iii a different order of SNP accumulations (mprF≫rpoB≫yycG; (iv a different cadre and locations of such SNPs. Thus, MRSA strains are not “pre-programmed” to phenotypically and/or genotypically adapt in an identical manner during induction of DAP resistance.

  8. Adaptations to vision-for-action in primate brain evolution: Comment on "Towards a Computational Comparative Neuroprimatology: Framing the language-ready brain" by Michael A. Arbib

    Hecht, Erin

    2016-03-01

    As Arbib [1] notes, the two-streams hypothesis [5] has provided a powerful explanatory framework for understanding visual processing. The inferotemporal ventral stream recognizes objects and agents - "what" one is seeing. The dorsal "how" or "where" stream through parietal cortex processes motion, spatial location, and visuo-proprioceptive relationships - "vision for action." Hickock and Poeppel's [3] extension of this model to the auditory system raises the question of deeper, multi- or supra-sensory themes in dorsal vs. ventral processing. Petrides and Pandya [10] postulate that the evolution of language may have been influenced by the fact that the dorsal stream terminates in posterior Broca's area (BA44) while the ventral stream terminates in anterior Broca's area (BA45). In an intriguing potential parallel, a recent ALE metanalysis of 54 fMRI studies found that semantic processing is located more anteriorly and superiorly than syntactic processing in Broca's area [13]. But clearly, macaques do not have language, nor other likely pre- or co-adaptations to language, such as complex imitation and tool use. What changed in the brain that enabled these functions to evolve?

  9. Hotspots of biased nucleotide substitutions in human genes.

    Jonas Berglund

    2009-01-01

    Full Text Available Genes that have experienced accelerated evolutionary rates on the human lineage during recent evolution are candidates for involvement in human-specific adaptations. To determine the forces that cause increased evolutionary rates in certain genes, we analyzed alignments of 10,238 human genes to their orthologues in chimpanzee and macaque. Using a likelihood ratio test, we identified protein-coding sequences with an accelerated rate of base substitutions along the human lineage. Exons evolving at a fast rate in humans have a significant tendency to contain clusters of AT-to-GC (weak-to-strong biased substitutions. This pattern is also observed in noncoding sequence flanking rapidly evolving exons. Accelerated exons occur in regions with elevated male recombination rates and exhibit an excess of nonsynonymous substitutions relative to the genomic average. We next analyzed genes with significantly elevated ratios of nonsynonymous to synonymous rates of base substitution (dN/dS along the human lineage, and those with an excess of amino acid replacement substitutions relative to human polymorphism. These genes also show evidence of clusters of weak-to-strong biased substitutions. These findings indicate that a recombination-associated process, such as biased gene conversion (BGC, is driving fixation of GC alleles in the human genome. This process can lead to accelerated evolution in coding sequences and excess amino acid replacement substitutions, thereby generating significant results for tests of positive selection.

  10. The prevalence of toxic hotspots in former Soviet countries.

    Sharov, Petr; Dowling, Russell; Gogishvili, Megi; Jones, Barbara; Caravanos, Jack; McCartor, Andrew; Kashdan, Zachary; Fuller, Richard

    2016-04-01

    Using a global database of contaminated sites, toxic hotspots in eight former Soviet countries were analyzed to identify the prevalence, types and sources of toxic pollution, as well as their associated potential public health impacts. For this analysis, polluted sites in Armenia, Azerbaijan, Kazakhstan, Kyrgyzstan, Russia, Tajikistan, Ukraine, and Uzbekistan were compiled and analyzed. The levels of contamination of seven key pollutants were assessed in each country. 424 contaminated sites were identified using data from Blacksmith Institute. Pesticides, lead (Pb), radioactive metals, arsenic (As), mercury (Hg), chromium (Cr), and cadmium (Cd) were the most commonly identified key pollutants. Collectively, these sites pose health risks to an estimated 6.2 million residents. The existing data on toxic hotspots in former Soviet countries likely captures only a small percentage of actual contaminated sites, but suggests potentially severe public health consequences. Additional assessments are needed to understand the risks posed by toxic pollution in the region. PMID:26796744

  11. Recent hotspot volcanism on Venus from VIRTIS emissivity data.

    Smrekar, Suzanne E; Stofan, Ellen R; Mueller, Nils; Treiman, Allan; Elkins-Tanton, Linda; Helbert, Joern; Piccioni, Giuseppe; Drossart, Pierre

    2010-04-30

    The questions of whether Venus is geologically active and how the planet has resurfaced over the past billion years have major implications for interior dynamics and climate change. Nine "hotspots"--areas analogous to Hawaii, with volcanism, broad topographic rises, and large positive gravity anomalies suggesting mantle plumes at depth--have been identified as possibly active. This study used variations in the thermal emissivity of the surface observed by the Visible and Infrared Thermal Imaging Spectrometer on the European Space Agency's Venus Express spacecraft to identify compositional differences in lava flows at three hotspots. The anomalies are interpreted as a lack of surface weathering. We estimate the flows to be younger than 2.5 million years and probably much younger, about 250,000 years or less, indicating that Venus is actively resurfacing. PMID:20378775

  12. Detecting Hotspots from Taxi Trajectory Data Using Spatial Cluster Analysis

    Zhao, P. X.; Qin, K.; Zhou, Q.; Liu, C. K.; Chen, Y. X.

    2015-07-01

    A method of trajectory clustering based on decision graph and data field is proposed in this paper. The method utilizes data field to describe spatial distribution of trajectory points, and uses decision graph to discover cluster centres. It can automatically determine cluster parameters and is suitable to trajectory clustering. The method is applied to trajectory clustering on taxi trajectory data, which are on the holiday (May 1st, 2014), weekday (Wednesday, May 7th, 2014) and weekend (Saturday, May 10th, 2014) respectively, in Wuhan City, China. The hotspots in four hours (8:00-9:00, 12:00-13:00, 18:00-19:00 and 23:00-24:00) for three days are discovered and visualized in heat maps. In the future, we will further research the spatiotemporal distribution and laws of these hotspots, and use more data to carry out the experiments.

  13. Mapping marginality hotspots: Geographical targeting for poverty reduction

    Graw, Valerie; Ladenburger, Christine

    2012-01-01

    This mapping approach aims to make the marginalized and poor visible by identifying areas with difficult biophysical and socio-economic conditions. Mapping using different data sources and data types gives deeper insight into possible causal interlinkages and offers the opportunity for comprehensive analysis. The maps highlight areas where different dimensions of marginality overlap – the marginality hotspots – based on proxies for marginality dimensions representing different spheres of life...

  14. Seamounts are hotspots of pelagic biodiversity in the open ocean

    Morato, Telmo; Hoyle, Simon D.; Allain, Valerie; Nicol, Simon J.

    2010-01-01

    The identification of biodiversity hotspots and their management for conservation have been hypothesized as effective ways to protect many species. There has been a significant effort to identify and map these areas at a global scale, but the coarse resolution of most datasets masks the small-scale patterns associated with coastal habitats or seamounts. Here we used tuna longline observer data to investigate the role of seamounts in aggregating large pelagic biodiversity and to identify which...

  15. Online Forums Hotspot Prediction Based on Sentiment Analysis

    V. Murali Bhaskarn; K. Nirmala Devi

    2012-01-01

    Problem statement: Online forums hotspot prediction is one of the significant research areas in web mining, which can help people make proper decision in daily life. Online forums, news reports and blogs, are containing large volume of public opinion information. Rapid growth of network arouses much attention on public opinion, it is important to analyse the public opinion in time and understands the trends of their opinion correctly. Approach: The sentiment analysis and text mining are impor...

