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Sample records for adaptive clinal variation

  1. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy.

    PubMed

    Silva, Gonçalo; Lima, Fernando P; Martel, Paulo; Castilho, Rita

    2014-10-01

    Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy. PMID:25143035

  2. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

    PubMed Central

    Silva, Gonçalo; Lima, Fernando P.; Martel, Paulo; Castilho, Rita

    2014-01-01

    Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy. PMID:25143035

  3. Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster.

    PubMed

    Bergland, Alan O; Tobler, Ray; González, Josefa; Schmidt, Paul; Petrov, Dmitri

    2016-03-01

    Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this hybridization event likely contributed to genome-wide patterns of parallel clinal variation between continents. The pervasive effects of admixture mean that differentiation at only several hundred loci can be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation in D. melanogaster and provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as temperate endemics. PMID:26547394

  4. Rapid Development of Adaptive, Climate-Driven Clinal Variation in Seed Mass in the Invasive Annual Forb Echium plantagineum L.

    PubMed Central

    Konarzewski, Tara K.; Murray, Brad R.; Godfree, Robert C.

    2012-01-01

    We examined adaptive clinal variation in seed mass among populations of an invasive annual species, Echium plantagineum, in response to climatic selection. We collected seeds from 34 field populations from a 1,000 km long temperature and rainfall gradient across the species' introduced range in south-eastern Australia. Seeds were germinated, grown to reproductive age under common glasshouse conditions, and progeny seeds were harvested and weighed. Analyses showed that seed mass was significantly related to climatic factors, with populations sourced from hotter, more arid sites producing heavier seeds than populations from cooler and wetter sites. Seed mass was not related to edaphic factors. We also found that seed mass was significantly related to both longitude and latitude with each degree of longitude west and latitude north increasing seed mass by around 2.5% and 4% on average. There was little evidence that within-population or between-population variation in seed mass varied in a systematic manner across the study region. Our findings provide compelling evidence for development of a strong cline in seed mass across the geographic range of a widespread and highly successful invasive annual forb. Since large seed mass is known to provide reproductive assurance for plants in arid environments, our results support the hypothesis that the fitness and range potential of invasive species can increase as a result of genetic divergence of populations along broad climatic gradients. In E. plantagineum population-level differentiation has occurred in 150 years or less, indicating that the adaptation process can be rapid. PMID:23284621

  5. Clinal variation of some mammals during the Holocene in Missouri

    NASA Astrophysics Data System (ADS)

    Purdue, James R.

    1980-03-01

    Eastern cottontail ( Sylvilagus floridanus), fox squirrel ( Sciurus niger), and gray squirrel ( Sciurus carolinensis) were examined for clinal variation during the Holocene. Modern samples of all three species displayed strong east-west patterns along the western edge of the eastern deciduous forest: S. floridanus and S. niger decrease and S. carolinensis increases in size. Archeological samples of S. carolinensis from Rodgers Shelter (23BE125), Benton County, Missouri, and Graham Cave (23MT2), Montgomery County, Missouri, indicated an increase in size from early to middle Holocene. Sylvilagus floridanus from Rodgers Shelter decreased in size from early to middle Holocene and then increased during the late Holocene to modern proportions. A literature survey reveals that clinal variation is a common phenomenon among modern homeotherms. In introduced species, clinal variation has developed after relatively few generations, indicating rapid adaptations to environmental conditions; often winter climatic variables are implicated. Morphological variation in the study species during the Holocene is interpreted as a response to changing climates. Studies of morphological clines may lead to another valuable data source for reconstructing past ecologies.

  6. Clinal variation for amino acid polymorphisms at the Pgm locus in Drosophila melanogaster.

    PubMed Central

    Verrelli, B C; Eanes, W F

    2001-01-01

    Clinal variation is common for enzymes in the glycolytic pathway for Drosophila melanogaster and is generally accepted as an adaptive response to different climates. Although the enzyme phosphoglucomutase (PGM) possesses several allozyme polymorphisms, it is unique in that it had been reported to show no clinal variation. Our recent DNA sequence investigation of Pgm found extensive cryptic amino acid polymorphism segregating with the allozyme alleles. In this study, we characterize the geographic variation of Pgm amino acid polymorphisms at the nucleotide level along a latitudinal cline in the eastern United States. A survey of 15 SNPs across the Pgm gene finds significant clinal differentiation for the allozyme polymorphisms as well as for many of the cryptic amino acid polymorphisms. A test of independence shows that pervasive linkage disequilibrium across this gene region can explain many of the amino acid clines. A single Pgm haplotype defined by two amino acid polymorphisms shows the strongest correlation with latitude and the steepest change in allele frequency across the cline. We propose that clinal selection at Pgm may in part explain the extensive amino acid polymorphism at this locus and is consistent with a multilocus response to selection in the glycolytic pathway. PMID:11290720

  7. Altitudinal Clinal Variation in Wing Size & Shape in African Drosophila melanogaster: One Cline or Many?

    PubMed Central

    Pitchers, William; Pool, John E.; Dworkin, Ian

    2013-01-01

    Geographical patterns of morphological variation have been useful in addressing hypotheses about environmental adaptation. In particular, latitudinal clines in phenotypes have been studied in a number of Drosophila species. Some environmental conditions along latitudinal clines – e.g. temperature – also vary along altitudinal clines, but these have been studied infrequently and it remains unclear whether these environmental factors are similar enough for convergence or parallel evolution. Most clinal studies in Drosophila have dealt exclusively with univariate phenotypes, allowing for the detection of clinal relationships, but not for estimating the directions of co-variation between them. We measured variation in wing shape and size in Drosophila melanogaster derived from populations at varying altitudes and latitudes across sub-Saharan Africa. Geometric morphometrics allows us to compare shape changes associated with latitude and altitude, and manipulating rearing temperature allows us to quantify the extent to which thermal plasticity recapitulates clinal effects. Comparing effect vectors demonstrates that altitude, latitude and temperature are only partly associated, and that the altitudinal shape effect may differ between Eastern and Western Africa. Our results suggest that selection responsible for these phenotypic clines may be more complex than just thermal adaptation. PMID:23356616

  8. Genomics of clinal variation in Drosophila: disentangling the interactions of selection and demography.

    PubMed

    Flatt, Thomas

    2016-03-01

    Clines in phenotypes and genotype frequencies across environmental gradients are commonly taken as evidence for spatially varying selection. Classical examples include the latitudinal clines in various species of Drosophila, which often occur in parallel fashion on multiple continents. Today, genomewide analysis of such clinal systems provides a fantastic opportunity for unravelling the genetics of adaptation, yet major challenges remain. A well-known but often neglected problem is that demographic processes can also generate clinality, independent of or coincident with selection. A closely related issue is how to identify true genic targets of clinal selection. In this issue of Molecular Ecology, three studies illustrate these challenges and how they might be met. Bergland et al. report evidence suggesting that the well-known parallel latitudinal clines in North American and Australian D. melanogaster are confounded by admixture from Africa and Europe, highlighting the importance of distinguishing demographic from adaptive clines. In a companion study, Machado et al. provide the first genomic comparison of latitudinal differentiation in D. melanogaster and its sister species D. simulans. While D. simulans is less clinal than D. melanogaster, a significant fraction of clinal genes is shared between both species, suggesting the existence of convergent adaptation to clinaly varying selection pressures. Finally, by drawing on several independent sources of evidence, Božičević et al. identify a functional network of eight clinal genes that are likely involved in cold adaptation. Together, these studies remind us that clinality does not necessarily imply selection and that separating adaptive signal from demographic noise requires great effort and care. PMID:26919307

  9. Clinal variation at phenology-related genes in spruce: parallel evolution in FTL2 and Gigantea?

    PubMed

    Chen, Jun; Tsuda, Yoshiaki; Stocks, Michael; Källman, Thomas; Xu, Nannan; Kärkkäinen, Katri; Huotari, Tea; Semerikov, Vladimir L; Vendramin, Giovanni G; Lascoux, Martin

    2014-07-01

    Parallel clines in different species, or in different geographical regions of the same species, are an important source of information on the genetic basis of local adaptation. We recently detected latitudinal clines in SNPs frequencies and gene expression of candidate genes for growth cessation in Scandinavian populations of Norway spruce (Picea abies). Here we test whether the same clines are also present in Siberian spruce (P. obovata), a close relative of Norway spruce with a different Quaternary history. We sequenced nine candidate genes and 27 control loci and genotyped 14 SSR loci in six populations of P. obovata located along the Yenisei river from latitude 56°N to latitude 67°N. In contrast to Scandinavian Norway spruce that both departs from the standard neutral model (SNM) and shows a clear population structure, Siberian spruce populations along the Yenisei do not depart from the SNM and are genetically unstructured. Nonetheless, as in Norway spruce, growth cessation is significantly clinal. Polymorphisms in photoperiodic (FTL2) and circadian clock (Gigantea, GI, PRR3) genes also show significant clinal variation and/or evidence of local selection. In GI, one of the variants is the same as in Norway spruce. Finally, a strong cline in gene expression is observed for FTL2, but not for GI. These results, together with recent physiological studies, confirm the key role played by FTL2 and circadian clock genes in the control of growth cessation in spruce species and suggest the presence of parallel adaptation in these two species. PMID:24814465

  10. Clinal variation in the juvenal plumage of American kestrels

    USGS Publications Warehouse

    Smallwood, J.A.; Natale, C.; Steenhof, K.; Meetz, M.; Marti, C.D.; Melvin, R.J.; Bortolotti, G.R.; Robertson, R.; Robertson, S.; Shuford, W.R.; Lindemann, S.A.; Tornwall, B.

    1999-01-01

    The American Kestrel(Falco sparverius) is a sexually dichromatic falcon that exhibits considerable individual plumage variability. For example, the anterior extent of the black dorsal barring in juvenile males has been used throughout North America as one of several aging criteria, but recent data demonstrate that the variability among individual Southeastern American Kestrels(E S. paulus)exceeds that accounted for by age. The objective of this study was to search for geographic patterns in the variability of juvenal plumage, particularly those characteristics considered indicative of age. Nestling kestrels (n = 610) were examined prior to fledging during the 1997 breeding season at nest box programs across a large portion of the North American breeding range. From south to north (1) the crown patches of both males and females become more completely rufous, and (2) shaft streaks on forehead and crown feathers become more pronounced, especially in males. Male Southeastern American Kestrels differed from other males (E s. sparverius) in that the anterior extent of dorsal barring averaged less but was more variable. The variability observed in North America appears to be part of a cline extending across the species range in the Western Hemisphere, where tropical subspecies are small and have reduced dorsal barring. Both body size and, especially in males, dorsal barring increases with increasing north and south latitude. We suggest that this geographic pattern is adaptive in terms of thermoregulation, and that differences in the sex roles may explain why males become less barred with maturity while females do not.

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

    PubMed

    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. Clinal variation or validation of a subspecies? A case study of the Graptemys nigrinoda complex (Testudines: Emydidae)

    USGS Publications Warehouse

    Ennen, Joshua R.; Kalis, Marley E.; Patterson, Adam L.; Kreiser, Brian R.; Lovich, Jeffrey E.; Godwin, James; Qualls, Carl P.

    2014-01-01

    Widely distributed species often display intraspecific morphological variation due to the abiotic and biotic gradients experienced across their ranges. Historically, in many vertebrate taxa, such as birds and reptiles, these morphological differences within a species were used to delimit subspecies. Graptemys nigrinoda is an aquatic turtle species endemic to the Mobile Bay Basin. Colour pattern and morphological variability were used to describe a subspecies (G. n. delticola) from the lower reaches of the system, although it and the nominate subspecies also reportedly intergrade over a large portion of the range. Other researchers have suggested that these morphological differences merely reflect clinal variation. Our molecular data (mtDNA) did not support the existence of the subspecies, as the haplotypes were differentiated by only a few base pairs and one haplotype was shared between the putative subspecies. While there were significant morphological and pattern differences among putative specimens of G. n. nigrinoda, G. n. delticola and G. n. nigrinoda × delticola, these differences probably represent clinal variation as they were also related to environmental variables [i.e. cumulative drainage area and drainage (categorical)]. Specimens occupying slow-current, high-turbidity river reaches (e.g. the Tensaw River) exhibited greater relative carapace heights and more dark pigmentation, while specimens occupying fast-current, clearer rivers (e.g. the upper Alabama, Cahaba and Tallapoosa rivers) exhibited lower carapace heights and more yellow pigmentation. Given the absence of clear molecular and morphological differences that are related to drainage characteristics, we suggest that there is not sufficient evidence for the recognition of G. n. delticola as a distinct subspecies.

  13. Sympatric divergence and clinal variation in multiple coloration traits of Ficedula flycatchers.

    PubMed

    Laaksonen, T; Sirkiä, P M; Calhim, S; Brommer, J E; Leskinen, P K; Primmer, C R; Adamík, P; Artemyev, A V; Belskii, E; Both, C; Bureš, S; Burgess, M D; Doligez, B; Forsman, J T; Grinkov, V; Hoffmann, U; Ivankina, E; Král, M; Krams, I; Lampe, H M; Moreno, J; Mägi, M; Nord, A; Potti, J; Ravussin, P-A; Sokolov, L

    2015-04-01

    Geographic variation in phenotypes plays a key role in fundamental evolutionary processes such as local adaptation, population differentiation and speciation, but the selective forces behind it are rarely known. We found support for the hypothesis that geographic variation in plumage traits of the pied flycatcher Ficedula hypoleuca is explained by character displacement with the collared flycatcher Ficedula albicollis in the contact zone. The plumage traits of the pied flycatcher differed strongly from the more conspicuous collared flycatcher in a sympatric area but increased in conspicuousness with increasing distance to there. Phenotypic differentiation (PST ) was higher than that in neutral genetic markers (FST ), and the effect of geographic distance remained when statistically controlling for neutral genetic differentiation. This suggests that a cline created by character displacement and gene flow explains phenotypic variation across the distribution of this species. The different plumage traits of the pied flycatcher are strongly to moderately correlated, indicating that they evolve non-independently from each other. The flycatchers provide an example of plumage patterns diverging in two species that differ in several aspects of appearance. The divergence in sympatry and convergence in allopatry in these birds provide a possibility to study the evolutionary mechanisms behind the highly divergent avian plumage patterns. PMID:25683091

  14. Recent ecological selection on regulatory divergence is shaping clinal variation in senecio on Mount Etna.

    PubMed

    Muir, Graham; Osborne, Owen G; Sarasa, Jonas; Hiscock, Simon J; Filatov, Dmitry A

    2013-10-01

    The hybrid zone on Mount Etna (Sicily) between Senecio aethnensis and Senecio chrysanthemifolius (two morphologically and physiologically distinct species) is a classic example of an altitudinal cline. Hybridization at intermediate altitudes and gradients in phenotypic and life-history traits occur along altitudinal transects of the volcano. The cline is considered to be a good example of ecological selection with species differences arising by divergent selection opposing gene flow. However, the possibility that the cline formed from recent secondary contact following an allopatric phase is difficult to exclude. We demonstrate a recent split between S. aethnensis and S. chrysanthemifolius (as recent as ∼32,000 years ago) and sufficient gene flow (2Nm > 1) to have prevented divergence (implicating a role for diversifying selection in the maintenance of the cline). Differentially expressed genes between S. aethnensis and S. chrysanthemifolius exhibit significantly higher genetic divergence relative to "expression invariant" controls, suggesting that species differences may in part be mediated by divergent selection on differentially expressed genes involved with altitude-related adaptation. The recent split time and the absence of fixed differences between these two ecologically distinct species suggest the rapid evolution to an altitudinal cline involving selection on both sequence and expression variation. PMID:24094352

  15. Clinal morphological variation along a depth gradient in the living scleractinian reef coral Favia pallida: Effects on perceived evolutionary tempos in the fossil record

    SciTech Connect

    Cuffey, R.J. ); Pachut, J.F. )

    1990-12-01

    The Holocene reef-building coral Favia pallida was sampled at 4.5 m depth increments (to 40 m) from two reefs on Enewetak Atoll to examine intraspecific environmental effects. An exposed outer reef was massive and wall-like, whereas a sheltered lagoonal reef grew as a slender pinnacle. Corallite diameter and growth rate, two attributes retrievable in fossil corals, were measured with data partitioned into shallow (<20 m), intermediate (20 to 29 m), and deep-water (>29 m) subsets. Highly significant differences between depth zone populations were found for both corallite diameters and growth rates in analyses of individual and combined reef data sets. Canonical variates analyses (CVA) separated populations from depth zones along single, highly significant, functions. Centroids and 95% confidence intervals, calculated from CVA scores of colonies in each population, are widely separated for the lagoon reef and combined data sets. Conversely, populations from shallow and intermediate depths on the outer reef display overlapping confidence bars indicative of more gradational morphologic changes. When CV's were used to classify specimens to groups, misassignments of intermediate depth specimens to shallow or deep-water populations underscored the gradational nature of the environment. Completely intergrading populations of Favia pallida collected from different depths can be morphologically separated into statistically distinct groupings. A stratigraphic succession of such morphotypes might be interpreted as abruptly appearing separate species if sampling were not as uniform, systematic, and detailed as was possible on modern reefs. Analyses of evolutionary patterns must carefully assess potential effects of clinal variation if past evolutionary patterns are to be interpreted correctly.

  16. Clinal variation in colony breeding structure and level of inbreeding in the subterranean termites Reticulitermes flavipes and R. grassei.

    PubMed

    Vargo, Edward L; Leniaud, Laurianne; Swoboda, Lois E; Diamond, Sarah E; Weiser, Michael D; Miller, Dini M; Bagnères, Anne-Geneviève

    2013-03-01

    Social insects exhibit remarkable variation in their colony breeding structures, both within and among species. Ecological factors are believed to be important in shaping reproductive traits of social insect colonies, yet there is little information linking specific environmental variables with differences in breeding structure. Subterranean termites (Rhinotermitidae) show exceptional variation in colony breeding structure, differing in the number of reproductives and degree of inbreeding; colonies can be simple families headed by a single pair of monogamous reproductives (king and queen) or they can be extended families headed by multiple inbreeding neotenic reproductives (wingless individuals). Using microsatellite markers, we characterized colony breeding structure and levels of inbreeding in populations over large parts of the range of the subterranean termites Reticulitermes flavipes in the USA and R. grassei in Europe. Combining these new data with previous results on populations of both species, we found that latitude had a strong effect on the proportion of extended-family colonies in R. flavipes and on levels of inbreeding in both species. We examined the effect of several environmental variables that vary latitudinally; while the degree of inbreeding was greatest in cool, moist habitats in both species, seasonality affected the species differently. Inbreeding in R. flavipes was most strongly associated with climatic variables (mean annual temperature and seasonality), whereas nonclimatic variables, including the availability of wood substrate and soil composition, were important predictors of inbreeding in R. grassei. These results are the first showing that termite breeding structure is shaped by local environmental factors and that species can vary in their responses to these factors. PMID:23293875

  17. Plasticity of functional traits varies clinally along a rainfall gradient in Eucalyptus tricarpa.

    PubMed

    McLean, Elizabeth H; Prober, Suzanne M; Stock, William D; Steane, Dorothy A; Potts, Brad M; Vaillancourt, René E; Byrne, Margaret

    2014-06-01

    Widespread species often occur across a range of climatic conditions, through a combination of local genetic adaptations and phenotypic plasticity. Species with greater phenotypic plasticity are likely to be better positioned to cope with rapid anthropogenic climate changes, while those displaying strong local adaptations might benefit from translocations to assist the movement of adaptive genes as the climate changes. Eucalyptus tricarpa occurs across a climatic gradient in south-eastern Australia, a region of increasing aridity, and we hypothesized that this species would display local adaptation to climate. We measured morphological and physiological traits reflecting climate responses in nine provenances from sites of 460 to 1040 mm annual rainfall, in their natural habitat and in common gardens near each end of the gradient. Local adaptation was evident in functional traits and differential growth rates in the common gardens. Some traits displayed complex combinations of plasticity and genetic divergence among provenances, including clinal variation in plasticity itself. Provenances from drier locations were more plastic in leaf thickness, whereas leaf size was more plastic in provenances from higher rainfall locations. Leaf density and stomatal physiology (as indicated by δ(13)C and δ(18)O) were highly and uniformly plastic. In addition to variation in mean trait values, genetic variation in trait plasticity may play a role in climate adaptation. PMID:24329726

  18. Variational method for adaptive grid generation

    SciTech Connect

    Brackbill, J.U.

    1983-01-01

    A variational method for generating adaptive meshes is described. Functionals measuring smoothness, skewness, orientation, and the Jacobian are minimized to generate a mapping from a rectilinear domain in natural coordinate to an arbitrary domain in physical coordinates. From the mapping, a mesh is easily constructed. In using the method to adaptively zone computational problems, as few as one third the number of mesh points are required in each coordinate direction compared with a uniformly zoned mesh.

  19. Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation.

    PubMed

    Hedrick, Philip W

    2013-09-01

    Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans-species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non-native ancestry in an endangered native salamander, are examined. PMID:23906376

  20. Adaptation of US maize to temperature variations

    NASA Astrophysics Data System (ADS)

    Butler, Ethan E.; Huybers, Peter

    2013-01-01

    High temperatures are associated with reduced crop yields, and predictions for future warming have raised concerns regarding future productivity and food security. However, the extent to which adaptation can mitigate such heat-related losses remains unclear. Here we empirically demonstrate how maize is locally adapted to hot temperatures across US counties. Using this spatial adaptation as a surrogate for future adaptation, we find that losses to average US maize yields from a 2°C warming would be reduced from 14% to only 6% and that loss in net production is wholly averted. This result does not account for possible changes in temperature variability or water resources, nor does it account for all possible forms of adaptation, but it does show that adaptation is of first-order importance for predicting future changes in yield. Further research should be undertaken regarding the ability to adapt to a changing climate, including analysis of other crops and regions, the application of more sophisticated models of crop development, and field trials employing artificially increased temperature.

  1. Adaptive genetic variation and population differences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Humans are physiologically and morphologically diverse. Such diversities have been shaped by demographic history and adaptation to local environments, including regional climate, landscape, food source, culture, and pathogens since their expansion within and out of Africa between 50,000 and 100,000 ...

  2. Amplitude variations on the Extreme Adaptive Optics testbed

    SciTech Connect

    Evans, J; Thomas, S; Dillon, D; Gavel, D; Phillion, D; Macintosh, B

    2007-08-14

    High-contrast adaptive optics systems, such as those needed to image extrasolar planets, are known to require excellent wavefront control and diffraction suppression. At the Laboratory for Adaptive Optics on the Extreme Adaptive Optics testbed, we have already demonstrated wavefront control of better than 1 nm rms within controllable spatial frequencies. Corresponding contrast measurements, however, are limited by amplitude variations, including those introduced by the micro-electrical-mechanical-systems (MEMS) deformable mirror. Results from experimental measurements and wave optic simulations of amplitude variations on the ExAO testbed are presented. We find systematic intensity variations of about 2% rms, and intensity variations with the MEMS to be 6%. Some errors are introduced by phase and amplitude mixing because the MEMS is not conjugate to the pupil, but independent measurements of MEMS reflectivity suggest that some error is introduced by small non-uniformities in the reflectivity.

  3. Allele surfing promotes microbial adaptation from standing variation.

    PubMed

    Gralka, Matti; Stiewe, Fabian; Farrell, Fred; Möbius, Wolfram; Waclaw, Bartlomiej; Hallatschek, Oskar

    2016-08-01

    The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from 'soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges. PMID:27307400

  4. The role of standing variation in geographic convergent adaptation

    PubMed Central

    Ralph, Peter L.; Coop, Graham

    2016-01-01

    The extent to which populations experiencing shared selective pressures adapt through a shared genetic response is relevant to many questions in evolutionary biology. In a number of well studied traits and species, it appears that convergent evolution within species is common. In this paper, we explore how standing, genetic variation contributes to convergent genetic responses in a geographically spread population, extending our previous work on the topic. Geographically limited dispersal slows the spread of each selected allele, hence allowing other alleles – newly arisen mutants or present as standing variation – to spread before any one comes to dominate the population. When such alleles meet, their progress is substantially slowed – if the alleles are selectively equivalent, they mix slowly, dividing the species range into a random tessellation, which can be well understood by analogy to a Poisson process model of crystallization. In this framework, we derive the geographic scale over which a typical allele is expected to dominate, the time it takes the species to adapt as a whole, and the proportion of adaptive alleles that arise from standing variation. Finally, we explore how negative pleiotropic effects of alleles before an environment change can bias the subset of alleles that contribute to the species’ adaptive response. We apply the results to the many geographically localized G6PD deficiency alleles thought to confer resistance to malaria, where the large mutational target size makes it a likely candidate for adaptation from standing variation, despite the selective cost of G6PD deficiency alleles in the absence of malaria. We find the numbers and geographic spread of these alleles matches our predictions reasonably well, consistent with the view that they arose from a combination of standing variation and new mutations since the advent of malaria. Our results suggest that much of adaptation may be geographically local even when selection

  5. Adaptive latitudinal variation in Common Blackbird Turdus merula nest characteristics.

    PubMed

    Mainwaring, Mark C; Deeming, D Charles; Jones, Chris I; Hartley, Ian R

    2014-03-01

    Nest construction is taxonomically widespread, yet our understanding of adaptive intraspecific variation in nest design remains poor. Nest characteristics are expected to vary adaptively in response to predictable variation in spring temperatures over large spatial scales, yet such variation in nest design remains largely overlooked, particularly amongst open-cup-nesting birds. Here, we systematically examined the effects of latitudinal variation in spring temperatures and precipitation on the morphology, volume, composition, and insulatory properties of open-cup-nesting Common Blackbirds' Turdus merula nests to test the hypothesis that birds living in cooler environments at more northerly latitudes would build better insulated nests than conspecifics living in warmer environments at more southerly latitudes. As spring temperatures increased with decreasing latitude, the external diameter of nests decreased. However, as nest wall thickness also decreased, there was no variation in the diameter of the internal nest cups. Only the mass of dry grasses within nests decreased with warmer temperatures at lower latitudes. The insulatory properties of nests declined with warmer temperatures at lower latitudes and nests containing greater amounts of dry grasses had higher insulatory properties. The insulatory properties of nests decreased with warmer temperatures at lower latitudes, via changes in morphology (wall thickness) and composition (dry grasses). Meanwhile, spring precipitation did not vary with latitude, and none of the nest characteristics varied with spring precipitation. This suggests that Common Blackbirds nesting at higher latitudes were building nests with thicker walls in order to counteract the cooler temperatures. We have provided evidence that the nest construction behavior of open-cup-nesting birds systematically varies in response to large-scale spatial variation in spring temperatures. PMID:24683466

  6. Function-valued adaptive dynamics and the calculus of variations.

    PubMed

    Parvinen, Kalle; Dieckmann, Ulf; Heino, Mikko

    2006-01-01

    Adaptive dynamics has been widely used to study the evolution of scalar-valued, and occasionally vector-valued, strategies in ecologically realistic models. In many ecological situations, however, evolving strategies are best described as function-valued, and thus infinite-dimensional, traits. So far, such evolution has only been studied sporadically, mostly based on quantitative genetics models with limited ecological realism. In this article we show how to apply the calculus of variations to find evolutionarily singular strategies of function-valued adaptive dynamics: such a strategy has to satisfy Euler's equation with environmental feedback. We also demonstrate how second-order derivatives can be used to investigate whether or not a function-valued singular strategy is evolutionarily stable. We illustrate our approach by presenting several worked examples. PMID:16012801

  7. Loss of adaptive variation during evolutionary responses to climate change.

    PubMed

    Buckley, James; Bridle, Jon R

    2014-10-01

    The changes in species' geographical distribution demanded by climate change are often critically limited by the availability of key interacting species. In such cases, species' persistence will depend on the rapid evolution of biotic interactions. Understanding evolutionary limits to such adaptation is therefore crucial for predicting biological responses to environmental change. The recent poleward range expansion of the UK brown argus butterfly has been associated with a shift in female preference from its main host plant, rockrose (Cistaceae), onto Geraniaceae host plants throughout its new distribution. Using reciprocal transplants onto natural host plants across the UK range, we demonstrate reduced fitness of females from recently colonised Geraniaceae-dominated habitat when moved to ancestral rockrose habitats. By contrast, individuals from ancestral rockrose habitats show no reduction in fitness on Geraniaceae. Climate-driven range expansion in this species is therefore associated with the rapid evolution of biotic interactions and a significant loss of adaptive variation. PMID:25104062

  8. Rapid differentiation of sexual signals in invasive toads: call variation among populations

    PubMed Central

    Yasumiba, Kiyomi; Duffy, Richard L.; Parsons, Scott A.; Alford, Ross A.; Schwarzkopf, Lin

    2016-01-01

    Advertisement calls tend to differ among populations, based on morphological and environmental factors, or simply geographic distance, in many taxa. Invasive cane toads (Rhinella marina) were introduced to Australia in 1935 and their distribution has expanded at increasing rates over time. Rapid evolution occurred in morphological and behavioural characters that accelerate dispersal, but the effects of rapid expansion on sexual signals have not been examined. We collected advertisement calls from four populations of different ages since invasion, and analysed the geographic differentiation of seven call parameters. Our comparisons indicate that the calls of R. marina differ among Australian populations. The signal variation was not simply clinal with respect to population age, climate, or morphological differentiation. We suggest that selection on signalling among populations has been idiosyncratic and may reflect local female preferences or adaptation to environmental factors that are not clinal such as energy availability. PMID:27328666

  9. Rapid differentiation of sexual signals in invasive toads: call variation among populations.

    PubMed

    Yasumiba, Kiyomi; Duffy, Richard L; Parsons, Scott A; Alford, Ross A; Schwarzkopf, Lin

    2016-01-01

    Advertisement calls tend to differ among populations, based on morphological and environmental factors, or simply geographic distance, in many taxa. Invasive cane toads (Rhinella marina) were introduced to Australia in 1935 and their distribution has expanded at increasing rates over time. Rapid evolution occurred in morphological and behavioural characters that accelerate dispersal, but the effects of rapid expansion on sexual signals have not been examined. We collected advertisement calls from four populations of different ages since invasion, and analysed the geographic differentiation of seven call parameters. Our comparisons indicate that the calls of R. marina differ among Australian populations. The signal variation was not simply clinal with respect to population age, climate, or morphological differentiation. We suggest that selection on signalling among populations has been idiosyncratic and may reflect local female preferences or adaptation to environmental factors that are not clinal such as energy availability. PMID:27328666

  10. Epigenetic variation contributes to environmental adaptation of Arabidopsis thaliana

    PubMed Central

    Kooke, Rik; Keurentjes, Joost J B

    2015-01-01

    Epigenetic variation is frequently observed in plants and direct relationships between differences in DNA methylation and phenotypic responses to changing environments have often been described. The identification of contributing genetic loci, however, was until recently hampered by the lack of suitable genome wide mapping resources that specifically segregate for epigenetic marks. The development of epi-RIL populations in the model species Arabidopsis thaliana has alleviated this obstacle, enabling the accurate genetic analysis of epigenetic variation. Comprehensive morphological phenotyping of a ddm1 derived epi-RIL population in different environments and subsequent epi-QTL mapping revealed a high number of epi-QTLs and pleiotropic effects of several DMRs on numerous traits. For a number of these epi-QTLs epistatic interactions could be observed, further adding to the complexity of epigenetic regulation. Moreover, linkage to epigenetic marks indicated a specific role for DNA-methylation variation, rather than TE transposition, in plastic responses to changing environments. These findings provide supportive evidence for a role of epigenetic regulation in evolutionary and adaptive processes. PMID:26237693

  11. Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change.

    PubMed

    Thorpe, Roger S; Barlow, Axel; Malhotra, Anita; Surget-Groba, Yann

    2015-03-01

    Global warming will impact species in a number of ways, and it is important to know the extent to which natural populations can adapt to anthropogenic climate change by natural selection. Parallel microevolution within separate species can demonstrate natural selection, but several studies of homoplasy have not yet revealed examples of widespread parallel evolution in a generic radiation. Taking into account primary phylogeographic divisions, we investigate numerous quantitative traits (size, shape, scalation, colour pattern and hue) in anole radiations from the mountainous Lesser Antillean islands. Adaptation to climatic differences can lead to very pronounced differences between spatially close populations with all studied traits showing some evidence of parallel evolution. Traits from shape, scalation, pattern and hue (particularly the latter) show widespread evolutionary parallels within these species in response to altitudinal climate variation greater than extreme anthropogenic climate change predicted for 2080. This gives strong evidence of the ability to adapt to climate variation by natural selection throughout this radiation. As anoles can evolve very rapidly, it suggests anthropogenic climate change is likely to be less of a conservation threat than other factors, such as habitat loss and invasive species, in this, Lesser Antillean, biodiversity hot spot. PMID:25644484

  12. Frequency variations of discrete cranial traits in major human populations. I. Supernumerary ossicle variations

    PubMed Central

    HANIHARA, TSUNEHIKO; ISHIDA, HAJIME

    2001-01-01

    Four supernumerary ossicle variations—the ossicle at the lambda, the parietal notch bone, the asterionic bone, and the occipitomastoid bone—were examined for laterality differences, intertrait correlations, sex differences, and between group variations in the samples from around the world. Significant laterality differences were not detected in almost all samples. In some pairs of traits, significant association of occurrence were found. Several geographic samples were sexually dimorphic with respect to the asterionic bone and to a lesser extent for the parietal notch bone. East/Northeast Asians including the Arctic populations in general had lower frequencies of the 4 accessory ossicles. Australians, Melanesians and the majority of the New World peoples, on the other hand, generally had high frequencies. In the western hemisphere of the Old World, Subsaharan Africans had relatively high frequencies. Except for the ossicle at the lambda, the distribution pattern in incidence showed clinal variation from south to north. Any identifiable adaptive value related to environmental or subsistence factors may be expressed in such clinal variation. This may allow us to hypothesise that not only mechanical factors but a founder effect, genetic drift, and population structure could have been the underlying causes for interregional variation and possible clines in the incidences of the accessory ossicles. PMID:11465862

  13. Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

    PubMed Central

    Matuszewski, Sebastian; Hermisson, Joachim; Kopp, Michael

    2015-01-01

    Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from preexisting standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect and (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow. PMID:26038348

  14. Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum.

    PubMed

    Matuszewski, Sebastian; Hermisson, Joachim; Kopp, Michael

    2015-08-01

    Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from preexisting standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect and (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow. PMID:26038348

  15. Replicate altitudinal clines reveal that evolutionary flexibility underlies adaptation to drought stress in annual Mimulus guttatus.

    PubMed

    Kooyers, Nicholas J; Greenlee, Anna B; Colicchio, Jack M; Oh, Morgan; Blackman, Benjamin K

    2015-04-01

    Examining how morphology, life history and physiology vary along environmental clines can reveal functional insight into adaptations to climate and thus inform predictions about evolutionary responses to global change. Widespread species occurring over latitudinal and altitudinal gradients in seasonal water availability are excellent systems for investigating multivariate adaptation to drought stress. Under common garden conditions, we characterized variation in 27 traits for 52 annual populations of Mimulus guttatus sampled from 10 altitudinal transects. We also assessed variation in the critical photoperiod for flowering and surveyed neutral genetic markers to control for demography when analyzing clinal patterns. Many drought escape (e.g. flowering time) and drought avoidance (e.g. specific leaf area, succulence) traits exhibited geographic or climatic clines, which often remained significant after accounting for population structure. Critical photoperiod and flowering time in glasshouse conditions followed distinct clinal patterns, indicating different aspects of seasonal phenology confer adaptation to unique agents of selection. Although escape and avoidance traits were negatively correlated range-wide, populations from sites with short growing seasons produced both early flowering and dehydration avoidance phenotypes. Our results highlight how abundant genetic variation in the component traits that build multivariate adaptations to drought stress provides flexibility for intraspecific adaptation to diverse climates. PMID:25407964

  16. Biological adaptability under seasonal variation of light/dark cycles.

    PubMed

    Quiles, Caroline Luísa; de Oliveira, Melissa Alves Braga; Tonon, André Comiran; Hidalgo, Maria Paz Loayza

    2016-01-01

    3A substantial amount of experimental models designed to understand rhythms entrainment and the effects of different regimens of light exposure on health have been proposed. However, many of them do not relate to what occurs in real life. Our objective was to evaluate the influence of "seasonal-like" variation in light/dark cycles on biological rhythms. Twenty adult male Wistar rats were assigned to three groups: control (CT), kept in 12:12 light/dark (LD) cycle; long photoperiod/short photoperiod (LP/SP), kept in 16.5:7.5 LD cycle for 18 days (phase A), then 17 days of gradual reductions in light time (phase B), then 18 days of shorter exposure (7.5:16.5 LD cycle, phase C); short photoperiod/long photoperiod (SP/LP) group, with same modifications as the LP/SP group, but in reverse order, starting phase A in 7.5:16.5 LD cycle. Activity and temperature were recorded constantly, and melatonin and cortisol concentrations were measured twice. Activity and temperature acrophases of all groups changed according to light. The correlation between activity and temperature was, overall, significantly lower for SP/LP group compared with LP/SP and CT groups. Regarding melatonin concentration, LP/SP group showed significant positive correlation between phase A and C (p = 0.018). Animals changed temperature and activity according to photoperiod and demonstrated better adaptability in transitioning from long to short photoperiod. Since this model imitates seasonal variation in light in a species that is largely used in behavioral experiments, it reveals promising methods to improve the reliability of experimental models and of further environmental health research. PMID:27222076

  17. Human proximal femur bone adaptation to variations in hip geometry.

    PubMed

    Machado, M M; Fernandes, P R; Zymbal, V; Baptista, F

    2014-10-01

    The study of bone mass distribution at proximal femur may contribute to understand the role of hip geometry on hip fracture risk. We examined how bone mineral density (BMD) of proximal femur adapts to inter individual variations in the femoral neck length (FNL), femoral neck width (FNW) and neck shaft angle (NSA). A parameterized and dimensionally scalable 3-D finite element model of a reference proximal femur geometry was incrementally adjusted to adopt physiological ranges at FNL (3.90-6.90cm), FNW (2.90-3.46cm), and NSA (109-141º), yielding a set of femora with different geometries. The bone mass distribution for each femur was obtained with a suitable bone remodelling model. The BMDs at the integral femoral neck (FN) and at the intertrochanteric (ITR) region, as well as the BMD ratio of inferomedial to superolateral (IM:SL) regions of FN and BMD ratio of FN:ITR were used to represent bone mass distribution. Results revealed that longer FNLs present greater BMD (g/cm(3)) at the FN, mainly at the SL region, and at the ITR region. Wider FNs were associated with reduced BMD at the FN, particularly at the SL region, and at the ITR region. Larger NSAs up to 129° were associated with BMD diminutions at the FN and ITR regions and with increases of the IM:SL BMD ratio while NSAs larger than 129° resulted in decrease of the IM:SL BMD ratio. These findings suggest hip geometry as moderator of the mechanical loading influence on bone mass distribution at proximal femur with higher FNL favoring the BMD of FN and ITR regions and greater FNW and NSA having the opposite effect. Augmented values of FNL and FNW seem also to favor more the BMD at the superolateral than at the inferomedial FN region. PMID:25016094

  18. Speckle reduction in optical coherence tomography by adaptive total variation method

    NASA Astrophysics Data System (ADS)

    Wu, Tong; Shi, Yaoyao; Liu, Youwen; He, Chongjun

    2015-12-01

    An adaptive total variation method based on the combination of speckle statistics and total variation restoration is proposed and developed for reducing speckle noise in optical coherence tomography (OCT) images. The statistical distribution of the speckle noise in OCT image is investigated and measured. With the measured parameters such as the mean value and variance of the speckle noise, the OCT image is restored by the adaptive total variation restoration method. The adaptive total variation restoration algorithm was applied to the OCT images of a volunteer's hand skin, which showed effective speckle noise reduction and image quality improvement. For image quality comparison, the commonly used median filtering method was also applied to the same images to reduce the speckle noise. The measured results demonstrate the superior performance of the adaptive total variation restoration method in terms of image signal-to-noise ratio, equivalent number of looks, contrast-to-noise ratio, and mean square error.

  19. Population variation revealed high-altitude adaptation of Tibetan mastiffs.

    PubMed

    Li, Yan; Wu, Dong-Dong; Boyko, Adam R; Wang, Guo-Dong; Wu, Shi-Fang; Irwin, David M; Zhang, Ya-Ping

    2014-05-01

    With the assistance of their human companions, dogs have dispersed into new environments during the expansion of human civilization. Tibetan Mastiff (TM), a native of the Tibetan Plateau, was derived from the domesticated Chinese native dog and, like Tibetans, has adapted to the extreme environment of high altitude. Here, we genotyped genome-wide single-nucleotide polymorphisms (SNPs) from 32 TMs and compared them with SNPs from 20 Chinese native dogs and 14 gray wolves (Canis lupus). We identified 16 genes with signals of positive selection in the TM, with 12 of these candidate genes associated with functions that have roles in adaptation to high-altitude adaptation, such as EPAS1, SIRT7, PLXNA4, and MAFG that have roles in responses to hypoxia. This study provides important information on the genetic diversity of the TM and potential mechanisms for adaptation to hypoxia. PMID:24520091

  20. Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language.

    PubMed

    Rosser, Z H; Zerjal, T; Hurles, M E; Adojaan, M; Alavantic, D; Amorim, A; Amos, W; Armenteros, M; Arroyo, E; Barbujani, G; Beckman, G; Beckman, L; Bertranpetit, J; Bosch, E; Bradley, D G; Brede, G; Cooper, G; Côrte-Real, H B; de Knijff, P; Decorte, R; Dubrova, Y E; Evgrafov, O; Gilissen, A; Glisic, S; Gölge, M; Hill, E W; Jeziorowska, A; Kalaydjieva, L; Kayser, M; Kivisild, T; Kravchenko, S A; Krumina, A; Kucinskas, V; Lavinha, J; Livshits, L A; Malaspina, P; Maria, S; McElreavey, K; Meitinger, T A; Mikelsaar, A V; Mitchell, R J; Nafa, K; Nicholson, J; Nørby, S; Pandya, A; Parik, J; Patsalis, P C; Pereira, L; Peterlin, B; Pielberg, G; Prata, M J; Previderé, C; Roewer, L; Rootsi, S; Rubinsztein, D C; Saillard, J; Santos, F R; Stefanescu, G; Sykes, B C; Tolun, A; Villems, R; Tyler-Smith, C; Jobling, M A

    2000-12-01

    Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift. PMID:11078479

  1. Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language

    PubMed Central

    Rosser, Zoë H.; Zerjal, Tatiana; Hurles, Matthew E.; Adojaan, Maarja; Alavantic, Dragan; Amorim, António; Amos, William; Armenteros, Manuel; Arroyo, Eduardo; Barbujani, Guido; Beckman, Gunhild; Beckman, Lars; Bertranpetit, Jaume; Bosch, Elena; Bradley, Daniel G.; Brede, Gaute; Cooper, Gillian; Côrte-Real, Helena B. S. M.; de Knijff, Peter; Decorte, Ronny; Dubrova, Yuri E.; Evgrafov, Oleg; Gilissen, Anja; Glisic, Sanja; Gölge, Mukaddes; Hill, Emmeline W.; Jeziorowska, Anna; Kalaydjieva, Luba; Kayser, Manfred; Kivisild, Toomas; Kravchenko, Sergey A.; Krumina, Astrida; Kučinskas, Vaidutis; Lavinha, João; Livshits, Ludmila A.; Malaspina, Patrizia; Maria, Syrrou; McElreavey, Ken; Meitinger, Thomas A.; Mikelsaar, Aavo-Valdur; Mitchell, R. John; Nafa, Khedoudja; Nicholson, Jayne; Nørby, Søren; Pandya, Arpita; Parik, Jüri; Patsalis, Philippos C.; Pereira, Luísa; Peterlin, Borut; Pielberg, Gerli; Prata, Maria João; Previderé, Carlo; Roewer, Lutz; Rootsi, Siiri; Rubinsztein, D. C.; Saillard, Juliette; Santos, Fabrício R.; Stefanescu, Gheorghe; Sykes, Bryan C.; Tolun, Aslihan; Villems, Richard; Tyler-Smith, Chris; Jobling, Mark A.

    2000-01-01

    Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift. PMID:11078479

  2. Arenavirus Variations Due to Host-Specific Adaptation

    PubMed Central

    Zapata, Juan C.; Salvato, Maria S.

    2013-01-01

    Arenavirus particles are enveloped and contain two single-strand RNA genomic segments with ambisense coding. Genetic plasticity of the arenaviruses comes from transcription errors, segment reassortment, and permissive genomic packaging, and results in their remarkable ability, as a group, to infect a wide variety of hosts. In this review, we discuss some in vitro studies of virus genetic and phenotypic variation after exposure to selective pressures such as high viral dose, mutagens and antivirals. Additionally, we discuss the variation in vivo of selected isolates of Old World arenaviruses, particularly after infection of different animal species. We also discuss the recent emergence of new arenaviruses in the context of our observations of sequence variations that appear to be host-specific. PMID:23344562

  3. Circumpolar variation in morphological characteristics of Greater White-fronted Geese Anser albifrons

    USGS Publications Warehouse

    Ely, C.R.; Fox, A.D.; Alisauskas, R.T.; Andreev, A.; Bromley, R.G.; Degtyarev, A.G.; Ebbinge, B.; Gurtovaya, E.N.; Kerbes, R.; Kondratyev, A.V.; Kostin, I.; Krechmar, A.V.; Litvin, K.E.; Miyabayashi, Y.; Moou, J.H.; Oates, R.M.; Orthmeyer, D.L.; Sabano, Y.; Simpson, S.G.; Solovieva, D.V.; Spindler, Michael A.; Syroechkovsky, Y.V.; Takekawa, J.Y.; Walsh, A.

    2005-01-01

    Capsule: Greater White-fronted Geese show significant variation in body size from sampling locations throughout their circumpolar breeding range. Aims: To determine the degree of geographical variation in body size of Greater White-fronted Geese and identify factors contributing to any apparent patterns in variation. Methods: Structural measures of >3000 geese from 16 breeding areas throughout the Holarctic breeding range of the species were compared statistically. Results: Palearctic forms varied clinally, and increased in size from the smallest forms on the Kanin and Taimyr peninsulas in western Eurasia to the largest forms breeding in the Anadyr Lowlands of eastern Chukotka. Clinal variation was less apparent in the Nearctic, as both the smallest form in the Nearctic and the largest form overall (the Tule Goose) were from different breeding areas in Alaska. The Tule Goose was 25% larger than the smallest form. Birds from Greenland (A. a. flavirostris) were the second largest, although only slightly larger than geese from several North American populations. Body size was not correlated with breeding latitude but was positively correlated with temperature on the breeding grounds, breeding habitat, and migration distance. Body mass of Greater White-fronted Geese from all populations remained relatively constant during the period of wing moult. Morphological distinctness of eastern and western Palearctic forms concurs with earlier findings of complete range disjunction. Conclusions: Patterns of morphological variation in Greater White-fronted Geese across the Holarctic can be generally attributed to adaptation to variable breeding environments, migration requirements, and phylo-geographical histories. 

  4. Effects of founding genetic variation on adaptation to a novel resource.

    PubMed

    Agashe, Deepa; Falk, Jay J; Bolnick, Daniel I

    2011-09-01

    Population genetic theory predicts that adaptation in novel environments is enhanced by genetic variation for fitness. However, theory also predicts that under strong selection, demographic stochasticity can drive populations to extinction before they can adapt. We exposed wheat-adapted populations of the flour beetle (Tribolium castaneum) to a novel suboptimal corn resource, to test the effects of founding genetic variation on population decline and subsequent extinction or adaptation. As previously reported, genetically diverse populations were less likely to go extinct. Here, we show that among surviving populations, genetically diverse groups recovered faster after the initial population decline. Within two years, surviving populations significantly increased their fitness on corn via increased fecundity, increased egg survival, faster larval development, and higher rate of egg cannibalism. However, founding genetic variation only enhanced the increase in fecundity, despite existing genetic variation-and apparent lack of trade-offs-for egg survival and larval development time. Thus, during adaptation to novel habitats the positive impact of genetic variation may be restricted to only a few traits, although change in many life-history traits may be necessary to avoid extinction. Despite severe initial maladaptation and low population size, genetic diversity can thus overcome the predicted high extinction risk in new habitats. PMID:21884051

  5. Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field.

    PubMed

    Manel, Stéphanie; Joost, Stéphane; Epperson, Bryan K; Holderegger, Rolf; Storfer, Andrew; Rosenberg, Michael S; Scribner, Kim T; Bonin, Aurélie; Fortin, Marie-Josée

    2010-09-01

    Understanding the genetic basis of species adaptation in the context of global change poses one of the greatest challenges of this century. Although we have begun to understand the molecular basis of adaptation in those species for which whole genome sequences are available, the molecular basis of adaptation is still poorly understood for most non-model species. In this paper, we outline major challenges and future research directions for correlating environmental factors with molecular markers to identify adaptive genetic variation, and point to research gaps in the application of landscape genetics to real-world problems arising from global change, such as the ability of organisms to adapt over rapid time scales. High throughput sequencing generates vast quantities of molecular data to address the challenge of studying adaptive genetic variation in non-model species. Here, we suggest that improvements in the sampling design should consider spatial dependence among sampled individuals. Then, we describe available statistical approaches for integrating spatial dependence into landscape analyses of adaptive genetic variation. PMID:20723056

  6. Adaptive potential of genomic structural variation in human and mammalian evolution.

    PubMed

    Radke, David W; Lee, Charles

    2015-09-01

    Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification. PMID:26003631

  7. The effect of adaptive mutagenesis on genetic variation at a linked, neutral locus

    SciTech Connect

    Colby, C.; Williams, S.M.

    1995-07-01

    Based on recent studies in single-celled organisms, it has been argued that a fitness benefit associated with a mutation will increase the probability of that mutation occurring. This increase is independent of mutation rates at other loci and is called adaptive mutagenesis. We modeled the effect of adaptive mutagenesis on populations of haploid organisms with adaptive mutation rates ranging from 0 to 1 x 10{sup -5}. Allele frequencies at the selected locus and a neutral linked locus were tracked. We also observed the amount of linkage disequilibrium during the selective sweep and the final heterozygosity after the sweep. The presence of adaptive mutagenesis increases the number of genetic backgrounds carrying the new fitter allele, making the outcomes more representative of the population before the selection. Therefore, more neutral genetic variation is preserved in simulations with adaptive mutagenesis than in those without it due to hitchhiking. Since adaptive mutagensis is time-dependent, it can generate mutants when other mechanisms of mutation cannot. In addition, adaptive mutagenesis has the potential to confound both phylogeny construction and the detection of natural selection from patterns of nucleotide variation. 27 refs., 4 figs.

  8. Does Genetic Variation Maintained by Environmental Heterogeneity Facilitate Adaptation to Novel Selection?

    PubMed

    Huang, Yuheng; Tran, Ivan; Agrawal, Aneil F

    2016-07-01

    Environmental heterogeneity helps maintain genetic variation in fitness. Therefore, one might predict that populations living in heterogeneous environments have higher adaptive potential than populations living in homogeneous environments. Such a prediction could be useful in guiding conservation priorities without requiring detailed genetic studies. However, this prediction will be true only if the additional genetic variation maintained by environmental heterogeneity can be used to respond to novel selection. Here we examine the effect of environmental heterogeneity on future adaptability using replicated experimental Drosophila melanogaster populations that had previously evolved for ∼100 generations under one of four selective regimes: constant salt-enriched larvae medium, constant cadmium-enriched larvae medium, and two heterogeneous regimes that vary either temporally or spatially between the two media. Replicates of these experimental populations were subjected to a novel heat stress while being maintained in their original larval diet selection regimes. Adaptation to increased temperature was measured with respect to female productivity and male siring success after ∼20 generations. For female productivity, there was evidence of adaptation overall and heterogeneous populations had a larger adaptive response than homogeneous populations. There was less evidence of adaptation overall for male siring success and no support for faster adaptation in heterogeneous populations. PMID:27322119

  9. Algorithme d'adaptation du filtre de Kalman aux variations soudaines de bruit

    NASA Astrophysics Data System (ADS)

    Canciu, Vintila

    This research targets the case of Kalman filtering as applied to linear time-invariant systems having unknown process noise covariance and measurement noise covariance matrices and addresses the problem represented by the incomplete a priori knowledge of these two filter initialization parameters. The goal of this research is to determine in realtime both the process covariance matrix and the noise covariance matrix in the context of adaptive Kalman filtering. The resultant filter, called evolutionary adaptive Kalman filter, is able to adapt to sudden noise variations and constitutes a hybrid solution for adaptive Kalman filtering based on metaheuristic algorithms. MATLAB/Simulink simulation using several processes and covariance matrices plus comparison with other filters was selected as validation method. The Cramer-Rae Lower Bound (CRLB) was used as performance criterion. The thesis begins with a description of the problem under consideration (the design of a Kalman filter that is able to adapt to sudden noise variations) followed by a typical application (INS-GPS integrated navigation system) and by a statistical analysis of publications related to adaptive Kalman filtering. Next, the thesis presents the current architectures of the adaptive Kalman filtering: the innovation adaptive estimator (IAE) and the multiple model adaptive estimator (MMAE). It briefly presents their formulation, their behavior, and the limit of their performances. The thesis continues with the architectural synthesis of the evolutionary adaptive Kalman filter. The steps involved in the solution of the problem under consideration is also presented: an analysis of Kalman filtering and sub-optimal filtering methods, a comparison of current adaptive Kalman and sub-optimal filtering methods, the emergence of evolutionary adaptive Kalman filter as an enrichment of sub-optimal filtering with the help of biological-inspired computational intelligence methods, and the step-by-step architectural

  10. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations.

    PubMed

    Trotter, Meredith V; Weissman, Daniel B; Peterson, Grant I; Peck, Kayla M; Masel, Joanna

    2014-12-01

    The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations. PMID:25178652

  11. Geographic variation of floral traits in Nicotiana glauca : Relationships with biotic and abiotic factors

    NASA Astrophysics Data System (ADS)

    Nattero, Julieta; Sérsic, Alicia N.; Cocucci, Andrea A.

    2011-09-01

    Geographic pattern of phenotypic variation can appear in a clinal or a mosaic fashion and can evidence adaptive or non-adaptive variation. To shed light on the mechanisms underlying this variation, we studied the relationships between geographic variation of floral traits and both biotic and abiotic factors of the hummingbird-pollinated plant, Nicotiana glauca, across its natural range. We obtained floral measures of 38 populations from an area about 1600 km long and 1050 km wide and an altitude range from 7 to over 3400 m. We used a MANOVA to detect between-population differentiations in flower traits and a DFA to determine the traits that best discriminate between populations. To test for associations between floral traits and climatic variables we used correlation analysis. We explored any possible distance-based pattern of variation (either geographic or altitudinal) in floral traits or bill length of pollinators using Mantel tests. Finally, we used a multiple regression to analyze simultaneously the effects and relative importance of abiotic predictor variables and bill length on corolla length. We found a high variation in flower traits among populations. Morphometric traits were the ones that best discriminated across populations. There was a clinal pattern of floral phenotypic variation explained by climatic factors. Differences in floral phenotypic distances were structured by altitudinal distances but not by geographic distances. Bill length of the hummingbird pollinators was structured both by altitudinal and geographic distances. Differences in bill length of hummingbird pollinators explained differences in corolla length across populations. Our findings support the assumption of flower evolution at a broad geographic scale. Floral traits seem to be structured not only by altitude but also by climatic factors.

  12. Genetic variation in parthenogenetic Artemia from the Shandong Peninsula, P.R.C.

    NASA Astrophysics Data System (ADS)

    King, Charles E.; Zhao, Yuqi; Liu, Xin; Li, Mingren

    1988-06-01

    Results are presented of a survey of isozyme frequencies in parthenogenetic Artimia from six salterns in the Shandong Peninsula, P.R.C. Three of the eleven enzymes we scored using polyacryamide gel electrophoresis proved to be useful for analysis of electromorph frequency variation. These enzymes are tetrazolium oxidase (TO), lactate dehydrogenase (LDH), and malate dehydrogenase (MDH). Each of these systems showed extensive isozyme variation both within and between salterns. In addition, we have examined the possibility that electromorph frequencies may vary as the result of natural selection for adaptation to specific salinity, or salinity-associated environmental conditions. An indication of clinal variation was found in two series of ponds differing in salinity, however more extensive data are needed before it is possible to conclude that these patterns are the result of natural selection. Finally, the use of isozyme analyses such as ours, for unraveling taxonomic problems in Artemia is discussed.

  13. Tropically adapted cattle of Africa: perspectives on potential role of copy number variations.

    PubMed

    Wang, M D; Dzama, K; Rees, D J G; Muchadeyi, F C

    2016-04-01

    Africa is host to diverse and locally adapted cattle breeds that are expected to survive the harsh and extreme tropical environments associated with diseases and parasite infections, heat stress and episodes of feed and water scarcity. Genomic copy number variations (CNVs) are considered to be primary role players in cattle breed formation and adaptation where isolation and genetic drift together with subsequent mutations have created an enormous diversity of local populations. CNVs are modifications in DNA structure comprising deletions, duplications and insertions that are >1 kb in size. Despite attracting much attention, the frequency and pattern of bovine CNV events, especially in African cattle breeds, are for the most part largely unknown. Characterization of genetic variation in the indigenous cattle of Africa will be a vital step toward dissecting the molecular mechanisms underlying phenotypic variation and local adaptation. This review therefore aims to describe the current knowledge regarding bovine CNVs and the implications and potentials they encompass for dissecting genetic adaptation and the genotypic skeleton of tropical African cattle populations. PMID:26644080

  14. Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass

    PubMed Central

    Grabowski, Paul P; Morris, Geoffrey P; Casler, Michael D; Borevitz, Justin O

    2014-01-01

    Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass. PMID:24962137

  15. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

    PubMed Central

    Pease, James B.; Haak, David C.; Hahn, Matthew W.; Moyle, Leonie C.

    2016-01-01

    Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a “PhyloGWAS” approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations. PMID:26871574

  16. Mating system and environmental variation drive patterns of adaptation in Boechera spatifolia (Brassicaceae).

    PubMed

    Lovell, John T; Grogan, Kelsi; Sharbel, Timothy F; McKay, John K

    2014-09-01

    Determining the relative contribution of population genetic processes to the distribution of natural variation is a major goal of evolutionary biology. Here, we take advantage of variation in mating system to test the hypothesis that local adaptation is constrained by asexual reproduction. We explored patterns of variation in ecological traits and genome-wide molecular markers in Boechera spatifolia (Brassicaceae), a species that contains both apomictic (asexual) and sexual individuals. Using a combination of quantitative genetics, neutral genetic (SSR) and genome-wide single nucleotide polymorphism, we assessed the hypothesis that asexual lineages should have reduced signatures of adaptation relative to sexual conspecifics. All three measures (traits, SSRs, SNPs) demonstrated that apomicts are genetically distinct from sexuals, regardless of population location. Additionally, phylogenetic clustering revealed that the apomictic group shared a single common ancestor. Across the landscape, sexual genome-wide SNP variation was strongly associated with latitude (r(2)  > 0.9), indicating that sexual populations have differentiated across an environmental gradient. Furthermore, flowering time and growth rate, as assessed in a common garden, strongly covary with the elevation and latitude of the source population. Despite a wide geographic distribution that largely overlaps with sexual populations, there was little evidence for differentiation in molecular markers or quantitative characters among apomictic populations. Combined, these data indicated that, in contrast to asexual populations, sexual populations show evidence of local adaptation. PMID:25112786

  17. A novel spatially adaptive guide-filter total variation (SAGFTV) regularization for image restoration

    NASA Astrophysics Data System (ADS)

    Fang, Hao; Li, Qian; Huang, Zhenghua

    2015-12-01

    Denoising algorithms based on gradient dependent energy functionals, such as Perona-Malik, total variation and adaptive total variation denoising, modify images towards piecewise constant functions. Although edge sharpness and location is well preserved, important information, encoded in image features like textures or certain details, is often compromised in the process of denoising. In this paper, We propose a novel Spatially Adaptive Guide-Filtering Total Variation (SAGFTV) regularization with image restoration algorithm for denoising images. The guide-filter is extended to the variational formulations of imaging problem, and the spatially adaptive operator can easily distinguish flat areas from texture areas. Our simulating experiments show the improvement of peak signal noise ratio (PSNR), root mean square error (RMSE) and structure similarity increment measurement (SSIM) over other prior algorithms. The results of both simulating and practical experiments are more appealing visually. This type of processing can be used for a variety of tasks in PDE-based image processing and computer vision, and is stable and meaningful from a mathematical viewpoint.

  18. Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment

    PubMed Central

    Xu, Qin; Zhu, Caiyun; Fan, Yangyang; Song, Zhihong; Xing, Shilai; Liu, Wei; Yan, Juan; Sang, Tao

    2016-01-01

    Expression variation plays an important role in plant adaptation, but little is known about the factors impacting the expression variation when population adapts to changing environment. We used RNA-seq data from 80 individuals in 14 Miscanthus lutarioriparius populations, which were transplanted into a harsh environment from native habitat, to investigate the expression level, expression diversity and genetic diversity for genes expressed in both environments. The expression level of genes with lower expression level or without SNP tended to be more changeable in new environment, which suggested highly expressed genes experienced stronger purifying selection than those at lower level. Low proportion of genes with population effect confirmed the weak population structure and frequent gene flow in these populations. Meanwhile, the number of genes with environment effect was the most frequent compared with that with population effect. Our results showed that environment and genetic diversity were the main factors determining gene expression variation in population. This study could facilitate understanding the mechanisms of global gene expression variation when plant population adapts to changing environment. PMID:27150248

  19. Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem

    PubMed Central

    Rudman, Seth M.; Rodriguez-Cabal, Mariano A.; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W.; Crutsinger, Gregory M.

    2015-01-01

    Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. PMID:26203004

  20. Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem.

