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Sample records for lake constance phylogeny

  1. Lake Constance

    Atmospheric Science Data Center

    2013-04-17

    ... Swiss shores of Lake Constance at the town of Rorschach. Eutrophication, or the process of nutrient enrichment, is rapidly accelerated ... of the value of Lake Constance, efforts to mitigate eutrophication were initiated in the 1970's. MISR was built and is managed ...

  2. Seasonal variation of solitary wave properties in Lake Constance

    NASA Astrophysics Data System (ADS)

    Preusse, M.; Freistühler, H.; Peeters, F.

    2012-04-01

    The properties of internal solitary waves (ISWs) depend on the stratification of the water body. In most climatic regions the stratification in lakes and oceans varies during the year, and hence the properties of the ISWs can also be expected to change over the seasons. On the basis of a long-term temperature time series recorded over 6 years, this paper investigates seasonal changes in the characteristic properties of ISWs in Lake Überlingen, a subbasin of Lake Constance. A large number of ISWs with amplitudes ranging from 3 m to 30 m were identified. More than 15% of the leading ISWs of a wave train were associated with density inversions, often indicating shear instabilities or trapped cores. For all waves the propagation depth and the value of a nonlinearity index nlp providing the degree of nonlinearity were determined, propagation depth being the rest height of the isotherm undergoing maximum displacement and nlp the ratio between wave amplitude and propagation depth. The index nlp was found to be a good parameter for predicting the occurrence of inversions. The statistical analysis of the wave properties derived from the observations revealed that the degree of nonlinearity of the ISWs changes with season. Complementary to the statistical analysis, the seasonally averaged ISW properties were compared with wave prototypes obtained numerically from the Dubreil-Jacotin-Long (DJL) and the stratified Korteweg-deVries (KdV) models. The simulations indicate that the typical stratification and its seasonal variation are responsible for the degree and the seasonality of nonlinearity of the ISWs.

  3. ["Constanze": a trinational project on avian influenza in wild birds at Lake Constance].

    PubMed

    Brunhart, I; Baumer, A; Reist, M; Stärk, K; Griot, C

    2010-11-01

    When highly pathogenic avian influenza H5N1 (HPAI H5N1) arrived at Lake Constance in February 2006, little was known about its ecology and epidemiology in wild birds. In order to prevent virus transmission from wild birds to poultry, the adjacent countries initiated the tri-national, interdisciplinary research program «Constanze» to investigate avian influenza infections in water birds at Lake Constance. In collaboration with government agencies scientists examined the prevalence of AI virus in the region of Lake Constance for a period of 33 months, compared the effectiveness of different surveillance methods and analysed the migration behaviour of water birds. Although virus introduction from regions as far as the Ural Mountains seemed possible based on the migration behaviour of certain species, no influenza A viruses of the highly pathogenic subtype H5N1 (HPAIV) was found. However, influenza A viruses of different low pathogenic subtypes were isolated in 2.2 % of the sampled birds (swabs). Of the different surveillance methods utilised in the program the sampling of so called sentinel birds was particularly efficient. PMID:21043024

  4. Seasonal and habitat-related distribution pattern of Synechococcus genotypes in Lake Constance.

    PubMed

    Becker, Sven; Richl, Petra; Ernst, Anneliese

    2007-10-01

    The abundance and distribution of Synechococcus spp. in the autotrophic picoplankton of Lake Constance, were followed in the pelagic and littoral habitat by qPCR over 2 years. One genotype, represented by isolated phycoerythrin-rich strain BO 8807, showed a seasonal distribution pattern in both habitats. Before a stable thermal stratification, the maximum of both the Synechococcus population and genotype BO 8807 occurred at 15 or 20 m water depth in the pelagic habitat. During the summer stratification, when the absolute abundance of all Synechococcus spp. was highest above 15 m, the absolute and relative abundance of genotype BO 8807 was maximal at 20 m. These results indicate that Synechococcus spp. or single genotypes are present in deep maxima in Lake Constance. The in situ dynamics of genotype BO 8807 is consistent with the observation that isolated strain BO 8807 requires higher phosphate concentrations for maximum growth rates than a strain from the same phylogenetic cluster that dominates the pelagic summer population. In contrast to these findings, low genome numbers of phycocyanin-rich genotype BO 8805 were found temporarily only in both the littoral and pelagic plankton. Microscopy revealed that PC-rich cells in general occurred preferentially in the littoral habitat. We discuss our results with respect to the versatility of picocyanobacteria of the evolutionary lineage VI of cyanobacteria, and a habitat-related distribution pattern of Synechococcus genotypes. PMID:17825073

  5. Underflows in Lake Constance - Numerical Modeling, Instrumental Observations and Sediment Data

    NASA Astrophysics Data System (ADS)

    Eder, Magdalena; Wessels, Martin; Dare, Julian

    2014-05-01

    A torrential rain event in the western Alps in August 2005 caused high flood flows in the rivers Alpine Rhine and Bregenzer Ache which are the main tributaries into Lake Constance. The discharge of the Alpine Rhine reached 2200 m³/s, which is little below a centennial flood event. Discharge of the Bregenzer Ache was estimated to 1350 m³/s which statistically occurs every 100 yr but with a 1000 yr frequency in selected smaller tributaries. The high concentration of suspended solids in the fluvial water increased its density and created an underflow with considerable influence on the lake's hydrodynamics and water quality. Consequences within the lake were directly registered by a mooring (equipped with thermistor chain, sediment trap, current meter, oxygen sensor). Spatial data of the path and form of suspended matter cloud within the lake were gathered using echo sounder and probe measurements (turbidity, temperature, salinity). An underflow with a temperature of 14°C flew with 1.4 km/h some 20 km into the lake. Several days after the event, the fluvial sediments were detected as increased turbidity at the drinking water outtakes around the lake. Sediment cores recovered from the lake bottom show the distribution pattern of the sediments while sidescan data give a picture from proximal sediment structures originating from this event. Further, we modelled this underflow using the three dimensional hydrodynamic and water quality model ELCOM-CAEDYM. The suspended solids module of the model accounts for the impact of the sediment load on water density. Settling is considered using Stokes Law, and resuspension can also be included. The simulation of the August 2005 flood event and comparison with measured data impressively showed the ability to reproduce the most important effects of the flood flow on the lake. Comparative simulations with and without consideration of the coriolis effect indicate an influence of the coriolis force on the flow path of the density

  6. Dust transport and palaeoclimate during the Oldest Dryas in Central Europe - implications from varves (Lake Constance)

    SciTech Connect

    Niessen, F.; Lister, G.; Giovanoli, F.

    1992-10-01

    This paper evaluates evidence for seasonal loess deposits in peri-Alpine Lake Constance at the end of the last Glacial (Oldest Dryas chronozone). The sedimentology of laminated couplets comprising yellow and grey silts evaluates the couplets as varves comprising alternations of loess and glacial silt and clay. The laminae, less than 1 mm thick, include from bottom to top: (1) a matrix of well-sorted, non-graded fine yellow silt with sand-size intraclasts, (2) coarsening-upward grey silt with a cap of fining-upward silt to clay. This is typical and reflects summer and winter deposits (silt and clay, respectively). The authors propose that the lack of grading and the matrix supported fabric is indicative of aeolian transport and interpret the yellow laminae as loess deposits. Volcanic glass intraclasts in the loess layers are probably derived from volcanic terrain to the west of the lake, indicating an easterly palaeowind direction. Deposition of loess in the lake occurred regularly at the beginning of each annual cycle, suggesting the palaeowinds were associated with winter and/or spring conditions. Two transport scenarios are suggested to explain the sand grains scattered in this deep-water lacustrine record. 1. The grains may have been transported as bedload over the annual winter ice-cover of the lake under moderate wind strengths, frozen into the ice, and released for deposition during spring melt. 2. The sand grains were blown directly out onto the lake water by very strong winds during spring. The first scenario is contrary to the general view that loess was transported during summer, and that loess deposits thus reflect summer conditions only. Loess input to the lake shows a transitional decrease after ca. 14.3 kyr BP and cessation at ca. 14 kyr BP, probably as a result of a change of wind behaviour, increased humidity and/or vegetational changes during the Oldest Dryas in central Europe. 62 refs., 8 figs.

  7. Genetic diversity and distribution of periphytic Synechococcus spp. in biofilms and picoplankton of Lake Constance.

    PubMed

    Becker, Sven; Singh, Arvind Kumar; Postius, Christine; Böger, Peter; Ernst, Anneliese

    2004-08-01

    In various water depths of the littoral zone of Lake Constance (Bodensee) cyanobacteria of the Synechococcus-type were isolated from biofilms (periphyton) on three natural substrates and an artificial one (unglazed tiles). From one tile three strains of phycoerythrin (PE)-rich Synechococcus spp. were isolated, the first examples of these organisms in the epibenthos. Phylogenetic inference based on the 16S-23S rRNA intergenic spacer (ITS-1) assigned all periphytic isolates to two clusters of the picophytoplankton clade (evolutionary lineage VI of cyanobacteria). The sequence divergence in the ITS-1 was used to design specific PCR primers to allow direct, culture-independent detection and quantification of isolated Synechococcus strains in natural periphytic and pelagic samples. Denaturing gradient gel electrophoresis (DGGE) analysis revealed depth-related differences of Synechococcus spp. distribution on tiles placed in the littoral zone. Synechococcus genotypes were observed which occurred in both the periphyton (on tiles) and in the pelagic picoplankton. A strain with one of these genotypes, Synechococcus sp. BO 8805, was isolated from the pelagic zone in 1988. Its genotype was found on tiles that had been exposed at different water depths in the littoral zone in spring and autumn of the year 2000. Quantitative analysis with a genotype-specific TaqMan probe and real-time Taq nuclease assays (TNA) confirmed its presence in the pelagic zone, although appearance of this and related genotypes was highly irregular and exhibited strong differences between consecutive years. Our results show that the ability to form significant subpopulations in pelagic and periphytic communities exists in three out of four phylogenetic clusters of Synechococcus spp. in Lake Constance. This versatility may be a key feature in the ubiquity of the evolutionary lineage VI of cyanobacteria. PMID:19712413

  8. Spatially explicit exposure assessment for small streams in catchments of the orchard growing region `Lake Constance

    NASA Astrophysics Data System (ADS)

    Golla, B.; Bach, M.; Krumpe, J.

    2009-04-01

    1. Introduction Small streams differ greatly from the standardised water body used in the context of aquatic risk assessment for the regulation of plant protection products in Germany. The standard water body is static, with a depth of 0.3 m and a width of 1.0 m. No dilution or water replacement takes place. Spray drift happens always in direction to the water body. There is no variability in drift deposition rate (90th percentile spray drift deposition values [2]). There is no spray drift filtering by vegetation. The application takes place directly adjacent to the water body. In order to establish a more realistic risk assessment procedure the Federal Office for Consumer Protection and Food Safety (BVL) and the Federal Environment Agency (UBA) aggreed to replace deterministic assumptions with data distributions and spatially explicit data and introduce probabilistic methods [3, 4, 5]. To consider the spatial and temporal variability in the exposure situations of small streams the hydraulic and morphological characteristics of catchments need to be described as well as the spatial distribution of fields treated with pesticides. As small streams are the dominant type of water body in most German orchard regions, we use the growing region Lake Constance as pilot region. 2. Materials and methods During field surveys we derive basic morphological parameters for small streams in the Lake Constance region. The mean water width/depth ratio is 13 with a mean depth of 0.12 m. The average residence time is 5.6 s/m (n=87) [1]. Orchards are mostly located in the upper parts of the catchments. Based on an authoritative dataset on rivers and streams of Germany (ATKIS DLM25) we constructed a directed network topology for the Lake Constance region. The gradient of the riverbed is calculated for river stretches of > 500 m length. The network for the pilot region consists of 2000 km rivers and streams. 500 km stream length are located within a distance of 150 m to orchards. Within

  9. Impact of submerged aquatic macrophytes on 3-dim current systems and hydrodynamic transport processes in Lake Constance

    NASA Astrophysics Data System (ADS)

    Wolf, Thomas; Lüddeke, Frauke; Thiange, Christophe

    2015-04-01

    According to the assessment criteria of the European water framework directive Lake Constance is having a good water quality. Nevertheless upcoming criteria using environmental quality measures show that there are still problems with respect to micropollutants. In fact, we observe significantly enhanced concentrations of micropollutants close to river mouths and in the areas of shallow water zones within Lake Constance compared to deep water concentrations. These findings are caused by river water plumes which can flow over distances of kilometers in the lake without being diluted or mixed only weakly with the surrounding lake water body. Besides, in the area of interest exist large populations of submerged aquatic macrophytes (SAM). There is only little knowledge, how these influence the distribution and transport processes of micropollutants. In order to assess the impact and distribution of river water plumes in different areas of the lake we implemented a 3-dim hydrodynamic model using DELFT3D-FLOW on a locally refined numerical grid which enables to cover different process scales of the distribution of river water bodies ranging from a few meters up to basin wide scales in the order of a few kilometers. We used numerical tracers (conservative and non-conservative) in order to quantify the impact of different abstract substance classes which are distinguished by their decay rates. In order to asses the influence of SAM populations on current field and transport processes we used a special simulation technique - the trachytope concept. The results of our 3-dim hydrodynamic model showed significantly changed current velocities, residence times and age of water parameters within the SAM areas compared to the control simulation without SAM. By simulating the propagation of coliform bacteria using numerical tracers with spatially and temporarily variable decay rates, we found complex impact pattern of the SAM on the distribution of these potentially harmful

  10. Role of pressure, temperature, salinity, lithology, and structure in hydrocarbon accumulation in Constance Bayou, Deep Lake, and southeast Little Pecan Lake Fields, Cameron Parish, Louisiana

    SciTech Connect

    Harrison, F.W. III

    1980-01-01

    Pressure, temperature, salinity, lithology, and structural studies indicate that hydrocarbons in Deep Lake, Constance Bayou, and Little Pecan Lake Fields, were generated in the shale beds of the hard geopressured zone and migrated upward along major growth faults. The hydrocarbons were originally dissolved in hot fresh pore water and came out of solution in the overlying low temperature and pressure zones, accumulating in the sand beds of the first structural traps encountered. By examining regional cross sections and anomaly maps, fluid escape routes taken by the hot pore water containing dissolved hydrocarbons can be identified. Areas below which a vertical flush of hot fresh pore water from the hard geopressured zone has occurred have 3 identifying characteristics: low fluid pressures, high formation water salinity values, and presence of residual high pressure areas. These areas are considered to be highly prospective places to search for hydrocarbon accumulations.

  11. Pb isotopes in sediments of Lake Constance, Central Europe constrain the heavy metal pathways and the pollution history of the catchment, the lake and the regional atmosphere

    SciTech Connect

    Kober, B.; Wessels, M.; Bollhoefer, A.; Mangini

    1999-05-01

    Pb isotope ratios and Pb concentrations of well-dated sediments of Lake Constance, Central Europe have been analyzed using thermal ion mass spectrometry. Sequential extraction studies indicated isotope homogeneity of the leachable Pb components within the investigated layers. Since the middle of the 19th century a significant anthropogenic Pb component appeared in the lake sediments, and rapidly approaches concentration levels similar to that of the geogenic Pb background (20 ppm) at the beginning of the 20th century. Anthropogenic Pb was predominantly transferred to the lake sediments via the atmosphere. Pb sources were coal combustion, industrial ore processing and leaded gasoline. The flux of a fluvial Pb component to the lake sediments, additive to atmospheric Pb deposition, peaked in about 1960. This flux is attributed to (re)mobilization of Pb from polluted parts of the lake catchment, and indicates the change of catchment soils from a pollution sink to a heavy metal source. The strong reduction of anthropogenic Pb in the uppermost lake sediments since the 1960s has been caused by advances of environmental protection. The lake sediments record the changing fluxes and the isotope composition of the deposited aeolian Pb pollution. During the 20th century aeolian Pb fluxes to the lake sediments were in the range of 1--4 {micro}g/cm{sup 2}/a. During peak emission periods of gasoline Pb to the atmosphere (1960--1990) the aerosol Pb isotope composition was rather constant ({sup 206}Pb/{sup 207}Pb: 1.12--1.13) and probably a mixture of Canadian and Australian with Russian and Central European Pb types. Aeolian Pb isotope and Pb flux trends in the lake sediments as a whole agree well with the trends found in Alpine glaciers (Doering et al., 1997a,b) and in ombrotrophic peat bogs of Switzerland (Shotyk et al., 1996). However, different industrial Pb components were deposited in the archives of aeolian pollution during the early 20th century.

  12. Multi-level approach for the integrated assessment of polar organic micropollutants in an international lake catchment: the example of Lake Constance.

    PubMed

    Moschet, Christoph; Götz, Christian; Longrée, Philipp; Hollender, Juliane; Singer, Heinz

    2013-07-01

    Polar organic micropollutants (MPs) can have ecotoxicological effects on aquatic ecosystems and their occurrence in drinking water is a threat to public health. An extensive exposure assessment of MPs in large river and lake catchments is a necessary but challenging proposition for researchers and regulators. To get a complete picture of MP exposure in a large catchment, we employed a novel integrated strategy including MP measurement in the international catchment of Lake Constance and mass-flux modeling. A comprehensive screening of 252 MPs in the lake water by high-resolution mass spectrometry was used to identify the most commonly present MPs for the study site. It was found that the wastewater borne MPs diclofenac, carbamazepine, sulfamethoxazole, acesulfame, sucralose, benzotriazole, and methylbenzotriazole accounted for the most frequent and prominent findings. The concentration pattern of these compounds in the catchment was calculated based on regionalized inputs from wastewater treatment plants (WWTPs) and substance specific elimination rates. In 52, 8, and 3 of the 112 investigated river locations the concentration exceeded the predicted no-effect levels for diclofenac, sulfamethoxazole and carbamazepine, respectively. By coupling the catchment and lake model the effect of future trends in usage as well as possible mitigation options were evaluated for the tributaries and the lake. The upgrade of the major WWTPs in the catchment with a postozonation step would lead to a load reduction between 32% and 52% for all substances except for sucralose (10%). PMID:23441970

  13. Water Quality Monitoring for Lake Constance with a Physically Based Algorithm for MERIS Data

    PubMed Central

    Odermatt, Daniel; Heege, Thomas; Nieke, Jens; Kneubühler, Mathias; Itten, Klaus

    2008-01-01

    A physically based algorithm is used for automatic processing of MERIS level 1B full resolution data. The algorithm is originally used with input variables for optimization with different sensors (i.e. channel recalibration and weighting), aquatic regions (i.e. specific inherent optical properties) or atmospheric conditions (i.e. aerosol models). For operational use, however, a lake-specific parameterization is required, representing an approximation of the spatio-temporal variation in atmospheric and hydrooptic conditions, and accounting for sensor properties. The algorithm performs atmospheric correction with a LUT for at-sensor radiance, and a downhill simplex inversion of chl-a, sm and y from subsurface irradiance reflectance. These outputs are enhanced by a selective filter, which makes use of the retrieval residuals. Regular chl-a sampling measurements by the Lake's protection authority coinciding with MERIS acquisitions were used for parameterization, training and validation.

  14. Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance.

    PubMed

    Bornemann, Maren; Bussmann, Ingeborg; Tichy, Lucas; Deutzmann, Jörg; Schink, Bernhard; Pester, Michael

    2016-08-01

    Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters. PMID:27267930

  15. First evidence for postzygotic reproductive isolation between two populations of Eurasian perch (Perca fluviatilis L.) within Lake Constance

    PubMed Central

    Behrmann-Godel, Jasminca; Gerlach, Gabriele

    2008-01-01

    Background The evolution of reproductive traits, such as hybrid incompatibility (postzygotic isolation) and species recognition (prezygotic isolation), have shown their key role in speciation. Theoretical modeling has recently predicted that close linkage between genes controlling pre- and postzygotic reproductive isolation could accelerate the conditions for speciation. Postzygotic isolation could develop during the sympatric speciation process contributing to the divergence of populations. Using hybrid fitness as a measure of postzygotic reproductive isolation, we empirically studied population divergence in perch (Perca fluviatilis L.) from two genetically divergent populations within a lake. Results During spawning time of perch we artificially created parental offspring and F1 hybrids of the two populations and studied fertilization rate and hatching success under laboratory conditions. The combined fitness measure (product of fertilization rate and hatching success) of F1 hybrids was significantly reduced compared to offspring from within population crosses. Conclusion Our results suggest intrinsic genetic incompatibility between the two populations and indicate that population divergence between two populations of perch inhabiting the same lake may indeed be promoted by postzygotic isolation. PMID:18218080

  16. Rethinking Colour Constancy.

    PubMed

    Logvinenko, Alexander D; Funt, Brian; Mirzaei, Hamidreza; Tokunaga, Rumi

    2015-01-01

    Colour constancy needs to be reconsidered in light of the limits imposed by metamer mismatching. Metamer mismatching refers to the fact that two objects reflecting metameric light under one illumination may reflect non-metameric light under a second; so two objects appearing as having the same colour under one illuminant can appear as having different colours under a second. Yet since Helmholtz, object colour has generally been believed to remain relatively constant. The deviations from colour constancy registered in experiments are usually thought to be small enough that they do not contradict the notion of colour constancy. However, it is important to determine how the deviations from colour constancy relate to the limits metamer mismatching imposes on constancy. Hence, we calculated metamer mismatching's effect for the 20 Munsell papers and 8 pairs of illuminants employed in the colour constancy study by Logvinenko and Tokunaga and found it to be so extensive that the two notions-metamer mismatching and colour constancy-must be mutually exclusive. In particular, the notion of colour constancy leads to some paradoxical phenomena such as the possibility of 20 objects having the same colour under chromatic light dispersing into a hue circle of colours under neutral light. Thus, colour constancy refers to a phenomenon, which because of metamer mismatching, simply cannot exist. Moreover, it obscures the really important visual phenomenon; namely, the alteration of object colours induced by illumination change. We show that colour is not an independent, intrinsic attribute of an object, but rather an attribute of an object/light pair, and then define a concept of material colour in terms of equivalence classes of such object/light pairs. We suggest that studying the shift in material colour under a change in illuminant will be more fruitful than pursuing colour constancy's false premise that colour is an intrinsic attribute of an object. PMID:26356217

  17. Rethinking Colour Constancy

    PubMed Central

    Logvinenko, Alexander D.; Funt, Brian; Mirzaei, Hamidreza; Tokunaga, Rumi

    2015-01-01

    Colour constancy needs to be reconsidered in light of the limits imposed by metamer mismatching. Metamer mismatching refers to the fact that two objects reflecting metameric light under one illumination may reflect non-metameric light under a second; so two objects appearing as having the same colour under one illuminant can appear as having different colours under a second. Yet since Helmholtz, object colour has generally been believed to remain relatively constant. The deviations from colour constancy registered in experiments are usually thought to be small enough that they do not contradict the notion of colour constancy. However, it is important to determine how the deviations from colour constancy relate to the limits metamer mismatching imposes on constancy. Hence, we calculated metamer mismatching’s effect for the 20 Munsell papers and 8 pairs of illuminants employed in the colour constancy study by Logvinenko and Tokunaga and found it to be so extensive that the two notions—metamer mismatching and colour constancy—must be mutually exclusive. In particular, the notion of colour constancy leads to some paradoxical phenomena such as the possibility of 20 objects having the same colour under chromatic light dispersing into a hue circle of colours under neutral light. Thus, colour constancy refers to a phenomenon, which because of metamer mismatching, simply cannot exist. Moreover, it obscures the really important visual phenomenon; namely, the alteration of object colours induced by illumination change. We show that colour is not an independent, intrinsic attribute of an object, but rather an attribute of an object/light pair, and then define a concept of material colour in terms of equivalence classes of such object/light pairs. We suggest that studying the shift in material colour under a change in illuminant will be more fruitful than pursuing colour constancy’s false premise that colour is an intrinsic attribute of an object. PMID:26356217

  18. Stereoscopic depth constancy.

    PubMed

    Guan, Phillip; Banks, Martin S

    2016-06-19

    Depth constancy is the ability to perceive a fixed depth interval in the world as constant despite changes in viewing distance and the spatial scale of depth variation. It is well known that the spatial frequency of depth variation has a large effect on threshold. In the first experiment, we determined that the visual system compensates for this differential sensitivity when the change in disparity is suprathreshold, thereby attaining constancy similar to contrast constancy in the luminance domain. In a second experiment, we examined the ability to perceive constant depth when the spatial frequency and viewing distance both changed. To attain constancy in this situation, the visual system has to estimate distance. We investigated this ability when vergence, accommodation and vertical disparity are all presented accurately and therefore provided veridical information about viewing distance. We found that constancy is nearly complete across changes in viewing distance. Depth constancy is most complete when the scale of the depth relief is constant in the world rather than when it is constant in angular units at the retina. These results bear on the efficacy of algorithms for creating stereo content.This article is part of the themed issue 'Vision in our three-dimensional world'. PMID:27269596

  19. Colour constancy in insects.

    PubMed

    Chittka, Lars; Faruq, Samia; Skorupski, Peter; Werner, Annette

    2014-06-01

    Colour constancy is the perceptual phenomenon that the colour of an object appears largely unchanged, even if the spectral composition of the illuminating light changes. Colour constancy has been found in all insect species so far tested. Especially the pollinating insects offer a remarkable opportunity to study the ecological significance of colour constancy since they spend much of their adult lives identifying and choosing between colour targets (flowers) under continuously changing ambient lighting conditions. In bees, whose colour vision is best studied among the insects, the compensation provided by colour constancy is only partial and its efficiency depends on the area of colour space. There is no evidence for complete 'discounting' of the illuminant in bees, and the spectral composition of the light can itself be used as adaptive information. In patchy illumination, bees adjust their spatial foraging to minimise transitions between variously illuminated zones. Modelling allows the quantification of the adaptive benefits of various colour constancy mechanisms in the economy of nature. We also discuss the neural mechanisms and cognitive operations that might underpin colour constancy in insects. PMID:24647930

  20. Stereoscopic depth constancy

    PubMed Central

    Guan, Phillip

    2016-01-01

    Depth constancy is the ability to perceive a fixed depth interval in the world as constant despite changes in viewing distance and the spatial scale of depth variation. It is well known that the spatial frequency of depth variation has a large effect on threshold. In the first experiment, we determined that the visual system compensates for this differential sensitivity when the change in disparity is suprathreshold, thereby attaining constancy similar to contrast constancy in the luminance domain. In a second experiment, we examined the ability to perceive constant depth when the spatial frequency and viewing distance both changed. To attain constancy in this situation, the visual system has to estimate distance. We investigated this ability when vergence, accommodation and vertical disparity are all presented accurately and therefore provided veridical information about viewing distance. We found that constancy is nearly complete across changes in viewing distance. Depth constancy is most complete when the scale of the depth relief is constant in the world rather than when it is constant in angular units at the retina. These results bear on the efficacy of algorithms for creating stereo content. This article is part of the themed issue ‘Vision in our three-dimensional world’. PMID:27269596

  1. Auditory color constancy

    NASA Astrophysics Data System (ADS)

    Kluender, Keith R.; Kiefte, Michael

    2003-10-01

    It is both true and efficient that sensorineural systems respond to change and little else. Perceptual systems do not record absolute level be it loudness, pitch, brightness, or color. This fact has been demonstrated in every sensory domain. For example, the visual system is remarkable at maintaining color constancy over widely varying illumination such as sunlight and varieties of artificial light (incandescent, fluorescent, etc.) for which spectra reflected from objects differ dramatically. Results will be reported for a series of experiments demonstrating how auditory systems similarly compensate for reliable characteristics of spectral shape in acoustic signals. Specifically, listeners' perception of vowel sounds, characterized by both local (e.g., formants) and broad (e.g., tilt) spectral composition, changes radically depending upon reliable spectral composition of precursor signals. These experiments have been conducted using a variety of precursor signals consisting of meaningful and time-reversed vocoded sentences, as well as novel nonspeech precursors consisting of multiple filter poles modulating sinusoidally across a source spectrum with specific local and broad spectral characteristics. Constancy across widely varying spectral compositions shares much in common with visual color constancy. However, auditory spectral constancy appears to be more effective than visual constancy in compensating for local spectral fluctuations. [Work supported by NIDCD DC-04072.