  16. BENCHMARKING UPGRADED HOTSPOT DOSE CALCULATIONS AGAINST MACCS2 RESULTS

    Brotherton, Kevin

    2009-04-30

    The radiological consequence of interest for a documented safety analysis (DSA) is the centerline Total Effective Dose Equivalent (TEDE) incurred by the Maximally Exposed Offsite Individual (MOI) evaluated at the 95th percentile consequence level. An upgraded version of HotSpot (Version 2.07) has been developed with the capabilities to read site meteorological data and perform the necessary statistical calculations to determine the 95th percentile consequence result. These capabilities should allow HotSpot to join MACCS2 (Version 1.13.1) and GENII (Version 1.485) as radiological consequence toolbox codes in the Department of Energy (DOE) Safety Software Central Registry. Using the same meteorological data file, scenarios involving a one curie release of {sup 239}Pu were modeled in both HotSpot and MACCS2. Several sets of release conditions were modeled, and the results compared. In each case, input parameter specifications for each code were chosen to match one another as much as the codes would allow. The results from the two codes are in excellent agreement. Slight differences observed in results are explained by algorithm differences.

  17. Páramo is the world’s fastest evolving and coolest biodiversity hotspot

    Santiago eMadriñán

    2013-10-01

    Full Text Available Understanding the processes that cause speciation is a key aim of evolutionary biology. Lineages or biomes that exhibit recent and rapid diversification are ideal model systems for determining these processes. Species rich biomes reported to be of relatively recent origin, i.e., since the beginning of the Miocene, include Mediterranean ecosystems such as the California Floristic Province, oceanic islands such as the Hawaiian archipelago and the Neotropical high elevation ecosystem of the Páramos. Páramos constitute grasslands above the forest tree-line (at elevations of c. 2800–4700 m with high species endemism. Organisms that occupy this ecosystem are a likely product of unique adaptations to an extreme environment that evolved during the last three to five million years when the Andes reached an altitude that was capable of sustaining this type of vegetation. We compared net diversification rates of lineages in fast evolving biomes using 73 dated molecular phylogenies. Based on our sample, we demonstrate that average net diversification rates of Páramo plant lineages are faster than those of other reportedly fast evolving hotspots and that the faster evolving lineages are more likely to be found in Páramos than the other hotspots. Páramos therefore represent the ideal model system for studying diversification processes. Most of the speciation events that we observed in the Páramos (144 out of 177 occurred during the Pleistocene possibly due to the effects of species range contraction and expansion that may have resulted from the well-documented climatic changes during that period. Understanding these effects will assist with efforts to determine how future climatic changes will impact plant populations.

  18. Medical Building Evolution and Illumination Design Adaptability%医疗建筑的演进与照明设计的适应性

    戴德慈

    2014-01-01

    With the continuous evolution of society and technology , the illumination design should also take actions to develop accordingly .There are various modern and contemporary illumination design concepts , such as being close to natural light , function supreme , expression light , humanism , etc.Analysis has been made toward the impact of these concepts on the luminous environment of medical buildings . The illumination design concept of respect for nature and the combination of satisfying functional requirements and humanistic care is introduced , and the adaptability principle of compliance with visual comfort , visual performance and visual security .The characteristics and technical essentials of illumination design for the large space area , medical technical area and ward area inside medical buildings have been explained as well .%医疗建筑随着社会与科技的发展不断演进,其照明设计需采取相应的对策。通过对近现代医疗建筑照明设计中亲近天然光、功能至上、表现灯光、人本主义等不同照明设计理念对医疗建筑光环境影响的分析,推出尊重自然、满足功能和人文关怀相结合的照明设计理念和遵循视觉舒适、视觉功效与视觉安全的适应原则,并阐述医疗建筑中大空间区域、医技区域和病房区域照明设计的特点与技术要点。

  19. Food Security Hotspots in India under Changing Climate and Growing Populatio

    Singh, N.; Cherkauer, K. A.; Ashfaq, M.; Rastogi, D.

    2015-12-01

    Global climate change, unprecedented population growth, and rapid urbanization have elevated the possibility of food and water shortages in many regions across the world. The likelihood of such shortages in the future is further exacerbated by the fact that increased greenhouse forcing and rapid growth in human population will continue for at least the next several decades. These socio-environmental changes will likely put some regions under enormous economic and environmental stress by forcing them to adapt to new conditions. India with its rapidly growing population and high rates of urbanization and industrialization is one such region whose agricultural resources will be particularly vulnerable to the impact of these changes. This study collectively reviews and analyses the possible impacts of climate change, population growth and resulting land use change on the availability of food and water in the coming decades for India. By analyzing and fusing a wide variety of existing data and research on the impact of land use change, population, and climate change, on water and food resources this study develops an understanding of the broader implications of each of the changes on food security in the region. In addition, the study focuses on the need to assess and quantify the combination of such impacts at a regional level and identify food security hotspots spatially across India that will help to narrow down regions in the country which will be severely affected and need priority adaptation and mitigation measures.

  20. Patterns and perceptions of climate change in a biodiversity conservation hotspot.

    Hartter, Joel; Stampone, Mary D; Ryan, Sadie J; Kirner, Karen; Chapman, Colin A; Goldman, Abraham

    2012-01-01

    Quantifying local people's perceptions to climate change, and their assessments of which changes matter, is fundamental to addressing the dual challenge of land conservation and poverty alleviation in densely populated tropical regions To develop appropriate policies and responses, it will be important not only to anticipate the nature of expected changes, but also how they are perceived, interpreted and adapted to by local residents. The Albertine Rift region in East Africa is one of the world's most threatened biodiversity hotspots due to dense smallholder agriculture, high levels of land and resource pressures, and habitat loss and conversion. Results of three separate household surveys conducted in the vicinity of Kibale National Park during the late 2000s indicate that farmers are concerned with variable precipitation. Many survey respondents reported that conditions are drier and rainfall timing is becoming less predictable. Analysis of daily rainfall data for the climate normal period 1981 to 2010 indicates that total rainfall both within and across seasons has not changed significantly, although the timing and transitions of seasons has been highly variable. Results of rainfall data analysis also indicate significant changes in the intra-seasonal rainfall distribution, including longer dry periods within rainy seasons, which may contribute to the perceived decrease in rainfall and can compromise food security. Our results highlight the need for fine-scale climate information to assist agro-ecological communities in developing effective adaptive management. PMID:22384244

  1. Key Role of European Rabbits in the Conservation of the Western Mediterranean Basin Hotspot

    Delibes Mateos, Miguel; Delibes, M.; Ferreras, Pablo; Villafuerte, Rafael

    2008-01-01

    The Mediterranean Basin is a global hotspot of biodiversity. Hotspots are said to be experiencing a major loss of habitat, but an added risk could be the decline of some species having a special role in ecological relationships of the system. We reviewed the role of European rabbits (Oryctolagus cuniculus) as a keystone species in the Iberian Peninsula portion of the Mediterranean hotspot. Rabbits conspicuously alter plant species composition and vegetation structure through grazing and see...

  2. Applying Hotspot Detection Methods in Forestry: A Case Study of Chestnut Oak Regeneration

    Songlin Fei

    2010-01-01

    Hotspot detection has been widely adopted in health sciences for disease surveillance, but rarely in natural resource disciplines. In this paper, two spatial scan statistics (SaTScan and ClusterSeer) and a nonspatial classification and regression trees method were evaluated as techniques for identifying chestnut oak (Quercus Montana) regeneration hotspots among 50 mixed-oak stands in the central Appalachian region of the eastern United States. Hotspots defined by the three methods had a moder...