    PubMed

    Rudman, Seth M; Rodriguez-Cabal, Mariano A; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W; Crutsinger, Gregory M

    2015-08-01

    Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. PMID:26203004

  1. Hedgehog signaling mediates adaptive variation in a dynamic functional system in the cichlid feeding apparatus

    PubMed Central

    Hu, Yinan; Albertson, R. Craig

    2014-01-01

    Adaptive variation in the craniofacial skeleton is a key component of resource specialization and habitat divergence in vertebrates, but the proximate genetic mechanisms that underlie complex patterns of craniofacial variation are largely unknown. Here we demonstrate that the Hedgehog (Hh) signaling pathway mediates widespread variation across a complex functional system that affects the kinematics of lower jaw depression—the opercular four-bar linkage apparatus—among Lake Malawi cichlids. By using a combined quantitative trait locus mapping and population genetics approach, we show that allelic variation in the Hh receptor, ptch1, affects the development of distinct bony elements in the head that represent two of three movable links in this functional system. The evolutionarily derived allele is found in species that feed from the water column, and is associated with shifts in anatomy that translate to a four-bar system capable of faster jaw rotation. Alternatively, the ancestral allele is found in species that feed on attached algae, and is associated with the development of a four-bar system that predicts slower jaw movement. Experimental manipulation of the Hh pathway during cichlid development recapitulates functionally salient natural variation in craniofacial geometry. In all, these results significantly extend our understanding of the mechanisms that fine-tune the craniofacial skeletal complex during adaptation to new foraging niches. PMID:24912175

  2. Responses of leaf traits to climatic gradients: adaptive variation versus compositional shifts

    NASA Astrophysics Data System (ADS)

    Meng, T.-T.; Wang, H.; Harrison, S. P.; Prentice, I. C.; Ni, J.; Wang, G.

    2015-09-01

    Dynamic global vegetation models (DGVMs) typically rely on plant functional types (PFTs), which are assigned distinct environmental tolerances and replace one another progressively along environmental gradients. Fixed values of traits are assigned to each PFT; modelled trait variation along gradients is thus driven by PFT replacement. But empirical studies have revealed "universal" scaling relationships (quantitative trait variations with climate that are similar within and between species, PFTs and communities); and continuous, adaptive trait variation has been proposed to replace PFTs as the basis for next-generation DGVMs. Here we analyse quantitative leaf-trait variation on long temperature and moisture gradients in China with a view to understanding the relative importance of PFT replacement vs. continuous adaptive variation within PFTs. Leaf area (LA), specific leaf area (SLA), leaf dry matter content (LDMC) and nitrogen content of dry matter were measured on all species at 80 sites ranging from temperate to tropical climates and from dense forests to deserts. Chlorophyll fluorescence traits and carbon, phosphorus and potassium contents were measured at 47 sites. Generalized linear models were used to relate log-transformed trait values to growing-season temperature and moisture indices, with or without PFT identity as a predictor, and to test for differences in trait responses among PFTs. Continuous trait variation was found to be ubiquitous. Responses to moisture availability were generally similar within and between PFTs, but biophysical traits (LA, SLA and LDMC) of forbs and grasses responded differently from woody plants. SLA and LDMC responses to temperature were dominated by the prevalence of evergreen PFTs with thick, dense leaves at the warm end of the gradient. Nutrient (N, P and K) responses to climate gradients were generally similar within all PFTs. Area-based nutrients generally declined with moisture; Narea and Karea declined with temperature

  3. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.

    PubMed

    Hess, Jon E; Campbell, Nathan R; Close, David A; Docker, Margaret F; Narum, Shawn R

    2013-06-01

    Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (F(CT) = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow. PMID:23205767

  4. Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation

    PubMed Central

    MANEL, STÉPHANIE; GUGERLI, FELIX; THUILLER, WILFRIED; ALVAREZ, NADIR; LEGENDRE, PIERRE; HOLDEREGGER, ROLF; GIELLY, LUDOVIC; TABERLET, PIERRE

    2014-01-01

    Identifying adaptive genetic variation is a challenging task, in particular in non-model species for which genomic information is still limited or absent. Here, we studied distribution patterns of amplified fragment length polymorphisms (AFLPs) in response to environmental variation, in 13 alpine plant species consistently sampled across the entire European Alps. Multiple linear regressions were performed between AFLP allele frequencies per site as dependent variables and two categories of independent variables, namely Moran’s eigenvector map MEM variables (to account for spatial and unaccounted environmental variation, and historical demographic processes) and environmental variables. These associations allowed the identification of 153 loci of ecological relevance. Univariate regressions between allele frequency and each environmental factor further showed that loci of ecological relevance were mainly correlated with MEM variables. We found that precipitation and temperature were the best environmental predictors, whereas topographic factors were rarely involved in environmental associations. Climatic factors, subject to rapid variation as a result of the current global warming, are known to strongly influence the fate of alpine plants. Our study shows, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps. PMID:22680783

  5. Histoplasma variation and adaptive strategies for parasitism: new perspectives on histoplasmosis.

    PubMed

    Eissenberg, L G; Goldman, W E

    1991-10-01

    This review summarizes the biology of Histoplasma capsulatum in relation to a wide variety of corresponding pathologies in histoplasmosis. Features of these disease syndromes can be explained in part by natural variations within the fungal population and adaptations made by individual organisms to specific environments. H. capsulatum grows as mycelia and conidia in the soil; once inhaled, the organism undergoes a dramatic morphological and physiological conversion to a yeast form. The yeasts proliferate within the phagolysosomes of macrophages, using a variety of specific strategies for intracellular survival. Even avirulent strains or variants are able to avoid being killed by macrophages and instead establish inapparent or persistent infections. The ingested avirulent organisms assume enlarged shapes similar in appearance to those seen in histological sections of tissues from patients with histoplasmosis. Respiratory tract epithelial cells also appear to play a role in persistence: within them yeasts undergo phenotypic switching akin to the phase variation observed in other pathogens. This particular change involves the loss or modification of cell wall alpha-(1,3)-glucan, which is also correlated with the spontaneous appearance of avirulent variants. The repertoire of adaptive responses and natural variations within this species probably evolved from the need to adjust to a wide range of dynamic environments. In combination with the immune status of the host, these characteristics of H. capsulatum appear to influence the epidemiology, extent, and persistence of histoplasmosis. PMID:1747859

  6. Genetic Variation and Adaptation in Africa: Implications for Human Evolution and Disease

    PubMed Central

    Gomez, Felicia; Hirbo, Jibril; Tishkoff, Sarah A.

    2014-01-01

    Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent. PMID:24984772

  7. Coselected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana.

    PubMed

    Brachi, Benjamin; Meyer, Christopher G; Villoutreix, Romain; Platt, Alexander; Morton, Timothy C; Roux, Fabrice; Bergelson, Joy

    2015-03-31

    The "mustard oil bomb" is a major defense mechanism in the Brassicaceae, which includes crops such as canola and the model plant Arabidopsis thaliana. These plants produce and store blends of amino acid-derived secondary metabolites called glucosinolates. Upon tissue rupture by natural enemies, the myrosinase enzyme hydrolyses glucosinolates, releasing defense molecules. Brassicaceae display extensive variation in the mixture of glucosinolates that they produce. To investigate the genetics underlying natural variation in glucosinolate profiles, we conducted a large genome-wide association study of 22 methionine-derived glucosinolates using A. thaliana accessions from across Europe. We found that 36% of among accession variation in overall glucosinolate profile was explained by genetic differentiation at only three known loci from the glucosinolate pathway. Glucosinolate-related SNPs were up to 490-fold enriched in the extreme tail of the genome-wide [Formula: see text] scan, indicating strong selection on loci controlling this pathway. Glucosinolate profiles displayed a striking longitudinal gradient with alkenyl and hydroxyalkenyl glucosinolates enriched in the West. We detected a significant contribution of glucosinolate loci toward general herbivore resistance and lifetime fitness in common garden experiments conducted in France, where accessions are enriched in hydroxyalkenyls. In addition to demonstrating the adaptive value of glucosinolate profile variation, we also detected long-distance linkage disequilibrium at two underlying loci, GS-OH and GS-ELONG. Locally cooccurring alleles at these loci display epistatic effects on herbivore resistance and fitness in ecologically realistic conditions. Together, our results suggest that natural selection has favored a locally adaptive configuration of physically unlinked loci in Western Europe. PMID:25775585

  8. Coselected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana

    PubMed Central

    Meyer, Christopher G.; Villoutreix, Romain; Platt, Alexander; Morton, Timothy C.; Roux, Fabrice; Bergelson, Joy

    2015-01-01

    The “mustard oil bomb” is a major defense mechanism in the Brassicaceae, which includes crops such as canola and the model plant Arabidopsis thaliana. These plants produce and store blends of amino acid-derived secondary metabolites called glucosinolates. Upon tissue rupture by natural enemies, the myrosinase enzyme hydrolyses glucosinolates, releasing defense molecules. Brassicaceae display extensive variation in the mixture of glucosinolates that they produce. To investigate the genetics underlying natural variation in glucosinolate profiles, we conducted a large genome-wide association study of 22 methionine-derived glucosinolates using A. thaliana accessions from across Europe. We found that 36% of among accession variation in overall glucosinolate profile was explained by genetic differentiation at only three known loci from the glucosinolate pathway. Glucosinolate-related SNPs were up to 490-fold enriched in the extreme tail of the genome-wide FST scan, indicating strong selection on loci controlling this pathway. Glucosinolate profiles displayed a striking longitudinal gradient with alkenyl and hydroxyalkenyl glucosinolates enriched in the West. We detected a significant contribution of glucosinolate loci toward general herbivore resistance and lifetime fitness in common garden experiments conducted in France, where accessions are enriched in hydroxyalkenyls. In addition to demonstrating the adaptive value of glucosinolate profile variation, we also detected long-distance linkage disequilibrium at two underlying loci, GS-OH and GS-ELONG. Locally cooccurring alleles at these loci display epistatic effects on herbivore resistance and fitness in ecologically realistic conditions. Together, our results suggest that natural selection has favored a locally adaptive configuration of physically unlinked loci in Western Europe. PMID:25775585

  9. Comparative population genomics of latitudinal variation in Drosophila simulans and Drosophila melanogaster.

    PubMed

    Machado, Heather E; Bergland, Alan O; O'Brien, Katherine R; Behrman, Emily L; Schmidt, Paul S; Petrov, Dmitri A

    2016-02-01

    Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and Drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple time points over 2 years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, we find that clinally varying loci in D. simulans are less stable over multiple years than comparable clines in D. melanogaster. D. simulans shows a significantly weaker pattern of isolation by distance than D. melanogaster and we find evidence for a stronger contribution of migration to D. simulans population genetic structure. While population bottlenecks and migration can plausibly explain the differences in stability of clinal variation between the two species, we also observe a significant enrichment of shared clinal genes, suggesting that the selective forces associated with climate are acting on the same genes and phenotypes in D. simulans and D. melanogaster. PMID:26523848

  10. Space-time adaptive approach to variational data assimilation using wavelets

    NASA Astrophysics Data System (ADS)

    Souopgui, Innocent; Wieland, Scott A.; Yousuff Hussaini, M.; Vasilyev, Oleg V.

    2016-02-01

    This paper focuses on one of the main challenges of 4-dimensional variational data assimilation, namely the requirement to have a forward solution available when solving the adjoint problem. The issue is addressed by considering the time in the same fashion as the space variables, reformulating the mathematical model in the entire space-time domain, and solving the problem on a near optimal computational mesh that automatically adapts to spatio-temporal structures of the solution. The compressed form of the solution eliminates the need to save or recompute data for every time slice as it is typically done in traditional time marching approaches to 4-dimensional variational data assimilation. The reduction of the required computational degrees of freedom is achieved using the compression properties of multi-dimensional second generation wavelets. The simultaneous space-time discretization of both the forward and the adjoint models makes it possible to solve both models either concurrently or sequentially. In addition, the grid adaptation reduces the amount of saved data to the strict minimum for a given a priori controlled accuracy of the solution. The proposed approach is demonstrated for the advection diffusion problem in two space-time dimensions.

  11. Adaptive force produced by stress-induced regulation of random variation intensity.

    PubMed

    Shimansky, Yury P

    2010-08-01

    The Darwinian theory of life evolution is capable of explaining the majority of related phenomena. At the same time, the mechanisms of optimizing traits beneficial to a population as a whole but not directly to an individual remain largely unclear. There are also significant problems with explaining the phenomenon of punctuated equilibrium. From another perspective, multiple mechanisms for the regulation of the rate of genetic mutations according to the environmental stress have been discovered, but their precise functional role is not well understood yet. Here a novel mathematical paradigm called a Kinetic-Force Principle (KFP), which can serve as a general basis for biologically plausible optimization methods, is introduced and its rigorous derivation is provided. Based on this principle, it is shown that, if the rate of random changes in a biological system is proportional, even only roughly, to the amount of environmental stress, a virtual force is created, acting in the direction of stress relief. It is demonstrated that KFP can provide important insights into solving the above problems. Evidence is presented in support of a hypothesis that the nature employs KFP for accelerating adaptation in biological systems. A detailed comparison between KFP and the principle of variation and natural selection is presented and their complementarity is revealed. It is concluded that KFP is not a competing alternative, but a powerful addition to the principle of variation and natural selection. It is also shown KFP can be used in multiple ways for adaptation of individual biological organisms. PMID:20361203

  12. Adaptive plasticity and epigenetic variation in response to warming in an Alpine plant

    PubMed Central

    Nicotra, Adrienne B; Segal, Deborah L; Hoyle, Gemma L; Schrey, Aaron W; Verhoeven, Koen J F; Richards, Christina L

    2015-01-01

    Environmentally induced phenotypic plasticity may be a critical component of response to changing environments. We examined local differentiation and adaptive phenotypic plasticity in response to elevated temperature in half-sib lines collected across an elevation gradient for the alpine herb, Wahlenbergia ceracea. Using Amplified Fragment Length Polymorphism (AFLP), we found low but significant genetic differentiation between low- and high-elevation seedlings, and seedlings originating from low elevations grew faster and showed stronger temperature responses (more plasticity) than those from medium and high elevations. Furthermore, plasticity was more often adaptive for plants of low-elevation origin and maladaptive for plants of high elevation. With methylation sensitive-AFLP (MS-AFLP), we revealed an increase in epigenetic variation in response to temperature in low-elevation seedlings. Although we did not find significant direct correlations between MS-AFLP loci and phenotypes, our results demonstrate that adaptive plasticity in temperature response to warming varies over fine spatial scales and suggest the involvement of epigenetic mechanisms in this response. PMID:25691987

  13. European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

    PubMed Central

    Tine, Mbaye; Kuhl, Heiner; Gagnaire, Pierre-Alexandre; Louro, Bruno; Desmarais, Erick; Martins, Rute S.T.; Hecht, Jochen; Knaust, Florian; Belkhir, Khalid; Klages, Sven; Dieterich, Roland; Stueber, Kurt; Piferrer, Francesc; Guinand, Bruno; Bierne, Nicolas; Volckaert, Filip A. M.; Bargelloni, Luca; Power, Deborah M.; Bonhomme, François; Canario, Adelino V. M.; Reinhardt, Richard

    2014-01-01

    The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation. PMID:25534655

  14. Body Size Adaptations to Altitudinal Climatic Variation in Neotropical Grasshoppers of the Genus Sphenarium (Orthoptera: Pyrgomorphidae).

    PubMed

    Sanabria-Urbán, Salomón; Song, Hojun; Oyama, Ken; González-Rodríguez, Antonio; Serrano-Meneses, Martin A; Cueva Del Castillo, Raúl

    2015-01-01

    Altitudinal clines in body size can result from the effects of natural and sexual selection on growth rates and developing times in seasonal environments. Short growing and reproductive seasons constrain the body size that adults can attain and their reproductive success. Little is known about the effects of altitudinal climatic variation on the diversification of Neotropical insects. In central Mexico, in addition to altitude, highly heterogeneous topography generates diverse climates that can occur even at the same latitude. Altitudinal variation and heterogeneous topography open an opportunity to test the relative impact of climatic variation on body size adaptations. In this study, we investigated the relationship between altitudinal climatic variation and body size, and the divergence rates of sexual size dimorphism (SSD) in Neotropical grasshoppers of the genus Sphenarium using a phylogenetic comparative approach. In order to distinguish the relative impact of natural and sexual selection on the diversification of the group, we also tracked the altitudinal distribution of the species and trends of both body size and SSD on the phylogeny of Sphenarium. The correlative evidence suggests no relationship between altitude and body size. However, larger species were associated with places having a warmer winter season in which the temporal window for development and reproduction can be longer. Nonetheless, the largest species were also associated with highly seasonal environments. Moreover, large body size and high levels of SSD have evolved independently several times throughout the history of the group and male body size has experienced a greater evolutionary divergence than females. These lines of evidence suggest that natural selection, associated with seasonality and sexual selection, on maturation time and body size could have enhanced the diversification of this insect group. PMID:26684616

  15. Body Size Adaptations to Altitudinal Climatic Variation in Neotropical Grasshoppers of the Genus Sphenarium (Orthoptera: Pyrgomorphidae)

    PubMed Central

    2015-01-01

    Altitudinal clines in body size can result from the effects of natural and sexual selection on growth rates and developing times in seasonal environments. Short growing and reproductive seasons constrain the body size that adults can attain and their reproductive success. Little is known about the effects of altitudinal climatic variation on the diversification of Neotropical insects. In central Mexico, in addition to altitude, highly heterogeneous topography generates diverse climates that can occur even at the same latitude. Altitudinal variation and heterogeneous topography open an opportunity to test the relative impact of climatic variation on body size adaptations. In this study, we investigated the relationship between altitudinal climatic variation and body size, and the divergence rates of sexual size dimorphism (SSD) in Neotropical grasshoppers of the genus Sphenarium using a phylogenetic comparative approach. In order to distinguish the relative impact of natural and sexual selection on the diversification of the group, we also tracked the altitudinal distribution of the species and trends of both body size and SSD on the phylogeny of Sphenarium. The correlative evidence suggests no relationship between altitude and body size. However, larger species were associated with places having a warmer winter season in which the temporal window for development and reproduction can be longer. Nonetheless, the largest species were also associated with highly seasonal environments. Moreover, large body size and high levels of SSD have evolved independently several times throughout the history of the group and male body size has experienced a greater evolutionary divergence than females. These lines of evidence suggest that natural selection, associated with seasonality and sexual selection, on maturation time and body size could have enhanced the diversification of this insect group. PMID:26684616

  16. Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics.

    PubMed

    Hand, Brian K; Muhlfeld, Clint C; Wade, Alisa A; Kovach, Ryan P; Whited, Diane C; Narum, Shawn R; Matala, Andrew P; Ackerman, Michael W; Garner, Brittany A; Kimball, John S; Stanford, Jack A; Luikart, Gordon

    2016-02-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics. PMID:26677031

  17. Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

    USGS Publications Warehouse

    Hand, Brian K; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R; Matala, Andrew P; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

    2016-01-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  18. EnVO: a hybrid ensemble/variational adaptive observation algorithm

    NASA Astrophysics Data System (ADS)

    Zhang, David; Bewley, Thomas

    2009-11-01

    Advances in autonomous technology enable the development of Adaptive Observation (AO) strategies, which identify future sensor locations to reduce forecast error. The approaches to AO strategies are mainly divided into two techniques, the ``uncertainty'' based techniques such as the Ensemble Transform Kalman Filter by Bishop et al. 2001 and the ``sensitivity'' based techniques such as the Singular Vector by Palmer et al. 1998. Both approaches have their advantages and disadvantages; hence the combination of both is perhaps ideal. We propose a hybrid ensemble/adjoint AO technique, dubbed Ensemble Variational Observation (EnVO). The EnVO technique uses both sensitivity and uncertainty information, and can be applied in such a way as to ensure its optimized sensor trajectories are both feasible and efficient over the time window between the present and forecast time. Integrated statistic results indicates EnVO is able to consistently identifies target sites that produce lower forecast errors.

  19. Cluster-based spike detection algorithm adapts to interpatient and intrapatient variation in spike morphology.

    PubMed

    Nonclercq, Antoine; Foulon, Martine; Verheulpen, Denis; De Cock, Cathy; Buzatu, Marga; Mathys, Pierre; Van Bogaert, Patrick

    2012-09-30

    Visual quantification of interictal epileptiform activity is time consuming and requires a high level of expert's vigilance. This is especially true for overnight recordings of patient suffering from epileptic encephalopathy with continuous spike and waves during slow-wave sleep (CSWS) as they can show tens of thousands of spikes. Automatic spike detection would be attractive for this condition, but available algorithms have methodological limitations related to variation in spike morphology both between patients and within a single recording. We propose a fully automated method of interictal spike detection that adapts to interpatient and intrapatient variation in spike morphology. The algorithm works in five steps. (1) Spikes are detected using parameters suitable for highly sensitive detection. (2) Detected spikes are separated into clusters. (3) The number of clusters is automatically adjusted. (4) Centroids are used as templates for more specific spike detections, therefore adapting to the types of spike morphology. (5) Detected spikes are summed. The algorithm was evaluated on EEG samples from 20 children suffering from epilepsy with CSWS. When compared to the manual scoring of 3 EEG experts (3 records), the algorithm demonstrated similar performance since sensitivity and selectivity were 0.3% higher and 0.4% lower, respectively. The algorithm showed little difference compared to the manual scoring of another expert for the spike-and-wave index evaluation in 17 additional records (the mean absolute difference was 3.8%). This algorithm is therefore efficient for the count of interictal spikes and determination of a spike-and-wave index. PMID:22850558

  20. A spatially adaptive total variation regularization method for electrical resistance tomography

    NASA Astrophysics Data System (ADS)

    Song, Xizi; Xu, Yanbin; Dong, Feng

    2015-12-01

    The total variation (TV) regularization method has been used to solve the ill-posed inverse problem of electrical resistance tomography (ERT), owing to its good ability to preserve edges. However, the quality of the reconstructed images, especially in the flat region, is often degraded by noise. To optimize the regularization term and the regularization factor according to the spatial feature and to improve the resolution of reconstructed images, a spatially adaptive total variation (SATV) regularization method is proposed. A kind of effective spatial feature indicator named difference curvature is used to identify which region is a flat or edge region. According to different spatial features, the SATV regularization method can automatically adjust both the regularization term and regularization factor. At edge regions, the regularization term is approximate to the TV functional to preserve the edges; in flat regions, it is approximate to the first-order Tikhonov (FOT) functional to make the solution stable. Meanwhile, the adaptive regularization factor determined by the spatial feature is used to constrain the regularization strength of the SATV regularization method for different regions. Besides, a numerical scheme is adopted for the implementation of the second derivatives of difference curvature to improve the numerical stability. Several reconstruction image metrics are used to quantitatively evaluate the performance of the reconstructed results. Both simulation and experimental results indicate that, compared with the TV (mean relative error 0.288, mean correlation coefficient 0.627) and FOT (mean relative error 0.295, mean correlation coefficient 0.638) regularization methods, the proposed SATV (mean relative error 0.259, mean correlation coefficient 0.738) regularization method can endure a relatively high level of noise and improve the resolution of reconstructed images.

  1. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

    PubMed Central

    Svetec, Nicolas; Cridland, Julie M.; Zhao, Li; Begun, David J.

    2016-01-01

    Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216

  2. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster.

    PubMed

    Svetec, Nicolas; Cridland, Julie M; Zhao, Li; Begun, David J

    2016-03-01

    Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216

  3. Life History Variation in an Alpine Caddisfly: Local Adaptation or Phenotypic Plasticity?

    NASA Astrophysics Data System (ADS)

    Shama, L. N.; Robinson, C. T.

    2005-05-01

    Facultative species that inhabit permanent and temporary streams can be locally adapted to their stream of origin or exhibit life history plasticity. Temporary stream populations should respond to environmental cues signalling stream drying, whereas permanent stream populations may not. We used a common garden experiment to test whether males and females of an alpine caddisfly from six populations (3 permanent/3 temporary streams) differed in their life history responses to combined changes in photoperiod (ambient/late) and hydroperiod (constant/drying). Responses varied by sex, time-constraint cue and population. Both sexes shortened development time in the late photoperiod, and males emerged before females in all treatments. Growth rates were higher in the late photoperiod for both sexes, and females had higher growth rates and mass at emergence than males. Growth rate compensation in the late photoperiod resulted in similar masses at emergence for both photoperiods. Population-level differences in responses varied according to microgeographic co-gradient variation. Our results suggest that while stream drying cues may not exert sufficient selection pressure to promote faster development in temporary streams, populations may be locally adapted to differences in growing season length associated with stream-specific environmental characteristics.

  4. Direct evidence for the adaptive role of copy number variation on antifolate susceptibility in Plasmodium falciparum

    PubMed Central

    Heinberg, Adina; Siu, Edwin; Stern, Chaya; Lawrence, Elizabeth A; Ferdig, Michael T; Deitsch, Kirk W; Kirkman, Laura A

    2013-01-01

    Summary Resistance to antimalarials targeting the folate pathway is widespread. GTP-cyclohydrolase (gch1), the first enzyme in this pathway, exhibits extensive copy number variation (CNV) in parasite isolates from areas with a history of longstanding antifolate use. Increased CN of gch1 is associated with a greater number of point mutations in enzymes targeted by the antifolates, pyrimethamine and sulfadoxine. While these observations suggest that increases in gch1 CN are an adaptation to drug pressure, changes in CN have not been experimentally demonstrated to directly alter drug susceptibility. To determine if changes in gch1 expression alone modify pyrimethamine sensitivity, we manipulated gch1 CN in several parasite lines to test the effect on drug sensitivity. We report that increases in gch1 CN alter pyrimethamine resistance in most parasites lines. However we find evidence of a detrimental effect of very high levels of gch1 overexpression in parasite lines with high endogenous levels of gch1 expression, revealing the importance of maintaining balance in the folate pathway and implicating changes in gch1 expression in preserving proper metabolic flux. This work expands our understanding of parasite adaptation to drug pressure and provides a possible mechanism for how specific mutations become fixed within parasite populations. PMID:23347134

  5. Does Variation in Genome Sizes Reflect Adaptive or Neutral Processes? New Clues from Passiflora

    PubMed Central

    Fonseca, Tamara C.; Salzano, Francisco M.; Bonatto, Sandro L.; Freitas, Loreta B.

    2011-01-01

    One of the long-standing paradoxes in genomic evolution is the observation that much of the genome is composed of repetitive DNA which has been typically regarded as superfluous to the function of the genome in generating phenotypes. In this work, we used comparative phylogenetic approaches to investigate if the variations in genome sizes (GS) should be considered as adaptive or neutral processes by the comparison between GS and flower diameters (FD) of 50 Passiflora species, more specifically, within its two most species-rich subgenera, Passiflora and Decaloba. For this, we have constructed a phylogenetic tree of these species, estimated GS and FD of them, inferred the tempo and mode of evolution of these traits and their correlations, using both current and phylogenetically independent contrasted values. We found significant correlations among the traits, when considering the complete set of data or only the subgenus Passiflora, whereas no correlations were observed within Decaloba. Herein, we present convincing evidence of adaptive evolution of GS, as well as clues that this pattern is limited by a minimum genome size, which could reduce both the possibilities of changes in GS and the possibility of phenotypic responses to environment changes. PMID:21464897

  6. A Fast Variational Method for the Construction of Resolution Adaptive C-Smooth Molecular Surfaces.

    PubMed

    Bajaj, Chandrajit L; Xu, Guoliang; Zhang, Qin

    2009-05-01

    We present a variational approach to smooth molecular (proteins, nucleic acids) surface constructions, starting from atomic coordinates, as available from the protein and nucleic-acid data banks. Molecular dynamics (MD) simulations traditionally used in understanding protein and nucleic-acid folding processes, are based on molecular force fields, and require smooth models of these molecular surfaces. To accelerate MD simulations, a popular methodology is to employ coarse grained molecular models, which represent clusters of atoms with similar physical properties by psuedo- atoms, resulting in coarser resolution molecular surfaces. We consider generation of these mixed-resolution or adaptive molecular surfaces. Our approach starts from deriving a general form second order geometric partial differential equation in the level-set formulation, by minimizing a first order energy functional which additionally includes a regularization term to minimize the occurrence of chemically infeasible molecular surface pockets or tunnel-like artifacts. To achieve even higher computational efficiency, a fast cubic B-spline C(2) interpolation algorithm is also utilized. A narrow band, tri-cubic B-spline level-set method is then used to provide C(2) smooth and resolution adaptive molecular surfaces. PMID:19802355

  7. Local adaptation of stream communities to intraspecific variation in a terrestrial ecosystem subsidy.

    PubMed

    Jackrel, Sara L; Wootton, J Timothy

    2014-01-01

    Cross-ecosystem fluxes can intertwine otherwise disparate food webs, but the effects of biodiversity at the genotypic level on fluxes across ecosystems boundaries is not known. Fresh leaves, which vary in traits such as defensive compounds against terrestrial herbivores, drop off trees and enter streams, providing a vital resource for riverine organisms. We demonstrate substantial variation in decomposition rates among individual trees in four different rivers in the Olympic Peninsula of Washington State, USA. We show that locally derived red alder leaf litter decomposes on average 24% faster than red alder leaf litter introduced from other riparian zones. Within rivers, leaves downstream of their parent trees decompose nearly as quickly as leaves from local trees. Leaves upstream of the parent tree decomposed as slowly as leaves from trees growing alongside different rivers. Over time, aquatic decomposer communities have locally adapted to the specific trees supplying the riparian subsidies. In energy-limited environments, such as small shaded streams, consumers must be efficient foragers. Our results indicate that this pressure for efficiency has led to adaptation at a particularly fine scale. More broadly, these results illustrate how genetic diversity and the effects of selection in one ecosystem can indirectly shape the structure of other ecosystems through ecological fluxes across boundaries. PMID:24649644

  8. Robust dynamic myocardial perfusion CT deconvolution using adaptive-weighted tensor total variation regularization

    NASA Astrophysics Data System (ADS)

    Gong, Changfei; Zeng, Dong; Bian, Zhaoying; Huang, Jing; Zhang, Xinyu; Zhang, Hua; Lu, Lijun; Feng, Qianjin; Liang, Zhengrong; Ma, Jianhua

    2016-03-01

    Dynamic myocardial perfusion computed tomography (MPCT) is a promising technique for diagnosis and risk stratification of coronary artery disease by assessing the myocardial perfusion hemodynamic maps (MPHM). Meanwhile, the repeated scanning of the same region results in a relatively large radiation dose to patients potentially. In this work, we present a robust MPCT deconvolution algorithm with adaptive-weighted tensor total variation regularization to estimate residue function accurately under the low-dose context, which is termed `MPD-AwTTV'. More specifically, the AwTTV regularization takes into account the anisotropic edge property of the MPCT images compared with the conventional total variation (TV) regularization, which can mitigate the drawbacks of TV regularization. Subsequently, an effective iterative algorithm was adopted to minimize the associative objective function. Experimental results on a modified XCAT phantom demonstrated that the present MPD-AwTTV algorithm outperforms and is superior to other existing deconvolution algorithms in terms of noise-induced artifacts suppression, edge details preservation and accurate MPHM estimation.

  9. A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation.

    PubMed

    Lange, Jeremy D; Pool, John E

    2016-07-01

    Identifying genomic targets of population-specific positive selection is a major goal in several areas of basic and applied biology. However, it is unclear how often such selection should act on new mutations versus standing genetic variation or recurrent mutation, and furthermore, favoured alleles may either become fixed or remain variable in the population. Very few population genetic statistics are sensitive to all of these modes of selection. Here, we introduce and evaluate the Comparative Haplotype Identity statistic (χMD ), which assesses whether pairwise haplotype sharing at a locus in one population is unusually large compared with another population, relative to genomewide trends. Using simulations that emulate human and Drosophila genetic variation, we find that χMD is sensitive to a wide range of selection scenarios, and for some very challenging cases (e.g. partial soft sweeps), it outperforms other two-population statistics. We also find that, as with FST , our haplotype approach has the ability to detect surprisingly ancient selective sweeps. Particularly for the scenarios resembling human variation, we find that χMD outperforms other frequency- and haplotype-based statistics for soft and/or partial selective sweeps. Applying χMD and other between-population statistics to published population genomic data from D. melanogaster, we find both shared and unique genes and functional categories identified by each statistic. The broad utility and computational simplicity of χMD will make it an especially valuable tool in the search for genes targeted by local adaptation. PMID:27135633

  10. Life history trait differentiation and local adaptation in invasive populations of Ambrosia artemisiifolia in China.

    PubMed

    Li, Xiao-Meng; She, Deng-Ying; Zhang, Da-Yong; Liao, Wan-Jin

    2015-03-01

    Local adaptation has been suggested to play an important role in range expansion, particularly among invasive species. However, the extent to which local adaptation affects the success of an invasive species and the factors that contribute to local adaptation are still unclear. This study aimed to investigate a case of population divergence that may have contributed to the local adaptation of invasive populations of Ambrosia artemisiifolia in China. Common garden experiments in seven populations indicated clinal variations along latitudinal gradients, with plants from higher latitudes exhibiting earlier flowering and smaller sizes at flowering. In reciprocal transplant experiments, plants of a northern Beijing origin produced more seeds at their home site than plants of a southern Wuhan origin, and the Wuhan-origin plants had grown taller at flowering than the Beijing-origin plants in Wuhan, which is believed to facilitate pollen dispersal. These results suggest that plants of Beijing origin may be locally adapted through female fitness and plants from Wuhan possibly locally adapted through male fitness. Selection and path analysis suggested that the phenological and growth traits of both populations have been influenced by natural selection and that flowering time has played an important role through its direct and indirect effects on the relative fitness of each individual. This study evidences the life history trait differentiation and local adaptation during range expansion of invasive A. artemisiifolia in China. PMID:25362583

  11. Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

    PubMed Central

    2013-01-01

    Background Copy number variable regions (CNVRs) can result in drastic phenotypic differences and may therefore be subject to selection during domestication. Studying copy number variation in relation to domestication is highly relevant in pigs because of their very rich natural and domestication history that resulted in many different phenotypes. To investigate the evolutionary dynamic of CNVRs, we applied read depth method on next generation sequence data from 16 individuals, comprising wild boars and domestic pigs from Europe and Asia. Results We identified 3,118 CNVRs with an average size of 13 kilobases comprising a total of 39.2 megabases of the pig genome and 545 overlapping genes. Functional analyses revealed that CNVRs are enriched with genes related to sensory perception, neurological process and response to stimulus, suggesting their contribution to adaptation in the wild and behavioral changes during domestication. Variations of copy number (CN) of antimicrobial related genes suggest an ongoing process of evolution of these genes to combat food-borne pathogens. Likewise, some genes related to the omnivorous lifestyle of pigs, like genes involved in detoxification, were observed to be CN variable. A small portion of CNVRs was unique to domestic pigs and may have been selected during domestication. The majority of CNVRs, however, is shared between wild and domesticated individuals, indicating that domestication had minor effect on the overall diversity of CNVRs. Also, the excess of CNVRs in non-genic regions implies that a major part of these variations is likely to be (nearly) neutral. Comparison between different populations showed that larger populations have more CNVRs, highlighting that CNVRs are, like other genetic variation such as SNPs and microsatellites, reflecting demographic history rather than phenotypic diversity. Conclusion CNVRs in pigs are enriched for genes related to sensory perception, neurological process, and response to stimulus. The

  12. Phase Variation in the Helicobacter pylori Phospholipase A Gene and Its Role in Acid Adaptation

    PubMed Central

    Tannæs, Tone; Dekker, Niek; Bukholm, Geir; Bijlsma, Jetta J. E.; Appelmelk, Ben J.

    2001-01-01

    Previously, we have shown that Helicobacter pylori can spontaneously and reversibly change its membrane lipid composition, producing variants with low or high content of lysophospholipids. The “lyso” variant contains a high percentage of lysophospholipids, adheres better to epithelial cells, and releases more proteins such as urease and VacA, compared to the “normal” variant, which has a low content of lysophospholipids. Prolonged growth of the normal variant at pH 3.5, but not under neutral conditions, leads to enrichment of lyso variant colonies, suggesting that the colony switch is relevant to acid adaptation. In this study we show that the change in membrane lipid composition is due to phase variation in the pldA gene. A change in the (C) tract length of this gene results in reversible frameshifts, translation of a full-length or truncated pldA, and the production of active or inactive outer membrane phospholipase A (OMPLA). The role of OMPLA in determining the colony morphology was confirmed by the construction of an OMPLA-negative mutant. Furthermore, variants with an active OMPLA were able to survive acidic conditions better than variants with the inactive form. This explains why the lyso variant is selected at low pH. Our studies demonstrate that phase variation in the pldA gene, resulting in an active form of OMPLA, is important for survival under acidic conditions. We also demonstrated the active OMPLA genotype in fresh isolates of H. pylori from patients referred to gastroscopy for dyspepsia. PMID:11705905

  13. Genotype-by-Environment Interactions and Adaptation to Local Temperature Affect Immunity and Fecundity in Drosophila melanogaster

    PubMed Central

    Lazzaro, Brian P.; Flores, Heather A.; Lorigan, James G.; Yourth, Christopher P.

    2008-01-01

    Natural populations of most organisms harbor substantial genetic variation for resistance to infection. The continued existence of such variation is unexpected under simple evolutionary models that either posit direct and continuous natural selection on the immune system or an evolved life history “balance” between immunity and other fitness traits in a constant environment. However, both local adaptation to heterogeneous environments and genotype-by-environment interactions can maintain genetic variation in a species. In this study, we test Drosophila melanogaster genotypes sampled from tropical Africa, temperate northeastern North America, and semi-tropical southeastern North America for resistance to bacterial infection and fecundity at three different environmental temperatures. Environmental temperature had absolute effects on all traits, but there were also marked genotype-by-environment interactions that may limit the global efficiency of natural selection on both traits. African flies performed more poorly than North American flies in both immunity and fecundity at the lowest temperature, but not at the higher temperatures, suggesting that the African population is maladapted to low temperature. In contrast, there was no evidence for clinal variation driven by thermal adaptation within North America for either trait. Resistance to infection and reproductive success were generally uncorrelated across genotypes, so this study finds no evidence for a fitness tradeoff between immunity and fecundity under the conditions tested. Both local adaptation to geographically heterogeneous environments and genotype-by-environment interactions may explain the persistence of genetic variation for resistance to infection in natural populations. PMID:18369474

  14. Genetic variation in adaptive traits and seed transfer zones for Pseudoroegneria spicata (bluebunch wheatgrass) in the northwestern United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A genecological approach was used to explore genetic variation in adaptive traits in Pseudoroegneria spicata, a key restoration grass, in the intermountain western United States. Common garden experiments were established at three contrasting sites with seedlings from two maternal parents from each ...

  15. Adaptive Feedforward Compensation by Specified Step Settling Considering Resonance Frequency Variation and Constraint on Control Input Amplitude

    NASA Astrophysics Data System (ADS)

    Maeda, Yoshihiro; Wada, Masatake; Iwasaki, Makoto; Hirai, Hiromu

    This paper presents an adaptive feedfowad (FF) compensation method based on a deadbeat control framework for fast and precise positioning in mechatronic systems. The conventional FF compensation approach can design a FF compensator by considering both the frequency shaping and amplitude of FF control input, to suppress the response variations due to the perturbations in plant resonance frequency. However, since the conventional approach is not adaptive against frequency variations, an overshoot and/or undershoot response at the settling region would deteriorate the positioning performance. In this research, therefore, the proposed FF compensation approach with an adaptive identification system for the resonance frequency is adopted to achieve the desired positioning performance. The effectiveness of the proposed FF compensation approach has been verified by experiments using a prototype of an industrial positioning device.

  16. An adaptive total variation image reconstruction method for speckles through disordered media

    NASA Astrophysics Data System (ADS)

    Gong, Changmei; Shao, Xiaopeng; Wu, Tengfei

    2013-09-01

    Multiple scattering of light in highly disordered medium can break the diffraction limit of conventional optical system combined with image reconstruction method. Once the transmission matrix of the imaging system is obtained, the target image can be reconstructed from its speckle pattern by image reconstruction algorithm. Nevertheless, the restored image attained by common image reconstruction algorithms such as Tikhonov regularization has a relatively low signal-tonoise ratio (SNR) due to the experimental noise and reconstruction noise, greatly reducing the quality of the result image. In this paper, the speckle pattern of the test image is simulated by the combination of light propagation theories and statistical optics theories. Subsequently, an adaptive total variation (ATV) algorithm—the TV minimization by augmented Lagrangian and alternating direction algorithms (TVAL3), which is based on augmented Lagrangian and alternating direction algorithm, is utilized to reconstruct the target image. Numerical simulation experimental results show that, the TVAL3 algorithm can effectively suppress the noise of the restored image and preserve more image details, thus greatly boosts the SNR of the restored image. It also indicates that, compared with the image directly formed by `clean' system, the reconstructed results can overcoming the diffraction limit of the `clean' system, therefore being conductive to the observation of cells and protein molecules in biological tissues and other structures in micro/nano scale.

  17. Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes

    PubMed Central

    Steiner, Cynthia C; Weber, Jesse N; Hoekstra, Hopi E

    2007-01-01

    Little is known about the genetic basis of ecologically important morphological variation such as the diverse color patterns of mammals. Here we identify genetic changes contributing to an adaptive difference in color pattern between two subspecies of oldfield mice (Peromyscus polionotus). One mainland subspecies has a cryptic dark brown dorsal coat, while a younger beach-dwelling subspecies has a lighter coat produced by natural selection for camouflage on pale coastal sand dunes. Using genome-wide linkage mapping, we identified three chromosomal regions (two of major and one of minor effect) associated with differences in pigmentation traits. Two candidate genes, the melanocortin-1 receptor (Mc1r) and its antagonist, the Agouti signaling protein (Agouti), map to independent regions that together are responsible for most of the difference in pigmentation between subspecies. A derived mutation in the coding region of Mc1r, rather than change in its expression level, contributes to light pigmentation. Conversely, beach mice have a derived increase in Agouti mRNA expression but no changes in protein sequence. These two genes also interact epistatically: the phenotypic effects of Mc1r are visible only in genetic backgrounds containing the derived Agouti allele. These results demonstrate that cryptic coloration can be based largely on a few interacting genes of major effect. PMID:17696646

  18. Adaptation to Pronunciation Variations in Indonesian Spoken Query-Based Information Retrieval

    NASA Astrophysics Data System (ADS)

    Lestari, Dessi Puji; Furui, Sadaoki

    Recognition errors of proper nouns and foreign words significantly decrease the performance of ASR-based speech applications such as voice dialing systems, speech summarization, spoken document retrieval, and spoken query-based information retrieval (IR). The reason is that proper nouns and words that come from other languages are usually the most important key words. The loss of such words due to misrecognition in turn leads to a loss of significant information from the speech source. This paper focuses on how to improve the performance of Indonesian ASR by alleviating the problem of pronunciation variation of proper nouns and foreign words (English words in particular). To improve the proper noun recognition accuracy, proper-noun specific acoustic models are created by supervised adaptation using maximum likelihood linear regression (MLLR). To improve English word recognition, the pronunciation of English words contained in the lexicon is fixed by using rule-based English-to-Indonesian phoneme mapping. The effectiveness of the proposed method was confirmed through spoken query based Indonesian IR. We used Inference Network-based (IN-based) IR and compared its results with those of the classical Vector Space Model (VSM) IR, both using a tf-idf weighting schema. Experimental results show that IN-based IR outperforms VSM IR.

  19. Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history

    PubMed Central

    2013-01-01

    Background The presence of a southeast to northwest gradient across Europe in human genetic diversity is a well-established observation and has recently been confirmed by genome-wide single nucleotide polymorphism (SNP) data. This pattern is traditionally explained by major prehistoric human migration events in Palaeolithic and Neolithic times. Here, we investigate whether (similar) spatial patterns in human genomic diversity also occur on a micro-geographic scale within Europe, such as in the Netherlands, and if so, whether these patterns could also be explained by more recent demographic events, such as those that occurred in Dutch population history. Methods We newly collected data on a total of 999 Dutch individuals sampled at 54 sites across the country at 443,816 autosomal SNPs using the Genome-Wide Human SNP Array 5.0 (Affymetrix). We studied the individual genetic relationships by means of classical multidimensional scaling (MDS) using different genetic distance matrices, spatial ancestry analysis (SPA), and ADMIXTURE software. We further performed dedicated analyses to search for spatial patterns in the genomic variation and conducted simulations (SPLATCHE2) to provide a historical interpretation of the observed spatial patterns. Results We detected a subtle but clearly noticeable genomic population substructure in the Dutch population, allowing differentiation of a north-eastern, central-western, central-northern and a southern group. Furthermore, we observed a statistically significant southeast to northwest cline in the distribution of genomic diversity across the Netherlands, similar to earlier findings from across Europe. Simulation analyses indicate that this genomic gradient could similarly be caused by ancient as well as by the more recent events in Dutch history. Conclusions Considering the strong archaeological evidence for genetic discontinuity in the Netherlands, we interpret the observed clinal pattern of genomic diversity as being caused by

  20. Adaptive dynamic resource allocation in annual eusocial insects: environmental variation will not necessarily promote graded control

    PubMed Central

    Mitesser, Oliver; Weissel, Norbert; Strohm, Erhard; Poethke, Hans-Joachim

    2007-01-01

    Background According to the classical model of Macevicz and Oster, annual eusocial insects should show a clear dichotomous "bang-bang" strategy of resource allocation; colony fitness is maximised when a period of pure colony growth (exclusive production of workers) is followed by a single reproductive period characterised by the exclusive production of sexuals. However, in several species graded investment strategies with a simultaneous production of workers and sexuals have been observed. Such deviations from the "bang-bang" strategy are usually interpreted as an adaptive (bet-hedging) response to environmental fluctuations such as variation in season length or food availability. To generate predictions about the optimal investment pattern of insect colonies in fluctuating environments, we slightly modified Macevicz and Oster's classical model of annual colony dynamics and used a dynamic programming approach nested into a recurrence procedure for the solution of the stochastic optimal control problem. Results 1) The optimal switching time between pure colony growth and the exclusive production of sexuals decreases with increasing environmental variance. 2) Yet, for reasonable levels of environmental fluctuations no deviation from the typical bang-bang strategy is predicted. 3) Model calculations for the halictid bee Lasioglossum malachurum reveal that bet-hedging is not likely to be the reason for the graded allocation into sexuals versus workers observed in this species. 4) When environmental variance reaches a critical level our model predicts an abrupt change from dichotomous behaviour to graded allocation strategies, but the transition between colony growth and production of sexuals is not necessarily monotonic. Both, the critical level of environmental variance as well as the characteristic pattern of resource allocation strongly depend on the type of function used to describe environmental fluctuations. Conclusion Up to now bet-hedging as an evolutionary

  1. Adaptation in the asexual false spider mite Brevipalpus phoenicis: evidence for frozen niche variation.

    PubMed

    Groot, Thomas V M; Janssen, Arne; Pallini, Angelo; Breeuwer, Johannes A J

    2005-01-01

    Because asexual species lack recombination, they have little opportunity to produce genetically variable offspring and cannot adapt to changes in their environment. However, a number of asexual species are very successful and appear to contradict this general view. One such species is the phytophagous mite Brevipalpus phoenicis (Geijskes), a species that is found in a wide range of environments. There are two general explanations for this pattern, the General Purpose Genotype (GPG) and Frozen Niche Variation (FNV). According to the GPG model, an asexual species consists of clones that can all survive and reproduce in all the different niches. Alternatively, the FNV model postulates that different clones are specialized to different niches. We have performed a test to distinguish between these models in B. phoenicis. Mites from three populations from three different host plant species (citrus, hibiscus and acerola) were transplanted to their own and the two alternative host plants and mite survival and egg production were measured. Additionally, the mite populations were genotyped using microsatellites. Fitness was seriously reduced when mites were transplanted to the alternative host plant species, except when the alternative host was acerola. We concluded that B. phoenicis clones are specialized to different niches and thus the FNV best describes the broad ecological niche of this species but that there is also some evidence for host plant generalization. This conclusion was strengthened by the observations that on each host plant species the native mite population performed better than the introduced ones, and that three microsatellite markers showed that the mite populations are genetically distinct. PMID:16132731

  2. A region-appearance-based adaptive variational model for 3D liver segmentation

    SciTech Connect

    Peng, Jialin; Dong, Fangfang; Chen, Yunmei; Kong, Dexing

    2014-04-15

    Purpose: Liver segmentation from computed tomography images is a challenging task owing to pixel intensity overlapping, ambiguous edges, and complex backgrounds. The authors address this problem with a novel active surface scheme, which minimizes an energy functional combining both edge- and region-based information. Methods: In this semiautomatic method, the evolving surface is principally attracted to strong edges but is facilitated by the region-based information where edge information is missing. As avoiding oversegmentation is the primary challenge, the authors take into account multiple features and appearance context information. Discriminative cues, such as multilayer consecutiveness and local organ deformation are also implicitly incorporated. Case-specific intensity and appearance constraints are included to cope with the typically large appearance variations over multiple images. Spatially adaptive balancing weights are employed to handle the nonuniformity of image features. Results: Comparisons and validations on difficult cases showed that the authors’ model can effectively discriminate the liver from adhering background tissues. Boundaries weak in gradient or with no local evidence (e.g., small edge gaps or parts with similar intensity to the background) were delineated without additional user constraint. With an average surface distance of 0.9 mm and an average volume overlap of 93.9% on the MICCAI data set, the authors’ model outperformed most state-of-the-art methods. Validations on eight volumes with different initial conditions had segmentation score variances mostly less than unity. Conclusions: The proposed model can efficiently delineate ambiguous liver edges from complex tissue backgrounds with reproducibility. Quantitative validations and comparative results demonstrate the accuracy and efficacy of the model.

  3. Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation.

    PubMed

    Portnoy, D S; Puritz, J B; Hollenbeck, C M; Gelsleichter, J; Chapman, D; Gold, J R

    2015-12-01

    Sex-biased dispersal is expected to homogenize nuclear genetic variation relative to variation in genetic material inherited through the philopatric sex. When site fidelity occurs across a heterogeneous environment, local selective regimes may alter this pattern. We assessed spatial patterns of variation in nuclear-encoded, single nucleotide polymorphisms (SNPs) and sequences of the mitochondrial control region in bonnethead sharks (Sphyrna tiburo), a species thought to exhibit female philopatry, collected from summer habitats used for gestation. Geographic patterns of mtDNA haplotypes and putatively neutral SNPs confirmed female philopatry and male-mediated gene flow along the northeastern coast of the Gulf of Mexico. A total of 30 outlier SNP loci were identified; alleles at over half of these loci exhibited signatures of latitude-associated selection. Our results indicate that in species with sex-biased dispersal, philopatry can facilitate sorting of locally adaptive variation, with the dispersing sex facilitating movement of potentially adaptive variation among locations and environments. PMID:26518727

  4. High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation?

    PubMed

    Roulin, Anne C; Mariadassou, Mahendra; Hall, Matthew D; Walser, Jean-Claude; Haag, Christoph; Ebert, Dieter

    2015-10-01

    Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy, as resting stages can only be produced sexually. In this species, on a continental scale, resting-stage production is locally adapted--that is, it is induced when the photoperiod indicates the imminence of habitat deterioration. Here, we aimed to explore whether selection is strong enough to maintain local adaptation at a scale of a few kilometers. We assessed life-history traits of 64 D. magna clones originating from 11 populations of a metapopulation with permanent and intermittent pool habitats. We found large within- and between-population variation for all dormancy-related traits, but no evidence for the hypothesized higher resting-stage production in animals from intermittent habitats. We discuss how gene flow, founder events, or other forms of selection might interfere with the process of local adaptation. PMID:26418426

  5. A CT reconstruction approach from sparse projection with adaptive-weighted diagonal total-variation in biomedical application.

    PubMed

    Deng, Luzhen; Mi, Deling; He, Peng; Feng, Peng; Yu, Pengwei; Chen, Mianyi; Li, Zhichao; Wang, Jian; Wei, Biao

    2015-01-01

    For lack of directivity in Total Variation (TV) which only uses x-coordinate and y-coordinate gradient transform as its sparse representation approach during the iteration process, this paper brought in Adaptive-weighted Diagonal Total Variation (AwDTV) that uses the diagonal direction gradient to constraint reconstructed image and adds associated weights which are expressed as an exponential function and can be adaptively adjusted by the local image-intensity diagonal gradient for the purpose of preserving the edge details, then using the steepest descent method to solve the optimization problem. Finally, we did two sets of numerical simulation and the results show that the proposed algorithm can reconstruct high-quality CT images from few-views projection, which has lower Root Mean Square Error (RMSE) and higher Universal Quality Index (UQI) than Algebraic Reconstruction Technique (ART) and TV-based reconstruction method. PMID:26405935

  6. Adaptation.

    PubMed

    Broom, Donald M

    2006-01-01

    The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

  7. High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

    PubMed Central

    2013-01-01

    Background Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is

  8. Genomic, transcriptomic and phenomic variation reveals the complex adaptation to stress response of modern maize breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Early maize adaptation to different agricultural environments was an important process associated with the creation of a stable food supply that allowed the evolution of human civilization in the Americas. To explore the mechanisms of maize adaptation, genomic, transcriptomic and phenomic data were ...

  9. Situational variations in ethnic identity across immigration generations: Implications for acculturative change and cross-cultural adaptation.

    PubMed

    Noels, Kimberly A; Clément, Richard

    2015-12-01

    This study examined whether the acculturation of ethnic identity is first evident in more public situations with greater opportunity for intercultural interaction and eventually penetrates more intimate situations. It also investigated whether situational variations in identity are associated with cross-cultural adaptation. First-generation (G1), second-generation (G2) and mixed-parentage second-generation (G2.5) young adult Canadians (n = 137, n = 169, and n = 91, respectively) completed a questionnaire assessing their heritage and Canadian identities across four situational domains (family, friends, university and community), global heritage identity and cross-cultural adaptation. Consistent with the acculturation penetration hypothesis, the results showed Canadian identity was stronger than heritage identity in public domains, but the converse was true in the family domain; moreover, the difference between the identities in the family domain was attenuated in later generations. Situational variability indicated better adaptation for the G1 cohort, but poorer adaptation for the G2.5 cohort. For the G2 cohort, facets of global identity moderated the relation, such that those with a weaker global identity experienced greater difficulties and hassles with greater identity variability but those with a stronger identity did not. These results are interpreted in light of potential interpersonal issues implied by situational variation for each generation cohort. PMID:26271917

  10. Behavioural variation in 172 small-scale societies indicates that social learning is the main mode of human adaptation

    PubMed Central

    Mathew, Sarah; Perreault, Charles

    2015-01-01

    The behavioural variation among human societies is vast and unmatched in the animal world. It is unclear whether this variation is due to variation in the ecological environment or to differences in cultural traditions. Underlying this debate is a more fundamental question: is the richness of humans’ behavioural repertoire due to non-cultural mechanisms, such as causal reasoning, inventiveness, reaction norms, trial-and-error learning and evoked culture, or is it due to the population-level dynamics of cultural transmission? Here, we measure the relative contribution of environment and cultural history in explaining the behavioural variation of 172 Native American tribes at the time of European contact. We find that the effect of cultural history is typically larger than that of environment. Behaviours also persist over millennia within cultural lineages. This indicates that human behaviour is not predominantly determined by single-generation adaptive responses, contra theories that emphasize non-cultural mechanisms as determinants of human behaviour. Rather, the main mode of human adaptation is social learning mechanisms that operate over multiple generations. PMID:26085589

  11. Behavioural variation in 172 small-scale societies indicates that social learning is the main mode of human adaptation.

    PubMed

    Mathew, Sarah; Perreault, Charles

    2015-07-01

    The behavioural variation among human societies is vast and unmatched in the animal world. It is unclear whether this variation is due to variation in the ecological environment or to differences in cultural traditions. Underlying this debate is a more fundamental question: is the richness of humans' behavioural repertoire due to non-cultural mechanisms, such as causal reasoning, inventiveness, reaction norms, trial-and-error learning and evoked culture, or is it due to the population-level dynamics of cultural transmission? Here, we measure the relative contribution of environment and cultural history in explaining the behavioural variation of 172 Native American tribes at the time of European contact. We find that the effect of cultural history is typically larger than that of environment. Behaviours also persist over millennia within cultural lineages. This indicates that human behaviour is not predominantly determined by single-generation adaptive responses, contra theories that emphasize non-cultural mechanisms as determinants of human behaviour. Rather, the main mode of human adaptation is social learning mechanisms that operate over multiple generations. PMID:26085589

  12. Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.

    PubMed

    Schrider, Daniel R; Hahn, Matthew W; Begun, David J

    2016-05-01

    Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. PMID:26809315

  13. Natural variation and the capacity to adapt to ocean acidification in the keystone sea urchin Strongylocentrotus purpuratus.

    PubMed

    Kelly, Morgan W; Padilla-Gamiño, Jacqueline L; Hofmann, Gretchen E

    2013-08-01

    A rapidly growing body of literature documents the potential negative effects of CO2 -driven ocean acidification (OA) on marine organisms. However, nearly all this work has focused on the effects of future conditions on modern populations, neglecting the role of adaptation. Rapid evolution can alter demographic responses to environmental change, ultimately affecting the likelihood of population persistence, but the capacity for adaptation will differ among populations and species. Here, we measure the capacity of the ecologically important purple sea urchin Strongylocentrotus purpuratus to adapt to OA, using a breeding experiment to estimate additive genetic variance for larval size (an important component of fitness) under future high-pCO2 /low-pH conditions. Although larvae reared under future conditions were smaller than those reared under present-day conditions, we show that there is also abundant genetic variation for body size under elevated pCO2 , indicating that this trait can evolve. The observed heritability of size was 0.40 ± 0.32 (95% CI) under low pCO2 , and 0.50 ± 0.30 under high-pCO2 conditions. Accounting for the observed genetic variation in models of future larval size and demographic rates substantially alters projections of performance for this species in the future ocean. Importantly, our model shows that after incorporating the effects of adaptation, the OA-driven decrease in population growth rate is up to 50% smaller, than that predicted by the 'no-adaptation' scenario. Adults used in the experiment were collected from two sites on the coast of the Northeast Pacific that are characterized by different pH regimes, as measured by autonomous sensors. Comparing results between sites, we also found subtle differences in larval size under high-pCO2 rearing conditions, consistent with local adaptation to carbonate chemistry in the field. These results suggest that spatially varying selection may help to maintain genetic variation necessary

  14. Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic structural variations, including segmental duplications (SD) and copy number variations (CNV), contribute significantly to individual health and disease in primates and rodents. As a part of the bovine genome annotation effort, we performed the first genome-wide analysis of SD in cattle usin...

  15. Genetic variation in adaptive traits and seed transfer zones for Pseudoroegneria spicata (bluebunch wheatgrass) in the northwestern United States

    PubMed Central

    Bradley St. Clair, John; Kilkenny, Francis F; Johnson, Richard C; Shaw, Nancy L; Weaver, George

    2013-01-01

    A genecological approach was used to explore genetic variation in adaptive traits in Pseudoroegneria spicata, a key restoration grass, in the intermountain western United States. Common garden experiments were established at three contrasting sites with seedlings from two maternal parents from each of 114 populations along with five commercial releases commonly used in restoration. Traits associated with size, flowering phenology, and leaf width varied considerably among populations and were moderately correlated with the climates of the seed sources. Pseudoroegneria spicata populations from warm, arid source environments were smaller with earlier phenology and had relatively narrow leaves than those from mild climates with cool summers, warm winters, low seasonal temperature differentials, high precipitation, and low aridity. Later phenology was generally associated with populations from colder climates. Releases were larger and more fecund than most of the native ecotypes, but were similar to native populations near their source of origin. Differences among native populations associated with source climates that are logical for survival, growth, and reproduction indicate that genetic variation across the landscape is adaptive and should be considered during restoration. Results were used to delineate seed transfer zones and population movement guidelines to ensure adapted plant materials for restoration activities. PMID:24062802

  16. Experimental studies of adaptation in Clarkia xantiana. II. Fitness variation across a subspecies border.

    PubMed

    Geber, Monica A; Eckhart, Vincent M

    2005-03-01

    Because the range boundary is the locale beyond which a taxon fails to persist, it provides a unique opportunity for studying the limits on adaptive evolution. Adaptive constraints on range expansion are perplexing in view of widespread ecotypic differentiation by habitat and region within a species' range (regional adaptation) and rapid evolutionary response to novel environments. In this study of two parapatric subspecies, Clarkia xantiana ssp. xantiana and C. x. ssp. parviflora, we compared the fitness of population transplants within their native region, in a non-native region within the native range, and in the non-native range to assess whether range expansion might be limited by a greater intensity of selection on colonists of a new range versus a new region within the range. The combined range of the two subspecies spans a west-to-east gradient of declining precipitation in the Sierra Nevada of California, with ssp. xantiana in the west being replaced by ssp. parviflora in the east. Both subspecies had significantly higher fitness in the native range (range adaptation), whereas regional adaptation was weak and was found only in the predominantly outcrossing ssp. xantiana but was absent in the inbreeding ssp. parvifilora. Because selection intensity on transplants was much stronger in the non-native range relative to non-native regions, there is a larger adaptive barrier to range versus regional expansion. Three of five sequential fitness components accounted for regional and range adaptation, but only one of them, survivorship from germination to flowering, contributed to both. Flower number contributed to regional adaptation in ssp. xantiana and fruit set (number of fruits per flower) to range adaptation. Differential survivorship of the two taxa or regional populations of ssp. xantiana in non-native environments was attributable, in part, to biotic interactions, including competition, herbivory, and pollination. For example, low fruit set in ssp. xantiana

  17. Geographic variation in the songs of neotropical singing mice: testing the relative importance of drift and local adaptation.

    PubMed

    Campbell, Polly; Pasch, Bret; Pino, Jorge L; Crino, Ondi L; Phillips, Molly; Phelps, Steven M

    2010-07-01

    Patterns of geographic variation in communication systems can provide insight into the processes that drive phenotypic evolution. Although work in birds, anurans, and insects demonstrates that acoustic signals are sensitive to diverse selective and stochastic forces, processes that shape variation in mammalian vocalizations are poorly understood. We quantified geographic variation in the advertisement songs of sister species of singing mice, montane rodents with a unique mode of vocal communication. We tested three hypotheses to explain spatial variation in the song of the lower altitude species, Scotinomys teguina: selection for species recognition in sympatry with congener, S. xerampelinus, acoustic adaptation to different environments, and stochastic divergence. Mice were sampled at seven sites in Costa Rica and Panamá; genetic distances were estimated from mitochondrial control region sequences, between-site differences in acoustic environment were estimated from climatic data. Acoustic, genetic and geographic distances were all highly correlated in S. teguina, suggesting that population differentiation in song is largely shaped by genetic drift. Contrasts between interspecific genetic-acoustic distances were significantly greater than expectations derived from intraspecific contrasts, indicating accelerated evolution of species-specific song. We propose that, although much intraspecific acoustic variation is effectively neutral, selection has been important in shaping species differences in song. PMID:20148958

  18. Adapt

    NASA Astrophysics Data System (ADS)

    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

  19. Heritable variation in heat shock gene expression: a potential mechanism for adaptation to thermal stress in embryos of sea turtles.