  2. Binaural Loudness Constancy.

    PubMed

    Culling, John F; Dare, Helen

    2016-01-01

    In binaural loudness summation, diotic presentation of a sound usually produces greater loudness than monaural presentation. However, experiments using loudspeaker presentation with and without earplugs find that magnitude estimates of loudness are little altered by the earplug, suggesting a form of loudness constancy. We explored the significance of controlling stimulation of the second ear using meatal occlusion as opposed to the deactivation of one earphone. We measured the point of subjective loudness equality (PSLE) for monaural vs. binaural presentation using an adaptive technique for both speech and noise. These stimuli were presented in a reverberant room over a loudspeaker to the right of the listener, or over lightweight headphones. Using the headphones, stimuli were either presented dry, or matched to those of the loudspeaker by convolution with impulse responses measured from the loudspeaker to the listener position, using an acoustic manikin. The headphone response was also compensated. Using the loudspeaker, monaural presentation was achieved by instructing the listener to block the left ear with a finger. Near perfect binaural loudness constancy was observed using loudspeaker presentation, while there was a summation effect of 3-6 dB for both headphone conditions. However, only partial constancy was observed when meatal occlusion was simulated. These results suggest that there may be contributions to binaural loudness constancy from residual low frequencies at the occluded ear as well as a cognitive element, which is activated by the knowledge that one ear is occluded. PMID:27080647

  3. Phylogenies of microcystin-producing cyanobacteria in the lower Laurentian Great Lakes suggest extensive genetic connectivity.

    PubMed

    Davis, Timothy W; Watson, Susan B; Rozmarynowycz, Mark J; Ciborowski, Jan J H; McKay, Robert Michael; Bullerjahn, George S

    2014-01-01

    Lake St. Clair is the smallest lake in the Laurentian Great Lakes system. MODIS satellite imagery suggests that high algal biomass events have occurred annually along the southern shore during late summer. In this study, we evaluated these events and tested the hypothesis that summer bloom material derived from Lake St. Clair may enter Lake Erie via the Detroit River and represent an overlooked source of potentially toxic Microcystis biomass to the western basin of Lake Erie. We conducted a seasonally and spatially resolved study carried out in the summer of 2013. Our goals were to: 1) track the development of the 2013 summer south-east shore bloom 2) conduct a spatial survey to characterize the extent of toxicity, taxonomic diversity of the total phytoplankton population and the phylogenetic diversity of potential MC-producing cyanobacteria (Microcystis, Planktothrix and Anabaena) during a high biomass event, and 3) compare the strains of potential MC-producers in Lake St. Clair with strains from Lake Erie and Lake Ontario. Our results demonstrated a clear predominance of cyanobacteria during a late August bloom event, primarily dominated by Microcystis, which we traced along the Lake St. Clair coastline downstream to the Detroit River's outflow at Lake Erie. Microcystin levels exceeded the Province of Ontario Drinking Water Quality Standard (1.5 µg L(-1)) for safe drinking water at most sites, reaching up to five times this level in some areas. Microcystis was the predominant microcystin producer, and all toxic Microcystis strains found in Lake St. Clair were genetically similar to toxic Microcystis strains found in lakes Erie and Ontario. These findings suggest extensive genetic connectivity among the three systems. PMID:25207941

  4. Phylogenies of Microcystin-Producing Cyanobacteria in the Lower Laurentian Great Lakes Suggest Extensive Genetic Connectivity

    PubMed Central

    Davis, Timothy W.; Watson, Susan B.; Rozmarynowycz, Mark J.; Ciborowski, Jan J. H.; McKay, Robert Michael; Bullerjahn, George S.

    2014-01-01

    Lake St. Clair is the smallest lake in the Laurentian Great Lakes system. MODIS satellite imagery suggests that high algal biomass events have occurred annually along the southern shore during late summer. In this study, we evaluated these events and tested the hypothesis that summer bloom material derived from Lake St. Clair may enter Lake Erie via the Detroit River and represent an overlooked source of potentially toxic Microcystis biomass to the western basin of Lake Erie. We conducted a seasonally and spatially resolved study carried out in the summer of 2013. Our goals were to: 1) track the development of the 2013 summer south-east shore bloom 2) conduct a spatial survey to characterize the extent of toxicity, taxonomic diversity of the total phytoplankton population and the phylogenetic diversity of potential MC-producing cyanobacteria (Microcystis, Planktothrix and Anabaena) during a high biomass event, and 3) compare the strains of potential MC-producers in Lake St. Clair with strains from Lake Erie and Lake Ontario. Our results demonstrated a clear predominance of cyanobacteria during a late August bloom event, primarily dominated by Microcystis, which we traced along the Lake St. Clair coastline downstream to the Detroit River's outflow at Lake Erie. Microcystin levels exceeded the Province of Ontario Drinking Water Quality Standard (1.5 µg L−1) for safe drinking water at most sites, reaching up to five times this level in some areas. Microcystis was the predominant microcystin producer, and all toxic Microcystis strains found in Lake St. Clair were genetically similar to toxic Microcystis strains found in lakes Erie and Ontario. These findings suggest extensive genetic connectivity among the three systems. PMID:25207941

  5. Flower constancy in insect pollinators

    PubMed Central

    Ratnieks, Francis L.W.

    2011-01-01

    As first noted by Aristotle in honeybee workers, many insect pollinators show a preference to visit flowers of just one species during a foraging trip. This “flower constancy” probably benefits plants, because pollen is more likely to be deposited on conspecific stigmas. But it is less clear why insects should ignore rewarding alternative flowers. Many researchers have argued that flower constancy is caused by constraints imposed by insect nervous systems rather than because flower constancy is itself an efficient foraging method. We argue that this view is unsatisfactory because it both fails to explain why foragers flexibly adjust the degree of flower constancy and does not explain why foragers of closely related species show different degrees of constancy. While limitations of the nervous system exist and are likely to influence flower constancy to some degree, the observed behavioural flexibility suggests that flower constancy is a successful foraging strategy given the insect’s own information about different foraging options. PMID:22446521

  6. Origin and Phylogeny of Microbes Living in Permanent Antarctic Lake Ice.

    PubMed

    Gordon, D. A.; Priscu, J.; Giovannoni, S.

    2000-04-01

    A BSTRACTThe phylogenetic diversity of bacteria and cyanobacteria colonizing sediment particles in the permanent ice cover of an Antarctic lake was characterized by analyses of 16S rRNA genes amplified from environmental DNA. Samples of mineral particles were collected from a depth of 2.5 m in the 4-m-thick ice cover of Lake Bonney, McMurdo Dry Valleys, Antarctica. A rRNA gene clone library of 198 clones was made and characterized by sequencing and oligonucleotide probe hybridization. The library was dominated by representatives of the cyanobacteria, proteobacteria, and Planctomycetales, but also contained diverse clones representing many other microbial groups, including the Acidobacterium/Holophaga division, the Green Non-Sulfur division, and the Actinobacteria. Six oligonucleotide probes were made for the most abundant clades recovered in the library. To determine whether the ice microbial community might originate from wind dispersal of the algal mats found elsewhere in Taylor Valley, the probes were hybridized to 16S rDNAs amplified from three samples of terrestrial cyanobacterial mats collected at nearby sites, as well as to bacterial 16S rDNAs from the lake ice community. The results demonstrate the presence of a diverse microbial community dominated by cyanobacteria in the lake ice, and also show that the dominant members of the lake ice microbial community are found in terrestrial mats elsewhere in the area. The lake ice microbial community appears to be dominated by organisms that are not uniquely adapted to the lake ice ecosystem, but instead are species that originate elsewhere in the surrounding region and opportunistically colonize the unusual habitat provided by the sediments suspended in lake ice. PMID:12035096

  7. Synaesthesia and colour constancy.

    PubMed

    Erskine, Holly; Mattingley, Jason B; Arnold, Derek H

    2013-04-01

    Grapheme-colour synaesthesia is an atypical condition characterized by the perception of colours when reading achromatic text. We investigated the level of colour processing responsible for these experiences. To do so, we tapped a central characteristic of colour perception. In different lighting conditions the same wavelength of light can prompt the perception of different colours. This helps humans recognize distinctive coloured objects despite changes in illumination. We wanted to see if synaesthetic colours were generated at a neural locus that was susceptible to colour constancy analyses. We used colour matching and naming tasks to examine interactions between simulated coloured illuminants and synaesthetic colours. Neither synaesthetic colour matching or naming was impacted. This contrasted with non-synaesthetic control participants, who performed the colour-matching task with graphemes physically coloured to mimic synaesthesia. Our data suggest that synaesthetic colour signals are not generated at lower-levels of colour processing, but are introduced at higher levels of analysis and are therefore not impacted by the processes responsible for perceptual constancy. PMID:22487049

  8. Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem.

    PubMed

    Preheim, Sarah P; Olesen, Scott W; Spencer, Sarah J; Materna, Arne; Varadharajan, Charuleka; Blackburn, Matthew; Friedman, Jonathan; Rodríguez, Jorge; Hemond, Harold; Alm, Eric J

    2016-01-01

    Much remains unknown about what drives microbial community structure and diversity. Highly structured environments might offer clues. For example, it may be possible to identify metabolically similar species as groups of organisms that correlate spatially with the geochemical processes they carry out. Here, we use a 16S ribosomal RNA gene survey in a lake that has chemical gradients across its depth to identify groups of spatially correlated but phylogenetically diverse organisms. Some groups had distributions across depth that aligned with the distributions of metabolic processes predicted by a biogeochemical model, suggesting that these groups performed biogeochemical functions. A single-cell genetic assay showed, however, that the groups associated with one biogeochemical process, sulfate reduction, contained only a few organisms that have the genes required to reduce sulfate. These results raise the possibility that some of these spatially correlated groups are consortia of phylogenetically diverse and metabolically different microbes that cooperate to carry out geochemical functions. PMID:27562262

  9. Invertebrates as indicators for chemical stress in sewage-influenced stream systems: toxic and endocrine effects in gammarids and reactions at the community level in two tributaries of Lake Constance, Schussen and Argen.

    PubMed

    Peschke, Katharina; Geburzi, Jonas; Köhler, Heinz-R; Wurm, Karl; Triebskorn, Rita

    2014-08-01

    The present study investigates the impact of releases from waste water treatment plants and storm water overflow basins on gammarids and other macrozoobenthos. The study relates to a recent upgrading of a waste water treatment plant (Langwiese) at the Schussen river, an important tributary to Lake Constance. Samples were taken at different sites at the Schussen river upstream and downstream of a storm water overflow basin and the waste water treatment plant Langwiese and, in parallel, at the Argen river, a less polluted reference stream. We assessed the influence of water quality on the distribution of macrozoobenthos and on the health of gammarid populations by a variety of ecotoxicological methods including biomarkers prior to the expansion of the waste water treatment plant. Through histopathological studies, the impact of parasites on host tissue health was evaluated. Analyses of heat shock protein (hsp70) levels allowed us to draw conclusions about the proteotoxicity-related stress status of the organisms. Furthermore, gammarid populations from all sites were investigated in respect to sex ratio, parasitism rate, and fecundity. Macrozoobenthos community integrity was determined by means of the saprobic index and the abundance as well as by the number of taxa. In gammarids, the sex ratio was significantly shifted towards females, fecundity was significantly decreased, and the hsp70 level was significantly increased downstream of the waste water treatment plant Langwiese, compared to the upstream sampling site. Similarly, these effects could be detected downstream of three small storm water overflow basins. In the macrozoobenthos communities, the abundance of taxa, the number of taxa, the number of ephemeroptera, plecoptera, and trichoptera taxa (EPT-taxa), and the number of sensitive taxa decreased downstream of the storm water overflow basin Mariatal as well as downstream of the waste water treatment plant Langwiese. Our study showed, that waste water

  10. Adaptive Color Constancy Using Faces.

    PubMed

    Bianco, Simone; Schettini, Raimondo

    2014-08-01

    In this work we design an adaptive color constancy algorithm that, exploiting the skin regions found in faces, is able to estimate and correct the scene illumination. The algorithm automatically switches from global to spatially varying color correction on the basis of the illuminant estimations on the different faces detected in the image. An extensive comparison with both global and local color constancy algorithms is carried out to validate the effectiveness of the proposed algorithm in terms of both statistical and perceptual significance on a large heterogeneous data set of RAW images containing faces. PMID:26353334

  11. Gender Constancy and Television Viewing.

    ERIC Educational Resources Information Center

    Luecke-Aleksa, Diane; And Others

    1995-01-01

    Explored gender constancy's interaction with television viewing, using videotapes of television viewing and viewing diaries for 5-year olds. Gender-constant boys focused on more male characters and watched more action and sports programs than preconstant boys. Gender-constant girls viewed more action programming than preconstant girls. Acquisition…

  12. Lightness Constancy in Surface Visualization.

    PubMed

    Szafir, Danielle Albers; Sarikaya, Alper; Gleicher, Michael

    2016-09-01

    Color is a common channel for displaying data in surface visualization, but is affected by the shadows and shading used to convey surface depth and shape. Understanding encoded data in the context of surface structure is critical for effective analysis in a variety of domains, such as in molecular biology. In the physical world, lightness constancy allows people to accurately perceive shadowed colors; however, its effectiveness in complex synthetic environments such as surface visualizations is not well understood. We report a series of crowdsourced and laboratory studies that confirm the existence of lightness constancy effects for molecular surface visualizations using ambient occlusion. We provide empirical evidence of how common visualization design decisions can impact viewers' abilities to accurately identify encoded surface colors. These findings suggest that lightness constancy aids in understanding color encodings in surface visualization and reveal a correlation between visualization techniques that improve color interpretation in shadow and those that enhance perceptions of surface depth. These results collectively suggest that understanding constancy in practice can inform effective visualization design. PMID:26584495

  13. Constructing Phylogenies.

    ERIC Educational Resources Information Center

    Bilardello, Nicholas; Valdes, Linda

    1998-01-01

    Introduces a method for constructing phylogenies using molecular traits and elementary graph theory. Discusses analyzing molecular data and using weighted graphs, minimum-weight spanning trees, and rooted cube phylogenies to display the data. (DDR)

  14. Color constancy in Japanese animation

    NASA Astrophysics Data System (ADS)

    Ichihara, Yasuyo G.

    2006-01-01

    In this study, we measure the colors used in a Japanese Animations. The result can be seen on CIE-xy color spaces. It clearly shows that the color system is not a natural appearance system but an imagined and artistic appearance system. Color constancy of human vision can tell the difference in skin and hair colors between under moonlight and day light. Human brain generates a match to the memorized color of an object from daylight viewing conditions to the color of the object in different viewing conditions. For example, Japanese people always perceive the color of the Rising Sun in the Japanese flag as red even in a different viewing condition such as under moonlight. Color images captured by a camera cannot present those human perceptions. However, Japanese colorists in Animation succeeded in painting the effects of color constancy not only under moonlight but also added the memory matching colors. They aim to create a greater impact on viewer's perceptions by using the effect of the memory matching colors. In this paper, we propose the Imagined Japanese Animation Color System. This system in art is currently a subject of research in Japan. Its importance is that it could also provide an explanation on how human brain perceives the same color under different viewing conditions.

  15. Flower Constancy, Insect Psychology, and Plant Evolution

    NASA Astrophysics Data System (ADS)

    Chittka, Lars; Thomson, James D.; Waser, Nickolas M.

    Individuals of some species of pollinating insects tend to restrict their visits to only a few of the available plant species, in the process bypassing valuable food sources. The question of why this flower constancy exists is a rich and important one with implications for the organization of natural communities of plants, floral evolution, and our understanding of the learning processes involved in finding food. Some scientists have assumed that flower constancy is adaptive per se. Others argued that constancy occurs because memory capacity for floral features in insects is limited, but attempts to identify the limitations often remained rather simplistic. We elucidate now different sensory and motor memories from natural foraging tasks are stored and retrieved, using concepts from modern learning science and visual search, and conclude that flower constancy is likely to have multiple causes. Possible constraints favoring constancy are interference sensitivity of short-term memory, and temporal limitations on retrieving information from long-term memory as rapidly as from short-term memory, but further empirical evidence is needed to substantiate these possibilities. In addition, retrieving memories may be slower and more prone to errors when there are several options than when an insect copes with only a single task. In addition to memory limitations, we also point out alternative explanations for flower constancy. We then consider the way in which floral parameters, such as interplant distances, nectar rewards, flower morphology, and floral color (as seen through bees' eyes) affect constancy. Finally, we discuss the implications of pollinator constancy for plant evolution. To date there is no evidence that flowers have diverged to favor constancy, although the appropriate tests may not have yet been conducted. However, there is good evidence against the notion that pollinator constancy is involved in speciation or maintenance of plant species integrity.

  16. A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach.

    PubMed

    Meyer, Britta S; Matschiner, Michael; Salzburger, Walter

    2015-02-01

    The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, the oldest of the lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains the highest number of endemic cichlid genera of all African lakes. Based on morphological grounds, the Tanganyikan cichlid species have been grouped into 12-16 distinct lineages, so-called tribes. While the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes remain largely elusive. Here, we present a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18kb. Using next-generation amplicon sequencing with the 454 pyrosequencing technology, we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the 'H-lineage', which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the 'H-lineage', as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic relationships at the base of the 'H-lineage' received less support, which is likely due to high speciation rates in the early phase of the radiation. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid

  17. Lightness constancy and illumination discounting.

    PubMed

    Logvinenko, Alexander D; Tokunaga, Rumi

    2011-08-01

    Contrary to the implication of the term "lightness constancy", asymmetric lightness matching has never been found to be perfect unless the scene is highly articulated (i.e., contains a number of different reflectances). Also, lightness constancy has been found to vary for different observers, and an effect of instruction (lightness vs. brightness) has been reported. The elusiveness of lightness constancy presents a great challenge to visual science; we revisit these issues in the following experiment, which involved 44 observers in total. The stimuli consisted of a large sheet of black paper with a rectangular spotlight projected onto the lower half and 40 squares of various shades of grey printed on the upper half. The luminance ratio at the edge of the spotlight was 25, while that of the squares varied from 2 to 16. Three different instructions were given to observers: They were asked to find a square in the upper half that (i) looked as if it was made of the same paper as that on which the spotlight fell (lightness match), (ii) had the same luminance contrast as the spotlight edge (contrast match), or (iii) had the same brightness as the spotlight (brightness match). Observers made 10 matches of each of the three types. Great interindividual variability was found for all three types of matches. In particular, the individual Brunswik ratios were found to vary over a broad range (from .47 to .85). That is, lightness matches were found to be far from veridical. Contrast matches were also found to be inaccurate, being on average, underestimated by a factor of 3.4. Articulation was found to essentially affect not only lightness, but contrast and brightness matches as well. No difference was found between the lightness and luminance contrast matches. While the brightness matches significantly differed from the other matches, the difference was small. Furthermore, the brightness matches were found to be subject to the same interindividual variability and the same

  18. White constancy method for mobile displays

    NASA Astrophysics Data System (ADS)

    Yum, Ji Young; Park, Hyun Hee; Jang, Seul Ki; Lee, Jae Hyang; Kim, Jong Ho; Yi, Ji Young; Lee, Min Woo

    2014-03-01

    In these days, consumer's needs for image quality of mobile devices are increasing as smartphone is widely used. For example, colors may be perceived differently when displayed contents under different illuminants. Displayed white in incandescent lamp is perceived as bluish, while same content in LED light is perceived as yellowish. When changed in perceived white under illuminant environment, image quality would be degraded. Objective of the proposed white constancy method is restricted to maintain consistent output colors regardless of the illuminants utilized. Human visual experiments are performed to analyze viewers'perceptual constancy. Participants are asked to choose the displayed white in a variety of illuminants. Relationship between the illuminants and the selected colors with white are modeled by mapping function based on the results of human visual experiments. White constancy values for image control are determined on the predesigned functions. Experimental results indicate that propsed method yields better image quality by keeping the display white.

  19. Color constancy by characterization of illumination chromaticity

    NASA Astrophysics Data System (ADS)

    Nikkanen, Jarno T.

    2011-05-01

    Computational color constancy algorithms play a key role in achieving desired color reproduction in digital cameras. Failure to estimate illumination chromaticity correctly will result in invalid overall colour cast in the image that will be easily detected by human observers. A new algorithm is presented for computational color constancy. Low computational complexity and low memory requirement make the algorithm suitable for resource-limited camera devices, such as consumer digital cameras and camera phones. Operation of the algorithm relies on characterization of the range of possible illumination chromaticities in terms of camera sensor response. The fact that only illumination chromaticity is characterized instead of the full color gamut, for example, increases robustness against variations in sensor characteristics and against failure of diagonal model of illumination change. Multiple databases are used in order to demonstrate the good performance of the algorithm in comparison to the state-of-the-art color constancy algorithms.

  20. Color constancy influenced by unnatural spatial structure.

    PubMed

    Mizokami, Yoko; Yaguchi, Hirohisa

    2014-04-01

    The recognition of spatial structures is important for color constancy because we cannot identify an object's color under different illuminations without knowing which space it is in and how that space is illuminated. To show the importance of the natural structure of environments on color constancy, we investigated the way in which color appearance was affected by unnatural viewing conditions in which a spatial structure was distorted. Observers judged the color of a test patch placed in the center of a small room illuminated by white or reddish lights, as well as two rooms illuminated by white and reddish light, respectively. In the natural viewing condition, an observer saw the room(s) through a viewing window, whereas in an unnatural viewing condition, the scene structure was scrambled by a kaleidoscope-type viewing box. Results of single room condition with one illuminant color showed little difference in color constancy between the two viewing conditions. However, it decreased in the two-rooms condition with a more complex arrangement of space and illumination. The patch's appearance under the unnatural viewing condition was more influenced by simultaneous contrast than its appearance under the natural viewing condition. It also appears that color appearance under white illumination is more stable compared to that under reddish illumination. These findings suggest that natural spatial structure plays an important role for color constancy in a complex environment. PMID:24695167

  1. Constance mirror program: Progress and plans

    NASA Astrophysics Data System (ADS)

    Klinkowstein, R. E.; Mauel, M. E.; Irby, J. H.; Smullin, L. D.; Voldman, S. H.

    1981-03-01

    The current state of the mechanics of the Constance II experiment, the physics results gathered, the motivation background, and future plans for the Constance II experiment are reviewed. Several improvements have been made and several experimental investigations have been completed. These include the construction/installation/testing of: (1) liquid-nitrogen cooled, Ioffe bars installed, (2) a diverter coil (3) the 100 kW ICRF generator, (4) the data acquisition system, and (5) the optimum hot-iron operation of the machine with Titanium and pulsed-gas plasma guns. Measurements were made of the density, temperature, and radius of the plasma. Ion-cyclotron fluctuations were observed, their bandwidth measured, and data collected demonstrating resonance heating. New X-ray diagnostics were designed and purchased, and progress on the Thomson scattering was made. Finally, a new hot cathode gun was designed and constructed.

  2. Constance mirror program: Progress and plans

    NASA Technical Reports Server (NTRS)

    Klinkowstein, R. E.; Mauel, M. E.; Irby, J. H.; Smullin, L. D.; Voldman, S. H.

    1981-01-01

    The current state of the mechanics of the Constance II experiment, the physics results gathered, the motivation background, and future plans for the Constance II experiment are reviewed. Several improvements have been made and several experimental investigations have been completed. These include the construction/installation/testing of: (1) liquid-nitrogen cooled, Ioffe bars installed, (2) a diverter coil (3) the 100 kW ICRF generator, (4) the data acquisition system, and (5) the optimum hot-iron operation of the machine with Titanium and pulsed-gas plasma guns. Measurements were made of the density, temperature, and radius of the plasma. Ion-cyclotron fluctuations were observed, their bandwidth measured, and data collected demonstrating resonance heating. New X-ray diagnostics were designed and purchased, and progress on the Thomson scattering was made. Finally, a new hot cathode gun was designed and constructed.