  3. Sampling effects on the identification of roadkill hotspots: Implications for survey design.

    Santos, Sara M; Marques, J Tiago; Lourenço, André; Medinas, Denis; Barbosa, A Márcia; Beja, Pedro; Mira, António

    2015-10-01

    Although locating wildlife roadkill hotspots is essential to mitigate road impacts, the influence of study design on hotspot identification remains uncertain. We evaluated how sampling frequency affects the accuracy of hotspot identification, using a dataset of vertebrate roadkills (n = 4427) recorded over a year of daily surveys along 37 km of roads. "True" hotspots were identified using this baseline dataset, as the 500-m segments where the number of road-killed vertebrates exceeded the upper 95% confidence limit of the mean, assuming a Poisson distribution of road-kills per segment. "Estimated" hotspots were identified likewise, using datasets representing progressively lower sampling frequencies, which were produced by extracting data from the baseline dataset at appropriate time intervals (1-30 days). Overall, 24.3% of segments were "true" hotspots, concentrating 40.4% of roadkills. For different groups, "true" hotspots accounted from 6.8% (bats) to 29.7% (small birds) of road segments, concentrating from 60% (lizards, lagomorphs, carnivores) of roadkills. Spatial congruence between "true" and "estimated" hotspots declined rapidly with increasing time interval between surveys, due primarily to increasing false negatives (i.e., missing "true" hotspots). There were also false positives (i.e., wrong "estimated" hotspots), particularly at low sampling frequencies. Spatial accuracy decay with increasing time interval between surveys was higher for smaller-bodied (amphibians, reptiles, small birds, small mammals) than for larger-bodied species (birds of prey, hedgehogs, lagomorphs, carnivores). Results suggest that widely used surveys at weekly or longer intervals may produce poor estimates of roadkill hotspots, particularly for small-bodied species. Surveying daily or at two-day intervals may be required to achieve high accuracy in hotspot identification for multiple species. PMID:26232568

  4. Outlier Detection on Hotspots Data in Riau Province using DBSCAN Algorithm

    Sukmasetya, Pristi; Sitanggang, Imas S.

    2016-01-01

    Indonesia has serious problems in forest fires. One of the potential factors which indicates forest fires is hotspot. Hotspot is a forest fires indicator that detects a location with relatively higher temperature in comparison with nearby positions. One possible prevention efforts for forest fires is by detecting outliers on hotspots data. This study detects outlier on hotspots data in Riau Province in between year 2001 to 2012 using the DBSCAN algorithm and determines the distribution of outlier hotspots by region and time. The experiment results show that the highest occurrence of outliers is in 2005. The number of outliers on hotspots data reaches 1241 hotspots with the sum of square error (SSE) is 0.084. Outlier hotspots in Riau Province in 2005 spread across 11 districts/cities and 136 districts. In 2005 the highest outlier are found in Rokan Hulu with the number of outliers is 186 points. The highest frequency of hotspot that is considered as outliers is found in August 2005, with a total of 355 outliers in which as many 97 of these outliers are occurred in Rokan Hulu District.

  5. Global diversity hotspots and conservation priorities for sharks.

    Luis O Lucifora

    Full Text Available Sharks are one of the most threatened groups of marine animals, as high exploitation rates coupled with low resilience to fishing pressure have resulted in population declines worldwide. Designing conservation strategies for this group depends on basic knowledge of the geographic distribution and diversity of known species. So far, this information has been fragmented and incomplete. Here, we have synthesized the first global shark diversity pattern from a new database of published sources, including all 507 species described at present, and have identified hotspots of shark species richness, functional diversity and endemicity from these data. We have evaluated the congruence of these diversity measures and demonstrate their potential use in setting priority areas for shark conservation. Our results show that shark diversity across all species peaks on the continental shelves and at mid-latitudes (30-40 degrees N and S. Global hotspots of species richness, functional diversity and endemicity were found off Japan, Taiwan, the East and West coasts of Australia, Southeast Africa, Southeast Brazil and Southeast USA. Moreover, some areas with low to moderate species richness such as Southern Australia, Angola, North Chile and Western Continental Europe stood out as places of high functional diversity. Finally, species affected by shark finning showed different patterns of diversity, with peaks closer to the Equator and a more oceanic distribution overall. Our results show that the global pattern of shark diversity is uniquely different from land, and other well-studied marine taxa, and may provide guidance for spatial approaches to shark conservation. However, similar to terrestrial ecosystems, protected areas based on hotspots of diversity and endemism alone would provide insufficient means for safeguarding the diverse functional roles that sharks play in marine ecosystems.

  6. Global diversity hotspots and conservation priorities for sharks.

    Lucifora, Luis O; García, Verónica B; Worm, Boris

    2011-01-01

    Sharks are one of the most threatened groups of marine animals, as high exploitation rates coupled with low resilience to fishing pressure have resulted in population declines worldwide. Designing conservation strategies for this group depends on basic knowledge of the geographic distribution and diversity of known species. So far, this information has been fragmented and incomplete. Here, we have synthesized the first global shark diversity pattern from a new database of published sources, including all 507 species described at present, and have identified hotspots of shark species richness, functional diversity and endemicity from these data. We have evaluated the congruence of these diversity measures and demonstrate their potential use in setting priority areas for shark conservation. Our results show that shark diversity across all species peaks on the continental shelves and at mid-latitudes (30-40 degrees N and S). Global hotspots of species richness, functional diversity and endemicity were found off Japan, Taiwan, the East and West coasts of Australia, Southeast Africa, Southeast Brazil and Southeast USA. Moreover, some areas with low to moderate species richness such as Southern Australia, Angola, North Chile and Western Continental Europe stood out as places of high functional diversity. Finally, species affected by shark finning showed different patterns of diversity, with peaks closer to the Equator and a more oceanic distribution overall. Our results show that the global pattern of shark diversity is uniquely different from land, and other well-studied marine taxa, and may provide guidance for spatial approaches to shark conservation. However, similar to terrestrial ecosystems, protected areas based on hotspots of diversity and endemism alone would provide insufficient means for safeguarding the diverse functional roles that sharks play in marine ecosystems. PMID:21573162

  7. Has Human Evolution Stopped?

    Alan R. Templeton

    2010-07-01

    Full Text Available It has been argued that human evolution has stopped because humans now adapt to their environment via cultural evolution and not biological evolution. However, all organisms adapt to their environment, and humans are no exception. Culture defines much of the human environment, so cultural evolution has actually led to adaptive evolution in humans. Examples are given to illustrate the rapid pace of adaptive evolution in response to cultural innovations. These adaptive responses have important implications for infectious diseases, Mendelian genetic diseases, and systemic diseases in current human populations. Moreover, evolution proceeds by mechanisms other than natural selection. The recent growth in human population size has greatly increased the reservoir of mutational variants in the human gene pool, thereby enhancing the potential for human evolution. The increase in human population size coupled with our increased capacity to move across the globe has induced a rapid and ongoing evolutionary shift in how genetic variation is distributed within and among local human populations. In particular, genetic differences between human populations are rapidly diminishing and individual heterozygosity is increasing, with beneficial health effects. Finally, even when cultural evolution eliminates selection on a trait, the trait can still evolve due to natural selection on other traits. Our traits are not isolated, independent units, but rather are integrated into a functional whole, so selection on one trait can cause evolution to occur on another trait, sometimes with mildly maladaptive consequences.