    PubMed

    Tedeschi, J N; Kennington, W J; Tomkins, J L; Berry, O; Whiting, S; Meekan, M G; Mitchell, N J

    2016-01-13

    The capacity of species to respond adaptively to warming temperatures will be key to their survival in the Anthropocene. The embryos of egg-laying species such as sea turtles have limited behavioural means for avoiding high nest temperatures, and responses at the physiological level may be critical to coping with predicted global temperature increases. Using the loggerhead sea turtle (Caretta caretta) as a model, we used quantitative PCR to characterise variation in the expression response of heat-shock genes (hsp60, hsp70 and hsp90; molecular chaperones involved in cellular stress response) to an acute non-lethal heat shock. We show significant variation in gene expression at the clutch and population levels for some, but not all hsp genes. Using pedigree information, we estimated heritabilities of the expression response of hsp genes to heat shock and demonstrated both maternal and additive genetic effects. This is the first evidence that the heat-shock response is heritable in sea turtles and operates at the embryonic stage in any reptile. The presence of heritable variation in the expression of key thermotolerance genes is necessary for sea turtles to adapt at a molecular level to warming incubation environments. PMID:26763709

  20. Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum.

    PubMed

    Hardigan, Michael A; Crisovan, Emily; Hamilton, John P; Kim, Jeongwoon; Laimbeer, Parker; Leisner, Courtney P; Manrique-Carpintero, Norma C; Newton, Linsey; Pham, Gina M; Vaillancourt, Brieanne; Yang, Xueming; Zeng, Zixian; Douches, David S; Jiang, Jiming; Veilleux, Richard E; Buell, C Robin

    2016-02-01

    Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways. PMID:26772996

  1. An Intronic Polymorphism in couch potato Is Not Distributed Clinally in European Drosophila melanogaster Populations nor Does It Affect Diapause Inducibility.

    PubMed

    Zonato, Valeria; Fedele, Giorgio; Kyriacou, Charalambos P

    2016-01-01

    couch potato (cpo) encodes an RNA binding protein that has been reported to be expressed in the peripheral and central nervous system of embryos, larvae and adults, including the major endocrine organ, the ring gland. A polymorphism in the D. melanogaster cpo gene coding region displays a latitudinal cline in frequency in North American populations, but as cpo lies within the inversion In(3R)Payne, which is at high frequencies and itself shows a strong cline on this continent, interpretation of the cpo cline is not straightforward. A second downstream SNP in strong linkage disequilibrium with the first has been claimed to be primarily responsible for the latitudinal cline in diapause incidence in USA populations.Here, we investigate the frequencies of these two cpo SNPs in populations of Drosophila throughout continental Europe. The advantage of studying cpo variation in Europe is the very low frequency of In(3R)Payne, which we reveal here, does not appear to be clinally distributed. We observe a very different geographical scenario for cpo variation from the one in North America, suggesting that the downstream SNP does not play a role in diapause. In an attempt to verify whether the SNPs influence diapause we subsequently generated lines with different combinations of the two cpo SNPs on known timeless (tim) genetic backgrounds, because polymorphism in the clock gene tim plays a significant role in diapause inducibility. Our results reveal that the downstream cpo SNP does not seem to play any role in diapause induction in European populations in contrast to the upstream coding cpo SNP. Consequently, all future diapause studies on strains of D. melanogaster should initially determine their tim and cpo status. PMID:27598401

  2. Distribution and clinal trends of the ABO and Rh genes in select Middle Eastern countries.

    PubMed

    AlSuhaibani, E S; Kizilbash, N A; Afshan, K; Malik, S

    2015-01-01

    An understanding of the ABO and Rh blood group systems is important for blood transfusions and is also pertinent due to their potential association with certain morbidities and susceptibilities to infections. To investigate the diversity and differentiation of the ABO and Rh loci in Middle Eastern populations, data from twelve representative Middle Eastern populations were analyzed. Six populations were in conformity with Hardy-Weinberg equilibrium at the ABO locus. The pooled heterozygosity at both loci was calculated to be highest in the sample from Jordan and lowest in Bahrain. Heterogeneity was pronounced in the Northern compared to the Southern Middle Eastern populations. Overall, the absolute gene diversity was 0.0046 and gene differentiation was calculated to be 0.0100. Genetic diversity of the studied loci across all populations (HT) was estimated to be 0.4594, while the diversity within the populations (HS) was 0.4548. Nei's genetic distance analyses revealed highest affinities between the populations of Kuwait and Qatar, Oman and Yemen, and between Qatar and the United Arab Emirates. These results were displayed through a UGPMA dendrogram and principal component analyses, which established clustering of certain populations. Clinal trends of the allelic systems were observed by generating contour maps that allow a detailed appreciation of the distributions of alleles across the geography of the Arabian Peninsula and the Middle East. Taken together, these analyses are helpful in understanding the differentiation of blood group loci and for designing prospective studies for establishing the associations of these loci with health variables in the populations studied. PMID:26400302

  3. Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration, and natural selection. Switchgrass (Panicum virgatum L.) has strong ecotypic differentiation despite life history characteristics that promote high levels of gene flow and can ...

  4. Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks

    PubMed Central

    2013-01-01

    Background Variation of gene expression can lead to phenotypic variation and have therefore been assumed to contribute the diversity of wine yeast (Saccharomyces cerevisiae) properties. However, the molecular bases of this variation of gene expression are unknown. We addressed these questions by carrying out an integrated genetical-genomic study in fermentation conditions. We report here quantitative trait loci (QTL) mapping based on expression profiling in a segregating population generated by a cross between a derivative of the popular wine strain EC1118 and the laboratory strain S288c. Results Most of the fermentation traits studied appeared to be under multi-allelic control. We mapped five phenotypic QTLs and 1465 expression QTLs. Several expression QTLs overlapped in hotspots. Among the linkages unraveled here, several were associated with metabolic processes essential for wine fermentation such as glucose sensing or nitrogen and vitamin metabolism. Variations affecting the regulation of drug detoxification and export (TPO1, PDR12 or QDR2) were linked to variation in four genes encoding transcription factors (PDR8, WAR1, YRR1 and HAP1). We demonstrated that the allelic variation of WAR1 and TPO1 affected sorbic and octanoic acid resistance, respectively. Moreover, analysis of the transcription factors phylogeny suggests they evolved with a specific adaptation of the strains to wine fermentation conditions. Unexpectedly, we found that the variation of fermentation rates was associated with a partial disomy of chromosome 16. This disomy resulted from the well known 8–16 translocation. Conclusions This large data set made it possible to decipher the effects of genetic variation on gene expression during fermentation and certain wine fermentation properties. Our findings shed a new light on the adaptation mechanisms required by yeast to cope with the multiple stresses generated by wine fermentation. In this context, the detoxification and export systems appear

  5. Extensive variation, but not local adaptation in an Australian alpine daisy.

    PubMed

    Hirst, Megan J; Sexton, Jason P; Hoffmann, Ary A

    2016-08-01

    Alpine plants often occupy diverse habitats within a similar elevation range, but most research on local adaptation in these plants has focused on elevation gradients. In testing for habitat-related local adaptation, local effects on seed quality and initial plant growth should be considered in designs that encompass multiple populations and habitats. We tested for local adaptation across alpine habitats in a morphologically variable daisy species, Brachyscome decipiens, in the Bogong High Plains in Victoria, Australia. We collected seed from different habitats, controlled for maternal effects through initial seed size estimates, and characterized seedling survival and growth in a field transplant experiment. We found little evidence for local adaptation for survival or plant size, based on three adaptation measures: Home versus Away, Local versus Foreign, and Sympatric versus Allopatric (SA). The SA measure controlled for planting site and population (site-of-origin) effects. There were significant differences due to site-of-origin and planting site effects. An important confounding factor was the size of plants directly after transplantation of seedlings, which had a large impact on subsequent seedling survival and growth. Initial differences in plant width and height influenced subsequent survival across the growing season but in opposing directions: wide plants had higher survival, but tall plants had lower survival. In an additional controlled garden experiment at Cranbourne Royal Botanic Gardens, site-of-origin effects detected in the field experiments disappeared under more benign homogeneous conditions. Although B. decipiens from different source areas varied significantly when grown across a range of alpine habitats, these differences did not translate into a local or habitat-related fitness advantage. This lack of local advantage may signal weak past selection, and/or weak adaptive transgeneration (plasticity) effects. PMID:27551396

  6. Fine-scale geographic variation in photosynthetic-related traits of Picea glauca seedlings indicates local adaptation to climate.

    PubMed

    Benomar, Lahcen; Lamhamedi, Mohammed S; Villeneuve, Isabelle; Rainville, André; Beaulieu, Jean; Bousquet, Jean; Margolis, Hank A

    2015-08-01

    Climate-related variations in functional traits of boreal tree species can result both from physiological acclimation and genetic adaptation of local populations to their biophysical environment. To improve our understanding and prediction of the physiological and growth responses of populations to climate change, we studied the role of climate of seed origin in determining variations in functional traits and its implications for tree improvement programs for a commonly reforested boreal conifer, white spruce (Picea glauca (Moench) Voss). We evaluated growth, root-to-shoot ratio (R/S), specific leaf area (SLA), needle nitrogen (N(mass)), total non-structural carbohydrates (NSC) and photosynthetic traits of 3-year-old seedlings in a greenhouse experiment using seed from six seed orchards (SO) representing the different regions where white spruce is reforested in Québec. Height and total dry mass (TDM) were positively correlated with photosynthetic capacity (A(max)), stomatal conductance (g(s)) and mesophyll conductance (g(m)). Total dry mass, but not height growth, was strongly correlated with latitude of seed origin (SO) and associated climate variables. A(max), g(s), g(m) and more marginally, photosynthetic nitrogen-use efficiency (PNUE) were positively associated with the mean July temperature of the SO, while water use efficiency (WUE) was negatively associated. Maximum rates of carboxylation (V(cmax)), maximum rates of electron transport (J(max)), SLA, N(mass), NSC and R/S showed no pattern. Our results did not demonstrate a higher Amax for northern seed orchards, although this has been previously hypothesized as an adaptation mechanism for maintaining carbon uptake in northern regions. We suggest that gs, gm, WUE and PNUE are the functional traits most associated with fine-scale geographic clines and with the degree of local adaptation of white spruce populations to their biophysical environments. These geographic patterns may reflect in situ adaptive genetic

  7. Genetic variation and local adaptation at a cheatgrass (Bromus tectorum) invasion edge in western Nevada.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cheatgrass (Bromus tectorum) is an invasive weed in western North America primarily found growing at elevations less than 2200 m. We asked whether cheatgrass is capable of becoming adapted to high elevations at a population near a high elevation invasion edge, using a combination of methods, includi...

  8. Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding.

    PubMed

    Liu, Haijun; Wang, Xiaqing; Warburton, Marilyn L; Wen, Weiwei; Jin, Minliang; Deng, Min; Liu, Jie; Tong, Hao; Pan, Qingchun; Yang, Xiaohong; Yan, Jianbing

    2015-06-01

    The temperate-tropical division of early maize germplasms to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from examining 558 529 single nucleotide polymorphisms, expression data of 28 769 genes, and 662 traits collected from 368 diverse temperate and tropical maize inbred lines in this study. This is a new attempt to systematically exploit the mechanisms of the adaptation process in maize. Our results indicate that divergence between tropical and temperate lines apparently occurred 3400-6700 years ago. Seven hundred and one genomic selection signals and transcriptomic variants including 2700 differentially expressed individual genes and 389 rewired co-expression network genes were identified. These candidate signals were found to be functionally related to stress responses, and most were associated with directionally selected traits, which may have been an advantage under widely varying environmental conditions faced by maize as it was migrated away from its domestication center. Our study also clearly indicates that such stress adaptation could involve evolution of protein-coding sequences as well as transcriptome-level regulatory changes. The latter process may be a more flexible and dynamic way for maize to adapt to environmental changes along its short evolutionary history. PMID:25620769

  9. Multi-allelic major effect genes interact with minor effect QTLs to control adaptive color pattern variation in Heliconius erato.

    PubMed

    Papa, Riccardo; Kapan, Durrell D; Counterman, Brian A; Maldonado, Karla; Lindstrom, Daniel P; Reed, Robert D; Nijhout, H Frederik; Hrbek, Tomas; McMillan, W Owen

    2013-01-01

    Recent studies indicate that relatively few genomic regions are repeatedly involved in the evolution of Heliconius butterfly wing patterns. Although this work demonstrates a number of cases where homologous loci underlie both convergent and divergent wing pattern change among different Heliconius species, it is still unclear exactly how many loci underlie pattern variation across the genus. To address this question for Heliconius erato, we created fifteen independent crosses utilizing the four most distinct color pattern races and analyzed color pattern segregation across a total of 1271 F2 and backcross offspring. Additionally, we used the most variable brood, an F2 cross between H. himera and the east Ecuadorian H. erato notabilis, to perform a quantitative genetic analysis of color pattern variation and produce a detailed map of the loci likely involved in the H. erato color pattern radiation. Using AFLP and gene based markers, we show that fewer major genes than previously envisioned control the color pattern variation in H. erato. We describe for the first time the genetic architecture of H. erato wing color pattern by assessing quantitative variation in addition to traditional linkage mapping. In particular, our data suggest three genomic intervals modulate the bulk of the observed variation in color. Furthermore, we also identify several modifier loci of moderate effect size that contribute to the quantitative wing pattern variation. Our results are consistent with the two-step model for the evolution of mimetic wing patterns in Heliconius and support a growing body of empirical data demonstrating the importance of major effect loci in adaptive change. PMID:23533571

  10. Transcriptional variation associated with cactus host plant adaptation in Drosophila mettleri populations.

    PubMed

    Hoang, Kim; Matzkin, Luciano M; Bono, Jeremy M

    2015-10-01

    Although the importance of host plant chemistry in plant-insect interactions is widely accepted, the genetic basis of adaptation to host plants is not well understood. Here, we investigate transcriptional changes associated with a host plant shift in Drosophila mettleri. While D. mettleri is distributed mainly throughout the Sonoran Desert where it specializes on columnar cacti (Carnegiea gigantea and Pachycereus pringleii), a population on Santa Catalina Island has shifted to chemically divergent coastal prickly pear cactus (Opuntia littoralis). We compared gene expression of larvae from the Sonoran Desert and Santa Catalina Island when reared on saguaro (C. gigantea), coastal prickly pear and laboratory food. Consistent with expectations based on the complexity and toxicity of cactus relative to laboratory food, within-population comparisons between larvae reared on these food sources revealed transcriptional differences in detoxification and other metabolic pathways. The majority of transcriptional differences between populations on the cactus hosts were independent of the rearing environment and included a disproportionate number of genes involved in processes relevant to host plant adaptation (e.g. detoxification, central metabolism and chemosensory pathways). Comparisons of transcriptional reaction norms between the two populations revealed extensive shared plasticity that likely allowed colonization of coastal prickly pear on Santa Catalina Island. We also found that while plasticity may have facilitated subsequent adaptive divergence in gene expression between populations, the majority of genes that differed in expression on the novel host were not transcriptionally plastic in the presumed ancestral state. PMID:26384860

  11. The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean.

    PubMed

    Burri, Reto; Antoniazza, Sylvain; Gaigher, Arnaud; Ducrest, Anne-Lyse; Simon, Céline; Fumagalli, Luca; Goudet, Jérôme; Roulin, Alexandre

    2016-01-01

    Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that barn owls colonized the Western Palearctic in a ring-like manner around the Mediterranean and meet in secondary contact in Greece. Rufous coloration appears to be linked to a recently evolved nonsynonymous-derived variant of the melanocortin 1 receptor (MC1R) gene, which according to quantitative genetic analyses evolved under local adaptation during or following the colonization of Central Europe. Admixture patterns and linkage disequilibrium between the neutral genetic background and color found exclusively within the secondary contact zone suggest limited introgression at secondary contact. These results from a system reminiscent of ring species provide a striking example of how local adaptation can evolve from derived genetic variation. PMID:26773815

  12. Population genomic variation reveals roles of history, adaptation, and ploidy in switchgrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diversity within a species is shaped by many processes, including mutation, migration, and natural selection. These processes leave signatures in geographic and genomic patterns of variation, and characterizing the patterns provides insight into the roles of different factors in shaping diversity. W...

  13. Endopolyploidy as a potential alternative adaptive strategy for Arabidopsis leaf size variation in response to UV-B

    PubMed Central

    Gegas, Vasilis C.; Wargent, Jason J.; Pesquet, Edouard; Granqvist, Emma; Paul, Nigel D.; Doonan, John H.

    2014-01-01

    The extent of endoreduplication in leaf growth is group- or even species-specific, and its adaptive role is still unclear. A survey of Arabidopsis accessions for variation at the level of endopolyploidy, cell number, and cell size in leaves revealed extensive genetic variation in endopolyploidy level. High endopolyploidy is associated with increased leaf size, both in natural and in genetically unstructured (mapping) populations. The underlying genes were identified as quantitative trait loci that control endopolyploidy in nature by modulating the progression of successive endocycles during organ development. This complex genetic architecture indicates an adaptive mechanism that allows differential organ growth over a broad geographic range and under stressful environmental conditions. UV-B radiation was identified as a significant positive climatic predictor for high endopolyploidy. Arabidopsis accessions carrying the increasing alleles for endopolyploidy also have enhanced tolerance to UV-B radiation. UV-absorbing secondary metabolites provide an additional protective strategy in accessions that display low endopolyploidy. Taken together, these results demonstrate that high constitutive endopolyploidy is a significant predictor for organ size in natural populations and is likely to contribute to sustaining plant growth under high incident UV radiation. Endopolyploidy may therefore form part of the range of UV-B tolerance mechanisms that exist in natural populations. PMID:24470468

  14. Performance variations among clinically available deformable image registration tools in adaptive radiotherapy - how should we evaluate and interpret the result?

    PubMed

    Nie, Ke; Pouliot, Jean; Smith, Eric; Chuang, Cynthia

    2016-01-01

    The purpose of this study is to evaluate the performance variations in commercial deformable image registration (DIR) tools for adaptive radiation therapy and further to interpret the differences using clinically available terms. Three clinical examples (prostate, head and neck (HN), and cranial spinal irradiation (CSI) with L-spine boost) were evaluated in this study. Firstly, computerized deformed CT images were generated using simulation QA software with virtual deformations of bladder filling (prostate), neck flexion/bite-block repositioning/tumor shrinkage (HN), and vertebral body rotation (CSI). The corresponding transformation matrices served as a "reference" for the following comparisons. Three commercialized DIR algorithms: the free-form deformation from MIMVista 5.5 and the RegRefine from MIMMaestro 6.0, the multipass B-spline from VelocityAI v3.0.1, and the adap-tive demons from OnQ rts 2.1.15, were applied between the initial images and the deformed CT sets. The generated adaptive contours and dose distributions were compared with the "reference" and among each other. The performance in transfer-ring contours was comparable among all three tools with an average Dice similarity coefficient of 0.81 for all the organs. However, the dose warping accuracy appeared to rely on the evaluation end points and methodologies. Point-dose differences could show a difference of up to 23.3 Gy inside the PTVs and to overestimate up to 13.2 Gy for OARs, which was substantial for a 72 Gy prescription dose. Dose-volume histogram-based evaluation might not be sensitive enough to illustrate all the detailed variations, while isodose assessment on a slice-by-slice basis could be tedious. We further explored the possibility of using 3D gamma index analysis for warping dose variation assessment, and observed differences in dose warping using different DIR tools. Overall, our results demonstrated that evaluation based only on the performance of contour transformation could not

  15. Adaptive Human CDKAL1 Variants Underlie Hormonal Response Variations at the Enteroinsular Axis

    PubMed Central

    Chang, Chia Lin; Cai, James J.; Huang, Shang Yu; Cheng, Po Jen; Chueh, Ho Yen; Hsu, Sheau Yu Teddy

    2014-01-01

    Recent analyses have identified positively selected loci that explain differences in immune responses, body forms, and adaptations to extreme climates, but variants that describe adaptations in energy-balance regulation remain underexplored. To identify variants that confer adaptations in energy-balance regulation, we explored the evolutionary history and functional associations of candidate variants in 207 genes. We screened single nucleotide polymorphisms in genes that had been associated with energy-balance regulation for unusual genetic patterns in human populations, followed by studying associations among selected variants and serum levels of GIP, insulin, and C-peptide in pregnant women after an oral glucose tolerance test. Our analysis indicated that 5′ variants in CDKAL1, CYB5R4, GAD2, and PPARG are marked with statistically significant signals of gene–environment interactions. Importantly, studies of serum hormone levels showed that variants in CDKAL1 are associated with glucose-induced GIP and insulin responses (p<0.05). On the other hand, a GAD2 variant exhibited a significant association with glucose-induced C-peptide response. In addition, simulation analysis indicated that a type 2 diabetes risk variant in CDKAL1 (rs7754840) was selected in East Asians ∼6,900 years ago. Taken together, these data indicated that variants in CDKAL1 and GAD2 were targets of prior environmental selection. Because the selection of the CDKAL1 variant overlapped with the selection of a cluster of GIP variants in the same population ∼11,800 to 2,000 years ago, we speculate that these regulatory genes at the human enteroinsular axis could be highly responsive to environmental selection in recent human history. PMID:25222615

  16. Adaptive variation in offspring size in the terrestrial isopod, Armadillidium vulgare

    USGS Publications Warehouse

    Brody, M.S.; Lawlor, L.R.

    1984-01-01

    Variation in the birth size of offspring of the terrestrial isopod, Armadillidium vulgare, was observed in laboratory experiments and in field populations. In the laboratory, larger offspring were produced when the mother's food supply was reduced. In field populations, larger offspring were produced during the summer, a period of reduced food availability. Smaller offspring are produced in the spring, when food is readily available. Females may be making larger young to increase survival during the more severe conditions of the summer breeding period.

  17. Adaptive significance of natural variations in maternal care in rats: a translational perspective.

    PubMed

    Beery, Annaliese K; Francis, Darlene D

    2011-06-01

    A wealth of data from the last fifty years documents the potency of early life experiences including maternal care on developing offspring. A majority of this research has focused on the developing stress axis and stress-sensitive behaviors in hopes of identifying factors impacting resilience and risk-sensitivity. The power of early life experience to shape later development is profound and has the potential to increase fitness of individuals for their environments. Current findings in a rat maternal care paradigm highlight the complex and dynamic relation between early experiences and a variety of outcomes. In this review we propose adaptive hypotheses for alternate maternal strategies and resulting offspring phenotypes, and suggest means of distinguishing between these hypotheses. We also provide evidence underscoring the critical role of context in interpreting the adaptive significance of early experiences. If our goal is to identify risk-factors relevant to humans, we must better explore the role of the social and physical environment in our basic animal models. PMID:21458485

  18. GNBP domain of Anopheles darlingi: are polymorphic inversions and gene variation related to adaptive evolution?

    PubMed

    Bridi, L C; Rafael, M S

    2016-02-01

    Anopheles darlingi is the main malaria vector in humans in South America. In the Amazon basin, it lives along the banks of rivers and lakes, which responds to the annual hydrological cycle (dry season and rainy season). In these breeding sites, the larvae of this mosquito feed on decomposing organic and microorganisms, which can be pathogenic and trigger the activation of innate immune system pathways, such as proteins Gram-negative binding protein (GNBP). Such environmental changes affect the occurrence of polymorphic inversions especially at the heterozygote frequency, which confer adaptative advantage compared to homozygous inversions. We mapped the GNBP probe to the An. darlingi 2Rd inversion by fluorescent in situ hybridization (FISH), which was a good indicator of the GNBP immune response related to the chromosomal polymorphic inversions and adaptative evolution. To better understand the evolutionary relations and time of divergence of the GNBP of An. darlingi, we compared it with nine other mosquito GNBPs. The results of the phylogenetic analysis of the GNBP sequence between the species of mosquitoes demonstrated three clades. Clade I and II included the GNBPB5 sequence, and clade III the sequence of GNBPB1. Most of these sequences of GNBP analyzed were homologous with that of subfamily B, including that of An. gambiae (87 %), therefore suggesting that GNBP of An. darling belongs to subfamily B. This work helps us understand the role of inversion polymorphism in evolution of An. darlingi. PMID:26767379

  19. Variation in genes involved in epigenetic processes offers insights into tropically adapted cattle diversity.

    PubMed

    Porto-Neto, Laercio R; Fortes, Marina R S; McWilliam, Sean M; Lehnert, Sigrid A; Reverter, Antonio

    2014-01-01

    We evaluated the relevance of the BovineHD Illumina SNP chip with respect to genes involved in epigenetic processes. Genotypes for 729,068 SNP on two tropical cattle breeds of Australia were used: Brahman (n = 2112) and Tropical Composite (n = 2550). We used data mining approaches to compile a list of bovine protein-coding genes involved in epigenetic processes. These genes represent 9 functional categories that contain between one (histone demethylases) and 99 (chromatin remodeling factors) genes. A total of 3091 SNP mapped to positions within 3000 bp of the 193 coding regions of those genes, including 113 SNP in transcribed regions, 2738 in intronic regions and 240 in up- or down-stream regions. For all these SNP categories, we observed differences in the allelic frequencies between Brahman and Tropical Composite cattle. These differences were larger than those observed for the entire set of 729,068 SNP (P = 1.79 x 10(-5)). A multidimensional scaling analysis using only the 113 SNP in transcribed regions allowed for the separation of the two populations and this separation was comparable to the one obtained with a random set of 113 SNP (Principal Component 1 r (2) > 0.84). To further characterize the differences between the breeds we defined a gene-differentiation metric based on the average genotypic frequencies of SNP connected to each gene and compared both cattle populations. The 10% most differentiated genes were distributed across 10 chromosomes, with significant (P < 0.05) enrichment on BTA 3 and 10. The 10% most conserved genes were located in 12 chromosomes. We conclude that there is variation between cattle populations in genes connected to epigenetic processes, and this variation can be used to differentiate cattle breeds. More research is needed to fully characterize the use of these SNP and its potential as means to further our understanding of biological variation and epigenetic processes. PMID:24795751

  20. Variation in genes involved in epigenetic processes offers insights into tropically adapted cattle diversity

    PubMed Central

    Porto-Neto, Laercio R.; Fortes, Marina R. S.; McWilliam, Sean M.; Lehnert, Sigrid A.; Reverter, Antonio

    2014-01-01

    We evaluated the relevance of the BovineHD Illumina SNP chip with respect to genes involved in epigenetic processes. Genotypes for 729,068 SNP on two tropical cattle breeds of Australia were used: Brahman (n = 2112) and Tropical Composite (n = 2550). We used data mining approaches to compile a list of bovine protein-coding genes involved in epigenetic processes. These genes represent 9 functional categories that contain between one (histone demethylases) and 99 (chromatin remodeling factors) genes. A total of 3091 SNP mapped to positions within 3000 bp of the 193 coding regions of those genes, including 113 SNP in transcribed regions, 2738 in intronic regions and 240 in up- or down-stream regions. For all these SNP categories, we observed differences in the allelic frequencies between Brahman and Tropical Composite cattle. These differences were larger than those observed for the entire set of 729,068 SNP (P = 1.79 x 10−5). A multidimensional scaling analysis using only the 113 SNP in transcribed regions allowed for the separation of the two populations and this separation was comparable to the one obtained with a random set of 113 SNP (Principal Component 1 r2 > 0.84). To further characterize the differences between the breeds we defined a gene-differentiation metric based on the average genotypic frequencies of SNP connected to each gene and compared both cattle populations. The 10% most differentiated genes were distributed across 10 chromosomes, with significant (P < 0.05) enrichment on BTA 3 and 10. The 10% most conserved genes were located in 12 chromosomes. We conclude that there is variation between cattle populations in genes connected to epigenetic processes, and this variation can be used to differentiate cattle breeds. More research is needed to fully characterize the use of these SNP and its potential as means to further our understanding of biological variation and epigenetic processes. PMID:24795751

  1. Phenotypic Variation in Mangrove Cuckoo (Coccyzus minor) across Its Geographic Range

    PubMed Central

    Lloyd, John D.

    2016-01-01

    Mangrove Cuckoo (Coccyzus minor) exhibits substantial phenotypic variation across its geographic range, but the significance of this variation for taxonomy remains unresolved. Using measurements of bill size and ventral color recorded from 274 museum specimens, I found that variation in these traits was clinal. No named subspecies was reciprocally diagnosable from all others, and none was distinguishable from the nominate form, such that previously recognized subspecific distinctions are invalid. Greatest differences in phenotype occurred between populations in Florida, the Bahamas, and the Greater Antilles–characteristically small-billed–and those in the Lesser Antilles, which had larger bills. Phenotypically intermediate individuals on the geographically intermediate islands of Barbuda and Antigua linked these two extremes. Individuals intermediate in bill size and color also characterized populations from throughout the remainder of the range in northern South America and Middle America. Mechanisms maintaining the fairly pronounced phenotypic differences between nearby populations of Greater and Lesser Antillean birds are unknown, yet the geographic proximity of these populations suggests that they probably persist despite occasional gene flow, and may be adaptive. PMID:27008380

  2. Pattern and scale of geographic variation in environmental sex determination in the Atlantic silverside, Menidia menidia.

    PubMed

    Duffy, Tara A; Hice, Lyndie A; Conover, David O

    2015-08-01

    The Atlantic silverside, Menidia menidia (Pisces: Atherinidae), exhibits an exceptionally high level of clinal variation in sex determination across its geographic range. Previous work suggested linear changes in the level of temperature-dependent sex determination (TSD) with increasing latitude. Based on comparisons at 31 sites encompassing the entire species' range, we find that the change in level of TSD with latitude is instead highly nonlinear. The level of TSD is uniformly high in the south (Florida to New Jersey), then declines rapidly into the northern Gulf of Maine where genotypic sex determination (GSD) predominates and then rebounds to moderate levels of TSD in the northern-most populations of the Gulf of St. Lawrence. Major latitudinal breakpoints occur in central New Jersey (40(o)N) and the northern Gulf of Maine (44(o)N). No populations display pure TSD or GSD. Length of the growing season is the likely agent of selection driving variation in TSD with a threshold at 210 days. Because gene flow among populations is high, such distinct patterns of geographic variation in TSD/GSD are likely maintained by contemporary selection thereby demonstrating the adaptive fine tuning of sex determining mechanisms. PMID:26177746

  3. Phenotypic Variation in Mangrove Cuckoo (Coccyzus minor) across Its Geographic Range.

    PubMed

    Lloyd, John D

    2016-01-01

    Mangrove Cuckoo (Coccyzus minor) exhibits substantial phenotypic variation across its geographic range, but the significance of this variation for taxonomy remains unresolved. Using measurements of bill size and ventral color recorded from 274 museum specimens, I found that variation in these traits was clinal. No named subspecies was reciprocally diagnosable from all others, and none was distinguishable from the nominate form, such that previously recognized subspecific distinctions are invalid. Greatest differences in phenotype occurred between populations in Florida, the Bahamas, and the Greater Antilles--characteristically small-billed--and those in the Lesser Antilles, which had larger bills. Phenotypically intermediate individuals on the geographically intermediate islands of Barbuda and Antigua linked these two extremes. Individuals intermediate in bill size and color also characterized populations from throughout the remainder of the range in northern South America and Middle America. Mechanisms maintaining the fairly pronounced phenotypic differences between nearby populations of Greater and Lesser Antillean birds are unknown, yet the geographic proximity of these populations suggests that they probably persist despite occasional gene flow, and may be adaptive. PMID:27008380

  4. Extreme phenotypic variation in Cetraria aculeata (lichenized Ascomycota): adaptation or incidental modification?

    PubMed Central

    Pérez-Ortega, Sergio; Fernández-Mendoza, Fernando; Raggio, José; Vivas, Mercedes; Ascaso, Carmen; Sancho, Leopoldo G.; Printzen, Christian; de los Ríos, Asunción

    2012-01-01

    Background and Aims Phenotypic variability is a successful strategy in lichens for colonizing different habitats. Vagrancy has been reported as a specific adaptation for lichens living in steppe habitats around the world. Among the facultatively vagrant species, the cosmopolitan Cetraria aculeata apparently forms extremely modified vagrant thalli in steppe habitats of Central Spain. The aim of this study was to investigate whether these changes are phenotypic plasticity (a single genotype producing different phenotypes), by characterizing the anatomical and ultrastructural changes observed in vagrant morphs, and measuring differences in ecophysiological performance. Methods Specimens of vagrant and attached populations of C. aculeata were collected on the steppes of Central Spain. The fungal internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GPD) and the large sub-unit of the mitochondrial ribosomal DNA (mtLSUm), and the algal ITS and actin were studied within a population genetics framework. Semi-thin and ultrathin sections were analysed by means of optical, scanning electron and transmission electron microscopy. Gas exchange and chlorophyll fluorescence were used to compare the physiological performance of both morphs. Key Results and Conclusions Vagrant and attached morphs share multilocus haplotypes which may indicate that they belong to the same species in spite of their completely different anatomy. However, differentiation tests suggested that vagrant specimens do not represent a random sub-set of the surrounding population. The morphological differences were related to anatomical and ultrastructural differences. Large intercalary growth rates of thalli after the loss of the basal–apical thallus polarity may be the cause of the increased growth shown by vagrant specimens. The anatomical and morphological changes lead to greater duration of ecophysiological activity in vagrant specimens. Although the anatomical and physiological

  5. Time-dependent post-imperative negative variation indicates adaptation and problem solving in migraine patients.

    PubMed

    Kropp, Peter; Brecht, Ines-Beatrice; Niederberger, Uwe; Kowalski, Jens; Schröder, Dietmar; Thome, Johannes; Meyer, Wolfgang; Wallasch, Thomas-Martin; Hilgendorf, Inken; Gerber, Wolf-Dieter

    2012-10-01

    According to the Seligman theory of learned helplessness, depression is caused by a repetitive experience of loss of control resulting in internal, stable and global attributional styles for negative events. In depressed patients and healthy controls experiencing such events, an increased amplitude of the post-imperative negative variation (PINV) has been described. The aim of the study was to investigate a possible correlation between migraine, depression, learned helplessness and PINV. 24 patients suffering from migraine without aura and 24 healthy controls were exposed to a situation of loss of control whilst the contingent negative variation (CNV) from C3, C4 and Cz were recorded. Before conducting the experiment, the subjects were asked to answer the Beck Depression Inventory (BDI) and the German attributional style questionnaire (GASQ). Amplitudes of total CNV, early and late component and PINV were calculated in eight blocks of four recordings each. The results confirm findings of a pronounced PINV in situations of loss of control, though high amplitudes were not correlated with low values in the GASQ and therefore with learned helplessness. High PINV in migraine patients correlated with high scores in the BDI and the list of the complaints questionnaire. However, this was not the case in healthy controls. In this experimental situation, PINV in migraine patients can be interpreted as an expectancy potential in order to avoid failure and helplessness. PMID:22688673

  6. Adaptation of epithelial sodium-dependent phosphate transport in jejunum and kidney of hens to variations in dietary phosphorus intake.

    PubMed

    Huber, K; Hempel, R; Rodehutscord, M

    2006-11-01

    The objective of this study was to explore the homeostatic response of jejunal and renal epithelia regarding the inorganic phosphate (P(i)) transport capacities to variations in dietary total phosphorus (tP) supply in hens. Adaptive processes were determined by quantitative measures of intake and excretion, P(i) transport studies across brush border membranes, and semiquantitative detection of sodium-dependent phosphate transporters (NaPi II) based on mRNA expression in the jejunum and kidney. Twelve hens (4/group) were adapted to 3 tP feeding levels in a pair-fed manner (60 g/d): low P diet with 0.073% tP, medium P diet with 0.204% tP, and high P diet with 0.343% tP. Excretion was measured during the last 5 d of a 16-d feeding period. After slaughtering, jejunal mucosa and renal cortex were removed. Tissues were used for (32)P uptake studies in brush-border membrane vesicles by rapid filtration technique and NaPi II mRNA expression studies by northern analyses. Plasma P(i) concentrations were additionally measured. The NaPi II transporter mRNA could specifically be detected in chicken jejunum and kidney. Functional parameters of Na(+)-dependent P(i) transport indicated that these transporters were involved in chicken P(i) transport across the apical membranes of jejunal and renal epithelia. Increased tP intake resulted in an increased overall tP excretion. Correlating individual data from all animals by linear regression highlighted that the adaptive decrease of renal P(i) transport capacity and NaPi IIa mRNA expression was associated with an increase in plasma P(i) levels and resulted in a higher tP excretion. Jejunal P(i) transport capacity and NaPi IIb mRNA expression did not react to variations in dietary tP supply. In conclusion, the homeostatic response was mainly based on the adaptive capacity of the kidney in hens. PMID:17032833

  7. Allelic variation in Salmonella: an underappreciated driver of adaptation and virulence

    PubMed Central

    Yue, Min; Schifferli, Dieter M.

    2014-01-01

    Salmonella enterica causes substantial morbidity and mortality in humans and animals. Infection and intestinal colonization by S. enterica require virulence factors that mediate bacterial binding and invasion of enterocytes and innate immune cells. Some S. enterica colonization factors and their alleles are host restricted, suggesting a potential role in regulation of host specificity. Recent data also suggest that colonization factors promote horizontal gene transfer of antimicrobial resistance genes by increasing the local density of Salmonella in colonized intestines. Although a profusion of genes are involved in Salmonella pathogenesis, the relative importance of their allelic variation has only been studied intensely in the type 1 fimbrial adhesin FimH. Although other Salmonella virulence factors demonstrate allelic variation, their association with specific metadata (e.g., host species, disease or carrier state, time and geographic place of isolation, antibiotic resistance profile, etc.) remains to be interrogated. To date, genome-wide association studies (GWAS) in bacteriology have been limited by the paucity of relevant metadata. In addition, due to the many variables amid metadata categories, a very large number of strains must be assessed to attain statistically significant results. However, targeted approaches in which genes of interest (e.g., virulence factors) are specifically sequenced alleviates the time-consuming and costly statistical GWAS analysis and increases statistical power, as larger numbers of strains can be screened for non-synonymous single nucleotide polymorphisms (SNPs) that are associated with available metadata. Congruence of specific allelic variants with specific metadata from strains that have a relevant clinical and epidemiological history will help to prioritize functional wet-lab and animal studies aimed at determining cause-effect relationships. Such an approach should be applicable to other pathogens that are being collected

  8. Adaptive Variation Regulates the Expression of the Human SGK1 Gene in Response to Stress

    PubMed Central

    Luca, Francesca; Kashyap, Sonal; Southard, Catherine; Zou, Min; Witonsky, David; Di Rienzo, Anna; Conzen, Suzanne D.

    2009-01-01

    The Serum and Glucocorticoid-regulated Kinase1 (SGK1) gene is a target of the glucocorticoid receptor (GR) and is central to the stress response in many human tissues. Because environmental stress varies across habitats, we hypothesized that natural selection shaped the geographic distribution of genetic variants regulating the level of SGK1 expression following GR activation. By combining population genetics and molecular biology methods, we identified a variant (rs9493857) with marked allele frequency differences between populations of African and European ancestry and with a strong correlation between allele frequency and latitude in worldwide population samples. This SNP is located in a GR-binding region upstream of SGK1 that was identified using a GR ChIP-chip. SNP rs9493857 also lies within a predicted binding site for Oct1, a transcription factor known to cooperate with the GR in the transactivation of target genes. Using ChIP assays, we show that both GR and Oct1 bind to this region and that the ancestral allele at rs9493857 binds the GR-Oct1 complex more efficiently than the derived allele. Finally, using a reporter gene assay, we demonstrate that the ancestral allele is associated with increased glucocorticoid-dependent gene expression when compared to the derived allele. Our results suggest a novel paradigm in which hormonal responsiveness is modulated by sequence variation in the regulatory regions of nuclear receptor target genes. Identifying such functional variants may shed light on the mechanisms underlying inter-individual variation in response to environmental stressors and to hormonal therapy, as well as in the susceptibility to hormone-dependent diseases. PMID:19461886

  9. Carbon allocation changes: an adaptive response to variations in atmospheric CO2

    NASA Astrophysics Data System (ADS)

    Harrison, Sandy; Li, Guangqi; Prentice, Iain Colin

    2016-04-01

    Given the ubiquity of nutrient constraints on primary production, an optimal carbon allocation strategy is expected to increase total below-ground allocation (fine root production and turnover, allocation to mycorrhizae and carbon exudation to the rhizophere) as atmospheric CO2 concentration increases. Conversely, below-ground allocation should be reduced when atmospheric CO2 concentrations were low, as occurred during glacial times. Using a coupled generic primary production and tree-growth model, we quantify the changes in carbon allocation that are required to explain the apparent homoeostasis of tree radial growth during recent decades and between glacial and interglacial conditions. These results suggest a resolution of the apparent paradox of continuing terrestrial CO2 uptake (a consequence of CO2 fertilization) and the widespread lack of observed enhancement of stem growth in trees. Adaptive shifts in carbon allocation are thus a key feature that should to be accounted for in models to predict tree growth and future timber harvests, as well as in large-scale ecosystem and carbon cycle models.

  10. Cyclic variations in incubation conditions induce adaptive responses to later heat exposure in chickens: a review.

    PubMed

    Loyau, T; Bedrani, L; Berri, C; Métayer-Coustard, S; Praud, C; Coustham, V; Mignon-Grasteau, S; Duclos, M J; Tesseraud, S; Rideau, N; Hennequet-Antier, C; Everaert, N; Yahav, S; Collin, A

    2015-01-01

    Selection programs have enabled broiler chickens to gain muscle mass without similar enlargement of the cardiovascular and respiratory systems that are essential for thermoregulatory efficiency. Meat-type chickens cope with high ambient temperature by reducing feed intake and growth during chronic and moderate heat exposure. In case of acute heat exposure, a dramatic increase in morbidity and mortality can occur. In order to alleviate heat stress in the long term, research has recently focused on early thermal manipulation. Aimed at stimulation of long-term thermotolerance, the thermal manipulation of embryos is a method based on fine tuning of incubation conditions, taking into account the level and duration of increases in temperature and relative humidity during a critical period of embryogenesis. The consequences of thermal manipulation on the performance and meat quality of broiler chickens have been explored to ensure the potential application of this strategy. The physiological basis of the method is the induction of epigenetic and metabolic mechanisms that control body temperature in the long term. Early thermal manipulation can enhance poultry resistance to environmental changes without much effect on growth performance. This review presents the main strategies of early heat exposure and the physiological concepts on which these methods were based. The cellular mechanisms potentially underlying the adaptive response are discussed as well as the potential interest of thermal manipulation of embryos for poultry production. PMID:25118598

  11. Edge preserved enhancement of medical images using adaptive fusion-based denoising by shearlet transform and total variation algorithm

    NASA Astrophysics Data System (ADS)

    Gupta, Deep; Anand, Radhey Shyam; Tyagi, Barjeev

    2013-10-01

    Edge preserved enhancement is of great interest in medical images. Noise present in medical images affects the quality, contrast resolution, and most importantly, texture information and can make post-processing difficult also. An enhancement approach using an adaptive fusion algorithm is proposed which utilizes the features of shearlet transform (ST) and total variation (TV) approach. In the proposed method, three different denoised images processed with TV method, shearlet denoising, and edge information recovered from the remnant of the TV method and processed with the ST are fused adaptively. The result of enhanced images processed with the proposed method helps to improve the visibility and detectability of medical images. For the proposed method, different weights are evaluated from the different variance maps of individual denoised image and the edge extracted information from the remnant of the TV approach. The performance of the proposed method is evaluated by conducting various experiments on both the standard images and different medical images such as computed tomography, magnetic resonance, and ultrasound. Experiments show that the proposed method provides an improvement not only in noise reduction but also in the preservation of more edges and image details as compared to the others.

  12. Adaptive-weighted total variation minimization for sparse data toward low-dose x-ray computed tomography image reconstruction

    NASA Astrophysics Data System (ADS)

    Liu, Yan; Ma, Jianhua; Fan, Yi; Liang, Zhengrong

    2012-12-01

    Previous studies have shown that by minimizing the total variation (TV) of the to-be-estimated image with some data and other constraints, piecewise-smooth x-ray computed tomography (CT) can be reconstructed from sparse-view projection data without introducing notable artifacts. However, due to the piecewise constant assumption for the image, a conventional TV minimization algorithm often suffers from over-smoothness on the edges of the resulting image. To mitigate this drawback, we present an adaptive-weighted TV (AwTV) minimization algorithm in this paper. The presented AwTV model is derived by considering the anisotropic edge property among neighboring image voxels, where the associated weights are expressed as an exponential function and can be adaptively adjusted by the local image-intensity gradient for the purpose of preserving the edge details. Inspired by the previously reported TV-POCS (projection onto convex sets) implementation, a similar AwTV-POCS implementation was developed to minimize the AwTV subject to data and other constraints for the purpose of sparse-view low-dose CT image reconstruction. To evaluate the presented AwTV-POCS algorithm, both qualitative and quantitative studies were performed by computer simulations and phantom experiments. The results show that the presented AwTV-POCS algorithm can yield images with several notable gains, in terms of noise-resolution tradeoff plots and full-width at half-maximum values, as compared to the corresponding conventional TV-POCS algorithm.

  13. Active noise control using noise source having adaptive resonant frequency tuning through stiffness variation

    NASA Technical Reports Server (NTRS)

    Pla, Frederic G. (Inventor); Rajiyah, Harindra (Inventor); Renshaw, Anthony A. (Inventor); Hedeen, Robert A. (Inventor)

    1995-01-01

    A noise source for an aircraft engine active noise cancellation system in which the resonant frequency of a noise radiating element is tuned to permit noise cancellation over a wide range of frequencies. The resonant frequency of the noise radiating element is tuned by a plurality of force transmitting mechanisms which contact the noise radiating element. Each one of the force transmitting mechanisms includes an expandable element and a spring in contact with the noise radiating element so that excitation of the element varies the spring force applied to the noise radiating element. The elements are actuated by a controller which receives input of a signal proportional to displacement of the noise radiating element and a signal corresponding to the blade passage frequency of the engine's fan. In response, the controller determines a control signal which is sent to the elements and causes the spring force applied to the noise radiating element to be varied. The force transmitting mechanisms can be arranged to either produce bending or linear stiffness variations in the noise radiating element.

  14. Revisiting the Clinal Concept of Evolution and Dispersal for the Tick-Borne Flaviviruses by Using Phylogenetic and Biogeographic Analyses

    PubMed Central

    Heinze, D. M.; Gould, E. A.

    2012-01-01

    Tick-borne flaviviruses (TBF) are widely dispersed across Africa, Europe, Asia, Oceania, and North America, and some present a significant threat to human health. Seminal studies on tick-borne encephalitis viruses (TBEV), based on partial envelope gene sequences, predicted a westward clinal pattern of evolution and dispersal across northern Eurasia, terminating in the British Isles. We tested this hypothesis using all available full-length open reading frame (ORF) TBF sequences. Phylogenetic analysis was consistent with current reports. However, linear and nonlinear regression analysis of genetic versus geographic distance combined with BEAST analysis identified two separate clines, suggesting that TBEV spread both east and west from a central point. In addition, BEAST analysis suggested that TBF emerged and dispersed more than 16,000 years ago, significantly earlier than previously predicted. Thus, climatic and ecological changes may have played a greater role in TBF dispersal than humans. PMID:22674986

  15. Tikhonov adaptively regularized gamma variate fitting to assess plasma clearance of inert renal markers

    PubMed Central

    Puetter, Richard C.; Ling, Lin; Babyn, Paul S.

    2010-01-01

    The Tk-GV model fits Gamma Variates (GV) to data by Tikhonov regularization (Tk) with shrinkage constant, λ, chosen to minimize the relative error in plasma clearance, CL (ml/min). Using 169Yb-DTPA and 99mTc-DTPA (n = 46, 8–9 samples, 5–240 min) bolus-dilution curves, results were obtained for fit methods: (1) Ordinary Least Squares (OLS) one and two exponential term (E1 and E2), (2) OLS-GV and (3) Tk-GV. Four tests examined the fit results for: (1) physicality of ranges of model parameters, (2) effects on parameter values when different data subsets are fit, (3) characterization of residuals, and (4) extrapolative error and agreement with published correction factors. Test 1 showed physical Tk-GV results, where OLS-GV fits sometimes-produced nonphysical CL. Test 2 showed the Tk-GV model produced good results with 4 or more samples drawn between 10 and 240 min. Test 3 showed that E1 and E2 failed goodness-of-fit testing whereas GV fits for t > 20 min were acceptably good. Test 4 showed CLTk-GV clearance values agreed with published CL corrections with the general result that CLE1 > CLE2 > CLTk-GV and finally that CLTk-GV were considerably more robust, precise and accurate than CLE2, and should replace the use of CLE2 for these renal markers. PMID:20865304

  16. Spatial and temporal variation of an ice-adapted predator's feeding ecology in a changing Arctic marine ecosystem.

    PubMed

    Yurkowski, David J; Ferguson, Steven H; Semeniuk, Christina A D; Brown, Tanya M; Muir, Derek C G; Fisk, Aaron T

    2016-03-01

    Spatial and temporal variation can confound interpretations of relationships within and between species in terms of diet composition, niche size, and trophic position (TP). The cause of dietary variation within species is commonly an ontogenetic niche shift, which is a key dynamic influencing community structure. We quantified spatial and temporal variations in ringed seal (Pusa hispida) diet, niche size, and TP during ontogeny across the Arctic-a rapidly changing ecosystem. Stable carbon and nitrogen isotope analysis was performed on 558 liver and 630 muscle samples from ringed seals and on likely prey species from five locations ranging from the High to the Low Arctic. A modest ontogenetic diet shift occurred, with adult ringed seals consuming more forage fish (approximately 80 versus 60 %) and having a higher TP than subadults, which generally decreased with latitude. However, the degree of shift varied spatially, with adults in the High Arctic presenting a more restricted niche size and consuming more Arctic cod (Boreogadus saida) than subadults (87 versus 44 %) and adults at the lowest latitude (29 %). The TPs of adult and subadult ringed seals generally decreased with latitude (4.7-3.3), which was mainly driven by greater complexity in trophic structure within the zooplankton communities. Adult isotopic niche size increased over time, likely due to the recent circumpolar increases in subarctic forage fish distribution and abundance. Given the spatial and temporal variability in ringed seal foraging ecology, ringed seals exhibit dietary plasticity as a species, suggesting adaptability in terms of their diet to climate change. PMID:26210748

  17. Design and conduct of Caudwell Xtreme Everest: an observational cohort study of variation in human adaptation to progressive environmental hypoxia

    PubMed Central

    2010-01-01

    Background The physiological responses to hypoxaemia and cellular hypoxia are poorly understood, and inter-individual differences in performance at altitude and outcome in critical illness remain unexplained. We propose a model for exploring adaptation to hypoxia in the critically ill: the study of healthy humans, progressively exposed to environmental hypobaric hypoxia (EHH). The aim of this study was to describe the spectrum of adaptive responses in humans exposed to graded EHH and identify factors (physiological and genetic) associated with inter-individual variation in these responses. Methods Design Observational cohort study of progressive incremental exposure to EHH. Setting University human physiology laboratory in London, UK (75 m) and 7 field laboratories in Nepal at 1300 m, 3500 m, 4250 m, 5300 m, 6400 m, 7950 m and 8400 m. Participants 198 healthy volunteers and 24 investigators trekking to Everest Base Camp (EBC) (5300 m). A subgroup of 14 investigators studied at altitudes up to 8400 m on Everest. Main outcome measures Exercise capacity, exercise efficiency and economy, brain and muscle Near Infrared Spectroscopy, plasma biomarkers (including markers of inflammation), allele frequencies of known or suspected hypoxia responsive genes, spirometry, neurocognitive testing, retinal imaging, pupilometry. In nested subgroups: microcirculatory imaging, muscle biopsies with proteomic and transcriptomic tissue analysis, continuous cardiac output measurement, arterial blood gas measurement, trans-cranial Doppler, gastrointestinal tonometry, thromboelastography and ocular saccadometry. Results Of 198 healthy volunteers leaving Kathmandu, 190 reached EBC (5300 m). All 24 investigators reached EBC. The completion rate for planned testing was more than 99% in the investigator group and more than 95% in the trekkers. Unique measurements were safely performed at extreme altitude, including the highest (altitude) field measurements of exercise capacity, cerebral blood

  18. Adaptive-weighted total variation minimization for sparse data toward low-dose x-ray computed tomography image reconstruction.

    PubMed

    Liu, Yan; Ma, Jianhua; Fan, Yi; Liang, Zhengrong

    2012-12-01

    Previous studies have shown that by minimizing the total variation (TV) of the to-be-estimated image with some data and other constraints, piecewise-smooth x-ray computed tomography (CT) can be reconstructed from sparse-view projection data without introducing notable artifacts. However, due to the piecewise constant assumption for the image, a conventional TV minimization algorithm often suffers from over-smoothness on the edges of the resulting image. To mitigate this drawback, we present an adaptive-weighted TV (AwTV) minimization algorithm in this paper. The presented AwTV model is derived by considering the anisotropic edge property among neighboring image voxels, where the associated weights are expressed as an exponential function and can be adaptively adjusted by the local image-intensity gradient for the purpose of preserving the edge details. Inspired by the previously reported TV-POCS (projection onto convex sets) implementation, a similar AwTV-POCS implementation was developed to minimize the AwTV subject to data and other constraints for the purpose of sparse-view low-dose CT image reconstruction. To evaluate the presented AwTV-POCS algorithm, both qualitative and quantitative studies were performed by computer simulations and phantom experiments. The results show that the presented AwTV-POCS algorithm can yield images with several notable gains, in terms of noise-resolution tradeoff plots and full-width at half-maximum values, as compared to the corresponding conventional TV-POCS algorithm. PMID:23154621

  19. Habitat Choice and Temporal Variation Alter the Balance between Adaptation by Genetic Differentiation, a Jack-of-All-Trades Strategy, and Phenotypic Plasticity.

    PubMed

    Scheiner, Samuel M

    2016-05-01

    Confronted with variable environments, species adapt in several ways, including genetic differentiation, a jack-of-all-trades strategy, or phenotypic plasticity. Adaptive habitat choice favors genetic differentiation and local adaptation over a generalist, jack-of-all-trades strategy. Models predict that, absent plasticity costs, variable environments generally favor phenotypic plasticity over genetic differentiation and being a jack-of-all-trades generalist. It is unknown how habitat choice might affect the evolution of plasticity. Using an individual-based simulation model, I explored the interaction of choice and plasticity. With only spatial variation, habitat choice promotes genetic differentiation over a jack-of-all-trades strategy or phenotypic plasticity. In the absence of plasticity, temporal variation favors a jack-of-all-trades strategy over choice-mediated genetic differentiation; when plasticity is an option, it is favored. This occurs because habitat choice creates a feedback between genetic differentiation and dispersal rates. As demes become better adapted to their local environments, the effective dispersal rate decreases, because more individuals have very high fitness and so choose not to disperse, reinforcing local stabilizing selection and negating selection for plasticity. Temporal variation breaks that feedback. These results point to a potential data paradox: systems with habitat choice may have the lowest actual movement rates. The potential for adaptive habitat choice may be very common, but its existence may reduce observed dispersal rates enough that we do not recognize systems where it may be present, warranting further exploration of likely systems. PMID:27104995

  20. Variational solution of the three-dimensional Schrödinger equation using plane waves in adaptive coordinates.

    PubMed

    Pérez-Jordá, José M

    2011-11-28

    A series of improvements for the solution of the three-dimensional Schrödinger equation over a method introduced by Gygi [F. Gygi, Europhys. Lett. 19, 617 (1992); F. Gygi, Phys. Rev. B 48, 11692 (1993)] are presented. As in the original Gygi's method, the solution (orbital) is expressed by means of plane waves in adaptive coordinates u, where u is mapped from Cartesian coordinates, u=f(r). The improvements implemented are threefold. First, maps are introduced that allow the application of the method to atoms and molecules without the assistance of the supercell approximation. Second, the electron-nucleus singularities are exactly removed, so that pseudo-potentials are no longer required. Third, the sampling error during integral evaluation is made negligible, which results in a true variational, second-order energy error procedure. The method is tested on the hydrogen atom (ground and excited states) and the H(2)(+) molecule, resulting in milli-Hartree accuracy with a moderate number of plane waves. PMID:22128925

  1. Volume and dosimetric variations during two-phase adaptive intensity-modulated radiotherapy for locally advanced nasopharyngeal carcinoma.

    PubMed

    Wang, Rui-hao; Zhang, Shu-xu; Zhou, Ling-hong; Zhang, Guo-qian; Yu, Hui; Lin, Xiao-dan; Lin, Shengqu

    2014-01-01

    The aims of this study were to evaluate the volume and dosimetric variations during IMRT for locally advanced NPC and to identify the benefits of a two-phase adaptive IMRT method. Twenty patients with locally advanced NPC having received IMRT treatment were included. Each patient had both an initial planning CT (CT-1) and a repeated CT scan (CT-2) after treatment at a dose of 40 Gy. Three IMRT planning scenarios were compared: (1) the initial plan on the CT-1 (plan-1); (2) the hybrid plan recalculated the initial plan on the CT-2 (plan-2); (3) the replan generated on the CT-2 being used to complete the course of IMRT (plan-3). The mean gross target volume and mean volumes of the positive neck lymph nodes, high-risk clinical target volume, and the left and right parotid glands significantly decreased by 30.2%, 45.1%, 21.1%, 14.7% and 18.2%, respectively on the CT-2. Comparing plan-2 with plan-1, the dose coverage of the targets remained unchanged, whereas the dose delivered to the parotid glands and spinal cord increased significantly. These patients with locally advanced NPC might benefit from replanning because of the sparing of the parotid glands and spinal cord. PMID:24212016

  2. Complex Patterns of Local Adaptation in Teosinte

    PubMed Central

    Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

    2013-01-01

    Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

  3. Linking Genetic Variation in Adaptive Plant Traits to Climate in Tetraploid and Octoploid Basin Wildrye [Leymus cinereus (Scribn. & Merr.) A. Love] in the Western U.S.

    PubMed Central

    Johnson, R. C.; Vance-Borland, Ken

    2016-01-01

    Few studies have assessed how ploidy type within a species affects genetic variation among populations in relation to source climates. Basin wildrye (Leymus cinereus (Scribn. & Merr.) A. Love) is a large bunchgrass common in the intermountain Western U.S. found in both octoploid and tetraploid types. In common gardens at two sites over two years differences in both ploidy type and genetic variation within ploidy were observed in phenology, morphology, and production traits on 57 octoploid and 52 tetraploid basin wildrye from the intermountain Western U.S. (P<0.01). Octoploids had larger leaves, longer culms, and greater crown circumference than tetraploids but the numerical ranges of plant traits and their source climates overlapped between ploidy types. Still, among populations octoploids often had greater genetic variation for traits and occupied more diverse climates than tetraploids. Genetic variation for both ploidy types was linked to source climates in canonical correlation analysis, with the first two variates explaining 70% of the variation. Regression of those canonical variates with seed source climate variables produced models that explained 64% and 38% of the variation, respectively, and were used to map 15 seed zones covering 673258 km2. Utilization of these seed zones will help ensure restoration with adaptive seed sources for both ploidy types. The link between genetic traits and seed source climates suggests climate driven natural selection and adaptive evolution in basin wildrye. The more diverse climates occupied by octoploids and higher trait variation suggests a higher capacity for ecological differentiation than tetraploids in the intermountain Western U.S. PMID:26881894

  4. Linking Genetic Variation in Adaptive Plant Traits to Climate in Tetraploid and Octoploid Basin Wildrye [Leymus cinereus (Scribn. & Merr.) A. Love] in the Western U.S.

    PubMed

    Johnson, R C; Vance-Borland, Ken

    2016-01-01

    Few studies have assessed how ploidy type within a species affects genetic variation among populations in relation to source climates. Basin wildrye (Leymus cinereus (Scribn. & Merr.) A. Love) is a large bunchgrass common in the intermountain Western U.S. found in both octoploid and tetraploid types. In common gardens at two sites over two years differences in both ploidy type and genetic variation within ploidy were observed in phenology, morphology, and production traits on 57 octoploid and 52 tetraploid basin wildrye from the intermountain Western U.S. (P<0.01). Octoploids had larger leaves, longer culms, and greater crown circumference than tetraploids but the numerical ranges of plant traits and their source climates overlapped between ploidy types. Still, among populations octoploids often had greater genetic variation for traits and occupied more diverse climates than tetraploids. Genetic variation for both ploidy types was linked to source climates in canonical correlation analysis, with the first two variates explaining 70% of the variation. Regression of those canonical variates with seed source climate variables produced models that explained 64% and 38% of the variation, respectively, and were used to map 15 seed zones covering 673,258 km2. Utilization of these seed zones will help ensure restoration with adaptive seed sources for both ploidy types. The link between genetic traits and seed source climates suggests climate driven natural selection and adaptive evolution in basin wildrye. The more diverse climates occupied by octoploids and higher trait variation suggests a higher capacity for ecological differentiation than tetraploids in the intermountain Western U.S. PMID:26881894

  5. Bring in the genes: genetic-ecophysiological modeling of the adaptive response of trees to environmental change. With application to the annual cycle

    PubMed Central

    Kramer, Koen; van der Werf, Bert; Schelhaas, Mart-Jan

    2015-01-01

    The observation of strong latitudinal clines in the date of bud burst of tree species indicate that populations of these species are genetically adapted to local environmental conditions. Existing phenological models rarely address this clinal variation, so that adaptive responses of tree populations to changes in environmental conditions are not taken into account, e.g., in models on species distributions that use phenological sub-models. This omission of simulating adaptive response in tree models may over- or underestimate the effects of climate change on tree species distributions, as well as the impacts of climate change on tree growth and productivity. Here, we present an approach to model the adaptive response of traits to environmental change based on an integrated process-based eco-physiological and quantitative genetic model of adaptive traits. Thus, the parameter values of phenological traits are expressed in genetic terms (allele effects and—frequencies, number of loci) for individual trees. These individual trees thereby differ in their ability to acquire resources, grow and reproduce as described by the process-based model, leading to differential survival. Differential survival is thus the consequence of both differences in parameters values and their genetic composition. By simulating recombination and dispersal of pollen, the genetic composition of the offspring will differ from that of their parents. Over time, the distribution of both trait values and the frequency of the underlying alleles in the population change as a consequence of changes in environmental drivers leading to adaptation of trees to local environmental conditions. This approach is applied to an individual-tree growth model that includes a phenological model on the annual cycle of trees whose parameters are allowed to adapt. An example of the adaptive response of the onset of the growing season across Europe is presented. PMID:25628628

  6. Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains' precipitation gradient: implications for grassland restoration with climate change.