  3. Improving dermoscopy image classification using color constancy.

    PubMed

    Barata, Catarina; Celebi, M Emre; Marques, Jorge S

    2015-05-01

    Robustness is one of the most important characteristics of computer-aided diagnosis systems designed for dermoscopy images. However, it is difficult to ensure this characteristic if the systems operate with multisource images acquired under different setups. Changes in the illumination and acquisition devices alter the color of images and often reduce the performance of the systems. Thus, it is important to normalize the colors of dermoscopy images before training and testing any system. In this paper, we investigate four color constancy algorithms: Gray World, max-RGB, Shades of Gray, and General Gray World. Our results show that color constancy improves the classification of multisource images, increasing the sensitivity of a bag-of-features system from 71.0% to 79.7% and the specificity from 55.2% to 76% using only 1-D RGB histograms as features. PMID:25073179

  4. Reflectance, illumination, and appearance in color constancy

    PubMed Central

    McCann, John J.; Parraman, Carinna; Rizzi, Alessandro

    2013-01-01

    We studied color constancy using a pair of identical 3-D Color Mondrian displays. We viewed one 3-D Mondrian in nearly uniform illumination, and the other in directional, nonuniform illumination. We used the three dimensional structures to modulate the light falling on the painted surfaces. The 3-D structures in the displays were a matching set of wooden blocks. Across Mondrian displays, each corresponding facet had the same paint on its surface. We used only 6 chromatic, and 5 achromatic paints applied to 104 block facets. The 3-D blocks add shadows and multiple reflections not found in flat Mondrians. Both 3-D Mondrians were viewed simultaneously, side-by-side. We used two techniques to measure correlation of appearance with surface reflectance. First, observers made magnitude estimates of changes in the appearances of identical reflectances. Second, an author painted a watercolor of the 3-D Mondrians. The watercolor's reflectances quantified the changes in appearances. While constancy generalizations about illumination and reflectance hold for flat Mondrians, they do not for 3-D Mondrians. A constant paint does not exhibit perfect color constancy, but rather shows significant shifts in lightness, hue and chroma in response to the structure in the nonuniform illumination. Color appearance depends on the spatial information in both the illumination and the reflectances of objects. The spatial information of the quanta catch from the array of retinal receptors generates sensations that have variable correlation with surface reflectance. Models of appearance in humans need to calculate the departures from perfect constancy measured here. This article provides a dataset of measurements of color appearances for computational models of sensation. PMID:24478738

  5. Reflectance, illumination, and appearance in color constancy.

    PubMed

    McCann, John J; Parraman, Carinna; Rizzi, Alessandro

    2014-01-01

    We studied color constancy using a pair of identical 3-D Color Mondrian displays. We viewed one 3-D Mondrian in nearly uniform illumination, and the other in directional, nonuniform illumination. We used the three dimensional structures to modulate the light falling on the painted surfaces. The 3-D structures in the displays were a matching set of wooden blocks. Across Mondrian displays, each corresponding facet had the same paint on its surface. We used only 6 chromatic, and 5 achromatic paints applied to 104 block facets. The 3-D blocks add shadows and multiple reflections not found in flat Mondrians. Both 3-D Mondrians were viewed simultaneously, side-by-side. We used two techniques to measure correlation of appearance with surface reflectance. First, observers made magnitude estimates of changes in the appearances of identical reflectances. Second, an author painted a watercolor of the 3-D Mondrians. The watercolor's reflectances quantified the changes in appearances. While constancy generalizations about illumination and reflectance hold for flat Mondrians, they do not for 3-D Mondrians. A constant paint does not exhibit perfect color constancy, but rather shows significant shifts in lightness, hue and chroma in response to the structure in the nonuniform illumination. Color appearance depends on the spatial information in both the illumination and the reflectances of objects. The spatial information of the quanta catch from the array of retinal receptors generates sensations that have variable correlation with surface reflectance. Models of appearance in humans need to calculate the departures from perfect constancy measured here. This article provides a dataset of measurements of color appearances for computational models of sensation. PMID:24478738

  6. Color Constancy Using Double-Opponency.

    PubMed

    Gao, Shao-Bing; Yang, Kai-Fu; Li, Chao-Yi; Li, Yong-Jie

    2015-10-01

    The double-opponent (DO) color-sensitive cells in the primary visual cortex (V1) of the human visual system (HVS) have long been recognized as the physiological basis of color constancy. In this work we propose a new color constancy model by imitating the functional properties of the HVS from the single-opponent (SO) cells in the retina to the DO cells in V1 and the possible neurons in the higher visual cortexes. The idea behind the proposed double-opponency based color constancy (DOCC) model originates from the substantial observation that the color distribution of the responses of DO cells to the color-biased images coincides well with the vector denoting the light source color. Then the illuminant color is easily estimated by pooling the responses of DO cells in separate channels in LMS space with the pooling mechanism of sum or max. Extensive evaluations on three commonly used datasets, including the test with the dataset dependent optimal parameters, as well as the intra- and inter-dataset cross validation, show that our physiologically inspired DOCC model can produce quite competitive results in comparison to the state-of-the-art approaches, but with a relative simple implementation and without requiring fine-tuning of the method for each different dataset. PMID:26353182

  7. Pre-constancy Vision in Infants.

    PubMed

    Yang, Jiale; Kanazawa, So; Yamaguchi, Masami K; Motoyoshi, Isamu

    2015-12-21

    Our visual system can easily estimate the constant color and material of external objects despite dynamic changes in the retinal image across viewpoints and illuminations in natural scenes. It is commonly believed that this high-level visual function, called "perceptual constancy," is acquired through postnatal learning [1], building upon low-level functions that have developed earlier, such as image discrimination. However, we demonstrate here that before developing perceptual constancy, 3- to 4-month-old infants have a striking ability to discriminate slight image changes due to illumination that are not salient for adults. These young infants lose this ability after 5 months of age and then develop an ability to perceive distal surface properties (glossy or matte) at 7-8 months of age. Moreover, we identify the transition period between these two functions at 5-6 months of age, wherein infants show difficulty in both image and surface discrimination. These findings support the notion that acquiring perceptual constancy leads to a loss of sensitivity to variant information, which is negligible for constant surface material perception. We suggest that the immature visual system may initially directly access local image features and then develops a complementary constant neural representation of the properties of an object. PMID:26671667

  8. Lake

    ERIC Educational Resources Information Center

    Wien, Carol Anne

    2008-01-01

    The lake is blue black and deep. It is a glaciated finger lake, clawed out of rock when ice retracted across Nova Scotia in a northerly direction during the last ice age. The lake is narrow, a little over a mile long, and deep, 90 to 190 feet in places according to local lore, off the charts in others. The author loves to swim there, with a sense…

  9. A Retinal Mechanism Inspired Color Constancy Model.

    PubMed

    Zhang, Xian-Shi; Gao, Shao-Bing; Li, Ruo-Xuan; Du, Xin-Yu; Li, Chao-Yi; Li, Yong-Jie

    2016-03-01

    In this paper, we propose a novel model for the computational color constancy, inspired by the amazing ability of the human vision system (HVS) to perceive the color of objects largely constant as the light source color changes. The proposed model imitates the color processing mechanisms in the specific level of the retina, the first stage of the HVS, from the adaptation emerging in the layers of cone photoreceptors and horizontal cells (HCs) to the color-opponent mechanism and disinhibition effect of the non-classical receptive field in the layer of retinal ganglion cells (RGCs). In particular, HC modulation provides a global color correction with cone-specific lateral gain control, and the following RGCs refine the processing with iterative adaptation until all the three opponent channels reach their stable states (i.e., obtain stable outputs). Instead of explicitly estimating the scene illuminant(s), such as most existing algorithms, our model directly removes the effect of scene illuminant. Evaluations on four commonly used color constancy data sets show that the proposed model produces competitive results in comparison with the state-of-the-art methods for the scenes under either single or multiple illuminants. The results indicate that single opponency, especially the disinhibitory effect emerging in the receptive field's subunit-structured surround of RGCs, plays an important role in removing scene illuminant(s) by inherently distinguishing the spatial structures of surfaces from extensive illuminant(s). PMID:26766375

  10. Color constancy in a naturalistic, goal-directed task

    PubMed Central

    Radonjić, Ana; Cottaris, Nicolas P.; Brainard, David H.

    2015-01-01

    In daily life, we use color information to select objects that will best serve a particular goal (e.g., pick the best-tasting fruit or avoid spoiled food). This is challenging when judgments must be made across changes in illumination as the spectrum reflected from an object to the eye varies with the illumination. Color constancy mechanisms serve to partially stabilize object color appearance across illumination changes, but whether and to what degree constancy supports accurate cross-illumination object selection is not well understood. To get closer to understanding how constancy operates in real-life tasks, we developed a paradigm in which subjects engage in a goal-directed task for which color is instrumental. Specifically, in each trial, subjects re-created an arrangement of colored blocks (the model) across a change in illumination. By analyzing the re-creations, we were able to infer and quantify the degree of color constancy that mediated subjects' performance. In Experiments 1 and 2, we used our paradigm to characterize constancy for two different sets of block reflectances, two different illuminant changes, and two different groups of subjects. On average, constancy was good in our naturalistic task, but it varied considerably across subjects. In Experiment 3, we tested whether varying scene complexity and the validity of local contrast as a cue to the illumination change modulated constancy. Increasing complexity did not lead to improved constancy; silencing local contrast significantly reduced constancy. Our results establish a novel goal-directed task that enables us to approach color constancy as it emerges in real life. PMID:26381834

  11. Color constancy in a naturalistic, goal-directed task.

    PubMed

    Radonjic, Ana; Cottaris, Nicolas P; Brainard, David H

    2015-01-01

    In daily life, we use color information to select objects that will best serve a particular goal (e.g., pick the best-tasting fruit or avoid spoiled food). This is challenging when judgments must be made across changes in illumination as the spectrum reflected from an object to the eye varies with the illumination. Color constancy mechanisms serve to partially stabilize object color appearance across illumination changes, but whether and to what degree constancy supports accurate cross-illumination object selection is not well understood. To get closer to understanding how constancy operates in real-life tasks, we developed a paradigm in which subjects engage in a goal-directed task for which color is instrumental. Specifically, in each trial, subjects re-created an arrangement of colored blocks (the model) across a change in illumination. By analyzing the re-creations, we were able to infer and quantify the degree of color constancy that mediated subjects' performance. In Experiments 1 and 2, we used our paradigm to characterize constancy for two different sets of block reflectances, two different illuminant changes, and two different groups of subjects. On average, constancy was good in our naturalistic task, but it varied considerably across subjects. In Experiment 3, we tested whether varying scene complexity and the validity of local contrast as a cue to the illumination change modulated constancy. Increasing complexity did not lead to improved constancy; silencing local contrast significantly reduced constancy. Our results establish a novel goal-directed task that enables us to approach color constancy as it emerges in real life. PMID:26381834

  12. Color constancy supports cross-illumination color selection

    PubMed Central

    Radonjić, Ana; Cottaris, Nicolas P.; Brainard, David H.

    2015-01-01

    We rely on color to select objects as the targets of our actions (e.g., the freshest fish, the ripest fruit). To be useful for selection, color must provide accurate guidance about object identity across changes in illumination. Although the visual system partially stabilizes object color appearance across illumination changes, how such color constancy supports object selection is not understood. To study how constancy operates in real-life tasks, we developed a novel paradigm in which subjects selected which of two test objects presented under a test illumination appeared closer in color to a target object presented under a standard illumination. From subjects' choices, we inferred a selection-based match for the target via a variant of maximum likelihood difference scaling, and used it to quantify constancy. Selection-based constancy was good when measured using naturalistic stimuli, but was dramatically reduced when the stimuli were simplified, indicating that a naturalistic stimulus context is critical for good constancy. Overall, our results suggest that color supports accurate object selection across illumination changes when both stimuli and task match how color is used in real life. We compared our selection-based constancy results with data obtained using a classic asymmetric matching task and found that the adjustment-based matches predicted selection well for our stimuli and instructions, indicating that the appearance literature provides useful guidance for the emerging study of constancy in natural tasks. PMID:26024460

  13. Scene Context Dependency of Pattern Constancy of Time Series Imagery

    NASA Technical Reports Server (NTRS)

    Woodell, Glenn A.; Jobson, Daniel J.; Rahman, Zia-ur

    2008-01-01

    A fundamental element of future generic pattern recognition technology is the ability to extract similar patterns for the same scene despite wide ranging extraneous variables, including lighting, turbidity, sensor exposure variations, and signal noise. In the process of demonstrating pattern constancy of this kind for retinex/visual servo (RVS) image enhancement processing, we found that the pattern constancy performance depended somewhat on scene content. Most notably, the scene topography and, in particular, the scale and extent of the topography in an image, affects the pattern constancy the most. This paper will explore these effects in more depth and present experimental data from several time series tests. These results further quantify the impact of topography on pattern constancy. Despite this residual inconstancy, the results of overall pattern constancy testing support the idea that RVS image processing can be a universal front-end for generic visual pattern recognition. While the effects on pattern constancy were significant, the RVS processing still does achieve a high degree of pattern constancy over a wide spectrum of scene content diversity, and wide ranging extraneousness variations in lighting, turbidity, and sensor exposure.

  14. Color constancy supports cross-illumination color selection.

    PubMed

    Radonjić, Ana; Cottaris, Nicolas P; Brainard, David H

    2015-01-01

    We rely on color to select objects as the targets of our actions (e.g., the freshest fish, the ripest fruit). To be useful for selection, color must provide accurate guidance about object identity across changes in illumination. Although the visual system partially stabilizes object color appearance across illumination changes, how such color constancy supports object selection is not understood. To study how constancy operates in real-life tasks, we developed a novel paradigm in which subjects selected which of two test objects presented under a test illumination appeared closer in color to a target object presented under a standard illumination. From subjects' choices, we inferred a selection-based match for the target via a variant of maximum likelihood difference scaling, and used it to quantify constancy. Selection-based constancy was good when measured using naturalistic stimuli, but was dramatically reduced when the stimuli were simplified, indicating that a naturalistic stimulus context is critical for good constancy. Overall, our results suggest that color supports accurate object selection across illumination changes when both stimuli and task match how color is used in real life. We compared our selection-based constancy results with data obtained using a classic asymmetric matching task and found that the adjustment-based matches predicted selection well for our stimuli and instructions, indicating that the appearance literature provides useful guidance for the emerging study of constancy in natural tasks. PMID:26024460

  15. Open problems in color constancy: discussion.

    PubMed

    van Trigt, C

    2014-02-01

    This paper discusses a number of open problems in color constancy theory whose correct solution is a prerequisite for the theory of the phenomenon. Solutions employing suitable visually meaningful versus physically meaningful basis functions (principal components) are examined. In the former case the starting point is an estimate of the first derivative of the reflectance (illuminant), essential for defining color, instead of an estimate of the reflectance (illuminant), as in the latter. Conceptual consequences are discussed. Mathematical and physical constraints are identified. We compare the results of theories that do or do not ignore them. The following questions are considered. (1) Do unique solutions of the estimation problem exist everywhere in the object-color solid belonging to the illuminant? (2) Are they physically meaningful, i.e., at least nonnegative? (3) Are they representative for reflectance and spectral distribution functions? (4) What role plays metamerism? PMID:24562033

  16. Extending "color constancy" outside the visible region.

    PubMed

    Ratnasingam, Sivalogeswaran; Collins, Steve; Hernández-Andrés, Javier

    2011-04-01

    In this paper, the results of an investigation of the possibility of extending "color constancy" to obtain illuminant-invariant reflectance features from data in the near-ultraviolet (UV) and near-infrared (IR) wavelength regions are reported. These features are obtained by extending a blackbody-model-based color constancy algorithm proposed by Ratnasingam and Collins [J. Opt. Soc. Am. A27, 286 (2010)] to these additional wavelengths. Ratnasingam and Collins applied the model-based algorithm in the visible region to extract two illuminant-invariant features related to the wavelength-dependent reflectance of a surface from the responses of four sensors. In this paper, this model-based algorithm is extended to extract two illuminant-invariant reflectance features from the responses of sensors that cover the visible and either the near-UV or near-IR wavelength. In this investigation, test reflectance data sets are generated using the goodness-fitness coefficient (GFC). The appropriateness of the GFC for generating the test data sets is demonstrated by comparing the results obtained with these data with those obtained from data sets generated using the CIELab distance. Results based upon the GFC are then presented that suggest that the model-based algorithm can extract useful features from data from the visible and near-IR wavelengths. Finally, results are presented that show that, although the spectrum of daylight in the near UV is very different from a blackbody spectrum, the algorithm can be modified to extract useful features from visible and near-UV wavelengths. PMID:21478947

  17. Spectral sharpening of color sensors: diagonal color constancy and beyond.

    PubMed

    Vazquez-Corral, Javier; Bertalmío, Marcelo

    2014-01-01

    It has now been 20 years since the seminal work by Finlayson et al. on the use of spectral sharpening of sensors to achieve diagonal color constancy. Spectral sharpening is still used today by numerous researchers for different goals unrelated to the original goal of diagonal color constancy e.g., multispectral processing, shadow removal, location of unique hues. This paper reviews the idea of spectral sharpening through the lens of what is known today in color constancy, describes the different methods used for obtaining a set of sharpening sensors and presents an overview of the many different uses that have been found for spectral sharpening over the years. PMID:24577523

  18. Spectral Sharpening of Color Sensors: Diagonal Color Constancy and Beyond

    PubMed Central

    Vazquez-Corral, Javier; Bertalmío, Marcelo

    2014-01-01

    It has now been 20 years since the seminal work by Finlayson et al. on the use of spectral sharpening of sensors to achieve diagonal color constancy. Spectral sharpening is still used today by numerous researchers for different goals unrelated to the original goal of diagonal color constancy e.g., multispectral processing, shadow removal, location of unique hues. This paper reviews the idea of spectral sharpening through the lens of what is known today in color constancy, describes the different methods used for obtaining a set of sharpening sensors and presents an overview of the many different uses that have been found for spectral sharpening over the years. PMID:24577523

  19. The nature of instructional effects in color constancy.

    PubMed

    Radonjić, Ana; Brainard, David H

    2016-06-01

    The instructions subjects receive can have a large effect on experimentally measured color constancy, but the nature of these effects and how their existence should inform our understanding of color perception remains unclear. We used a factorial design to measure how instructional effects on constancy vary with experimental task and stimulus set. In each of 2 experiments, we employed both a classic adjustment-based asymmetric matching task and a novel color selection task. Four groups of naive subjects were instructed to make adjustments/selections based on (a) color (neutral instructions); (b) the light reaching the eye (physical spectrum instructions); (c) the actual surface reflectance of an object (objective reflectance instructions); or (d) the apparent surface reflectance of an object (apparent reflectance instructions). Across the 2 experiments we varied the naturalness of the stimuli. We find clear interactions between instructions, task, and stimuli. With simplified stimuli (Experiment 1), instructional effects were large and the data revealed 2 instruction-dependent patterns. In 1 (neutral and physical spectrum instructions) constancy was low, intersubject variability was also low, and adjustment-based and selection-based constancy were in agreement. In the other (reflectance instructions) constancy was high, intersubject variability was large, adjustment-based constancy deviated from selection-based constancy and for some subjects selection-based constancy increased across sessions. Similar patterns held for naturalistic stimuli (Experiment 2), although instructional effects were smaller. We interpret these 2 patterns as signatures of distinct task strategies-1 is perceptual, with judgments based primarily on the perceptual representation of color; the other involves explicit instruction-driven reasoning. (PsycINFO Database Record PMID:26727021

  20. Color constancy for an unseen surface.

    PubMed

    Norman, Liam J; Akins, Kathleen; Heywood, Charles A; Kentridge, Robert W

    2014-12-01

    The illumination of a scene strongly affects our perception of objects in that scene, e.g., the pages of a book illuminated by candlelight will appear quite yellow relative to other types of artificial illuminants. Yet at the same time, the reader still judges the pages as white, their surface color unaffected by the interplay of paper and illuminant. It has been shown empirically that we can indeed report two quite different interpretations of "color": one is dependent on the constant surface spectral reflectance of an object (surface color) and the other on the power of light of different wavelengths reflected from that object (reflected color). How then are these two representations related? The common view, dating from Aristotle, is that our experience of surface color is derived from reflected color or, in more familiar terms, that color perception follows from color sensation. By definition, color constancy requires that vision "discounts the illuminant"; thus, it seems reasonable that vision begins with the color of objects as they naively appear and that we infer from their appearances their surface color. Here, we question this classic view. We use metacontrast-masked priming and, by presenting the unseen prime and the visible mask under different illuminants, dissociate two ways in which the prime matched the mask: in surface color or in reflected color. We find that priming of the mask occurs when it matches the prime in surface color, not reflected color. It follows that color perception can arise without prior color sensation. PMID:25456450

  1. Crater Lake: blue through time

    USGS Publications Warehouse

    Larson, Gary L.; Buktenica, Mark; Collier, Robert

    2003-01-01

    Blue is the color of constancy, hence the term true blue. The unearthly blueness of Crater Lake reflects its pristine character and gives scientists a focal point for studying human impacts on aquatic environments over long periods of time. Scientists with the U.S. Geological Survey (USGS), National Park Service, and Oregon State University have systematically studied the lake for the last two decades. Long-term monitoring of this lake is a priority of Crater Lake National Park and will continue far into the future.

  2. Accommodation and size-constancy of virtual objects.

    PubMed

    Kenyon, Robert V; Phenany, Moses; Sandin, Daniel; Defanti, Thomas

    2008-02-01

    Accommodation has been suspected as a contributor to size illusions in virtual environments (VE) due to the lack of appropriate accommodative stimuli in a VE for the objects displayed. Previous experiments examining size-constancy in VE have shown that monocular cues to depth that accompany the object are a major contributor to correct size perception. When these accompanying cues are removed perceived size varied with the object's distance from the subject, i.e., visual angle. If accommodation were the dominant mechanism contributing to a visual angle response [due to its action to keep physical objects clear] in this condition, an open-loop accommodation viewing condition might restore size-constancy to this condition. Pinhole apertures were used to open-loop accommodation and examine if size-constancy might be restored when few accompanying monocular cues to depth were present. Visual angle performance when viewing a low cue environment was found with and without the use of the pinhole apertures. Thus, these results signify that accommodation does not play a dominate role in the loss of size-constancy in sparse visual environments often used in VE. These results suggest that size-constancy is driven by the inclusion of the remaining monocular cues to depth in VE as it is in the physical world. PMID:18066664

  3. Chromatic settings and the structural color constancy index.

    PubMed

    Roca-Vila, Jordi; Parraga, C Alejandro; Vanrell, Maria

    2013-01-01

    Color constancy is usually measured by achromatic setting, asymmetric matching, or color naming paradigms, whose results are interpreted in terms of indexes and models that arguably do not capture the full complexity of the phenomenon. Here we propose a new paradigm, chromatic setting, which allows a more comprehensive characterization of color constancy through the measurement of multiple points in color space under immersive adaptation. We demonstrated its feasibility by assessing the consistency of subjects' responses over time. The paradigm was applied to two-dimensional (2-D) Mondrian stimuli under three different illuminants, and the results were used to fit a set of linear color constancy models. The use of multiple colors improved the precision of more complex linear models compared to the popular diagonal model computed from gray. Our results show that a diagonal plus translation matrix that models mechanisms other than cone gain might be best suited to explain the phenomenon. Additionally, we calculated a number of color constancy indices for several points in color space, and our results suggest that interrelations among colors are not as uniform as previously believed. To account for this variability, we developed a new structural color constancy index that takes into account the magnitude and orientation of the chromatic shift in addition to the interrelations among colors and memory effects. PMID:23479473

  4. Life/Work Planning: Change and Constancy in the World of Work.

    ERIC Educational Resources Information Center

    Bolles, Richard N.

    1983-01-01

    To plan for our future we must consider both change and constancy, but most futurists today pay insufficient attention to constancy. As individuals plan their lives, they must assess their desire for change or constancy in geography, goals, special knowledge, people environments, working conditions, salary, and transferable skills. (IS)

  5. "God Made Me a Girl": Sex-Category Constancy Judgments and Explanations Revisited.

    ERIC Educational Resources Information Center

    Szkrybalo, Joel; Ruble, Diane N.

    1999-01-01

    Studied children's sex-category constancy judgments and accompanying explanations over three years. Found that constancy improvements were linked to explanations based on operational reasoning. Lower constancy scores were linked to explanations emphasizing gender-role norms and external appearances. Judgment-explanation relationships were stronger…

  6. Sensory, computational and cognitive components of human colour constancy

    PubMed Central

    Smithson, H.E

    2005-01-01

    When the illumination on a scene changes, so do the visual signals elicited by that scene. In spite of these changes, the objects within a scene tend to remain constant in their apparent colour. We start this review by discussing the psychophysical procedures that have been used to quantify colour constancy. The transformation imposed on the visual signals by a change in illumination dictates what the visual system must ‘undo’ to achieve constancy. The problem is mathematically underdetermined, and can be solved only by exploiting regularities of the visual world. The last decade has seen a substantial increase in our knowledge of such regularities as technical advances have made it possible to make empirical measurements of large numbers of environmental scenes and illuminants. This review provides a taxonomy of models of human colour constancy based first on the assumptions they make about how the inverse transformation might be simplified, and second, on how the parameters of the inverse transformation might be set by elements of a complex scene. Candidate algorithms for human colour constancy are represented graphically and pictorially, and the availability and utility of an accurate estimate of the illuminant is discussed. Throughout this review, we consider both the information that is, in principle, available and empirical assessments of what information the visual system actually uses. In the final section we discuss where in our visual systems these computations might be implemented. PMID:16147525

  7. Gender Constancy and Same-Sex Imitation: A Developmental Study.

    ERIC Educational Resources Information Center

    Perloff, Richard M.

    1982-01-01

    Fifty-one preschool children were interviewed individually to assess awareness of gender constancy and choice of same-sex models. Differences emerged between high and low gender-constant children when they were given a choice between imitating a same-sex model performing a relatively unpleasant task and imitating an opposite-sex model enacting a…

  8. Constance D'Arcy Mackay: A Historiographical Perspective.

    ERIC Educational Resources Information Center

    van de Water, Manon

    1995-01-01

    States that Constance D'Arcy Mackay was instrumental in defining the genre of children's theater in the early 20th century. Discusses her career highlights. Concludes that Mackay played a pivotal role in the "making" of the history of children's theater in the United States, and that while little of her personal history is known, her theories are…

  9. Constance Mellon's "Library Anxiety": An Appreciation and a Critique

    ERIC Educational Resources Information Center

    Gremmels, Gillian S.

    2015-01-01

    In this article, the author recollects her memories reading Constance A. Mellon's article, "Library Anxiety: A Grounded Theory and Its Development," when it appeared in the March 1986 issue of "College & Research Libraries." She was a reference librarian at at DePauw University in Indiana at the time, helping students…

  10. Exemplar-Based Color Constancy and Multiple Illumination.

    PubMed

    Joze, Hamid Reza Vaezi; Drew, Mark S

    2014-05-01

    Exemplar-based learning or, equally, nearest neighbor methods have recently gained interest from researchers in a variety of computer science domains because of the prevalence of large amounts of accessible data and storage capacity. In computer vision, these types of technique have been successful in several problems such as scene recognition, shape matching, image parsing, character recognition, and object detection. Applying the concept of exemplar-based learning to the problem of color constancy seems odd at first glance since, in the first place, similar nearest neighbor images are not usually affected by precisely similar illuminants and, in the second place, gathering a dataset consisting of all possible real-world images, including indoor and outdoor scenes and for all possible illuminant colors and intensities, is indeed impossible. In this paper, we instead focus on surfaces in the image and address the color constancy problem by unsupervised learning of an appropriate model for each training surface in training images. We find nearest neighbor models for each surface in a test image and estimate its illumination based on comparing the statistics of pixels belonging to nearest neighbor surfaces and the target surface. The final illumination estimation results from combining these estimated illuminants over surfaces to generate a unique estimate. We show that it performs very well, for standard datasets, compared to current color constancy algorithms, including when learning based on one image dataset is applied to tests from a different dataset. The proposed method has the advantage of overcoming multi-illuminant situations, which is not possible for most current methods since they assume the color of the illuminant is constant all over the image. We show a technique to overcome the multiple illuminant situation using the proposed method and test our technique on images with two distinct sources of illumination using a multiple-illuminant color constancy

  11. Depth perception in the framework of General Object Constancy.

    PubMed

    Qian, Jiehui; Petrov, Yury

    2013-01-01

    Size constancy is a well-known example of perceptual stabilization accounting for the effect of viewing distance on retinal image size. In a recent study (Qian & Petrov, 2012), we demonstrated a similar stabilization mechanism for contrast perception and suggested that the brain accounts for effects of perceived distance on various other object features in a similar way, a hypothesis that we called General Object Constancy. Here we report a new illusion of depth further supporting this hypothesis. Pairs of disks moved across the screen in a pattern of radial optic flow. A pair comprised a small black disk floating in front of a large white disk, creating the percept of a pencil tip viewed head on. As these "pencils" moved away, they appeared to grow in contrast, in diameter, and also appeared to be getting "sharper." The contrast and size illusions replicated our previous findings, while the depth gradient (sharpness) illusion revealed a depth constancy phenomenon. We discovered that depth and size constancies were related, e.g., the two illusions were strongly correlated across observers. Whereas the illusory diameter increase could not be canceled by any degree of depth modulation, decreasing the diameter of the "pencils" during optic flow motion (thus increasing their disparity gradient) weakened the illusory depth gradient increase. This paradoxical result, as well as our other results, is explained by the General Object Constancy model: Besides using the same scaling factor to account for size, contrast, and depth variations with distance, the brain uses the apparent object size to additionally scale contrast and depth signals. PMID:24023274

  12. Building a Twig Phylogeny

    ERIC Educational Resources Information Center

    Flinn, Kathryn M.