  8. Ecosystem characteristics and processes facilitating persistent macrobenthic biomass hotspots and associated benthivory in the Pacific Arctic

    Grebmeier, Jacqueline M.; Bluhm, Bodil A.; Cooper, Lee W.; Danielson, Seth L.; Arrigo, Kevin R.; Blanchard, Arny L.; Clarke, Janet T.; Day, Robert H.; Frey, Karen E.; Gradinger, Rolf R.; Kędra, Monika; Konar, Brenda; Kuletz, Kathy J.; Lee, Sang H.; Lovvorn, James R.; Norcross, Brenda L.; Okkonen, Stephen R.

    2015-08-01

    The northern Bering and Chukchi Seas are areas in the Pacific Arctic characterized by high northward advection of Pacific Ocean water, with seasonal variability in sea ice cover, water mass characteristics, and benthic processes. In this review, we evaluate the biological and environmental factors that support communities of benthic prey on the continental shelves, with a focus on four macrofaunal biomass "hotspots." For the purpose of this study, we define hotspots as macrofaunal benthic communities with high biomass that support a corresponding ecological guild of benthivorous seabird and marine mammal populations. These four benthic hotspots are regions within the influence of the St. Lawrence Island Polynya (SLIP), the Chirikov Basin between St. Lawrence Island and Bering Strait (Chirikov), north of Bering Strait in the southeast Chukchi Sea (SECS), and in the northeast Chukchi Sea (NECS). Detailed benthic macrofaunal sampling indicates that these hotspot regions have been persistent over four decades of sampling due to annual reoccurrence of seasonally consistent, moderate-to-high water column production with significant export of carbon to the underlying sediments. We also evaluate the usage of the four benthic hotspot regions by benthic prey consumers to illuminate predator-prey connectivity. In the SLIP hotspot, spectacled eiders and walruses are important winter consumers of infaunal bivalves and polychaetes, along with epibenthic gastropods and crabs. In the Chirikov hotspot, gray whales have historically been the largest summer consumers of benthic macrofauna, primarily feeding on ampeliscid amphipods in the summer, but they are also foraging further northward in the SECS and NECS hotspots. Areas of concentrated walrus foraging occur in the SLIP hotspot in winter and early spring, the NECS hotspot in summer, and the SECS hotspot in fall. Bottom up forcing by hydrography and food supply to the benthos influences persistence and composition of benthic prey

  9. On Exploiting Hotspot and Entropy for Data Forwarding in Delay Tolerant Networks

    Yuan, Peiyan; Tang, Shaojie

    2012-01-01

    Performance of data forwarding in Delay Tolerant Networks (DTNs) benefits considerably if one can make use of human mobility in terms of social structures. However, it is difficult and time-consuming to calculate the centrality and similarity of nodes by using solutions for traditional social networks, this is mainly because of the transient node contact and the intermittently connected environment. In this work, we are interested in the following question: Can we explore some other stable social attributes to quantify the centrality and similarity of nodes? Taking GPS traces of human walks from the real world, we find that there exist two known phenomena. One is public hotspot, the other is personal hotspot. Motivated by this observation, we present Hoten (hotspot and entropy), a novel routing metric to improve routing performance in DTNs. First, we use the relative entropy between the public hotspots and the personal hotspots to compute the centrality of nodes. Then we utilize the inverse symmetrized entrop...

  10. Applying Hotspot Detection Methods in Forestry: A Case Study of Chestnut Oak Regeneration

    Songlin Fei

    2010-01-01

    Full Text Available Hotspot detection has been widely adopted in health sciences for disease surveillance, but rarely in natural resource disciplines. In this paper, two spatial scan statistics (SaTScan and ClusterSeer and a nonspatial classification and regression trees method were evaluated as techniques for identifying chestnut oak (Quercus Montana regeneration hotspots among 50 mixed-oak stands in the central Appalachian region of the eastern United States. Hotspots defined by the three methods had a moderate level of conformity and revealed similar chestnut oak regeneration site affinity. Chestnut oak regeneration hotspots were positively associated with the abundance of chestnut oak trees in the overstory and a moderate cover of heather species (Vaccinium and Gaylussacia spp. but were negatively associated with the abundance of hayscented fern (Dennstaedtia punctilobula and mountain laurel (Kalmia latiforia. In general, hotspot detection is a viable tool for assisting natural resource managers with identifying areas possessing significantly high or low tree regeneration.

  11. Diagnostic for determining the mix in inertial confinement fusion capsule hotspot

    He, Shibei; Ding, Yongkun; Miao, Wenyong; Zhang, Xing; Tu, Shaoyong; Yuan, Yongteng; Pu, Yudong; Yan, Ji; Wei, Minxi; Yin, Chuansheng

    2016-07-01

    A diagnostic is developed for determining the hotspot mix in inertial confinement fusion experiments. A multi-channel pinhole camera measures Bremsstrahlung emissions from implosion capsules ranging from 6 keV to 30 keV and records an image of the hotspot. Meanwhile, a planar crystal spectrometer measures Ar line emissions used to deduce the electron density of the hotspot. An X-ray streaked camera records the burn duration. With the Bremsstrahlung spectrum, electron density, hotspot volume, and burn duration, the mix quantity is determined by solving a pair of linear equations. This inferred mix amount has an uncertainty due to the uncertainty of the electron density, but with the help of the measured neutron product, the most likely mix quantity value can be determined. This technique is applied to experimental images to infer the quantity of CH ablator mix into the hotspot.

  12. Cloud Computing Application for Hotspot Clustering Using Recursive Density Based Clustering (RDBC)

    Santoso, Aries; Khiyarin Nisa, Karlina

    2016-01-01

    Indonesia has vast areas of tropical forest, but are often burned which causes extensive damage to property and human life. Monitoring hotspots can be one of the forest fire management. Each hotspot is recorded in dataset so that it can be processed and analyzed. This research aims to build a cloud computing application which visualizes hotspots clustering. This application uses the R programming language with Shiny web framework and implements Recursive Density Based Clustering (RDBC) algorithm. Clustering is done on hotspot dataset of the Kalimantan Island and South Sumatra Province to find the spread pattern of hotspots. The clustering results are evaluated using the Silhouette's Coefficient (SC) which yield best value 0.3220798 for Kalimantan dataset. Clustering pattern are displayed in the form of web pages so that it can be widely accessed and become the reference for fire occurrence prediction.

  13. Modelling Regional Hotspots of Water Pollution Induced by Salinization

    Malsy, M.; Floerke, M.