    PubMed

    Johnson, Loretta C; Olsen, Jacob T; Tetreault, Hannah; DeLaCruz, Angel; Bryant, Johnny; Morgan, Theodore J; Knapp, Mary; Bello, Nora M; Baer, Sara G; Maricle, Brian R

    2015-08-01

    Identifying suitable genetic stock for restoration often employs a 'best guess' approach. Without adaptive variation studies, restoration may be misguided. We test the extent to which climate in central US grasslands exerts selection pressure on a foundation grass big bluestem (Andropogon gerardii), widely used in restorations, and resulting in local adaptation. We seeded three regional ecotypes of A. gerardii in reciprocal transplant garden communities across 1150 km precipitation gradient. We measured ecological responses over several timescales (instantaneous gas exchange, medium-term chlorophyll absorbance, and long-term responses of establishment and cover) in response to climate and biotic factors and tested if ecotypes could expand range. The ecotype from the driest region exhibited greatest cover under low rainfall, suggesting local adaptation under abiotic stress. Unexpectedly, no evidence for cover differences between ecotypes exists at mesic sites where establishment and cover of all ecotypes were low, perhaps due to strong biotic pressures. Expression of adaptive differences is strongly environment specific. Given observed adaptive variation, the most conservative restoration strategy would be to plant the local ecotype, especially in drier locations. With superior performance of the most xeric ecotype under dry conditions and predicted drought, this ecotype may migrate eastward, naturally or with assistance in restorations. PMID:26240607

  7. Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains’ precipitation gradient: implications for grassland restoration with climate change

    PubMed Central

    Johnson, Loretta C; Olsen, Jacob T; Tetreault, Hannah; DeLaCruz, Angel; Bryant, Johnny; Morgan, Theodore J; Knapp, Mary; Bello, Nora M; Baer, Sara G; Maricle, Brian R

    2015-01-01

    Identifying suitable genetic stock for restoration often employs a ‘best guess’ approach. Without adaptive variation studies, restoration may be misguided. We test the extent to which climate in central US grasslands exerts selection pressure on a foundation grass big bluestem (Andropogon gerardii), widely used in restorations, and resulting in local adaptation. We seeded three regional ecotypes of A. gerardii in reciprocal transplant garden communities across 1150 km precipitation gradient. We measured ecological responses over several timescales (instantaneous gas exchange, medium-term chlorophyll absorbance, and long-term responses of establishment and cover) in response to climate and biotic factors and tested if ecotypes could expand range. The ecotype from the driest region exhibited greatest cover under low rainfall, suggesting local adaptation under abiotic stress. Unexpectedly, no evidence for cover differences between ecotypes exists at mesic sites where establishment and cover of all ecotypes were low, perhaps due to strong biotic pressures. Expression of adaptive differences is strongly environment specific. Given observed adaptive variation, the most conservative restoration strategy would be to plant the local ecotype, especially in drier locations. With superior performance of the most xeric ecotype under dry conditions and predicted drought, this ecotype may migrate eastward, naturally or with assistance in restorations. PMID:26240607

  8. Interindividual Variation in Functionally Adapted Trait Sets Is Established During Postnatal Growth and Predictable Based on Bone Robustness

    PubMed Central

    Pandey, Nirnimesh; Bhola, Siddharth; Goldstone, Andrew; Chen, Fred; Chrzanowski, Jessica; Terranova, Carl J.; Ghillani, Richard

    2009-01-01

    Adults acquire unique sets of morphological and tissue-quality bone traits that are predictable based on robustness and deterministic of strength and fragility. How and when individual trait sets arise during growth has not been established. Longitudinal structural changes of the metacarpal diaphysis were measured for boys and girls from 3 mo to 8 yr of age using hand radiographs obtained from the Bolton-Brush collection. Robustness varied ∼2-fold among boys and girls, and individual values were established by 2 yr of age, indicating that genetic and environmental factors controlling the relationship between growth in width and growth in length were established early during postnatal growth. Significant negative correlations between robustness and relative cortical area and a significant positive correlation between robustness and a novel measure capturing the efficiency of growth indicated that coordination of the subperiosteal and endocortical surfaces was responsible for this population acquiring a narrow range of trait sets that was predictable based on robustness. Boys and girls with robust diaphyses had proportionally thinner cortices to minimize mass, whereas children with slender diaphyses had proportionally thicker cortices to maximize stiffness. Girls had more slender metacarpals with proportionally thicker cortices compared with boys at all prepubertal ages. Although postnatal growth patterns varied in fundamentally different ways with sex and robustness, the dependence of trait sets on robustness indicated that children sustained variants affecting subperiosteal growth because they shared a common biological factor regulating functional adaptation. Considering the natural variation in acquired trait sets may help identify determinants of fracture risk, because age-related bone loss and gain will affect slender and robust structures differently. PMID:20001599

  9. Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis.

    PubMed

    Suter, Léonie; Rüegg, Marlene; Zemp, Niklaus; Hennig, Lars; Widmer, Alex

    2014-12-01

    Steep environmental gradients provide ideal settings for studies of potentially adaptive phenotypic and genetic variation in plants. The accurate timing of flowering is crucial for reproductive success and is regulated by several pathways, including the vernalization pathway. Among the numerous genes known to enable flowering in response to vernalization, the most prominent is FLOWERING LOCUS C (FLC). FLC and other genes of the vernalization pathway vary extensively among natural populations and are thus candidates for the adaptation of flowering time to environmental gradients such as altitude. We used 15 natural Arabidopsis (Arabidopsis thaliana) genotypes originating from an altitudinal gradient (800-2,700 m above sea level) in the Swiss Alps to test whether flowering time correlated with altitude under different vernalization scenarios. Additionally, we measured the expression of 12 genes of the vernalization pathway and its downstream targets. Flowering time correlated with altitude in a nonlinear manner for vernalized plants. Flowering time could be explained by the expression and regulation of the vernalization pathway, most notably by AGAMOUS LIKE19 (AGL19), FLOWERING LOCUS T (FT), and FLC. The expression of AGL19, FT, and VERNALIZATION INSENSITIVE3 was associated with altitude, and the regulation of MADS AFFECTING FLOWERING2 (MAF2) and MAF3 differed between low- and high-altitude genotypes. In conclusion, we found clinal variation across an altitudinal gradient both in flowering time and the expression and regulation of genes in the flowering time control network, often independent of FLC, suggesting that the timing of flowering may contribute to altitudinal adaptation. PMID:25339407

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

    PubMed

    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

  11. Spatial patterns of neutral and functional genetic variations reveal patterns of local adaptation in raccoon (Procyon lotor) populations exposed to raccoon rabies.

    PubMed

    Kyle, Christopher J; Rico, Yessica; Castillo, Sarrah; Srithayakumar, Vythegi; Cullingham, Catherine I; White, Bradley N; Pond, Bruce A

    2014-05-01

    Local adaptation is necessary for population survival and depends on the interplay between responses to selective forces and demographic processes that introduce or retain adaptive and maladaptive attributes. Host-parasite systems are dynamic, varying in space and time, where both host and parasites must adapt to their ever-changing environment in order to survive. We investigated patterns of local adaptation in raccoon populations with varying temporal exposure to the raccoon rabies virus (RRV). RRV infects approximately 85% of the population when epizootic and has been presumed to be completely lethal once contracted; however, disease challenge experiments and varying spatial patterns of RRV spread suggest some level of immunity may exist. We first assessed patterns of local adaptation in raccoon populations along the eastern seaboard of North America by contrasting spatial patterns of neutral (microsatellite loci) and functional, major histocompatibility complex (MHC) genetic diversity and structure. We explored variation of MHC allele frequencies in the light of temporal population exposure to RRV (0-60 years) and specific RRV strains in infected raccoons. Our results revealed high levels of MHC variation (66 DRB exon 2 alleles) and pronounced genetic structure relative to neutral microsatellite loci, indicative of local adaptation. We found a positive association linking MHC genetic diversity and temporal RRV exposure, but no association with susceptibility and resistance to RRV strains. These results have implications for landscape epidemiology studies seeking to predict the spread of RRV and present an example of how population demographics influence the degree to which populations adapt to local selective pressures. PMID:24655158

  12. Genetic Adaptation vs. Ecophysiological Plasticity of Photosynthetic-Related Traits in Young Picea glauca Trees along a Regional Climatic Gradient

    PubMed Central

    Benomar, Lahcen; Lamhamedi, Mohammed S.; Rainville, André; Beaulieu, Jean; Bousquet, Jean; Margolis, Hank A.

    2016-01-01

    correlated and decreased with a reduction of the average temperature of the growing season at seed origin. The clinal variation in H2014 and Amax appeared to be driven by CO2 conductance. The presence of locally adapted functional traits suggests that the use of APM may have advantages for optimizing seed source productivity in future local climates. PMID:26870067

  13. Genetic Adaptation vs. Ecophysiological Plasticity of Photosynthetic-Related Traits in Young Picea glauca Trees along a Regional Climatic Gradient.

    PubMed

    Benomar, Lahcen; Lamhamedi, Mohammed S; Rainville, André; Beaulieu, Jean; Bousquet, Jean; Margolis, Hank A

    2016-01-01

    cmax), were correlated and decreased with a reduction of the average temperature of the growing season at seed origin. The clinal variation in H2014 and A max appeared to be driven by CO2 conductance. The presence of locally adapted functional traits suggests that the use of APM may have advantages for optimizing seed source productivity in future local climates. PMID:26870067

  14. Role of adaptive and non-adaptive mechanisms forming complex patterns of genome size variation in six cytotypes of polyploid Allium oleraceum (Amaryllidaceae) on a continental scale

    PubMed Central

    Duchoslav, Martin; Šafářová, Lenka; Jandová, Michaela

    2013-01-01

    Background and Aims Although the large variation in genome size among different species is widely acknowledged, the occurrence and extent of variation below the species level are still controversial and have not yet been satisfactorily analysed. The aim of this study was to assess genome size variation in six ploidy levels (2n = 3x–8x) of the polyploid Allium oleraceum over a large geographical gradient and to search for potential interpretations of the size variation. Methods The genome sizes of 407 individuals of A. oleraceum collected from 114 populations across Europe were determined by flow cytometry using propidium iodide staining. The genome size variation was correlated with spatial, climatic and habitat variables. Key Results The mean holoploid genome size (2C DNA) was 42·49, 52·14, 63·34, 71·94, 85·51 and 92·12 pg at the tri-, tetra-, penta-, hexa-, hepta- and octoploid levels, respectively. Genome size varied from a minimum of 2·3 % in the octoploids to a maximum of 18·3 % in the tetraploids. Spatial structuring of genome size was observed within the tetra- and pentaploids, where 2C DNA significantly increased with both latitude and longitude, and correlated with several climatic variables, suggesting a gradient of continentality. Genome size in hexaploids showed low variation, weak correlation with climatic variables and no spatial structuring. Downsizing in monoploid genome size was observed between all cytotypes except for heptaploids. Splitting populations into western and eastern European groups resulted in strong differences in monoploid genome size between groups in tetra- and pentaploids but not in hexaploids. The monoploid genome sizes of the cytotypes were similar in the western group but diverged in the eastern group. Conclusions Complex patterns of holoploid and monoploid genome size variation found both within and between A. oleraceum cytotypes are most likely the result of several interacting factors, including different

  15. Genotypic Variation in Growth and Physiological Response to Drought Stress and Re-Watering Reveals the Critical Role of Recovery in Drought Adaptation in Maize Seedlings

    PubMed Central

    Chen, Daoqian; Wang, Shiwen; Cao, Beibei; Cao, Dan; Leng, Guohui; Li, Hongbing; Yin, Lina; Shan, Lun; Deng, Xiping

    2016-01-01

    Non-irrigated crops in temperate climates and irrigated crops in arid climates are subjected to continuous cycles of water stress and re-watering. Thus, fast and efficient recovery from water stress may be among the key determinants of plant drought adaptation. The present study was designed to comparatively analyze the roles of drought resistance and drought recovery in drought adaptation and to investigate the physiological basis of genotypic variation in drought adaptation in maize (Zea mays) seedlings. As the seedlings behavior in growth associate with yield under drought, it could partly reflect the potential of drought adaptability. Growth and physiological responses to progressive drought stress and recovery were observed in seedlings of 10 maize lines. The results showed that drought adaptability is closely related to drought recovery (r = 0.714**), but not to drought resistance (r = 0.332). Drought induced decreases in leaf water content, water potential, osmotic potential, gas exchange parameters, chlorophyll content, Fv/Fm and nitrogen content, and increased H2O2 accumulation and lipid peroxidation. After recovery, most of these physiological parameters rapidly returned to normal levels. The physiological responses varied between lines. Further correlation analysis indicated that the physiological bases of drought resistance and drought recovery are definitely different, and that maintaining higher chlorophyll content (r = 0.874***) and Fv/Fm (r = 0.626*) under drought stress contributes to drought recovery. Our results suggest that both drought resistance and recovery are key determinants of plant drought adaptation, and that drought recovery may play a more important role than previously thought. In addition, leaf water potential, chlorophyll content and Fv/Fm could be used as efficient reference indicators in the selection of drought-adaptive genotypes. PMID:26793218

  16. Genotypic Variation in Growth and Physiological Response to Drought Stress and Re-Watering Reveals the Critical Role of Recovery in Drought Adaptation in Maize Seedlings.

    PubMed

    Chen, Daoqian; Wang, Shiwen; Cao, Beibei; Cao, Dan; Leng, Guohui; Li, Hongbing; Yin, Lina; Shan, Lun; Deng, Xiping

    2015-01-01

    Non-irrigated crops in temperate climates and irrigated crops in arid climates are subjected to continuous cycles of water stress and re-watering. Thus, fast and efficient recovery from water stress may be among the key determinants of plant drought adaptation. The present study was designed to comparatively analyze the roles of drought resistance and drought recovery in drought adaptation and to investigate the physiological basis of genotypic variation in drought adaptation in maize (Zea mays) seedlings. As the seedlings behavior in growth associate with yield under drought, it could partly reflect the potential of drought adaptability. Growth and physiological responses to progressive drought stress and recovery were observed in seedlings of 10 maize lines. The results showed that drought adaptability is closely related to drought recovery (r = 0.714(**)), but not to drought resistance (r = 0.332). Drought induced decreases in leaf water content, water potential, osmotic potential, gas exchange parameters, chlorophyll content, Fv/Fm and nitrogen content, and increased H2O2 accumulation and lipid peroxidation. After recovery, most of these physiological parameters rapidly returned to normal levels. The physiological responses varied between lines. Further correlation analysis indicated that the physiological bases of drought resistance and drought recovery are definitely different, and that maintaining higher chlorophyll content (r = 0.874(***)) and Fv/Fm (r = 0.626(*)) under drought stress contributes to drought recovery. Our results suggest that both drought resistance and recovery are key determinants of plant drought adaptation, and that drought recovery may play a more important role than previously thought. In addition, leaf water potential, chlorophyll content and Fv/Fm could be used as efficient reference indicators in the selection of drought-adaptive genotypes. PMID:26793218

  17. Tolerable Variation in Item Parameter Estimates for Linear and Adaptive Computer-Based Testing. Research Report No. 04-28

    ERIC Educational Resources Information Center

    Rizavi, Saba; Way, Walter D.; Davey, Tim; Herbert, Erin

    2004-01-01

    Item parameter estimates vary for a variety of reasons, including estimation error, characteristics of the examinee samples, and context effects (e.g., item location effects, section location effects, etc.). Although we expect variation based on theory, there is reason to believe that observed variation in item parameter estimates exceeds what…

  18. Gene Regulatory Variation Mediates Flowering Responses to Vernalization along an Altitudinal Gradient in Arabidopsis1[W][OPEN

    PubMed Central

    Suter, Léonie; Rüegg, Marlene; Zemp, Niklaus

    2014-01-01

    Steep environmental gradients provide ideal settings for studies of potentially adaptive phenotypic and genetic variation in plants. The accurate timing of flowering is crucial for reproductive success and is regulated by several pathways, including the vernalization pathway. Among the numerous genes known to enable flowering in response to vernalization, the most prominent is FLOWERING LOCUS C (FLC). FLC and other genes of the vernalization pathway vary extensively among natural populations and are thus candidates for the adaptation of flowering time to environmental gradients such as altitude. We used 15 natural Arabidopsis (Arabidopsis thaliana) genotypes originating from an altitudinal gradient (800–2,700 m above sea level) in the Swiss Alps to test whether flowering time correlated with altitude under different vernalization scenarios. Additionally, we measured the expression of 12 genes of the vernalization pathway and its downstream targets. Flowering time correlated with altitude in a nonlinear manner for vernalized plants. Flowering time could be explained by the expression and regulation of the vernalization pathway, most notably by AGAMOUS LIKE19 (AGL19), FLOWERING LOCUS T (FT), and FLC. The expression of AGL19, FT, and VERNALIZATION INSENSITIVE3 was associated with altitude, and the regulation of MADS AFFECTING FLOWERING2 (MAF2) and MAF3 differed between low- and high-altitude genotypes. In conclusion, we found clinal variation across an altitudinal gradient both in flowering time and the expression and regulation of genes in the flowering time control network, often independent of FLC, suggesting that the timing of flowering may contribute to altitudinal adaptation. PMID:25339407

  19. Local adaptations and climate change: converging sensitivity of bud break in black spruce provenances.

    PubMed

    Rossi, Sergio

    2015-07-01

    Species with transcontinental distribution or spread over wide geographical regions develop populations with growth traits genetically adapted to the local climate. The aim of this study was to investigate the ecotypic sensitivity of bud break, a strong adaptive trait, to a changing environment. Six phenological phases of bud break were monitored daily on black spruce [Picea mariana (Mill.) BSP] seedlings submitted to different temperatures (12, 16 and 20 °C) and photoperiods (14, 18 and 22 h). Six provenances were tested in growth chambers, produced from seeds collected along the whole latitudinal range of the closed boreal forest in Quebec, Canada. Bud break lasted 13.3 days on average and occurred earlier in seedlings from colder sites. The annual temperature of the sites suitably tracked the clinal variation among ecotypes, providing a clear biological explanation for the environmental signal driving the adaptive divergence of populations to the local climate. Increasing temperature induced an earlier bud break according to a non-linear pattern with greater advancements observed between 12 and 16 °C. Photoperiod was significant, but sensitivity analysis indicated that its effect on bud break was marginal with respect to temperature. No interaction of provenance × treatment was observed, demonstrating an ecotypic convergence of the responses to both factors. Changes in the growing conditions could substantially modify the synchronization between bud phenology and climate, thus exposing the developing meristems of black spruce to frost damage. However, similar advancements of bud break could be expected in the different ecotypes subjected to warmer temperatures or longer day lengths. PMID:25225116

  20. Local adaptations and climate change: converging sensitivity of bud break in black spruce provenances

    NASA Astrophysics Data System (ADS)

    Rossi, Sergio

    2015-07-01

    Species with transcontinental distribution or spread over wide geographical regions develop populations with growth traits genetically adapted to the local climate. The aim of this study was to investigate the ecotypic sensitivity of bud break, a strong adaptive trait, to a changing environment. Six phenological phases of bud break were monitored daily on black spruce [ Picea mariana (Mill.) BSP] seedlings submitted to different temperatures (12, 16 and 20 °C) and photoperiods (14, 18 and 22 h). Six provenances were tested in growth chambers, produced from seeds collected along the whole latitudinal range of the closed boreal forest in Quebec, Canada. Bud break lasted 13.3 days on average and occurred earlier in seedlings from colder sites. The annual temperature of the sites suitably tracked the clinal variation among ecotypes, providing a clear biological explanation for the environmental signal driving the adaptive divergence of populations to the local climate. Increasing temperature induced an earlier bud break according to a non-linear pattern with greater advancements observed between 12 and 16 °C. Photoperiod was significant, but sensitivity analysis indicated that its effect on bud break was marginal with respect to temperature. No interaction of provenance × treatment was observed, demonstrating an ecotypic convergence of the responses to both factors. Changes in the growing conditions could substantially modify the synchronization between bud phenology and climate, thus exposing the developing meristems of black spruce to frost damage. However, similar advancements of bud break could be expected in the different ecotypes subjected to warmer temperatures or longer day lengths.

  1. Effects of body-size variation on flight-related traits in latitudinal populations of Drosophila melanogaster.

    PubMed

    Bhan, Veer; Parkash, Ravi; Aggarwal, Dau Dayal

    2014-04-01

    In the present study, we tested the hypothesis whether flight-related traits such as wing area, flight-muscle ratio, wing loading and dispersal yield evidence of geographical variation in nine wild-collected as well as laboratory-reared (at 21°C) latitudinal populations of Drosophila melanogaster from the Indian subcontinent. We observed positive clinal variation in the wing-thorax ratio, wing aspect ratio and wing area, along a latitudinal gradient for both the sexes. In contrast, geographical changes in three parameters of flight ability, i.e. flight-muscle ratio, wing loading and dispersal, showed negative correlation with latitude. On the basis of isofemale line variability, we observed positive correlation of wing loading with flight-muscle ratio as well as dispersal behaviour in both the sexes. We also found positive correlation between duration of development and wing area. Interestingly, southern populations of D. melanogaster from warm and humid habitats exhibited higher flight-muscle ratio as well as the higher wing loading than northern populations which occur in cooler and drier climatic conditions. Laboratory tests for dispersal-related walking behaviour showed significantly higher values for southern populations compared with northern populations of D. melanogaster. Multiple regression analysis of geographical changes in flight-muscle ratio, wing loading as well as walking behaviour as a function of average temperature and relative humidity of the origin of populations in wild-collected flies have suggested adaptive changes in flight-related traits in response to steeper gradients of climatic factors in the Indian subcontinent. Finally, adaptive latitudinal variations in flight-related traits in D. melanogaster are consistent with results of other studies from different continents despite differences due to specific climatic conditions in the Indian subcontinent. PMID:24840827

  2. Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum[OPEN

    PubMed Central

    Hardigan, Michael A.; Crisovan, Emily; Hamilton, John P.; Laimbeer, Parker; Leisner, Courtney P.; Manrique-Carpintero, Norma C.; Newton, Linsey; Pham, Gina M.; Vaillancourt, Brieanne; Zeng, Zixian; Jiang, Jiming

    2016-01-01

    Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways. PMID:26772996

  3. Adaptive Agent Modeling of Distributed Language: Investigations on the Effects of Cultural Variation and Internal Action Representations

    ERIC Educational Resources Information Center

    Cangelosi, Angelo

    2007-01-01

    In this paper we present the "grounded adaptive agent" computational framework for studying the emergence of communication and language. This modeling framework is based on simulations of population of cognitive agents that evolve linguistic capabilities by interacting with their social and physical environment (internal and external symbol…

  4. Accurate relativistic adapted Gaussian basis sets for francium through Ununoctium without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models.

    PubMed

    Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade

    2013-10-15

    Accurate relativistic adapted Gaussian basis sets (RAGBSs) for 87 Fr up to 118 Uuo atoms without variational prolapse were developed here with the use of a polynomial version of the Generator Coordinate Dirac-Fock method. Two finite nuclear models have been used, the Gaussian and uniform sphere models. The largest RAGBS error, with respect to numerical Dirac-Fock results, is 15.4 miliHartree for Ununoctium with a basis set size of 33s30p19d14f functions. PMID:23913741

  5. Audience effects, but not environmental influences, explain variation in gorilla close distance vocalizations-A test of the acoustic adaptation hypothesis.

    PubMed

    Hedwig, Daniela; Mundry, Roger; Robbins, Martha M; Boesch, Christophe

    2015-12-01

    Close distance vocalizations are an integral part of primate vocal communication. They exhibit large acoustic variation which has been suggested to constitute flexible responses to the highly variable social setting of group living animals. However, a recent study suggested that acoustic variation in close distance calls of baboons may also arise from acoustic adaptations to environmental factors in order to counteract sound degradation. We tested whether the variation in calling rate and acoustic structure of gorilla close distance vocalizations may serve to counteract distorting effects of vegetation during sound propagation. Using focal animal sampling we recorded the vocal behavior of 15 adult individuals living in two groups: one group of western lowland gorillas Gorilla gorilla gorilla and one group of mountain gorillas Gorilla beringei beringei. We considered the distance between the caller and its nearest neighbor as the minimum transmission distance of calls; while vegetation density was quantified through measures of visibility. Our analysis revealed vocal plasticity in gorilla close calls in relation to changes in visibility and nearest neighbor distance. However, the observed changes in fundamental frequency and calling rate are unlikely to counteract degrading effects of vegetation, but rather seem to reflect reactions to variation in spatial and visual separation from other group members, similar to the audience effects demonstrated in a range of other species. We propose that vocal plasticity to counteract distorting environmental effects may not be prevalent across taxa and perhaps confined to species living in heterogeneous habitats with highly variable transmission conditions. PMID:26352614

  6. Evidence of Convergent Evolution in Humans and Macaques Supports an Adaptive Role for Copy Number Variation of the β-Defensin-2 Gene

    PubMed Central

    Ottolini, Barbara; Hornsby, Michael J.; Abujaber, Razan; MacArthur, Jacqueline A.L.; Badge, Richard M.; Schwarzacher, Trude; Albertson, Donna G.; Bevins, Charles L.; Solnick, Jay V.; Hollox, Edward J.

    2014-01-01

    β-defensins are a family of important peptides of innate immunity, involved in host defense, immunomodulation, reproduction, and pigmentation. Genes encoding β-defensins show evidence of birth-and-death evolution, adaptation by amino acid sequence changes, and extensive copy number variation (CNV) within humans and other species. The role of CNV in the adaptation of β-defensins to new functions remains unclear, as does the adaptive role of CNV in general. Here, we fine-map CNV of a cluster of β-defensins in humans and rhesus macaques. Remarkably, we found that the structure of the CNV is different between primates, with distinct mutational origins and CNV boundaries defined by retroviral long terminal repeat elements. Although the human β-defensin CNV region is 322 kb and encompasses several genes, including β-defensins, a long noncoding RNA gene, and testes-specific zinc-finger transcription factors, the orthologous region in the rhesus macaque shows CNV of a 20-kb region, containing only a single gene, the ortholog of the human β-defensin-2 gene. Despite its independent origins, the range of gene copy numbers in the rhesus macaque is similar to humans. In addition, the rhesus macaque gene has been subject to divergent positive selection at the amino acid level following its initial duplication event between 3 and 9.5 Ma, suggesting adaptation of this gene as the macaque successfully colonized novel environments outside Africa. Therefore, the molecular phenotype of β-defensin-2 CNV has undergone convergent evolution, and this gene shows evidence of adaptation at the amino acid level in rhesus macaques. PMID:25349268

  7. Evidence of convergent evolution in humans and macaques supports an adaptive role for copy number variation of the β-defensin-2 gene.

    PubMed

    Ottolini, Barbara; Hornsby, Michael J; Abujaber, Razan; MacArthur, Jacqueline A L; Badge, Richard M; Schwarzacher, Trude; Albertson, Donna G; Bevins, Charles L; Solnick, Jay V; Hollox, Edward J

    2014-01-01

    β-defensins are a family of important peptides of innate immunity, involved in host defense, immunomodulation, reproduction, and pigmentation. Genes encoding β-defensins show evidence of birth-and-death evolution, adaptation by amino acid sequence changes, and extensive copy number variation (CNV) within humans and other species. The role of CNV in the adaptation of β-defensins to new functions remains unclear, as does the adaptive role of CNV in general. Here, we fine-map CNV of a cluster of β-defensins in humans and rhesus macaques. Remarkably, we found that the structure of the CNV is different between primates, with distinct mutational origins and CNV boundaries defined by retroviral long terminal repeat elements. Although the human β-defensin CNV region is 322 kb and encompasses several genes, including β-defensins, a long noncoding RNA gene, and testes-specific zinc-finger transcription factors, the orthologous region in the rhesus macaque shows CNV of a 20-kb region, containing only a single gene, the ortholog of the human β-defensin-2 gene. Despite its independent origins, the range of gene copy numbers in the rhesus macaque is similar to humans. In addition, the rhesus macaque gene has been subject to divergent positive selection at the amino acid level following its initial duplication event between 3 and 9.5 Ma, suggesting adaptation of this gene as the macaque successfully colonized novel environments outside Africa. Therefore, the molecular phenotype of β-defensin-2 CNV has undergone convergent evolution, and this gene shows evidence of adaptation at the amino acid level in rhesus macaques. PMID:25349268

  8. Rainfall can explain adaptive phenotypic variation with high gene flow in the New Holland Honeyeater (Phylidonyris novaehollandiae)

    PubMed Central

    Myers, Steven A; Donnellan, Stephen; Kleindorfer, Sonia

    2012-01-01

    Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex-specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall-related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits – shorter, deeper bills, longer tarsi, and longer wings – would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex-biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill-head length, deeper bills, and shorter tarsi. Bill depth in males in high-rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill-head length, bill-nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale. PMID:23145327

  9. Rainfall can explain adaptive phenotypic variation with high gene flow in the New Holland Honeyeater (Phylidonyris novaehollandiae).

    PubMed

    Myers, Steven A; Donnellan, Stephen; Kleindorfer, Sonia

    2012-10-01

    Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex-specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall-related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits - shorter, deeper bills, longer tarsi, and longer wings - would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex-biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill-head length, deeper bills, and shorter tarsi. Bill depth in males in high-rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill-head length, bill-nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale. PMID:23145327

  10. Inversions and adaptation to the plant toxin ouabain shape DNA sequence variation within and between chromosomal inversions of Drosophila subobscura.

    PubMed Central

    Pegueroles, Cinta; Ferrés-Coy, Albert; Martí-Solano, Maria; Aquadro, Charles F; Pascual, Marta; Mestres, Francesc

    2016-01-01

    Adaptation is defined as an evolutionary process allowing organisms to succeed in certain habitats or conditions. Chromosomal inversions have the potential to be key in the adaptation processes, since they can contribute to the maintenance of favoured combinations of adaptive alleles through reduced recombination between individuals carrying different inversions. We have analysed six genes (Pif1A, Abi, Sqd, Yrt, Atpα and Fmr1), located inside and outside three inversions of the O chromosome in European populations of Drosophila subobscura. Genetic differentiation was significant between inversions despite extensive recombination inside inverted regions, irrespective of gene distance to the inversion breakpoints. Surprisingly, the highest level of genetic differentiation between arrangements was found for the Atpα gene, which is located outside the O1 and O7 inversions. Two derived unrelated arrangements (O3+4+1 and O3+4+7) are nearly fixed for several amino acid substitutions at the Atpα gene that have been described to confer resistance in other species to the cardenolide ouabain, a plant toxin capable of blocking ATPases. Similarities in the Atpα variants, conferring ouabain resistance in both arrangements, may be the result of convergent substitution and be favoured in response to selective pressures presumably related to the presence of plants containing ouabain in the geographic locations where both inversions are present. PMID:27029337

  11. In situ adaptive response to climate and habitat quality variation: spatial and temporal variation in European badger (Meles meles) body weight.

    PubMed

    Byrne, Andrew W; Fogarty, Ursula; O'Keeffe, James; Newman, Chris

    2015-09-01

    Variation in climatic and habitat conditions can affect populations through a variety of mechanisms, and these relationships can act at different temporal and spatial scales. Using post-mortem badger body weight records from 15 878 individuals captured across the Republic of Ireland (7224 setts across ca. 15 000 km(2) ; 2009-2012), we employed a hierarchical multilevel mixed model to evaluate the effects of climate (rainfall and temperature) and habitat quality (landscape suitability), while controlling for local abundance (unique badgers caught/sett/year). Body weight was affected strongly by temperature across a number of temporal scales (preceding month or season), with badgers being heavier if preceding temperatures (particularly during winter/spring) were warmer than the long-term seasonal mean. There was less support for rainfall across different temporal scales, although badgers did exhibit heavier weights when greater rainfall occurred one or 2 months prior to capture. Badgers were also heavier in areas with higher landscape habitat quality, modulated by the number of individuals captured per sett, consistent with density-dependent effects reducing weights. Overall, the mean badger body weight of culled individuals rose during the study period (2009-2012), more so for males than for females. With predicted increases in temperature, and rainfall, augmented by ongoing agricultural land conversion in this region, we project heavier individual badger body weights in the future. Increased body weight has been associated with higher fecundity, recruitment and survival rates in badgers, due to improved food availability and energetic budgets. We thus predict that climate change could increase the badger population across the Republic of Ireland. Nevertheless, we emphasize that, locally, populations could still be vulnerable to extreme weather variability coupled with detrimental agricultural practice, including population management. PMID:25846328

  12. Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus × viridis Hybrid Zone in Southwestern New Mexico

    PubMed Central

    Zancolli, Giulia; Baker, Timothy G.; Barlow, Axel; Bradley, Rebecca K.; Calvete, Juan J.; Carter, Kimberley C.; de Jager, Kaylah; Owens, John Benjamin; Price, Jenny Forrester; Sanz, Libia; Scholes-Higham, Amy; Shier, Liam; Wood, Liam; Wüster, Catharine E.; Wüster, Wolfgang

    2016-01-01

    Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter- and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species. PMID:27322321

  13. Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus × viridis Hybrid Zone in Southwestern New Mexico.

    PubMed

    Zancolli, Giulia; Baker, Timothy G; Barlow, Axel; Bradley, Rebecca K; Calvete, Juan J; Carter, Kimberley C; de Jager, Kaylah; Owens, John Benjamin; Price, Jenny Forrester; Sanz, Libia; Scholes-Higham, Amy; Shier, Liam; Wood, Liam; Wüster, Catharine E; Wüster, Wolfgang

    2016-01-01

    Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter- and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A₂ such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species. PMID:27322321

  14. Evolutionary significance of geographic variation in a plumage-based foraging adaptation: an experimental test in the slate-throated redstart (Myioborus miniatus).

    PubMed

    Mumme, Ronald L; Galatowitsch, Mark L; Jabłoński, Piotr G; Stawarczyk, Tadeusz M; Cygan, Jakub P

    2006-05-01

    two hypotheses for geographic variation in plumage pattern: (1) that geographic variation is a nonadaptive result of genetic drift, and (2) that selection for enhanced flush-pursuit foraging performance generally favors increased white in the plumage, but evolutionary trade-offs constrain the evolution of extensive patches of white in some geographic regions. Instead, our results suggest that geographic variation in the plumage pattern of Myioborus redstarts reflects adaptation to regional habitat characteristics that enhances flush-pursuit foraging performance. PMID:16817547

  15. Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors.

    PubMed

    Dannemann, Michael; Andrés, Aida M; Kelso, Janet

    2016-01-01

    Pathogens and the diseases they cause have been among the most important selective forces experienced by humans during their evolutionary history. Although adaptive alleles generally arise by mutation, introgression can also be a valuable source of beneficial alleles. Archaic humans, who lived in Europe and Western Asia for more than 200,000 years, were probably well adapted to this environment and its local pathogens. It is therefore conceivable that modern humans entering Europe and Western Asia who admixed with them obtained a substantial immune advantage from the introgression of archaic alleles. Here we document a cluster of three Toll-like receptors (TLR6-TLR1-TLR10) in modern humans that carries three distinct archaic haplotypes, indicating repeated introgression from archaic humans. Two of these haplotypes are most similar to the Neandertal genome, and the third haplotype is most similar to the Denisovan genome. The Toll-like receptors are key components of innate immunity and provide an important first line of immune defense against bacteria, fungi, and parasites. The unusually high allele frequencies and unexpected levels of population differentiation indicate that there has been local positive selection on multiple haplotypes at this locus. We show that the introgressed alleles have clear functional effects in modern humans; archaic-like alleles underlie differences in the expression of the TLR genes and are associated with increased [corrected] microbial resistance and increased allergic disease in large cohorts. This provides strong evidence for recurrent adaptive introgression at the TLR6-TLR1-TLR10 locus, resulting in differences in disease phenotypes in modern humans. PMID:26748514

  16. Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors

    PubMed Central

    Dannemann, Michael; Andrés, Aida M.; Kelso, Janet

    2016-01-01

    Pathogens and the diseases they cause have been among the most important selective forces experienced by humans during their evolutionary history. Although adaptive alleles generally arise by mutation, introgression can also be a valuable source of beneficial alleles. Archaic humans, who lived in Europe and Western Asia for more than 200,000 years, were probably well adapted to this environment and its local pathogens. It is therefore conceivable that modern humans entering Europe and Western Asia who admixed with them obtained a substantial immune advantage from the introgression of archaic alleles. Here we document a cluster of three Toll-like receptors (TLR6-TLR1-TLR10) in modern humans that carries three distinct archaic haplotypes, indicating repeated introgression from archaic humans. Two of these haplotypes are most similar to the Neandertal genome, and the third haplotype is most similar to the Denisovan genome. The Toll-like receptors are key components of innate immunity and provide an important first line of immune defense against bacteria, fungi, and parasites. The unusually high allele frequencies and unexpected levels of population differentiation indicate that there has been local positive selection on multiple haplotypes at this locus. We show that the introgressed alleles have clear functional effects in modern humans; archaic-like alleles underlie differences in the expression of the TLR genes and are associated with reduced microbial resistance and increased allergic disease in large cohorts. This provides strong evidence for recurrent adaptive introgression at the TLR6-TLR1-TLR10 locus, resulting in differences in disease phenotypes in modern humans. PMID:26748514

  17. Functional adaptations in the craniofacial morphology of Malagasy primates: shape variations associated with gummivory in the family Cheirogaleidae.

    PubMed

    Viguier, Bénédicte

    2004-12-01

    The infraorder Lemuriformes is characterized by a high level of homoplasy that clouds the evolutionary signal. The analysis of the morphological disparity of the Malagasy primates' crania and mandibles demonstrates the high determinism of functional specializations and developmental constraints, regardless of the phylogeny. In the present work, the weight of functional constraints linked to diet--a putative source of homoplasy--is analyzed first at the level of the infraorder Lemuriformes as a whole, and secondly at the level of a single family, the Cheirogaleidae, chosen because it contains taxa with two different diets (omnivory and gummivory). Malagasy primates are characterized by a great variety of dietary habits: some of them are omnivores, folivores, frugivores, gummivores, insectivores or even specialized hard-object feeders. All cheirogaleids feed on tree exudates, but while gum consumption is occasional or limited for Microcebus, Cheirogaleus and Mirza, gums are the dominant food source for Phaner and Allocebus. Craniofacial shape variations are analyzed using geometric morphometrics: methods based on landmark identification (Procrustes superimpositions) are chosen for cranium shape analysis, and methods based on outline decomposition (elliptical Fourier functions) for study of mandible shape. The morphospaces obtained at the level of the infraorder appear to be highly constrained by dietary habits, especially in the case of the mandibles. At the finer level of the family Cheirogaleidae, the analyses permit (1) separation of craniomandibular shape variation associated with the two dietary categories and (2) among the omnivorous category, to distinguish variation associated with the percentage of gum consumption. PMID:15646283

  18. An Evolutionary History of Defensins: A Role for Copy Number Variation in Maximizing Host Innate and Adaptive Immune Responses

    PubMed Central

    Machado, Lee R.; Ottolini, Barbara

    2015-01-01

    Defensins represent an evolutionary ancient family of antimicrobial peptides that play diverse roles in human health and disease. Defensins are cationic cysteine-containing multifunctional peptides predominantly expressed by epithelial cells or neutrophils. Defensins play a key role in host innate immune responses to infection and, in addition to their classically described role as antimicrobial peptides, have also been implicated in immune modulation, fertility, development, and wound healing. Aberrant expression of defensins is important in a number of inflammatory diseases as well as modulating host immune responses to bacteria, unicellular pathogens, and viruses. In parallel with their role in immunity, in other species, defensins have evolved alternative functions, including the control of coat color in dogs. Defensin genes reside in complex genomic regions that are prone to structural variations and some defensin family members exhibit copy number variation (CNV). Structural variations have mediated, and continue to influence, the diversification and expression of defensin family members. This review highlights the work currently being done to better understand the genomic architecture of the β-defensin locus. It evaluates current evidence linking defensin CNV to autoimmune disease (i.e., Crohn’s disease and psoriasis) as well as the contribution CNV has in influencing immune responses to HIV infection. PMID:25852686

  19. Leaf thickness controls variation in leaf mass per area (LMA) among grazing-adapted grasses in Serengeti.

    PubMed

    Griffith, Daniel M; Quigley, Kathleen M; Anderson, T Michael

    2016-08-01

    Leaf mass per area (LMA) is a primary plant functional trait that represents the cost of constructing a leaf. Ultimately, plants modify LMA by altering leaf thickness (LT), leaf dry matter content (LDMC), or both. While LMA can be modified through both of these constituents, studies of LMA have found that there is variation in whether LT or LDMC changes are responsible for LMA-and the relationships change depending on the species or functional groups being compared. In this study, we used a phylogenetic framework to determine that evolutionary shifts in LMA are driven by LT, and not LDMC, among 45 Serengeti grass species. We considered two alternative hypotheses that could result in evolutionary correlation of LMA on LT but not LDMC: either (1) LT is more labile than LDMC-and is therefore a less costly means to change LMA or (2) LDMC is tightly coupled to a different dimension of leaf variation (e.g., leaf hydraulics), leaving LT as the source of variation in LMA. LT was not more labile than LDMC, leading us to conclude that the evolution of LMA has been shaped by LT because LDMC is responding to other demands on leaf physiology. We speculate that leaf hydraulics provide this constraint on LDMC. The decoupling of LDMC from LT may allow plants to better optimize resource allocation in ecosystems where gradients in light competition, herbivory, and aridity place competing demands on leaf economics. PMID:27098527

  20. Genetic relationships and variation in reproductive strategies in four closely related bromeliads adapted to neotropical ‘inselbergs’: Alcantarea glaziouana, A. regina, A. geniculata and A. imperialis (Bromeliaceae)

    PubMed Central

    Barbará, Thelma; Martinelli, Gustavo; Palma-Silva, Clarisse; Fay, Michael F.; Mayo, Simon; Lexer, Christian

    2009-01-01

    Background and Aims Bromeliads (Bromeliaceae) adapted to rock outcrops or ‘inselbergs’ in neotropical rain forests have been identified as suitable plant models for studying population divergence and speciation during continental plant radiations. Little is known about genetic relationships and variation in reproductive strategies within and among inselberg-adapted species, yet knowledge of these parameters is important for understanding divergence processes and for conservation planning. Methods Nuclear microsatellites were used to assess the role of clonal reproduction, estimate genetic diversity and explore genetic relationships and variation in reproductive strategies for a total of 15 populations of four closely related Alcantarea inselberg species in south-eastern Brazil: A. glaziouana, A. regina, A. geniculata and A. imperialis. Key Results Clonal propagation is frequent in coastal populations of A. glaziouana and A. regina, but absent in the high-altitude species A. geniculata and A. imperialis. Considerable variation in clonal diversity, gene diversity (He), allelic richness, and Wright's inbreeding coefficient (FIS) exists within and between species of Alcantarea. A Bayesian analysis of coastal inselberg species indicated pronounced genetic structure. A neighbor-joining analysis grouped populations of each species together with moderate bootstrap support, except for the high altitude species A. imperialis. Conclusions The coastal inselberg species A. glaziouana and A. regina tend to propagate asexually via vegetative clonal growth, and both reproductive strategies and breeding systems vary greatly between populations and species of Alcantarea. The microsatellite data indicate a history of hybridization and reticulation involving the high-altitude species A. geniculata and A. imperialis in areas of co-occurrence. The results highlight the need to understand similarities and differences in reproductive strategies both within and between related species

  1. The impact of spatial scale and habitat configuration on patterns of trait variation and local adaptation in a wild plant parasite.

    PubMed

    Tack, Ayco J M; Horns, Felix; Laine, Anna-Liisa

    2014-01-01

    Theory indicates that spatial scale and habitat configuration are fundamental for coevolutionary dynamics and how diversity is maintained in host-pathogen interactions. Yet, we lack empirical data to translate the theory to natural host-parasite systems. In this study, we conduct a multiscale cross-inoculation study using the specialist wild plant pathogen Podosphaera plantaginis on its host plant Plantago lanceolata. We apply the same sampling scheme to a region with highly fragmented (Åland) and continuous (Saaremaa) host populations. Although theory predicts higher parasite virulence in continuous regions, we did not detect differences in traits conferring virulence among the regions. Patterns of adaptation were highly scale dependent. We detected parasite maladaptation among regions, and among populations separated by intermediate distances (6.0-40.0 km) within the fragmented region. In contrast, parasite performance did not vary significantly according to host origin in the continuous landscape. For both regions, differentiation among populations was much larger for genetic variation than for phenotypic variation, indicating balancing selection maintaining phenotypic variation within populations. Our findings illustrate the critical role of spatial scale and habitat configuration in driving host-parasite coevolution. The absence of more aggressive strains in the continuous landscape, in contrast to theoretical predictions, has major implications for long-term decision making in conservation, agriculture, and public health. PMID:24372603

  2. Adaptive evolution of interleukin-3 (IL3), a gene associated with brain volume variation in general human populations.

    PubMed

    Li, Ming; Huang, Liang; Li, Kaiqin; Huo, Yongxia; Chen, Chunhui; Wang, Jinkai; Liu, Jiewei; Luo, Zhenwu; Chen, Chuansheng; Dong, Qi; Yao, Yong-Gang; Su, Bing; Luo, Xiong-Jian

    2016-04-01

    Greatly expanded brain volume is one of the most characteristic traits that distinguish humans from other primates. Recent studies have revealed genes responsible for the dramatically enlarged human brain size (i.e., the microcephaly genes), and it has been well documented that many microcephaly genes have undergone accelerated evolution along the human lineage. In addition to being far larger than other primates, human brain volume is also highly variable in general populations. However, the genetic basis underlying human brain volume variation remains elusive and it is not known whether genes regulating human brain volume variation also have experienced positive selection. We have previously shown that genetic variants (near the IL3 gene) on 5q33 were significantly associated with brain volume in Chinese population. Here, we provide further evidence that support the significant association of genetic variants on 5q33 with brain volume. Bioinformatic analyses suggested that rs31480 is likely to be the causal variant among the studied SNPs. Molecular evolutionary analyses suggested that IL3 might have undergone positive selection in primates and humans. Neutrality tests further revealed signatures of positive selection of IL3 in Han Chinese and Europeans. Finally, extended haplotype homozygosity (EHH) and relative EHH analyses showed that the C allele of SNP rs31480 might have experienced recent positive selection in Han Chinese. Our results suggest that IL3 is an important genetic regulator for human brain volume variation and implied that IL3 might have experienced weak or modest positive selection in the evolutionary history of humans, which may be due to its contribution to human brain volume. PMID:26875095

  3. Strain variation in the adaptation of C57Bl6 and BALBc mice to chronic hypobaric hypoxia.

    PubMed

    Cramer, Nathan P; Xu, Xiufen; Christensen, Christine; Bierman, Alexis; Tankersley, Clarke G; Galdzicki, Zygmunt

    2015-05-01

    The interplay of environmental and genetic factors may lead to a spectrum of physiological and behavioral outcomes. How environmental stress factors interact with the diverse mouse genomes is still poorly understood and elucidating the underlying interactions requires specific stress models that can target integrated physiological systems. Here, we employ behavioral tests and whole-body plethysmography to examine the effects of 12 weeks of simulated high altitude (HA) exposure on two inbred mouse strains, BALBc and C57Bl6. We find that HA induced- weight loss recovers at significantly different rates in these two strains. Even at 12 weeks, however, both strains fail to reach body weight levels of controls. Performance on two motor tasks, rotarod and treadmill, improve with HA exposure but more prominently in BALBc mice. Whole-body plethysmography outcomes indicate that compensation to chronic HA includes increased respiratory frequencies and tidal volumes in both strains. However, the effects on tidal volume are significantly greater in BALBc mice and showed a biphasic course. Whole- body metabolic rates are also increased in both strains with prolonged HA exposure, but were more pronounced in BALBc mice suggestive of less successful adaptation in this strain. These adaptations occur in the absence of gross pathological changes in all major organs. Together these results indicate that chronic HA exposure results in environmental stressors that impact the specific physiological responses of BALBc more than C57Bl6 mice. Thus, these strains provide a promising platform for investigating how genetic backgrounds can differentially reinforce the effects of long-lasting environmental stressors and their potential to interact with psychological stressors. PMID:25647362

  4. Geographic body size variation in the periodical cicadas Magicicada: implications for life cycle divergence and local adaptation.

    PubMed

    Koyama, T; Ito, H; Kakishima, S; Yoshimura, J; Cooley, J R; Simon, C; Sota, T

    2015-06-01

    Seven species in three species groups (Decim, Cassini and Decula) of periodical cicadas (Magicicada) occupy a wide latitudinal range in the eastern United States. To clarify how adult body size, a key trait affecting fitness, varies geographically with climate conditions and life cycle, we analysed the relationships of population mean head width to geographic variables (latitude, longitude, altitude), habitat annual mean temperature (AMT), life cycle and species differences. Within species, body size was larger in females than males and decreased with increasing latitude (and decreasing habitat AMT), following the converse Bergmann's rule. For the pair of recently diverged 13- and 17-year species in each group, 13-year cicadas were equal in size or slightly smaller on average than their 17-year counterparts despite their shorter developmental time. This fact suggests that, under the same climatic conditions, 17-year cicadas have lowered growth rates compared to their 13-years counterparts, allowing 13-year cicadas with faster growth rates to achieve body sizes equivalent to those of their 17-year counterparts at the same locations. However, in the Decim group, which includes two 13-year species, the more southerly, anciently diverged 13-year species (Magicicada tredecim) was characterized by a larger body size than the other, more northerly 13- and 17-year species, suggesting that local adaptation in warmer habitats may ultimately lead to evolution of larger body sizes. Our results demonstrate how geographic clines in body size may be maintained in sister species possessing different life cycles. PMID:25975714

  5. Constant phycobilisome size in chromatically adapted cells of the cyanobacterium Tolypothrix tenuis, and variation in Nostoc sp

    SciTech Connect

    Ohki, K.; Gantt, E.; Lipschultz, C.A.; Ernst, M.C.

    1985-12-01

    Phycobilisomes of Tolypothrix tenuis, a cyanobacterium capable of complete chromatic adaptation, were studied from cells grown in red and green light, and in darkness. The phycobilisome size remained constant irrespective of the light quality. The hemidiscoidal phycobilisomes had an average diameter of about 52 nanometers and height of about 33 nanometers, by negative staining. The thickness was equivalent to a physocyanin molecule (about 10 nanometers). The molar ratio of allophycocyanin, relative to other phycobiliproteins always remained at about 1:3. Phycobilisomes from red light grown cells and cells grown heterotrophically in darkness were indistinguishable in their pigment composition, polypeptide pattern, and size. Eight polypeptides were resolved in the phycobilin region (17.5 to 23.5 kilodaltons) by isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Half of these were invariable, while others were variable in green and red light. It is inferred that phycoerythrin synthesis in green light resulted in a one for one substitution of phycocyanin, thus retaining a constant phycobilisome size. Tolypothrix appears to be one of the best examples of phycobiliprotein regulation with wavelength. By contrast, in Nostoc sp., the decrease in phycoerythrin in red light cells was accompanied by a decrease in phycobilisome size but not a regulated substitution.

  6. SU-E-J-102: Performance Variations Among Clinically Available Deformable Image Registration Tools in Adaptive Radiotherapy: How Should We Evaluate and Interpret the Result?

    SciTech Connect

    Nie, K; Pouliot, J; Smith, E; Chuang, C

    2015-06-15

    Purpose: To evaluate the performance variations in commercial deformable image registration (DIR) tools for adaptive radiation therapy. Methods: Representative plans from three different anatomical sites, prostate, head-and-neck (HN) and cranial spinal irradiation (CSI) with L-spine boost, were included. Computerized deformed CT images were first generated using virtual DIR QA software (ImSimQA) for each case. The corresponding transformations served as the “reference”. Three commercial software packages MIMVista v5.5 and MIMMaestro v6.0, VelocityAI v2.6.2, and OnQ rts v2.1.15 were tested. The warped contours and doses were compared with the “reference” and among each other. Results: The performance in transferring contours was comparable among all three tools with an average DICE coefficient of 0.81 for all the organs. However, the performance of dose warping accuracy appeared to rely on the evaluation end points. Volume based DVH comparisons were not sensitive enough to illustrate all the detailed variations while isodose assessment on a slice-by-slice basis could be tedious. Point-based evaluation was over-sensitive by having up to 30% hot/cold-spot differences. If adapting the 3mm/3% gamma analysis into the evaluation of dose warping, all three algorithms presented a reasonable level of equivalency. One algorithm had over 10% of the voxels not meeting this criterion for the HN case while another showed disagreement for the CSI case. Conclusion: Overall, our results demonstrated that evaluation based only on the performance of contour transformation could not guarantee the accuracy in dose warping. However, the performance of dose warping accuracy relied on the evaluation methodologies. Nevertheless, as more DIR tools are available for clinical use, the performance could vary at certain degrees. A standard quality assurance criterion with clinical meaning should be established for DIR QA, similar to the gamma index concept, in the near future.

  7. Genome-Wide Association Study in Arabidopsis thaliana of Natural Variation in Seed Oil Melting Point: A Widespread Adaptive Trait in Plants.

    PubMed

    Branham, Sandra E; Wright, Sara J; Reba, Aaron; Morrison, Ginnie D; Linder, C Randal

    2016-05-01

    Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of 15 a priori oil synthesis candidate genes, 2 (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others' molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions. PMID:26865732

  8. Host plant and latitude-related diapause variation in Rhagoletis pomonella: a test for multifaceted life history adaptation on different stages of diapause development.

    PubMed

    Dambroski, H R; Feder, J L

    2007-11-01

    Variation in the overwintering pupal diapause of Rhagoletis pomonella appears to adapt sympatric populations of the fly to seasonal differences in the fruiting times of their host plants, generating ecological reproductive isolation. Here, we investigate what aspects of diapause development are differentially affected (1) by comparing the propensities of apple vs. hawthorn-infesting host races of R. pomonella to forgo an initially deep diapause and directly develop into adults, and (2) by determining the chronological order that R. pomonella races and sibling species break diapause and eclose when reared under standardized environmental conditions. The results imply that factors affecting initial diapause depth (and/or differential mortality during the prewintering period) and those determining the timing of diapause termination or rates of post-diapause development are both under differential selection and are to some degree genetically uncoupled in flies. The modular nature of diapause life history adaptation in Rhagoletis suggests that phenology may involve multiple genetic changes and represent a stronger ecological barrier separating phytophagous specialists than is generally appreciated. PMID:17956381

  9. Variational solution of the Schrödinger equation using plane waves in adaptive coordinates: The radial case.

    PubMed

    Pérez-Jordá, José M

    2010-01-14

    A new method for solving the Schrödinger equation is proposed, based on the following details. First, a map u=u(r) from Cartesian coordinates r to a new coordinate system u is chosen. Second, the solution (orbital) psi(r) is written in terms of a function U depending on u so that psi(r)=/J(u)/(-1/2)U(u), where /J(u)/ is the Jacobian determinant of the map. Third, U is expressed as a linear combination of plane waves in the u coordinate, U(u)= sum (k)c(k)e(ik x u). Finally, the coefficients c(k) are variationally optimized to obtain the best energy, using a generalization of an algorithm originally developed for the Coulomb potential [J. M. Perez-Jorda, Phys. Rev. B 58, 1230 (1998)]. The method is tested for the radial Schrödinger equation in the hydrogen atom, resulting in micro-Hartree accuracy or better for the energy of ns and np orbitals (with n up to 5) using expansions of moderate length. PMID:20095666

  10. Preceding vehicle detection and tracking adaptive to illumination variation in night traffic scenes based on relevance analysis.

    PubMed

    Guo, Junbin; Wang, Jianqiang; Guo, Xiaosong; Yu, Chuanqiang; Sun, Xiaoyan

    2014-01-01

    Preceding vehicle detection and tracking at nighttime are challenging problems due to the disturbance of other extraneous illuminant sources coexisting with the vehicle lights. To improve the detection accuracy and robustness of vehicle detection, a novel method for vehicle detection and tracking at nighttime is proposed in this paper. The characteristics of taillights in the gray level are applied to determine the lower boundary of the threshold for taillights segmentation, and the optimal threshold for taillight segmentation is calculated using the OTSU algorithm between the lower boundary and the highest grayscale of the region of interest. The candidate taillight pairs are extracted based on the similarity between left and right taillights, and the non-vehicle taillight pairs are removed based on the relevance analysis of vehicle location between frames. To reduce the false negative rate of vehicle detection, a vehicle tracking method based on taillights estimation is applied. The taillight spot candidate is sought in the region predicted by Kalman filtering, and the disturbed taillight is estimated based on the symmetry and location of the other taillight of the same vehicle. Vehicle tracking is completed after estimating its location according to the two taillight spots. The results of experiments on a vehicle platform indicate that the proposed method could detect vehicles quickly, correctly and robustly in the actual traffic environments with illumination variation. PMID:25195855

  11. Preceding Vehicle Detection and Tracking Adaptive to Illumination Variation in Night Traffic Scenes Based on Relevance Analysis

    PubMed Central

    Guo, Junbin; Wang, Jianqiang; Guo, Xiaosong; Yu, Chuanqiang; Sun, Xiaoyan

    2014-01-01

    Preceding vehicle detection and tracking at nighttime are challenging problems due to the disturbance of other extraneous illuminant sources coexisting with the vehicle lights. To improve the detection accuracy and robustness of vehicle detection, a novel method for vehicle detection and tracking at nighttime is proposed in this paper. The characteristics of taillights in the gray level are applied to determine the lower boundary of the threshold for taillights segmentation, and the optimal threshold for taillight segmentation is calculated using the OTSU algorithm between the lower boundary and the highest grayscale of the region of interest. The candidate taillight pairs are extracted based on the similarity between left and right taillights, and the non-vehicle taillight pairs are removed based on the relevance analysis of vehicle location between frames. To reduce the false negative rate of vehicle detection, a vehicle tracking method based on taillights estimation is applied. The taillight spot candidate is sought in the region predicted by Kalman filtering, and the disturbed taillight is estimated based on the symmetry and location of the other taillight of the same vehicle. Vehicle tracking is completed after estimating its location according to the two taillight spots. The results of experiments on a vehicle platform indicate that the proposed method could detect vehicles quickly, correctly and robustly in the actual traffic environments with illumination variation. PMID:25195855

  12. An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster

    PubMed Central

    Glaser-Schmitt, Amanda; Duchen, Pablo; Parsch, John

    2016-01-01

    Insertions and deletions (indels) are a major source of genetic variation within species and may result in functional changes to coding or regulatory sequences. In this study we report that an indel polymorphism in the 3’ untranslated region (UTR) of the metallothionein gene MtnA is associated with gene expression variation in natural populations of Drosophila melanogaster. A derived allele of MtnA with a 49-bp deletion in the 3' UTR segregates at high frequency in populations outside of sub-Saharan Africa. The frequency of the deletion increases with latitude across multiple continents and approaches 100% in northern Europe. Flies with the deletion have more than 4-fold higher MtnA expression than flies with the ancestral sequence. Using reporter gene constructs in transgenic flies, we show that the 3' UTR deletion significantly contributes to the observed expression difference. Population genetic analyses uncovered signatures of a selective sweep in the MtnA region within populations from northern Europe. We also find that the 3’ UTR deletion is associated with increased oxidative stress tolerance. These results suggest that the 3' UTR deletion has been a target of selection for its ability to confer increased levels of MtnA expression in northern European populations, likely due to a local adaptive advantage of increased oxidative stress tolerance. PMID:27120580

  13. Circadian clock of Drosophila montana is adapted to high variation in summer day lengths and temperatures prevailing at high latitudes.

    PubMed

    Kauranen, Hannele; Ala-Honkola, Outi; Kankare, Maaria; Hoikkala, Anneli

    2016-06-01

    Photoperiodic regulation of the circadian rhythms in insect locomotor activity has been studied in several species, but seasonal entrainment of these rhythms is still poorly understood. We have traced the entrainment of activity rhythm of northern Drosophila montana flies in a climate chamber mimicking the photoperiods and day and night temperatures that the flies encounter in northern Finland during the summer. The experiment was started by transferring freshly emerged females into the chamber in early and late summer conditions to obtain both non-diapausing and diapausing females for the studies. The locomotor activity of the females and daily changes in the expression levels of two core circadian clock genes, timeless and period, in their heads were measured at different times of summer. The study revealed several features in fly rhythmicity that are likely to help the flies to cope with high variation in the day length and temperature typical to northern summers. First, both the non-diapausing and the diapausing females showed evening activity, which decreased towards the short day length as observed in the autumn in nature. Second, timeless and period genes showed concordant daily oscillations and seasonal shifts in their expression level in both types of females. Contrary to Drosophila melanogaster, oscillation profiles of these genes were similar to each other in all conditions, including the extremely long days in early summer and the cool temperatures in late summer, and their peak expression levels were not locked to lights-off transition in any photoperiod. Third, the diapausing females were less active than the non-diapausing ones, in spite of their younger age. Overall, the study showed that D. montana clock functions well under long day conditions, and that both the photoperiod and the daily temperature cycles are important zeitgebers for seasonal changes in the circadian rhythm of this species. PMID:26993661

  14. Stress avoidance in a common annual: reproductive timing is important for local adaptation and geographic distribution.