    2015-01-01

    In this classroom activity, students build a phylogeny for woody plant species based on the morphology of their twigs. Using any available twigs, students can practice the process of cladistics to test evolutionary hypotheses for real organisms. They identify homologous characters, determine polarity through outgroup comparison, and construct a…

  13. Color constancy using 3D scene geometry derived from a single image.

    PubMed

    Elfiky, Noha; Gevers, Theo; Gijsenij, Arjan; Gonzalez, Jordi

    2014-09-01

    The aim of color constancy is to remove the effect of the color of the light source. As color constancy is inherently an ill-posed problem, most of the existing color constancy algorithms are based on specific imaging assumptions (e.g., gray-world and white patch assumption). In this paper, 3D geometry models are used to determine which color constancy method to use for the different geometrical regions (depth/layer) found in images. The aim is to classify images into stages (rough 3D geometry models). According to stage models, images are divided into stage regions using hard and soft segmentation. After that, the best color constancy methods are selected for each geometry depth. To this end, we propose a method to combine color constancy algorithms by investigating the relation between depth, local image statistics, and color constancy. Image statistics are then exploited per depth to select the proper color constancy method. Our approach opens the possibility to estimate multiple illuminations by distinguishing nearby light source from distant illuminations. Experiments on state-of-the-art data sets show that the proposed algorithm outperforms state-of-the-art single color constancy algorithms with an improvement of almost 50% of median angular error. When using a perfect classifier (i.e, all of the test images are correctly classified into stages); the performance of the proposed method achieves an improvement of 52% of the median angular error compared with the best-performing single color constancy algorithm. PMID:25051548

  14. Constructing computer virus phylogenies

    SciTech Connect

    Goldberg, L.A.; Goldberg, P.W.; Phillips, C.A.; Sorkin, G.B.

    1996-03-01

    There has been much recent algorithmic work on the problem of reconstructing the evolutionary history of biological species. Computer virus specialists are interested in finding the evolutionary history of computer viruses--a virus is often written using code fragments from one or more other viruses, which are its immediate ancestors. A phylogeny for a collection of computer viruses is a directed acyclic graph whose nodes are the viruses and whose edges map ancestors to descendants and satisfy the property that each code fragment is ``invented`` only once. To provide a simple explanation for the data, we consider the problem of constructing such a phylogeny with a minimal number of edges. In general, this optimization problem cannot be solved in quasi-polynomial time unless NQP=QP; we present positive and negative results for associated approximated problems. When tree solutions exist, they can be constructed and randomly sampled in polynomial time.

  15. Color constancy - A method for recovering surface spectral reflectance

    NASA Technical Reports Server (NTRS)

    Maloney, L. T.; Wandell, B. A.

    1986-01-01

    An algorithm has been developed for estimating the surface reflectance functions of objects in a scene with incomplete knowledge of the spectral power distribution of the ambient light. An image processing system employing this algorithm can assign colors that are constant despite changes in the lighting of the scene; this capability is essential to correct color rendering in photography, TV, and in the construction of artificial visual systems for robotics. Attention is given to the way in which constraints on lights and surfaces in the environment make color-constancy possible for a visual system, and the algorithm's implications for human color vision are discussed.

  16. The Development of Sex-Gender Constancy Among Children in Four Cultures.

    ERIC Educational Resources Information Center

    Munroe, Ruth H.; Munroe, Robert L.

    The study examines the acquisition of gender constancy in children as it relates to cultural, socioenvironmental, or individual differences. Gender constancy refers to the stages from simple identification of biological sex of self and others, to the understanding that one's sex is stable over time, and to comprehension of one's sex as consistent…

  17. An Experimental Test of the Effects of Gender Constancy on Sex Typing

    ERIC Educational Resources Information Center

    Arthur, Andrea E.; Bigler, Rebecca S.; Ruble, Diane N.

    2009-01-01

    This study provides an experimental test of the hypothesis that level of gender constancy understanding affects children's sex typing. Preschool-age children (N = 62, mean age = 47 months) were randomly assigned to experimental lessons that taught that biological traits (including gender) are either fixed (pro-constancy condition) or mutable…

  18. Hippopotamus and whale phylogeny.

    PubMed

    Geisler, Jonathan H; Theodor, Jessica M

    2009-03-19

    Thewissen et al. describe new fossils from India that apparently support a phylogeny that places Cetacea (that is, whales, dolphins, porpoises) as the sister group to the extinct family Raoellidae, and Hippopotamidae as more closely related to pigs and peccaries (that is, Suina) than to cetaceans. However, our reanalysis of a modified version of the data set they used differs in retaining molecular characters and demonstrates that Hippopotamidae is the closest extant family to Cetacea and that raoellids are the closest extinct group, consistent with previous phylogenetic studies. This topology supports the view that the aquatic adaptations in hippopotamids and cetaceans are inherited from their common ancestor. PMID:19295550

  19. Color constancy in 3D-2D face recognition

    NASA Astrophysics Data System (ADS)

    Meyer, Manuel; Riess, Christian; Angelopoulou, Elli; Evangelopoulos, Georgios; Kakadiaris, Ioannis A.

    2013-05-01

    Face is one of the most popular biometric modalities. However, up to now, color is rarely actively used in face recognition. Yet, it is well-known that when a person recognizes a face, color cues can become as important as shape, especially when combined with the ability of people to identify the color of objects independent of illuminant color variations. In this paper, we examine the feasibility and effect of explicitly embedding illuminant color information in face recognition systems. We empirically examine the theoretical maximum gain of including known illuminant color to a 3D-2D face recognition system. We also investigate the impact of using computational color constancy methods for estimating the illuminant color, which is then incorporated into the face recognition framework. Our experiments show that under close-to-ideal illumination estimates, one can improve face recognition rates by 16%. When the illuminant color is algorithmically estimated, the improvement is approximately 5%. These results suggest that color constancy has a positive impact on face recognition, but the accuracy of the illuminant color estimate has a considerable effect on its benefits.

  20. The Development of Gender Constancy in Early Childhood and Its Relation to Time Comprehension and False-Belief Understanding

    ERIC Educational Resources Information Center

    Zmyj, Norbert; Bischof-Köhler, Doris

    2015-01-01

    What is the developmental course of children's gender constancy? Do other cognitive abilities such as time comprehension and false-belief understanding foster gender constancy and the subcomponents gender stability and gender consistency? We examined the development of gender constancy and its relation to time comprehension and false-belief…

  1. Constancy and diversity in the flavivirus fusion peptide

    PubMed Central

    Seligman, Stephen J

    2008-01-01

    Background Flaviviruses include the mosquito-borne dengue, Japanese encephalitis, yellow fever and West Nile and the tick-borne encephalitis viruses. They are responsible for considerable world-wide morbidity and mortality. Viral entry is mediated by a conserved fusion peptide containing 16 amino acids located in domain II of the envelope protein E. Highly orchestrated conformational changes initiated by exposure to acidic pH accompany the fusion process and are important factors limiting amino acid changes in the fusion peptide that still permit fusion with host cell membranes in both arthropod and vertebrate hosts. The cell-fusing related agents, growing only in mosquitoes or insect cell lines, possess a different homologous peptide. Results Analysis of 46 named flaviviruses deposited in the Entrez Nucleotides database extended the constancy in the canonical fusion peptide sequences of mosquito-borne, tick-borne and viruses with no known vector to include more recently-sequenced viruses. The mosquito-borne signature amino acid, G104, was also found in flaviviruses with no known vector and with the cell-fusion related viruses. Despite the constancy in the canonical sequences in pathogenic flaviviruses, mutations were surprisingly frequent with a 27% prevalence of nonsynonymous mutations in yellow fever virus fusion peptide sequences, and 0 to 7.4% prevalence in the others. Six of seven yellow fever patients whose virus had fusion peptide mutations died. In the cell-fusing related agents, not enough sequences have been deposited to estimate reliably the prevalence of fusion peptide mutations. However, the canonical sequences homologous to the fusion peptide and the pattern of disulfide linkages in protein E differed significantly from the other flaviviruses. Conclusion The constancy of the canonical fusion peptide sequences in the arthropod-borne flaviviruses contrasts with the high prevalence of mutations in most individual viruses. The discrepancy may be the

  2. Quantitative studies of animal colour constancy: using the chicken as model.

    PubMed

    Olsson, Peter; Wilby, David; Kelber, Almut

    2016-05-11

    Colour constancy is the capacity of visual systems to keep colour perception constant despite changes in the illumination spectrum. Colour constancy has been tested extensively in humans and has also been described in many animals. In humans, colour constancy is often studied quantitatively, but besides humans, this has only been done for the goldfish and the honeybee. In this study, we quantified colour constancy in the chicken by training the birds in a colour discrimination task and testing them in changed illumination spectra to find the largest illumination change in which they were able to remain colour-constant. We used the receptor noise limited model for animal colour vision to quantify the illumination changes, and found that colour constancy performance depended on the difference between the colours used in the discrimination task, the training procedure and the time the chickens were allowed to adapt to a new illumination before making a choice. We analysed literature data on goldfish and honeybee colour constancy with the same method and found that chickens can compensate for larger illumination changes than both. We suggest that future studies on colour constancy in non-human animals could use a similar approach to allow for comparison between species and populations. PMID:27170714

  3. Monitoring Linear Accelerator Output Constancy Using the PTW Linacheck

    SciTech Connect

    McDermott, Garry M.; Buckle, Andrew H.

    2011-04-01

    The PTW-Linacheck was assessed for its ability to monitor linear accelerator radiation output constancy. The key issues that were considered were the setup for daily output measurements, e.g., requirements for build-up and backscatter material, and the reproducibility and linearity of the device with linear accelerator output. An appropriate measurement setup includes a 10 x 10 cm field at 100 cm FSD, 5 cm backscatter, and no added build-up for 4 MeV electron beams, 1 cm added build-up for 6-16 MeV electron beams and 5 cm added build-up for 6-15 MV photon beams. Using this measurement setup, the dose linearity and short-term reproducibility were acceptable; however, the Linacheck should be recalibrated on a monthly basis to ensure acceptable long-term reproducibility.

  4. The intensity dependent spread model and color constancy

    NASA Technical Reports Server (NTRS)

    Kurrasch, Ellie

    1990-01-01

    Odetics is investigating the use of the intensity dependent spread (IDS) model for determining color constancy. Object segmentation is performed effortlessly by the human visual systems, but creating computer vision that takes an image as input and performs object identification on the basis of color has some difficulties. The unknown aspects of the light illuminating a scene in space or anywhere can seriously interfere with the use of color for object identification. The color of an image depends not only on the physical characteristics of the object, but also on the wavelength composition of the incident illumination. IDS processing provides the extraction of edges and of reflectance changes across edges, independent of variations in scene illumination. IDS depends solely on the ratio of the reflectances on the two sides of the edge. Researchers are in the process of using IDS to recover the reflectance image.

  5. TARA and constance B mirror confinement experiments and theory

    SciTech Connect

    Post, R.S.; Gerver, M.; Kesner, J.; Irby, J.H.; Lane, B.G.; Mauel, M.E.; McVey, B.D.; Ram, A.; Sevillano, E.; Smatlak, D.L.

    1984-01-01

    The axisymmetric TARA central cell has been heated using aperture and double half turn ICRF antennas to produce stable plasma with ..beta.. less than or equal to 0.2%. Parameters suitable for startup of thermal barriers with n = 3.5 x 10/sup 12//cm/sup 3/ and Ti/sub perpendiculer/ approx. 30 eV have been reached. Hot electron plasmas with ..beta.. less than or equal to 15% are obtained in the TARA and Constance quadrupoles. Electron cyclotron instabilities are analyzed. A new scheme for single frequency drift pumping with stochasticity by ICRF is proposed. ICRF modulated at the electron bounce frequency is shown to yield stochastic parallel electron heating for thermal barriers.

  6. Generalized Enhanced Multivariance Product Representation for Data Partitioning: Constancy Level

    SciTech Connect

    Tunga, M. Alper; Demiralp, Metin

    2011-09-14

    Enhanced Multivariance Product Representation (EMPR) method is used to represent multivariate functions in terms of less-variate structures. The EMPR method extends the HDMR expansion by inserting some additional support functions to increase the quality of the approximants obtained for dominantly or purely multiplicative analytical structures. This work aims to develop the generalized form of the EMPR method to be used in multivariate data partitioning approaches. For this purpose, the Generalized HDMR philosophy is taken into consideration to construct the details of the Generalized EMPR at constancy level as the introductory steps and encouraging results are obtained in data partitioning problems by using our new method. In addition, to examine this performance, a number of numerical implementations with concluding remarks are given at the end of this paper.

  7. Speed Constancy or Only Slowness: What Drives the Kappa Effect

    PubMed Central

    Chen, Youguo; Zhang, Bangwu; Kording, Konrad Paul

    2016-01-01

    In the Kappa effect, two visual stimuli are given, and their spatial distance affects their perceived temporal interval. The classical model assumes constant speed while a competing Bayesian model assumes a slow speed prior. The two models are based on different assumptions about the statistical structure of the environment. Here we introduce a new visual experiment to distinguish between these models. When fit to the data, both the two models replicated human response, but the slowness model makes better behavioral predictions than the speed constancy model, and the estimated constant speed is close to the absolute threshold of speed. Our findings suggest that the Kappa effect appears to be due to slow speeds, and also modulated by spatial variance. PMID:27100097

  8. Monitoring linear accelerator output constancy using the PTW Linacheck.

    PubMed

    McDermott, Garry M; Buckle, Andrew H

    2011-01-01

    The PTW-Linacheck was assessed for its ability to monitor linear accelerator radiation output constancy. The key issues that were considered were the setup for daily output measurements, e.g., requirements for build-up and backscatter material, and the reproducibility and linearity of the device with linear accelerator output. An appropriate measurement setup includes a 10 × 10 cm field at 100 cm FSD, 5 cm backscatter, and no added build-up for 4 MeV electron beams, 1 cm added build-up for 6-16 MeV electron beams and 5 cm added build-up for 6-15 MV photon beams. Using this measurement setup, the dose linearity and short-term reproducibility were acceptable; however, the Linacheck should be recalibrated on a monthly basis to ensure acceptable long-term reproducibility. PMID:20346645

  9. Electron-cyclotron heating in the Constance 2 mirror experiment

    SciTech Connect

    Mauel, Michael E.

    1982-09-01

    Electron cyclotron heating of a highly-ionized plasma in mirror geometry is investigated. The experimental diagnosis of the electron energy distribution and the comparison of the results of this diagnosis with a two dimensional, time-dependent Fokker-Planck simulation are accomplished in four steps. (1) First, the power balance of the heated and unheated Constance 2 plasma is analyzed experimentally. It is concluded that the heated electrons escape the mirror at a rate dominated by a combination of the influx of cool electrons from outside the mirror and the increased loss rate of the ions. (2) The microwave parameters at the resonance zones are then calculated by cold-plasma ray tracing. High N/sub parallel/ waves are launched and for these waves, strong first-pass absorption is predicted. The absorption strength is qualitatively checked in the experiment by surrounding the plasma with non-reflecting liners. (3) A simplified quasilinear theory including the effect of N/sub parallel/ is developed to model the electrons. An analytic expression is derived for the RF-induced pump-out of the magnetically-confined warm electrons. Results of the Fokker-Planck simulations show the development of the electron energy distribution for several plasma conditions and verify the scaling of the analytic expression for RF-induced diffusion into the loss cone. (4) Sample x-ray and endloss data are presented, and the overall comparison between the simulation and experiment is discussed. The x-ray signals indicate that, for greater RF power, the hot electrondensity increases more rapidly than its temperature. The time history of the endloss data, illustrating RF-enhancement, suggests the predicted scaling for warm-electron pump-out. Finally, a comparison between the measured and predicted energy distribution shows that the bulk, warm and hot components of the heated Constance 2 electrons are indeed reproduced by the simulation.

  10. Color constancy demonstrated in a photographic picture by means of a D-up viewer

    NASA Astrophysics Data System (ADS)

    Phuangsuwan, Chanprapha; Ikeda, Mitsuo; Katemake, Pichayada

    2013-01-01

    According to the recognized visual space of illumination concept, space perception is essential for color constancy. It should be possible to experience the color constancy in a picture if we perceive a three-dimensional space in the picture. A dimension-up (D-up) viewer was constructed to perceive a space for a picture. An experimental room illuminated by various color lights was used as the reference scene and the subject determined a picture in which the color impression was matched to that of the room by selecting from 13 different colored pictures of the room. The picture with the color nearest to the color of the room was selected with the D-up viewer implying the existence of color constancy in the picture. When subjects observed a picture in a normal way the picture of the room illuminated in white was selected regardless of the actual room illumination color, confirming no color constancy in the picture.

  11. Phylogeny of filamentous ascomycetes

    NASA Astrophysics Data System (ADS)

    Lumbsch, H. T.

    Phylogenetic studies of higher ascomycetes are enhanced by the introduction of molecular markers. Most studies employed sequences of the SSU rRNA gene, but recently data from additional genes (RPB2, LSU rRNA) have become available. Several groups defined by their ascoma-type, such as Pyrenomycetes, are supported while others, like the Discomycetes, appear to be paraphyletic. The Pezizales with operculate asci are basal to other eu-ascomycetes, while other Discomycetes appear to be derived eu-ascomycetes. The re-evaluation of classical characters using molecular data is discussed using three examples. Ascus types are often regarded as being of major importance in ascomycete systematics, but prototunicate asci were found to be of poor taxonomic value, since ascomycetes with prototunicate asci are polyphyletic. The independence of the Agyriales, assumed from their morphological characters, is supported by sequence data but the relationship to supposed sister groups remains dubious. The phylogeny of ascolocularous fungi and their circumscription requires further study. While a circumscription based on bitunicate asci can be rejected, it remains unclear whether fungi with ascolocularous ascoma development represent a monophyletic entity.

  12. Phylogeny of African cichlid fishes as revealed by molecular markers.

    PubMed

    Mayer, W E; Tichy, H; Klein, J

    1998-06-01

    The species flocks of cichlid fish in the three great East African Lakes, Victoria, Malawi, and Tanganyika, have arisen in each lake by explosive adaptive radiation. Various questions concerning their phylogeny have not yet been answered. In particular, the identity of the ancestral founder species and the monophyletic origin of the haplochromine cichlids from the East African lakes have not been established conclusively. In the present study, we used the anonymous nuclear DNA marker DXTU1 as a step towards answering these questions. A 280 bp-fragment of the DXTU1 locus was amplified by the polymerase chain reaction from East African lacustrine species, the East African riverine cichlid species Haplochromis bloyeti, H. burtoni and H. sparsidens, and other African cichlids. Sequencing revealed several indels and substitutions that were used as cladistically informative markers to support a phylogenetic tree constructed by the neighbor-joining method. The topology, although not supported by high bootstrap values, corresponds well to the geographical distribution and previous classification of the cichlids. Markers could be defined that: (i) differentiate East African from West African cichlids; (ii) distinguish the riverine and Lake Victoria/Malawi haplochromines from Lake Tanganyika cichlids; and (iii) indicate the existence of a monophyletic Lake Victoria cichlid superflock which includes haplochromines from satellite lakes and East African rivers. In order to resolve further the relationship of East African riverine and lacustrine species, mtDNA cytochrome b and control region segments were sequenced. The mtDNA-based trees support the notion of the monophyly of the Lake Victoria superflock but are ambiguous with respect to the phylogenetic position of the Lake Malawi flock. PMID:9675872

  13. Chromatic Illumination Discrimination Ability Reveals that Human Colour Constancy Is Optimised for Blue Daylight Illuminations

    PubMed Central

    Pearce, Bradley; Crichton, Stuart; Mackiewicz, Michal; Finlayson, Graham D.; Hurlbert, Anya

    2014-01-01

    The phenomenon of colour constancy in human visual perception keeps surface colours constant, despite changes in their reflected light due to changing illumination. Although colour constancy has evolved under a constrained subset of illuminations, it is unknown whether its underlying mechanisms, thought to involve multiple components from retina to cortex, are optimised for particular environmental variations. Here we demonstrate a new method for investigating colour constancy using illumination matching in real scenes which, unlike previous methods using surface matching and simulated scenes, allows testing of multiple, real illuminations. We use real scenes consisting of solid familiar or unfamiliar objects against uniform or variegated backgrounds and compare discrimination performance for typical illuminations from the daylight chromaticity locus (approximately blue-yellow) and atypical spectra from an orthogonal locus (approximately red-green, at correlated colour temperature 6700 K), all produced in real time by a 10-channel LED illuminator. We find that discrimination of illumination changes is poorer along the daylight locus than the atypical locus, and is poorest particularly for bluer illumination changes, demonstrating conversely that surface colour constancy is best for blue daylight illuminations. Illumination discrimination is also enhanced, and therefore colour constancy diminished, for uniform backgrounds, irrespective of the object type. These results are not explained by statistical properties of the scene signal changes at the retinal level. We conclude that high-level mechanisms of colour constancy are biased for the blue daylight illuminations and variegated backgrounds to which the human visual system has typically been exposed. PMID:24586299

  14. Chromatic illumination discrimination ability reveals that human colour constancy is optimised for blue daylight illuminations.

    PubMed

    Pearce, Bradley; Crichton, Stuart; Mackiewicz, Michal; Finlayson, Graham D; Hurlbert, Anya

    2014-01-01

    The phenomenon of colour constancy in human visual perception keeps surface colours constant, despite changes in their reflected light due to changing illumination. Although colour constancy has evolved under a constrained subset of illuminations, it is unknown whether its underlying mechanisms, thought to involve multiple components from retina to cortex, are optimised for particular environmental variations. Here we demonstrate a new method for investigating colour constancy using illumination matching in real scenes which, unlike previous methods using surface matching and simulated scenes, allows testing of multiple, real illuminations. We use real scenes consisting of solid familiar or unfamiliar objects against uniform or variegated backgrounds and compare discrimination performance for typical illuminations from the daylight chromaticity locus (approximately blue-yellow) and atypical spectra from an orthogonal locus (approximately red-green, at correlated colour temperature 6700 K), all produced in real time by a 10-channel LED illuminator. We find that discrimination of illumination changes is poorer along the daylight locus than the atypical locus, and is poorest particularly for bluer illumination changes, demonstrating conversely that surface colour constancy is best for blue daylight illuminations. Illumination discrimination is also enhanced, and therefore colour constancy diminished, for uniform backgrounds, irrespective of the object type. These results are not explained by statistical properties of the scene signal changes at the retinal level. We conclude that high-level mechanisms of colour constancy are biased for the blue daylight illuminations and variegated backgrounds to which the human visual system has typically been exposed. PMID:24586299

  15. Repeated Lake-Stream Divergence in Stickleback Life History within a Central European Lake Basin

    PubMed Central

    Moser, Dario; Roesti, Marius; Berner, Daniel

    2012-01-01

    Life history divergence between populations inhabiting ecologically distinct habitats might be a potent source of reproductive isolation, but has received little attention in the context of speciation. We here test for life history divergence between threespine stickleback inhabiting Lake Constance (Central Europe) and multiple tributary streams. Otolith analysis shows that lake fish generally reproduce at two years of age, while their conspecifics in all streams have shifted to a primarily annual life cycle. This divergence is paralleled by a striking and consistent reduction in body size and fecundity in stream fish relative to lake fish. Stomach content analysis suggests that life history divergence might reflect a genetic or plastic response to pelagic versus benthic foraging modes in the lake and the streams. Microsatellite and mitochondrial markers further reveal that life history shifts in the different streams have occurred independently following the colonization by Lake Constance stickleback, and indicate the presence of strong barriers to gene flow across at least some of the lake-stream habitat transitions. Given that body size is known to strongly influence stickleback mating behavior, these barriers might well be related to life history divergence. PMID:23226528

  16. The effect of exposure on MaxRGB color constancy

    NASA Astrophysics Data System (ADS)

    Funt, Brian; Shi, Lilong

    2010-02-01

    The performance of the MaxRGB illumination-estimation method for color constancy and automatic white balancing has been reported in the literature as being mediocre at best; however, MaxRGB has usually been tested on images of only 8-bits per channel. The question arises as to whether the method itself is inadequate, or rather whether it has simply been tested on data of inadequate dynamic range. To address this question, a database of sets of exposure-bracketed images was created. The image sets include exposures ranging from very underexposed to slightly overexposed. The color of the scene illumination was determined by taking an extra image of the scene containing 4 Gretag Macbeth mini Colorcheckers placed at an angle to one another. MaxRGB was then run on the images of increasing exposure. The results clearly show that its performance drops dramatically when the 14-bit exposure range of the Nikon D700 camera is exceeded, thereby resulting in clipping of high values. For those images exposed such that no clipping occurs, the median error in MaxRGB's estimate of the color of the scene illumination is found to be relatively small.