    2014-12-01

    Insufficient water quality is one of the main global topics causing risk to human health, biodiversity, and food security. At this, salinization of water and land resources is widely spread especially in arid to semi-arid climates, where salinization, often induced by irrigation agriculture, is a fundamental aspect of land degradation. High salinity is crucial to water use for drinking, irrigation, and industrial purposes, and therefore poses a risk to human health and ecosystem status. However, salinization is also an economic problem, in particular in those regions where agriculture makes a significant contribution to the economy and/or where agriculture is mainly based on irrigation. Agricultural production is exposed to high salinity of irrigation water resulting in lower yields. Hence, not only the quantity of irrigation water is of importance for growing cops but also its quality, which may further reduce the available resources. Thereby a major concern for food production and security persists, as irrigated agriculture accounts for over 30% of the total agricultural production. In this study, the large scale water quality model WorldQual was applied to simulate recent total dissolved solids (TDS) loadings and in-stream concentrations from point and diffuse sources to get an insight on potential environmental impacts as well as risks to food security. Regional focus in this study is on developing countries, as these are most threatened by water pollution. Furthermore, insufficient water quality for irrigation and therefore restrictions in irrigation water use were examined, indicating limitations to crop production. For this purpose, model simulations were conducted for the year 2010 to show the recent status of surface water quality and to identify hotspots and main causes of pollution. Our results show that salinity hotspots mainly occur in peak irrigation regions as irrigated agriculture is by far the dominant sector contributing to water abstractions as

  14. Adaptive Laboratory Evolution Of Escherichia Coli Reveals Arduous Resistance Development To A Combination Of Three Novel Antimicrobial Compounds And To The Short Amp P9-4

    Citterio, Linda; Franzyk, Henrik; Gram, Lone

    2015-01-01

    Antimicrobial peptides (AMPs) were for long considered as promising new antimicrobials since resistance was not expected. However, adaptive evolution experiments have demonstrated that bacteria may indeed develop resistance also to AMPs. However, we and others hypothesize that the risk of...... resistance development decreases when two or more compounds are combined as compared to single-drug treatments. The purpose of this study was to determine if resistance could develop in Escherichia coli ATCC 25922 to the peptidomimetic HF-1002 2 and the AMPs novicidin and P9-4. The mentioned compounds were...... adaptation to 32 x MIC. This shows that resistance to novicidin and HF-1002 2, administered alone, developed more easily than it occurred in lineages exposed to the combination of three drugs. This result further supports combinatorial treatment as a way to circumvent resistance development. Surprisingly...

  15. Adaptive Evolution Technology for Collaborative SaaS Platform of Industrial Chains%支撑产业链协同的SaaS平台自适应演化技术

    王淑营

    2012-01-01

    An adaptive evolution method for a collaborative SaaS ( software as a service) platform of industrial chains was proposed based on dynamic binding, implicit authority, and autonomous model for enterprises, to adapt itself to frequent changes in users and their businesses. An adaptive evolution model for business functions and data, and a synchronous evolution algorithm for online update of the business functions and database were presented, which represent the adaptive evolution mechanism of a SaaS platform. The proposed method was applied to the an research and development project of a collaborative SaaS platform for an automobile part industrial chain, showing that it meets the needs of online update of user businesses without disturbance to continuous service.%为实现产业链协同SaaS平台在运行服务过程中面向各企业群及其业务需求变化的动态演化支持,针对平台企业联盟和用户的动态性,提出了基于动态绑定与隐式授权的企业联盟自适应演化管理和基于企业自治模型的用户自适应演化管理方法;针对平台各企业联盟业务协同需求的动态性,建立了面向演化的业务功能与业务数据管理模型,提出了业务功能在线更新与业务数据库的同步演化算法,建立了SaaS平台自适应演化机制.通过在汽车零部件产业链协同SaaS平台研发过程中的应用表明,自适应演化方法能有效支持平台在不间断服务条件下,通过业务功能和业务数据库的在线演化满足各企业联盟业务功能扩展和动态更新的需求.

  16. Hotspots of anaerobic ammonia oxidation in land - freshwater interfaces

    Zhu, Guibing; Wang, Shanyun; Wang, Weidong;

    2013-01-01

    sampled fromlake riparian zones in North China. Laboratory incubations in the presence of ammonium or nitrate—at concentrations equivalent to no more than 10% of those detected in situ—yielded some of the highest potential anammox activities reported for natural environments to date. Potential rates of......For decades, the conversion of organic nitrogen to dinitrogen gas by heterotrophic bacteria, termed heterotrophic denitrification, was assumed to be the main pathway of nitrogen loss in natural ecosystems. Recently, however, autotrophic bacteria have been shown to oxidize ammonium in the absence of...... anammox peaked in sediments sampled from the interface between the land and the water, as did the abundance of annamox bacteria. Scaling our findings up to the entire lake system, we estimate that interfacial anammox hotspots account for the loss of 103 gNm-2 yr-1 from this lake region, and around one...

  17. Future of endemic flora of biodiversity hotspots in India.

    Vishwas Sudhir Chitale

    Full Text Available India is one of the 12 mega biodiversity countries of the world, which represents 11% of world's flora in about 2.4% of global land mass. Approximately 28% of the total Indian flora and 33% of angiosperms occurring in India are endemic. Higher human population density in biodiversity hotspots in India puts undue pressure on these sensitive eco-regions. In the present study, we predict the future distribution of 637 endemic plant species from three biodiversity hotspots in India; Himalaya, Western Ghats, Indo-Burma, based on A1B scenario for year 2050 and 2080. We develop individual variable based models as well as mixed models in MaxEnt by combining ten least co-related bioclimatic variables, two disturbance variables and one physiography variable as predictor variables. The projected changes suggest that the endemic flora will be adversely impacted, even under such a moderate climate scenario. The future distribution is predicted to shift in northern and north-eastern direction in Himalaya and Indo-Burma, while in southern and south-western direction in Western Ghats, due to cooler climatic conditions in these regions. In the future distribution of endemic plants, we observe a significant shift and reduction in the distribution range compared to the present distribution. The model predicts a 23.99% range reduction and a 7.70% range expansion in future distribution by 2050, while a 41.34% range reduction and a 24.10% range expansion by 2080. Integration of disturbance and physiography variables along with bioclimatic variables in the models improved the prediction accuracy. Mixed models provide most accurate results for most of the combinations of climatic and non-climatic variables as compared to individual variable based models. We conclude that a regions with cooler climates and higher moisture availability could serve as refugia for endemic plants in future climatic conditions; b mixed models provide more accurate results, compared to single

  18. Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

    Krause, Stefan; Lewandowski, Joerg; Hannah, David; McDonald, Karlie; Folegot, Silvia; Baranov, Victor

    2016-04-01

    Ecohydrological interfaces, represent the boundaries between water-dependent ecosystems that can alter substantially the fluxes of energy and matter. There is still a critical gap of understanding the organisational principles of the drivers and controls of spatially and temporally variable ecohydrological interface functions. This knowledge gap limits our capacity to efficiently quantify, predict and manage the services provided by complex ecosystems. Many ecohydrological interfaces are characterized by step changes in microbial metabolic activity, steep redox gradients and often even thermodynamic phase shifts, for instance at the interfaces between atmosphere and water or soil matrix and macro-pores interfaces. This paper integrates investigations from point scale laboratory microcosm experiments with reach and subcatchment scale tracer experiments and numerical modeling studies to elaborate similarities in the drivers and controls that constitute the enhanced biogeochemical activity of different types of ecohydrologica interfaces across a range of spatial and temporal scales. We therefore combine smart metabolic activity tracers to quantify the impact of bioturbating benthic fauna onto ecosystem respiration and oxygen consumption and investigate at larger scale, how microbial metabolic activity and carbon turnover at the water-sediment interface are controlled by sediment physical and chemical properties as well as water temperatures. Numerical modeling confirmed that experimentally identified hotspots of streambed biogeochemical cycling were controlled by patterns of physical properties such as hydraulic conductivities or bioavailability of organic matter, impacting on residence time distributions and hence reaction times. In contrast to previous research, our investigations thus confirmed that small-scale variability of physical and chemical interface properties had a major impact on biogeochemical processing at the investigated ecohydrological interfaces