    PubMed

    Griffith, T M; Watson, M A

    2005-11-01

    Adaptation to local environments may be an important determinant of species' geographic range. However, little is known about which traits contribute to adaptation or whether their further evolution would facilitate range expansion. In this study, we assessed the adaptive value of stress avoidance traits in the common annual Cocklebur (Xanthium strumarium) by performing a reciprocal transplant across a broad latitudinal gradient extending to the species' northern border. Populations were locally adapted and stress avoidance traits accounted for most fitness differences between populations. At the northern border where growing seasons are cooler and shorter, native populations had evolved to reproduce earlier than native populations in the lower latitude gardens. This clinal pattern in reproductive timing corresponded to a shift in selection from favouring later to earlier reproduction. Thus, earlier reproduction is an important adaptation to northern latitudes and constraint on the further evolution of this trait in marginal populations could potentially limit distribution. PMID:16313471

  15. P. falciparum Infection Durations and Infectiousness Are Shaped by Antigenic Variation and Innate and Adaptive Host Immunity in a Mathematical Model

    PubMed Central

    Eckhoff, Philip

    2012-01-01

    Many questions remain about P. falciparum within-host dynamics, immunity, and transmission–issues that may affect public health campaign planning. These gaps in knowledge concern the distribution of durations of malaria infections, determination of peak parasitemia during acute infection, the relationships among gametocytes and immune responses and infectiousness to mosquitoes, and the effect of antigenic structure on reinfection outcomes. The present model of intra-host dynamics of P. falciparum implements detailed representations of parasite and immune dynamics, with structures based on minimal extrapolations from first-principles biology in its foundations. The model is designed to quickly and readily accommodate gains in mechanistic understanding and to evaluate effects of alternative biological hypothesis through in silico experiments. Simulations follow the parasite from the liver-stage through the detailed asexual cycle to clearance while tracking gametocyte populations. The modeled immune system includes innate inflammatory and specific antibody responses to a repertoire of antigens. The mechanistic focus provides clear explanations for the structure of the distribution of infection durations through the interaction of antigenic variation and innate and adaptive immunity. Infectiousness to mosquitoes appears to be determined not only by the density of gametocytes but also by the level of inflammatory cytokines, which harmonizes an extensive series of study results. Finally, pre-existing immunity can either decrease or increase the duration of infections upon reinfection, depending on the degree of overlap in antigenic repertoires and the strength of the pre-existing immunity. PMID:23028698

  16. The Sampling Scheme Matters: Pan troglodytes troglodytes and P. t. schweinfurthii Are Characterized by Clinal Genetic Variation Rather Than a Strong Subspecies Break

    PubMed Central

    Fünfstück, Tillmann; Arandjelovic, Mimi; Morgan, David B.; Sanz, Crickette; Reed, Patricia; Olson, Sarah H.; Cameron, Ken; Ondzie, Alain; Peeters, Martine; Vigilant, Linda

    2015-01-01

    Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions. PMID:25330245

  17. The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break.

    PubMed

    Fünfstück, Tillmann; Arandjelovic, Mimi; Morgan, David B; Sanz, Crickette; Reed, Patricia; Olson, Sarah H; Cameron, Ken; Ondzie, Alain; Peeters, Martine; Vigilant, Linda

    2015-02-01

    Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions. PMID:25330245

  18. Frequency variations of discrete cranial traits in major human populations. III. Hyperostotic variations

    PubMed Central

    HANIHARA, TSUNEHIKO; ISHIDA, HAJIME

    2001-01-01

    Seven discrete cranial traits usually categorised as hyperostotic characters, the medial palatine canal, hypoglossal canal bridging, precondylar tubercle, condylus tertius, jugular foramen bridging, auditory exostosis, and mylohyoid bridging were investigated in 81 major human population samples from around the world. Significant asymmetric occurrences of the bilateral traits were detected in the medial palatine canal and jugular foramen bridging in several samples. Significant intertrait associations were found between some pairs of the traits, but not consistently across the large geographical samples. The auditory exostosis showed a predominant occurrence in males. With the exception of the auditory exostosis and mylohyoid bridging in a few samples, significant sex differences were slight. The frequency distributions of the traits (except for the auditory exostosis) showed some interregional clinality and intraregional discontinuity, suggesting that genetic drift could have contributed to the observed pattern of variation. PMID:11554504

  19. Adaptive re-tracking algorithm for retrieval of water level variations and wave heights from satellite altimetry data for middle-sized inland water bodies

    NASA Astrophysics Data System (ADS)

    Troitskaya, Yuliya; Lebedev, Sergey; Soustova, Irina; Rybushkina, Galina; Papko, Vladislav; Baidakov, Georgy; Panyutin, Andrey

    by the improved threshold algorithm. The possibility of determination of significant wave height (SWH) in the lakes through a two-step adaptive retracking is also studied. Calculation of the parameter SWH for Gorky Reservoir from May 2010 to March 2014 showed the anomalously high values of SWH, derived from altimetry data [15], which means that the calibration of this SWH for inland waters is required. Calibration ground measurements were performed at Gorky reservoir in 2011-2013, when wave height, wind speed and air temperature were collected by equipment placed on a buoy [15] collocated with Jason-1 and Jason-2 altimetry data acquisition. The results obtained on the basis of standard algorithm and method for adaptive re-tracking at Rybinsk , Gorky , Kuibyshev , Saratov and Volgograd reservoirs and middle-sized lakes of Russia: Chany, Segozero, Hanko, Oneko, Beloye, water areas of which are intersected by the Jason-1,2 tracks, were compared and their correlation with the observed data of hydrological stations in reservoirs and lakes was investigated. It was noted that the Volgograd reservoir regional re-tracking to determine the water level , while the standard GDR data are practically absent. REFERENCES [1] AVISO/Altimetry. User Handbook. Merged TOPEX/ POSEIDON Products. Edition 3.0. AVISO. Toulouse., 1996. [2] C.M. Birkett et al., “Surface water dynamics in the Amazon Basin: Application of satellite radar altimetry,” J. Geophys. Res., vol. 107, pp. 8059, 2002. [3] G. Brown, “The average impulse response of a rough surface and its applications,” IEEE Trans. Antennas Propagat., vol. 25, pp. 67-74, 1977. [4] I.O. Campos et al., “Temporal variations of river basin waters from Topex/Poseidon satellite altimetry. Application to the Amazon basin,” Earth and Planetary Sciences, vol. 333, pp. 633-643, 2001. [5] A.V. Kouraev et al., “Ob’ river discharge from TOPEX/Poseidon satellite altimetry (1992-2002),” Rem. Sens. Environ., vol. 93, pp. 238-245, 2004

  20. Contrast adaptive total p-norm variation minimization approach to CT reconstruction for artifact reduction in reduced-view brain perfusion CT

    NASA Astrophysics Data System (ADS)

    Kim, Chang-Won; Kim, Jong-Hyo

    2011-03-01

    Perfusion CT (PCT) examinations are getting more frequently used for diagnosis of acute brain diseases such as hemorrhage and infarction, because the functional map images it produces such as regional cerebral blood flow (rCBF), regional cerebral blood volume (rCBV), and mean transit time (MTT) may provide critical information in the emergency work-up of patient care. However, a typical PCT scans the same slices several tens of times after injection of contrast agent, which leads to much increased radiation dose and is inevitability of growing concern for radiation-induced cancer risk. Reducing the number of views in projection in combination of TV minimization reconstruction technique is being regarded as an option for radiation reduction. However, reconstruction artifacts due to insufficient number of X-ray projections become problematic especially when high contrast enhancement signals are present or patient's motion occurred. In this study, we present a novel reconstruction technique using contrast-adaptive TpV minimization that can reduce reconstruction artifacts effectively by using different p-norms in high contrast and low contrast objects. In the proposed method, high contrast components are first reconstructed using thresholded projection data and low p-norm total variation to reflect sparseness in both projection and reconstruction spaces. Next, projection data are modified to contain only low contrast objects by creating projection data of reconstructed high contrast components and subtracting them from original projection data. Then, the low contrast projection data are reconstructed by using relatively high p-norm TV minimization technique, and are combined with the reconstructed high contrast component images to produce final reconstructed images. The proposed algorithm was applied to numerical phantom and a clinical data set of brain PCT exam, and the resultant images were compared with those using filtered back projection (FBP) and conventional TV

  1. Similarities and differences in altitudinal versus latitudinal variation for morphological traits in Drosophila melanogaster.

    PubMed

    Klepsatel, Peter; Gáliková, Martina; Huber, Christian D; Flatt, Thomas

    2014-05-01

    Understanding how natural environments shape phenotypic variation is a major aim in evolutionary biology. Here, we have examined clinal, likely genetically based variation in morphology among 19 populations of the fruit fly (Drosophila melanogaster) from Africa and Europe, spanning a range from sea level to 3000 m altitude and including locations approximating the southern and northern range limit. We were interested in testing whether latitude and altitude have similar phenotypic effects, as has often been postulated. Both latitude and altitude were positively correlated with wing area, ovariole number, and cell number. In contrast, latitude and altitude had opposite effects on the ratio between ovariole number and body size, which was negatively correlated with egg production rate per ovariole. We also used transgenic manipulation to examine how increased cell number affects morphology and found that larger transgenic flies, due to a higher number of cells, had more ovarioles, larger wings, and, unlike flies from natural populations, increased wing loading. Clinal patterns in morphology are thus not a simple function of changes in body size; instead, each trait might be subject to different selection pressures. Together, our results provide compelling evidence for profound similarities as well as differences between phenotypic effects of latitude and altitude. PMID:24410363

  2. Integrating Evolutionary and Functional Tests of Adaptive Hypotheses: A Case Study of Altitudinal Differentiation in Hemoglobin Function in an Andean Sparrow, Zonotrichia capensis

    PubMed Central

    Cheviron, Zachary A.; Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Eddy, Douglas K.; Jones, Jennifer; Carling, Matthew D.; Witt, Christopher C.; Moriyama, Hideaki; Weber, Roy E.; Fago, Angela; Storz, Jay F.

    2014-01-01

    In air-breathing vertebrates, the physiologically optimal blood-O2 affinity is jointly determined by the prevailing partial pressure of atmospheric O2, the efficacy of pulmonary O2 transfer, and internal metabolic demands. Consequently, genetic variation in the oxygenation properties of hemoglobin (Hb) may be subject to spatially varying selection in species with broad elevational distributions. Here we report the results of a combined functional and evolutionary analysis of Hb polymorphism in the rufous-collared sparrow (Zonotrichia capensis), a species that is continuously distributed across a steep elevational gradient on the Pacific slope of the Peruvian Andes. We integrated a population genomic analysis that included all postnatally expressed Hb genes with functional studies of naturally occurring Hb variants, as well as recombinant Hb (rHb) mutants that were engineered through site-directed mutagenesis. We identified three clinally varying amino acid polymorphisms: Two in the αA-globin gene, which encodes the α-chain subunits of the major HbA isoform, and one in the αD-globin gene, which encodes the α-chain subunits of the minor HbD isoform. We then constructed and experimentally tested single- and double-mutant rHbs representing each of the alternative αA-globin genotypes that predominate at different elevations. Although the locus-specific patterns of altitudinal differentiation suggested a history of spatially varying selection acting on Hb polymorphism, the experimental tests demonstrated that the observed amino acid mutations have no discernible effect on respiratory properties of the HbA or HbD isoforms. These results highlight the importance of experimentally validating the hypothesized effects of genetic changes in protein function to avoid the pitfalls of adaptive storytelling. PMID:25135942

  3. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea

    PubMed Central

    Stock, Amanda J.; Campitelli, Brandon E.; Stinchcombe, John R.

    2014-01-01

    Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range. PMID:25002704

  4. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea.

    PubMed

    Stock, Amanda J; Campitelli, Brandon E; Stinchcombe, John R

    2014-08-19

    Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range. PMID:25002704

  5. Genome-wide association study in arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to co-vary with germination temperatures because of a trade-o...

  6. Variation in infectivity and adaptation of wild duck- and poultry-origin high pathogenicity and low pathogenicity avian influenza viruses for poultry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Avian influenza (AI) viruses vary in their adaptation which impacts transmission between and infection of different bird species. We determine the intranasal mean bird infectious doses (BID50) for 11 high pathogenicity (HP) AI viruses for layer type chickens (LC), and three low pathogenicity (LP) A...

  7. Quantifying genetic variations and phenotypic plasticity of leaf phenology and growth for two temperate Fagaceae species (sessile oak and european beech)

    NASA Astrophysics Data System (ADS)

    Delzon, Sylvain; Vitasse, Yann; Alberto, Florian; Bresson, Caroline; Kremer, Antoine

    2010-05-01

    Under current climate change, research on inherent adaptive capacities of organisms is crucial to assess future evolutionary changes of natural populations. Genetic diversity and phenotypic plasticity constitute adaptative capacities that could allow populations to respond to new environmental conditions. The aim of the present study was (i) to determine whether there are genetic variations among populations from altitudinal gradients using a lowland common garden experiment and (ii) to assess the magnitude of phenotypic plasticity using a reciprocal transplant experiment (5 elevations from 100 to 1600 m asl.) for leaf phenology (flushing and senescence) and growth of two fagaceae species (Fagus sylvatica and Quercus petraea). We found significant differences in phenology among provenances for most species, and evidenced that these among-population differences in phenology were related to annual temperature of the provenance sites for both species. It's noteworthy that, along the same climatic gradient, the species exhibited opposite genetic clines: beech populations from high elevation flushed earlier than those of low elevation, whereas we observed an opposite trend for oak. Finally, we highlighted that both phenology timing and growth rate were highly consistent year to year. The results demonstrated that in spite of the proximity of the populations in their natural area, altitude led to genetic differentiations in their phenology and growth. Moreover, a high phenological plasticity was found for both species. We evidenced that reaction norms of flushing timing to temperature followed linear clinal trends for both species with an average shift of 5.7 days per degree increase. Timing of leaf senescence exhibited hyperbolic trends for beech and no or slight trends for oak. Furthermore, within species, there was no difference in magnitude of phenological plasticity among populations neither for flushing, nor for senescence. Consequently, for both species, the

  8. Genomic Evidence for Adaptive Inversion Clines in Drosophila melanogaster.

    PubMed

    Kapun, Martin; Fabian, Daniel K; Goudet, Jérôme; Flatt, Thomas

    2016-05-01

    Clines in chromosomal inversion polymorphisms-presumably driven by climatic gradients-are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic single nucleotide polymorphism (SNP) markers to estimate inversion frequencies from 28 whole-genome Pool-seq samples collected from 10 populations along the North American east coast. Inversions In(3L)P, In(3R)Mo, and In(3R)Payne showed clear latitudinal clines, and for In(2L)t, In(2R)NS, and In(3R)Payne the steepness of the clinal slopes changed between summer and fall. Consistent with an effect of seasonality on inversion frequencies, we detected small but stable seasonal fluctuations of In(2R)NS and In(3R)Payne in a temperate Pennsylvanian population over 4 years. In support of spatially varying selection, we observed that the cline in In(3R)Payne has remained stable for >40 years and that the frequencies of In(2L)t and In(3R)Payne are strongly correlated with climatic factors that vary latitudinally, independent of population structure. To test whether these patterns are adaptive, we compared the amount of genetic differentiation of inversions versus neutral SNPs and found that the clines in In(2L)t and In(3R)Payne are maintained nonneutrally and independent of admixture. We also identified numerous clinal inversion-associated SNPs, many of which exhibit parallel differentiation along the Australian cline and reside in genes known to affect fitness-related traits. Together, our results provide strong evidence that inversion clines are maintained by spatially-and perhaps also temporally-varying selection. We interpret our data in light of current hypotheses about how inversions are established and maintained. PMID:26796550

  9. Adaptive antennas

    NASA Astrophysics Data System (ADS)

    Barton, P.

    1987-04-01

    The basic principles of adaptive antennas are outlined in terms of the Wiener-Hopf expression for maximizing signal to noise ratio in an arbitrary noise environment; the analogy with generalized matched filter theory provides a useful aid to understanding. For many applications, there is insufficient information to achieve the above solution and thus non-optimum constrained null steering algorithms are also described, together with a summary of methods for preventing wanted signals being nulled by the adaptive system. The three generic approaches to adaptive weight control are discussed; correlation steepest descent, weight perturbation and direct solutions based on sample matrix conversion. The tradeoffs between hardware complexity and performance in terms of null depth and convergence rate are outlined. The sidelobe cancellor technique is described. Performance variation with jammer power and angular distribution is summarized and the key performance limitations identified. The configuration and performance characteristics of both multiple beam and phase scan array antennas are covered, with a brief discussion of performance factors.

  10. Climate adaption and post-fire restoration of a foundational perennial in cold desert: Insights from intraspecific variation in response to weather

    USGS Publications Warehouse

    Brabec, Martha M.; Germino, Matthew; Richardson, Bryce A.

    2016-01-01

    1.The loss of foundational but fire-intolerant perennials such as sagebrush due to increases in fire size and frequency in semiarid regions has motivated efforts to restore them, often with mixed or even no success. Seeds of sagebrush Artemisia tridentata and related species must be moved considerable distances from seed source to planting sites, but such transfers have not been guided by an understanding of local climate adaptation. Initial seedling establishment and its response to weather are a key demographic bottleneck that likely varies among subspecies and populations of sagebrush. 2.We assessed differences in survival, growth, and physiological responses of sagebrush to weather among eleven seed sources that varied in subspecies, cytotype, and climates-of-origin over 18 months following outplanting. Diploid or polyploid populations of mountain, Wyoming, and basin big sagebrush (A.tridentata ssp. vaseyana, A.tridentata ssp. wyomingensis, and A.tridentata ssp. tridentata, respectively) were planted onto five burned sites that normally support A.t.wyomingensis with some A.t.tridentata. 3.A.t.wyomingensis had the most growth and survival, and tetraploid populations had greater survival and height than diploids. Seasonal timing of mortality varied among the subspecies/cytotypes and was more closely related to minimum temperatures than water deficit. 4.Temperatures required to induce ice formation were up to 6°C more negative in 4n-A.t.tridentata and A.t.wyomingensis than other subspecies/cytotypes, indicating greater freezing avoidance. In contrast, freezing resistance of photosynthesis varied only 1°C among subspecies/cytotypes, being greatest in A.t.wyomingensis and least in the subspecies normally considered most cold-adapted,A.t.vaseyana. A large spectrum of reliance on freezing-avoidance vs. freezing-tolerance was observed and corresponded to differences in post-fire survivorship among subspecies/cytotypes. Differences in water deficit

  11. Cranial allometry and geographic variation in slow lorises (Nycticebus)

    PubMed

    Ravosa, M J

    1998-01-01

    A series of 20 craniodental measurements was obtained for two sister taxa: Nycticebus coucang (common slow loris) and N. pygmaeus (pygmy slow loris). Multivariate analysis of variance was performed with adult data to describe patterns of subspecific and specific variation in this genus. The geometric mean of adult cranial dimensions was compared to field data on latitudinal coordinates for available specimens to investigate if size variation in Nycticebus is clinal in nature. Ontogenetic series for larger-bodied N. coucang and smaller-bodied N. pygmaeus were compared to test the hypothesis that species and subspecific variation in skull form results from the differential extension of common patterns of relative growth. A MANOVA provides independent support of Groves's [pp. 44-53 in Proceedings of the Third International Congress on Primatology, Vol. 1 (Basel: S. Karger), in 1971)] classification of Nycticebus into two species, with four subspecies in the common slow loris and one form of the pygmy slow loris. Within N. coucang, cranial proportions for all four subspecies are ontogenetically scaled, and size differentiation is mainly clinal (Bergmann's Rule). N. c. bengalensis represents the most northerly disposed and the largest form. N. c. javanicus represents the next-largest form and is located in a southerly direction the next-farthest away from the equator. N. c. coucang and N. c. menagensis are both equatorial; however, the latter subspecies is the smallest. A genetic basis for some of the taxonomic variation between N. c. coucang and N. c. menagensis is supported by such nonclinal variation in body size. Variation in the presence/absence of I2 is not size-related but rather tracks geographic proximity and isolating factors which predate the most recent inundation of the Sunda Shelf. Although they inhabit a nonequatorial environment, pygmy slow lorises are the smallest of all Nycticebus. As N. pygmaeus is sympatric with N. c. bengalensis, the largest slow

  12. Genomic variation in cline shape across a hybrid zone.

    PubMed

    Kingston, Sarah E; Jernigan, Robert W; Fagan, William F; Braun, David; Braun, Michael J

    2012-11-01

    Hybrid zones are unique biological interfaces that reveal both population level and species level evolutionary processes. A genome-scale approach to assess gene flow across hybrid zones is vital, and now possible. In Mexican towhees (genus Pipilo), several morphological hybrid gradients exist. We completed a genome survey across one such gradient (9 populations, 140 birds) using mitochondrial DNA, 28 isozyme, and 377 AFLP markers. To assess variation in introgression among loci, cline parameters (i.e., width, center) for the 61 clinally varying loci were estimated and compiled into genomic distributions for tests against three empirical models spanning the range of observed cline shape. No single model accounts for observed variation in cline shape among loci. Numerous backcross individuals near the gradient center confirm a hybrid origin for these populations, contrary to a previous hypothesis based on social mimicry and character displacement. In addition, the observed variation does not bin into well-defined categories of locus types (e.g., neutral vs. highly selected). Our multi-locus analysis reveals cross-genomic variation in selective constraints on gene flow and locus-specific flexibility in the permeability of the interspecies membrane. PMID:23170209

  13. Genomic variation in cline shape across a hybrid zone

    PubMed Central

    Kingston, Sarah E; Jernigan, Robert W; Fagan, William F; Braun, David; Braun, Michael J

    2012-01-01

    Hybrid zones are unique biological interfaces that reveal both population level and species level evolutionary processes. A genome-scale approach to assess gene flow across hybrid zones is vital, and now possible. In Mexican towhees (genus Pipilo), several morphological hybrid gradients exist. We completed a genome survey across one such gradient (9 populations, 140 birds) using mitochondrial DNA, 28 isozyme, and 377 AFLP markers. To assess variation in introgression among loci, cline parameters (i.e., width, center) for the 61 clinally varying loci were estimated and compiled into genomic distributions for tests against three empirical models spanning the range of observed cline shape. No single model accounts for observed variation in cline shape among loci. Numerous backcross individuals near the gradient center confirm a hybrid origin for these populations, contrary to a previous hypothesis based on social mimicry and character displacement. In addition, the observed variation does not bin into well-defined categories of locus types (e.g., neutral vs. highly selected). Our multi-locus analysis reveals cross-genomic variation in selective constraints on gene flow and locus-specific flexibility in the permeability of the interspecies membrane. PMID:23170209

  14. Geographical variation of St. Lucia Parrot flight vocalizations

    USGS Publications Warehouse

    Kleeman, P.M.; Gilardi, J.D.

    2005-01-01

    Parrots are vocal learners and many species of parrots are capable of learning new calls, even as adults. This capability gives parrots the potential to develop communication systems that can vary dramatically over space. St. Lucia Parrot (Amazona versicolor) flight vocalizations were examined for geographic variation between four different sites on the island of St. Lucia. Spectrographic cross-correlation analysis of a commonly used flight vocalization, the p-chow call, demonstrated quantitative differences between sites. Additionally, the similarity of p-chows decreased as the distance between sites increased. Flight call repertoires also differed among sites; parrots at the Des Bottes and Quilesse sites each used one flight call unique to those sites, while parrots at the Barre de L'Isle site used a flight call that Quilesse parrots gave only while perched. It is unclear whether the vocal variation changed clinally with distance, or whether there were discrete dialect boundaries as in a congener, the Yellow-naped Parrot (Amazona auropalliata, Wright 1996). The geographical scale over which the St. Lucia Parrot's vocal variation occurred was dramatically smaller than that of the Yellow-naped Parrot. Similar patterns of fine-scale vocal variation may be more widespread among other parrot species in the Caribbean than previously documented.

  15. East Greenland and Barents Sea polar bears (Ursus maritimus): adaptive variation between two populations using skull morphometrics as an indicator of environmental and genetic differences.

    PubMed

    Pertoldi, Cino; Sonne, Christian; Wiig, Øystein; Baagøe, Hans J; Loeschcke, Volker; Bechshøft, Thea Østergaard

    2012-06-01

    A morphometric study was conducted on four skull traits of 37 male and 18 female adult East Greenland polar bears (Ursus maritimus) collected 1892-1968, and on 54 male and 44 female adult Barents Sea polar bears collected 1950-1969. The aim was to compare differences in size and shape of the bear skulls using a multivariate approach, characterizing the variation between the two populations using morphometric traits as an indicator of environmental and genetic differences. Mixture analysis testing for geographic differentiation within each population revealed three clusters for Barents Sea males and three clusters for Barents Sea females. East Greenland consisted of one female and one male cluster. A principal component analysis (PCA) conducted on the clusters defined by the mixture analysis, showed that East Greenland and Barents Sea polar bear populations overlapped to a large degree, especially with regards to females. Multivariate analyses of variance (MANOVA) showed no significant differences in morphometric means between the two populations, but differences were detected between clusters from each respective geographic locality. To estimate the importance of genetics and environment in the morphometric differences between the bears, a PCA was performed on the covariance matrix derived from the skull measurements. Skull trait size (PC1) explained approx. 80% of the morphometric variation, whereas shape (PC2) defined approx. 15%, indicating some genetic differentiation. Hence, both environmental and genetic factors seem to have contributed to the observed skull differences between the two populations. Overall, results indicate that many Barents Sea polar bears are morphometrically similar to the East Greenland ones, suggesting an exchange of individuals between the two populations. Furthermore, a subpopulation structure in the Barents Sea population was also indicated from the present analyses, which should be considered with regards to future management

  16. Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution.

    PubMed

    Modahl, Cassandra M; Mackessy, Stephen P

    2016-06-01

    Envenomation of humans by snakes is a complex and continuously evolving medical emergency, and treatment is made that much more difficult by the diverse biochemical composition of many venoms. Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation and genotype-phenotype relationships. To compare venom complexity and protein sequences, venom gland transcriptomes are assembled, which usually requires the sacrifice of snakes for tissue. However, toxin transcripts are also present in venoms, offering the possibility of obtaining cDNA sequences directly from venom. This study provides evidence that unknown full-length venom protein transcripts can be obtained from the venoms of multiple species from all major venomous snake families. These unknown venom protein cDNAs are obtained by the use of primers designed from conserved signal peptide sequences within each venom protein superfamily. This technique was used to assemble a partial venom gland transcriptome for the Middle American Rattlesnake (Crotalus simus tzabcan) by amplifying sequences for phospholipases A2, serine proteases, C-lectins, and metalloproteinases from within venom. Phospholipase A2 sequences were also recovered from the venoms of several rattlesnakes and an elapid snake (Pseudechis porphyriacus), and three-finger toxin sequences were recovered from multiple rear-fanged snake species, demonstrating that the three major clades of advanced snakes (Elapidae, Viperidae, Colubridae) have stable mRNA present in their venoms. These cDNA sequences from venom were then used to explore potential activities derived from protein sequence similarities and evolutionary histories within these large multigene superfamilies. Venom-derived sequences can also be used to aid in characterizing venoms that lack proteomic profiles and identify sequence characteristics indicating specific envenomation profiles. This approach, requiring only venom, provides

  17. Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution

    PubMed Central

    Modahl, Cassandra M.; Mackessy, Stephen P.

    2016-01-01

    Envenomation of humans by snakes is a complex and continuously evolving medical emergency, and treatment is made that much more difficult by the diverse biochemical composition of many venoms. Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation and genotype-phenotype relationships. To compare venom complexity and protein sequences, venom gland transcriptomes are assembled, which usually requires the sacrifice of snakes for tissue. However, toxin transcripts are also present in venoms, offering the possibility of obtaining cDNA sequences directly from venom. This study provides evidence that unknown full-length venom protein transcripts can be obtained from the venoms of multiple species from all major venomous snake families. These unknown venom protein cDNAs are obtained by the use of primers designed from conserved signal peptide sequences within each venom protein superfamily. This technique was used to assemble a partial venom gland transcriptome for the Middle American Rattlesnake (Crotalus simus tzabcan) by amplifying sequences for phospholipases A2, serine proteases, C-lectins, and metalloproteinases from within venom. Phospholipase A2 sequences were also recovered from the venoms of several rattlesnakes and an elapid snake (Pseudechis porphyriacus), and three-finger toxin sequences were recovered from multiple rear-fanged snake species, demonstrating that the three major clades of advanced snakes (Elapidae, Viperidae, Colubridae) have stable mRNA present in their venoms. These cDNA sequences from venom were then used to explore potential activities derived from protein sequence similarities and evolutionary histories within these large multigene superfamilies. Venom-derived sequences can also be used to aid in characterizing venoms that lack proteomic profiles and identify sequence characteristics indicating specific envenomation profiles. This approach, requiring only venom, provides

  18. Variation in rod and cone density from the fovea to the mid-periphery in healthy human retinas using adaptive optics scanning laser ophthalmoscopy.

    PubMed

    Wells-Gray, E M; Choi, S S; Bries, A; Doble, N

    2016-08-01

    PurposeTo characterize the rod and cone photoreceptor mosaic at retinal locations spanning the central 60° in vivo using adaptive optics scanning laser ophthalmoscopy (AO-SLO) in healthy human eyes.MethodsAO-SLO images (0.7 × 0.9°) were acquired at 680 nm from 14 locations from 30° nasal retina (NR) to 30° temporal retina (TR) in 5 subjects. Registered averaged images were used to measure rod and cone density and spacing within 60 × 60 μm regions of interest. Voronoi analysis was performed to examine packing geometry at all locations.ResultsAverage peak cone density near the fovea was 164 000±24 000 cones/mm(2) and decreased to 6700±1500 and 5400±700 cones/mm(2) at 30° NR and 30° TR, respectively. Cone-to-cone spacing increased from 2.7±0.2 μm at the fovea to 14.6±1.4 μm at 30° NR and 16.3±0.7 μm at 30° TR. Rod density peaked at 25° NR (124 000±20 000 rods/mm(2)) and 20° TR (120 000±12 000 rods/mm(2)) and decreased at higher eccentricities. Center-to-center rod spacing was lowest nasally at 25° (2.1±0.1 μm). Temporally, rod spacing was lowest at 20° (2.2±0.1 μm) before increasing to 2.3±0.1 μm at 30° TR.ConclusionsBoth rod and cone densities showed good agreement with histology and prior AO-SLO studies. The results demonstrate the ability to image at higher retinal eccentricities than reported previously. This has clinical importance in diseases that initially affect the peripheral retina such as retinitis pigmentosa. PMID:27229708

  19. Adaptive genetic variation and heart disease risk

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Purpose of review: Obesity, dyslipidemia and cardiovascular disease are complex and determined by both genetic and environmental factors and their interrelationships. Many associations from genome-wide association studies (GWAS) and candidate gene approaches have described a multitude of polymorphis...

  20. Transformational adaptation when incremental adaptations to climate change are insufficient

    PubMed Central

    Kates, Robert W.; Travis, William R.; Wilbanks, Thomas J.

    2012-01-01

    All human–environment systems adapt to climate and its natural variation. Adaptation to human-induced change in climate has largely been envisioned as increments of these adaptations intended to avoid disruptions of systems at their current locations. In some places, for some systems, however, vulnerabilities and risks may be so sizeable that they require transformational rather than incremental adaptations. Three classes of transformational adaptations are those that are adopted at a much larger scale, that are truly new to a particular region or resource system, and that transform places and shift locations. We illustrate these with examples drawn from Africa, Europe, and North America. Two conditions set the stage for transformational adaptation to climate change: large vulnerability in certain regions, populations, or resource systems; and severe climate change that overwhelms even robust human use systems. However, anticipatory transformational adaptation may be difficult to implement because of uncertainties about climate change risks and adaptation benefits, the high costs of transformational actions, and institutional and behavioral actions that tend to maintain existing resource systems and policies. Implementing transformational adaptation requires effort to initiate it and then to sustain the effort over time. In initiating transformational adaptation focusing events and multiple stresses are important, combined with local leadership. In sustaining transformational adaptation, it seems likely that supportive social contexts and the availability of acceptable options and resources for actions are key enabling factors. Early steps would include incorporating transformation adaptation into risk management and initiating research to expand the menu of innovative transformational adaptations. PMID:22509036

  1. Adaptive Management

    EPA Science Inventory

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive managem...

  2. The genomics of adaptation.

    PubMed

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    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 are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation. PMID:23097510

  3. Biogeographic variation in the baboon: dissecting the cline

    PubMed Central

    Dunn, Jason; Cardini, Andrea; Elton, Sarah

    2013-01-01

    All species demonstrate intraspecific anatomical variation. While generalisations such as Bergman's and Allen's rules have attempted to explain the geographic structuring of variation with some success, recent work has demonstrated limited support for these in certain Old World monkeys. This study extends this research to the baboon: a species that is widely distributed across sub-Saharan Africa and exhibits clinal variation across an environmentally disparate range. This study uses trend surface analysis to map the pattern of skull variation in size and shape in order to visualise the main axes of morphological variation. Patterns of shape and size-controlled shape are compared to highlight morphological variation that is underpinned by allometry alone. Partial regression is used to dissociate the effects of environmental terms, such as rainfall, temperature and spatial position. The diminutive Kinda baboon is outlying in size, so analyses were carried out with and without this taxon. Skull size variation demonstrates an east–west pattern, with small animals at the two extremes and large animals in Central and Southern Africa. Shape variation demonstrates the same geographical pattern as skull size, with small-sized animals exhibiting classic paedomorphic morphology. However, an additional north–south axis of variation emerges. After controlling for skull size, the diminutive Kinda baboon is no longer an outlier for size and shape. Also, the east–west component is no longer evident and discriminant function analysis shows an increased misclassification of adjacent taxa previously differentiated by size. This demonstrates the east–west component of shape variation is underpinned by skull size, while the north–south axis is not. The latter axis is explicable in phylogenetic terms: baboons arose in Southern Africa and colonised East and West Africa to the north, diverging in the process, aided by climate-mediated isolating mechanisms. Environmental terms

  4. Local climatic adaptation in a widespread microorganism

    PubMed Central

    Leducq, Jean-Baptiste; Charron, Guillaume; Samani, Pedram; Dubé, Alexandre K.; Sylvester, Kayla; James, Brielle; Almeida, Pedro; Sampaio, José Paulo; Hittinger, Chris Todd; Bell, Graham; Landry, Christian R.

    2014-01-01

    Exploring the ability of organisms to locally adapt is critical for determining the outcome of rapid climate changes, yet few studies have addressed this question in microorganisms. We investigated the role of a heterogeneous climate on adaptation of North American populations of the wild yeast Saccharomyces paradoxus. We found abundant among-strain variation for fitness components across a range of temperatures, but this variation was only partially explained by climatic variation in the distribution area. Most of fitness variation was explained by the divergence of genetically distinct groups, distributed along a north–south cline, suggesting that these groups have adapted to distinct climatic conditions. Within-group fitness components were correlated with climatic conditions, illustrating that even ubiquitous microorganisms locally adapt and harbour standing genetic variation for climate-related traits. Our results suggest that global climatic changes could lead to adaptation to new conditions within groups, or changes in their geographical distributions. PMID:24403328

  5. Iterative adaption of the bidimensional wall of the French T2 wind tunnel around a C5 axisymmetrical model: Infinite variation of the Mach number at zero incidence and a test at increased incidence

    NASA Technical Reports Server (NTRS)

    Archambaud, J. P.; Dor, J. B.; Payry, M. J.; Lamarche, L.

    1986-01-01

    The top and bottom two-dimensional walls of the T2 wind tunnel are adapted through an iterative process. The adaptation calculation takes into account the flow three-dimensionally. This method makes it possible to start with any shape of walls. The tests were performed with a C5 axisymmetric model at ambient temperature. Comparisons are made with the results of a true three-dimensional adaptation.

  6. Adaptive SPECT

    PubMed Central

    Barrett, Harrison H.; Furenlid, Lars R.; Freed, Melanie; Hesterman, Jacob Y.; Kupinski, Matthew A.; Clarkson, Eric; Whitaker, Meredith K.

    2008-01-01

    Adaptive imaging systems alter their data-acquisition configuration or protocol in response to the image information received. An adaptive pinhole single-photon emission computed tomography (SPECT) system might acquire an initial scout image to obtain preliminary information about the radiotracer distribution and then adjust the configuration or sizes of the pinholes, the magnifications, or the projection angles in order to improve performance. This paper briefly describes two small-animal SPECT systems that allow this flexibility and then presents a framework for evaluating adaptive systems in general, and adaptive SPECT systems in particular. The evaluation is in terms of the performance of linear observers on detection or estimation tasks. Expressions are derived for the ideal linear (Hotelling) observer and the ideal linear (Wiener) estimator with adaptive imaging. Detailed expressions for the performance figures of merit are given, and possible adaptation rules are discussed. PMID:18541485

  7. Population genetic evidence for cold adaptation in European Drosophila melanogaster populations.

    PubMed

    Božičević, Vedran; Hutter, Stephan; Stephan, Wolfgang; Wollstein, Andreas

    2016-03-01

    We studied Drosophila melanogaster populations from Europe (the Netherlands and France) and Africa (Rwanda and Zambia) to uncover genetic evidence of adaptation to cold. We present here four lines of evidence for genes involved in cold adaptation from four perspectives: (i) the frequency of SNPs at genes previously known to be associated with chill-coma recovery time (CCRT), startle reflex (SR) and resistance to starvation stress (RSS) vary along environmental gradients and therefore among populations; (ii) SNPs of genes that correlate significantly with latitude and altitude in African and European populations overlap with SNPs that correlate with a latitudinal cline from North America; (iii) at the genomewide level, the top candidate genes are enriched in gene ontology (GO) terms that are related to cold tolerance; (iv) GO enriched terms from North American clinal genes overlap significantly with those from Africa and Europe. Each SNP was tested in 10 independent runs of Bayenv2, using the median Bayes factors to ascertain candidate genes. None of the candidate genes were found close to the breakpoints of cosmopolitan inversions, and only four candidate genes were linked to QTLs related to CCRT. To overcome the limitation that we used only four populations to test correlations with environmental gradients, we performed simulations to estimate the power of our approach for detecting selection. Based on our results, we propose a novel network of genes that is involved in cold adaptation. PMID:26558479

  8. Adaptive colouration in amphibians.

    PubMed

    Rudh, Andreas; Qvarnström, Anna

    2013-01-01

    Amphibians, i.e. salamanders, frogs and caecilians show a wide range of bright colours in combination with contrasting patterns. There is variation among species, populations and also within species and populations. Furthermore, individuals often change colours during developmental stages or in response to environmental factors. This extraordinary variation means that there are excellent opportunities to test hypotheses of the adaptive significance of colours using amphibian species as models. We review the present view of functions of colouration in amphibians with the main focus on relatively unexplored topics. Variation in colouration has been found to play a role in thermoregulation, UV protection, predator avoidance and sexual signalling. However, many proposed cases of adaptive functions of colouration in amphibians remain virtually scientifically unexplored and surprisingly few genes influencing pigmentation or patterning have been detected. We would like to especially encourage more studies that take advantage of recent developments in measurement of visual properties of several possible signalling receivers (e.g. predators, competitors or mates). Future investigations on interactions between behaviour, ecology and vision have the potential to challenge our current view of the adaptive function of colouration in amphibians. PMID:23664831

  9. Marked intra-strain variation in response of Listeria monocytogenes dairy isolates to acid or salt stress and the effect of acid or salt adaptation on adherence to abiotic surfaces.

    PubMed

    Adrião, A; Vieira, M; Fernandes, I; Barbosa, M; Sol, M; Tenreiro, R P; Chambel, L; Barata, B; Zilhao, I; Shama, G; Perni, S; Jordan, S J; Andrew, P W; Faleiro, M L

    2008-03-31

    During food processing, and particularly in cheese manufacturing processes, Listeria monocytogenes may be exposed routinely to environments of low pH or high salt concentration. It has been suggested that these environmental conditions may contribute to bacterial adherence to abiotic surfaces and increased resistance to disinfection. In this study strains isolated from the environment of artisanal cheese-making dairies were used to investigate the behaviour of L. monocytogenes in response to acid and salt stress and clear differences between strains was observed. In planktonic culture, strains varied in resistance to low pH or high NaCl concentration and in the occurrence of an adaptive response to moderate acid or NaCl. There was dislocation in responses to salt and acid. Strains resistant, or adaptive, to acid were not resistant or adaptive to NaCl. The reverse also was observed. Exposure to moderate acid did not promote adherence to polystyrene but survival, at low pH or high NaCl concentration, of cells adherent to stainless steel was increased, even for strains that had no adaptive response planktonically, but the detail of these observations varied between strains. In contrast to acid adaptation, with some strains salt adaptation enhanced adherence of L. monocytogenes to polystyrene but this was not true for all strains. For some strains salt- or acid adaptation may enhance the survival of sessile cells exposed to hypochlorite disinfection. PMID:18258322

  10. Individual predictors of sensorimotor adaptability

    PubMed Central

    Seidler, Rachael D.; Mulavara, Ajitkumar P.; Bloomberg, Jacob J.; Peters, Brian T.

    2015-01-01

    There are large individual variations in strategies and rates of sensorimotor adaptation to spaceflight. This is seen in both the magnitude of performance disruptions when crewmembers are first exposed to microgravity, and in the rate of re-adaptation when they return to Earth’s gravitational environment. Understanding the sources of this variation can lead to a better understanding of the processes underlying adaptation, as well as provide insight into potential routes for facilitating performance of “slow adapters”. Here we review the literature on brain, behavioral, and genetic predictors of motor learning, recovery of motor function following neural insult, and sensorimotor adaptation. For example, recent studies have identified specific genetic polymorphisms that are associated with faster adaptation on manual joystick tasks and faster recovery of function following a stroke. Moreover, the extent of recruitment of specific brain regions during learning and adaptation has been shown to be predictive of the magnitude of subsequent learning. We close with suggestions for forward work aimed at identifying predictors of spaceflight adaptation success. Identification of “slow adapters” prior to spaceflight exposure would allow for more targeted preflight training and/or provision of booster training and adaptation adjuncts during spaceflight. PMID:26217197

  11. Revisiting classic clines in Drosophila melanogaster in the age of genomics

    PubMed Central

    Adrion, Jeffrey R.; Hahn, Matthew W.; Cooper, Brandon S.

    2015-01-01

    Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review, we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discuss instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and a number of other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature. PMID:26072452

  12. Revisiting classic clines in Drosophila melanogaster in the age of genomics.

    PubMed

    Adrion, Jeffrey R; Hahn, Matthew W; Cooper, Brandon S

    2015-08-01

    Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discussing instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and several other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature. PMID:26072452

  13. Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

    PubMed Central

    Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

    2016-01-01

    Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact

  14. Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster.

    PubMed

    Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

    2016-01-01

    Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact

  15. Probabilistic Finite Element: Variational Theory

    NASA Technical Reports Server (NTRS)

    Belytschko, T.; Liu, W. K.

    1985-01-01

    The goal of this research is to provide techniques which are cost-effective and enable the engineer to evaluate the effect of uncertainties in complex finite element models. Embedding the probabilistic aspects in a variational formulation is a natural approach. In addition, a variational approach to probabilistic finite elements enables it to be incorporated within standard finite element methodologies. Therefore, once the procedures are developed, they can easily be adapted to existing general purpose programs. Furthermore, the variational basis for these methods enables them to be adapted to a wide variety of structural elements and to provide a consistent basis for incorporating probabilistic features in many aspects of the structural problem. Tasks concluded include the theoretical development of probabilistic variational equations for structural dynamics, the development of efficient numerical algorithms for probabilistic sensitivity displacement and stress analysis, and integration of methodologies into a pilot computer code.

  16. A Preliminary Study of Genetic Variation in Populations of Monstera adansonii var. klotzschiana (Araceae) from North-East Brazil, Estimated with AFLP Molecular Markers

    PubMed Central

    Andrade, I. M.; Mayo, S. J.; van den Berg, C.; Fay, M. F.; Chester, M.; Lexer, C.; Kirkup, D.

    2007-01-01

    Background and Aims This study sought genetic evidence of long-term isolation in populations of Monstera adansonii var. klotzschiana (Araceae), a herbaceous, probably outbreeding, humid forest hemi-epiphyte, in the brejo forests of Ceará (north-east Brazil), and clarification of their relationships with populations in Amazonia and the Atlantic forest of Brazil. Methods Within-population genetic diversity and between-population dissimilarity were estimated using AFLP molecular markers in 75 individuals from eight populations located in Ceará, the Brazilian Atlantic Forest and Amazonia. Key Results The populations showed a clinal pattern of weak genetic differentiation over a large geographical region (FST = 0·1896). A strong correlation between genetic and geographical distance (Mantel test: r = 0·6903, P = 0·002) suggests a historical pattern of isolation by distance. Genetic structure analysis revealed at least two distinct gene pools in the data. The two isolated Ceará populations are significantly different from each other (pairwise ΦPT = 0·137, P = 0·003) and as diverse (Nei's gene diversity, average He = 0·1832, 0·1706) as those in the Atlantic and Amazon forest regions. The population in southern Brazil is less diverse (Nei's gene diversity, average He = 0·127) than the rest. The Ceará populations are related to those of the Atlantic forest rather than those from Amazonia (AMOVA, among-groups variation = 11·95 %, P = 0·037). Conclusions The gene pools detected within an overall pattern of clinal variation suggest distinct episodes of gene flow, possibly correlated with past humid forest expansions. The Ceará populations show no evidence of erosion of genetic diversity, although this was expected because of their isolation. Their genetic differentiation and relatively high diversity reinforce the importance of conserving the endangered brejo forests. PMID:17823112

  17. Adaptive control of robotic manipulators

    NASA Technical Reports Server (NTRS)

    Seraji, H.

    1987-01-01

    The author presents a novel approach to adaptive control of manipulators to achieve trajectory tracking by the joint angles. The central concept in this approach is the utilization of the manipulator inverse as a feedforward controller. The desired trajectory is applied as an input to the feedforward controller which behaves as the inverse of the manipulator at any operating point; the controller output is used as the driving torque for the manipulator. The controller gains are then updated by an adaptation algorithm derived from MRAC (model reference adaptive control) theory to cope with variations in the manipulator inverse due to changes of the operating point. An adaptive feedback controller and an auxiliary signal are also used to enhance closed-loop stability and to achieve faster adaptation. The proposed control scheme is computationally fast and does not require a priori knowledge of the complex dynamic model or the parameter values of the manipulator or the payload.

  18. Adaptive Development

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The goal of this research is to develop and demonstrate innovative adaptive seal technologies that can lead to dramatic improvements in engine performance, life, range, and emissions, and enhance operability for next generation gas turbine engines. This work is concentrated on the development of self-adaptive clearance control systems for gas turbine engines. Researchers have targeted the high-pressure turbine (HPT) blade tip seal location for following reasons: Current active clearance control (ACC) systems (e.g., thermal case-cooling schemes) cannot respond to blade tip clearance changes due to mechanical, thermal, and aerodynamic loads. As such they are prone to wear due to the required tight running clearances during operation. Blade tip seal wear (increased clearances) reduces engine efficiency, performance, and service life. Adaptive sealing technology research has inherent impact on all envisioned 21st century propulsion systems (e.g. distributed vectored, hybrid and electric drive propulsion concepts).

  19. Geographic patterns of craniofacial variation in pre-Hispanic populations from the Southern Cone of South America.

    PubMed

    Fabra, Mariana; Demarchi, Darío A

    2011-08-01

    In this study we analyzed the relationships and patterns of spatial variation from morphological cranial variability of 17 population samples representing the ancient inhabitants of the central territory of Argentina (archaeologically known as "Sierras Centrales") and other pre-Hispanic populations from different ecological and geographic regions of the Southern Cone of South America (Argentina and Uruguay), based on the analysis of 10 craniofacial measurements. Results obtained from D2 distances can be interpreted as evidence of a similar biological history for the populations that inhabited the Sierras Centrales and the population of Santiago del Estero. Matrix correlation analysis demonstrated that craniometric variation is significantly influenced by geography, suggesting that populations that lived at lower geographical distance share more biological similarity. Global spatial autocorrelation analysis suggests a clinal pattern for the biological variation, although Moran's I estimates calculated for each variable demonstrate that only nasal height and breadth show this spatial pattern of variation. Results from spatial regression techniques show a significant effect of altitude modeling nasal shape, in agreement with previous studies suggesting that nasal morphology is strongly influenced by environment variables. PMID:21846206

  20. Adaptive manifold learning.

    PubMed

    Zhang, Zhenyue; Wang, Jing; Zha, Hongyuan

    2012-02-01

    Manifold learning algorithms seek to find a low-dimensional parameterization of high-dimensional data. They heavily rely on the notion of what can be considered as local, how accurately the manifold can be approximated locally, and, last but not least, how the local structures can be patched together to produce the global parameterization. In this paper, we develop algorithms that address two key issues in manifold learning: 1) the adaptive selection of the local neighborhood sizes when imposing a connectivity structure on the given set of high-dimensional data points and 2) the adaptive bias reduction in the local low-dimensional embedding by accounting for the variations in the curvature of the manifold as well as its interplay with the sampling density of the data set. We demonstrate the effectiveness of our methods for improving the performance of manifold learning algorithms using both synthetic and real-world data sets. PMID:21670485

  1. Adapting Animals.

    ERIC Educational Resources Information Center

    Wedman, John; Wedman, Judy

    1985-01-01

    The "Animals" program found on the Apple II and IIe system master disk can be adapted for use in the mathematics classroom. Instructions for making the necessary changes and suggestions for using it in lessons related to geometric shapes are provided. (JN)

  2. Adaptive Thresholds

    SciTech Connect

    Bremer, P. -T.

    2014-08-26

    ADAPT is a topological analysis code that allow to compute local threshold, in particular relevance based thresholds for features defined in scalar fields. The initial target application is vortex detection but the software is more generally applicable to all threshold based feature definitions.

  3. Adaptive homeostasis.

    PubMed

    Davies, Kelvin J A

    2016-06-01

    Homeostasis is a central pillar of modern Physiology. The term homeostasis was invented by Walter Bradford Cannon in an attempt to extend and codify the principle of 'milieu intérieur,' or a constant interior bodily environment, that had previously been postulated by Claude Bernard. Clearly, 'milieu intérieur' and homeostasis have served us well for over a century. Nevertheless, research on signal transduction systems that regulate gene expression, or that cause biochemical alterations to existing enzymes, in response to external and internal stimuli, makes it clear that biological systems are continuously making short-term adaptations both to set-points, and to the range of 'normal' capacity. These transient adaptations typically occur in response to relatively mild changes in conditions, to programs of exercise training, or to sub-toxic, non-damaging levels of chemical agents; thus, the terms hormesis, heterostasis, and allostasis are not accurate descriptors. Therefore, an operational adjustment to our understanding of homeostasis suggests that the modified term, Adaptive Homeostasis, may be useful especially in studies of stress, toxicology, disease, and aging. Adaptive Homeostasis may be defined as follows: 'The transient expansion or contraction of the homeostatic range in response to exposure to sub-toxic, non-damaging, signaling molecules or events, or the removal or cessation of such molecules or events.' PMID:27112802

  4. Morphological variation and zoogeography of racers (Coluber constrictor) in the central Rocky Mountains

    USGS Publications Warehouse

    Corn, Paul Stephen; Bury, R. Bruce

    1986-01-01

    We examined 63 specimens of Coluber constrictor from Colorado and Utah using eight external morphological characters that have been used to distinguish C. c. mormon from C. c. flaviventris. We grouped the snakes into three Operational Taxonomic Units (OTU's) in a transect across the Rocky Mountains: the eastern Front Range foothills in Colorado; the inter-mountain region (western slope of Colorado and northeastern Utah); and the western foothills of the Wasatch Mountains in Utah. Statistically significant variation among the OTU's was discovered for ration of tail length to total length, number of central and subcaudal scales, and number of dentary teeth. However, variation is clinal with nearly complete overlap from one end f the transect to the other for each character, suggesting a wide zone of intergradiation in the inter-mountain region. We do not believe reported differences in reproductive parameters between Great Plains and Great Basin racers are sufficient grounds for recognition of species, because clutch size is both geographically variable and dependent on the environment. The distribution of C. constrictor is similar to that of other reptiles with transmontane distributions in the western United States, and we suggest two possible routes of dispersal across the Continental Divide in southwestern Wyoming. Thus, elevation of C. c. mormon to species status is not supported by morphological, reproductive, or zoogeographic evidence.

  5. Modelling reveals endogenous osmotic adaptation of storage tissue water potential as an important driver determining different stem diameter variation patterns in the mangrove species Avicennia marina and Rhizophora stylosa

    PubMed Central

    Vandegehuchte, Maurits W.; Guyot, Adrien; Hubeau, Michiel; De Swaef, Tom; Lockington, David A.; Steppe, Kathy

    2014-01-01

    Background Stem diameter variations are mainly determined by the radial water transport between xylem and storage tissues. This radial transport results from the water potential difference between these tissues, which is influenced by both hydraulic and carbon related processes. Measurements have shown that when subjected to the same environmental conditions, the co-occurring mangrove species Avicennia marina and Rhizophora stylosa unexpectedly show a totally different pattern in daily stem diameter variation. Methods Using in situ measurements of stem diameter variation, stem water potential and sap flow, a mechanistic flow and storage model based on the cohesion–tension theory was applied to assess the differences in osmotic storage water potential between Avicennia marina and Rhizophora stylosa. Key results Both species, subjected to the same environmental conditions, showed a resembling daily pattern in simulated osmotic storage water potential. However, the osmotic storage water potential of R. stylosa started to decrease slightly after that of A. marina in the morning and increased again slightly later in the evening. This small shift in osmotic storage water potential likely underlaid the marked differences in daily stem diameter variation pattern between the two species. Conclusions The results show that in addition to environmental dynamics, endogenous changes in the osmotic storage water potential must be taken into account in order to accurately predict stem diameter variations, and hence growth. PMID:24534674

  6. Adaptive compensation for an optical tracking telescope

    NASA Technical Reports Server (NTRS)

    Gilbart, J. W.; Winston, G. C.

    1974-01-01

    The application of model referenced adaptive control theory to an optical tracking telescope is discussed. The capability of the adaptive technique to compensate for mount irregularities such as inertial variations and bearing friction is demonstrated via field test results on a large tracking telescope. Results are presented which show a 6 to 1 improvement in tracking accuracy for a worst-case satellite trajectory.

  7. Adaptive WMMR filters for edge enhancement

    NASA Astrophysics Data System (ADS)

    Zhou, Jun; Longbotham, Harold G.

    1993-05-01

    In this paper, an adaptive WMMR filter is introduced, which adaptively changes its window size to accommodate edge width variations. We prove that for any given one dimensional input signal convergence is to fixed points, which are PICO (piecewise constant), by iterative application of the adaptive WMMR filter. An application of the filters to one-D data (non- PICO) and images of printed circuit boards are then provided. Application to images in general is discussed.

  8. Connector adapter

    NASA Technical Reports Server (NTRS)

    Hacker, Scott C. (Inventor); Dean, Richard J. (Inventor); Burge, Scott W. (Inventor); Dartez, Toby W. (Inventor)

    2007-01-01

    An adapter for installing a connector to a terminal post, wherein the connector is attached to a cable, is presented. In an embodiment, the adapter is comprised of an elongated collet member having a longitudinal axis comprised of a first collet member end, a second collet member end, an outer collet member surface, and an inner collet member surface. The inner collet member surface at the first collet member end is used to engage the connector. The outer collet member surface at the first collet member end is tapered for a predetermined first length at a predetermined taper angle. The collet includes a longitudinal slot that extends along the longitudinal axis initiating at the first collet member end for a predetermined second length. The first collet member end is formed of a predetermined number of sections segregated by a predetermined number of channels and the longitudinal slot.

  9. Adaptive sampler

    DOEpatents

    Watson, Bobby L.; Aeby, Ian

    1982-01-01

    An adaptive data compression device for compressing data having variable frequency content, including a plurality of digital filters for analyzing the content of the data over a plurality of frequency regions, a memory, and a control logic circuit for generating a variable rate memory clock corresponding to the analyzed frequency content of the data in the frequency region and for clocking the data into the memory in response to the variable rate memory clock.

  10. Adaptive sampler

    DOEpatents

    Watson, B.L.; Aeby, I.

    1980-08-26

    An adaptive data compression device for compressing data is described. The device has a frequency content, including a plurality of digital filters for analyzing the content of the data over a plurality of frequency regions, a memory, and a control logic circuit for generating a variable rate memory clock corresponding to the analyzed frequency content of the data in the frequency region and for clocking the data into the memory in response to the variable rate memory clock.

  11. Mitochondrial cytochrome B DNA variation in the high-fecundity atlantic cod: trans-atlantic clines and shallow gene genealogy.

    PubMed Central

    Arnason, Einar

    2004-01-01

    An analysis of sequence variation of 250 bp of the mitochondrial cytochrome b gene of 1278 Atlantic cod Gadus morhua ranging from Newfoundland to the Baltic shows four high-frequency (>8%) haplotypes and a number of rare and singleton haplotypes. Variation is primarily synonymous mutations. Natural selection acting directly on these variants is either absent or very weak. Common haplotypes show regular trans-Atlantic clines in frequencies and each of them reaches its highest frequency in a particular country. A shallow multifurcating constellation gene genealogy implies young age and recent turnover of polymorphism. Haplotypes characterizing populations at opposite ends of the geographic distribution in Newfoundland and the Baltic are mutationally closest together. The haplotypes are young and have risen rapidly in frequency. Observed differentiation among countries is due primarily to clinal variation. Hypotheses of historical isolation and polymorphisms balanced by local selection and gene flow are unlikely. Instead the results are explained by demic selection of mitochondria carried by highly fit females winning reproductive sweepstakes. By inference the Atlantic cod, a very high-fecundity vertebrate, is characterized by a high variance of offspring number and strong natural selection that leads to very low effective to actual population sizes. PMID:15126405

  12. Population extinction and the genetics of adaptation.

    PubMed

    Orr, H Allen; Unckless, Robert L

    2008-08-01

    Theories of adaptation typically ignore the effect of environmental change on population size. But some environmental challenges--challenges to which populations must adapt--may depress absolute fitness below 1, causing populations to decline. Under this scenario, adaptation is a race; beneficial alleles that adapt a population to the new environment must sweep to high frequency before the population becomes extinct. We derive simple, though approximate, solutions to the probability of successful adaptation (population survival) when adaptation involves new mutations, the standing genetic variation, or a mixture of the two. Our results show that adaptation to such environmental challenges can be difficult when relying on new mutations at one or a few loci, and populations will often decline to extinction. PMID:18662122

  13. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula

    PubMed Central

    Barral-Arca, Ruth; Pischedda, Sara; Gómez-Carballa, Alberto; Pastoriza, Ana; Mosquera-Miguel, Ana; López-Soto, Manuel; Martinón-Torres, Federico; Álvarez-Iglesias, Vanesa; Salas, Antonio

    2016-01-01

    The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies. PMID

  14. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

    PubMed

    Barral-Arca, Ruth; Pischedda, Sara; Gómez-Carballa, Alberto; Pastoriza, Ana; Mosquera-Miguel, Ana; López-Soto, Manuel; Martinón-Torres, Federico; Álvarez-Iglesias, Vanesa; Salas, Antonio

    2016-01-01

    The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies. PMID

  15. Adapting agriculture to climate change

    PubMed Central

    Howden, S. Mark; Soussana, Jean-François; Tubiello, Francesco N.; Chhetri, Netra; Dunlop, Michael; Meinke, Holger

    2007-01-01

    The strong trends in climate change already evident, the likelihood of further changes occurring, and the increasing scale of potential climate impacts give urgency to addressing agricultural adaptation more coherently. There are many potential adaptation options available for marginal change of existing agricultural systems, often variations of existing climate risk management. We show that implementation of these options is likely to have substantial benefits under moderate climate change for some cropping systems. However, there are limits to their effectiveness under more severe climate changes. Hence, more systemic changes in resource allocation need to be considered, such as targeted diversification of production systems and livelihoods. We argue that achieving increased adaptation action will necessitate integration of climate change-related issues with other risk factors, such as climate variability and market risk, and with other policy domains, such as sustainable development. Dealing with the many barriers to effective adaptation will require a comprehensive and dynamic policy approach covering a range of scales and issues, for example, from the understanding by farmers of change in risk profiles to the establishment of efficient markets that facilitate response strategies. Science, too, has to adapt. Multidisciplinary problems require multidisciplinary solutions, i.e., a focus on integrated rather than disciplinary science and a strengthening of the interface with decision makers. A crucial component of this approach is the implementation of adaptation assessment frameworks that are relevant, robust, and easily operated by all stakeholders, practitioners, policymakers, and scientists. PMID:18077402

  16. Adaptive Optics for Large Telescopes

    SciTech Connect

    Olivier, S

    2008-06-27

    The use of adaptive optics was originally conceived by astronomers seeking to correct the blurring of images made with large telescopes due to the effects of atmospheric turbulence. The basic idea is to use a device, a wave front corrector, to adjust the phase of light passing through an optical system, based on some measurement of the spatial variation of the phase transverse to the light propagation direction, using a wave front sensor. Although the original concept was intended for application to astronomical imaging, the technique can be more generally applied. For instance, adaptive optics systems have been used for several decades to correct for aberrations in high-power laser systems. At Lawrence Livermore National Laboratory (LLNL), the world's largest laser system, the National Ignition Facility, uses adaptive optics to correct for aberrations in each of the 192 beams, all of which must be precisely focused on a millimeter scale target in order to perform nuclear physics experiments.

  17. Adaptive encoding in the visual pathway.

    PubMed

    Lesica, Nicholas A; Boloori, Alireza S; Stanley, Garrett B

    2003-02-01

    In a natural setting, the mean luminance and contrast of the light within a visual neuron's receptive field are constantly changing as the eyes saccade across complex scenes. Adaptive mechanisms modulate filtering properties of the early visual pathway in response to these variations, allowing the system to maintain differential sensitivity to nonstationary stimuli. An adaptive variant of the reverse correlation technique is used to characterize these changes during single trials. Properties of the adaptive reverse correlation algorithm were investigated via simulation. Analysis of data collected from the mammalian visual system demonstrates the ability to continuously track adaptive changes in the encoding scheme. The adaptive estimation approach provides a framework for characterizing the role of adaptation in natural scene viewing. PMID:12613554

  18. Mitochondrial DNA Variation in Human Radiation and Disease

    PubMed Central

    Wallace, Douglas C.

    2016-01-01

    Environmental adaptation, predisposition to common diseases, and, potentially, speciation may all be linked through the adaptive potential of mitochondrial DNA (mtDNA) alterations of bioenergetics. This Perspective synthesizes evidence that human mtDNA variants may be adaptive or deleterious depending on environmental context and proposes that the accrual of mtDNA variation could contribute to animal speciation via adaptation to marginal environments. PMID:26406369

  19. Limited evidence for adaptive evolution and functional effect of allelic variation at rs702424 in the promoter of the TAS2R16 bitter taste receptor gene in Africa.

    PubMed

    Campbell, Michael C; Ranciaro, Alessia; Zinshteyn, Daniel; Rawlings-Goss, Renata; Hirbo, Jibril; Thompson, Simon; Woldemeskel, Dawit; Froment, Alain; Omar, Sabah A; Bodo, Jean-Marie; Nyambo, Thomas; Belay, Gurja; Drayna, Dennis; Breslin, Paul A S; Tishkoff, Sarah A

    2014-06-01

    Bitter taste perception, mediated by receptors encoded by the TAS2R loci, has important roles in human health and nutrition. Prior studies have demonstrated that nonsynonymous variation at site 516 in the coding exon of TAS2R16, a bitter taste receptor gene on chromosome 7, has been subject to positive selection and is strongly correlated with differences in sensitivity to salicin, a bitter anti-inflammatory compound, in human populations. However, a recent study suggested that the derived G-allele at rs702424 in the TAS2R16 promoter has also been the target of recent selection and may have an additional effect on the levels of salicin bitter taste perception. Here, we examined alleles at rs702424 for signatures of selection using Extended Haplotype Homozygosity (EHH) and FST statistics in diverse populations from West Central, Central and East Africa. We also performed a genotype-phenotype analysis of salicin sensitivity in a subset of 135 individuals from East Africa. Based on our data, we did not find evidence for positive selection at rs702424 in African populations, suggesting that nucleotide position 516 is likely the site under selection at TAS2R16. Moreover, we did not detect a significant association between rs702424 alleles and salicin bitter taste recognition, implying that this site does not contribute to salicin phenotypic variance. Overall, this study of African diversity provides further information regarding the genetic architecture and evolutionary history of a biologically-relevant trait in humans. PMID:24785689

  20. Limited Evidence for Adaptive Evolution and Functional Effect of Allelic Variation at rs702424 in the Promoter of the TAS2R16 Bitter Taste Receptor Gene in Africa

    PubMed Central

    Campbell, Michael C.; Ranciaro, Alessia; Zinshteyn, Daniel; Rawlings-Goss, Renata; Hirbo, Jibril; Thompson, Simon; Woldemeskel, Dawit; Froment, Alain; Omar, Sabah A.; Bodo, Jean-Marie; Nyambo, Thomas; Belay, Gurja; Drayna, Dennis; Breslin, Paul A.S.; Tishkoff, Sarah A.