  17. Colour constancy across the life span: evidence for compensatory mechanisms.

    PubMed

    Wuerger, Sophie

    2013-01-01

    It is well known that the peripheral visual system declines with age: the yellowing of the lens causes a selective reduction of short-wavelength light and sensitivity losses occur in the cone receptor mechanisms. At the same time, our subjective experience of colour does not change with age. The main purpose of this large-scale study (n = 185) covering a wide age range of colour-normal observers (18-75 years of age) was to assess the extent to which the human visual system is able to compensate for the changes in the optical media and at which level of processing this compensation is likely to occur. We report two main results: (1) Supra-threshold parafoveal colour perception remains largely unaffected by the age-related changes in the optical media (yellowing of the lens) whereas our ability to discriminate between small colour differences is compromised with an increase in age. (2) Significant changes in colour appearance are only found for unique green settings under daylight viewing condition which is consistent with the idea that the yellow-blue mechanism is most affected by an increase in age due to selective attenuation of short-wavelength light. The data on the invariance of hue perception, in conjunction with the age-related decline in chromatic sensitivity, provides evidence for compensatory mechanisms that enable colour-normal human observers a large degree of colour constancy across the life span. These compensatory mechanisms are likely to originate at cortical sites. PMID:23667689

  18. ON THE CONSTANCY OF THE SOLAR RADIUS. III

    SciTech Connect

    Bush, R. I.; Emilio, M.; Kuhn, J. R. E-mail: memilio@uepg.b

    2010-06-20

    The Michelson Doppler Imager on board the Solar and Heliospheric Observatory satellite has operated for over a sunspot cycle. This instrument is now relatively well understood and provides a nearly continuous record of the solar radius in combination with previously developed algorithms. Because these data are obtained from above Earth's atmosphere, they are uniquely sensitive to possible long-term changes of the Sun's size. We report here on the first homogeneous, highly precise, and complete solar-cycle measurement of the Sun's radius variability. Our results show that any intrinsic changes in the solar radius that are synchronous with the sunspot cycle must be smaller than 23 mas peak to peak. In addition, we find that the average solar radius must not be changing (on average) by more than 1.2 mas yr{sup -1}. If ground- and space-based measurements are both correct, the pervasive difference between the constancy of the solar radius seen from space and the apparent ground-based solar astrometric variability can only be accounted for by long-term changes in the terrestrial atmosphere.

  19. Surface-illuminant ambiguity and color constancy: effects of scene complexity and depth cues.

    PubMed

    Kraft, James M; Maloney, Shannon I; Brainard, David H

    2002-01-01

    Two experiments were conducted to study how scene complexity and cues to depth affect human color constancy. Specifically, two levels of scene complexity were compared. The low-complexity scene contained two walls with the same surface reflectance and a test patch which provided no information about the illuminant. In addition to the surfaces visible in the low-complexity scene, the high-complexity scene contained two rectangular solid objects and 24 paper samples with diverse surface reflectances. Observers viewed illuminated objects in an experimental chamber and adjusted the test patch until it appeared achromatic. Achromatic settings made tinder two different illuminants were used to compute an index that quantified the degree of constancy. Two experiments were conducted: one in which observers viewed the stimuli directly, and one in which they viewed the scenes through an optical system that reduced cues to depth. In each experiment, constancy was assessed for two conditions. In the valid-cue condition, many cues provided valid information about the illuminant change. In the invalid-cue condition, some image cues provided invalid information. Four broad conclusions are drawn from the data: (a) constancy is generally better in the valid-cue condition than in the invalid-cue condition: (b) for the stimulus configuration used, increasing image complexity has little effect in the valid-cue condition but leads to increased constancy in the invalid-cue condition; (c) for the stimulus configuration used, reducing cues to depth has little effect for either constancy condition: and (d) there is moderate individual variation in the degree of constancy exhibited, particularly in the degree to which the complexity manipulation affects performance. PMID:11922136

  20. Chlorine-36 dating of saline sediments: Preliminary results from Searles Lake, California

    USGS Publications Warehouse

    Phillips, F.M.; Smith, G.I.; Bentley, H.W.; Elmore, D.; Gove, H.E.

    1983-01-01

    Measurements have been made of the ratios of chlorine-36 to chlorine in five halite samples from Searles Lake sediments, previously dated by carbon-14, thorium-230, and magnetostratigraphic techniques. The ages calculated from the chlorine ratios are generally concordant with those from the other methods, implying the constancy of the chlorine input ratio over the last million years.

  1. Research on color constancy computation based on YCbCr color space and gray surface

    NASA Astrophysics Data System (ADS)

    Wang, Hong; Yang, Jianfeng; Xue, Bin; Yan, Xingtao; Liang, Xiaofen

    2014-11-01

    Color constancy is of important for many computer vision applications, such as image classification, color object recognition, object tracking and so on. But unlike the human visual system, imaging device cannot be able to compute color constant descriptors which do not vary with the color of the illuminant, so solving color constancy problem is necessary. In the calculation of color constancy, illuminant estimation is the key. Because grey surfaces can perfectly reflect the color of the scene illumination, many methods have been proposed to identify grey surfaces to estimate the illuminant. But they either rely on the camera's parameters, lacking universality, or work inaccurate in worse conditions. In order to solve these problems, in this paper, an iterative method is proposed. The quality of the proposed method is tested and compared to the previous color constancy methods on the Macbeth Chart and two data sets of synthetic and real images. Through MATLAB simulation, experimental pictures and quantitative data for performance evaluation were gotten. The simulated results show that the proposed algorithm is accurate and efficient in identification of the grey surfaces, even in worse condition. And it performs well in color constancy computation on both synthetic and real images.

  2. No Measured Effect of a Familiar Contextual Object on Color Constancy.

    PubMed

    Kanematsu, Erika; Brainard, David H

    2014-08-01

    Some familiar objects have a typical color, such as the yellow of a banana. The presence of such objects in a scene is a potential cue to the scene illumination, since the light reflected from them should on average be consistent with their typical surface reflectance. Although there are many studies on how the identity of an object affects how its color is perceived, little is known about whether the presence of a familiar object in a scene helps the visual system stabilize the color appearance of other objects with respect to changes in illumination. We used a successive color matching procedure in three experiments designed to address this question. Across the experiments we studied a total of 6 subjects (2 in Experiment 1, 3 in Experiment 2, and 4 in Experiment 3) with partial overlap of subjects between experiments. We compared measured color constancy across conditions in which a familiar object cue to the illuminant was available with conditions in which such a cue was not present. Overall, our results do not reveal a reliable improvement in color constancy with the addition of a familiar object to a scene. An analysis of the experimental power of our data suggests that if there is such an effect, it is small: less than approximately a change of 0.09 in a constancy index where an absence of constancy corresponds to an index value of 0 and perfect constancy corresponds to an index value of 1. PMID:25313267

  3. Effects of memory colour on colour constancy for unknown coloured objects

    PubMed Central

    Granzier, Jeroen J M; Gegenfurtner, Karl R

    2012-01-01

    The perception of an object's colour remains constant despite large variations in the chromaticity of the illumination—colour constancy. Hering suggested that memory colours, the typical colours of objects, could help in estimating the illuminant's colour and therefore be an important factor in establishing colour constancy. Here we test whether the presence of objects with diagnostical colours (fruits, vegetables, etc) within a scene influence colour constancy for unknown coloured objects in the scene. Subjects matched one of four Munsell papers placed in a scene illuminated under either a reddish or a greenish lamp with the Munsell book of colour illuminated by a neutral lamp. The Munsell papers were embedded in four different scenes—one scene containing diagnostically coloured objects, one scene containing incongruent coloured objects, a third scene with geometrical objects of the same colour as the diagnostically coloured objects, and one scene containing non-diagnostically coloured objects (eg, a yellow coffee mug). All objects were placed against a black background. Colour constancy was on average significantly higher for the scene containing the diagnostically coloured objects compared with the other scenes tested. We conclude that the colours of familiar objects help in obtaining colour constancy for unknown objects. PMID:23145282

  4. The effects of surface gloss and roughness on color constancy for real 3-D objects.

    PubMed

    Granzier, Jeroen J M; Vergne, Romain; Gegenfurtner, Karl R

    2014-01-01

    Color constancy denotes the phenomenon that the appearance of an object remains fairly stable under changes in illumination and background color. Most of what we know about color constancy comes from experiments using flat, matte surfaces placed on a single plane under diffuse illumination simulated on a computer monitor. Here we investigate whether material properties (glossiness and roughness) have an effect on color constancy for real objects. Subjects matched the color and brightness of cylinders (painted red, green, or blue) illuminated by simulated daylight (D65) or by a reddish light with a Munsell color book illuminated by a tungsten lamp. The cylinders were either glossy or matte and either smooth or rough. The object was placed in front of a black background or a colored checkerboard. We found that color constancy was significantly higher for the glossy objects compared to the matte objects, and higher for the smooth objects compared to the rough objects. This was independent of the background. We conclude that material properties like glossiness and roughness can have significant effects on color constancy. PMID:24563527

  5. No Measured Effect of a Familiar Contextual Object on Color Constancy

    PubMed Central

    Kanematsu, Erika; Brainard, David H.

    2013-01-01

    Some familiar objects have a typical color, such as the yellow of a banana. The presence of such objects in a scene is a potential cue to the scene illumination, since the light reflected from them should on average be consistent with their typical surface reflectance. Although there are many studies on how the identity of an object affects how its color is perceived, little is known about whether the presence of a familiar object in a scene helps the visual system stabilize the color appearance of other objects with respect to changes in illumination. We used a successive color matching procedure in three experiments designed to address this question. Across the experiments we studied a total of 6 subjects (2 in Experiment 1, 3 in Experiment 2, and 4 in Experiment 3) with partial overlap of subjects between experiments. We compared measured color constancy across conditions in which a familiar object cue to the illuminant was available with conditions in which such a cue was not present. Overall, our results do not reveal a reliable improvement in color constancy with the addition of a familiar object to a scene. An analysis of the experimental power of our data suggests that if there is such an effect, it is small: less than approximately a change of 0.09 in a constancy index where an absence of constancy corresponds to an index value of 0 and perfect constancy corresponds to an index value of 1. PMID:25313267

  6. Determination of Sectional Constancy of Organic Coal-Water Fuel Compositions

    NASA Astrophysics Data System (ADS)

    Dmitrienko, Margarita A.; Nyashina, Galina S.; Strizhak, Pavel A.

    2016-02-01

    To use widespreadly the waste of coals and oils processing in the great and the small-scale power generation, the key parameter, which is sectional constancy of promising organic coal-water fuels (OCWF), was studied. The compo-sitions of OCWF from brown and bituminous coals, filter cakes, used motor, turbine and dielectrical oils, water-oil emul-sion and special wetting agent (plasticizer) were investigated. Two modes of preparation were considered. They are with homogenizer and cavitator. It was established that the constancy did not exceed 5-7 days for the compositions of OCWF with brown coals, and 12-15 days for that compositions with bituminous coals and filter cakes. The injection of used oils in a composition of OCWF led to increase in viscosity of fuel compositions and their sectional constancy.

  7. Demonstration of color constancy in photographs by two techniques: Stereoscope and D-up viewer

    NASA Astrophysics Data System (ADS)

    Phuangsuwan, Chanprapha; Ikeda, Mitsuo; Shinoda, Hiroyuki

    2014-11-01

    When we look, under daylight, at a scene in a photograph taken under an incandescent lamp, it appears very reddish, showing that color constancy is not maintained. According to the recognized visual space of illumination (RVSI) concept, color constancy should exist in a photograph if one can perceive three dimensions in it. This prediction was confirmed by applying two viewing techniques to perceive a 3D space in a 2D photograph: a stereoscope viewed with two eyes and a D-up viewer viewed with one eye. A wide range of illumination color was investigated, covering range from vivid blue through to vivid orange, and the color constancy index became larger with the 3D perception than with the 2D perception of the photographs produced by the two techniques.

  8. Brunswik ratios: a ratio scale for comparative analyses of size constancy data from different experiments.

    PubMed

    Smith, O W; Smith, P C; Zimmermann, R R; Geist, C

    1977-12-01

    The literature on visual size constancy implicitly assumes that the perceived size of any dimension of a thing is evidence of how well (a) any other dimension of the thing will be perceived and (b) any visible dimension of any other thing will be perceived under comparable conditions of perception. For tests of these assumptions Brunswik ratios (1956) are described as a common conceptual and numerical basis, a ratio scale, for testing statistically for differences among or the equivalence of two or more sets of data from different experiments on visual size constancy. PMID:604909

  9. Iterative color constancy with temporal filtering for an image sequence with no relative motion between the camera and the scene.

    PubMed

    Simão, Josemar; Jörg Andreas Schneebeli, Hans; Vassallo, Raquel Frizera

    2015-11-01

    Color constancy is the ability to perceive the color of a surface as invariant even under changing illumination. In outdoor applications, such as mobile robot navigation or surveillance, the lack of this ability harms the segmentation, tracking, and object recognition tasks. The main approaches for color constancy are generally targeted to static images and intend to estimate the scene illuminant color from the images. We present an iterative color constancy method with temporal filtering applied to image sequences in which reference colors are estimated from previous corrected images. Furthermore, two strategies to sample colors from the images are tested. The proposed method has been tested using image sequences with no relative movement between the scene and the camera. It also has been compared with known color constancy algorithms such as gray-world, max-RGB, and gray-edge. In most cases, the iterative color constancy method achieved better results than the other approaches. PMID:26560917

  10. Support Values for Genome Phylogenies

    PubMed Central

    Klötzl, Fabian; Haubold, Bernhard

    2016-01-01

    We have recently developed a distance metric for efficiently estimating the number of substitutions per site between unaligned genome sequences. These substitution rates are called “anchor distances” and can be used for phylogeny reconstruction. Most phylogenies come with bootstrap support values, which are computed by resampling with replacement columns of homologous residues from the original alignment. Unfortunately, this method cannot be applied to anchor distances, as they are based on approximate pairwise local alignments rather than the full multiple sequence alignment necessary for the classical bootstrap. We explore two alternatives: pairwise bootstrap and quartet analysis, which we compare to classical bootstrap. With simulated sequences and 53 human primate mitochondrial genomes, pairwise bootstrap gives better results than quartet analysis. However, when applied to 29 E. coli genomes, quartet analysis comes closer to the classical bootstrap. PMID:26959064

  11. Phylogeny and diversification of bryophytes.

    PubMed

    Shaw, Jonathan; Renzaglia, Karen

    2004-10-01

    The bryophytes comprise three phyla of embryophytes that are well established to occupy the first nodes among extant lineages in the land-plant tree of life. The three bryophyte groups (hornworts, liverworts, mosses) may not form a monophyletic clade, but they share life history features including dominant free-living gametophytes and matrotrophic monosporangiate sporophytes. Because of their unique vegetative and reproductive innovations and their critical position in embryophyte phylogeny, studies of bryophytes are crucial to understanding the evolution of land plant morphology and genomes. This review focuses on phylogenetic relationships within each of the three divisions of bryophytes and relates morphological diversity to new insights about those relationships. Most previous work has been on the mosses, but progress on understanding the phylogeny of hornworts and liverworts is advancing at a rapid pace. Multilocus multigenome studies have been successful at resolving deep relationships within the mosses and liverworts, whereas single-gene analyses have advanced understanding of hornwort evolution. PMID:21652309

  12. High-Performance Phylogeny Reconstruction

    SciTech Connect

    Tiffani L. Williams

    2004-11-10

    Under the Alfred P. Sloan Fellowship in Computational Biology, I have been afforded the opportunity to study phylogenetics--one of the most important and exciting disciplines in computational biology. A phylogeny depicts an evolutionary relationship among a set of organisms (or taxa). Typically, a phylogeny is represented by a binary tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with the edges of the tree denoting evolutionary relationships. The task of phylogenetics is to infer this tree from observations upon present-day organisms. Reconstructing phylogenies is a major component of modern research programs in many areas of biology and medicine, but it is enormously expensive. The most commonly used techniques attempt to solve NP-hard problems such as maximum likelihood and maximum parsimony, typically by bounded searches through an exponentially-sized tree-space. For example, there are over 13 billion possible trees for 13 organisms. Phylogenetic heuristics that quickly analyze large amounts of data accurately will revolutionize the biological field. This final report highlights my activities in phylogenetics during the two-year postdoctoral period at the University of New Mexico under Prof. Bernard Moret. Specifically, this report reports my scientific, community and professional activities as an Alfred P. Sloan Postdoctoral Fellow in Computational Biology.

  13. The Relation between Gender Labelling and Gender Constancy in Preschool Children.

    ERIC Educational Resources Information Center

    Zucker, Kenneth J.; Yoannidis, Tom

    The relationship between preschool children's level of gender understanding and their ability to identify gender-linked attributes was examined. Participants were 26 3-year-old and 30 4-year-old children who were administered a single-cue gender labelling task, Slaby and Frey's (1975) gender constancy test, and the Peabody Picture Vocabulary Test.…

  14. Restructuring Philadelphia's Neighborhood High Schools: A Conversation with Constance Clayton and Michelle Fine.

    ERIC Educational Resources Information Center

    Schwartz, Robert

    1994-01-01

    This interview with Constance Clayton, superintendent of the Philadelphia (Pennsylvania) public schools, and Michelle Fine, professor of psychology and consultant, discusses the Philadelphia Schools Collaborative, a nonprofit organization established to lead the restructuring of the city's high schools. Central to the effort is the concept of…

  15. Surface color perception under two illuminants: the second illuminant reduces color constancy

    NASA Technical Reports Server (NTRS)

    Yang, Joong Nam; Shevell, Steven K.

    2003-01-01

    This study investigates color perception in a scene with two different illuminants. The two illuminants, in opposite corners, simultaneously shine on a (simulated) scene with an opaque dividing wall, which controls how much of the scene is illuminated by each source. In the first experiment, the height of the dividing wall was varied. This changed the amount of each illuminant reaching objects on the opposite side of the wall. Results showed that the degree of color constancy decreased when a region on one side of the wall had cues to both illuminants, suggesting that cues from the second illuminant are detrimental to color constancy. In a later experiment, color constancy was found to improve when the specular highlight cues from the second illuminant were altered to be consistent with the first illuminant. This corroborates the influence of specular highlights in surface color perception, and suggests that the reduced color constancy in the first experiment is due to the inconsistent, though physically correct, cues from the two illuminants.

  16. Morphological Constancy in Spelling: A Comparison of Children with Dyslexia and Typically Developing Children

    ERIC Educational Resources Information Center

    Bourassa, Derrick C.; Treiman, Rebecca

    2008-01-01

    The spellings of many English words follow a principle of morphological constancy. For example, "musician" includes the c of "music", even though the pronunciation of this letter changes. With other words, such as "explanation" and "explain", the spellings of morphemes are not retained when affixes are added. We asked whether children with…

  17. A Neural Model of Distance-Dependent Percept of Object Size Constancy

    PubMed Central

    Qian, Jiehui; Yazdanbakhsh, Arash

    2015-01-01

    Size constancy is one of the well-known visual phenomena that demonstrates perceptual stability to account for the effect of viewing distance on retinal image size. Although theories involving distance scaling to achieve size constancy have flourished based on psychophysical studies, its underlying neural mechanisms remain unknown. Single cell recordings show that distance-dependent size tuned cells are common along the ventral stream, originating from V1, V2, and V4 leading to IT. In addition, recent research employing fMRI demonstrates that an object’s perceived size, associated with its perceived egocentric distance, modulates its retinotopic representation in V1. These results suggest that V1 contributes to size constancy, and its activity is possibly regulated by feedback of distance information from other brain areas. Here, we propose a neural model based on these findings. First, we construct an egocentric distance map in LIP by integrating horizontal disparity and vergence through gain-modulated MT neurons. Second, LIP neurons send modulatory feedback of distance information to size tuned cells in V1, resulting in a spread of V1 cortical activity. This process provides V1 with distance-dependent size representations. The model supports that size constancy is preserved by scaling retinal image size to compensate for changes in perceived distance, and suggests a possible neural circuit capable of implementing this process. PMID:26132106

  18. The role of size constancy for the integration of local elements into a global shape

    PubMed Central

    Rennig, Johannes; Karnath, Hans-Otto; Huberle, Elisabeth

    2013-01-01

    Visual perception depends on the visual context and is likely to be influenced by size constancy, which predicts a size and distance invariant perception of objects. However, size constancy can also result in optical illusions that allow the manipulation of the perceived size. We thus asked whether the integration of local elements into a global object can be influenced by manipulations of the visual context and size constancy? A set of stimuli was applied in healthy individuals that took advantage of the “Kanizsa” illusion, in which three circles with open wedges oriented toward a center point are placed to form an illusionary perception of a triangle. In addition, a 3D-perspective view was implemented in which the global target (“Kanizsa” triangle) was placed in combination with several distractor circles either in a close or a distant position. Subjects were engaged in a global recognition task on the location of the “Kanizsa” triangle. Global recognition of “Kanizsa” triangles improved with a decreasing length of the illusory contour. Interestingly, recognition of “Kanizsa” triangles decreased when they were perceived as if they were located further away. We conclude that the integration of local elements into a global object is dependent on the visual context and dominated by size constancy. PMID:23840187

  19. A Neural Model of Distance-Dependent Percept of Object Size Constancy.

    PubMed

    Qian, Jiehui; Yazdanbakhsh, Arash

    2015-01-01

    Size constancy is one of the well-known visual phenomena that demonstrates perceptual stability to account for the effect of viewing distance on retinal image size. Although theories involving distance scaling to achieve size constancy have flourished based on psychophysical studies, its underlying neural mechanisms remain unknown. Single cell recordings show that distance-dependent size tuned cells are common along the ventral stream, originating from V1, V2, and V4 leading to IT. In addition, recent research employing fMRI demonstrates that an object's perceived size, associated with its perceived egocentric distance, modulates its retinotopic representation in V1. These results suggest that V1 contributes to size constancy, and its activity is possibly regulated by feedback of distance information from other brain areas. Here, we propose a neural model based on these findings. First, we construct an egocentric distance map in LIP by integrating horizontal disparity and vergence through gain-modulated MT neurons. Second, LIP neurons send modulatory feedback of distance information to size tuned cells in V1, resulting in a spread of V1 cortical activity. This process provides V1 with distance-dependent size representations. The model supports that size constancy is preserved by scaling retinal image size to compensate for changes in perceived distance, and suggests a possible neural circuit capable of implementing this process. PMID:26132106

  20. The Development of Language Constancy: Attention to Native versus Nonnative Accents

    ERIC Educational Resources Information Center

    Kitamura, Christine; Panneton, Robin; Best, Catherine T.

    2013-01-01

    The time frame for infants' acquisition of language constancy was probed, using the phonetic variation in a rarely heard accent (South African English) or a frequently heard accent (American English). A total of 156 Australian infants were tested. Six-month-olds looked longer to Australian English than less commonly heard South African…

  1. Revisiting the Principle of Relative Constancy: Consumer Mass Media Expenditures in Belgium.

    ERIC Educational Resources Information Center

    Dupagne, Michel; Green, R. Jeffery

    1996-01-01

    Proposes two new econometric models for testing the principle of relative constancy (PRC). Reports on regression and cointegration analyses conducted with Belgian mass media expenditure data from 1953-91. Suggests that alternative mass media expenditure models should be developed because PRC lacks of economic foundation and sound empirical…

  2. CONSTANCY OF THE RELATION BETWEEN FLOC SIZE AND DENSITY IN SAN FRANCISCO BAY

    EPA Science Inventory

    Ganju, N.K., D.H. Schoellhamer, M.C. Murrell, J.W. Gartner and S.A. Wright. In press. Constancy of the Relation Between Floc Size and Density in San Francisco Bay. In: INTERCOH 2003: Proceedings of the 7th International Conference on Nearshore and Estuarine Cohesive Sediment Tran...

  3. Spatial and temporal aspects of chromatic adaptation and their functional significance for colour constancy.

    PubMed

    Werner, Annette

    2014-11-01

    Illumination in natural scenes changes at multiple temporal and spatial scales: slow changes in global illumination occur in the course of a day, and we encounter fast and localised illumination changes when visually exploring the non-uniform light field of three-dimensional scenes; in addition, very long-term chromatic variations may come from the environment, like for example seasonal changes. In this context, I consider the temporal and spatial properties of chromatic adaptation and discuss their functional significance for colour constancy in three-dimensional scenes. A process of fast spatial tuning in chromatic adaptation is proposed as a possible sensory mechanism for linking colour constancy to the spatial structure of a scene. The observed middlewavelength selectivity of this process is particularly suitable for adaptation to the mean chromaticity and the compensation of interreflections in natural scenes. Two types of sensory colour constancy are distinguished, based on the functional differences of their temporal and spatial scales: a slow type, operating at a global scale for the compensation of the ambient illumination; and a fast colour constancy, which is locally restricted and well suited to compensate region-specific variations in the light field of three dimensional scenes. PMID:25449338

  4. Right Temporal Cortex is Critical for Utilization of Melodic Contextual Cues in a Pitch Constancy Task

    ERIC Educational Resources Information Center

    Warrier, Catherine M.; Zatorre, Robert J.

    2004-01-01

    Pitch constancy, perceiving the same pitch from tones with differing spectral shapes, requires one to extract the fundamental frequency from two sets of harmonics and compare them. We previously showed this difficult task to be easier when tonal context is present, presumably because the context creates a tonal reference point from which to judge…

  5. Constance "Connie" Hanf (1917-2002): The Mentor and the Model

    ERIC Educational Resources Information Center

    Reitman, David; McMahon, Robert J.

    2013-01-01

    This article provides an account of the impact of Constance Hanf, Ph.D., developer of the well-known two-stage parent training model that bears her name. Past colleagues, interns, postdoctoral students, and undergraduate trainees reflect on their experiences with Dr. Hanf and comment on her influence on their careers, as well as the impact of the…

  6. Lake Life.

    ERIC Educational Resources Information Center

    Ohrn, Deborah Gore, Ed.

    1993-01-01

    This quarterly publication of the State Historical Society of Iowa features articles and activities for elementary school students. This summer issue focuses on the topic of lake life. The issue includes the following features: (1) "Where the Lakes Are Map"; (2) "Letter from the Lake"; (3) "Lake People"; (4) "Spirit Lake"; (5) "Lake Manawa"; (6)…

  7. Phylogeny and subgeneric taxonomy of Aspergillus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylogeny of the genus Aspergillus and its teleomorphs is discussed based on multilocus sequence data. DNA sequence analysis was used to formulate a nucleotide sequence framework of the genus and to analyze character changes in relationship to the phylogeny hypothesized from the DNA sequence an...

  8. Phylogeny of major intrinsic proteins.

    PubMed

    Danielson, Jonas A H; Johanson, Urban

    2010-01-01

    Major intrinsic proteins (MIPs) form a large superfamily of proteins that can be divided into different subfamilies and groups according to phylogenetic analyses. Plants encode more MIPs than o ther organisms and se ven subfamilies have been defined, whereofthe Nodulin26-like major intrinsic proteins (NIPs) have been shown to permeate metalloids. In this chapter we review the phylogeny of MIPs in general and especially of the plant MIPs. We also identify bacterial NIP-like MIPs and discuss the evolutionary implications of this finding regarding the origin and ancestral transport specificity of the NIPs. PMID:20666221

  9. Advances in estimating the climate sensibility of a large lake using scenario simulations

    NASA Astrophysics Data System (ADS)

    Eder, M. M.; Schlabing, D.; Frassl, M. A.; Rinke, K.; Bárdossy, A.