  19. Methodology and software to detect viral integration site hot-spots

    Kim Namshin

    2011-09-01

    Full Text Available Abstract Background Modern gene therapy methods have limited control over where a therapeutic viral vector inserts into the host genome. Vector integration can activate local gene expression, which can cause cancer if the vector inserts near an oncogene. Viral integration hot-spots or 'common insertion sites' (CIS are scrutinized to evaluate and predict patient safety. CIS are typically defined by a minimum density of insertions (such as 2-4 within a 30-100 kb region, which unfortunately depends on the total number of observed VIS. This is problematic for comparing hot-spot distributions across data sets and patients, where the VIS numbers may vary. Results We develop two new methods for defining hot-spots that are relatively independent of data set size. Both methods operate on distributions of VIS across consecutive 1 Mb 'bins' of the genome. The first method 'z-threshold' tallies the number of VIS per bin, converts these counts to z-scores, and applies a threshold to define high density bins. The second method 'BCP' applies a Bayesian change-point model to the z-scores to define hot-spots. The novel hot-spot methods are compared with a conventional CIS method using simulated data sets and data sets from five published human studies, including the X-linked ALD (adrenoleukodystrophy, CGD (chronic granulomatous disease and SCID-X1 (X-linked severe combined immunodeficiency trials. The BCP analysis of the human X-linked ALD data for two patients separately (774 and 1627 VIS and combined (2401 VIS resulted in 5-6 hot-spots covering 0.17-0.251% of the genome and containing 5.56-7.74% of the total VIS. In comparison, the CIS analysis resulted in 12-110 hot-spots covering 0.018-0.246% of the genome and containing 5.81-22.7% of the VIS, corresponding to a greater number of hot-spots as the data set size increased. Our hot-spot methods enable one to evaluate the extent of VIS clustering, and formally compare data sets in terms of hot-spot overlap

  20. Methodology and software to detect viral integration site hot-spots

    2011-01-01

    Background Modern gene therapy methods have limited control over where a therapeutic viral vector inserts into the host genome. Vector integration can activate local gene expression, which can cause cancer if the vector inserts near an oncogene. Viral integration hot-spots or 'common insertion sites' (CIS) are scrutinized to evaluate and predict patient safety. CIS are typically defined by a minimum density of insertions (such as 2-4 within a 30-100 kb region), which unfortunately depends on the total number of observed VIS. This is problematic for comparing hot-spot distributions across data sets and patients, where the VIS numbers may vary. Results We develop two new methods for defining hot-spots that are relatively independent of data set size. Both methods operate on distributions of VIS across consecutive 1 Mb 'bins' of the genome. The first method 'z-threshold' tallies the number of VIS per bin, converts these counts to z-scores, and applies a threshold to define high density bins. The second method 'BCP' applies a Bayesian change-point model to the z-scores to define hot-spots. The novel hot-spot methods are compared with a conventional CIS method using simulated data sets and data sets from five published human studies, including the X-linked ALD (adrenoleukodystrophy), CGD (chronic granulomatous disease) and SCID-X1 (X-linked severe combined immunodeficiency) trials. The BCP analysis of the human X-linked ALD data for two patients separately (774 and 1627 VIS) and combined (2401 VIS) resulted in 5-6 hot-spots covering 0.17-0.251% of the genome and containing 5.56-7.74% of the total VIS. In comparison, the CIS analysis resulted in 12-110 hot-spots covering 0.018-0.246% of the genome and containing 5.81-22.7% of the VIS, corresponding to a greater number of hot-spots as the data set size increased. Our hot-spot methods enable one to evaluate the extent of VIS clustering, and formally compare data sets in terms of hot-spot overlap. Finally, we show that the

  1. Coral-mucus-associated Vibrio integrons in the Great Barrier Reef: genomic hotspots for environmental adaptation.

    Koenig, Jeremy E; Bourne, David G; Curtis, Bruce; Dlutek, Marlena; Stokes, H W; Doolittle, W Ford; Boucher, Yan

    2011-06-01

    Integron cassette arrays in a dozen cultivars of the most prevalent group of Vibrio isolates obtained from mucus expelled by a scleractinian coral (Pocillopora damicornis) colony living on the Great Barrier Reef were sequenced and compared. Although all cultivars showed >99% identity across recA, pyrH and rpoB genes, no two had more than 10% of their integron-associated gene cassettes in common, and some individuals shared cassettes exclusively with distantly-related members of the genus. Of cassettes shared within the population, a number appear to have been transferred between Vibrio isolates, as assessed by phylogenetic analysis. Prominent among the mucus Vibrio cassettes with potentially inferable functions are acetyltransferases, some with close similarity to known antibiotic-resistance determinants. A subset of these potential resistance cassettes were shared exclusively between the mucus Vibrio cultivars, Vibrio coral pathogens and human pathogens, thus illustrating a direct link between these microbial niches through exchange of integron-associated gene cassettes. PMID:21270840

  2. Coral-mucus-associated Vibrio integrons in the Great Barrier Reef: genomic hotspots for environmental adaptation

    Koenig, Jeremy E.; Bourne, David G; Curtis, Bruce; Dlutek, Marlena; Stokes, H. W.; Doolittle, W Ford; Boucher, Yan

    2011-01-01

    Integron cassette arrays in a dozen cultivars of the most prevalent group of Vibrio isolates obtained from mucus expelled by a scleractinian coral (Pocillopora damicornis) colony living on the Great Barrier Reef were sequenced and compared. Although all cultivars showed >99% identity across recA, pyrH and rpoB genes, no two had more than 10% of their integron-associated gene cassettes in common, and some individuals shared cassettes exclusively with distantly-related members of the genus. Of ...

  3. Crustal and uppermost mantle structure variation beneath La Réunion hotspot track

    Fontaine, Fabrice R.; Barruol, Guilhem; Tkalčić, Hrvoje; Wölbern, Ingo; Rümpker, Georg; Bodin, Thomas; Haugmard, Méric

    2015-10-01

    The Piton de la Fournaise basaltic volcano, on La Réunion Island in the western Indian Ocean, is one of the most active volcanoes in the world. This volcano is classically considered as the surface expression of an upwelling mantle plume and its activity is continuously monitored, providing detailed information on its superficial dynamics and on the edifice structure. Deeper crustal and upper mantle structure under La Réunion Island is surprisingly poorly constrained, motivating this study. We used receiver function techniques to determine a shear wave velocity profile through the crust and uppermost mantle beneath La Réunion, but also at other seismic stations located on the hotspot track, to investigate the plume and lithosphere interaction and its evolution through time. Receiver functions (RFs) were computed at permanent broad-band seismic stations from the GEOSCOPE network (on La Réunion and Rodrigues), at IRIS stations MRIV and DGAR installed on Mauritius and Diego Garcia islands, and at the GEOFON stations KAAM and HMDM on the Maldives. We performed non-linear inversions of RFs through modelling of P-to-S conversions at various crustal and upper mantle interfaces. Joint inversion of RF and surface wave dispersion data suggests a much deeper Mohorovičić discontinuity (Moho) beneath Mauritius (˜21 km) compared to La Réunion (˜12 km). A magmatic underplated body may be present under La Réunion as a thin layer (≤3 km thick), as suggested by a previous seismic refraction study, and as a much thicker layer beneath other stations located on the hotspot track, suggesting that underplating is an important process resulting from the plume-lithosphere interaction. We find evidence for a strikingly low velocity layer starting at about 33 km depth beneath La Réunion that we interpret as a zone of partial melt beneath the active volcano. We finally observe low velocities below 70 km beneath La Réunion and below 50 km beneath Mauritius that could represent