    2014-01-01

    Bitter taste perception, mediated by receptors encoded by the TAS2R loci, plays important roles in human health and nutrition. Prior studies have demonstrated that nonsynonymous variation at site 516 in the coding exon of TAS2R16, a bitter taste receptor gene on chromosome 7, has been subject to positive selection and is strongly correlated with differences in sensitivity to salicin, a bitter anti-inflammatory compound, in human populations. However, a recent study suggested that the derived G-allele at rs702424 in the TAS2R16 promoter has also been the target of recent selection and may have an additional effect on levels of salicin bitter taste perception. Here, we examined alleles at rs702424 for signatures of selection using Extended Haplotype Homozygosity (EHH) and FST statistics in 44 diverse populations from West Central, Central and East Africa. We also performed a genotype-phenotype analysis of salicin sensitivity in a subset of 135 individuals from East Africa. Based on our data, we did not find evidence for positive selection at rs702424 in African populations, suggesting that site 516 is likely the variant under selection at TAS2R16. Additionally, we did not detect a significant association between rs702424 alleles and salicin bitter taste recognition, implying that this site does not contribute to salicin phenotypic variance. Overall, this study of African diversity provides further information regarding the genetic architecture and evolutionary history of a biologically-relevant trait in humans. PMID:24785689

  1. Molecular evolution and thermal adaptation

    NASA Astrophysics Data System (ADS)

    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

  2. Adaptive control applied to Space Station attitude control system

    NASA Technical Reports Server (NTRS)

    Lam, Quang M.; Chipman, Richard; Hu, Tsay-Hsin G.; Holmes, Eric B.; Sunkel, John

    1992-01-01

    This paper presents an adaptive control approach to enhance the performance of current attitude control system used by the Space Station Freedom. The proposed control law was developed based on the direct adaptive control or model reference adaptive control scheme. Performance comparisons, subject to inertia variation, of the adaptive controller and the fixed-gain linear quadratic regulator currently implemented for the Space Station are conducted. Both the fixed-gain and the adaptive gain controllers are able to maintain the Station stability for inertia variations of up to 35 percent. However, when a 50 percent inertia variation is applied to the Station, only the adaptive controller is able to maintain the Station attitude.

  3. ADAPTATION AND ADAPTABILITY, THE BELLEFAIRE FOLLOWUP STUDY.

    ERIC Educational Resources Information Center

    ALLERHAND, MELVIN E.; AND OTHERS

    A RESEARCH TEAM STUDIED INFLUENCES, ADAPTATION, AND ADAPTABILITY IN 50 POORLY ADAPTING BOYS AT BELLEFAIRE, A REGIONAL CHILD CARE CENTER FOR EMOTIONALLY DISTURBED CHILDREN. THE TEAM ATTEMPTED TO GAUGE THE SUCCESS OF THE RESIDENTIAL TREATMENT CENTER IN TERMS OF THE PSYCHOLOGICAL PATTERNS AND ROLE PERFORMANCES OF THE BOYS DURING INDIVIDUAL CASEWORK…

  4. Biochemical adaptation to ocean acidification.

    PubMed

    Stillman, Jonathon H; Paganini, Adam W

    2015-06-01

    The change in oceanic carbonate chemistry due to increased atmospheric PCO2  has caused pH to decline in marine surface waters, a phenomenon known as ocean acidification (OA). The effects of OA on organisms have been shown to be widespread among diverse taxa from a wide range of habitats. The majority of studies of organismal response to OA are in short-term exposures to future levels of PCO2 . From such studies, much information has been gathered on plastic responses organisms may make in the future that are beneficial or harmful to fitness. Relatively few studies have examined whether organisms can adapt to negative-fitness consequences of plastic responses to OA. We outline major approaches that have been used to study the adaptive potential for organisms to OA, which include comparative studies and experimental evolution. Organisms that inhabit a range of pH environments (e.g. pH gradients at volcanic CO2 seeps or in upwelling zones) have great potential for studies that identify adaptive shifts that have occurred through evolution. Comparative studies have advanced our understanding of adaptation to OA by linking whole-organism responses with cellular mechanisms. Such optimization of function provides a link between genetic variation and adaptive evolution in tuning optimal function of rate-limiting cellular processes in different pH conditions. For example, in experimental evolution studies of organisms with short generation times (e.g. phytoplankton), hundreds of generations of growth under future conditions has resulted in fixed differences in gene expression related to acid-base regulation. However, biochemical mechanisms for adaptive responses to OA have yet to be fully characterized, and are likely to be more complex than simply changes in gene expression or protein modification. Finally, we present a hypothesis regarding an unexplored area for biochemical adaptation to ocean acidification. In this hypothesis, proteins and membranes exposed to the

  5. Adaptive Image Denoising by Mixture Adaptation.

    PubMed

    Luo, Enming; Chan, Stanley H; Nguyen, Truong Q

    2016-10-01

    We propose an adaptive learning procedure to learn patch-based image priors for image denoising. The new algorithm, called the expectation-maximization (EM) adaptation, takes a generic prior learned from a generic external database and adapts it to the noisy image to generate a specific prior. Different from existing methods that combine internal and external statistics in ad hoc ways, the proposed algorithm is rigorously derived from a Bayesian hyper-prior perspective. There are two contributions of this paper. First, we provide full derivation of the EM adaptation algorithm and demonstrate methods to improve the computational complexity. Second, in the absence of the latent clean image, we show how EM adaptation can be modified based on pre-filtering. The experimental results show that the proposed adaptation algorithm yields consistently better denoising results than the one without adaptation and is superior to several state-of-the-art algorithms. PMID:27416593

  6. An adaptive grid with directional control

    NASA Technical Reports Server (NTRS)

    Brackbill, J. U.

    1993-01-01

    An adaptive grid generator for adaptive node movement is here derived by combining a variational formulation of Winslow's (1981) variable-diffusion method with a directional control functional. By applying harmonic-function theory, it becomes possible to define conditions under which there exist unique solutions of the resulting elliptic equations. The results obtained for the grid generator's application to the complex problem posed by the fluid instability-driven magnetic field reconnection demonstrate one-tenth the computational cost of either a Eulerian grid or an adaptive grid without directional control.

  7. Population Genomics of Human Adaptation.

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2013-11-01

    Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 - 100,000 years ago. Movement into new environments, as well as changes in culture and technology including plant and animal domestication, resulted in local adaptation to diverse environments. We summarize statistical approaches for detecting targets of natural selection and for distinguishing the effects of demographic history from natural selection. On a genome-wide scale, immune-related genes appear to be major targets of positive selection. Genes associated with reproduction and fertility also appear to be fast evolving. Additional examples of recent human adaptation include genes associated with lactase persistence, eccrine glands, and response to hypoxia. Lastly, we emphasize the need to supplement scans of selection with functional studies to demonstrate the physiologic impact of candidate loci. PMID:25383060

  8. Population Genomics of Human Adaptation

    PubMed Central

    Lachance, Joseph; Tishkoff, Sarah A.

    2014-01-01

    Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 – 100,000 years ago. Movement into new environments, as well as changes in culture and technology including plant and animal domestication, resulted in local adaptation to diverse environments. We summarize statistical approaches for detecting targets of natural selection and for distinguishing the effects of demographic history from natural selection. On a genome-wide scale, immune-related genes appear to be major targets of positive selection. Genes associated with reproduction and fertility also appear to be fast evolving. Additional examples of recent human adaptation include genes associated with lactase persistence, eccrine glands, and response to hypoxia. Lastly, we emphasize the need to supplement scans of selection with functional studies to demonstrate the physiologic impact of candidate loci. PMID:25383060

  9. HLA variation reveals genetic continuity rather than population group structure in East Asia.

    PubMed

    Di, Da; Sanchez-Mazas, Alicia

    2014-03-01

    Genetic differences between Northeast Asian (NEA) and Southeast Asian (SEA) populations have been observed in numerous studies. At the among-population level, despite a clear north-south differentiation observed for many genetic markers, debates were led between abrupt differences and a continuous pattern. At the within-population level, whether NEA or SEA populations have higher genetic diversity is also highly controversial. In this study, we analyzed a large set of HLA data from East Asia in order to map the genetic variation among and within populations in this continent and to clarify the distribution pattern of HLA lineages and alleles. We observed a genetic differentiation between NEA and SEA populations following a continuous pattern from north to south, and we show a significant and continuous decrease of HLA diversity by the same direction. This continuity is shaped by clinal distributions of many HLA lineages and alleles with increasing or decreasing frequencies along the latitude. These results bring new evidence in favor of the "overlapping model" proposed previously for East Asian peopling history, whereby modern humans migrated eastward from western Eurasia via two independent routes along each side of the Himalayas and, later, overlapped in East Asia across open land areas. Our study strongly suggests that intensive gene flow between NEA and SEA populations occurred and shaped the latitude-related continuous pattern of genetic variation and the peculiar HLA lineage and allele distributions observed in this continent. Probably for a very long period, the exact duration of these events remains to be estimated. PMID:24449274

  10. Adaptive compressive sensing camera

    NASA Astrophysics Data System (ADS)

    Hsu, Charles; Hsu, Ming K.; Cha, Jae; Iwamura, Tomo; Landa, Joseph; Nguyen, Charles; Szu, Harold

    2013-05-01

    We have embedded Adaptive Compressive Sensing (ACS) algorithm on Charge-Coupled-Device (CCD) camera based on the simplest concept that each pixel is a charge bucket, and the charges comes from Einstein photoelectric conversion effect. Applying the manufactory design principle, we only allow altering each working component at a minimum one step. We then simulated what would be such a camera can do for real world persistent surveillance taking into account of diurnal, all weather, and seasonal variations. The data storage has saved immensely, and the order of magnitude of saving is inversely proportional to target angular speed. We did design two new components of CCD camera. Due to the matured CMOS (Complementary metal-oxide-semiconductor) technology, the on-chip Sample and Hold (SAH) circuitry can be designed for a dual Photon Detector (PD) analog circuitry for changedetection that predicts skipping or going forward at a sufficient sampling frame rate. For an admitted frame, there is a purely random sparse matrix [Φ] which is implemented at each bucket pixel level the charge transport bias voltage toward its neighborhood buckets or not, and if not, it goes to the ground drainage. Since the snapshot image is not a video, we could not apply the usual MPEG video compression and Hoffman entropy codec as well as powerful WaveNet Wrapper on sensor level. We shall compare (i) Pre-Processing FFT and a threshold of significant Fourier mode components and inverse FFT to check PSNR; (ii) Post-Processing image recovery will be selectively done by CDT&D adaptive version of linear programming at L1 minimization and L2 similarity. For (ii) we need to determine in new frames selection by SAH circuitry (i) the degree of information (d.o.i) K(t) dictates the purely random linear sparse combination of measurement data a la [Φ]M,N M(t) = K(t) Log N(t).

  11. Geometric constrained variational calculus. III: The second variation (Part II)

    NASA Astrophysics Data System (ADS)

    Massa, Enrico; Luria, Gianvittorio; Pagani, Enrico

    2016-03-01

    The problem of minimality for constrained variational calculus is analyzed within the class of piecewise differentiable extremaloids. A fully covariant representation of the second variation of the action functional based on a family of local gauge transformations of the original Lagrangian is proposed. The necessity of pursuing a local adaptation process, rather than the global one described in [1] is seen to depend on the value of certain scalar attributes of the extremaloid, here called the corners’ strengths. On this basis, both the necessary and the sufficient conditions for minimality are worked out. In the discussion, a crucial role is played by an analysis of the prolongability of the Jacobi fields across the corners. Eventually, in the appendix, an alternative approach to the concept of strength of a corner, more closely related to Pontryagin’s maximum principle, is presented.

  12. Variations of biorhythm composition in healthy people

    NASA Astrophysics Data System (ADS)

    Aptikaeva, O. I.; Gamburtsev, A. G.; Stepanova, S. I.

    2010-12-01

    We have investigated variations in the spectral composition of some physiological characteristics (heart rate, sublingual temperature, potassium renal excretion, and respiratory rate). It has been shown that, in regular social and domestic conditions, the human responses to permanently changing external influences are different and depend on their individual adaptation ability. Some test subjects show a prevalence of the major circadian rhythm in the rhythmic composition of physiological characteristics, which stays almost unchanged under significant variations in external factors; other test subjects are characterized by a rapid change in the rhythmic composition following variations, for example, of solar activity; for a third type of test subject, this change occurs with a significant time delay.

  13. Evolutionary Adaptations to Dietary Changes

    PubMed Central

    Luca, F.; Perry, G.H.; Di Rienzo, A.

    2014-01-01

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  14. Evolutionary adaptations to dietary changes.

    PubMed

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  15. Habituation of visual adaptation

    PubMed Central

    Dong, Xue; Gao, Yi; Lv, Lili; Bao, Min

    2016-01-01

    Our sensory system adjusts its function driven by both shorter-term (e.g. adaptation) and longer-term (e.g. learning) experiences. Most past adaptation literature focuses on short-term adaptation. Only recently researchers have begun to investigate how adaptation changes over a span of days. This question is important, since in real life many environmental changes stretch over multiple days or longer. However, the answer to the question remains largely unclear. Here we addressed this issue by tracking perceptual bias (also known as aftereffect) induced by motion or contrast adaptation across multiple daily adaptation sessions. Aftereffects were measured every day after adaptation, which corresponded to the degree of adaptation on each day. For passively viewed adapters, repeated adaptation attenuated aftereffects. Once adapters were presented with an attentional task, aftereffects could either reduce for easy tasks, or initially show an increase followed by a later decrease for demanding tasks. Quantitative analysis of the decay rates in contrast adaptation showed that repeated exposure of the adapter appeared to be equivalent to adaptation to a weaker stimulus. These results suggest that both attention and a non-attentional habituation-like mechanism jointly determine how adaptation develops across multiple daily sessions. PMID:26739917

  16. Habituation of visual adaptation.

    PubMed

    Dong, Xue; Gao, Yi; Lv, Lili; Bao, Min

    2016-01-01

    Our sensory system adjusts its function driven by both shorter-term (e.g. adaptation) and longer-term (e.g. learning) experiences. Most past adaptation literature focuses on short-term adaptation. Only recently researchers have begun to investigate how adaptation changes over a span of days. This question is important, since in real life many environmental changes stretch over multiple days or longer. However, the answer to the question remains largely unclear. Here we addressed this issue by tracking perceptual bias (also known as aftereffect) induced by motion or contrast adaptation across multiple daily adaptation sessions. Aftereffects were measured every day after adaptation, which corresponded to the degree of adaptation on each day. For passively viewed adapters, repeated adaptation attenuated aftereffects. Once adapters were presented with an attentional task, aftereffects could either reduce for easy tasks, or initially show an increase followed by a later decrease for demanding tasks. Quantitative analysis of the decay rates in contrast adaptation showed that repeated exposure of the adapter appeared to be equivalent to adaptation to a weaker stimulus. These results suggest that both attention and a non-attentional habituation-like mechanism jointly determine how adaptation develops across multiple daily sessions. PMID:26739917

  17. A liquid crystal adaptive lens

    NASA Technical Reports Server (NTRS)

    Kowel, S. T.; Cleverly, D.

    1981-01-01

    Creation of an electronically controlled liquid crystal lens for use as a focusing mechanism in a multi-element lens system or as an adaptive optical element is analyzed. Varying the index of refraction is shown to be equivalent to the shaping of a solid refracting material. Basic characteristics of liquid crystals, essential for the creation of a lens, are reviewed. The required variation of index of refraction is provided by choosing appropriate electrode voltages. The configuration required for any incoming polarization is given and its theoretical performance in terms of modulation transfer function derived.

  18. A local adaptive image descriptor

    NASA Astrophysics Data System (ADS)

    Zahid Ishraque, S. M.; Shoyaib, Mohammad; Abdullah-Al-Wadud, M.; Monirul Hoque, Md; Chae, Oksam

    2013-12-01

    The local binary pattern (LBP) is a robust but computationally simple approach in texture analysis. However, LBP performs poorly in the presence of noise and large illumination variation. Thus, a local adaptive image descriptor termed as LAID is introduced in this proposal. It is a ternary pattern and is able to generate persistent codes to represent microtextures in a given image, especially in noisy conditions. It can also generate stable texture codes if the pixel intensities change abruptly due to the illumination changes. Experimental results also show the superiority of the proposed method over other state-of-the-art methods.

  19. Chromatic adaptation performance of different RGB sensors

    NASA Astrophysics Data System (ADS)

    Susstrunk, Sabine E.; Holm, Jack M.; Finlayson, Graham D.

    2000-12-01

    Chromatic adaptation transforms are used in imaging system to map image appearance to colorimetry under different illumination sources. In this paper, the performance of different chromatic adaptation transforms (CAT) is compared with the performance of transforms based on RGB primaries that have been investigated in relation to standard color spaces for digital still camera characterization and image interchange. The chromatic adaptation transforms studied are von Kries, Bradford, Sharp, and CMCCAT2000. The RGB primaries investigated are ROMM, ITU-R BT.709, and 'prime wavelength' RGB. The chromatic adaptation model used is a von Kries model that linearly scales post-adaptation cone response with illuminant dependent coefficients. The transforms were evaluated using 16 sets of corresponding color dat. The actual and predicted tristimulus values were converted to CIELAB, and three different error prediction metrics, (Delta) ELab, (Delta) ECIE94, and (Delta) ECMC(1:1) were applied to the results. One-tail Student-t tests for matched pairs were calculated to compare if the variations in errors are statistically significant. For the given corresponding color data sets, the traditional chromatic adaptation transforms, Sharp CAT and CMCCAT2000, performed best. However, some transforms based on RGB primaries also exhibit good chromatic adaptation behavior, leading to the conclusion that white-point independent RGB spaces for image encoding can be defined. This conclusion holds only if the linear von Kries model is considered adequate to predict chromatic adaptation behavior.

  20. Genome-environment associations in sorghum landraces predict adaptive traits.

    PubMed

    Lasky, Jesse R; Upadhyaya, Hari D; Ramu, Punna; Deshpande, Santosh; Hash, C Tom; Bonnette, Jason; Juenger, Thomas E; Hyma, Katie; Acharya, Charlotte; Mitchell, Sharon E; Buckler, Edward S; Brenton, Zachary; Kresovich, Stephen; Morris, Geoffrey P

    2015-07-01

    Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation. PMID:26601206

  1. Genome-environment associations in sorghum landraces predict adaptive traits

    PubMed Central

    Lasky, Jesse R.; Upadhyaya, Hari D.; Ramu, Punna; Deshpande, Santosh; Hash, C. Tom; Bonnette, Jason; Juenger, Thomas E.; Hyma, Katie; Acharya, Charlotte; Mitchell, Sharon E.; Buckler, Edward S.; Brenton, Zachary; Kresovich, Stephen; Morris, Geoffrey P.

    2015-01-01

    Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation. PMID:26601206

  2. Atmospheric and adaptive optics

    NASA Astrophysics Data System (ADS)

    Hickson, Paul

    2014-11-01

    Atmospheric optics is the study of optical effects induced by the atmosphere on light propagating from distant sources. Of particular concern to astronomers is atmospheric turbulence, which limits the performance of ground-based telescopes. The past two decades have seen remarkable growth in the capabilities and performance of adaptive optics (AO) systems. These opto-mechanical systems actively compensate for the blurring effect of the Earth's turbulent atmosphere. By sensing, and correcting, wavefront distortion introduced by atmospheric index-of-refraction variations, AO systems can produce images with resolution approaching the diffraction limit of the telescope at near-infrared wavelengths. This review highlights the physical processes and fundamental relations of atmospheric optics that are most relevant to astronomy, and discusses the techniques used to characterize atmospheric turbulence. The fundamentals of AO are then introduced and the many types of advanced AO systems that have been developed are described. The principles of each are outlined, and the performance and limitations are examined. Aspects of photometric and astrometric measurements of AO-corrected images are considered. The paper concludes with a discussion of some of the challenges related to current and future AO systems, particularly those that will equip the next generation of large, ground-based optical and infrared telescopes.

  3. Expressing Adaptation Strategies Using Adaptation Patterns

    ERIC Educational Resources Information Center

    Zemirline, N.; Bourda, Y.; Reynaud, C.

    2012-01-01

    Today, there is a real challenge to enable personalized access to information. Several systems have been proposed to address this challenge including Adaptive Hypermedia Systems (AHSs). However, the specification of adaptation strategies remains a difficult task for creators of such systems. In this paper, we consider the problem of the definition…

  4. Multi-level adaptive finite element methods. 1: Variation problems

    NASA Technical Reports Server (NTRS)

    Brandt, A.

    1979-01-01

    A general numerical strategy for solving partial differential equations and other functional problems by cycling between coarser and finer levels of discretization is described. Optimal discretization schemes are provided together with very fast general solvers. It is described in terms of finite element discretizations of general nonlinear minimization problems. The basic processes (relaxation sweeps, fine-grid-to-coarse-grid transfers of residuals, coarse-to-fine interpolations of corrections) are directly and naturally determined by the objective functional and the sequence of approximation spaces. The natural processes, however, are not always optimal. Concrete examples are given and some new techniques are reviewed. Including the local truncation extrapolation and a multilevel procedure for inexpensively solving chains of many boundary value problems, such as those arising in the solution of time-dependent problems.

  5. Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)

    PubMed Central

    Muir, A P; Biek, R; Thomas, R; Mable, B K

    2014-01-01

    Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. The aim of this study was to assess whether local adaptation occurs in the face of high gene flow and to identify potential environmental selection pressures that drive adaptation. Phenotypic variation in larval traits was quantified in R. temporaria from paired high- and low-altitude sites using three common temperature treatments. Local adaptation was assessed using QST–FST analyses, and quantitative phenotypic divergence was related to environmental parameters using Mantel tests. Although evidence of local adaptation was found for all traits measured, only variation in larval period and growth rate was consistent with adaptation to altitude. Moreover, this was only evident in the three mountains with the highest high-altitude sites. This variation was correlated with mean summer and winter temperatures, suggesting that temperature parameters are potentially strong selective pressures maintaining local adaptation, despite high gene flow. PMID:24330274

  6. Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature.

    PubMed

    Ghalambor, Cameron K; Hoke, Kim L; Ruell, Emily W; Fischer, Eva K; Reznick, David N; Hughes, Kimberly A

    2015-09-17

    Phenotypic plasticity is the capacity for an individual genotype to produce different phenotypes in response to environmental variation. Most traits are plastic, but the degree to which plasticity is adaptive or non-adaptive depends on whether environmentally induced phenotypes are closer or further away from the local optimum. Existing theories make conflicting predictions about whether plasticity constrains or facilitates adaptive evolution. Debate persists because few empirical studies have tested the relationship between initial plasticity and subsequent adaptive evolution in natural populations. Here we show that the direction of plasticity in gene expression is generally opposite to the direction of adaptive evolution. We experimentally transplanted Trinidadian guppies (Poecilia reticulata) adapted to living with cichlid predators to cichlid-free streams, and tested for evolutionary divergence in brain gene expression patterns after three to four generations. We find 135 transcripts that evolved parallel changes in expression within the replicated introduction populations. These changes are in the same direction exhibited in a native cichlid-free population, suggesting rapid adaptive evolution. We find 89% of these transcripts exhibited non-adaptive plastic changes in expression when the source population was reared in the absence of predators, as they are in the opposite direction to the evolved changes. By contrast, the remaining transcripts exhibiting adaptive plasticity show reduced population divergence. Furthermore, the most plastic transcripts in the source population evolved reduced plasticity in the introduction populations, suggesting strong selection against non-adaptive plasticity. These results support models predicting that adaptive plasticity constrains evolution, whereas non-adaptive plasticity potentiates evolution by increasing the strength of directional selection. The role of non-adaptive plasticity in evolution has received relatively

  7. The adaptive evolution of the mammalian mitochondrial genome

    PubMed Central

    da Fonseca, Rute R; Johnson, Warren E; O'Brien, Stephen J; Ramos, Maria João; Antunes, Agostinho

    2008-01-01

    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. PMID:18318906

  8. Epigenetic variation in asexually reproducing organisms.

    PubMed

    Verhoeven, Koen J F; Preite, Veronica

    2014-03-01

    The role that epigenetic inheritance can play in adaptation may differ between sexuals and asexuals because (1) the dynamics of adaptation differ under sexual and asexual reproduction and the opportunities offered by epigenetic inheritance may affect these dynamics differently; and (2) in asexual reproduction epigenetic reprogramming mechanisms that are associated with meiosis can be bypassed, which could promote the buildup of epigenetic variation in asexuals. Here, we evaluate current evidence for an epigenetic contribution to adaptation in asexuals. We argue that two aspects of epigenetic variation should have particular relevance for asexuals, namely epigenetics-mediated phenotypic plasticity within and between generations, and heritable variation via stochastic epimutations. An evaluation of epigenetic reprogramming mechanisms suggests that some, but not all, forms of asexual reproduction enhance the likelihood of stable transmission of epigenetic marks across generations compared to sexual reproduction. However, direct tests of these predicted sexual-asexual differences are virtually lacking. Stable transmission of DNA methylation, transcriptomes, and phenotypes from parent to clonal offspring are demonstrated in various asexual species, and clonal genotypes from natural populations show habitat-specific DNA methylation. We discuss how these initial observations can be extended to demonstrate an epigenetic contribution to adaptation. PMID:24274255

  9. Online adaptation and verification of VMAT

    SciTech Connect

    Crijns, Wouter; Defraene, Gilles; Depuydt, Tom; Haustermans, Karin; Van Herck, Hans; Maes, Frederik; Van den Heuvel, Frank

    2015-07-15

    Purpose: This work presents a method for fast volumetric modulated arc therapy (VMAT) adaptation in response to interfraction anatomical variations. Additionally, plan parameters extracted from the adapted plans are used to verify the quality of these plans. The methods were tested as a prostate class solution and compared to replanning and to their current clinical practice. Methods: The proposed VMAT adaptation is an extension of their previous intensity modulated radiotherapy (IMRT) adaptation. It follows a direct (forward) planning approach: the multileaf collimator (MLC) apertures are corrected in the beam’s eye view (BEV) and the monitor units (MUs) are corrected using point dose calculations. All MLC and MU corrections are driven by the positions of four fiducial points only, without need for a full contour set. Quality assurance (QA) of the adapted plans is performed using plan parameters that can be calculated online and that have a relation to the delivered dose or the plan quality. Five potential parameters are studied for this purpose: the number of MU, the equivalent field size (EqFS), the modulation complexity score (MCS), and the components of the MCS: the aperture area variability (AAV) and the leaf sequence variability (LSV). The full adaptation and its separate steps were evaluated in simulation experiments involving a prostate phantom subjected to various interfraction transformations. The efficacy of the current VMAT adaptation was scored by target mean dose (CTV{sub mean}), conformity (CI{sub 95%}), tumor control probability (TCP), and normal tissue complication probability (NTCP). The impact of the adaptation on the plan parameters (QA) was assessed by comparison with prediction intervals (PI) derived from a statistical model of the typical variation of these parameters in a population of VMAT prostate plans (n = 63). These prediction intervals are the adaptation equivalent of the tolerance tables for couch shifts in the current clinical

  10. Admixture facilitates genetic adaptations to high altitude in Tibet

    PubMed Central

    Jeong, Choongwon; Alkorta-Aranburu, Gorka; Basnyat, Buddha; Neupane, Maniraj; Witonsky, David B.; Pritchard, Jonathan K.; Beall, Cynthia M.; Di Rienzo, Anna

    2015-01-01

    Admixture is recognized as a widespread feature of human populations, renewing interest in the possibility that genetic exchange can facilitate adaptations to new environments. Studies of Tibetans revealed candidates for high-altitude adaptations in the EGLN1 and EPAS1 genes, associated with lower hemoglobin concentration. However, the history of these variants or that of Tibetans remains poorly understood. Here, we analyze genotype data for the Nepalese Sherpa, and find that Tibetans are a mixture of ancestral populations related to the Sherpa and Han Chinese. EGLN1 and EPAS1 genes show a striking enrichment of high-altitude ancestry in the Tibetan genome, indicating that migrants from low altitude acquired adaptive alleles from the highlanders. Accordingly, the Sherpa and Tibetans share adaptive hemoglobin traits. This admixture-mediated adaptation shares important features with adaptive introgression. Therefore, we identify a novel mechanism, beyond selection on new mutations or on standing variation, through which populations can adapt to local environments. PMID:24513612

  11. Adaptive radiations: From field to genomic studies

    PubMed Central

    Hodges, Scott A.; Derieg, Nathan J.

    2009-01-01

    Adaptive radiations were central to Darwin's formation of his theory of natural selection, and today they are still the centerpiece for many studies of adaptation and speciation. Here, we review the advantages of adaptive radiations, especially recent ones, for detecting evolutionary trends and the genetic dissection of adaptive traits. We focus on Aquilegia as a primary example of these advantages and highlight progress in understanding the genetic basis of flower color. Phylogenetic analysis of Aquilegia indicates that flower color transitions proceed by changes in the types of anthocyanin pigments produced or their complete loss. Biochemical, crossing, and gene expression studies have provided a wealth of information about the genetic basis of these transitions in Aquilegia. To obtain both enzymatic and regulatory candidate genes for the entire flavonoid pathway, which produces anthocyanins, we used a combination of sequence searches of the Aquilegia Gene Index, phylogenetic analyses, and the isolation of novel sequences by using degenerate PCR and RACE. In total we identified 34 genes that are likely involved in the flavonoid pathway. A number of these genes appear to be single copy in Aquilegia and thus variation in their expression may have been key for floral color evolution. Future studies will be able to use these sequences along with next-generation sequencing technologies to follow expression and sequence variation at the population level. The genetic dissection of other adaptive traits in Aquilegia should also be possible soon as genomic resources such as whole-genome sequencing become available. PMID:19528644

  12. Adaptive radiations: from field to genomic studies.

    PubMed

    Hodges, Scott A; Derieg, Nathan J

    2009-06-16

    Adaptive radiations were central to Darwin's formation of his theory of natural selection, and today they are still the centerpiece for many studies of adaptation and speciation. Here, we review the advantages of adaptive radiations, especially recent ones, for detecting evolutionary trends and the genetic dissection of adaptive traits. We focus on Aquilegia as a primary example of these advantages and highlight progress in understanding the genetic basis of flower color. Phylogenetic analysis of Aquilegia indicates that flower color transitions proceed by changes in the types of anthocyanin pigments produced or their complete loss. Biochemical, crossing, and gene expression studies have provided a wealth of information about the genetic basis of these transitions in Aquilegia. To obtain both enzymatic and regulatory candidate genes for the entire flavonoid pathway, which produces anthocyanins, we used a combination of sequence searches of the Aquilegia Gene Index, phylogenetic analyses, and the isolation of novel sequences by using degenerate PCR and RACE. In total we identified 34 genes that are likely involved in the flavonoid pathway. A number of these genes appear to be single copy in Aquilegia and thus variation in their expression may have been key for floral color evolution. Future studies will be able to use these sequences along with next-generation sequencing technologies to follow expression and sequence variation at the population level. The genetic dissection of other adaptive traits in Aquilegia should also be possible soon as genomic resources such as whole-genome sequencing become available. PMID:19528644

  13. Adaptation potential of European agriculture in response to climate change

    NASA Astrophysics Data System (ADS)

    Moore, Frances C.; Lobell, David B.

    2014-07-01

    Projecting the impacts of climate change on agriculture requires knowing or assuming how farmers will adapt. However, empirical estimates of the effectiveness of this private adaptation are scarce and the sensitivity of impact assessments to adaptation assumptions is not well understood. Here we assess the potential effectiveness of private farmer adaptation in Europe by jointly estimating both short-run and long-run response functions using time-series and cross-sectional variation in subnational yield and profit data. The difference between the impacts of climate change projected using the short-run (limited adaptation) and long-run (substantial adaptation) response curves can be interpreted as the private adaptation potential. We find high adaptation potential for maize to future warming but large negative effects and only limited adaptation potential for wheat and barley. Overall, agricultural profits could increase slightly under climate change if farmers adapt but could decrease in many areas if there is no adaptation. Decomposing the variance in 2040 projected yields and farm profits using an ensemble of 13 climate model runs, we find that the rate at which farmers will adapt to rising temperatures is an important source of uncertainty.

  14. Decentralized digital adaptive control of robot motion

    NASA Technical Reports Server (NTRS)

    Tarokh, M.

    1990-01-01

    A decentralized model reference adaptive scheme is developed for digital control of robot manipulators. The adaptation laws are derived using hyperstability theory, which guarantees asymptotic trajectory tracking despite gross robot parameter variations. The control scheme has a decentralized structure in the sense that each local controller receives only its joint angle measurement to produce its joint torque. The independent joint controllers have simple structures and can be programmed using a very simple and computationally fast algorithm. As a result, the scheme is suitable for real-time motion control.

  15. Organizational Adaptation and Higher Education.

    ERIC Educational Resources Information Center

    Cameron, Kim S.

    1984-01-01

    Organizational adaptation and types of adaptation needed in academe in the future are reviewed and major conceptual approaches to organizational adaptation are presented. The probable environment that institutions will face in the future that will require adaptation is discussed. (MLW)

  16. Origins of adaptive immunity.

    PubMed

    Liongue, Clifford; John, Liza B; Ward, Alister

    2011-01-01

    Adaptive immunity, involving distinctive antibody- and cell-mediated responses to specific antigens based on "memory" of previous exposure, is a hallmark of higher vertebrates. It has been argued that adaptive immunity arose rapidly, as articulated in the "big bang theory" surrounding its origins, which stresses the importance of coincident whole-genome duplications. Through a close examination of the key molecules and molecular processes underpinning adaptive immunity, this review suggests a less-extreme model, in which adaptive immunity emerged as part of longer evolutionary journey. Clearly, whole-genome duplications provided additional raw genetic materials that were vital to the emergence of adaptive immunity, but a variety of other genetic events were also required to generate some of the key molecules, whereas others were preexisting and simply co-opted into adaptive immunity. PMID:21395512

  17. Parallel Anisotropic Tetrahedral Adaptation

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Darmofal, David L.

    2008-01-01

    An adaptive method that robustly produces high aspect ratio tetrahedra to a general 3D metric specification without introducing hybrid semi-structured regions is presented. The elemental operators and higher-level logic is described with their respective domain-decomposed parallelizations. An anisotropic tetrahedral grid adaptation scheme is demonstrated for 1000-1 stretching for a simple cube geometry. This form of adaptation is applicable to more complex domain boundaries via a cut-cell approach as demonstrated by a parallel 3D supersonic simulation of a complex fighter aircraft. To avoid the assumptions and approximations required to form a metric to specify adaptation, an approach is introduced that directly evaluates interpolation error. The grid is adapted to reduce and equidistribute this interpolation error calculation without the use of an intervening anisotropic metric. Direct interpolation error adaptation is illustrated for 1D and 3D domains.

  18. Gravitational adaptation of animals

    NASA Technical Reports Server (NTRS)

    Smith, A. H.; Burton, R. R.

    1982-01-01

    The effect of gravitational adaptation is studied in a group of five Leghorn cocks which had become physiologically adapted to 2 G after 162 days of centrifugation. After this period of adaptation, they are periodically exposed to a 2 G field, accompanied by five previously unexposed hatch-mates, and the degree of retained acceleration adaptation is estimated from the decrease in lymphocyte frequency after 24 hr at 2 G. Results show that the previously adapted birds exhibit an 84% greater lymphopenia than the unexposed birds, and that the lymphocyte frequency does not decrease to a level below that found at the end of 162 days at 2 G. In addition, the capacity for adaptation to chronic acceleration is found to be highly heritable. An acceleration tolerant strain of birds shows lesser mortality during chronic acceleration, particularly in intermediate fields, although the result of acceleration selection is largely quantitative (a greater number of survivors) rather than qualitative (behavioral or physiological changes).

  19. Technology transfer for adaptation

    NASA Astrophysics Data System (ADS)

    Biagini, Bonizella; Kuhl, Laura; Gallagher, Kelly Sims; Ortiz, Claudia

    2014-09-01

    Technology alone will not be able to solve adaptation challenges, but it is likely to play an important role. As a result of the role of technology in adaptation and the importance of international collaboration for climate change, technology transfer for adaptation is a critical but understudied issue. Through an analysis of Global Environment Facility-managed adaptation projects, we find there is significantly more technology transfer occurring in adaptation projects than might be expected given the pessimistic rhetoric surrounding technology transfer for adaptation. Most projects focused on demonstration and early deployment/niche formation for existing technologies rather than earlier stages of innovation, which is understandable considering the pilot nature of the projects. Key challenges for the transfer process, including technology selection and appropriateness under climate change, markets and access to technology, and diffusion strategies are discussed in more detail.

  20. Adaptation as organism design

    PubMed Central

    Gardner, Andy

    2009-01-01

    The problem of adaptation is to explain the apparent design of organisms. Darwin solved this problem with the theory of natural selection. However, population geneticists, whose responsibility it is to formalize evolutionary theory, have long neglected the link between natural selection and organismal design. Here, I review the major historical developments in theory of organismal adaptation, clarifying what adaptation is and what it is not, and I point out future avenues for research. PMID:19793739

  1. Phase Adaptation and Correction by Adaptive Optics

    NASA Astrophysics Data System (ADS)

    Tiziani, Hans J.

    2010-04-01

    Adaptive optical elements and systems for imaging or laser beam propagation are used for some time in particular in astronomy, where the image quality is degraded by atmospheric turbulence. In astronomical telescopes a deformable mirror is frequently used to compensate wavefront-errors due to deformations of the large mirror, vibrations as well as turbulence and hence to increase the image quality. In the last few years interesting elements like Spatial Light Modulators, SLM's, such as photorefractive crystals, liquid crystals and micro mirrors and membrane mirrors were introduced. The development of liquid crystals and micro mirrors was driven by data projectors as consumer products. They contain typically a matrix of individually addressable pixels of liquid crystals and flip mirrors respectively or more recently piston mirrors for special applications. Pixel sizes are in the order of a few microns and therefore also appropriate as active diffractive elements in digital holography or miniature masks. Although liquid crystals are mainly optimized for intensity modulation; they can be used for phase modulation. Adaptive optics is a technology for beam shaping and wavefront adaptation. The application of spatial light modulators for wavefront adaptation and correction and defect analysis as well as sensing will be discussed. Dynamic digital holograms are generated with liquid crystal devices (LCD) and used for wavefront correction as well as for beam shaping and phase manipulation, for instance. Furthermore, adaptive optics is very useful to extend the measuring range of wavefront sensors and for the wavefront adaptation in order to measure and compare the shape of high precision aspherical surfaces.

  2. Limits to adaptation along environmental gradients.

    PubMed

    Polechová, Jitka; Barton, Nicholas H

    2015-05-19

    Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible. PMID:25941385

  3. Human adaptation to smog

    SciTech Connect

    Evans, G.W. Jacobs, S.V.; Frager, N.B.

    1982-10-01

    This study examined the health effects of human adaptation to photochemical smog. A group of recent arrivals to the Los Angeles air basin were compared to long-term residents of the basin. Evidence for adaptation included greater irritation and respiratory problems among the recent arrivals and desensitization among the long-term residents in their judgments of the severity of the smog problem to their health. There was no evidence for biochemical adaptation as measured by hemoglobin response to oxidant challenge. The results were discussed in terms of psychological adaption to chronic environmental stressors.

  4. Adaptive parallel logic networks

    NASA Technical Reports Server (NTRS)

    Martinez, Tony R.; Vidal, Jacques J.

    1988-01-01

    Adaptive, self-organizing concurrent systems (ASOCS) that combine self-organization with massive parallelism for such applications as adaptive logic devices, robotics, process control, and system malfunction management, are presently discussed. In ASOCS, an adaptive network composed of many simple computing elements operating in combinational and asynchronous fashion is used and problems are specified by presenting if-then rules to the system in the form of Boolean conjunctions. During data processing, which is a different operational phase from adaptation, the network acts as a parallel hardware circuit.

  5. Quantifying the Adaptive Cycle

    PubMed Central

    Angeler, David G.; Allen, Craig R.; Garmestani, Ahjond S.; Gunderson, Lance H.; Hjerne, Olle; Winder, Monika

    2015-01-01

    The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems. PMID:26716453

  6. Decentralized adaptive control

    NASA Technical Reports Server (NTRS)

    Oh, B. J.; Jamshidi, M.; Seraji, H.

    1988-01-01

    A decentralized adaptive control is proposed to stabilize and track the nonlinear, interconnected subsystems with unknown parameters. The adaptation of the controller gain is derived by using model reference adaptive control theory based on Lyapunov's direct method. The adaptive gains consist of sigma, proportional, and integral combination of the measured and reference values of the corresponding subsystem. The proposed control is applied to the joint control of a two-link robot manipulator, and the performance in computer simulation corresponds with what is expected in theoretical development.

  7. Structured adaptive grid generation using algebraic methods

    NASA Technical Reports Server (NTRS)

    Yang, Jiann-Cherng; Soni, Bharat K.; Roger, R. P.; Chan, Stephen C.

    1993-01-01

    The accuracy of the numerical algorithm depends not only on the formal order of approximation but also on the distribution of grid points in the computational domain. Grid adaptation is a procedure which allows optimal grid redistribution as the solution progresses. It offers the prospect of accurate flow field simulations without the use of an excessively timely, computationally expensive, grid. Grid adaptive schemes are divided into two basic categories: differential and algebraic. The differential method is based on a variational approach where a function which contains a measure of grid smoothness, orthogonality and volume variation is minimized by using a variational principle. This approach provided a solid mathematical basis for the adaptive method, but the Euler-Lagrange equations must be solved in addition to the original governing equations. On the other hand, the algebraic method requires much less computational effort, but the grid may not be smooth. The algebraic techniques are based on devising an algorithm where the grid movement is governed by estimates of the local error in the numerical solution. This is achieved by requiring the points in the large error regions to attract other points and points in the low error region to repel other points. The development of a fast, efficient, and robust algebraic adaptive algorithm for structured flow simulation applications is presented. This development is accomplished in a three step process. The first step is to define an adaptive weighting mesh (distribution mesh) on the basis of the equidistribution law applied to the flow field solution. The second, and probably the most crucial step, is to redistribute grid points in the computational domain according to the aforementioned weighting mesh. The third and the last step is to reevaluate the flow property by an appropriate search/interpolate scheme at the new grid locations. The adaptive weighting mesh provides the information on the desired concentration

  8. Adaptive Mesh Refinement for Microelectronic Device Design

    NASA Technical Reports Server (NTRS)

    Cwik, Tom; Lou, John; Norton, Charles

    1999-01-01

    Finite element and finite volume methods are used in a variety of design simulations when it is necessary to compute fields throughout regions that contain varying materials or geometry. Convergence of the simulation can be assessed by uniformly increasing the mesh density until an observable quantity stabilizes. Depending on the electrical size of the problem, uniform refinement of the mesh may be computationally infeasible due to memory limitations. Similarly, depending on the geometric complexity of the object being modeled, uniform refinement can be inefficient since regions that do not need refinement add to the computational expense. In either case, convergence to the correct (measured) solution is not guaranteed. Adaptive mesh refinement methods attempt to selectively refine the region of the mesh that is estimated to contain proportionally higher solution errors. The refinement may be obtained by decreasing the element size (h-refinement), by increasing the order of the element (p-refinement) or by a combination of the two (h-p refinement). A successful adaptive strategy refines the mesh to produce an accurate solution measured against the correct fields without undue computational expense. This is accomplished by the use of a) reliable a posteriori error estimates, b) hierarchal elements, and c) automatic adaptive mesh generation. Adaptive methods are also useful when problems with multi-scale field variations are encountered. These occur in active electronic devices that have thin doped layers and also when mixed physics is used in the calculation. The mesh needs to be fine at and near the thin layer to capture rapid field or charge variations, but can coarsen away from these layers where field variations smoothen and charge densities are uniform. This poster will present an adaptive mesh refinement package that runs on parallel computers and is applied to specific microelectronic device simulations. Passive sensors that operate in the infrared portion of

  9. Applying Adaptive Variables in Computerised Adaptive Testing

    ERIC Educational Resources Information Center

    Triantafillou, Evangelos; Georgiadou, Elissavet; Economides, Anastasios A.

    2007-01-01

    Current research in computerised adaptive testing (CAT) focuses on applications, in small and large scale, that address self assessment, training, employment, teacher professional development for schools, industry, military, assessment of non-cognitive skills, etc. Dynamic item generation tools and automated scoring of complex, constructed…

  10. Physiologic adaptation to space - Space adaptation syndrome

    NASA Technical Reports Server (NTRS)

    Vanderploeg, J. M.

    1985-01-01

    The adaptive changes of the neurovestibular system to microgravity, which result in space motion sickness (SMS), are studied. A list of symptoms, which range from vomiting to drowsiness, is provided. The two patterns of symptom development, rapid and gradual, and the duration of the symptoms are described. The concept of sensory conflict and rearrangements to explain SMS is being investigated.

  11. Protandry, sexual size dimorphism, and adaptive growth.

    PubMed

    Morbey, Yolanda E

    2013-12-21

    Adaptive growth refers to the strategic adjustment of growth rate by individuals to maximize some component of fitness. The concept of adaptive growth proliferated in the 1990s, in part due to an influential theoretical paper by Peter Abrams and colleagues. In their 1996 paper, Abrams et al. explored the effects of time stress on optimal growth rate, development time, and adult size in seasonal organisms. In this review, I explore how the concept of adaptive growth informs our understanding of protandry (the earlier arrival of males to sites of reproduction than females) and sexual size dimorphism in seasonal organisms. I conclude that growth rate variation is an important mechanism that helps to conserve optimal levels of protandry and sexual size dimorphism in changing environments. PMID:23688825

  12. Intraspecific variation in social organization by genetic variation, developmental plasticity, social flexibility or entirely extrinsic factors

    PubMed Central

    Schradin, Carsten

    2013-01-01

    Previously, it was widely believed that each species has a specific social organization, but we know now that many species show intraspecific variation in their social organization. Four different processes can lead to intraspecific variation in social organization: (i) genetic variation between individuals owing to local adaptation (between populations) or evolutionarily stable strategies within populations; (ii) developmental plasticity evolved in long-term (more than one generation) unpredictable and short-term (one generation) predictable environments, which is mediated by organizational physiological effects during early ontogeny; (iii) social flexibility evolved in highly unpredictable environments, which is mediated by activational physiological effects in adults; (iv) entirely extrinsic factors such as the death of a dominant breeder. Variation in social behaviour occurs between individuals in the case of genetic variation and developmental plasticity, but within individuals in the case of social flexibility. It is important to study intraspecific variation in social organization to understand the social systems of species because it reveals the mechanisms by which species can adapt to changing environments, offers a useful tool to study the ultimate and proximate causes of sociality, and is an interesting phenomenon by itself that needs scientific explanation. PMID:23569294

  13. Adaptive learning based heartbeat classification.

    PubMed

    Srinivas, M; Basil, Tony; Mohan, C Krishna

    2015-01-01

    Cardiovascular diseases (CVD) are a leading cause of unnecessary hospital admissions as well as fatalities placing an immense burden on the healthcare industry. A process to provide timely intervention can reduce the morbidity rate as well as control rising costs. Patients with cardiovascular diseases require quick intervention. Towards that end, automated detection of abnormal heartbeats captured by electronic cardiogram (ECG) signals is vital. While cardiologists can identify different heartbeat morphologies quite accurately among different patients, the manual evaluation is tedious and time consuming. In this chapter, we propose new features from the time and frequency domains and furthermore, feature normalization techniques to reduce inter-patient and intra-patient variations in heartbeat cycles. Our results using the adaptive learning based classifier emulate those reported in existing literature and in most cases deliver improved performance, while eliminating the need for labeling of signals by domain experts. PMID:26484555

  14. Parallel genotypic adaptation: when evolution repeats itself

    PubMed Central

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

    2008-01-01

    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 literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together. PMID:15881688

  15. Retinal Imaging: Adaptive Optics

    NASA Astrophysics Data System (ADS)

    Goncharov, A. S.; Iroshnikov, N. G.; Larichev, Andrey V.

    This chapter describes several factors influencing the performance of ophthalmic diagnostic systems with adaptive optics compensation of human eye aberration. Particular attention is paid to speckle modulation, temporal behavior of aberrations, and anisoplanatic effects. The implementation of a fundus camera with adaptive optics is considered.

  16. Uncertainty in adaptive capacity

    NASA Astrophysics Data System (ADS)

    Adger, W. Neil; Vincent, Katharine

    2005-03-01

    The capacity to adapt is a critical element of the process of adaptation: it is the vector of resources that represent the asset base from which adaptation actions can be made. Adaptive capacity can in theory be identified and measured at various scales, from the individual to the nation. The assessment of uncertainty within such measures comes from the contested knowledge domain and theories surrounding the nature of the determinants of adaptive capacity and the human action of adaptation. While generic adaptive capacity at the national level, for example, is often postulated as being dependent on health, governance and political rights, and literacy, and economic well-being, the determinants of these variables at national levels are not widely understood. We outline the nature of this uncertainty for the major elements of adaptive capacity and illustrate these issues with the example of a social vulnerability index for countries in Africa. To cite this article: W.N. Adger, K. Vincent, C. R. Geoscience 337 (2005).

  17. Water Resource Adaptation Program

    EPA Science Inventory

    The Water Resource Adaptation Program (WRAP) contributes to the U.S. Environmental Protection Agency’s (U.S. EPA) efforts to provide water resource managers and decision makers with the tools needed to adapt water resources to demographic and economic development, and future clim...

  18. Adaptive Sampling Proxy Application

    2012-10-22

    ASPA is an implementation of an adaptive sampling algorithm [1-3], which is used to reduce the computational expense of computer simulations that couple disparate physical scales. The purpose of ASPA is to encapsulate the algorithms required for adaptive sampling independently from any specific application, so that alternative algorithms and programming models for exascale computers can be investigated more easily.

  19. Adaptive Wavelet Transforms

    SciTech Connect

    Szu, H.; Hsu, C.

    1996-12-31

    Human sensors systems (HSS) may be approximately described as an adaptive or self-learning version of the Wavelet Transforms (WT) that are capable to learn from several input-output associative pairs of suitable transform mother wavelets. Such an Adaptive WT (AWT) is a redundant combination of mother wavelets to either represent or classify inputs.

  20. Robust adaptive transient damping in power systems

    SciTech Connect

    Pierre, D.A.; Sadighi, I.; Trudnowski, D.J.; Smith, J.R.; Nehrir, M.H. . Dept. of Electrical Engineering)

    1992-09-01

    This Volume 1 of the final report on RP2665-1 contains two parts. part 1 consists of the following: (1) a literature review of real-time parameter identification algorithms which may be used in self-tuning adaptive control; (2) a description of mathematical discrete-time models that are linear in the parameters and that are useful for self-tuning adaptive control; (3) detailed descriptions of several variations of recursive-least-squares algorithms (RLS algorithms) and a unified representation of some of these algorithms; (4) a new variation of RLS called Corrector Least Squares (CLS); (5) a set of practical issues that need to be addressed in the implementation of RLS-based algorithms; (6) a set of simulation examples that illustrate properties of the identification methods; and (7) appendices With FORTRAN listings of several identification codes. Part 2 of this volume addresses the problem of damping electromechanical oscillations in power systems using advanced control theory. Two control strategies are developed. Controllers are then applied to a power system as power system stabilizer (PSS) units. The primary strategy is a decentralized indirect adaptive control scheme where multiple self-tuning adaptive controllers are coordinated. This adaptive scheme is presented in a general format and the stabilizing properties are demonstrated using examples. Both the adaptive and the conventional strategies are applied to a 17-machine computer-simulated power system. PSS units are applied to four generators in the system. Detailed simulation results are presented that show the feasibility and properties of both control schemes. FORTRAN codes for the control simulations are given in appendices of Part 2, as also are FORTRAN codes for the Prony identification method.

  1. Adaptation is automatic.

    PubMed

    Samuel, A G; Kat, D

    1998-04-01

    Two experiments were used to test whether selective adaptation for speech occurs automatically or instead requires attentional resources. A control condition demonstrated the usual large identification shifts caused by repeatedly presenting an adapting sound (/wa/, with listeners identifying members of a /ba/-/wa/ test series). Two types of distractor tasks were used: (1) Subjects did a rapid series of arithmetic problems during the adaptation periods (Experiments 1 and 2), or (2) they made a series of rhyming judgments, requiring phonetic coding (Experiment 2). A control experiment (Experiment 3) demonstrated that these tasks normally impose a heavy attentional cost on phonetic processing. Despite this, for both experimental conditions, the observed adaptation effect was just as large as in the control condition. This result indicates that adaptation is automatic, operating at an early, preattentive level. The implications of these results for current models of speech perception are discussed. PMID:9599999

  2. A RE-EXAMINATION OF VARIATION ASSOCIATED WITH ENVIRONMENTALLY STRESSED ORGANISMS

    EPA Science Inventory

    Variation is an essential feature of biological systems. Populations adapt to dynamic environments, in part, because of this variation. In this review, we re-examine phenotypic variation, especially in organisms living in polluted environments. A recent goal of ecotoxicology is t...

  3. Adaptive capture of expert behavior

    SciTech Connect

    Jones, R.D.; Barrett, C.L.; Hand, U.; Gordon, R.C.

    1994-08-01

    The authors smoothed and captured a set of expert rules with adaptive networks. The motivation for doing this is discussed. (1) Smoothing leads to stabler control actions. (2) For some sets of rules, the evaluation of the rules can be sped up. This is important in large-scale simulations where many intelligent elements are present. (3) Variability of the intelligent elements can be achieved by adjusting the weights in an adaptive network. (4) After capture has occurred, the weights can be adjusted based on performance criteria. The authors thus have the capability of learning a new set of rules that lead to better performance. The set of rules the authors chose to capture were based on a set of threat determining rules for tank commanders. The approach in this paper: (1) They smoothed the rules. The rule set was converted into a simple set of arithmetic statements. Continuous, non-binary inputs, are now permitted. (2) An operational measure of capturability was developed. (3) They chose four candidate networks for the rule set capture: (a) multi-linear network, (b) adaptive partial least squares, (c) connectionist normalized local spline (CNLS) network, and (d) CNLS net with a PLS preprocessor. These networks were able to capture the rule set to within a few percent. For the simple tank rule set, the multi-linear network performed the best. When the rules were modified to include more nonlinear behavior, CNLS net performed better than the other three nets which made linear assumptions. (4) The networks were tested for robustness to input noise. Noise levels of plus or minus 10% had no real effect on the network performance. Noise levels in the plus or minus 30% range degraded performance by a factor of two. Some performance enhancement occurred when the networks were trained with noisy data. (5) The scaling of the evaluation time was calculated. (6) Human variation can be mimicked in all the networks by perturbing the weights.

  4. Jovimagnetic secular variation

    NASA Technical Reports Server (NTRS)

    Connerney, J. E. P.; Acuna, M. H.

    1982-01-01

    Long term variations of a planetary magnetic field are one of the few observables available in the study of planetary interiors and dynamo theory. While variations of the geomagnetic field were accessible to direct measurement for centuries, knowledge of the secular variations of other planetary dynamos is limited. New limits on Jovimagnetic secular variations were found by comparison of a Jovian internal field model obtained from the Voyager 1 magnetic field observations at epoch 1979.2 with the epoch 1974.9 Pioneer 11 O4 model. No significant secular variation of either the magnitude or position of the Jovidipole is found for the years 1974.9 through 1979.2, although a small Earth-like variation cannot be ruled out.

  5. Morphological variation, advertisement call, and tadpoles of Bokermannohyla nanuzae (Bokermann, 1973), and taxonomic status of B. feioi (Napoli & Caramaschi, 2004) (Anura, Hylidae, Cophomantini).

    PubMed

    Walker, Marina; Lourenço, Ana Carolina Calijorne; Pimenta, Bruno V S; Nascimento, Luciana Barreto

    2015-01-01

    Bokermannohyla nanuzae (Bokermann & Sazima 1973) and B. feioi (Napoli & Caramaschi 2004) belong to the B. cir-cumdata species group. The type locality of the former is Serra do Cipó, Espinhaço mountain range, and of the latter is Parque Estadual do Ibitipoca, Mantiqueira mountain range, both in Minas Gerais State, Brazil. Differences on dorsal draw-ing pattern of adults, oral disc morphology of tadpoles, and temporal properties of calls were proposed to distinguish these two species. However, several specimens found between the two type localities remain unidentified because diagnostic characters and states occur in all of these populations. Thus, in order to assess these characters variations, we performed an analysis of the morphology and morphometry of adults, vocalization, and morphology of tadpoles. Specimens were divided into three operational taxonomic units (OTUs): B. nanuzae (Serra do Cipó and northwards, Espinhaço mountain range), B. cf. nanuzae (Quadrilátero Ferrífero, Espinhaço mountain range, south of Serra do Cipó), and B. feioi (Serra do Ibitipoca, Mantiqueira mountain range). Drawing patterns of the dorsum and limbs show clinal variation and the three units are morphometrically very similar. Temporal and spectral properties of calls overlap in these three units. The diagnostic differences originally proposed for tadpoles are intrapopulational variations and occur in specimens from all of the locations analyzed. We found that these three units are morphologically indistinguishable. Therefore, we designate Bok-ermannohyla feioi (Napoli & Caramaschi 2004) as a junior synonym of Bokermannohyla nanuzae (Bokermann & Sazima 1973), extending its geographical distribution to the Mantiqueira mountain range. PMID:25947466

  6. Heterogeneous treatment in the variational nodal method

    SciTech Connect

    Fanning, T.H.; Palmiotti, G.

    1995-06-01

    The variational nodal transport method is reduced to its diffusion form and generalized for the treatment of heterogeneous nodes while maintaining nodal balances. Adapting variational methods to heterogeneous nodes requires the ability to integrate over a node with discontinuous cross sections. In this work, integrals are evaluated using composite gaussian quadrature rules, which permit accurate integration while minimizing computing time. Allowing structure within a nodal solution scheme avoids some of the necessity of cross section homogenization, and more accurately defines the intra-nodal flux shape. Ideally, any desired heterogeneity can be constructed within the node; but in reality, the finite set of basis functions limits the practical resolution to which fine detail can be defined within the node. Preliminary comparison tests show that the heterogeneous variational nodal method provides satisfactory results even if some improvements are needed for very difficult, configurations.

  7. Dynamical Adaptation in Photoreceptors

    PubMed Central

    Clark, Damon A.; Benichou, Raphael; Meister, Markus; Azeredo da Silveira, Rava

    2013-01-01

    Adaptation is at the heart of sensation and nowhere is it more salient than in early visual processing. Light adaptation in photoreceptors is doubly dynamical: it depends upon the temporal structure of the input and it affects the temporal structure of the response. We introduce a non-linear dynamical adaptation model of photoreceptors. It is simple enough that it can be solved exactly and simulated with ease; analytical and numerical approaches combined provide both intuition on the behavior of dynamical adaptation and quantitative results to be compared with data. Yet the model is rich enough to capture intricate phenomenology. First, we show that it reproduces the known phenomenology of light response and short-term adaptation. Second, we present new recordings and demonstrate that the model reproduces cone response with great precision. Third, we derive a number of predictions on the response of photoreceptors to sophisticated stimuli such as periodic inputs, various forms of flickering inputs, and natural inputs. In particular, we demonstrate that photoreceptors undergo rapid adaptation of response gain and time scale, over ∼ 300 ms—i. e., over the time scale of the response itself—and we confirm this prediction with data. For natural inputs, this fast adaptation can modulate the response gain more than tenfold and is hence physiologically relevant. PMID:24244119

  8. A new approach to adaptive control of manipulators

    NASA Technical Reports Server (NTRS)

    Seraji, H.

    1987-01-01

    An approach in which the manipulator inverse is used as a feedforward controller is employed in the adaptive control of manipulators in order to achieve trajectory tracking by the joint angles. The desired trajectory is applied as an input to the feedforward controller, and the controller output is used as the driving torque for the manipulator. An adaptive algorithm obtained from MRAC theory is used to update the controller gains to cope with variations in the manipulator inverse due to changes of the operating point. An adaptive feedback controller and an auxiliary signal enhance closed-loop stability and achieve faster adaptation. Simulation results demonstrate the effectiveness of the proposed control scheme for different reference trajectories, and despite large variations in the payload.

  9. Adaptive network countermeasures.

    SciTech Connect

    McClelland-Bane, Randy; Van Randwyk, Jamie A.; Carathimas, Anthony G.; Thomas, Eric D.

    2003-10-01

    This report describes the results of a two-year LDRD funded by the Differentiating Technologies investment area. The project investigated the use of countermeasures in protecting computer networks as well as how current countermeasures could be changed in order to adapt with both evolving networks and evolving attackers. The work involved collaboration between Sandia employees and students in the Sandia - California Center for Cyber Defenders (CCD) program. We include an explanation of the need for adaptive countermeasures, a description of the architecture we designed to provide adaptive countermeasures, and evaluations of the system.

  10. [Adaptive optics for ophthalmology].

    PubMed

    Saleh, M

    2016-04-01

    Adaptive optics is a technology enhancing the visual performance of an optical system by correcting its optical aberrations. Adaptive optics have already enabled several breakthroughs in the field of visual sciences, such as improvement of visual acuity in normal and diseased eyes beyond physiologic limits, and the correction of presbyopia. Adaptive optics technology also provides high-resolution, in vivo imaging of the retina that may eventually help to detect the onset of retinal conditions at an early stage and provide better assessment of treatment efficacy. PMID:27019970

  11. Climatic selection on genes and traits after a 100 year-old invasion: a critical look at the temperate-tropical clines in Drosophila melanogaster from eastern Australia.