    2012-04-01

    The vertical mixing behaviour of large deep lakes as e.g. Lake Constance is reflecting the long-term meteorological conditions and therefore is likely to be sensible to climate change. Today, Lake Constance does not mix completely every year, but only once in 2-3 years, which leads to the typical saw-tooth pattern in the deep water temperature. Whether complete mixing does occur is not only depending on the meteorological conditions in the respective winter period, but also on the thermal conditions in the lake and hence on the meteorological conditions in the preceding years. The lake's response to climate change thus depends on the temperature increase itself as well as on its gradient and on the inter-annual variability of the meteorological variables. Last year we showed first steps towards a model system to evaluate possible effects of climate change on Lake Constance: The Vector-Autoregressive Weathergenerator VG produces time series of meteorological data, which are used as boundary conditions for the 3D hydrodynamic lake model ELCOM (Centre of Water Research, University of Western Australia). As VG gives the opportunity to change mean and variability of selected variables, "What if?" - scenarios for process understanding can be performed. The time scales of variability turned out to be a critical point in the artificial time series for modelling the hydrodynamics of Lake Constance, as the big water body integrates over time and thus the hydrodynamics overlook the variability of air temperature on short time scales. Therefore, VG was developed further, especially with respect to the time scales of variability. While for heat input, the time scale of several days to weeks seems to be more important, wind and, when biology is modelled, short-wave radiation should be given at a sub-daily timestep. Besides producing user-defined scenario time-series, VG can also be used to stochastical downscale output of global climate model IPCC scenarios for lake modelling

  10. Eumetazoan Cryptochrome Phylogeny and Evolution

    PubMed Central

    Haug, Marion F.; Gesemann, Matthias; Lazović, Viktor; Neuhauss, Stephan C.F.

    2015-01-01

    Cryptochromes (Crys) are light sensing receptors that are present in all eukaryotes. They mainly absorb light in the UV/blue spectrum. The extant Crys consist of two subfamilies, which are descendants of photolyases but are now involved in the regulation of circadian rhythms. So far, knowledge about the evolution, phylogeny, and expression of cry genes is still scarce. The inclusion of cry sequences from a wide range of bilaterian species allowed us to analyze their phylogeny in detail, identifying six major Cry subgroups. Selective gene inactivations and stabilizations in multiple chordate as well as arthropod lineages suggest several sub- and/or neofunctionalization events. An expression study performed in zebrafish, the model organism harboring the largest amount of crys, showed indeed only partially overlapping expression of paralogous mRNA, supporting gene sub- and/or neofunctionalization. Moreover, the daily cry expression in the adult zebrafish retina indicated varying oscillation patterns in different cell types. Our extensive phylogenetic analysis provides for the first time an overview of cry evolutionary history. Although several, especially parasitic or blind species, have lost all cry genes, crustaceans have retained up to three crys, teleosts possess up to seven, and tetrapods up to four crys. The broad and cyclic expression pattern of all cry transcripts in zebrafish retinal layers implies an involvement in retinal circadian processes and supports the hypothesis of several autonomous circadian clocks present in the vertebrate retina. PMID:25601102

  11. The phylogeny of amphibian metamorphosis.

    PubMed

    Reiss, John O

    2002-01-01

    Frogs have one of the most extreme metamorphoses among vertebrates. How did this metamorphosis evolve? By combining the methods previously proposed by Mabee and Humphries (1993) and Velhagen (1997), I develop a phylogenetic method suited for rigorous analysis of this question. In a preliminary analysis using 12 transformation sequence characters and 36 associated event sequence characters, all drawn from the osteology of the skull, the evolution of metamorphosis is traced on an assumed phylogeny. This phylogeny has lissamphibians (frogs, salamanders, and caecilians) monophyletic, with frogs the sister group of salamanders. Successive outgroups used are temnospondyls and discosauriscids, both of which are fossil groups for which ontogenetic data are available. In the reconstruction of character evolution, an unambiguous change (synapomorphy) along the branch leading to lissamphibians is a delay in the lengthening of the maxilla until metamorphosis, in accordance with my previous suggestion (Reiss, 1996). However, widening of the interpterygoid vacuity does not appear as a synapomophy of lissamphibians, due to variation in the character states in the outgroups. From a more theoretical perspective, the reconstructed evolution of amphibian metamorphosis involves examples of heterochrony, through the shift of ancestral premetamorphic events to the metamorphic period, caenogenesis, through the origin of new larval features, and terminal addition, through the origin of new adult features. Other changes don't readily fit these categories. This preliminary study provides evidence that metamorphic changes in frogs arose as further modifications of changes unique to lissamphibians, as well as a new method by which such questions can be examined. PMID:16351859

  12. Reconciling molecular phylogenies with the fossil record.

    PubMed

    Morlon, Hélène; Parsons, Todd L; Plotkin, Joshua B

    2011-09-27

    Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ~10 Myr. PMID:21930899

  13. Reconciling molecular phylogenies with the fossil record

    PubMed Central

    Morlon, Hélène; Parsons, Todd L.; Plotkin, Joshua B.

    2011-01-01

    Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr. PMID:21930899

  14. The biological significance of color constancy: an agent-based model with bees foraging from flowers under varied illumination.

    PubMed

    Faruq, Samia; McOwan, Peter W; Chittka, Lars

    2013-01-01

    The perceived color of an object depends on its spectral reflectance and the spectral composition of the illuminant. Thus when the illumination changes, the light reflected from the object also varies. This would result in a different color sensation if no color constancy mechanism is put in place-that is, the ability to form consistent representation of colors across various illuminants and background scenes. We explore the quantitative benefits of various color constancy algorithms in an agent-based model of foraging bees, where agents select flower color based on reward. Each simulation is based on 100 "meadows" with five randomly selected flower species with empirically determined spectral reflectance properties, and each flower species is associated with realistic distributions of nectar rewards. Simulated foraging bees memorize the colors of flowers that they have experienced as most rewarding, and their task is to discriminate against other flower colors with lower rewards, even in the face of changing illumination conditions. We compared the performance of von Kries, White Patch, and Gray World constancy models with (hypothetical) bees with perfect color constancy, and color-blind bees. A bee equipped with trichromatic color vision but no color constancy performed only ∼20% better than a color-blind bee (relative to a maximum improvement at 100% for perfect color constancy), whereas the most powerful recovery of reflectance in the face of changing illumination was generated by a combination of von Kries photoreceptor adaptation and a White Patch calibration (∼30% improvement relative to a bee without color constancy). However, none of the tested algorithms generated perfect color constancy. PMID:23962735

  15. Morphological constancy in spelling: a comparison of children with dyslexia and typically developing children.

    PubMed

    Bourassa, Derrick C; Treiman, Rebecca

    2008-08-01

    The spellings of many English words follow a principle of morphological constancy. For example, musician includes the c of music, even though the pronunciation of this letter changes. With other words, such as explanation and explain, the spellings of morphemes are not retained when affixes are added. We asked whether children with dyslexia use root morphemes to aid their spelling of morphologically complex words. If so, they should sometimes produce misspellings such as 'explaination' for explanation. Our results suggest that children with dyslexia adhere to the principle of morphological constancy to the same extent as typically developing younger children of the same spelling level. In this and other ways, the spellings of older dyslexic children are remarkably similar to those of typical younger children. PMID:18720405

  16. Transparent layer constancy under changes in illumination color: Does task matter?

    PubMed

    Faul, Franz; Falkenberg, Charlotte

    2015-11-01

    If the perceived transmittances of transparent objects are matched across illuminants, only incomplete constancy is found. This implies that physically identical objects may appear different. Nevertheless, it was reported in the literature that subjects could almost perfectly identify such objects across illuminants, even if a transparency impression was suppressed by violating geometric transparency conditions. A potential interpretation of these findings is that (a) identification and matching rely on different criteria and processes and that (b) identification is solely based on low-level color information. We here present evidence against these hypotheses. Our results show that the best match, that is, the transparent object under the test illuminant that appears most similar to the standard, is also the preferred object in the identification task. Furthermore, we found that the degree of constancy increases in both tasks, if figural cues support a transparency impression and the accompanying color scission. We discuss the relation between matching and identification suggested by these findings. PMID:26409045

  17. Color constancy in a scene with bright colors that do not have a fully natural surface appearance.

    PubMed

    Fukuda, Kazuho; Uchikawa, Keiji

    2014-04-01

    Theoretical and experimental approaches have proposed that color constancy involves a correction related to some average of stimulation over the scene, and some of the studies showed that the average gives greater weight to surrounding bright colors. However, in a natural scene, high-luminance elements do not necessarily carry information about the scene illuminant when the luminance is too high for it to appear as a natural object color. The question is how a surrounding color's appearance mode influences its contribution to the degree of color constancy. Here the stimuli were simple geometric patterns, and the luminance of surrounding colors was tested over the range beyond the luminosity threshold. Observers performed perceptual achromatic setting on the test patch in order to measure the degree of color constancy and evaluated the surrounding bright colors' appearance mode. Broadly, our results support the assumption that the visual system counts only the colors in the object-color appearance for color constancy. However, detailed analysis indicated that surrounding colors without a fully natural object-color appearance had some sort of influence on color constancy. Consideration of this contribution of unnatural object color might be important for precise modeling of human color constancy. PMID:24695177

  18. SU-E-T-257: Output Constancy: Reducing Measurement Variations in a Large Practice Group

    SciTech Connect

    Hedrick, K; Fitzgerald, T; Miller, R

    2014-06-01

    Purpose: To standardize output constancy check procedures in a large medical physics practice group covering multiple sites, in order to identify and reduce small systematic errors caused by differences in equipment and the procedures of multiple physicists. Methods: A standardized machine output constancy check for both photons and electrons was instituted within the practice group in 2010. After conducting annual TG-51 measurements in water and adjusting the linac to deliver 1.00 cGy/MU at Dmax, an acrylic phantom (comparable at all sites) and PTW farmer ion chamber are used to obtain monthly output constancy reference readings. From the collected charge reading, measurements of air pressure and temperature, and chamber Ndw and Pelec, a value we call the Kacrylic factor is determined, relating the chamber reading in acrylic to the dose in water with standard set-up conditions. This procedure easily allows for multiple equipment combinations to be used at any site. The Kacrylic factors and output results from all sites and machines are logged monthly in a central database and used to monitor trends in calibration and output. Results: The practice group consists of 19 sites, currently with 34 Varian and 8 Elekta linacs (24 Varian and 5 Elekta linacs in 2010). Over the past three years, the standard deviation of Kacrylic factors measured on all machines decreased by 20% for photons and high energy electrons as systematic errors were found and reduced. Low energy electrons showed very little change in the distribution of Kacrylic values. Small errors in linac beam data were found by investigating outlier Kacrylic values. Conclusion: While the use of acrylic phantoms introduces an additional source of error through small differences in depth and effective depth, the new standardized procedure eliminates potential sources of error from using many different phantoms and results in more consistent output constancy measurements.

  19. Genome downsizing and karyotype constancy in diploid and polyploid congeners: a model of genome size variation

    PubMed Central

    Poggio, Lidia; Realini, María Florencia; Fourastié, María Florencia; García, Ana María; González, Graciela Esther

    2014-01-01

    Evolutionary chromosome change involves significant variation in DNA amount in diploids and genome downsizing in polyploids. Genome size and karyotype parameters of Hippeastrum species with different ploidy level were analysed. In Hippeastrum, polyploid species show less DNA content per basic genome than diploid species. The rate of variation is lower at higher ploidy levels. All the species have a basic number x = 11 and bimodal karyotypes. The basic karyotypes consist of four short metacentric chromosomes and seven large chromosomes (submetacentric and subtelocentric). The bimodal karyotype is preserved maintaining the relative proportions of members of the haploid chromosome set, even in the presence of genome downsizing. The constancy of the karyotype is maintained because changes in DNA amount are proportional to the length of the whole-chromosome complement and vary independently in the long and short sets of chromosomes. This karyotype constancy in taxa of Hippeastrum with different genome size and ploidy level indicates that the distribution of extra DNA within the complement is not at random and suggests the presence of mechanisms selecting for constancy, or against changes, in karyotype morphology. PMID:24969503

  20. Temporal-envelope constancy of speech in rooms and the perceptual weighting of frequency bands.

    PubMed

    Watkins, Anthony J; Raimond, Andrew P; Makin, Simon J

    2011-11-01

    Three experiments measured constancy in speech perception, using natural-speech messages or noise-band vocoder versions of them. The eight vocoder-bands had equally log-spaced center-frequencies and the shapes of corresponding "auditory" filters. Consequently, the bands had the temporal envelopes that arise in these auditory filters when the speech is played. The "sir" or "stir" test-words were distinguished by degrees of amplitude modulation, and played in the context; "next you'll get _ to click on." Listeners identified test-words appropriately, even in the vocoder conditions where the speech had a "noise-like" quality. Constancy was assessed by comparing the identification of test-words with low or high levels of room reflections across conditions where the context had either a low or a high level of reflections. Constancy was obtained with both the natural and the vocoded speech, indicating that the effect arises through temporal-envelope processing. Two further experiments assessed perceptual weighting of the different bands, both in the test word and in the context. The resulting weighting functions both increase monotonically with frequency, following the spectral characteristics of the test-word's [s]. It is suggested that these two weighting functions are similar because they both come about through the perceptual grouping of the test-word's bands. PMID:22087906

  1. Color constancy of color-deficient observers under illuminations defined by individual color discrimination ellipsoids.

    PubMed

    Ma, Ruiqing; Kawamoto, Ken-Ichiro; Shinomori, Keizo

    2016-03-01

    We explored the color constancy mechanisms of color-deficient observers under red, green, blue, and yellow illuminations. The red and green illuminations were defined individually by the longer axis of the color discrimination ellipsoid measured by the Cambridge Colour Test. Four dichromats (3 protanopes and 1 deuteranope), two anomalous trichromats (2 deuteranomalous observers), and five color-normal observers were asked to complete the color constancy task by making a simultaneous paper match under asymmetrical illuminations in haploscopic view on a monitor. The von Kries adaptation model was applied to estimate the cone responses. The model fits showed that for all color-deficient observers under all illuminations, the adjustment of the S-cone response or blue-yellow chromatically opponent responses modeled with the simple assumption of cone deletion in a certain type (S-M, S-L or S-(L+M)) was consistent with the principle of the von Kries model. The degree of adaptation was similar to that of color-normal observers. The results indicate that the color constancy of color-deficient observers is mediated by the simplified blue-yellow color system with a von Kries-type adaptation effect, even in the case of brightness match, as well as by a possible cone-level adaptation to the S-cone when the illumination produces a strong S-cone stimulation, such as blue illumination. PMID:26974935

  2. Effects of surrounding stimulus properties on color constancy based on luminance balance.

    PubMed

    Morimoto, Takuma; Fukuda, Kazuho; Uchikawa, Keiji

    2016-03-01

    The visual system needs to discount the influence of an illuminant to achieve color constancy. Uchikawa et al. [J. Opt. Soc. Am. A29, A133 (2012) showed that the luminance-balance change of surfaces in a scene contributes to illuminant estimation; however, its effect was substantially less than the chromaticity change. We conduct three experiments to reinforce the previous findings and investigate possible factors that can influence the effect of luminance balance. Experimental results replicate the previous finding; i.e., luminance balance makes a small, but significant, contribution to illuminant estimation. We find that stimulus dimensionality affects neither the degree of color constancy nor the effect of luminance balance. Unlike chromaticity-based color constancy, chromatic variation does not influence the effect of luminance balance. It is shown that luminance-balance-based estimation of an illuminant performs better for scenes with reddish or bluish surfaces. This suggests that the visual system exploits the optimal color distribution for illuminant estimation [J. Opt. Soc. Am. A 29, A133(2012)]. PMID:26974926

  3. Coding polymorphism for phylogeny reconstruction.

    PubMed

    Kornet, D J; Turner, H

    1999-06-01

    The methodology of coding polymorphic taxa has received limited attention to date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolutionary novelty, and methods that identify the new state with the fixation of a novelty. The methods of the first category introduce soft reversals, yielding signals that support cladograms incompatible with true phylogenies. We conclude that coding the plesiomorphy is the method to be preferred, unless the ancestral state is unknown, in which case coding as ambiguous is recommended. This holds for coding polymorphism in species as well as in supraspecific taxa. In this light we remark on methods proposed by previous authors. PMID:12066713

  4. Ontogeny and phylogeny of language

    PubMed Central

    Yang, Charles

    2013-01-01

    How did language evolve? A popular approach points to the similarities between the ontogeny and phylogeny of language. Young children’s language and nonhuman primates’ signing both appear formulaic with limited syntactic combinations, thereby suggesting a degree of continuity in their cognitive abilities. To evaluate the validity of this approach, as well as to develop a quantitative benchmark to assess children’s language development, I propose a formal analysis that characterizes the statistical profile of grammatical rules. I show that very young children’s language is consistent with a productive grammar rather than memorization of specific word combinations from caregivers’ speech. Furthermore, I provide a statistically rigorous demonstration that the sign use of Nim Chimpsky, the chimpanzee who was taught American Sign Language, does not show the expected productivity of a rule-based grammar. Implications for theories of language acquisition and evolution are discussed. PMID:23576720

  5. Untangling the phylogeny of amoeboid protists.

    PubMed

    Pawlowski, Jan; Burki, Fabien

    2009-01-01

    The amoebae and amoeboid protists form a large and diverse assemblage of eukaryotes characterized by various types of pseudopodia. For convenience, the traditional morphology-based classification grouped them together in a macrotaxon named Sarcodina. Molecular phylogenies contributed to the dismantlement of this assemblage, placing the majority of sarcodinids into two new supergroups: Amoebozoa and Rhizaria. In this review, we describe the taxonomic composition of both supergroups and present their small subunit rDNA-based phylogeny. We comment on the advantages and weaknesses of these phylogenies and emphasize the necessity of taxon-rich multigene datasets to resolve phylogenetic relationships within Amoebozoa and Rhizaria. We show the importance of environmental sequencing as a way of increasing taxon sampling in these supergroups. Finally, we highlight the interest of Amoebozoa and Rhizaria for understanding eukaryotic evolution and suggest that resolving their phylogenies will be among the main challenges for future phylogenomic analyses. PMID:19335771

  6. Reconstructing the prior probabilities of allelic phylogenies.

    PubMed Central

    Golding, G Brian

    2002-01-01

    In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually "rare" topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4N(mu) (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions. PMID:12072482

  7. Phylogeny of the Genus Flavivirus

    PubMed Central

    Kuno, Goro; Chang, Gwong-Jen J.; Tsuchiya, K. Richard; Karabatsos, Nick; Cropp, C. Bruce

    1998-01-01

    We undertook a comprehensive phylogenetic study to establish the genetic relationship among the viruses of the genus Flavivirus and to compare the classification based on molecular phylogeny with the existing serologic method. By using a combination of quantitative definitions (bootstrap support level and the pairwise nucleotide sequence identity), the viruses could be classified into clusters, clades, and species. Our phylogenetic study revealed for the first time that from the putative ancestor two branches, non-vector and vector-borne virus clusters, evolved and from the latter cluster emerged tick-borne and mosquito-borne virus clusters. Provided that the theory of arthropod association being an acquired trait was correct, pairwise nucleotide sequence identity among these three clusters provided supporting data for a possibility that the non-vector cluster evolved first, followed by the separation of tick-borne and mosquito-borne virus clusters in that order. Clades established in our study correlated significantly with existing antigenic complexes. We also resolved many of the past taxonomic problems by establishing phylogenetic relationships of the antigenically unclassified viruses with the well-established viruses and by identifying synonymous viruses. PMID:9420202

  8. Alveolate phylogeny inferred using concatenated ribosomal proteins.

    PubMed

    Bachvaroff, Tsvetan R; Handy, Sara M; Place, Allen R; Delwiche, Charles F

    2011-01-01

    Dinoflagellates and apicomplexans are a strongly supported monophyletic group in rDNA phylogenies, although this phylogeny is not without controversy, particularly between the two groups. Here we use concatenated protein-coding genes from expressed sequence tags or genomic data to construct phylogenies including "typical" dinophycean dinoflagellates, a parasitic syndinian dinoflagellate, Amoebophrya sp., and two related species, Oxyrrhis marina, and Perkinsus marinus. Seventeen genes encoding proteins associated with the ribosome were selected for phylogenetic analysis. The dataset was limited for the most part by data availability from the dinoflagellates. Forty-five taxa from four major lineages were used: the heterokont outgroup, ciliates, dinoflagellates, and apicomplexans. Amoebophrya sp. was included in this phylogeny as a sole representative of the enigmatic marine alveolate or syndinian lineage. The atypical dinoflagellate O. marina, usually excluded from rDNA analyses due to long branches, was also included. The resulting phylogenies were well supported in concatenated analyses with only a few unstable or weakly supported branches; most features were consistent when different lineages were pruned from the tree or different genes were concatenated. The least stable branches involved the placement of Cryptosporidium spp. within the Apicomplexa and the relationships between P. marinus, Amoebophrya sp., and O. marina. Both bootstrap and approximately unbiased test results confirmed that P. marinus, Amoebophrya sp., O. marina, and the remaining dinoflagellates form a monophyletic lineage to the exclusion of Apicomplexa. PMID:21518081

  9. Recovering of weather degraded images based on RGB response ratio constancy.

    PubMed

    Luzón-González, Raúl; Nieves, Juan L; Romero, Javier

    2015-02-01

    Images captured under bad weather conditions suffer from poor contrast and visibility. These effects are noticeable for haze, mist, fog, or dust storms. We have proposed a recovering method for images captured for several adverse weather conditions based on the RGB response ratio constancy under illuminant changes. This algorithm improves the visibility, contrast, and color in degraded images with low computational times. We obtain results similar to those from previously published deweathering methods but with no prior information about the image content or atmospheric parameters needed. PMID:25967830

  10. Juvenile morphology in baleen whale phylogeny

    NASA Astrophysics Data System (ADS)

    Tsai, Cheng-Hsiu; Fordyce, R. Ewan

    2014-09-01

    Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.

  11. Juvenile morphology in baleen whale phylogeny

    NASA Astrophysics Data System (ADS)

    Tsai, Cheng-Hsiu; Fordyce, R. Ewan

    2014-08-01

    Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.

  12. Development of Phonological Constancy: 19-Month-Olds, but Not 15-Month-Olds, Identify Words in a Non-Native Regional Accent

    ERIC Educational Resources Information Center

    Mulak, Karen E.; Best, Catherine T.; Tyler, Michael D.; Kitamura, Christine; Irwin, Julia R.

    2013-01-01

    By 12 months, children grasp that a phonetic change to a word can change its identity ("phonological distinctiveness"). However, they must also grasp that some phonetic changes do "not" ("phonological constancy"). To test development of phonological constancy, sixteen 15-month-olds and sixteen 19-month-olds completed…

  13. Israeli Kindergarten Children's Gender Constancy for Others' Counter-Stereotypic Toy Play and Appearance: The Role of Sibling Gender and Relative Age

    ERIC Educational Resources Information Center

    Karniol, Rachel

    2009-01-01

    To test divergent theoretical predictions as to the impact of having a younger or older, same-sex sibling or opposite-sex sibling on other gender constancy, Israeli kindergarten children in two-child families responded to a gender constancy task in which a male and female picture target engaged in counter-stereotypic toy play and adopted…

  14. Ribosomal RNA: a key to phylogeny

    NASA Technical Reports Server (NTRS)

    Olsen, G. J.; Woese, C. R.

    1993-01-01

    As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.

  15. Low levels of specularity support operational color constancy, particularly when surface and illumination geometry can be inferred

    PubMed Central

    Lee, Robert J.; Smithson, Hannah E.

    2016-01-01

    We tested whether surface specularity alone supports operational color constancy – the ability to discriminate changes in illumination or reflectance. Observers viewed short animations of illuminant or reflectance changes in rendered scenes containing a single spherical surface, and were asked to classify the change. Performance improved with increasing specularity, as predicted from regularities in chromatic statistics. Peak performance was impaired by spatial rearrangements of image pixels that disrupted the perception of illuminated surfaces, but was maintained with increased surface complexity. The characteristic chromatic transformations that are available with non-zero specularity are useful for operational color constancy, particularly if accompanied by appropriate perceptual organisation. PMID:26974938

  16. Low levels of specularity support operational color constancy, particularly when surface and illumination geometry can be inferred.

    PubMed

    Lee, Robert J; Smithson, Hannah E

    2016-03-01

    We tested whether surface specularity alone supports operational color constancy-the ability to discriminate changes in illumination or reflectance. Observers viewed short animations of illuminant or reflectance changes in rendered scenes containing a single spherical surface and were asked to classify the change. Performance improved with increasing specularity, as predicted from regularities in chromatic statistics. Peak performance was impaired by spatial rearrangements of image pixels that disrupted the perception of illuminated surfaces but was maintained with increased surface complexity. The characteristic chromatic transformations that are available with nonzero specularity are useful for operational color constancy, particularly if accompanied by appropriate perceptual organization. PMID:26974938

  17. Influence of gender constancy and social power on sex-linked modeling.

    PubMed

    Bussey, K; Bandura, A

    1984-12-01

    Competing predictions derived from cognitive-developmental theory and social learning theory concerning sex-linked modeling were tested. In cognitive-developmental theory, gender constancy is considered a necessary prerequisite for the emulation of same-sex models, whereas according to social learning theory, sex-role development is promoted through a vast system of social influences with modeling serving as a major conveyor of sex role information. In accord with social learning theory, even children at a lower level of gender conception emulated same-sex models in preference to opposite-sex ones. Level of gender constancy was associated with higher emulation of both male and female models rather than operating as a selective determinant of modeling. This finding corroborates modeling as a basic mechanism in the sex-typing process. In a second experiment we explored the limits of same-sex modeling by pitting social power against the force of collective modeling of different patterns of behavior by male and female models. Social power over activities and rewarding resources produced cross-sex modeling in boys, but not in girls. This unexpected pattern of cross-sex modeling is explained by the differential sex-typing pressures that exist for boys and girls and socialization experiences that heighten the attractiveness of social power for boys. PMID:6527216

  18. Experimental studies of instantaneous color constancy: dynamic color matching under rapid changes of illuminant

    NASA Astrophysics Data System (ADS)

    Barbur, John L.; de Cunha, Darryl; Williams, Cristyn B.; Plant, Gordon

    2002-06-01

    We have extended the experiments of McCann et al., (1976) by incorporating the Mondrian stimulus into a dynamic colour matching (DCM) technique that allows the subject to match accurately the colour of any test patch under sequential changes of illuminant. We have also studied how scattered light affects the measured instantaneous colour constancy (ICC) index. The results show that correction for forward light scatter in the eye can increase significantly the measured ICC index. The changes in the perceived colour of a central test stimulus as a result of surround illuminant changes was investigated in a number of successful binocular and dichoptic experiments. The contribution made by distant patches to ICC was found to be small with the immediate surround (i.e., less than 2 degree(s) separation) contributing over 50% of the constancy effect. A number of subjects with partial loss of ability to see and discriminate colours caused by damage to ventromedial pre-striate visual cortex were also investigated. In order to establish the site of ICC mechanisms, the dynamic colour matching technique was modified to make it suitable for studies in patients with unilateral damage to the primary visual cortex.