  4. Environmental change: prospects for conservation and agriculture in a southwest Australia biodiversity hotspot

    Neil E. Pettit

    2015-09-01

    Full Text Available Accelerating environmental change is perhaps the greatest challenge for natural resource management; successful strategies need to be effective for decades to come. Our objective is to identify opportunities that new environmental conditions may provide for conservation, restoration, and resource use in a globally recognized biodiversity hotspot in southwestern Australia. We describe a variety of changes to key taxonomic groups and system-scale characteristics as a consequence of environmental change (climate and land use, and outline strategies for conserving and restoring important ecological and agricultural characteristics. Opportunities for conservation and economic adaptation are substantial because of gradients in rainfall, temperature, and land use, extensive areas of remnant native vegetation, the ability to reduce and ameliorate areas affected by secondary salinization, and the existence of large national parks and an extensive network of nature reserves. Opportunities presented by the predicted environmental changes encompass agricultural as well as natural ecosystems. These may include expansion of aquaculture, transformation of agricultural systems to adapt to drier autumns and winters, and potential increases in spring and summer rain, carbon-offset plantings, and improving the network of conservation reserves. A central management dilemma is whether restoration/preservation efforts should have a commercial or biodiversity focus, and how they could be integrated. Although the grand challenge is conserving, protecting, restoring, and managing for a future environment, one that balances economic, social, and environmental values, the ultimate goal is to establish a regional culture that values the unique regional environment and balances the utilization of natural resources against protecting remaining natural ecosystems.

  5. How Can Evolution Learn?

    Watson, Richard A; Szathmáry, Eörs

    2016-02-01

    The theory of evolution links random variation and selection to incremental adaptation. In a different intellectual domain, learning theory links incremental adaptation (e.g., from positive and/or negative reinforcement) to intelligent behaviour. Specifically, learning theory explains how incremental adaptation can acquire knowledge from past experience and use it to direct future behaviours toward favourable outcomes. Until recently such cognitive learning seemed irrelevant to the 'uninformed' process of evolution. In our opinion, however, new results formally linking evolutionary processes to the principles of learning might provide solutions to several evolutionary puzzles - the evolution of evolvability, the evolution of ecological organisation, and evolutionary transitions in individuality. If so, the ability for evolution to learn might explain how it produces such apparently intelligent designs. PMID:26705684

  6. The genomics of adaptation

    Radwan, Jacek; Babik, Wiesław

    2012-01-01

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far ...

  7. Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome

    Favero, Francesco; McGranahan, Nicholas; Salm, Maximilian P.;

    2015-01-01

    chromosome also incorporating miR26a-2. The WGS analysis uncovered progressive evolution of the double minute chromosome converging on the KIT/PDGFRA/PI3K/mTOR axis, superseding the IDH1 mutation in dominance in a mutually exclusive manner at recurrence, consequently the patient was treated with imatinib...

  8. Health Aspects of Climate Change in Cities with Mediterranean Climate, and Local Adaptation Plans

    Shlomit Paz; Maya Negev; Alexandra Clermont; Green, Manfred S.

    2016-01-01

    Cities with a Mediterranean-type climate (Med-cities) are particularly susceptible to health risks from climate change since they are located in biogeographical hot-spots that experience some of the strongest effects of the changing climate. The study aims to highlight health impacts of climate change in Med-cities, analyze local climate adaptation plans and make adaptation policy recommendations for the Med-city level. We identified five Med-cities with a climate change adaptation plan: Adel...

  9. Implications of salinity pollution hotspots on agricultural production

    Floerke, Martina; Fink, Julia; Malsy, Marcus; Voelker, Jeanette; Alcamo, Joseph

    2016-04-01

    , large metropolitan regions are initially loading hotspots and pollution, too, and prevention becomes important as point sources are dependent on sewer connection rates and treatment levels. In conclusion, this study provides a detailed picture of the spatial and temporal distribution of salinity pollution and identifies hotspot areas as well as the dominant sources. Furthermore, impacts of water quality degradation on agricultural production and food security are quantified, which aim for a better understanding of the risks for food security caused by water quality impairment.

  10. Plumes, Hotspot & Slabs Imaged by Global Adjoint Tomography

    Bozdag, E.; Lefebvre, M. P.; Lei, W.; Peter, D. B.; Smith, J. A.; Komatitsch, D.; Tromp, J.

    2015-12-01

    We present the "first generation" global adjoint tomography model based on 3D wave simulations, which is the result of 15 conjugate-gradient iterations with confined transverse isotropy to the upper mantle. Our starting model is the 3D mantle and crustal models S362ANI (Kustowski et al. 2008) and Crust2.0 (Bassin et al. 2000), respectively. We take into account the full nonlinearity of wave propagation in numerical simulations including attenuation (both in forward and adjoint simulations), topography/bathymetry, etc., using the GPU version of the SPECFEM3D_GLOBE package. We invert for crust and mantle together without crustal corrections to avoid any bias in mantle structure. We started with an initial selection of 253 global CMT events within the magnitude range 5.8 ≤ Mw ≤ 7.0 with numerical simulations having resolution down to 27 s combining 30-s body and 60-s surface waves. After the 12th iteration we increased the resolution to 17 s, including higher-frequency body waves as well as going down to 45 s in surface-wave measurements. We run 180-min seismograms and assimilate all minor- and major-arc body and surface waves. Our 15th iteration model update shows a tantalisingly enhanced image of the Tahiti plume as well as various other plumes and hotspots, such as Caroline, Galapagos, Yellowstone, Erebus, etc. Furthermore, we see clear improvements in slab resolution along the Hellenic and Japan Arcs, as well as subduction along the East of Scotia Plate, which does not exist in the initial model. Point-spread function tests (Fichtner & Trampert 2011) suggest that we are close to the resolution of continental-scale studies in our global inversions and able to confidently map features, for instance, at the scale of the Yellowstone hotspot. This is a clear consequence of our multi-scale smoothing strategy, in which we define our smoothing operator as a function of the approximate Hessian kernel and smooth our gradients less wherever we have good ray coverage

  11. Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua.

    Manousaki, Tereza; Hull, Pincelli M; Kusche, Henrik; Machado-Schiaffino, Gonzalo; Franchini, Paolo; Harrod, Chris; Elmer, Kathryn R; Meyer, Axel

    2013-02-01

    The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)-from two Great Lakes and two crater lakes in Nicaragua-to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ(13)C and δ(15)N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. PMID:23057963

  12. Learning and Evolution

    Nolfi, S.; Floreano, D.

    1999-01-01

    In the last few years several researchers have resorted to artificial evolution (e.g. genetic algorithms) and learning techniques (e.g. neural networks) for studying the interaction between learning and evolution. These studies have been conducted for two different purposes: (a) looking at the performance advantages obtained by combining these two adaptive techniques; (b) understanding the role of the interaction between learning and evolution in biological organisms. In this paper we describ...

  13. Relativistic and Slowing Down: The Flow in the Hotspots of Powerful Radio Galaxies and Quasars

    Kazanas, D.