    PubMed

    Hoffmann, Ary A; Weeks, Andrew R

    2007-02-01

    Drosophila melanogaster invaded Australia around 100 years ago, most likely through a northern invasion. The wide range of climatic conditions in eastern Australia across which D. melanogaster is now found provides an opportunity for researchers to identify traits and genes that are associated with climatic adaptation. Allozyme studies indicate clinal patterns for at least four loci including a strong linear cline in Adh and a non-linear cline in alpha-Gpdh. Inversion clines were initially established from cytological studies but have now been validated with larger sample sizes using molecular markers for breakpoints. Recent collections indicate that some genetic markers (Adh and In(3R)Payne) have changed over the last 20 years reflecting continuing evolution. Heritable clines have been established for quantitative traits including wing length/area, thorax length and cold and heat resistance. A cline in egg size independent of body size and a weak cline in competitive ability have also been established. Postulated clinal patterns for resistance to desiccation and starvation have not been supported by extensive sampling. Experiments under laboratory and semi-natural conditions have suggested selective factors generating clinal patterns, particularly for reproductive patterns over winter. Attempts are being made to link clinal variation in traits to specific genes using QTL analysis and the candidate locus approach, and to identify the genetic architecture of trait variation along the cline. This is proving difficult because of inversion polymorphisms that generate disequilibrium among genes. Substantial gaps still remain in linking clines to field selection and understanding the genetic and physiological basis of the adaptive shifts. However D. melanogaster populations in eastern Australia remain an excellent resource for understanding past and future evolutionary responses to climate change. PMID:16955331

  12. Rapid perceptual adaptation to high gravitoinertial force levels Evidence for context-specific adaptation

    NASA Technical Reports Server (NTRS)

    Lackner, J. R.; Graybiel, A.

    1982-01-01

    Subjects exposed to periodic variations in gravitoinertial force (2-G peak) in parabolic flight maneuvers quickly come to perceive the peak force level as having decreased in intensity. By the end of a 40-parabola flight, the decrease in apparent force is approximately 40%. On successive flight days, the apparent intensity of the force loads seems to decrease as well, indicating a cumulative adaptive effect. None of the subjects reported feeling abnormally 'light' for more than a minute or two after return to 1-G background force levels. The pattern of findings suggests a context-specific adaptation to high-force levels.

  13. Adaptive phenotypic plasticity and local adaptation for temperature tolerance in freshwater zooplankton

    PubMed Central

    Yampolsky, Lev Y.; Schaer, Tobias M. M.; Ebert, Dieter

    2014-01-01

    Many organisms have geographical distributions extending from the tropics to near polar regions or can experience up to 30°C temperature variation within the lifespan of an individual. Two forms of evolutionary adaptation to such wide ranges in ambient temperatures are frequently discussed: local adaptation and phenotypic plasticity. The freshwater planktonic crustacean Daphnia magna, whose range extends from South Africa to near arctic sites, shows strong phenotypic and genotypic variation in response to temperature. In this study, we use D. magna clones from 22 populations (one clone per population) ranging from latitude 0° (Kenya) to 66° North (White Sea) to explore the contributions of phenotypic plasticity and local adaptation to high temperature tolerance. Temperature tolerance was studied as knockout time (time until immobilization, Timm) at 37°C in clones acclimatized to either 20°C or 28°C. Acclimatization to 28°C strongly increased Timm, testifying to adaptive phenotypic plasticity. At the same time, Timm significantly correlated with average high temperature at the clones’ sites of origin, suggesting local adaptation. As earlier studies have found that haemoglobin expression contributes to temperature tolerance, we also quantified haemoglobin concentration in experimental animals and found that both acclimatization temperature (AccT) and temperature at the site of origin are positively correlated with haemoglobin concentration. Furthermore, Daphnia from warmer climates upregulate haemoglobin much more strongly in response to AccT, suggesting local adaptation for plasticity in haemoglobin expression. Our results show that both local adaptation and phenotypic plasticity contribute to temperature tolerance, and elucidate a possible role of haemoglobin in mediating these effects that differs along a cold–warm gradient. PMID:24352948

  14. Adaptations, exaptations, and spandrels.

    PubMed

    Buss, D M; Haselton, M G; Shackelford, T K; Bleske, A L; Wakefield, J C

    1998-05-01

    Adaptation and natural selection are central concepts in the emerging science of evolutionary psychology. Natural selection is the only known causal process capable of producing complex functional organic mechanisms. These adaptations, along with their incidental by-products and a residue of noise, comprise all forms of life. Recently, S. J. Gould (1991) proposed that exaptations and spandrels may be more important than adaptations for evolutionary psychology. These refer to features that did not originally arise for their current use but rather were co-opted for new purposes. He suggested that many important phenomena--such as art, language, commerce, and war--although evolutionary in origin, are incidental spandrels of the large human brain. The authors outline the conceptual and evidentiary standards that apply to adaptations, exaptations, and spandrels and discuss the relative utility of these concepts for psychological science. PMID:9612136

  15. Adaptive Space Structures

    NASA Technical Reports Server (NTRS)

    Wada, B.

    1993-01-01

    The term adaptive structures refers to a structural control approach in which sensors, actuators, electronics, materials, structures, structural concepts, and system-performance-validation strategies are integrated to achieve specific objectives.

  16. Adaptive Management of Ecosystems

    EPA Science Inventory

    Adaptive management is an approach to natural resource management that emphasizes learning through management. As such, management may be treated as experiment, with replication, or management may be conducted in an iterative manner. Although the concept has resonated with many...

  17. Adaptive Heat Engine

    NASA Astrophysics Data System (ADS)

    Allahverdyan, A. E.; Babajanyan, S. G.; Martirosyan, N. H.; Melkikh, A. V.

    2016-07-01

    A major limitation of many heat engines is that their functioning demands on-line control and/or an external fitting between the environmental parameters (e.g., temperatures of thermal baths) and internal parameters of the engine. We study a model for an adaptive heat engine, where—due to feedback from the functional part—the engine's structure adapts to given thermal baths. Hence, no on-line control and no external fitting are needed. The engine can employ unknown resources; it can also adapt to results of its own functioning that make the bath temperatures closer. We determine resources of adaptation and relate them to the prior information available about the environment.

  18. Limits to adaptation

    NASA Astrophysics Data System (ADS)

    Dow, Kirstin; Berkhout, Frans; Preston, Benjamin L.; Klein, Richard J. T.; Midgley, Guy; Shaw, M. Rebecca

    2013-04-01

    An actor-centered, risk-based approach to defining limits to social adaptation provides a useful analytic framing for identifying and anticipating these limits and informing debates over society's responses to climate change.

  19. Rocketing into Adaptive Inquiry.

    ERIC Educational Resources Information Center

    Farenga, Stephen J.; Joyce, Beverly A.; Dowling, Thomas W.

    2002-01-01

    Defines adaptive inquiry and argues for employing this method which allows lessons to be shaped in response to student needs. Illustrates this idea by detailing an activity in which teams of students build rockets. (DDR)

  20. Telescope Adaptive Optics Code

    SciTech Connect

    Phillion, D.

    2005-07-28

    The Telescope AO Code has general adaptive optics capabilities plus specialized models for three telescopes with either adaptive optics or active optics systems. It has the capability to generate either single-layer or distributed Kolmogorov turbulence phase screens using the FFT. Missing low order spatial frequencies are added using the Karhunen-Loeve expansion. The phase structure curve is extremely dose to the theoreUcal. Secondly, it has the capability to simulate an adaptive optics control systems. The default parameters are those of the Keck II adaptive optics system. Thirdly, it has a general wave optics capability to model the science camera halo due to scintillation from atmospheric turbulence and the telescope optics. Although this capability was implemented for the Gemini telescopes, the only default parameter specific to the Gemini telescopes is the primary mirror diameter. Finally, it has a model for the LSST active optics alignment strategy. This last model is highly specific to the LSST

  1. Adaptive Heat Engine.

    PubMed

    Allahverdyan, A E; Babajanyan, S G; Martirosyan, N H; Melkikh, A V

    2016-07-15

    A major limitation of many heat engines is that their functioning demands on-line control and/or an external fitting between the environmental parameters (e.g., temperatures of thermal baths) and internal parameters of the engine. We study a model for an adaptive heat engine, where-due to feedback from the functional part-the engine's structure adapts to given thermal baths. Hence, no on-line control and no external fitting are needed. The engine can employ unknown resources; it can also adapt to results of its own functioning that make the bath temperatures closer. We determine resources of adaptation and relate them to the prior information available about the environment. PMID:27472104

  2. Variations in Sexual Behavior.

    ERIC Educational Resources Information Center

    Juhasz, Anne McCreary

    1983-01-01

    Questions are raised about the difficulty of defining normal and atypical sexual behavior. Variations from normalcy that students, parents, and educators are most likely to encounter are discussed. The importance of dealing with variations in ways that are best for the individual and the group is emphasized. (PP)

  3. Saccadic adaptation to a systematically varying disturbance.

    PubMed

    Cassanello, Carlos R; Ohl, Sven; Rolfs, Martin

    2016-08-01

    Saccadic adaptation maintains the correct mapping between eye movements and their targets, yet the dynamics of saccadic gain changes in the presence of systematically varying disturbances has not been extensively studied. Here we assessed changes in the gain of saccade amplitudes induced by continuous and periodic postsaccadic visual feedback. Observers made saccades following a sequence of target steps either along the horizontal meridian (Two-way adaptation) or with unconstrained saccade directions (Global adaptation). An intrasaccadic step-following a sinusoidal variation as a function of the trial number (with 3 different frequencies tested in separate blocks)-consistently displaced the target along its vector. The oculomotor system responded to the resulting feedback error by modifying saccade amplitudes in a periodic fashion with similar frequency of variation but lagging the disturbance by a few tens of trials. This periodic response was superimposed on a drift toward stronger hypometria with similar asymptotes and decay rates across stimulus conditions. The magnitude of the periodic response decreased with increasing frequency and was smaller and more delayed for Global than Two-way adaptation. These results suggest that-in addition to the well-characterized return-to-baseline response observed in protocols using constant visual feedback-the oculomotor system attempts to minimize the feedback error by integrating its variation across trials. This process resembles a convolution with an internal response function, whose structure would be determined by coefficients of the learning model. Our protocol reveals this fast learning process in single short experimental sessions, qualifying it for the study of sensorimotor learning in health and disease. PMID:27098027

  4. Leak test adapter for containers

    DOEpatents

    Hallett, Brian H.; Hartley, Michael S.

    1996-01-01

    An adapter is provided for facilitating the charging of containers and leak testing penetration areas. The adapter comprises an adapter body and stem which are secured to the container's penetration areas. The container is then pressurized with a tracer gas. Manipulating the adapter stem installs a penetration plug allowing the adapter to be removed and the penetration to be leak tested with a mass spectrometer. Additionally, a method is provided for using the adapter.

  5. Adaptable DC offset correction

    NASA Technical Reports Server (NTRS)

    Golusky, John M. (Inventor); Muldoon, Kelly P. (Inventor)

    2009-01-01

    Methods and systems for adaptable DC offset correction are provided. An exemplary adaptable DC offset correction system evaluates an incoming baseband signal to determine an appropriate DC offset removal scheme; removes a DC offset from the incoming baseband signal based on the appropriate DC offset scheme in response to the evaluated incoming baseband signal; and outputs a reduced DC baseband signal in response to the DC offset removed from the incoming baseband signal.

  6. Robust Adaptive Control

    NASA Technical Reports Server (NTRS)

    Narendra, K. S.; Annaswamy, A. M.

    1985-01-01

    Several concepts and results in robust adaptive control are are discussed and is organized in three parts. The first part surveys existing algorithms. Different formulations of the problem and theoretical solutions that have been suggested are reviewed here. The second part contains new results related to the role of persistent excitation in robust adaptive systems and the use of hybrid control to improve robustness. In the third part promising new areas for future research are suggested which combine different approaches currently known.

  7. Adaptive transfer functions

    SciTech Connect

    Goulding, J.R. )

    1991-01-01

    This paper details the approach and methodology used to build adaptive transfer functions in a feed-forward Back-Propagation neural network, and provides insight into the structure dependent properties of using non-scaled analog inputs. The results of using adaptive transfer functions are shown to outperform conventional architectures in the implementation of a mechanical power transmission gearbox design expert system knowledge base. 4 refs., 4 figs., 1 tab.

  8. Shuffling Adaptive Clinical Trials.

    PubMed

    Gokhale, Sanjay G; Gokhale, Sankalp

    2016-01-01

    Clinical trials are interventional studies on human beings, designed to test the hypothesis for diagnostic techniques, treatments, and disease preventions. Any novel medical technology should be evaluated for its efficacy and safety by clinical trials. The costs associated with developing drugs have increased dramatically over the past decade, and fewer drugs are obtaining regulatory approval. Because of this, the pharmaceutical industry is continually exploring new ways of improving drug developments, and one area of focus is adaptive clinical trial designs. Adaptive designs, which allow for some types of prospectively planned mid-study changes, can improve the efficiency of a trial and maximize the chance of success without undermining validity and integrity of the trial. However it is felt that in adaptive trials; perhaps by using accrued data the actual patient population after the adaptations could deviate from the originally target patient population and so to overcome this drawback; special methods like Bayesian Statistics, predicted probability are used to deduce data-analysis. Here, in this study, mathematical model of a new adaptive design (shuffling adaptive trial) is suggested which uses real-time data, and because there is no gap between expected and observed data, statistical modifications are not needed. Results are obviously clinically relevant. PMID:23751329

  9. Adaptation and perceptual norms

    NASA Astrophysics Data System (ADS)

    Webster, Michael A.; Yasuda, Maiko; Haber, Sara; Leonard, Deanne; Ballardini, Nicole

    2007-02-01

    We used adaptation to examine the relationship between perceptual norms--the stimuli observers describe as psychologically neutral, and response norms--the stimulus levels that leave visual sensitivity in a neutral or balanced state. Adapting to stimuli on opposite sides of a neutral point (e.g. redder or greener than white) biases appearance in opposite ways. Thus the adapting stimulus can be titrated to find the unique adapting level that does not bias appearance. We compared these response norms to subjectively defined neutral points both within the same observer (at different retinal eccentricities) and between observers. These comparisons were made for visual judgments of color, image focus, and human faces, stimuli that are very different and may depend on very different levels of processing, yet which share the property that for each there is a well defined and perceptually salient norm. In each case the adaptation aftereffects were consistent with an underlying sensitivity basis for the perceptual norm. Specifically, response norms were similar to and thus covaried with the perceptual norm, and under common adaptation differences between subjectively defined norms were reduced. These results are consistent with models of norm-based codes and suggest that these codes underlie an important link between visual coding and visual experience.

  10. The Climate Adaptation Frontier

    SciTech Connect

    Preston, Benjamin L

    2013-01-01

    Climate adaptation has emerged as a mainstream risk management strategy for assisting in maintaining socio-ecological systems within the boundaries of a safe operating space. Yet, there are limits to the ability of systems to adapt. Here, we introduce the concept of an adaptation frontier , which is defined as a socio-ecological system s transitional adaptive operating space between safe and unsafe domains. A number of driving forces are responsible for determining the sustainability of systems on the frontier. These include path dependence, adaptation/development deficits, values conflicts and discounting of future loss and damage. The cumulative implications of these driving forces are highly uncertain. Nevertheless, the fact that a broad range of systems already persist at the edge of their frontiers suggests a high likelihood that some limits will eventually be exceeded. The resulting system transformation is likely to manifest as anticipatory modification of management objectives or loss and damage. These outcomes vary significantly with respect to their ethical implications. Successful navigation of the adaptation frontier will necessitate new paradigms of risk governance to elicit knowledge that encourages reflexive reevaluation of societal values that enable or constrain sustainability.

  11. Prism adaptation in schizophrenia.

    PubMed

    Bigelow, Nirav O; Turner, Beth M; Andreasen, Nancy C; Paulsen, Jane S; O'Leary, Daniel S; Ho, Beng-Choon

    2006-08-01

    The prism adaptation test examines procedural learning (PL) in which performance facilitation occurs with practice on tasks without the need for conscious awareness. Dynamic interactions between frontostriatal cortices, basal ganglia, and the cerebellum have been shown to play key roles in PL. Disruptions within these neural networks have also been implicated in schizophrenia, and such disruptions may manifest as impairment in prism adaptation test performance in schizophrenia patients. This study examined prism adaptation in a sample of patients diagnosed with schizophrenia (N=91) and healthy normal controls (N=58). Quantitative indices of performance during prism adaptation conditions with and without visual feedback were studied. Schizophrenia patients were significantly more impaired in adapting to prism distortion and demonstrated poorer quality of PL. Patients did not differ from healthy controls on aftereffects when the prisms were removed, but they had significantly greater difficulties in reorientation. Deficits in prism adaptation among schizophrenia patients may be due to abnormalities in motor programming arising from the disruptions within the neural networks that subserve PL. PMID:16510223

  12. Adaptation through proportion.

    PubMed

    Xiong, Liyang; Shi, Wenjia; Tang, Chao

    2016-01-01

    Adaptation is a ubiquitous feature in biological sensory and signaling networks. It has been suggested that adaptive systems may follow certain simple design principles across diverse organisms, cells and pathways. One class of networks that can achieve adaptation utilizes an incoherent feedforward control, in which two parallel signaling branches exert opposite but proportional effects on the output at steady state. In this paper, we generalize this adaptation mechanism by establishing a steady-state proportionality relationship among a subset of nodes in a network. Adaptation can be achieved by using any two nodes in the sub-network to respectively regulate the output node positively and negatively. We focus on enzyme networks and first identify basic regulation motifs consisting of two and three nodes that can be used to build small networks with proportional relationships. Larger proportional networks can then be constructed modularly similar to LEGOs. Our method provides a general framework to construct and analyze a class of proportional and/or adaptation networks with arbitrary size, flexibility and versatile functional features. PMID:27526863

  13. Adaptive parallel logic networks

    SciTech Connect

    Martinez, T.R.; Vidal, J.J.

    1988-02-01

    This paper presents a novel class of special purpose processors referred to as ASOCS (adaptive self-organizing concurrent systems). Intended applications include adaptive logic devices, robotics, process control, system malfunction management, and in general, applications of logic reasoning. ASOCS combines massive parallelism with self-organization to attain a distributed mechanism for adaptation. The ASOCS approach is based on an adaptive network composed of many simple computing elements (nodes) which operate in a combinational and asynchronous fashion. Problem specification (programming) is obtained by presenting to the system if-then rules expressed as Boolean conjunctions. New rules are added incrementally. In the current model, when conflicts occur, precedence is given to the most recent inputs. With each rule, desired network response is simply presented to the system, following which the network adjusts itself to maintain consistency and parsimony of representation. Data processing and adaptation form two separate phases of operation. During processing, the network acts as a parallel hardware circuit. Control of the adaptive process is distributed among the network nodes and efficiently exploits parallelism.

  14. The adaptive accuracy of flowers: measurement and microevolutionary patterns

    PubMed Central

    Armbruster, W. Scott; Hansen, Thomas F.; Pélabon, Christophe; Pérez-Barrales, Rocío; Maad, Johanne

    2009-01-01

    Background and Aims From Darwin's time onward, biologists have thought about adaptation as evolution toward optimal trait values, but they have not usually assessed the relative importance of the distinct causes of deviations from optima. This problem is investigated here by measuring adaptive inaccuracy (phenotypic deviation from the optimum), using flower pollination as an adaptive system. Methods Adaptive accuracy is shown to have at least three distinct components, two of which are optimality (deviation of the mean from the optimum) and precision (trait variance). We then describe adaptive accuracy of both individuals and populations. Individual inaccuracy comprises the deviation of the genotypic target (the mean phenotype of a genotype grown in a range of environments) from the optimum and the phenotypic variation around that genotypic target (phenotypic imprecision). Population inaccuracy has three basic components: deviation of the population mean from the optimum, variance in the genotypic targets and phenotypic imprecision. In addition, a fourth component is proposed, namely within-population variation in the optimum. These components are directly estimable, have additive relationships, and allow exploration of the causes of adaptive inaccuracy of both individuals and populations. Adaptive accuracy of a sample of flowers is estimated, relating floral phenotypes controlling pollen deposition on pollinators to adaptive optima defined as the site most likely to get pollen onto stigmas (male inaccuracy). Female inaccuracy is defined as the deviation of the position of stigma contact from the expected location of pollen on pollinators. Key Results A surprising amount of variation in estimated accuracy within and among similar species is found. Some of this variation is generated by developmental changes in positions of stigmas or anthers during anthesis (the floral receptive period), which can cause dramatic change in accuracy estimates. There seem to be trends

  15. Discrete-time adaptive control of robot manipulators

    NASA Technical Reports Server (NTRS)

    Tarokh, M.

    1989-01-01

    A discrete-time model reference adaptive control scheme is developed for trajectory tracking of robot manipulators. Hyperstability theory is utilized to derive the adaptation laws for the controller gain matrices. It is shown that asymptotic trajectory tracking is achieved despite gross robot parameter variation and uncertainties. The method offers considerable design flexibility and enables the designer to improve the performance of the control system by adjusting free design parameters. The discrete-time adaptation algorithm is extremely simple and is therefore suitable for real-time implementation.

  16. Adaptive controller for a needle free jet-injector system.

    PubMed

    Modak, Ashin; Hogan, N Catherine; Hunter, Ian W

    2015-08-01

    A nonlinear, sliding mode adaptive controller was created for a needle-free jet injection system. The controller was based on a simplified lumped-sum parameter model of the jet-injection mechanics. The adaptive control scheme was compared to a currently-used Feed-forward+PID controller in both ejection of water into air, and injection of dye into ex-vivo porcine tissue. The adaptive controller was more successful in trajectory tracking and was more robust to the biological variations caused by a tissue load. PMID:26737988

  17. Second Variation of Induced Curvature Term in Brane-World Action

    NASA Astrophysics Data System (ADS)

    Iofa, Mikhail Z.

    In a 5D spacetime with a 3-brane embedded we calculate the second variation of the scalar 4D curvature term on the brane under variations of the 5D metric. It is shown that the second variation of the 4D scalar curvature term in adapted coordinates is expressed only through variations of the components of the 5D metric with 4D indices.

  18. Understanding Farmer Perspectives on Climate Change Adaptation and Mitigation

    PubMed Central

    Morton, Lois Wright; Hobbs, Jon

    2015-01-01

    Agriculture is vulnerable to climate change and a source of greenhouse gases (GHGs). Farmers face pressures to adjust agricultural systems to make them more resilient in the face of increasingly variable weather (adaptation) and reduce GHG production (mitigation). This research examines relationships between Iowa farmers’ trust in environmental or agricultural interest groups as sources of climate information, climate change beliefs, perceived climate risks to agriculture, and support for adaptation and mitigation responses. Results indicate that beliefs varied with trust, and beliefs in turn had a significant direct effect on perceived risks from climate change. Support for adaptation varied with perceived risks, while attitudes toward GHG reduction (mitigation) were associated predominantly with variation in beliefs. Most farmers were supportive of adaptation responses, but few endorsed GHG reduction, suggesting that outreach should focus on interventions that have adaptive and mitigative properties (e.g., reduced tillage, improved fertilizer management). PMID:25983336

  19. Human variation databases

    PubMed Central

    Küntzer, Jan; Eggle, Daniela; Klostermann, Stefan; Burtscher, Helmut

    2010-01-01

    More than 100 000 human genetic variations have been described in various genes that are associated with a wide variety of diseases. Such data provides invaluable information for both clinical medicine and basic science. A number of locus-specific databases have been developed to exploit this huge amount of data. However, the scope, format and content of these databases differ strongly and as no standard for variation databases has yet been adopted, the way data is presented varies enormously. This review aims to give an overview of current resources for human variation data in public and commercial resources. PMID:20639550

  20. The state of climate change adaptation in the Arctic

    NASA Astrophysics Data System (ADS)

    Ford, James D.; McDowell, Graham; Jones, Julie

    2014-10-01

    The Arctic climate is rapidly changing, with wide ranging impacts on natural and social systems. A variety of adaptation policies, programs and practices have been adopted to this end, yet our understanding of if, how, and where adaptation is occurring is limited. In response, this paper develops a systematic approach to characterize the current state of adaptation in the Arctic. Using reported adaptations in the English language peer reviewed literature as our data source, we document 157 discrete adaptation initiatives between 2003 and 2013. Results indicate large variations in adaptation by region and sector, dominated by reporting from North America, particularly with regards to subsistence harvesting by Inuit communities. Few adaptations were documented in the European and Russian Arctic, or have a focus on the business and economy, or infrastructure sectors. Adaptations are being motivated primarily by the combination of climatic and non-climatic factors, have a strong emphasis on reducing current vulnerability involving incremental changes to existing risk management processes, and are primarily initiated and led at the individual/community level. There is limited evidence of trans-boundary adaptations or initiatives considering potential cross-scale/sector impacts.

  1. An explanatory framework for adaptive personality differences

    PubMed Central

    Wolf, Max; Weissing, Franz J.

    2010-01-01

    We develop a conceptual framework for the understanding of animal personalities in terms of adaptive evolution. We focus on two basic questions. First, why do behavioural types exhibit limited behavioural plasticity, that is, behavioural correlations both across contexts and over time? Second, how can multiple behavioural types coexist within a single population? We emphasize differences in ‘state’ among individuals in combination with state-dependent behaviour. Some states are inherently stable and individual differences in such states can explain stable differences in suites of behaviour if it is adaptive to make behaviour in various contexts dependent on such states. Behavioural stability and cross-context correlations in behaviour are more difficult to explain if individual states are potentially more variable. In such cases stable personalities can result from state-dependent behaviour if state and behaviour mutually reinforce each other by feedback mechanisms. We discuss various evolutionary mechanisms for the maintenance of variation (in states and/or behaviour), including frequency-dependent selection, spatial variation with incomplete matching between habitat and phenotype, bet-hedging in a temporally fluctuating environment, and non-equilibrium dynamics. Although state differences are important, we also discuss how social conventions and social signalling can give rise to adaptive personality differences in the absence of state differences. PMID:21078648

  2. INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCI

    PubMed Central

    Storz, Jay F.; Wheat, Christopher W.

    2010-01-01

    Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally, population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests to evaluate whether the functional variation is of adaptive significance. In other cases, studies may be initiated by genome scans of DNA variation to identify candidate loci for recent adaptation. Results of such analyses can then motivate experimental efforts to test whether the identified candidate loci do in fact contribute to functional variation in some fitness-related phenotype. Functional studies can provide corroborative evidence for positive selection at particular loci, and can potentially reveal specific molecular mechanisms of adaptation. PMID:20500215

  3. Adaptation and risk management

    SciTech Connect

    Preston, Benjamin L

    2011-01-01

    Adaptation assessment methods are compatible with the international risk management standard ISO:31000. Risk management approaches are increasingly being recommended for adaptation assessments at both national and local levels. Two orientations to assessments can commonly be identified: top-down and bottom-up, and prescriptive and diagnostic. Combinations of these orientations favor different types of assessments. The choice of orientation can be related to uncertainties in prediction and taking action, in the type of adaptation and in the degree of system stress. Adopting multiple viewpoints is to be encouraged, especially in complex situations. The bulk of current guidance material is consistent with top-down and predictive approaches, thus is most suitable for risk scoping and identification. Abroad range ofmaterial fromwithin and beyond the climate change literature can be used to select methods to be used in assessing and implementing adaptation. The framing of risk, correct formulation of the questions being investigated and assessment methodology are critical aspects of the scoping phase. Only when these issues have been addressed should be issue of specific methods and tools be addressed. The reorientation of adaptation from an assessment focused solely on anthropogenic climate change to broader issues of vulnerability/resilience, sustainable development and disaster risk, especially through a risk management framework, can draw from existing policy and management understanding in communities, professions and agencies, incorporating existing agendas, knowledge, risks, and issues they already face.

  4. Mechanisms of intestinal adaptation.

    PubMed

    Rubin, Deborah C; Levin, Marc S

    2016-04-01

    Following loss of functional small bowel surface area due to surgical resection for therapy of Crohn's disease, ischemia, trauma or other disorders, the remnant gut undergoes a morphometric and functional compensatory adaptive response which has been best characterized in preclinical models. Increased crypt cell proliferation results in increased villus height, crypt depth and villus hyperplasia, accompanied by increased nutrient, fluid and electrolyte absorption. Clinical observations suggest that functional adaptation occurs in humans. In the immediate postoperative period, patients with substantial small bowel resection have massive fluid and electrolyte loss with reduced nutrient absorption. For many patients, the adaptive response permits partial or complete weaning from parenteral nutrition (PN), within two years following resection. However, others have life-long PN dependence. An understanding of the molecular mechanisms that regulate the gut adaptive response is critical for developing novel therapies for short bowel syndrome. Herein we present a summary of key studies that seek to elucidate the mechanisms that regulate post-resection adaptation, focusing on stem and crypt cell proliferation, epithelial differentiation, apoptosis, enterocyte function and the role of growth factors and the enteric nervous system. PMID:27086888

  5. Adaptable Multivariate Calibration Models for Spectral Applications

    SciTech Connect

    THOMAS,EDWARD V.

    1999-12-20

    Multivariate calibration techniques have been used in a wide variety of spectroscopic situations. In many of these situations spectral variation can be partitioned into meaningful classes. For example, suppose that multiple spectra are obtained from each of a number of different objects wherein the level of the analyte of interest varies within each object over time. In such situations the total spectral variation observed across all measurements has two distinct general sources of variation: intra-object and inter-object. One might want to develop a global multivariate calibration model that predicts the analyte of interest accurately both within and across objects, including new objects not involved in developing the calibration model. However, this goal might be hard to realize if the inter-object spectral variation is complex and difficult to model. If the intra-object spectral variation is consistent across objects, an effective alternative approach might be to develop a generic intra-object model that can be adapted to each object separately. This paper contains recommendations for experimental protocols and data analysis in such situations. The approach is illustrated with an example involving the noninvasive measurement of glucose using near-infrared reflectance spectroscopy. Extensions to calibration maintenance and calibration transfer are discussed.

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

    PubMed

    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

  7. The Schwinger Variational Method

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    1995-01-01

    Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. For collisional problems they can be grouped into two types: those based on the Schroedinger equation and those based on the Lippmann-Schwinger equation. The application of the Schwinger variational (SV) method to e-molecule collisions and photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions.

  8. Generalized quasi variational inequalities

    SciTech Connect

    Noor, M.A.

    1996-12-31

    In this paper, we establish the equivalence between the generalized quasi variational inequalities and the generalized implicit Wiener-Hopf equations using essentially the projection technique. This equivalence is used to suggest and analyze a number of new iterative algorithms for solving generalized quasi variational inequalities and the related complementarity problems. The convergence criteria is also considered. The results proved in this paper represent a significant improvement and refinement of the previously known results.

  9. Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia.

    PubMed

    Chávez-Galarza, Julio; Henriques, Dora; Johnston, J Spencer; Carneiro, Miguel; Rufino, José; Patton, John C; Pinto, M Alice

    2015-06-01

    Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern-southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity. PMID:25930679

  10. Monitoring adaptive genetic responses to environmental change.

    PubMed

    Hansen, Michael M; Olivieri, Isabelle; Waller, Donald M; Nielsen, Einar E

    2012-03-01

    Widespread environmental changes including climate change, selective harvesting and landscape alterations now greatly affect selection regimes for most organisms. How animals and plants can adapt to these altered environments via contemporary evolution is thus of strong interest. We discuss how to use genetic monitoring to study adaptive responses via repeated analysis of the same populations over time, distinguishing between phenotypic and molecular genetics approaches. After describing monitoring designs, we develop explicit criteria for demonstrating adaptive responses, which include testing for selection and establishing clear links between genetic and environmental change. We then review a few exemplary studies that explore adaptive responses to climate change in Drosophila, selective responses to hunting and fishing, and contemporary evolution in Daphnia using resurrected resting eggs. We further review a broader set of 44 studies to assess how well they meet the proposed criteria, and conclude that only 23% fulfill all criteria. Approximately half (43%) of these studies failed to rule out the alternative hypothesis of replacement by a different, better-adapted population. Likewise, 34% of the studies based on phenotypic variation did not test for selection as opposed to drift. These shortcomings can be addressed via improved experimental designs and statistical testing. We foresee monitoring of adaptive responses as a future valuable tool in conservation biology, for identifying populations unable to evolve at sufficiently high rates and for identifying possible donor populations for genetic rescue. Technological advances will further augment the realization of this potential, especially next-generation sequencing technologies that allow for monitoring at the level of whole genomes. PMID:22269082

  11. Cardiovascular adaptation to spaceflight

    NASA Technical Reports Server (NTRS)

    Charles, John B.; Lathers, Claire M.

    1991-01-01

    Data are presented on the rate of adaptation of the human cardiovascular system to conditions of spaceflight, with particular attention given to data obtained during spaceflight in the U.S. Space Shuttle Program. It is pointed out that many of the cardiovascular changes that occurred during spaceflights that lasted from 2 to 11 days can be traced directly to changes in the body fluid volume. The beneficial effects of a fluid loading countermeasure (oral rehydration) and of the supine body position on the heart rate during the spaceflight are demonstrated. It is noted that, after hours or a few days of spaceflight, a state of adaptation is reached, in which the subject is well adapted and appropriately hydrated for the weightless environment. However, the return to the normal gravity of the earth leaves the individual especially sensitive to orthostatic stress.

  12. Cardiovascular adaptation to spaceflight

    NASA Technical Reports Server (NTRS)

    Hargens, A. R.; Watenpaugh, D. E.

    1996-01-01

    This article reviews recent flight and ground-based studies of cardiovascular adaptation to spaceflight. Prominent features of microgravity exposure include loss of gravitational pressures, relatively low venous pressures, headward fluid shifts, plasma volume loss, and postflight orthostatic intolerance and reduced exercise capacity. Many of these short-term responses to microgravity extend themselves during long-duration microgravity exposure and may be explained by altered pressures (blood and tissue) and fluid balance in local tissues nourished by the cardiovascular system. In this regard, it is particularly noteworthy that tissues of the lower body (e.g., foot) are well adapted to local hypertension on Earth, whereas tissues of the upper body (e.g., head) are not as well adapted to increase in local blood pressure. For these and other reasons, countermeasures for long-duration flight should include reestablishment of higher, Earth-like blood pressures in the lower body.

  13. Chromatic variations suppress suprathreshold brightness variations.

    PubMed

    Kingdom, Frederick A A; Bell, Jason; Gheorghiu, Elena; Malkoc, Gokhan

    2010-01-01

    Most objects in natural scenes are suprathreshold in both color (chromatic) and luminance contrast. How salient is each dimension? We have developed a novel method employing a stimulus similar to that used by B. C. Regan and J. D. Mollon (1997) who studied the relative saliencies of the two chromatic cardinal directions. Our stimuli consist of left- and right-oblique modulations of color and/or luminance defined within a lattice of circles. In the "separated" condition, the two modulations were presented separately as forced-choice pairs, and the task was to indicate which was more salient. In the "combined" condition, the two orthogonal-in-orientation modulations were added, and the task was to indicate the more salient orientation. The ratio of color to luminance contrast at the PSE was calculated for both conditions. Across color directions, 48% more luminance contrast relative to color contrast was required to achieve a PSE in the "combined" compared to the "separated" condition. A second experiment showed that the PSE difference was due to the luminance being masked by the color, rather than due to superior color grouping. We conclude that suprathreshold brightness variations are masked by suprathreshold color variations. PMID:20884478

  14. Adaptive triangular mesh generation

    NASA Technical Reports Server (NTRS)

    Erlebacher, G.; Eiseman, P. R.

    1984-01-01

    A general adaptive grid algorithm is developed on triangular grids. The adaptivity is provided by a combination of node addition, dynamic node connectivity and a simple node movement strategy. While the local restructuring process and the node addition mechanism take place in the physical plane, the nodes are displaced on a monitor surface, constructed from the salient features of the physical problem. An approximation to mean curvature detects changes in the direction of the monitor surface, and provides the pulling force on the nodes. Solutions to the axisymmetric Grad-Shafranov equation demonstrate the capturing, by triangles, of the plasma-vacuum interface in a free-boundary equilibrium configuration.

  15. Adaptive piezoelectric sensoriactuator

    NASA Technical Reports Server (NTRS)

    Clark, Jr., Robert L. (Inventor); Vipperman, Jeffrey S. (Inventor); Cole, Daniel G. (Inventor)

    1996-01-01

    An adaptive algorithm implemented in digital or analog form is used in conjunction with a voltage controlled amplifier to compensate for the feedthrough capacitance of piezoelectric sensoriactuator. The mechanical response of the piezoelectric sensoriactuator is resolved from the electrical response by adaptively altering the gain imposed on the electrical circuit used for compensation. For wideband, stochastic input disturbances, the feedthrough capacitance of the sensoriactuator can be identified on-line, providing a means of implementing direct-rate-feedback control in analog hardware. The device is capable of on-line system health monitoring since a quasi-stable dynamic capacitance is indicative of sustained health of the piezoelectric element.

  16. Adaptive optics revisited.

    PubMed

    Babcock, H W

    1990-07-20

    From the earliest days and nights of telescopic astronomy, atmospheric turbulence has been a serious detriment to optical performance. The new technology of adaptive optics can overcome this problem by compensating for the wavefront distortion that results from turbulence. The result will be large gains in resolving power and limiting magnitude, closely approaching the theoretical limit. In other words, telescopic images will be very significantly sharpened. Rapid and accelerating progress is being made today by several groups. Adaptive optics, together with the closely related technology of active optics, seems certain to be utilized in large astronomical telescopes of the future. This may entail significant changes in telescope design. PMID:17750109

  17. Learning and Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mansour, Yishay

    Domain adaptation is a fundamental learning problem where one wishes to use labeled data from one or several source domains to learn a hypothesis performing well on a different, yet related, domain for which no labeled data is available. This generalization across domains is a very significant challenge for many machine learning applications and arises in a variety of natural settings, including NLP tasks (document classification, sentiment analysis, etc.), speech recognition (speakers and noise or environment adaptation) and face recognition (different lighting conditions, different population composition).

  18. Verification of Adaptive Systems

    SciTech Connect

    Pullum, Laura L; Cui, Xiaohui; Vassev, Emil; Hinchey, Mike; Rouff, Christopher; Buskens, Richard

    2012-01-01

    Adaptive systems are critical for future space and other unmanned and intelligent systems. Verification of these systems is also critical for their use in systems with potential harm to human life or with large financial investments. Due to their nondeterministic nature and extremely large state space, current methods for verification of software systems are not adequate to provide a high level of assurance for them. The combination of stabilization science, high performance computing simulations, compositional verification and traditional verification techniques, plus operational monitors, provides a complete approach to verification and deployment of adaptive systems that has not been used before. This paper gives an overview of this approach.

  19. Adaptive Cruise Control (ACC)

    NASA Astrophysics Data System (ADS)

    Reif, Konrad

    Die adaptive Fahrgeschwindigkeitsregelung (ACC, Adaptive Cruise Control) ist eine Weiterentwicklung der konventionellen Fahrgeschwindigkeitsregelung, die eine konstante Fahrgeschwindigkeit einstellt. ACC überwacht mittels eines Radarsensors den Bereich vor dem Fahrzeug und passt die Geschwindigkeit den Gegebenheiten an. ACC reagiert auf langsamer vorausfahrende oder einscherende Fahrzeuge mit einer Reduzierung der Geschwindigkeit, sodass der vorgeschriebene Mindestabstand zum vorausfahrenden Fahrzeug nicht unterschritten wird. Hierzu greift ACC in Antrieb und Bremse ein. Sobald das vorausfahrende Fahrzeug beschleunigt oder die Spur verlässt, regelt ACC die Geschwindigkeit wieder auf die vorgegebene Sollgeschwindigkeit ein (Bild 1). ACC steht somit für eine Geschwindigkeitsregelung, die sich dem vorausfahrenden Verkehr anpasst.

  20. Adaptive background model

    NASA Astrophysics Data System (ADS)

    Lu, Xiaochun; Xiao, Yijun; Chai, Zhi; Wang, Bangping

    2007-11-01

    An adaptive background model aiming at outdoor vehicle detection is presented in this paper. This model is an improved model of PICA (pixel intensity classification algorithm), it classifies pixels into K-distributions by color similarity, and then a hypothesis that the background pixel color appears in image sequence with a high frequency is used to evaluate all the distributions to determine which presents the current background color. As experiments show, the model presented in this paper is a robust, adaptive and flexible model, which can deal with situations like camera motions, lighting changes and so on.

  1. Impact of pre-adapted HIV transmission.

    PubMed

    Carlson, Jonathan M; Du, Victor Y; Pfeifer, Nico; Bansal, Anju; Tan, Vincent Y F; Power, Karen; Brumme, Chanson J; Kreimer, Anat; DeZiel, Charles E; Fusi, Nicolo; Schaefer, Malinda; Brockman, Mark A; Gilmour, Jill; Price, Matt A; Kilembe, William; Haubrich, Richard; John, Mina; Mallal, Simon; Shapiro, Roger; Frater, John; Harrigan, P Richard; Ndung'u, Thumbi; Allen, Susan; Heckerman, David; Sidney, John; Allen, Todd M; Goulder, Philip J R; Brumme, Zabrina L; Hunter, Eric; Goepfert, Paul A

    2016-06-01

    Human leukocyte antigen class I (HLA)-restricted CD8(+) T lymphocyte (CTL) responses are crucial to HIV-1 control. Although HIV can evade these responses, the longer-term impact of viral escape mutants remains unclear, as these variants can also reduce intrinsic viral fitness. To address this, we here developed a metric to determine the degree of HIV adaptation to an HLA profile. We demonstrate that transmission of viruses that are pre-adapted to the HLA molecules expressed in the recipient is associated with impaired immunogenicity, elevated viral load and accelerated CD4(+) T cell decline. Furthermore, the extent of pre-adaptation among circulating viruses explains much of the variation in outcomes attributed to the expression of certain HLA alleles. Thus, viral pre-adaptation exploits 'holes' in the immune response. Accounting for these holes may be key for vaccine strategies seeking to elicit functional responses from viral variants, and to HIV cure strategies that require broad CTL responses to achieve successful eradication of HIV reservoirs. PMID:27183217

  2. Thin, nearly wireless adaptive optical device

    NASA Technical Reports Server (NTRS)

    Knowles, Gareth (Inventor); Hughes, Eli (Inventor)

    2008-01-01

    A thin, nearly wireless adaptive optical device capable of dynamically modulating the shape of a mirror in real time to compensate for atmospheric distortions and/or variations along an optical material is provided. The device includes an optical layer, a substrate, at least one electronic circuit layer with nearly wireless architecture, an array of actuators, power electronic switches, a reactive force element, and a digital controller. Actuators are aligned so that each axis of expansion and contraction intersects both substrate and reactive force element. Electronics layer with nearly wireless architecture, power electronic switches, and digital controller are provided within a thin-film substrate. The size and weight of the adaptive optical device is solely dominated by the size of the actuator elements rather than by the power distribution system.

  3. Thin, nearly wireless adaptive optical device

    NASA Technical Reports Server (NTRS)

    Knowles, Gareth (Inventor); Hughes, Eli (Inventor)

    2007-01-01

    A thin, nearly wireless adaptive optical device capable of dynamically modulating the shape of a mirror in real time to compensate for atmospheric distortions and/or variations along an optical material is provided. The device includes an optical layer, a substrate, at least one electronic circuit layer with nearly wireless architecture, an array of actuators, power electronic switches, a reactive force element, and a digital controller. Actuators are aligned so that each axis of expansion and contraction intersects both substrate and reactive force element. Electronics layer with nearly wireless architecture, power electronic switches, and digital controller are provided within a thin-film substrate. The size and weight of the adaptive optical device is solely dominated by the size of the actuator elements rather than by the power distribution system.

  4. Color demosaicking via robust adaptive sparse representation

    NASA Astrophysics Data System (ADS)

    Huang, Lili; Xiao, Liang; Chen, Qinghua; Wang, Kai

    2015-09-01

    A single sensor camera can capture scenes by means of a color filter array. Each pixel samples only one of the three primary colors. We use a color demosaicking (CDM) technique to produce full color images and propose a robust adaptive sparse representation model for high quality CDM. The data fidelity term is characterized by l1 norm to suppress the heavy-tailed visual artifacts with an adaptively learned dictionary, while the regularization term is encouraged to seek sparsity by forcing sparse coding close to its nonlocal means to reduce coding errors. Based on the classical quadratic penalty function technique in optimization and an operator splitting method in convex analysis, we further present an effective iterative algorithm to solve the variational problem. The efficiency of the proposed method is demonstrated by experimental results with simulated and real camera data.

  5. Thin nearly wireless adaptive optical device

    NASA Technical Reports Server (NTRS)

    Knowles, Gareth J. (Inventor); Hughes, Eli (Inventor)

    2009-01-01

    A thin nearly wireless adaptive optical device capable of dynamically modulating the shape of a mirror in real time to compensate for atmospheric distortions and/or variations along an optical material is provided. The device includes an optical layer, a substrate, at least one electronic circuit layer with nearly wireless architecture, an array of actuators, power electronic switches, a reactive force element, and a digital controller. Actuators are aligned so that each axis of expansion and contraction intersects both substrate and reactive force element. Electronics layer with nearly wireless architecture, power electronic switches, and digital controller are provided within a thin-film substrate. The size and weight of the adaptive optical device is solely dominated by the size of the actuator elements rather than by the power distribution system.

  6. Adaptive synchronization and anticipatory dynamical systems

    NASA Astrophysics Data System (ADS)

    Yang, Ying-Jen; Chen, Chun-Chung; Lai, Pik-Yin; Chan, C. K.

    2015-09-01

    Many biological systems can sense periodical variations in a stimulus input and produce well-timed, anticipatory responses after the input is removed. Such systems show memory effects for retaining timing information in the stimulus and cannot be understood from traditional synchronization consideration of passive oscillatory systems. To understand this anticipatory phenomena, we consider oscillators built from excitable systems with the addition of an adaptive dynamics. With such systems, well-timed post-stimulus responses similar to those from experiments can be obtained. Furthermore, a well-known model of working memory is shown to possess similar anticipatory dynamics when the adaptive mechanism is identified with synaptic facilitation. The last finding suggests that this type of oscillator can be common in neuronal systems with plasticity.

  7. Hybrid Adaptive Flight Control with Model Inversion Adaptation

    NASA Technical Reports Server (NTRS)

    Nguyen, Nhan

    2011-01-01

    This study investigates a hybrid adaptive flight control method as a design possibility for a flight control system that can enable an effective adaptation strategy to deal with off-nominal flight conditions. The hybrid adaptive control blends both direct and indirect adaptive control in a model inversion flight control architecture. The blending of both direct and indirect adaptive control provides a much more flexible and effective adaptive flight control architecture than that with either direct or indirect adaptive control alone. The indirect adaptive control is used to update the model inversion controller by an on-line parameter estimation of uncertain plant dynamics based on two methods. The first parameter estimation method is an indirect adaptive law based on the Lyapunov theory, and the second method is a recursive least-squares indirect adaptive law. The model inversion controller is therefore made to adapt to changes in the plant dynamics due to uncertainty. As a result, the modeling error is reduced that directly leads to a decrease in the tracking error. In conjunction with the indirect adaptive control that updates the model inversion controller, a direct adaptive control is implemented as an augmented command to further reduce any residual tracking error that is not entirely eliminated by the indirect adaptive control.

  8. Robust Optimal Adaptive Control Method with Large Adaptive Gain

    NASA Technical Reports Server (NTRS)

    Nguyen, Nhan T.

    2009-01-01

    In the presence of large uncertainties, a control system needs to be able to adapt rapidly to regain performance. Fast adaptation is referred to the implementation of adaptive control with a large adaptive gain to reduce the tracking error rapidly. However, a large adaptive gain can lead to high-frequency oscillations which can adversely affect robustness of an adaptive control law. A new adaptive control modification is presented that can achieve robust adaptation with a large adaptive gain without incurring high-frequency oscillations as with the standard model-reference adaptive control. The modification is based on the minimization of the Y2 norm of the tracking error, which is formulated as an optimal control problem. The optimality condition is used to derive the modification using the gradient method. The optimal control modification results in a stable adaptation and allows a large adaptive gain to be used for better tracking while providing sufficient stability robustness. Simulations were conducted for a damaged generic transport aircraft with both standard adaptive control and the adaptive optimal control modification technique. The results demonstrate the effectiveness of the proposed modification in tracking a reference model while maintaining a sufficient time delay margin.

  9. Morphological and Molecular Variation in Perennial Medicago (Alfalfa) Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Alfalfa (Medicago sativa L.) is one of the most important cultivated forage legumes worldwide. Understanding the areas of adaptation and genetic variation available in a crop species facilitates efforts to identify suitable germplasm for integration in plant breeding programs. Accessions that repr...

  10. Density fluctuations represent a key process maintaining personality variation in a wild passerine bird.

    PubMed

    Nicolaus, Marion; Tinbergen, Joost M; Ubels, Richard; Both, Christiaan; Dingemanse, Niels J

    2016-04-01

    Heritable personality variation is subject to fluctuating selection in many animal taxa; a major unresolved question is why this is the case. A parsimonious explanation must involve a general ecological process: a likely candidate is the omnipresent spatiotemporal variation in conspecific density. We tested whether spatiotemporal variation in density within and among nest box plots of great tits (Parus major) predicted variation in selection acting on exploratory behaviour (n = 48 episodes of selection). We found viability selection favouring faster explorers under lower densities but slower explorers under higher densities. Temporal variation in local density represented the primary factor explaining personality-related variation in viability selection. Importantly, birds did not anticipate changes in selection by means of adaptive density-dependent plasticity. This study thereby provides an unprecedented example of the key importance of the interplay between fluctuating selection and lack of adaptive behavioural plasticity in maintaining animal personality variation in the wild. PMID:26929092

  11. Adaptive divergence in embryonic thermal plasticity among Atlantic salmon populations.

    PubMed

    Côte, J; Roussel, J-M; Le Cam, S; Guillaume, F; Evanno, G

    2016-08-01

    In the context of global changes, the long-term viability of populations of endangered ectotherms may depend on their adaptive potential and ability to cope with temperature variations. We measured responses of Atlantic salmon embryos from four populations to temperature variations and used a QST -FST approach to study the adaptive divergence among these populations. Embryos were reared under two experimental conditions: a low temperature regime at 4 °C until eyed-stage and 10 °C until the end of embryonic development and a high temperature regime with a constant temperature of 10 °C throughout embryonic development. Significant variations among populations and population × temperature interactions were observed for embryo survival, incubation time and length. QST was higher than FST in all but one comparison suggesting an important effect of divergent selection. QST was also higher under the high-temperature treatment than at low temperature for length and survival due to a higher variance among populations under the stressful warmer treatment. Interestingly, heritability was lower for survival under high temperature in relation to a lower additive genetic variance under that treatment. Overall, these results reveal an adaptive divergence in thermal plasticity in embryonic life stages of Atlantic salmon suggesting that salmon populations may differentially respond to temperature variations induced by climate change. These results also suggest that changes in temperature may alter not only the adaptive potential of natural populations but also the selection regimes among them. PMID:27177256

  12. Variational time integrators in computational solid mechanics

    NASA Astrophysics Data System (ADS)

    Lew, Adrian Jose

    This thesis develops the theory and implementation of variational integrators for computational solid mechanics problems, and to some extent, for fluid mechanics problems as well. Variational integrators for finite dimensional mechanical systems are succinctly reviewed, and used as the foundations for the extension to continuum systems. The latter is accomplished by way of a space-tune formulation for Lagrangian continuum mechanics that unifies the derivation of tyre balance of linear momentum, energy and configurational forces, all of there as Euler-Lagrange equations of an extended Hamilton's principle. In this formulation, energy conservation and the path independence of the J- and L-integrals are conserved quantities emanating from Noether's theorem. Variational integrators for continuum mechanics are constructed by mimicking this variational structure, and a discrete Noether's theorem for rather general space-tune discretizations is presented. Additionally, the algorithms are automatically (multi)symplectic, and the (multi)symplectic form is uniquely defined by the theory. For instance, in nonlinear elastodynamics the algorithms exactly preserve linear and angular momenta, whenever the continuous system does. A class of variational algorithms is constructed, termed asynchronous variational integrators (AVI), which permit: the selection of independent time steps in each element of a finite element mesh, and the local time steps need riot bear an integral relation to each other. The conservation properties of both synchronous and asynchronous variational integrators are discussed in detail. In particular, AVI are found to nearly conserve energy both locally and globally, a distinguishing feature of variational integrators. The possibility of adapting the elemental time step to exactly satisfy the local energy balance equation, obtained from the extended variational principle, is analyzed. The AVI are also extended to include dissipative systems. The excellent

  13. Generalization of Prism Adaptation

    ERIC Educational Resources Information Center

    Redding, Gordon M.; Wallace, Benjamin

    2006-01-01

    Prism exposure produces 2 kinds of adaptive response. Recalibration is ordinary strategic remapping of spatially coded movement commands to rapidly reduce performance error. Realignment is the extraordinary process of transforming spatial maps to bring the origins of coordinate systems into correspondence. Realignment occurs when spatial…

  14. Prism Adaptation in Schizophrenia

    ERIC Educational Resources Information Center

    Bigelow, Nirav O.; Turner, Beth M.; Andreasen, Nancy C.; Paulsen, Jane S.; O'Leary, Daniel S.; Ho, Beng-Choon

    2006-01-01

    The prism adaptation test examines procedural learning (PL) in which performance facilitation occurs with practice on tasks without the need for conscious awareness. Dynamic interactions between frontostriatal cortices, basal ganglia, and the cerebellum have been shown to play key roles in PL. Disruptions within these neural networks have also…

  15. Adaptive Sampling Designs.

    ERIC Educational Resources Information Center

    Flournoy, Nancy

    Designs for sequential sampling procedures that adapt to cumulative information are discussed. A familiar illustration is the play-the-winner rule in which there are two treatments; after a random start, the same treatment is continued as long as each successive subject registers a success. When a failure occurs, the other treatment is used until…

  16. Adapting to the Environment.

    ERIC Educational Resources Information Center

    Kovach, Amy L.

    2003-01-01

    Presents an activity on natural selection and how the peppered moth's adaptive values for their colors changed during the Industrial Revolution in Manchester, England, influencing their survival and ultimately affecting the survival of their offspring. Includes activity objectives. (Author/KHR)

  17. Adaptive sequential controller

    DOEpatents

    El-Sharkawi, Mohamed A.; Xing, Jian; Butler, Nicholas G.; Rodriguez, Alonso

    1994-01-01

    An adaptive sequential controller (50/50') for controlling a circuit breaker (52) or other switching device to substantially eliminate transients on a distribution line caused by closing and opening the circuit breaker. The device adaptively compensates for changes in the response time of the circuit breaker due to aging and environmental effects. A potential transformer (70) provides a reference signal corresponding to the zero crossing of the voltage waveform, and a phase shift comparator circuit (96) compares the reference signal to the time at which any transient was produced when the circuit breaker closed, producing a signal indicative of the adaptive adjustment that should be made. Similarly, in controlling the opening of the circuit breaker, a current transformer (88) provides a reference signal that is compared against the time at which any transient is detected when the circuit breaker last opened. An adaptive adjustment circuit (102) produces a compensation time that is appropriately modified to account for changes in the circuit breaker response, including the effect of ambient conditions and aging. When next opened or closed, the circuit breaker is activated at an appropriately compensated time, so that it closes when the voltage crosses zero and opens when the current crosses zero, minimizing any transients on the distribution line. Phase angle can be used to control the opening of the circuit breaker relative to the reference signal provided by the potential transformer.

  18. Adaptive Computerized Instruction.

    ERIC Educational Resources Information Center

    Ray, Roger D.; And Others

    1995-01-01

    Describes an artificially intelligent multimedia computerized instruction system capable of developing a conceptual image of what a student is learning while the student is learning it. It focuses on principles of learning and adaptive behavioral control systems theory upon which the system is designed and demonstrates multiple user modes.…

  19. Adaptive MGS Phase Retrieval

    NASA Technical Reports Server (NTRS)

    Basinger, Scott A.; Bikkannavar, Siddarayappa; Cohen, David; Green, Joseph J.; Lou, John; Ohara, Catherine; Redding, David; Shi, Fang

    2008-01-01

    Adaptive MGS Phase Retrieval software uses the Modified Gerchberg-Saxton (MGS) algorithm, an image-based sensing method that can turn any focal plane science instrument into a wavefront sensor, avoiding the need to use external metrology equipment. Knowledge of the wavefront enables intelligent control of active optical systems.

  20. Adaptive Recreational Equipment.

    ERIC Educational Resources Information Center

    Schilling, Mary Lou, Ed.

    1983-01-01

    Designed for teachers interested in therapeutic recreation, the document lists sources of adaptive recreational equipment and their homemade counterparts. Brief descriptions for ordering or constructing recreational equipment for the visually impaired, poorly coordinated, physically impaired, and mentally retarded are given. Specific adaptations…

  1. Career Adaptability in Childhood

    ERIC Educational Resources Information Center

    Hartung, Paul J.; Porfeli, Erik J.; Vondracek, Fred W.

    2008-01-01

    Childhood marks the dawn of vocational development, involving developmental tasks, transitions, and change. Children must acquire the rudiments of career adaptability to envision a future, make educational and vocational decisions, explore self and occupations, and problem solve. The authors situate child vocational development within human life…

  2. Adapting to Environmental Jolts.

    ERIC Educational Resources Information Center

    Meyer, Alan D.

    1982-01-01

    Examines the reactions of three San Francisco (California) hospitals to the 1975 doctors' strike. Analyzes the anticipatory, responsive, and readjustment phases of the hospitals' adaptations in terms of each hospital's previous market strategy, organizational structure and ideology, and deployment of slack resources, including financial, human,…

  3. Coupled adaptive complex networks

    NASA Astrophysics Data System (ADS)

    Shai, S.; Dobson, S.

    2013-04-01

    Adaptive networks, which combine topological evolution of the network with dynamics on the network, are ubiquitous across disciplines. Examples include technical distribution networks such as road networks and the internet, natural and biological networks, and social science networks. These networks often interact with or depend upon other networks, resulting in coupled adaptive networks. In this paper we study susceptible-infected-susceptible (SIS) epidemic dynamics on coupled adaptive networks, where susceptible nodes are able to avoid contact with infected nodes by rewiring their intranetwork connections. However, infected nodes can pass the disease through internetwork connections, which do not change with time: The dependencies between the coupled networks remain constant. We develop an analytical formalism for these systems and validate it using extensive numerical simulation. We find that stability is increased by increasing the number of internetwork links, in the sense that the range of parameters over which both endemic and healthy states coexist (both states are reachable depending on the initial conditions) becomes smaller. Finally, we find a new stable state that does not appear in the case of a single adaptive network but only in the case of weakly coupled networks, in which the infection is endemic in one network but neither becomes endemic nor dies out in the other. Instead, it persists only at the nodes that are coupled to nodes in the other network through internetwork links. We speculate on the implications of these findings.

  4. Narrative, Adaptation, and Change

    ERIC Educational Resources Information Center

    Bateson, Mary Catherine

    2007-01-01

    This paper explores how individuals and communities orient themselves to the future by the way they story the past. There is a persistent tendency to think of such narratives as factual and therefore stable. The mutability of such narratives is actually a key adaptive characteristic, ranging from complete repression of individual traumas to public…

  5. Adapting Bulls to Florida

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The adaptation of bulls used for natural breeding purposes to the Gulf Coast region of the United States including all of Florida is an important topic. Nearly 40% of the U.S. cow/calf population resides in the Gulf Coast and Southeast. Thus, as A.I. is relatively rare, the number of bulls used for ...

  6. Aging and dark adaptation.

    PubMed

    Jackson, G R; Owsley, C; McGwin, G

    1999-11-01

    Older adults have serious difficulty seeing under low illumination and at night, even in the absence of ocular disease. Optical changes in the aged eye, such as pupillary miosis and increased lens density, cannot account for the severity of this problem, and little is known about its neural basis. Dark adaptation functions were measured on 94 adults ranging in age from the 20s to the 80s to assess the rate of rod-mediated sensitivity recovery after exposure to a 98% bleach. Fundus photography and a grading scale were used to characterize macular health in subjects over age 49 in order to control for macular disease. Thresholds for each subject were corrected for lens density based on individual estimates, and pupil diameter was controlled. Results indicated that during human aging there is a dramatic slowing in rod-mediated dark adaptation that can be attributed to delayed rhodopsin regeneration. During the second component of the rod-mediated phase of dark adaptation, the rate of sensitivity recovery decreased 0.02 log unit/min per decade, and the time constant of rhodopsin regeneration increased 8.4 s/decade. The amount of time to reach within 0.3 log units of baseline scotopic sensitivity increased 2.76 min/decade. These aging-related changes in rod-mediated dark adaptation may contribute to night vision problems commonly experienced by the elderly. PMID:10748929

  7. Telescope Adaptive Optics Code

    2005-07-28

    The Telescope AO Code has general adaptive optics capabilities plus specialized models for three telescopes with either adaptive optics or active optics systems. It has the capability to generate either single-layer or distributed Kolmogorov turbulence phase screens using the FFT. Missing low order spatial frequencies are added using the Karhunen-Loeve expansion. The phase structure curve is extremely dose to the theoreUcal. Secondly, it has the capability to simulate an adaptive optics control systems. The defaultmore » parameters are those of the Keck II adaptive optics system. Thirdly, it has a general wave optics capability to model the science camera halo due to scintillation from atmospheric turbulence and the telescope optics. Although this capability was implemented for the Gemini telescopes, the only default parameter specific to the Gemini telescopes is the primary mirror diameter. Finally, it has a model for the LSST active optics alignment strategy. This last model is highly specific to the LSST« less

  8. Flight test experience with an adaptive control system using a maximum likelihood parameter estimation technique

    NASA Technical Reports Server (NTRS)

    Hartmann, G.; Stein, G.; Powers, B.

    1979-01-01

    The flight test performance of an adaptive control system for the F-8 DFBW aircraft is summarized. The adaptive system is based on explicit identification of surface effectiveness parameters which are used for gain scheduling in a command augmentation system. Performance of this control law under various design parameter variations is presented. These include variations in test signal level, sample rate, and identification channel structure. Flight performance closely matches analysis and simulation predictions from previous references.