  19. Accurate moving cast shadow suppression based on local color constancy detection.

    PubMed

    Amato, Ariel; Mozerov, Mikhail G; Bagdanov, Andrew D; Gonzàlez, Jordi

    2011-10-01

    This paper describes a novel framework for detection and suppression of properly shadowed regions for most possible scenarios occurring in real video sequences. Our approach requires no prior knowledge about the scene, nor is it restricted to specific scene structures. Furthermore, the technique can detect both achromatic and chromatic shadows even in the presence of camouflage that occurs when foreground regions are very similar in color to shadowed regions. The method exploits local color constancy properties due to reflectance suppression over shadowed regions. To detect shadowed regions in a scene, the values of the background image are divided by values of the current frame in the RGB color space. We show how this luminance ratio can be used to identify segments with low gradient constancy, which in turn distinguish shadows from foreground. Experimental results on a collection of publicly available datasets illustrate the superior performance of our method compared with the most sophisticated, state-of-the-art shadow detection algorithms. These results show that our approach is robust and accurate over a broad range of shadow types and challenging video conditions. PMID:21435975

  20. Dodging the cosmic curvature to probe the constancy of the speed of light

    NASA Astrophysics Data System (ADS)

    Cai, Rong-Gen; Guo, Zong-Kuan; Yang, Tao

    2016-08-01

    We develop a new model-independent method to probe the constancy of the speed of light c. In our method, the degeneracy between the cosmic curvature and the speed of light can be eliminated, which makes the test more natural and general. Combining the independent observations of Hubble parameter H(z) and luminosity distance dL(z), we use the model-independent smoothing technique, Gaussian processes, to reconstruct them and then detect variation of the speed of light. We find no signal of deviation from the present value of the speed of light c0. Moreover, to demonstrate the improvement in probing the constancy of the speed of light from future experiments, we produce a series of simulated data. The Dark Energy Survey will be able to detect Δc/c0 ~ 1% at ~ 1.5σ confidence level and Δc/c0 ~ 2% at ~ 3σ confidence level. If the errors are reduced to one-tenth of the expected DES ones, it can detect a Δc/c0 ~ 0.1% variation at ~ 2σ confidence level.

  1. Modelling colour constancy in fish: implications for vision and signalling in water.

    PubMed

    Wilkins, Lucas; Marshall, N Justin; Johnsen, Sönke; Osorio, D

    2016-06-15

    Colour vision and colour signals are important to aquatic animals, but light scattering and absorption by water distorts spectral stimuli. To investigate the performance of colour vision in water, and to suggest how photoreceptor spectral sensitivities and body colours might evolve for visual communication, we model the effects of changes in viewing distance and depth on the appearance of fish colours for three teleosts: a barracuda, Sphyraena helleri, which is dichromatic and two damselfishes, Chromis verater and Chromis hanui, which are trichromatic. We assume that photoreceptors light-adapt to the background, thereby implementing the von Kries transformation, which can largely account for observed colour constancy in humans and other animals, including fish. This transformation does not, however, compensate for light scattering over variable viewing distances, which in less than a metre seriously impairs dichromatic colour vision, and makes judgement of colour saturation unreliable for trichromats. The von Kries transformation does substantially offset colour shifts caused by changing depth, so that from depths of 0 to 30 m modelled colour changes (i.e. failures of colour constancy) are sometimes negligible. However, the magnitudes and directions of remaining changes are complex, depending upon the specific spectral sensitivities of the receptors and the reflectance spectra. This predicts that when judgement of colour is important, the spectra of signalling colours and photoreceptor spectral sensitivities should be evolutionarily linked, with the colours dependent on photoreceptor spectral sensitivities, and vice versa. PMID:27045090

  2. Auditory color constancy: calibration to reliable spectral properties across nonspeech context and targets.

    PubMed

    Stilp, Christian E; Alexander, Joshua M; Kiefte, Michael; Kluender, Keith R

    2010-02-01

    Brief experience with reliable spectral characteristics of a listening context can markedly alter perception of subsequent speech sounds, and parallels have been drawn between auditory compensation for listening context and visual color constancy. In order to better evaluate such an analogy, the generality of acoustic context effects for sounds with spectral-temporal compositions distinct from speech was investigated. Listeners identified nonspeech sounds-extensively edited samples produced by a French horn and a tenor saxophone-following either resynthesized speech or a short passage of music. Preceding contexts were "colored" by spectral envelope difference filters, which were created to emphasize differences between French horn and saxophone spectra. Listeners were more likely to report hearing a saxophone when the stimulus followed a context filtered to emphasize spectral characteristics of the French horn, and vice versa. Despite clear changes in apparent acoustic source, the auditory system calibrated to relatively predictable spectral characteristics of filtered context, differentially affecting perception of subsequent target nonspeech sounds. This calibration to listening context and relative indifference to acoustic sources operates much like visual color constancy, for which reliable properties of the spectrum of illumination are factored out of perception of color. PMID:20139460

  3. A robust phylogeny among major lineages of the East African cichlids.

    PubMed

    Takahashi, Tetsumi; Sota, Teiji

    2016-07-01

    The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR. PMID:27068840

  4. Lake Powell

    Atmospheric Science Data Center

    2014-05-15

    article title:  Lake Powell     View Larger Image ... (14.42 mb)   This true-color image over Lake Powell was acquired by Multi-angle Imaging SpectroRadiometer (MISR) in late March 2000. Lake Powell was formed with the construction of the Glen Canyon Dam in 1963, on the ...

  5. CONNECTICUT LAKES

    EPA Science Inventory

    This is a 1:24,000-scale datalayer of named lakes in Connecticut. It is a polygon Shapefile that includes all lakes that are named on the U.S. Geologicial Survey (USGS) 7½ minute topographic quadrangle maps that cover the State of Connecticut, plus other officially named lakes i...

  6. Lake Eyre

    Atmospheric Science Data Center

    2013-04-16

    ...   View Larger Image Lake Eyre is a large salt lake situated between two deserts in one of Australia's driest regions. ... the effect of sunglint at the nadir camera view angle. Dry, salt encrusted parts of the lake appear bright white or gray. Purple areas have ...

  7. Does phylogeny control U37K -temperature sensitivity? Implications for lacustrine alkenone paleothermometry

    NASA Astrophysics Data System (ADS)

    D'Andrea, William J.; Theroux, Susanna; Bradley, Raymond S.; Huang, Xiaohui

    2016-02-01

    Alkenone paleothermometry (via the U37K and U37K‧ indices) has long been used to reconstruct sea surface temperature and has more recently been proven effective in lacustrine settings. Genetic analyses indicate that there is a diversity of different alkenone-producing lacustrine haptophytes, and differences among U37K -temperature calibrations suggest that unique calibrations might be required to quantify past temperature variation from individual lakes. The only term necessary to quantify U37K -inferred temperature relative to a reference period (e.g., modern temperature 20th Century mean) is the slope of the calibration regression, the U37K -temperature sensitivity (i.e., the change in U37K per °C temperature change). Here, we bring together all of the existing U37K -temperature calibrations in order to compare the variability among U37K -temperature sensitivities. We also report a new in situ U37K -temperature calibration along with environmental genomic analysis based on the 18S rRNA gene of an alkenone producing haptophyte from lake Vikvatnet in Norway. We propose and test the hypothesis that U37K -temperature sensitivity is controlled by phylogeny and that this term can be used to quantify past temperature variation from lake sediments if the genetic identity of the lake's alkenone-producer is known. Using the existing calibration data sets, we determine four phylotype-specific U37K -temperature sensitivities for use in cases where in situ calibration is unavailable but the phylogeny of the alkenone producers is known.

  8. Messages for Educational Leadership: The Constance E. Clayton Lectures 1998-2007. Black Studies and Critical Thinking. Volume 34

    ERIC Educational Resources Information Center

    Slaughter-Defoe, Diana T., Ed.

    2012-01-01

    Urban education is an interdisciplinary field, characterized by introducing many perspectives to research pertaining to educational policy and to the practice of educating youth whose lives unfold in densely populated urban metropolitan areas. This book celebrates Constance Clayton's eleven-year tenure as superintendent of the School District of…

  9. Stereotype Knowledge, Flexibility, and Gender Constancy: Applications of Gender Schema Theory to Sex-Typing by Preschoolers.

    ERIC Educational Resources Information Center

    Carter, D. Bruce; And Others

    An investigation was made of relationships between children's understanding of gender constancy, their conceptions of sex-role stereotypes, their perceptions of similarities between themselves and other children, and their schematic processing of gender-relevant choices. Forty-nine children between 36 and 73 months of age participated in a…

  10. How metamer mismatching decreases as the number of colour mechanisms increases with implications for colour and lightness constancy.

    PubMed

    Logvinenko, Alexander D; Funt, Brian; Godau, Christoph

    2015-08-01

    Metamer mismatching has been previously found to impose serious limitations on colour constancy. The extent of metamer mismatching is shown here to be considerably smaller for trichromats than for dichromats, and maximal for monochromats. The implications for achromatic colour perception are discussed. PMID:26054251

  11. Apparent size contrasts of retinal images and size constancy as determinants of the moon illusion.

    PubMed

    Smith, O W; Smith, P C; Geist, C C; Zimmermann, R R

    1978-06-01

    Kaufman and Rock (1962) and Rock and Kaufman (1962) concluded that the moon illusion is a function of and attributable to apparent distance. They also reported a large framing effect as an exception. Analysis of the effect suggests two components which can account for the illusion independently of apparent distance. These are apparent size contrasts of visual images of discriminable features or objects of the earth with the moon's image and size constancy of the features or objects plus the interactions of the two. Apparent distances to horizons are always a consequence of the necessary conditions for the illusion. They are related to the illusion but are not a determinant of it. PMID:673635

  12. Constancy adding space extension for ODE sets with second degree multinomial right hand side functions

    NASA Astrophysics Data System (ADS)

    Gözükirmizi, Coşar; Demiralp, Metin

    2014-10-01

    Constancy adding space extension is a technique to convert ODE of the form ẋ(t) = F0+F1x(t)+F2x(t)⊗2 to form ṡ = G1s+G2P-1s⊗2. There are arbitrary parameters in the representation. These parameters may be utilized in such a way that G1 becomes a multiple of identity matrix. Then, using a function transformation it is possible to obtain the form ds˜(u)/du = G2P-1s˜(u)⊗2. Therefore, a new universal representation for ODEs with second degree multinomial right hand side functions is proposed. There are remaining arbitrary parameters of the space extension and this paper also focuses on how to choose them.

  13. Motion Vector Field Estimation Using Brightness Constancy Assumption and Epipolar Geometry Constraint

    NASA Astrophysics Data System (ADS)

    Hosseinyalamdary, S.; Yilmaz, A.

    2014-11-01

    In most Photogrammetry and computer vision tasks, finding the corresponding points among images is required. Among many, the Lucas-Kanade optical flow estimation has been employed for tracking interest points as well as motion vector field estimation. This paper uses the IMU measurements to reconstruct the epipolar geometry and it integrates the epipolar geometry constraint with the brightness constancy assumption in the Lucas-Kanade method. The proposed method has been tested using the KITTI dataset. The results show the improvement in motion vector field estimation in comparison to the Lucas-Kanade optical flow estimation. The same approach has been used in the KLT tracker and it has been shown that using epipolar geometry constraint can improve the KLT tracker. It is recommended that the epipolar geometry constraint is used in advanced variational optical flow estimation methods.

  14. Verification of a novel method for tube voltage constancy measurement of orthovoltage x-ray irradiators

    PubMed Central

    Wang, Chu; Belley, Matthew D.; Chao, Nelson J.; Dewhirst, Mark W.; Yoshizumi, Terry

    2014-01-01

    Purpose: For orthovoltage x-ray irradiators, the tube voltage is one of the most fundamental system parameters as this directly relates to the dosimetry in radiation biology studies; however, to the best of our knowledge, there is no commercial portable quality assurance (QA) tool to directly test the constancy of the tube voltage greater than 160 kV. The purpose of this study is to establish the Beam Quality Index (BQI), a quantity strongly correlated to the tube voltage, as an alternative parameter for the verification of the tube voltage as part of the QA program of orthovoltage x-ray irradiators. Methods: A multipurpose QA meter and its associated data acquisition software were used to customize the measurement parameters to measure the BQI and collect its time-plot. BQI measurements were performed at 320 kV with four filtration levels on three orthovoltage x-ray irradiators of the same model, one of which had been recently energy-calibrated at the factory. Results: For each of the four filtration levels, the measured BQI values were in good agreement (<5%) between the three irradiators. BQI showed filtration-specificity, possibly due to the difference in beam quality. Conclusions: The BQI has been verified as a feasible alternative for monitoring the constancy of the tube voltage for orthovoltage irradiators. The time-plot of BQI offers information on the behavior of beam energy at different phases of the irradiation time line. In addition, this would provide power supply performance characteristics from initial ramp-up to plateau, and finally, the sharp drop-off at the end of the exposure. PMID:25086562

  15. Verification of a novel method for tube voltage constancy measurement of orthovoltage x-ray irradiators

    SciTech Connect

    Wang, Chu; Belley, Matthew D.; Chao, Nelson J.; Dewhirst, Mark W.; Yoshizumi, Terry

    2014-08-15

    Purpose: For orthovoltage x-ray irradiators, the tube voltage is one of the most fundamental system parameters as this directly relates to the dosimetry in radiation biology studies; however, to the best of our knowledge, there is no commercial portable quality assurance (QA) tool to directly test the constancy of the tube voltage greater than 160 kV. The purpose of this study is to establish the Beam Quality Index (BQI), a quantity strongly correlated to the tube voltage, as an alternative parameter for the verification of the tube voltage as part of the QA program of orthovoltage x-ray irradiators. Methods: A multipurpose QA meter and its associated data acquisition software were used to customize the measurement parameters to measure the BQI and collect its time-plot. BQI measurements were performed at 320 kV with four filtration levels on three orthovoltage x-ray irradiators of the same model, one of which had been recently energy-calibrated at the factory. Results: For each of the four filtration levels, the measured BQI values were in good agreement (<5%) between the three irradiators. BQI showed filtration-specificity, possibly due to the difference in beam quality. Conclusions: The BQI has been verified as a feasible alternative for monitoring the constancy of the tube voltage for orthovoltage irradiators. The time-plot of BQI offers information on the behavior of beam energy at different phases of the irradiation time line. In addition, this would provide power supply performance characteristics from initial ramp-up to plateau, and finally, the sharp drop-off at the end of the exposure.

  16. [Research on developping the spectral dataset for Dunhuang typical colors based on color constancy].

    PubMed

    Liu, Qiang; Wan, Xiao-Xia; Liu, Zhen; Li, Chan; Liang, Jin-Xing

    2013-11-01

    The present paper aims at developping a method to reasonably set up the typical spectral color dataset for different kinds of Chinese cultural heritage in color rendering process. The world famous wall paintings dating from more than 1700 years ago in Dunhuang Mogao Grottoes was taken as typical case in this research. In order to maintain the color constancy during the color rendering workflow of Dunhuang culture relics, a chromatic adaptation based method for developping the spectral dataset of typical colors for those wall paintings was proposed from the view point of human vision perception ability. Under the help and guidance of researchers in the art-research institution and protection-research institution of Dunhuang Academy and according to the existing research achievement of Dunhuang Research in the past years, 48 typical known Dunhuang pigments were chosen and 240 representative color samples were made with reflective spectral ranging from 360 to 750 nm was acquired by a spectrometer. In order to find the typical colors of the above mentioned color samples, the original dataset was devided into several subgroups by clustering analysis. The grouping number, together with the most typical samples for each subgroup which made up the firstly built typical color dataset, was determined by wilcoxon signed rank test according to the color inconstancy index comprehensively calculated under 6 typical illuminating conditions. Considering the completeness of gamut of Dunhuang wall paintings, 8 complementary colors was determined and finally the typical spectral color dataset was built up which contains 100 representative spectral colors. The analytical calculating results show that the median color inconstancy index of the built dataset in 99% confidence level by wilcoxon signed rank test was 3.28 and the 100 colors are distributing in the whole gamut uniformly, which ensures that this dataset can provide reasonable reference for choosing the color with highest

  17. Taxonomic triage and the poverty of phylogeny.

    PubMed Central

    Wheeler, Quentin D

    2004-01-01

    Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age. PMID:15253345

  18. A Molecular Phylogeny of Living Primates

    PubMed Central

    Perelman, Polina; Johnson, Warren E.; Roos, Christian; Seuánez, Hector N.; Horvath, Julie E.; Moreira, Miguel A. M.; Kessing, Bailey; Pontius, Joan; Roelke, Melody; Rumpler, Yves; Schneider, Maria Paula C.; Silva, Artur; O'Brien, Stephen J.; Pecon-Slattery, Jill

    2011-01-01

    Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. PMID:21436896

  19. Mammalian phylogeny reveals recent diversification rate shifts.

    PubMed

    Stadler, Tanja

    2011-04-12

    Phylogenetic trees of present-day species allow investigation of the rate of evolution that led to the present-day diversity. A recent analysis of the mammalian phylogeny challenged the view of explosive mammalian evolution after the Cretaceous-Tertiary (K/T) boundary (65 Mya). However, due to lack of appropriate methods, the diversification (speciation minus extinction) rates in the more recent past of mammalian evolution could not be determined. In this paper, I provide a method that reveals that the tempo of mammalian evolution did not change until ∼ 33 Mya. This constant period was followed by a peak of diversification rates between 33 and 30 Mya. Thereafter, diversification rates remained high and constant until 8.55 Mya. Diversification rates declined significantly at 8.55 and 3.35 Mya. Investigation of mammalian subgroups (marsupials, placentals, and the six largest placental subgroups) reveals that the diversification rate peak at 33-30 Mya is mainly driven by rodents, cetartiodactyla, and marsupials. The recent diversification rate decrease is significant for all analyzed subgroups but eulipotyphla, cetartiodactyla, and primates. My likelihood approach is not limited to mammalian evolution. It provides a robust framework to infer diversification rate changes and mass extinction events in phylogenies, reconstructed from, e.g., present-day species or virus data. In particular, the method is very robust toward noise and uncertainty in the phylogeny and can account for incomplete taxon sampling. PMID:21444816

  20. Phylogeny and evolution of RNA structure.

    PubMed

    Gesell, Tanja; Schuster, Peter

    2014-01-01

    Darwin's conviction that all living beings on Earth are related and the graph of relatedness is tree-shaped has been essentially confirmed by phylogenetic reconstruction first from morphology and later from data obtained by molecular sequencing. Limitations of the phylogenetic tree concept were recognized as more and more sequence information became available. The other path-breaking idea of Darwin, natural selection of fitter variants in populations, is cast into simple mathematical form and extended to mutation-selection dynamics. In this form the theory is directly applicable to RNA evolution in vitro and to virus evolution. Phylogeny and population dynamics of RNA provide complementary insights into evolution and the interplay between the two concepts will be pursued throughout this chapter. The two strategies for understanding evolution are ultimately related through the central paradigm of structural biology: sequence ⇒ structure ⇒ function. We elaborate on the state of the art in modeling both phylogeny and evolution of RNA driven by reproduction and mutation. Thereby the focus will be laid on models for phylogenetic sequence evolution as well as evolution and design of RNA structures with selected examples and notes on simulation methods. In the perspectives an attempt is made to combine molecular structure, population dynamics, and phylogeny in modeling evolution. PMID:24639167

  1. Development of phonological constancy: 19-month-olds, but not 15-month-olds, identify words in a non-native regional accent

    PubMed Central

    Mulak, Karen E.; Best, Catherine T.; Tyler, Michael D.; Kitamura, Christine; Irwin, Julia R.

    2014-01-01

    By 12 months, children grasp that a phonetic change to a word can change its identity (phonological distinctiveness). However, they must also grasp that some phonetic changes do not (phonological constancy). To test development of phonological constancy, 16 15-month-olds and 16 19-month-olds completed an eye-tracking task that tracked their gaze to named versus unnamed images for familiar words spoken in their native (Australian) and an unfamiliar non-native (Jamaican) regional accent of English. Both groups looked longer at named than unnamed images for Australian pronunciations, but only 19-month-olds did so for Jamaican pronunciations, indicating that phonological constancy emerges by 19 months. Vocabulary size predicted 15-month-olds' identifications for the Jamaican pronunciations, suggesting vocabulary growth is a viable predictor for phonological constancy development. PMID:23521607

  2. Development of phonological constancy: 19-month-olds, but not 15-month-olds, identify words in a non-native regional accent.

    PubMed

    Mulak, Karen E; Best, Catherine T; Tyler, Michael D; Kitamura, Christine; Irwin, Julia R

    2013-01-01

    By 12 months, children grasp that a phonetic change to a word can change its identity (phonological distinctiveness). However, they must also grasp that some phonetic changes do not (phonological constancy). To test development of phonological constancy, sixteen 15-month-olds and sixteen 19-month-olds completed an eye-tracking task that tracked their gaze to named versus unnamed images for familiar words spoken in their native (Australian) and an unfamiliar non-native (Jamaican) regional accent of English. Both groups looked longer at named than unnamed images for Australian pronunciations, but only 19-month-olds did so for Jamaican pronunciations, indicating that phonological constancy emerges by 19 months. Vocabulary size predicted 15-month-olds' identifications for the Jamaican pronunciations, suggesting vocabulary growth is a viable predictor for phonological constancy development. PMID:23521607

  3. LAKE FORK

    EPA Science Inventory

    The Lake Fork of the Arkansas River Watershed has been adversely affected through mining, water diversion and storage projects, grazing, logging, and other human influences over the past 120 years. It is the goals of the LFWWG to improve the health of Lake fork by addressing th...

  4. Retrospective analysis of linear accelerator output constancy checks using process control techniques.

    PubMed

    Sanghangthum, Taweap; Suriyapee, Sivalee; Srisatit, Somyot; Pawlicki, Todd

    2013-01-01

    Shewhart control charts have previously been suggested as a process control tool for use in routine linear accelerator (linac) output verifications. However, a comprehensive approach to process control has not been investigated for linac output verifications. The purpose of this work is to investigate a comprehensive process control approach to linac output constancy quality assurance (QA). The RBA-3 dose constancy check was used to verify outputs of photon beams and electron beams delivered by a Varian Clinac 21EX linac. The data were collected during 2009 to 2010. Shewhart-type control charts, exponentially weighted moving average (EWMA) charts, and capability indices were applied to these processes. The Shewhart-type individuals chart (X-chart) was used and the number of data points used to calculate the control limits was varied. The parameters tested for the EWMA charts (smoothing parameter (λ) and the control limit width (L)) were λ = 0.05, L = 2.492; λ = 0.10, L = 2.703; and λ = 0.20, L = 2.860, as well as the number of points used to estimate the initial process mean and variation. Lastly, the number of in-control data points used to determine process capability (C(p)) and acceptability (C(pk)) were investigated, comparing the first in-control run to the longest in-control run of the process data. C(p) and C(pk) values greater than 1.0 were considered acceptable. The 95% confidence intervals were reported. The X-charts detected systematic errors (e.g., device setup errors). In-control run lengths on the X-charts varied from 5 to 30 output measurements (about one to seven months). EWMA charts showed in-control runs ranging from 9 to 33 output measurements (about two to eight months). The C(p) and C(pk) ratios are higher than 1.0 for all energies, except 12 and 20 MeV. However, 10 MV and 6, 9, and 16 MeV were in question when considering the 95% confidence limits. The X-chart should be calculated using 8-12 data points. For EWMA chart, using 4 data points

  5. Hot electron plasma equilibrium and stability in the Constance B mirror experiment

    SciTech Connect

    Chen, Xing

    1988-04-01

    An experimental study of the equilibrium and macroscopic stability property of an electron cyclotron resonance heating (ECRH) generated plasma in a minimum-B mirror is presented. The Constance B mirror is a single cell quadrupole magnetic mirror in which high beta (..beta.. less than or equal to 0.3) hot electron plasmas (T/sub e/approx. =400 keV) are created with up to 4 kW of ECRH power. The plasma equilibrium profile is hollow and resembles the baseball seam geometry of the magnet which provides the confining magnetic field. This configuration coincides with the drift orbit of deeply trapped particles. The on-axis hollowness of the hot electron density profile is 50 /+-/ 10%, and the pressure profile is at least as hollow as, if not more than, the hot electron density profile. The hollow plasma equilibrium is macroscopically stable and generated in all the experimental conditions in which the machine has been operated. The hollowness of the plasma pressure profile is not limited by the marginal stability condition. Small macroscopic plasma fluctuations in the range of the hot electron curvature drift frequency sometimes occur but their growth rate is small (..omega../sub i//..omega../sub r/ less than or equal to 10/sup -2/) and saturate at very low level (deltaB//bar B/ less than or equal to 10/sup -3/). Particle drift reversal is predicted to occur for the model pressure profile which best fits the experimental data under the typical operating conditions. No strong instability is observed when the plasma is near the drift reversal parameter regime, despite a theoretical prediction of instability under such conditions. The experiment shows that the cold electron population has no stabilizing effect to the hot electrons, which disagrees with current hot electron stability theories and results of previous maximum-B experiments. A theoretical analysis using MHD theory shows that the compressibility can stabilize a plasma with a hollowness of 20--30% in the

  6. Trial of a proposed protocol for constancy control of digital mammography systems

    SciTech Connect

    Pedersen, Kristin; Landmark, Ingrid Dypvik

    2009-12-15

    Purpose: Evaluate the utility of tests in a proposed protocol for constancy control of digital mammography systems. Methods: The protocol contained tests for image acquisition, mechanical function and safety, monitors and printers, and viewing conditions. Nine sites with digital systems from four equipment manufacturers were recruited. Dedicated PMMA test objects and Excel spreadsheets were developed. Quantitative measurements were done on processed images for systems where these images were the ones most readily available. For daily assessment of the automatic exposure control system, a homogeneous PMMA phantom was exposed under clinical conditions. The mAs and signal to noise ratio (SNR) were recorded, the deviation from a target value calculated, and the resulting image inspected for artifacts. For thickness tracking, the signal difference to noise ratio obtained for three thicknesses was calculated. Detector uniformity was assessed through comparison of SNR values for regions of interest in the center and corners of an image of a homogeneous test object. Mechanical function and safety control included a compression test, a checklist for mechanical aspects, and control of field alignment. Monitor performance was evaluated by visual inspection of the AAPM TG 18 QC test image [E. Samei et al., ''Assessment of display performance for medical imaging systems,'' Task Group 18 (Madison, WI, April 2005)]. Results: For quantitative parameters, target values and tolerance limits were established. Test results exceeding the limits were registered. Most systems exhibited stable mAs values, indicating that the tolerance limit of {+-}10% was readily achievable. The SNR also showed little variation, indicating that the tolerance limit of {+-}20% was too wide. At one site, a defective grid caused artifacts that were visible in the test images. The monitor controls proved more difficult to implement due to both difficulties importing and displaying the test image, and the

  7. Detection of IMRT delivery errors based on a simple constancy check of transit dose by using an EPID

    NASA Astrophysics Data System (ADS)

    Baek, Tae Seong; Chung, Eun Ji; Son, Jaeman; Yoon, Myonggeun

    2015-11-01

    Beam delivery errors during intensity modulated radiotherapy (IMRT) were detected based on a simple constancy check of the transit dose by using an electronic portal imaging device (EPID). Twenty-one IMRT plans were selected from various treatment sites, and the transit doses during treatment were measured by using an EPID. Transit doses were measured 11 times for each course of treatment, and the constancy check was based on gamma index (3%/3 mm) comparisons between a reference dose map (the first measured transit dose) and test dose maps (the following ten measured dose maps). In a simulation using an anthropomorphic phantom, the average passing rate of the tested transit dose was 100% for three representative treatment sites (head & neck, chest, and pelvis), indicating that IMRT was highly constant for normal beam delivery. The average passing rate of the transit dose for 1224 IMRT fields from 21 actual patients was 97.6% ± 2.5%, with the lower rate possibly being due to inaccuracies of patient positioning or anatomic changes. An EPIDbased simple constancy check may provide information about IMRT beam delivery errors during treatment.