    2003-01-01

    The 'hotspots' of powerful radio galaxies (the compact, high brightness regions, where the jet flow collides with the intergalactic medium (IGM)) have been imaged in radio, optical and recently in X-ray frequencies. We propose a scheme that unifies their, at first sight, disparate broad band (radio to X-ray) spectral properties. This scheme involves a relativistic flow upstream of the hotspot that decelerates to the sub-relativistic speed of its inferred advance through the IGM and it is viewed at different angles to its direction of motion, as suggested by two independent orientation estimators (the presence or not of broad emission lines in their optical spectra and the core-to-extended radio luminosity). This scheme, besides providing an account of the hotspot spectral properties with jet orientation, it also suggests that the large-scale jets remain relativistic all the way to the hotspots.

  14. Shock-induced hotspot formation and chemical reaction initiation in PETN containing a spherical void

    We present results of reactive molecular dynamics simulations of hotspot formation and chemical reaction initiation in shock-induced compression of pentaerythritol tetranitrate (PETN) with the ReaxFF reactive force field. A supported shockwave is driven through a PETN crystal containing a 20 nm spherical void at a sub-threshold impact velocity of 2 km/s. Formation of a hotspot due to shock-induced void collapse is observed. During void collapse, NO2 is the dominant species ejected from the upstream void surface. Once the ejecta collide with the downstream void surface and the hotspot develops, formation of final products such as N2 and H2O is observed. The simulation provides a detailed picture of how void collapse and hotspot formation leads to initiation at sub-threshold impact velocities.

  15. Application of PCARES in locating the soil erosion Hotspots in the Manupali River Watershed

    Paningbatan, E.

    2004-01-01

    In this presentation the author covers: GIS mapping of land attributes, dynamic modeling of soil erosion at watershed scale using PCARES (Predicting Catchment Runoff and Soil Erosion for Sustainability), identifying soil erosion "hotspots" in the Manupali River watershed

  16. Hotspots of human nutrition: Micronutrient supply, demand, and pollinator dependence

    Dombeck, E.; Chaplin-Kramer, R.; Mueller, M.; Mueller, N. D.; Foley, J. A.

    2012-12-01

    While our caloric needs can mostly be met by wind-pollinated crops such as cereals, a recent analysis of USDA data shows that animal-pollinated crops contain the vast majority of many essential nutrients, including vitamins A and C, calcium, fluoride, and folic acid. In this work we combined global crop yield data with data on nutritional content in each crop to map nutrient production around the world, and to illustrate the value of pollination services to human nutrition. Spatially explicit crop yields (at 5 min resolution) were multiplied by crop nutrient content and by crop dependence on pollination to map where reductions in total nutrient production would occur if pollination services were removed. Nutrient demand maps (human nutrient requirements multiplied by population density) were generated to identify regions where local reduction in pollination services could threaten nutritional security. Nutrient deficiency maps (nutrient supply minus nutrient demand) were also created to identify hotspots where local crop production is not adequate to meet local nutritional needs.

  17. Pervasive defaunation of forest remnants in a tropical biodiversity hotspot.

    Gustavo R Canale

    Full Text Available Tropical deforestation and forest fragmentation are among the most important biodiversity conservation issues worldwide, yet local extinctions of millions of animal and plant populations stranded in unprotected forest remnants remain poorly explained. Here, we report unprecedented rates of local extinctions of medium to large-bodied mammals in one of the world's most important tropical biodiversity hotspots. We scrutinized 8,846 person-years of local knowledge to derive patch occupancy data for 18 mammal species within 196 forest patches across a 252,669-km(2 study region of the Brazilian Atlantic Forest. We uncovered a staggering rate of local extinctions in the mammal fauna, with only 767 from a possible 3,528 populations still persisting. On average, forest patches retained 3.9 out of 18 potential species occupancies, and geographic ranges had contracted to 0-14.4% of their former distributions, including five large-bodied species that had been extirpated at a regional scale. Forest fragments were highly accessible to hunters and exposed to edge effects and fires, thereby severely diminishing the predictive power of species-area relationships, with the power model explaining only ~9% of the variation in species richness per patch. Hence, conventional species-area curves provided over-optimistic estimates of species persistence in that most forest fragments had lost species at a much faster rate than predicted by habitat loss alone.

  18. Lead Polluted Hotspot: Environmental Implication of Unplanned Industrial Development

    Rikta Sharmin Yousuf

    2016-06-01

    Full Text Available In Rayer Bazaar, different industries like tannery, plastic, textile, battery recycling industry etc. are increasing rapidly without considering the environmental issues and deterioration. Since chromium (Cr pollution of this area has been widely investigated due to the presence of tannery industries, this study was focused on examining other environmental factors. Field visits and analytical results of semi-quantitative and quantitative analysis as well as three dimensional excitation emission matrix spectroscopy (3DEEM of water, soil and vegetative tissues indicated that, the area is highly polluted in term of different environmental parameters and metal content. The extremely high lead (Pb content of the soil (1171.7 mg/kg in summer, 2157.1 mg/kg in winter and blackish materials of vegetative tissues (6585.6 mg/kg in summer, 1974.1 mg/kg in winter indicates excessive lead deposition of this area that makes it a lead polluted hotspot. One of the possible sources of the extremely high lead concentration is adjacent battery recycling industry and/or other industries surrounding this area. So it is urgent to take necessary steps to find out immediate options for possible mitigation.

  19. Atmospheric gravity waves in the Red Sea: a new hotspot

    J. M. Magalhaes

    2011-02-01

    Full Text Available The region of the Middle East around the Red Sea (between 32° E and 44° E longitude and 12° N and 28° N latitude is a currently undocumented hotspot for atmospheric gravity waves (AGWs. Satellite imagery shows evidence that this region is prone to relatively high occurrence of AGWs compared to other areas in the world, and reveals the spatial characteristics of these waves. The favorable conditions for wave propagation in this region are illustrated with three typical cases of AGWs propagating in the lower troposphere over the sea. Using weakly nonlinear long wave theory and the observed characteristic wavelengths we obtain phase speeds which are consistent with those observed and typical for AGWs, with the Korteweg-de Vries theory performing slightly better than Benjamin-Davis-Acrivos-Ono theory as far as phase speeds are concerned. ERS-SAR and Envisat-ASAR satellite data analysis between 1993 and 2008 reveals signatures consistent with horizontally propagating large-scale internal waves. These signatures cover the entire Red Sea and are more frequently observed between April and September, although they also occur during the rest of the year. The region's (seasonal propagation conditions for AGWs, based upon average vertical atmospheric stratification profiles suggest that many of the signatures identified in the satellite images are atmospheric internal waves.

  20. Orchid conservation in the biodiversity hotspot of southwestern China.

    Liu, Qiang; Chen, Jin; Corlett, Richard T; Fan, XuLi; Yu, DongLi; Yang, HongPei; Gao, JiangYun

    2015-12-01

    Xishuangbanna is on the northern margins of tropical Asia in southwestern China and has the largest area of tropical forest remaining in the country. It is in the Indo-Burma hotspot and contains 16% of China's vascular flora in medicinal or ornamental value) was significantly related to endangerment. Expansion of rubber tree plantations was less of a threat to orchids than to other taxa because only 75 orchid species (17.6%) occurred below the 1000-m-elevation ceiling for rubber cultivation, and most of these (46) occurred in nature reserves. However, climate change is projected to lift this ceiling to around 1300 m by 2050, and the limited area at higher elevations reduces the potential for upslope range expansion. The Xishuangbanna Tropical Botanical Garden is committed to achieving zero plant extinctions in Xishuangbanna, and orchids are a high priority. Appropriate in and ex situ conservation strategies, including new protected areas and seed banking, have been developed for every threatened orchid species and are being implemented. PMID:26372504