  9. Strong selection barriers explain microgeographic adaptation in wild salamander populations.

    PubMed

    Richardson, Jonathan L; Urban, Mark C

    2013-06-01

    Microgeographic adaptation occurs when populations evolve divergent fitness advantages across the spatial scales at which focal organisms regularly disperse. Although an increasing number of studies find evidence for microgeographic adaptation, the underlying causes often remain unknown. Adaptive divergence requires some combination of limited gene flow and strong divergent natural selection among populations. In this study, we estimated the relative influence of selection, gene flow, and the spatial arrangement of populations in shaping patterns of adaptive divergence in natural populations of the spotted salamander (Ambystoma maculatum). Within the study region, A. maculatum co-occur with the predatory marbled salamander (Ambystoma opacum) in some ponds, and past studies have established a link between predation risk and adaptive trait variation in A. maculatum. Using 14 microsatellite loci, we found a significant pattern of genetic divergence among A. maculatum populations corresponding to levels of A. opacum predation risk. Additionally, A. maculatum foraging rate was strongly associated with predation risk, genetic divergence, and the spatial relationship of ponds on the landscape. Our results indicate the sorting of adaptive genotypes by selection regime and strongly suggest that substantial selective barriers operate against gene flow. This outcome suggests that microgeographic adaptation in A. maculatum is possible because strong antagonistic selection quickly eliminates maladapted phenotypes despite ongoing and substantial immigration. Increasing evidence for microgeographic adaptation suggests a strong role for selective barriers in counteracting the homogenizing influence of gene flow. PMID:23730765

  10. Variations in genome mass.

    PubMed

    Wachtel, S S; Tiersch, T R

    1993-02-01

    1. Genome size varies considerably among vertebrates, ranging from less than 1 pg to more than 200 pg; the amount of DNA differing among individuals in a population can equal the amount in the entire structural gene complement. 2. Recent technological advances permit evaluation of genome size variation at several levels including sub-chromosomal, chromosomal and cellular. 3. Genome size variation may also be viewed from taxonomic levels, and across evolutionary time frames. 4. As sources of genome size variation are identified and studied, the conundrum of the C-value paradox (lack of correlations among genome size, genomic complexity and phylogenetic status of organisms) may prove to be more apparent than real. 5. For example, the limited and relatively constant genome size of avians may be related to the physiological constraints of flight. PMID:8462275

  11. Essential Variational Poisson Cohomology

    NASA Astrophysics Data System (ADS)

    De Sole, Alberto; Kac, Victor G.

    2012-08-01

    In our recent paper "The variational Poisson cohomology" (2011) we computed the dimension of the variational Poisson cohomology {{{H}^bullet_K({V})}} for any quasiconstant coefficient ℓ × ℓ matrix differential operator K of order N with invertible leading coefficient, provided that {{{V}}} is a normal algebra of differential functions over a linearly closed differential field. In the present paper we show that, for K skewadjoint, the {{{Z}}} -graded Lie superalgebra {{{H}^bullet_K({V})}} is isomorphic to the finite dimensional Lie superalgebra {{widetilde{H}(Nell,S)}} . We also prove that the subalgebra of "essential" variational Poisson cohomology, consisting of classes vanishing on the Casimirs of K, is zero. This vanishing result has applications to the theory of bi-Hamiltonian structures and their deformations. At the end of the paper we consider also the translation invariant case.

  12. Mediterranean sea level variations.

    NASA Astrophysics Data System (ADS)

    Vigo, I.; Sánchez Reales, J. M.; García, D.; Chao, B. F.

    2009-04-01

    In this work we report an updated study of the sea level variations for the Mediterranean sea for the period from October 1992 to January 2008. The study addresses two mayor issues: (i)The analysis of the spatial and temporal variability of sea surface height (SSH) from radar altimetry measurements (from TOPEX/Poseidon (T/P) + Jason-1, etc.). We use EOF analysis to explain most of its interannual variation, and how the different basins interact. (ii) The analysis of dynamics and balance of water mass transport for the whole period. We estimate the steric SSH by combining the steric SSH estimated from temperature and salt profiles simulated by the ECCO model with time-variable gravity (TVG) data (from GRACE) for the Mediterranean Sea. The estimated steric SSH together with the SSH obtained from altimetry allow for a more realistic estimation of the water mass variations in the Mediterranean for the whole period.

  13. Natural Selection and Evolution: Using Multimedia Slide Shows to Emphasize the Role of Genetic Variation

    ERIC Educational Resources Information Center

    Malone, Molly

    2012-01-01

    Most middle school students comprehend that organisms have adaptations that enable their survival and that successful adaptations prevail in a population over time. Yet they often miss that those bird beaks, moth-wing colors, or whatever traits are the result of random, normal genetic variations that just happen to confer a negative, neutral, or…

  14. Earth orbital variations and vertebrate bioevolution

    NASA Technical Reports Server (NTRS)

    Mclean, Dewey M.

    1988-01-01

    Cause of the Pleistocene-Holocene transition mammalian extinctions at the end of the last age is the subject of debate between those advocating human predation and climate change. Identification of an ambient air temperature (AAT)-uterine blood flow (UBF) coupling phenomenon supports climate change as a factor in the extinctions, and couples the extinctions to earth orbital variations that drive ice age climatology. The AAT-UBF phenomenon couples mammalian bioevolution directly to climate change via effects of environmental heat upon blood flow to the female uterus and damage to developing embryos. Extinctions were in progress during climatic warming before the Younger Dryas event, and after, at times when the AAT-UBF couple would have been operative; however, impact of a sudden short-term cooling on mammals in the process of adapting to smaller size and relatively larger S/V would have been severe. Variations in earth's orbit, and orbital forcing of atmospheric CO2 concentrations, were causes of the succession of Pleistocene ice ages. Coincidence of mammalian extinctions with terminations of the more intense cold stages links mammalian bioevolution to variations in earth's orbit. Earth orbital variations are a driving source of vertebrate bioevolution.

  15. Customizing Countermeasure Prescriptions using Predictive Measures of Sensorimotor Adaptability

    NASA Technical Reports Server (NTRS)

    Bloomberg, J. J.; Peters, B. T.; Mulavara, A. P.; Miller, C. A.; Batson, C. D.; Wood, S. J.; Guined, J. R.; Cohen, H. S.; Buccello-Stout, R.; DeDios, Y. E.; Kofman, I. S.; Szecsy, D. L.; Erdeniz, B.; Koppelmans, V.; Seidler, R. D.

    2014-01-01

    Astronauts experience sensorimotor disturbances during the initial exposure to microgravity and during the readapation phase following a return to a gravitational environment. These alterations may lead to disruption in the ability to perform mission critical functional tasks during and after these gravitational transitions. Astronauts show significant inter-subject variation in adaptive capability following gravitational transitions. The ability to predict the manner and degree to which each individual astronaut will be affected would improve the effectiveness of a countermeasure comprised of a training program designed to enhance sensorimotor adaptability. Due to this inherent individual variability we need to develop predictive measures of sensorimotor adaptability that will allow us to predict, before actual space flight, which crewmember will experience challenges in adaptive capacity. Thus, obtaining this information will allow us to design and implement better sensorimotor adaptability training countermeasures that will be customized for each crewmember's unique adaptive capabilities. Therefore the goals of this project are to: 1) develop a set of predictive measures capable of identifying individual differences in sensorimotor adaptability, and 2) use this information to design sensorimotor adaptability training countermeasures that are customized for each crewmember's individual sensorimotor adaptive characteristics. To achieve these goals we are currently pursuing the following specific aims: Aim 1: Determine whether behavioral metrics of individual sensory bias predict sensorimotor adaptability. For this aim, subjects perform tests that delineate individual sensory biases in tests of visual, vestibular, and proprioceptive function. Aim 2: Determine if individual capability for strategic and plastic-adaptive responses predicts sensorimotor adaptability. For this aim, each subject's strategic and plastic-adaptive motor learning abilities are assessed using

  16. Genetic structure and local adaptation of European wheat yellow rust populations: the role of temperature-specific adaptation

    PubMed Central

    Mboup, Mamadou; Bahri, Bochra; Leconte, Marc; De Vallavieille-Pope, Claude; Kaltz, Oliver; Enjalbert, Jérôme

    2012-01-01

    Environmental heterogeneity influences coevolution and local adaptation in host–parasite systems. This also concerns applied issues, because the geographic range of parasites may depend on their capacity to adapt to abiotic conditions. We studied temperature-specific adaptation in the wheat yellow/stripe rust pathogen, Puccinia striiformis f.sp. tritici (PST). Using laboratory experiments, PST isolates from northern and southern France were studied for their ability to germinate and to infect bread and durum wheat cultivars over a temperature gradient. Pathogen origin × temperature interactions for infectivity and germination rate suggest local adaptation to high- versus low-temperature regimes in south and north. Competition experiments in southern and northern field sites showed a general competitive advantage of southern over northern isolates. This advantage was particularly pronounced in the southern ‘home’ site, consistent with a model integrating laboratory infectivity and field temperature variation. The stable PST population structure in France likely reflects adaptation to ecological and genetic factors: persistence of southern PST may be due to adaptation to the warmer Mediterranean climate; and persistence of northern PST can be explained by adaptation to commonly used cultivars, for which southern isolates are lacking the relevant virulence genes. Thus, understanding the role of temperature-specific adaptations may help to improve forecast models or breeding programmes. PMID:25568055

  17. Neural Control Adaptation to Motor Noise Manipulation

    PubMed Central

    Hasson, Christopher J.; Gelina, Olga; Woo, Garrett

    2016-01-01

    Antagonistic muscular co-activation can compensate for movement variability induced by motor noise at the expense of increased energetic costs. Greater antagonistic co-activation is commonly observed in older adults, which could be an adaptation to increased motor noise. The present study tested this hypothesis by manipulating motor noise in 12 young subjects while they practiced a goal-directed task using a myoelectric virtual arm, which was controlled by their biceps and triceps muscle activity. Motor noise was increased by increasing the coefficient of variation (CV) of the myoelectric signals. As hypothesized, subjects adapted by increasing antagonistic co-activation, and this was associated with reduced noise-induced performance decrements. A second hypothesis was that a virtual decrease in motor noise, achieved by smoothing the myoelectric signals, would have the opposite effect: co-activation would decrease and motor performance would improve. However, the results showed that a decrease in noise made performance worse instead of better, with no change in co-activation. Overall, these findings suggest that the nervous system adapts to virtual increases in motor noise by increasing antagonistic co-activation, and this preserves motor performance. Reducing noise may have failed to benefit performance due to characteristics of the filtering process itself, e.g., delays are introduced and muscle activity bursts are attenuated. The observed adaptations to increased noise may explain in part why older adults and many patient populations have greater antagonistic co-activation, which could represent an adaptation to increased motor noise, along with a desire for increased joint stability. PMID:26973487

  18. Neural Control Adaptation to Motor Noise Manipulation.

    PubMed

    Hasson, Christopher J; Gelina, Olga; Woo, Garrett

    2016-01-01

    Antagonistic muscular co-activation can compensate for movement variability induced by motor noise at the expense of increased energetic costs. Greater antagonistic co-activation is commonly observed in older adults, which could be an adaptation to increased motor noise. The present study tested this hypothesis by manipulating motor noise in 12 young subjects while they practiced a goal-directed task using a myoelectric virtual arm, which was controlled by their biceps and triceps muscle activity. Motor noise was increased by increasing the coefficient of variation (CV) of the myoelectric signals. As hypothesized, subjects adapted by increasing antagonistic co-activation, and this was associated with reduced noise-induced performance decrements. A second hypothesis was that a virtual decrease in motor noise, achieved by smoothing the myoelectric signals, would have the opposite effect: co-activation would decrease and motor performance would improve. However, the results showed that a decrease in noise made performance worse instead of better, with no change in co-activation. Overall, these findings suggest that the nervous system adapts to virtual increases in motor noise by increasing antagonistic co-activation, and this preserves motor performance. Reducing noise may have failed to benefit performance due to characteristics of the filtering process itself, e.g., delays are introduced and muscle activity bursts are attenuated. The observed adaptations to increased noise may explain in part why older adults and many patient populations have greater antagonistic co-activation, which could represent an adaptation to increased motor noise, along with a desire for increased joint stability. PMID:26973487

  19. Numerical design of an adaptive aileron

    NASA Astrophysics Data System (ADS)

    Amendola, Gianluca; Dimino, Ignazio; Concilio, Antonio; Magnifico, Marco; Pecora, Rosario

    2016-04-01

    The study herein described is aimed at investigating the feasibility of an innovative full-scale camber morphing aileron device. In the framework of the "Adaptive Aileron" project, an international cooperation between Italy and Canada, this goal was carried out with the integration of different morphing concepts in a wing-tip prototype. As widely demonstrated in recent European projects such as Clean Sky JTI and SARISTU, wing trailing edge morphing may lead to significant drag reduction (up to 6%) in off-design flight points by adapting chord-wise camber variations in cruise to compensate A/C weight reduction following fuel consumption. Those researches focused on the flap region as the most immediate solution to implement structural adaptations. However, there is also a growing interest in extending morphing functionalities to the aileron region preserving its main functionality in controlling aircraft directional stability. In fact, the external region of the wing seems to be the most effective in producing "lift over drag" improvements by morphing. Thus, the objective of the presented research is to achieve a certain drag reduction in off-design flight points by adapting wing shape and lift distribution following static deflections. In perspective, the developed device could also be used as a load alleviation system to reduce gust effects, augmenting its frequency bandwidth. In this paper, the preliminary design of the adaptive aileron is first presented, assessed on the base of the external aerodynamic loads. The primary structure is made of 5 segmented ribs, distributed along 4 bays, each splitted into three consecutive parts, connected with spanwise stringers. The aileron shape modification is then implemented by means of an actuation system, based on a classical quick-return mechanism, opportunely suited for the presented application. Finite element analyses were assessed for properly sizing the load-bearing structure and actuation systems and for

  20. SU-E-J-153: MRI Based, Daily Adaptive Radiotherapy for Rectal Cancer: Contour Adaptation

    SciTech Connect

    Kleijnen, J; Burbach, M; Verbraeken, T; Weggers, R; Zoetelief, A; Reerink, O; Lagendijk, J; Raaymakers, B; Asselen, B

    2014-06-01

    Purpose: A major hurdle in adaptive radiotherapy is the adaptation of the planning MRI's delineations to the daily anatomy. We therefore investigate the accuracy and time needed for online clinical target volume (CTV) adaptation by radiation therapists (RTT), to be used in MRI-guided adaptive treatments on a MRI-Linac (MRL). Methods: Sixteen patients, diagnosed with early stage rectal cancer, underwent a T2-weighted MRI prior to each fraction of short-course radiotherapy, resulting in 4–5 scans per patient. On these scans, the CTV was delineated according to guidelines by an experienced radiation oncologist (RO) and considered to be the gold standard. For each patient, the first MRI was considered as the planning MRI and matched on bony anatomy to the 3–4 daily MRIs. The planning MRI's CTV delineation was rigidly propagated to the daily MRI scans as a proposal for adaptation. Three RTTs in training started the adaptation of the CTV conform guidelines, after a two hour training lecture and a two patient (n=7) training set. To assess the inter-therapist variation, all three RTTs altered delineations of 3 patients (n=12). One RTT altered the CTV delineations (n=53) of the remaining 11 patients. Time needed for adaptation of the CTV to guidelines was registered.As a measure of agreement, the conformity index (CI) was determined between the RTTs' delineations as a group. Dice similarity coefficients were determined between delineations of the RTT and the RO. Results: We found good agreement between RTTs' and RO's delineations (average Dice=0.91, SD=0.03). Furthermore, the inter-observer agreement between the RTTs was high (average CI=0.94, SD=0.02). Adaptation time reduced from 10:33 min (SD= 3:46) to 2:56 min (SD=1:06) between the first and last ten delineations, respectively. Conclusion: Daily CTV adaptation by RTTs, seems a feasible and safe way to introduce daily, online MRI-based plan adaptation for a MRL.

  1. Contrast Adaptation Implies Two Spatiotemporal Channels but Three Adapting Processes

    ERIC Educational Resources Information Center

    Langley, Keith; Bex, Peter J.

    2007-01-01

    The contrast gain control model of adaptation predicts that the effects of contrast adaptation correlate with contrast sensitivity. This article reports that the effects of high contrast spatiotemporal adaptors are maximum when adapting around 19 Hz, which is a factor of two or more greater than the peak in contrast sensitivity. To explain the…

  2. 75 FR 57859 - Specially Adapted Housing and Special Home Adaptation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-23

    ..., 2009, (74 FR 67145), VA proposed to amend its regulations pertaining to eligibility for specially... AFFAIRS 38 CFR Part 3 RIN 2900-AN21 Specially Adapted Housing and Special Home Adaptation AGENCY... housing and special home adaptation grants. This final rule incorporates certain provisions from...

  3. Variation and Linguistic Theory.

    ERIC Educational Resources Information Center

    Bailey, Charles-James N.

    This volume presents principles and models for describing language variation, and introduces a time-based, dynamic framework for linguistic description. The book first summarizes some of the problems of grammatical description encountered from Saussure through the present and then outlines possibilities for new descriptions of language which take…

  4. Seasonal Variation in Epidemiology

    ERIC Educational Resources Information Center

    Marrero, Osvaldo

    2013-01-01

    Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

  5. Variational transition state theory

    SciTech Connect

    Truhlar, D.G.

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  6. (Genomic variation in maize)

    SciTech Connect

    Rivin, C.J.

    1991-01-01

    These studies have sought to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in Fl hybrids, tissue culture cells and regenerated plants. We describe the repetitive portion of the maize genome as composed primarily of sequences that vary markedly in copy number among different genetic stocks. The most highly variable is the 185 bp repeat associated with the heterochromatic chromosome knobs. Even in lines without visible knobs, there is a considerable quantity of tandemly arrayed repeats. We also found a high degree of variability for the tandemly arrayed 5S and ribosomal DNA repeats. While such variation might be expected as the result of unequal cross-over, we were surprised to find considerable variation among lower copy number, dispersed repeats as well. One highly repeated sequence that showed a complex tandem and dispersed arrangement stood out as showing no detectable variability among the maize lines. In striking contrast to the variability seen between the inbred stocks, individuals within a stock were indistinguishable with regard to their repeated sequence multiplicities.

  7. Sociolinguistic Variation and Change.

    ERIC Educational Resources Information Center

    Trudgill, Peter

    This book examines linguistic variation and change. Section 1, "Sociohistorical Linguistics," includes: (1) "British Vernacular Dialects in the Formation of American English: The Case of East Anglian 'Do'"; (2) "'Short o' in East Anglia and New England"; and (3) "Sociohistorical Linguistics and Dialect Survival: A Note on Another Nova Scotian…

  8. Determining Faculty Grading Variation.

    ERIC Educational Resources Information Center

    Demerjian, Marlene D.

    A study was undertaken at the College of the Canyons, in California, to assess the variation of grades given by mathematics instructors teaching intermediate algebra. A sample was drawn from all instructors who taught Math 070 repeatedly from fall 1990 to fall 1994, resulting in the examination of the grades of at least 200 students from classes…

  9. Fluency Variation in Adolescents

    ERIC Educational Resources Information Center

    De Andrade, Claudia Regina Furquim; Martins, Vanessa De Oliveira

    2007-01-01

    The Speech Fluency Profile of fluent adolescent speakers of Brazilian Portuguese, were examined with respect to gender and neurolinguistic variations. Speech samples of 130 male and female adolescents, aged between 12;0 and 17;11 years were gathered. They were analysed according to type of speech disruption; speech rate; and frequency of speech…

  10. NEEDS - Information Adaptive System

    NASA Technical Reports Server (NTRS)

    Kelly, W. L.; Benz, H. F.; Meredith, B. D.

    1980-01-01

    The Information Adaptive System (IAS) is an element of the NASA End-to-End Data System (NEEDS) Phase II and is focused toward onboard image processing. The IAS is a data preprocessing system which is closely coupled to the sensor system. Some of the functions planned for the IAS include sensor response nonuniformity correction, geometric correction, data set selection, data formatting, packetization, and adaptive system control. The inclusion of these sensor data preprocessing functions onboard the spacecraft will significantly improve the extraction of information from the sensor data in a timely and cost effective manner, and provide the opportunity to design sensor systems which can be reconfigured in near real-time for optimum performance. The purpose of this paper is to present the preliminary design of the IAS and the plans for its development.

  11. Adaptive control for accelerators

    DOEpatents

    Eaton, Lawrie E.; Jachim, Stephen P.; Natter, Eckard F.

    1991-01-01

    An adaptive feedforward control loop is provided to stabilize accelerator beam loading of the radio frequency field in an accelerator cavity during successive pulses of the beam into the cavity. A digital signal processor enables an adaptive algorithm to generate a feedforward error correcting signal functionally determined by the feedback error obtained by a beam pulse loading the cavity after the previous correcting signal was applied to the cavity. Each cavity feedforward correcting signal is successively stored in the digital processor and modified by the feedback error resulting from its application to generate the next feedforward error correcting signal. A feedforward error correcting signal is generated by the digital processor in advance of the beam pulse to enable a composite correcting signal and the beam pulse to arrive concurrently at the cavity.

  12. Unconsciously triggered conflict adaptation.

    PubMed

    van Gaal, Simon; Lamme, Victor A F; Ridderinkhof, K Richard

    2010-01-01

    In conflict tasks such as the Stroop, the Eriksen flanker or the Simon task, it is generally observed that the detection of conflict in the current trial reduces the impact of conflicting information in the subsequent trial; a phenomenon termed conflict adaptation. This higher-order cognitive control function has been assumed to be restricted to cases where conflict is experienced consciously. In the present experiment we manipulated the awareness of conflict-inducing stimuli in a metacontrast masking paradigm to directly test this assumption. Conflicting response tendencies were elicited either consciously (through primes that were weakly masked) or unconsciously (strongly masked primes). We demonstrate trial-by-trial conflict adaptation effects after conscious as well as unconscious conflict, which could not be explained by direct stimulus/response repetitions. These findings show that unconscious information can have a longer-lasting influence on our behavior than previously thought and further stretch the functional boundaries of unconscious cognition. PMID:20634898

  13. Bacterial surface adaptation

    NASA Astrophysics Data System (ADS)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  14. Intestinal mucosal adaptation

    PubMed Central

    Drozdowski, Laurie; Thomson, Alan BR

    2006-01-01

    Intestinal failure is a condition characterized by malnutrition and/or dehydration as a result of the inadequate digestion and absorption of nutrients. The most common cause of intestinal failure is short bowel syndrome, which occurs when the functional gut mass is reduced below the level necessary for adequate nutrient and water absorption. This condition may be congenital, or may be acquired as a result of a massive resection of the small bowel. Following resection, the intestine is capable of adaptation in response to enteral nutrients as well as other trophic stimuli. Identifying factors that may enhance the process of intestinal adaptation is an exciting area of research with important potential clinical applications. PMID:16937429

  15. Evolutionary adaptation to thermosensation.

    PubMed

    Gracheva, Elena O; Bagriantsev, Sviatoslav N

    2015-10-01

    Organisms continuously evolve to adapt to changing environmental conditions. Chief among these are daily and seasonal temperature fluctuations. Relatively small in terms of real physical values, temperature fluctuations of just a few degrees can profoundly affect organismal functions. In vertebrates, temperature is detected by primary afferents of somatosensory neurons, which express thermo-gated ion channels. Most of our knowledge about temperature receptors comes from seminal studies in mice and rats. Recent work uncovered thermosensory mechanisms in other vertebrates, shedding light onto the diversity of thermosensory adaptations. Here, we summarize molecular mechanisms of thermosensation in different species and discuss the need to use the standard laboratory rodents and non-standard species side-by-side in order to understand fundamental principles of somatosensation. PMID:25698346

  16. Adaptive sensor fusion

    NASA Astrophysics Data System (ADS)

    Kadar, Ivan

    1995-07-01

    A perceptual reasoning system adaptively extracting, associating, and fusing information from multiple sources, at various levels of abstraction, is considered as the building block for the next generation of surveillance systems. A system architecture is presented which makes use of both centralized and distributed predetection fusion combined with intelligent monitor and control coupling both on-platform and off-board track and decision level fusion results. The goal of this system is to create a `gestalt fused sensor system' whose information product is greater than the sum of the information products from the individual sensors and has performance superior to either individual or a sub-group of combined sensors. The application of this architectural concept to the law enforcement arena (e.g. drug interdiction) utilizing multiple spatially and temporally diverse surveillance platforms and/or information sources, is used to illustrate the benefits of the adaptive perceptual reasoning system concept.

  17. Adaptive Algebraic Multigrid Methods

    SciTech Connect

    Brezina, M; Falgout, R; MacLachlan, S; Manteuffel, T; McCormick, S; Ruge, J

    2004-04-09

    Our ability to simulate physical processes numerically is constrained by our ability to solve the resulting linear systems, prompting substantial research into the development of multiscale iterative methods capable of solving these linear systems with an optimal amount of effort. Overcoming the limitations of geometric multigrid methods to simple geometries and differential equations, algebraic multigrid methods construct the multigrid hierarchy based only on the given matrix. While this allows for efficient black-box solution of the linear systems associated with discretizations of many elliptic differential equations, it also results in a lack of robustness due to assumptions made on the near-null spaces of these matrices. This paper introduces an extension to algebraic multigrid methods that removes the need to make such assumptions by utilizing an adaptive process. The principles which guide the adaptivity are highlighted, as well as their application to algebraic multigrid solution of certain symmetric positive-definite linear systems.

  18. Reconfigurable environmentally adaptive computing

    NASA Technical Reports Server (NTRS)

    Coxe, Robin L. (Inventor); Galica, Gary E. (Inventor)

    2008-01-01

    Described are methods and apparatus, including computer program products, for reconfigurable environmentally adaptive computing technology. An environmental signal representative of an external environmental condition is received. A processing configuration is automatically selected, based on the environmental signal, from a plurality of processing configurations. A reconfigurable processing element is reconfigured to operate according to the selected processing configuration. In some examples, the environmental condition is detected and the environmental signal is generated based on the detected condition.

  19. Intelligent adaptive structures

    NASA Technical Reports Server (NTRS)

    Wada, Ben K.

    1990-01-01

    'Intelligent Adaptive Structures' (IAS) refers to structural systems whose geometric and intrinsic structural characteristics can be automatically changed to meet mission requirements with changing operational scenarios. An IAS is composed of actuators, sensors, and a control logic; these are integrated in a distributed fashion within the elements of the structure. The IAS concepts thus far developed for space antennas and other precision structures should be applicable to civil, marine, automotive, and aeronautical structural systems.

  20. Adaptive Structures Flight Experiments

    NASA Technical Reports Server (NTRS)

    Martin, Maurice

    1992-01-01

    The topics are presented in viewgraph form and include the following: adaptive structures flight experiments; enhanced resolution using active vibration suppression; Advanced Controls Technology Experiment (ACTEX); ACTEX program status; ACTEX-2; ACTEX-2 program status; modular control patch; STRV-1b Cryocooler Vibration Suppression Experiment; STRV-1b program status; Precision Optical Bench Experiment (PROBE); Clementine Spacecraft Configuration; TECHSAT all-composite spacecraft; Inexpensive Structures and Materials Flight Experiment (INFLEX); and INFLEX program status.

  1. Adaptive structures flight experiments

    NASA Astrophysics Data System (ADS)

    Martin, Maurice

    The topics are presented in viewgraph form and include the following: adaptive structures flight experiments; enhanced resolution using active vibration suppression; Advanced Controls Technology Experiment (ACTEX); ACTEX program status; ACTEX-2; ACTEX-2 program status; modular control patch; STRV-1b Cryocooler Vibration Suppression Experiment; STRV-1b program status; Precision Optical Bench Experiment (PROBE); Clementine Spacecraft Configuration; TECHSAT all-composite spacecraft; Inexpensive Structures and Materials Flight Experiment (INFLEX); and INFLEX program status.

  2. Adaptive optics ophthalmoscopy

    PubMed Central

    Roorda, Austin; Duncan, Jacque L.

    2016-01-01

    This review starts with a brief history and description of adaptive optics (AO) technology, followed by a showcase of the latest capabilities of AO systems for imaging the human retina and an extensive review of the literature on where AO is being used clinically. The review concludes with a discussion on future directions and guidance on usage and interpretation of images from AO systems for the eye. PMID:26973867

  3. Adaptive optical processors.

    PubMed

    Ghosh, A

    1989-06-15

    There are two different approaches for improving the accuracy of analog optical associative processors: postprocessing with a bimodal system and preprocessing with a preconditioner. These two approaches can be combined to develop an adaptive optical multiprocessor that can adjust the computational steps depending on the data and produce solutions of linear algebra problems with a specified accuracy in a given amount of time. PMID:19752909

  4. Adaptive bidirectional associative memories.

    PubMed

    Kosko, B

    1987-12-01

    Bidirectionality, forward and backward information flow, is introduced in neural networks to produce two-way associative search for stored stimulus-response associations (A(i),B(i)). Two fields of neurons, F(A) and F(B), are connected by an n x p synaptic marix M. Passing information through M gives one direction, passing information through its transpose M(T) gives the other. Every matrix is bidirectionally stable for bivalent and for continuous neurons. Paired data (A(i),B(i)) are encoded in M by summing bipolar correlation matrices. The bidirectional associative memory (BAM) behaves as a two-layer hierarchy of symmetrically connected neurons. When the neurons in F(A) and F(B) are activated, the network quickly evolves to a stable state of twopattern reverberation, or pseudoadaptive resonance, for every connection topology M. The stable reverberation corresponds to a system energy local minimum. An adaptive BAM allows M to rapidly learn associations without supervision. Stable short-term memory reverberations across F(A) and F(B) gradually seep pattern information into the long-term memory connections M, allowing input associations (A(i),B(i)) to dig their own energy wells in the network state space. The BAM correlation encoding scheme is extended to a general Hebbian learning law. Then every BAM adaptively resonates in the sense that all nodes and edges quickly equilibrate in a system energy local minimum. A sampling adaptive BAM results when many more training samples are presented than there are neurons in F(B) and F(B), but presented for brief pulses of learning, not allowing learning to fully or nearly converge. Learning tends to improve with sample size. Sampling adaptive BAMs can learn some simple continuous mappings and can rapidly abstract bivalent associations from several noisy gray-scale samples. PMID:20523473

  5. Diurnal variations of Titan

    NASA Astrophysics Data System (ADS)

    Cui, J.; Galand, M.; Yelle, R. V.; Vuitton, V.; Wahlund, J.-E.; Lavvas, P. P.; Mueller-Wodarg, I. C. F.; Kasprzak, W. T.; Waite, J. H.

    2009-04-01

    We present our analysis of the diurnal variations of Titan's ionosphere (between 1,000 and 1,400 km) based on a sample of Ion Neutral Mass Spectrometer (INMS) measurements in the Open Source Ion (OSI) mode obtained from 8 close encounters of the Cassini spacecraft with Titan. Though there is an overall ion depletion well beyond the terminator, the ion content on Titan's nightside is still appreciable, with a density plateau of ~700 cm-3 below ~1,300 km. Such a plateau is associated with the combination of distinct diurnal variations of light and heavy ions. Light ions (e.g. CH5+, HCNH+, C2H5+) show strong diurnal variation, with clear bite-outs in their nightside distributions. In contrast, heavy ions (e.g. c-C3H3+, C2H3CNH+, C6H7+) present modest diurnal variation, with significant densities observed on the nightside. We propose that the distinctions between light and heavy ions are associated with their different chemical loss pathways, with the former primarily through "fast" ion-neutral chemistry and the latter through "slow" electron dissociative recombination. The INMS data suggest day-to-night transport as an important source of ions on Titan's nightside, to be distinguished from the conventional scenario of auroral ionization by magnetospheric particles as the only ionizing source on the nightside. This is supported by the strong correlation between the observed night-to-day ion density ratios and the associated ion lifetimes. We construct a time-dependent ion chemistry model to investigate the effects of day-to-night transport on the ionospheric structures of Titan. The predicted diurnal variation has similar general characteristics to those observed, with some apparent discrepancies which could be reconciled by imposing fast horizontal thermal winds in Titan's upper atmosphere.

  6. Accelerated adaptive integration method.

    PubMed

    Kaus, Joseph W; Arrar, Mehrnoosh; McCammon, J Andrew

    2014-05-15

    Conformational changes that occur upon ligand binding may be too slow to observe on the time scales routinely accessible using molecular dynamics simulations. The adaptive integration method (AIM) leverages the notion that when a ligand is either fully coupled or decoupled, according to λ, barrier heights may change, making some conformational transitions more accessible at certain λ values. AIM adaptively changes the value of λ in a single simulation so that conformations sampled at one value of λ seed the conformational space sampled at another λ value. Adapting the value of λ throughout a simulation, however, does not resolve issues in sampling when barriers remain high regardless of the λ value. In this work, we introduce a new method, called Accelerated AIM (AcclAIM), in which the potential energy function is flattened at intermediate values of λ, promoting the exploration of conformational space as the ligand is decoupled from its receptor. We show, with both a simple model system (Bromocyclohexane) and the more complex biomolecule Thrombin, that AcclAIM is a promising approach to overcome high barriers in the calculation of free energies, without the need for any statistical reweighting or additional processors. PMID:24780083

  7. Accelerated Adaptive Integration Method

    PubMed Central

    2015-01-01

    Conformational changes that occur upon ligand binding may be too slow to observe on the time scales routinely accessible using molecular dynamics simulations. The adaptive integration method (AIM) leverages the notion that when a ligand is either fully coupled or decoupled, according to λ, barrier heights may change, making some conformational transitions more accessible at certain λ values. AIM adaptively changes the value of λ in a single simulation so that conformations sampled at one value of λ seed the conformational space sampled at another λ value. Adapting the value of λ throughout a simulation, however, does not resolve issues in sampling when barriers remain high regardless of the λ value. In this work, we introduce a new method, called Accelerated AIM (AcclAIM), in which the potential energy function is flattened at intermediate values of λ, promoting the exploration of conformational space as the ligand is decoupled from its receptor. We show, with both a simple model system (Bromocyclohexane) and the more complex biomolecule Thrombin, that AcclAIM is a promising approach to overcome high barriers in the calculation of free energies, without the need for any statistical reweighting or additional processors. PMID:24780083

  8. Vestibulospinal adaptation to microgravity

    NASA Technical Reports Server (NTRS)

    Paloski, W. H.

    1998-01-01

    Human balance control is known to be transiently disrupted after spaceflight; however, the mechanisms responsible for postflight postural ataxia are still under investigation. In this report, we propose a conceptual model of vestibulospinal adaptation based on theoretical adaptive control concepts and supported by the results from a comprehensive study of balance control recovery after spaceflight. The conceptual model predicts that immediately after spaceflight the balance control system of a returning astronaut does not expect to receive gravity-induced afferent inputs and that descending vestibulospinal control of balance is disrupted until the central nervous system is able to cope with the newly available vestibular otolith information. Predictions of the model are tested using data from a study of the neurosensory control of balance in astronauts immediately after landing. In that study, the mechanisms of sensorimotor balance control were assessed under normal, reduced, and/or altered (sway-referenced) visual and somatosensory input conditions. We conclude that the adaptive control model accurately describes the neurobehavioral responses to spaceflight and that similar models of altered sensory, motor, or environmental constraints are needed clinically to predict responses that patients with sensorimotor pathologies may have to various visual-vestibular or changing stimulus environments.

  9. Adaptive Dynamic Bayesian Networks

    SciTech Connect

    Ng, B M

    2007-10-26

    A discrete-time Markov process can be compactly modeled as a dynamic Bayesian network (DBN)--a graphical model with nodes representing random variables and directed edges indicating causality between variables. Each node has a probability distribution, conditional on the variables represented by the parent nodes. A DBN's graphical structure encodes fixed conditional dependencies between variables. But in real-world systems, conditional dependencies between variables may be unknown a priori or may vary over time. Model errors can result if the DBN fails to capture all possible interactions between variables. Thus, we explore the representational framework of adaptive DBNs, whose structure and parameters can change from one time step to the next: a distribution's parameters and its set of conditional variables are dynamic. This work builds on recent work in nonparametric Bayesian modeling, such as hierarchical Dirichlet processes, infinite-state hidden Markov networks and structured priors for Bayes net learning. In this paper, we will explain the motivation for our interest in adaptive DBNs, show how popular nonparametric methods are combined to formulate the foundations for adaptive DBNs, and present preliminary results.

  10. Adaptive building skin structures

    NASA Astrophysics Data System (ADS)

    Del Grosso, A. E.; Basso, P.

    2010-12-01

    The concept of adaptive and morphing structures has gained considerable attention in the recent years in many fields of engineering. In civil engineering very few practical applications are reported to date however. Non-conventional structural concepts like deployable, inflatable and morphing structures may indeed provide innovative solutions to some of the problems that the construction industry is being called to face. To give some examples, searches for low-energy consumption or even energy-harvesting green buildings are amongst such problems. This paper first presents a review of the above problems and technologies, which shows how the solution to these problems requires a multidisciplinary approach, involving the integration of architectural and engineering disciplines. The discussion continues with the presentation of a possible application of two adaptive and dynamically morphing structures which are proposed for the realization of an acoustic envelope. The core of the two applications is the use of a novel optimization process which leads the search for optimal solutions by means of an evolutionary technique while the compatibility of the resulting configurations of the adaptive envelope is ensured by the virtual force density method.

  11. Rapid local adaptation mediates zooplankton community assembly in experimental mesocosms.

    PubMed

    Pantel, Jelena H; Duvivier, Cathy; Meester, Luc De

    2015-10-01

    Adaptive evolution can occur over similar timescales as ecological processes such as community assembly, but its particular effects on community assembly and structure and their magnitude are poorly understood. In experimental evolution trials, Daphnia magna were exposed to varying environments (presence and absence of fish and artificial macrophytes) for 2 months. Then, in a common gardening experiment, we compared zooplankton community composition when either experimentally adapted or D. magna from the original population were present. Local adaptation of D. magna significantly altered zooplankton community composition, leading to a suppression of abundances for some zooplankton taxa and facilitation for others. The effect size of D. magna adaptation was similar to that of adding fish or macrophytes to mesocosms, two important drivers of zooplankton community structure. Our results suggest that substantial amounts of variation in community composition in natural systems may be unexplained if evolutionary dynamics are ignored. PMID:26251339

  12. Advanced Adaptive Optics Technology Development

    SciTech Connect

    Olivier, S

    2001-09-18

    The NSF Center for Adaptive Optics (CfAO) is supporting research on advanced adaptive optics technologies. CfAO research activities include development and characterization of micro-electro-mechanical systems (MEMS) deformable mirror (DM) technology, as well as development and characterization of high-resolution adaptive optics systems using liquid crystal (LC) spatial light modulator (SLM) technology. This paper presents an overview of the CfAO advanced adaptive optics technology development activities including current status and future plans.

  13. A variational principle for compressible fluid mechanics: Discussion of the multi-dimensional theory

    NASA Technical Reports Server (NTRS)

    Prozan, R. J.

    1982-01-01

    The variational principle for compressible fluid mechanics previously introduced is extended to two dimensional flow. The analysis is stable, exactly conservative, adaptable to coarse or fine grids, and very fast. Solutions for two dimensional problems are included. The excellent behavior and results lend further credence to the variational concept and its applicability to the numerical analysis of complex flow fields.

  14. Theory of psychological adaptive modes.

    PubMed

    Lehti, Juha

    2016-05-01

    When an individual is facing a stressor and normal stress-response mechanism cannot guarantee sufficient adaptation, special emotional states, adaptive modes, are activated (for example a depressive reaction). Adaptive modes are involuntary states of mind, they are of comprehensive nature, they interfere with normal functioning, and they cannot be repressed or controlled the same way as many emotions. Their transformational nature differentiates them from other emotional states. The object of the adaptive mode is to optimize the problem-solving abilities according to the situation that has provoked the mode. Cognitions and emotions during the adaptive mode are different than in a normal mental state. These altered cognitions and emotional reactions guide the individual to use the correct coping skills in order to deal with the stressor. Successful adaptation will cause the adaptive mode to fade off since the adaptive mode is no longer necessary, and the process as a whole will lead to raised well-being. However, if the adaptation process is inadequate, then the transformation period is prolonged, and the adaptive mode will turn into a dysfunctional state. Many psychiatric disorders are such maladaptive processes. The maladaptive processes can be turned into functional ones by using adaptive skills that are used in functional adaptive processes. PMID:27063089

  15. A New Look at Adaptation.

    ERIC Educational Resources Information Center

    Buttolph, Diana

    1992-01-01

    Examines terms used to describe the changing of an innovation by an adopter, including reinvention, fidelity, adaptation, and mutual adaptation. Three explanations for adaptation of innovation--interpretation, adopter innovativeness, and generative learning--are discussed; and the theory of generative learning is used to explain internal…

  16. Variation in Plant Traits Explains Global Biogeographic Variation in the Abundance of Major Forest Functional Types

    NASA Astrophysics Data System (ADS)

    Wang, Y.

    2015-12-01

    Contrasting leaf types (needle vs. broadleaf) with different lifespans (annual vs. perennial) represent different adaptive strategies of plants under different environmental conditions. Previous studies explained adaptive advantages of different strategies using empirical models but cannot adequately explain the co-dominance of multiple plant functional types (PFTs) as observed in many parts of the world. Here we used a process-based model to explore whether observed inter- and intra-PFT variation in key plant traits can explain global biogeographic variation in co-dominance of major forest functional types. Using a parameter screening method, we identified the four most important plant traits for simulating annual net primary production (NPP) using the Australian Community Atmosphere-Biosphere-Land Exchange model (CABLE). Using ensemble CABLE simulations, we estimated the fraction of global land cover attributed to each PFT by comparing the simulated NPP for all three PFTs at each land point, globally. Our results were consistent with land area cover fractions of major forest types estimated from remote sensing data products; i.e., evergreen needle-leaf forests dominate in boreal regions, evergreen broadleaf forests dominate in tropical regions, and deciduous broadleaf forests are distributed widely across a broad range of environmental conditions. More importantly our approach successfully explained a paradox that has puzzled ecologists for over a century: why evergreen leaf types dominate in both boreal and tropical regions. We conclude that variation in and co-variation between key plant traits can explain significant fractions of global biogeographic variation of three major forest types, and should be taken into account when simulating global vegetation dynamics.

  17. Low Temperature Adaptation Is Not the Opposite Process of High Temperature Adaptation in Terms of Changes in Amino Acid Composition

    PubMed Central

    Yang, Ling-Ling; Tang, Shu-Kun; Huang, Ying; Zhi, Xiao-Yang

    2015-01-01

    Previous studies focused on psychrophilic adaptation generally have demonstrated that multiple mechanisms work together to increase protein flexibility and activity, as well as to decrease the thermostability of proteins. However, the relationship between high and low temperature adaptations remains unclear. To investigate this issue, we collected the available predicted whole proteome sequences of species with different optimal growth temperatures, and analyzed amino acid variations and substitutional asymmetry in pairs of homologous proteins from related species. We found that changes in amino acid composition associated with low temperature adaptation did not exhibit a coherent opposite trend when compared with changes in amino acid composition associated with high temperature adaptation. This result indicates that during their evolutionary histories the proteome-scale evolutionary patterns associated with prokaryotes exposed to low temperature environments were distinct from the proteome-scale evolutionary patterns associated with prokaryotes exposed to high temperature environments in terms of changes in amino acid composition of the proteins. PMID:26614525

  18. Selective Pressure along a Latitudinal Gradient Affects Subindividual Variation in Plants

    PubMed Central

    Sobral, Mar; Guitián, José; Guitián, Pablo; Larrinaga, Asier R.

    2013-01-01

    Individual plants produce repeated structures such as leaves, flowers or fruits, which, although belonging to the same genotype, are not phenotypically identical. Such subindividual variation reflects the potential of individual genotypes to vary with micro-environmental conditions. Furthermore, variation in organ traits imposes costs to foraging animals such as time, energy and increased predation risk. Therefore, animals that interact with plants may respond to this variation and affect plant fitness. Thus, phenotypic variation within an individual plant could be, in part, an adaptive trait. Here we investigated this idea and we found that subindividual variation of fruit size of Crataegus monogyna, in different populations throughout the latitudinal gradient in Europe, was explained at some extent by the selective pressures exerted by seed-dispersing birds. These findings support the hypothesis that within-individual variation in plants is an adaptive trait selected by interacting animals which may have important implications for plant evolution. PMID:24069297

  19. Epigenetic mutations can both help and hinder adaptive evolution.

    PubMed

    Kronholm, Ilkka; Collins, Sinéad

    2016-04-01

    Epigenetic variation is being integrated into our understanding of adaptation, yet we lack models on how epigenetic mutations affect evolution that includes de novo genetic change. We model the effects of epigenetic mutations on the dynamics and endpoints of adaptive walks-a process where a series of beneficial mutations move a population towards a fitness optimum. We use an individual-based model of an asexual population, where mutational effects are drawn from Fisher's geometric model. We find cases where epigenetic mutations speed adaptation or result in populations with higher fitness. However, we also find cases where they slow adaptation or result in populations with lower fitness. The effect of epigenetic mutations on adaptive walks depends crucially on their stability and fitness effects relative to genetic mutations, with small-effect epigenetic mutations generally speeding adaptation, and epigenetic mutations with the same fitness effects as genetic mutations slowing adaptation. Our work reveals a complex relationship between epigenetic mutations and natural selection and highlights the need for empirical data. PMID:26139359

  20. Climate Change in Central Taiwan: Impact and Adaptive Capacity

    NASA Astrophysics Data System (ADS)

    Ho, Chih-Chao; Chang, Liang-Cheng; Tsai, Chan-Ming

    2013-04-01

    This study aims to evaluate the spatial vulnerability distribution of water resources and propose the adaptive strategies for centeral Taiwan. The main tasks of this study are future water demand estimation, Rainfall trend analysis, climate change impact analysis and adaptive strategy proposing. Future water demand estimation considers the impact of GDP and temperature on domestic use water demand. MK Test, MWP Test and KW Test are used to analyze the variation trend of precipitation, intensity and drought day. The water allocation simulation model build by Vensim are used to analyze climate change impact. Based on impact analysis result, multi-criteria analysis is used to optimize optimal adaptive strategies combination. For Miaoli and Nantou, the furture demand (2031) can be fulfilled under Tiahuahu reservoir and Niaozueitan artificial lake is finished. It is not necessary to propose adaptive strategy. For Taichung, the optimal adaptive combinations for A1B worse case are Water Saving and Futian Domestic Wastewater Treatment Plant. For Changhua, the optimal adaptive strategy for A1B worse case is seawater desalinization. For Yunlin, the optimal adaptive combinations for A1B worse case are Water Saving and tap water pipe replacement.

  1. Living on the edge: how philopatry maintains adaptive potential

    PubMed Central

    Stiebens, Victor A.; Merino, Sonia E.; Roder, Christian; Chain, Frédéric J. J.; Lee, Patricia L. M.; Eizaguirre, Christophe

    2013-01-01

    Without genetic variation, species cannot cope with changing environments, and evolution does not proceed. In endangered species, adaptive potential may be eroded by decreased population sizes and processes that further reduce gene flow such as philopatry and local adaptations. Here, we focused on the philopatric and endangered loggerhead sea turtle (Caretta caretta) nesting in Cape Verde as a model system to investigate the link between adaptive potential and philopatry. We produced a dataset of three complementary genomic regions to investigate female philopatric behaviour (mitochondrial DNA), male-mediated gene flow (microsatellites) and adaptive potential (major histocompatibility complex, MHC). Results revealed genetically distinct nesting colonies, indicating remarkably small-scale philopatric behaviour of females. Furthermore, these colonies also harboured local pools of MHC alleles, especially at the margins of the population's distribution, which are therefore important reserves of additional diversity for the population. Meanwhile, directional male-mediated gene flow from the margins of distribution sustains the adaptive potential for the entire rookery. We therefore present the first evidence for a positive association between philopatry and locally adapted genomic regions. Contrary to expectation, we propose that philopatry conserves a high adaptive potential at the margins of a distribution, while asymmetric gene flow maintains genetic connectivity with the rest of the population. PMID:23720544

  2. The Schwinger Variational Method

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    1995-01-01

    Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. The application of the Schwinger variational (SV) method to e-molecule collisions and molecular photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions. Since this is not a review of cross section data, cross sections are presented only to server as illustrative examples. In the SV method, the correct boundary condition is automatically incorporated through the use of Green's function. Thus SV calculations can employ basis functions with arbitrary boundary conditions. The iterative Schwinger method has been used extensively to study molecular photoionization. For e-molecule collisions, it is used at the static exchange level to study elastic scattering and coupled with the distorted wave approximation to study electronically inelastic scattering.

  3. Floral adaptation and diversification under pollen limitation

    PubMed Central

    Harder, Lawrence D.; Aizen, Marcelo A.

    2010-01-01

    Pollen limitation (PL) of seed production creates unique conditions for reproductive adaptation by angiosperms, in part because, unlike under ovule or resource limitation, floral interactions with pollen vectors can contribute to variation in female success. Although the ecological and conservation consequences of PL have received considerable attention in recent times, its evolutionary implications are poorly appreciated. To identify general influences of PL on reproductive adaptation compared with those under other seed-production limits and their implications for evolution in altered environments, we derive a model that incorporates pollination and post-pollination aspects of PL. Because PL always favours increased ovule fertilization, even when population dynamics are not seed limited, it should pervasively influence selection on reproductive traits. Significantly, under PL the intensity of inbreeding does not determine whether outcrossing or autonomous selfing can evolve, although it can affect which response is most likely. Because the causes of PL are multifaceted in both natural and anthropogenically altered environments, the possible outcrossing solutions are diverse and context dependent, which may contribute to the extensive variety of angiosperm reproductive characteristics. Finally, the increased adaptive options available under PL may be responsible for positive global associations between it and angiosperm diversity. PMID:20047878

  4. Dosimetric adaptive IMRT driven by fiducial points

    SciTech Connect

    Crijns, Wouter; Van Herck, Hans; Defraene, Gilles; Van den Bergh, Laura; Haustermans, Karin; Slagmolen, Pieter; Maes, Frederik; Van den Heuvel, Frank

    2014-06-15

    Purpose: Intensity modulated radiotherapy (IMRT) and volumetric modulated arc therapy have become standard treatments but are more sensitive to anatomical variations than 3D conformal techniques. To correct for inter- and intrafraction anatomical variations, fast and easy to implement methods are needed. Here, the authors propose a full dosimetric IMRT correction that finds a compromise in-between basic repositioning (the current clinical practice) and full replanning. It simplifies replanning by avoiding a recontouring step and a full dose calculation. It surpasses repositioning by updating the preoptimized fluence and monitor units (MU) using a limited number of fiducial points and a pretreatment (CB)CT. To adapt the fluence the fiducial points were projected in the beam's eye view (BEV). To adapt the MUs, point dose calculation towards the same fiducial points were performed. The proposed method is intrinsically fast and robust, and simple to understand for operators, because of the use of only four fiducial points and the beam data based point dose calculations. Methods: To perform our dosimetric adaptation, two fluence corrections in the BEV are combined with two MU correction steps along the beam's path. (1) A transformation of the fluence map such that it is realigned with the current target geometry. (2) A correction for an unintended scaling of the penumbra margin when the treatment beams scale to the current target size. (3) A correction for the target depth relative to the body contour and (4) a correction for the target distance to the source. The impact of the correction strategy and its individual components was evaluated by simulations on a virtual prostate phantom. This heterogeneous reference phantom was systematically subjected to population based prostate transformations to simulate interfraction variations. Additionally, a patient example illustrated the clinical practice. The correction strategy was evaluated using both dosimetric (CTV mean

  5. Geographically Related Variation in Epicuticular Wax Traits of Pinus nigra Populations from Southern Carpathians and Central Balkans - Taxonomic Considerations.

    PubMed

    Mitić, Zorica S; Zlatković, Bojan K; Jovanović, Snežana Č; Stojanović, Gordana S; Marin, Petar D

    2016-07-01

    The chemical composition of epicuticular waxes of nine populations from three Pinus nigra J. F. Arnold subspecies (namely subsp. nigra, subsp. banatica (Borbás) Novák, and subsp. pallasiana (Lamb.) Holmboe) from Southern Carpathians and central Balkan Peninsula were analyzed using GC/MS and GC/FID chromatography, and multivariate statistical techniques with respect to biogeography and taxonomy. In the needle waxes, four primary alcohols and 14 n-alkanes ranging from C21 to C33 were identified, and the most abundant compounds were the four odd-numbered n-alkanes C27 , C25 , C23 , and C29. Multivariate statistical analyses (CDA and CA) have shown existence of three P. nigra groups and suggested clinal differentiation as a mechanism of genetic variation across a geographic area: the first group consisted of the southernmost populations of subsp. pallasiana from Macedonia, the second consisted of the northernmost subsp. banatica populations from Romania, while all populations in Serbia described as three different subspecies (nigra, banatica, and pallasiana) formed the third group together with subsp. nigra population from Bosnia and Herzegovina. According to simple linear regression, geographic latitude and four bioclimatic parameters were moderately correlated with the contents of epicuticular wax compounds that are important in population discrimination, while stepwise multiple regression showed that latitude participated in most of the regression models for predicting the composition of the epicuticular waxes. These results agree with CDA and CA analysis, and confirmed the possibility of recognition of fine geographic differentiation of the analyzed P. nigra populations. PMID:27273147

  6. Adaptations between ecotypes and along environmental gradients in Panicum virgatum.

    PubMed

    Lowry, David B; Behrman, Kathrine D; Grabowski, Paul; Morris, Geoffrey P; Kiniry, James R; Juenger, Thomas E

    2014-05-01

    Determining the patterns and mechanisms of natural selection in the wild is of fundamental importance to understanding the differentiation of populations and the evolution of new species. However, it is often unknown the extent to which adaptive genetic variation is distributed among ecotypes between distinct habitats versus along large-scale geographic environmental gradients, such as those that track latitude. Classic studies of selection in the wild in switchgrass, Panicum virgatum, tested for adaptation at both of these levels of natural variation. Here we review what these field experiments and modern agronomic field trials have taught us about natural variation and selection at both the ecotype and environmental gradient levels in P. virgatum. With recent genome sequencing efforts in P. virgatum, it is poised to become an excellent system for understanding the adaptation of grassland species across the eastern half of North America. The identification of genetic loci involved in different types of adaptations will help to understand the evolutionary mechanisms of diversification within P. virgatum and provide useful information for the breeding of high-yielding cultivars for different ecoregions. PMID:24739200

  7. Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

    PubMed Central

    Ferriere, Regis; Legendre, Stéphane

    2013-01-01

    Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps. PMID:23209163

  8. Variation, Repetition, And Choice

    PubMed Central

    Abreu-Rodrigues, Josele; Lattal, Kennon A; dos Santos, Cristiano V; Matos, Ricardo A

    2005-01-01

    Experiment 1 investigated the controlling properties of variability contingencies on choice between repeated and variable responding. Pigeons were exposed to concurrent-chains schedules with two alternatives. In the REPEAT alternative, reinforcers in the terminal link depended on a single sequence of four responses. In the VARY alternative, a response sequence in the terminal link was reinforced only if it differed from the n previous sequences (lag criterion). The REPEAT contingency generated low, constant levels of sequence variation whereas the VARY contingency produced levels of sequence variation that increased with the lag criterion. Preference for the REPEAT alternative tended to increase directly with the degree of variation required for reinforcement. Experiment 2 examined the potential confounding effects in Experiment 1 of immediacy of reinforcement by yoking the interreinforcer intervals in the REPEAT alternative to those in the VARY alternative. Again, preference for REPEAT was a function of the lag criterion. Choice between varying and repeating behavior is discussed with respect to obtained behavioral variability, probability of reinforcement, delay of reinforcement, and switching within a sequence. PMID:15828592

  9. Cosmic ray biannual variation

    NASA Technical Reports Server (NTRS)

    Attolini, M. R.; Cecchini, S.; Cinicastagnoli, G.; Galli, M.

    1985-01-01

    The study of the cosmic ray (CR) power spectrum has revealed a significant variation with a period around 2 yr that cannot be explained as a high order harmonic of the 11 yr solar cycle. Comparative study of the correlation on different time scales between CR intensity and Rz, aa, high speed streams and polar hole size has put in evidence that a high degree of coherency exists between each couple of variables at 1.58 to 1.64 yr, except between CR and Rz. On the other hand cyclic variation on a short time scale, around 26 months, has been claimed to be present in the neutrino flux. Critical tests of this hypothesis are considered and a preliminary result seems to indicate that the hypothesis of the existence of a 1.6 yr periodicity in the neutrino data during the measurement time interval, has a significance or = 99.9%. The possible origin of this variation as due to a contribution either of CR interactions in the upper atmosphere or to the solar dynamics, are discussed.

  10. Canonical variate regression.

    PubMed

    Luo, Chongliang; Liu, Jin; Dey, Dipak K; Chen, Kun

    2016-07-01

    In many fields, multi-view datasets, measuring multiple distinct but interrelated sets of characteristics on the same set of subjects, together with data on certain outcomes or phenotypes, are routinely collected. The objective in such a problem is often two-fold: both to explore the association structures of multiple sets of measurements and to develop a parsimonious model for predicting the future outcomes. We study a unified canonical variate regression framework to tackle the two problems simultaneously. The proposed criterion integrates multiple canonical correlation analysis with predictive modeling, balancing between the association strength of the canonical variates and their joint predictive power on the outcomes. Moreover, the proposed criterion seeks multiple sets of canonical variates simultaneously to enable the examination of their joint effects on the outcomes, and is able to handle multivariate and non-Gaussian outcomes. An efficient algorithm based on variable splitting and Lagrangian multipliers is proposed. Simulation studies show the superior performance of the proposed approach. We demonstrate the effectiveness of the proposed approach in an [Formula: see text] intercross mice study and an alcohol dependence study. PMID:26861909

  11. Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

    PubMed

    Faulks, L K; Östman, Ö

    2016-04-01

    This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended. PMID:26940068

  12. Adaptive nonlinear flight control

    NASA Astrophysics Data System (ADS)

    Rysdyk, Rolf Theoduor

    1998-08-01

    Research under supervision of Dr. Calise and Dr. Prasad at the Georgia Institute of Technology, School of Aerospace Engineering. has demonstrated the applicability of an adaptive controller architecture. The architecture successfully combines model inversion control with adaptive neural network (NN) compensation to cancel the inversion error. The tiltrotor aircraft provides a specifically interesting control design challenge. The tiltrotor aircraft is capable of converting from stable responsive fixed wing flight to unstable sluggish hover in helicopter configuration. It is desirable to provide the pilot with consistency in handling qualities through a conversion from fixed wing flight to hover. The linear model inversion architecture was adapted by providing frequency separation in the command filter and the error-dynamics, while not exiting the actuator modes. This design of the architecture provides for a model following setup with guaranteed performance. This in turn allowed for convenient implementation of guaranteed handling qualities. A rigorous proof of boundedness is presented making use of compact sets and the LaSalle-Yoshizawa theorem. The analysis allows for the addition of the e-modification which guarantees boundedness of the NN weights in the absence of persistent excitation. The controller is demonstrated on the Generic Tiltrotor Simulator of Bell-Textron and NASA Ames R.C. The model inversion implementation is robustified with respect to unmodeled input dynamics, by adding dynamic nonlinear damping. A proof of boundedness of signals in the system is included. The effectiveness of the robustification is also demonstrated on the XV-15 tiltrotor. The SHL Perceptron NN provides a more powerful application, based on the universal approximation property of this type of NN. The SHL NN based architecture is also robustified with the dynamic nonlinear damping. A proof of boundedness extends the SHL NN augmentation with robustness to unmodeled actuator

  13. Adaptation in Collaborative Governance Regimes

    NASA Astrophysics Data System (ADS)

    Emerson, Kirk; Gerlak, Andrea K.

    2014-10-01

    Adaptation and the adaptive capacity of human and environmental systems have been of central concern to natural and social science scholars, many of whom characterize and promote the need for collaborative cross-boundary systems that are seen as flexible and adaptive by definition. Researchers who study collaborative governance systems in the public administration, planning and policy literature have paid less attention to adaptive capacity specifically and institutional adaptation in general. This paper bridges the two literatures and finds four common dimensions of capacity, including structural arrangements, leadership, knowledge and learning, and resources. In this paper, we focus on institutional adaptation in the context of collaborative governance regimes and try to clarify and distinguish collaborative capacity from adaptive capacity and their contributions to adaptive action. We posit further that collaborative capacities generate associated adaptive capacities thereby enabling institutional adaptation within collaborative governance regimes. We develop these distinctions and linkages between collaborative and adaptive capacities with the help of an illustrative case study in watershed management within the National Estuary Program.

  14. Adaptation in collaborative governance regimes.

    PubMed

    Emerson, Kirk; Gerlak, Andrea K

    2014-10-01

    Adaptation and the adaptive capacity of human and environmental systems have been of central concern to natural and social science scholars, many of whom characterize and promote the need for collaborative cross-boundary systems that are seen as flexible and adaptive by definition. Researchers who study collaborative governance systems in the public administration, planning and policy literature have paid less attention to adaptive capacity specifically and institutional adaptation in general. This paper bridges the two literatures and finds four common dimensions of capacity, including structural arrangements, leadership, knowledge and learning, and resources. In this paper, we focus on institutional adaptation in the context of collaborative governance regimes and try to clarify and distinguish collaborative capacity from adaptive capacity and their contributions to adaptive action. We posit further that collaborative capacities generate associated adaptive capacities thereby enabling institutional adaptation within collaborative governance regimes. We develop these distinctions and linkages between collaborative and adaptive capacities with the help of an illustrative case study in watershed management within the National Estuary Program. PMID:25073764

  15. Renal adaptation during hibernation

    PubMed Central

    Martin, Sandra L.; Jain, Swati; Keys, Daniel; Edelstein, Charles L.

    2013-01-01

    Hibernators periodically undergo profound physiological changes including dramatic reductions in metabolic, heart, and respiratory rates and core body temperature. This review discusses the effect of hypoperfusion and hypothermia observed during hibernation on glomerular filtration and renal plasma flow, as well as specific adaptations in renal architecture, vasculature, the renin-angiotensin system, and upregulation of possible protective mechanisms during the extreme conditions endured by hibernating mammals. Understanding the mechanisms of protection against organ injury during hibernation may provide insights into potential therapies for organ injury during cold storage and reimplantation during transplantation. PMID:24049148

  16. Adaptive Optical Scanning Holography

    PubMed Central

    Tsang, P. W. M.; Poon, Ting-Chung; Liu, J.-P.

    2016-01-01

    Optical Scanning Holography (OSH) is a powerful technique that employs a single-pixel sensor and a row-by-row scanning mechanism to capture the hologram of a wide-view, three-dimensional object. However, the time required to acquire a hologram with OSH is rather lengthy. In this paper, we propose an enhanced framework, which is referred to as Adaptive OSH (AOSH), to shorten the holographic recording process. We have demonstrated that the AOSH method is capable of decreasing the acquisition time by up to an order of magnitude, while preserving the content of the hologram favorably. PMID:26916866