  8. Synaptic depression in conjunction with A-current channels promote phase constancy in a rhythmic network.

    PubMed

    Greenberg, Idan; Manor, Yair

    2005-02-01

    In many central pattern generators, pairs of neurons maintain an approximately fixed phase despite large changes in the frequency. The mechanisms underlying phase maintenance are not clear. Previous theoretical work suggested that inhibitory synapses that show short-term depression could play a critical role in this respect. In this work we examine how the interaction between synaptic depression and the kinetics of a transient potassium (A-like) current could be advantageous for phase constancy in a rhythmic network. To demonstrate the mechanism in the context of a realistic central pattern generator, we constructed a detailed model of the crustacean pyloric circuit. The frequency of the rhythm was modified by changing the level of a ligand-activated current in one of the pyloric neurons. We examined how the time difference of firing activities between two selected neurons in this circuit is affected by synaptic depression, A-current, and a combination of the two. We tuned the parameters of the model such that with synaptic depression alone, or A-current alone, phase was not maintained between these two neurons. However, when these two components came together, they acted synergistically to maintain the phase across a wide range of cycle periods. This suggests that synaptic depression may be necessary to allow an A-current to delay a postsynaptic neuron in a frequency-dependent manner, such that phase invariance is ensured. PMID:15356180

  9. Julius Caesar Scaliger on plant generation and the question of species constancy.

    PubMed

    Blank, Andreas

    2010-01-01

    The sixteenth-century physician and philosopher Julius Caesar Scaliger combines the view that living beings are individuated by a single substantial form with the view that the constituents of the organic body retain their identity due to the continued existence and operation of their own substantial forms. This essay investigates the implications of Scaliger's account of subordinate and dominant substantial forms for the question of the constancy of biological species. According to Scaliger, biological mutability involves not only change on the ontological level of accidents but, in some cases, also change on the level of substantial forms. While he shares the received view that substantial forms themselves cannot undergo change, he maintains that relations of domination and subordination between substantial forms can undergo change. He uses his theory of how such changes can occur to explain cases of revertible plant degeneration. Moreover, in his view plants that belong to previously unknown biological species can emerge from changes in the relations between the many forms contained in plant seeds. PMID:20695395

  10. Recent results from the Tara tandem mirror and Constance-B mirror

    SciTech Connect

    Post, R.S.; Brau, K.; Casey, J.; Chen, X.; Coleman, J.; Garner, R.; Golovato, S.; Gerver, M.; Goodman, D.; Guss, W.

    1986-11-01

    The Tara tandem mirror program has studied anchor and ponderomotive stabilization, axicell plugging with ECH and ICRF, sloshing ion buildup in the axicells, and halo formation and stabilization by an axisymmetric divertor. Central cell plasma parameters achieved by midplane fueling and slow wave ICRF heating from a local magnetic hill are ..beta.. = 1.2%, n/sub e/ = 3 x 10/sup 12/ cm/sup -3/. The plasma is stabilized both by anchor ion ..beta.. and by ponderomotive stabilization with the central cell ICRF in combination with a magnetic divertor, realizing a completely axisymmetric configuration. Anchor ICRF creates non-Boltzman potential plugging of central cell ions. Neutral beam injection establishes a sloshing ion distribution for a cold dense central cell stream; the hot ion confinement is classical and dominated by electron drag. Axicell ECH plugging experiments lead to near total reduction in endloss, but also to a decrease in the central cell density, indicating increased radial losses. Single-ended ECH plugging shows no increase in opposite endloss. Single-ended plugging with axicell ICRF produces 50% reduction in ion endloss, with about half of the reflected ions observed in the opposite endloss. In the Constance-B quadrupole mirror the hot electron pressure profile is peaked off-axis and has the shape of a baseball seam.

  11. Constancy of the relation between floc size and density in San Francisco Bay

    USGS Publications Warehouse

    Ganju, N.K.; Schoellhamer, D.H.; Murrell, M.C.; Gartner, J.W.; Wright, S.A.

    2007-01-01

    The size and density of fine-sediment aggregates, or flocs, govern their transport and depositional properties. While the mass and volume concentrations of flocs can be measured directly or by optical methods, they must be determined simultaneously to gain an accurate density measurement. Results are presented from a tidal cycle study in San Francisco Bay, where mass concentration was determined directly, and volume concentration was measured in 32 logarithmically spaced size bins by laser-diffraction methods. The relation between floc size and density is investigated assuming a constant primary particle size and fractal floc dimension. This relation is validated with measurements from several sites throughout San Francisco Bay. The constancy of this relation implies a uniform primary particle size throughout the Bay, as well as uniform aggregation/disaggregation mechanisms (which modify fractal dimension). The exception to the relation is identified during near-bed measurements, when advected flocs mix with recently resuspended flocs from the bed, which typically have a higher fractal dimension than suspended flocs. The constant relation for suspended flocs simplifies monitoring and numerical modeling of suspended sediment in San Francisco Bay. ?? 2007 Elsevier B.V. All rights reserved.

  12. Edge-moment-based color constancy using illumination-coherent regularized regression.

    PubMed

    Wu, Meng; Luo, Kai; Dang, Jianjun; Zhou, Jun

    2015-09-01

    Considering no previous literature reveals the effectiveness of image similarity coherent with corresponding illuminant in color constancy, we propose an edge-moment-based algorithm using regularized regression in an illumination-coherent space in a divide-and-conquer way. To represent the scene images, we adopt color edge moments which are then projected into an illumination-coherent space using canonical correlation analysis (CCA). Further, a mixture of Gaussians (MoG) model is exploited to construct consistent subspaces, in each of which an iterative l2-norm regularized regression is used to learn the correlation between edge moments and illuminants. In the testing phase, estimations from each subspace are fused in a soft way according to the posterior possibility of the test image caused by the MoG. Extensive experiments on the standard datasets including the intra- and inter-dataset evaluations show that our approach outperforms the state-of-the-art algorithms. PMID:26367440

  13. Chromosomal phylogeny and evolution of gibbons (Hylobatidae).

    PubMed

    Müller, Stefan; Hollatz, Melanie; Wienberg, Johannes

    2003-11-01

    Although human and gibbons are classified in the same primate superfamily (Hominoidae), their karyotypes differ by extensive chromosome reshuffling. To date, there is still limited understanding of the events that shaped extant gibbon karyotypes. Further, the phylogeny and evolution of the twelve or more extant gibbon species (lesser apes, Hylobatidae) is poorly understood, and conflicting phylogenies have been published. We present a comprehensive analysis of gibbon chromosome rearrangements and a phylogenetic reconstruction of the four recognized subgenera based on molecular cytogenetics data. We have used two different approaches to interpret our data: (1) a cladistic reconstruction based on the identification of ancestral versus derived chromosome forms observed in extant gibbon species; (2) an approach in which adjacent homologous segments that have been changed by translocations and intra-chromosomal rearrangements are treated as discrete characters in a parsimony analysis (PAUP). The orangutan serves as an "outgroup", since it has a karyotype that is supposed to be most similar to the ancestral form of all humans and apes. Both approaches place the subgenus Bunopithecus as the most basal group of the Hylobatidae, followed by Hylobates, with Symphalangus and Nomascus as the last to diverge. Since most chromosome rearrangements observed in gibbons are either ancestral to all four subgenera or specific for individual species and only a few common derived rearrangements at subsequent branching points have been recorded, all extant gibbons may have diverged within relatively short evolutionary time. In general, chromosomal rearrangements produce changes that should be considered as unique landmarks at the divergence nodes. Thus, molecular cytogenetics could be an important tool to elucidate phylogenies in other species in which speciation may have occurred over very short evolutionary time with not enough genetic (DNA sequence) and other biological divergence to

  14. Explaining evolution via constrained persistent perfect phylogeny

    PubMed Central

    2014-01-01

    Background The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to

  15. Detecting Macroevolutionary Self-Destruction from Phylogenies.

    PubMed

    Bromham, Lindell; Hua, Xia; Cardillo, Marcel

    2016-01-01

    Phylogenetic analyses have lent support to the concept of lineage selection: that biological lineages can have heritable traits that influence their capacity to persist and diversify, and thereby affect their representation in biodiversity. While many discussions have focused on "positive" lineage selection, where stably heritable properties of lineages enhance their diversification rate, there are also intriguing examples that seem to represent "negative" lineage selection, where traits reduce the likelihood that a lineage will persist or speciate. In this article, we test whether a particular pattern of negative lineage selection is detectable from the distributions of the trait on a phylogeny. "Self-destructive" traits are those that arise often but then disappear again because they confer either a raised extinction rate or they are prone to a high rate of trait loss. For such a trait, the reconstructed origins will tend to be dispersed across the tips of the phylogeny, rather than defining large clades of related lineages that all share the trait. We examine the utility of four possible measures of "tippiness" as potential indicators of macroevolutionary self-destruction, applying them to phylogenies on which trait evolution has been simulated under different combinations of parameters for speciation, extinction, trait gain, and trait loss. We use an efficient simulation approach that starts with the required number of tips with and without the trait and uses a model to work "backwards" to construct different possible trees that result in that set of tips. We then apply these methods to a number of case studies: salt tolerance in grasses, color polymorphism in birds of prey, and selfing in nightshades. We find that the relative age of species, measured from tip length, can indicate a reduced speciation rate but does not identify traits that increase the extinction rate or the trait loss rate. We show that it is possible to detect cases of macroevolutionary self

  16. [Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

    PubMed

    Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

    2014-10-01

    Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax. PMID:25406249

  17. Mitochondrial phylogeny and systematics of baboons (Papio).

    PubMed

    Newman, Timothy K; Jolly, Clifford J; Rogers, Jeffrey

    2004-05-01

    Baboons (Papio, s.s.) comprise a series of parapatric allotaxa (subspecies or closely related species) widely distributed in sub-Saharan Africa. Despite extensive studies of their ecology, morphology, and behavior, disagreement about their phylogenetic relationships continues, as expressed in the current coexistence of at least three major, competing taxonomic treatments. To help resolve this situation, we sequenced approximately 900 bases of mitochondrial DNA of 40 individuals from five of the widely recognized "major" allotaxa. Total sequence diversity (>5%) is high compared to most primate species. Major mitochondrial clades correspond to recognized allotaxa, with the important exception that haplotypes from yellow and olive baboons form a single, monophyletic clade within which the two allotaxa do not comprise mutually exclusive clusters. The major clades fall unambiguously into the pattern: (chacma (Guinea (hamadryas (yellow + olive)))). This phylogeny does not support taxonomies that oppose hamadryas to all other baboons ("desert" vs. "savanna"), but is compatible with the view that all definable allotaxa should be recognized as coordinates, either as "phylogenetic" species or "biological" subspecies. The close relationship and unsegregated distribution of haplotypes from Kenyan and Tanzanian yellow and olive baboons are unexplained, but may reflect introgression across the documented hybrid zone. The overall phylogeny, when combined with paleontological data, suggests a southern African origin for extant Papio baboons, with all extant lineages sharing a common mitochondrial ancestor at approximately 1.8 Ma. PMID:15085544

  18. Molecular phylogeny of tintinnid ciliates (Tintinnida, Ciliophora).

    PubMed

    Bachy, Charles; Gómez, Fernando; López-García, Purificación; Dolan, John R; Moreira, David

    2012-11-01

    We investigated the phylogeny of tintinnids (Ciliophora, Tintinnida) with 62 new SSU-rDNA sequences from single cells of 32 marine and freshwater species in 20 genera, including the first SSU-rDNA sequences for Amphorides, Climacocylis, Codonaria, Cyttarocylis, Parundella, Petalotricha, Undella and Xystonella, and 23 ITS sequences of 17 species in 15 genera. SSU-rDNA phylogenies suggested a basal position for Eutintinnus, distant to other Tintinnidae. We propose Eutintinnidae fam. nov. for this divergent genus, keeping the family Tintinnidae for Amphorellopsis, Amphorides and Steenstrupiella. Tintinnopsis species branched in at least two separate groups and, unexpectedly, Climacocylis branched among Tintinnopsis sensu stricto species. Tintinnopsis does not belong to the family Codonellidae, which is restricted to Codonella, Codonaria, and also Dictyocysta (formerly in the family Dictyocystidae). The oceanic genus Undella branched close to an undescribed freshwater species. Metacylis, Rhabdonella and Cyttarocylis formed a well supported clade with several Tintinnopsis species at a basal position. Petalotricha ampulla and Cyttarocylis cassis SSU-rDNA and ITS sequences were identical or almost identical. Therefore, we propose Cyttarocylis ampulla comb. nov. for them. Intensive use of single-cell isolation and sequencing revealed unexpected complexity in the evolutionary history of these relatively well-studied ciliates. Notably, the diversity of freshwater forms suggests multiple marine-freshwater invasions. PMID:22321440

  19. Progress in nemertean biology: development and phylogeny.

    PubMed

    Turbeville, J M

    2002-07-01

    This paper reviews progress in developmental biology and phylogeny of the Nemertea, a common but poorly studied spiralian taxon of considerable ecological and evolutionary significance. Analyses of reproductive biology (including calcium dynamics during fertilization and oocyte maturation), larval morphology and development and developmental genetics have significantly extended our knowledge of spiralian developmental biology. Developmental genetics studies have in addition provided characters useful for reconstructing metazoan phylogeny. Reinvestigation of the cell lineage of Cerebratulus lacteus using fluorescent tracers revealed that endomesoderm forms from the 4d cell as in other spiralians and that ectomesoderm is derived from the 3a and 3b cells as in annelids, echiurans and molluscs. Studies examining blastomere specification show that cell fates are established precociously in direct developers and later in indirect developers. Morphological characters used to estimate the phylogenetic position of nemerteans are critically re-evaluated, and cladistic analyses of morphology reveal that conflicting hypotheses of nemertean relationships result because of different provisional homology statements. Analyses that include disputed homology statements (1, gliointerstitial cell system 2, coelomic circulatory system) suggest that nemerteans form the sister taxon to the coelomate spiralian taxa rather than the sister taxon to Platyhelminthes. Analyses of small subunit rRNA (18S rDNA) sequences alone or in combination with morphological characters support the inclusion of the nemerteans in a spiralian coelomate clade nested within a more inclusive lophotrochozoan clade. Ongoing evaluation of nemertean relationships with mitochondrial gene rearrangements and other molecular characters is discussed. PMID:21708766

  20. Phylogeny, host-parasite relationship and zoogeography

    PubMed Central

    1999-01-01

    Phylogeny is the evolutionary history of a group or the lineage of organisms and is reconstructed based on morphological, molecular and other characteristics. The genealogical relationship of a group of taxa is often expressed as a phylogenetic tree. The difficulty in categorizing the phylogeny is mainly due to the existence of frequent homoplasies that deceive observers. At the present time, cladistic analysis is believed to be one of the most effective methods of reconstructing a phylogenetic tree. Excellent computer program software for phylogenetic analysis is available. As an example, cladistic analysis was applied for nematode genera of the family Acuariidae, and the phylogenetic tree formed was compared with the system used currently. Nematodes in the genera Nippostrongylus and Heligmonoides were also analyzed, and the validity of the reconstructed phylogenetic trees was observed from a zoogeographical point of view. Some of the theories of parasite evolution were briefly reviewed as well. Coevolution of parasites and humans was discussed with special reference to the evolutionary relationship between Enterobius and primates. PMID:10634036

  1. On the Basis of Synaptic Integration Constancy during Growth of a Neuronal Circuit

    PubMed Central

    De-La-Rosa Tovar, Adriana; Mishra, Prashant K.; De-Miguel, Francisco F.

    2016-01-01

    We studied how a neuronal circuit composed of two neuron types connected by chemical and electrical synapses maintains constant its integrative capacities as neurons grow. For this we combined electrophysiological experiments with mathematical modeling in pairs of electrically-coupled Retzius neurons from postnatal to adult leeches. The electrically-coupled dendrites of both Retzius neurons receive a common chemical input, which produces excitatory postsynaptic potentials (EPSPs) with varying amplitudes. Each EPSP spreads to the soma, but also crosses the electrical synapse to arrive at the soma of the coupled neuron. The leak of synaptic current across the electrical synapse reduces the amplitude of the EPSPs in proportion to the coupling ratio. In addition, summation of EPSPs generated in both neurons generates the baseline action potentials of these serotonergic neurons. To study how integration is adjusted as neurons grow, we first studied the characteristics of the chemical and electrical connections onto the coupled dendrites of neuron pairs with soma diameters ranging from 21 to 75 μm. Then by feeding a mathematical model with the neuronal voltage responses to pseudorandom noise currents we obtained the values of the coupling ratio, the membrane resistance of the soma (rm) and dendrites (rdend), the space constant (λ) and the characteristic dendritic length (L = l/λ). We found that the EPSPs recorded from the somata were similar regardless on the neuron size. However, the amplitude of the EPSPs and the firing frequency of the neurons were inversely proportional to the coupling ratio of the neuron pair, which also was independent from the neuronal size. This data indicated that the integrative constancy relied on the passive membrane properties. We show that the growth of Retzius neurons was compensated by increasing the membrane resistance of the dendrites and therefore the λ value. By solely increasing the dendrite resistance this circuit maintains

  2. On the Basis of Synaptic Integration Constancy during Growth of a Neuronal Circuit.

    PubMed

    De-La-Rosa Tovar, Adriana; Mishra, Prashant K; De-Miguel, Francisco F

    2016-01-01

    We studied how a neuronal circuit composed of two neuron types connected by chemical and electrical synapses maintains constant its integrative capacities as neurons grow. For this we combined electrophysiological experiments with mathematical modeling in pairs of electrically-coupled Retzius neurons from postnatal to adult leeches. The electrically-coupled dendrites of both Retzius neurons receive a common chemical input, which produces excitatory postsynaptic potentials (EPSPs) with varying amplitudes. Each EPSP spreads to the soma, but also crosses the electrical synapse to arrive at the soma of the coupled neuron. The leak of synaptic current across the electrical synapse reduces the amplitude of the EPSPs in proportion to the coupling ratio. In addition, summation of EPSPs generated in both neurons generates the baseline action potentials of these serotonergic neurons. To study how integration is adjusted as neurons grow, we first studied the characteristics of the chemical and electrical connections onto the coupled dendrites of neuron pairs with soma diameters ranging from 21 to 75 μm. Then by feeding a mathematical model with the neuronal voltage responses to pseudorandom noise currents we obtained the values of the coupling ratio, the membrane resistance of the soma (rm ) and dendrites (r dend), the space constant (λ) and the characteristic dendritic length (L = l/λ). We found that the EPSPs recorded from the somata were similar regardless on the neuron size. However, the amplitude of the EPSPs and the firing frequency of the neurons were inversely proportional to the coupling ratio of the neuron pair, which also was independent from the neuronal size. This data indicated that the integrative constancy relied on the passive membrane properties. We show that the growth of Retzius neurons was compensated by increasing the membrane resistance of the dendrites and therefore the λ value. By solely increasing the dendrite resistance this circuit maintains

  3. ON THE CONSTANCY OF THE ELECTRON TEMPERATURE IN THE EXPANDING CORONA THROUGHOUT SOLAR CYCLE 23

    SciTech Connect

    Habbal, Shadia Rifai; Morgan, Huw; Druckmueller, Miloslav; Ding, Adalbert

    2010-03-10

    A recent analysis of Fe emission lines observed during the total solar eclipses of 2006 March 29 and 2008 August 1 established the first empirical link between the electron temperature in the expanding corona and Fe charge states measured in interplanetary space. In this Letter, we use this link to infer this temperature throughout solar cycle 23 from in situ charge state measurements from the Solar Wind Ion Composition Spectrometer (SWICS) on the Advanced Composition Explorer (ACE) and on Ulysses. The distribution of the SWICS/ACE Fe charge states, which span cycle 23 from 1998 to 2009, is skewed with a peak centered on Fe{sup 8+}, Fe{sup 9+}, and Fe{sup 10+} and a tail spanning Fe{sup 12+} to Fe{sup 20+}. An iterative process based on this distribution and on the Fe ion fraction as a function of electron temperature yields a narrow peak at 1.1 x 10{sup 6} K. The tail in the measured charge state distribution is attributed to the sporadic release of material hotter than 2 x 10{sup 6} K from closed magnetic structures within the bulges of streamers. The Fe Ulysses charge state measurements between 1992 and 1997 from cycle 22 peaked at Fe{sup 11+}, indicative of a slightly higher temperature of 1.5 x 10{sup 6} K. The relative constancy of the electron temperature in the expanding corona throughout solar cycle 23 points to the presence of an unknown mechanism regulating the energy input to electrons in the acceleration region of the solar wind at all latitudes during this cycle.

  4. [In-phantom dosimetric measurements as quality control for brachytherapy: System check and constancy check].

    PubMed

    Kollefrath, Michael; Bruggmoser, Gregor; Nanko, Norbert; Gainey, Mark

    2015-06-01

    In brachytherapy dosimetric measurements are difficult due to the inherent dose-inhomogenieties. Typically in routine clincal practice only the nominal dose rate is determined for computer controlled afterloading systems. The region of interest lies close to the source when measuring the spatial dose distribution. In this region small errors in the postioning of the detector, and its finite size, lead to large measurement uncertainties that exacerbate the routine dosimetric control of the system in the clinic. The size of the measurement chamber, its energy dependence, and the directional dependence of the measurement apparatus are the factors which have a significant influence on dosimetry. Although ionisation chambers are relatively large, they are employed since similar chambers are commonly found on clincal brachytherapy units. The dose is determined using DIN 6800 [11] since DIN 6809-2 [12], which deals with dosimetry in brachytherapy, is antiquated and is currently in the process of revision. Further information regarding dosimetry for brachytherapy can be found in textbooks [1] and [2]. The measurements for this work were performed with a HDR (High-Dose-Rate) (192)Ir source, type mHDR V2, and a Microselectron Afterloader V2 both from Nucletron/Elekta. In this work two dosimetric procedures are presented which, despite the aforemention difficulties, should assist in performing checks of the proper operation of the system. The first is a system check that measures the dose distribution along a line and is to be performed when first bringing the afterloader into operation, or after significant changes to the system. The other is a dosimetric constancy check, which with little effort can be performed monhtly or weekly. It simultaneously verifies the positioning of the source at two positions, the functionality of the system clock and the automatic re-calculation of the source activity. PMID:25791738

  5. Lake Powell

    NASA Technical Reports Server (NTRS)

    2007-01-01

    The white ring around Lake Powell tells the story. The surface is down 98 feet. This is critical, because Powell, Lake Mead, and other lakes along the Colorado River provide water for millions of people in five states. We are in the eighth year of a drought on the Colorado River. This year was the driest year ever reported in Southern California, and there is a severe drought in Northern California, down to less than 30-percent of snow pack. This ASTER image of part of Lake Powell was acquired in 2001. The gray area depicts the shrunken, reduced 2007 lake extent compared to the extended, larger black area in 2001.

    The image covers an area of 24 x 30 km, and is centered near 37.1 degrees north latitude, 111.3 degrees west longitude.

    The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

  6. Climate Change and its Potential Consequences to the Thermodynamics of an Alpine Lake

    NASA Astrophysics Data System (ADS)

    Fink, G.

    2012-04-01

    The characteristics of mixing processes as well as duration, frequency, and stability of an alpine lake's stratification are strongly coupled to the local climate conditions. These physical processes then again define the way in which life - from bacteria to human being - develops in this environment. Hence, probably economic and cultural lake uses are affected by climate change. Studies discovered reactions of lake physics due to global warming in central Europe in measured time series. The question is: What changes in alpine lake's thermodynamic processes do we have to expect in the next decades? This question is directed at first to general lake properties like water temperature, metalimnion depth, and heat balance and their behavior in space and time. Secondly, there is a need for information about mixing processes in these monomictic lakes. Mixing is important for the distribution of e.g. nutrients and oxygen. Thus, it is necessary to know how mixing intensity changes under likely future climate conditions. For this purpose three representative lakes were selected: Lake Constance (international), Lago di Viverone (Italy), and Woerthersee (Austria). For each lake a 1dv hydrodynamic model was built up, calibrated with an evolutionary algorithm, and finally validated. The model's source code is in an experimental state and it was provided by Deltares (Netherlands). During calibration the calculated mean monthly temperatures in different depths were compared to measurements. Then, based upon measured meteorological data "what if"-scenarios of air temperature, wind speed, cloud cover and relative humidity were developed by changing the mean value or by removing the old trend and adding a new one. When driving the model with this broad range of meteorology the result is a sensitivity study. This allows the determination of the lake's sensitivity e.g. regarding mixing intensity on changing climate, in a way that is independent from rough regional climate projections

  7. A Guide to the Natural History of Freshwater Lake Bacteria†

    PubMed Central

    Newton, Ryan J.; Jones, Stuart E.; Eiler, Alexander; McMahon, Katherine D.; Bertilsson, Stefan

    2011-01-01

    Summary: Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies. PMID:21372319

  8. Partitional Classification: A Complement to Phylogeny

    PubMed Central

    Salomon, Marc; Dassy, Bruno

    2016-01-01

    The tree of life is currently an active object of research, though next to vertical gene transmission non vertical gene transfers proved to play a significant role in the evolutionary process. To overcome this difficulty, trees of life are now constructed from genes hypothesized vital, on the assumption that these are all transmitted vertically. This view has been challenged. As a frame for this discussion, we developed a partitional taxonomical system clustering taxa at a high taxonomical rank. Our analysis (1) selects RNase P RNA sequences of bacterial, archaeal, and eucaryal genera from genetic databases, (2) submits the sequences, aligned, to k-medoid analysis to obtain clusters, (3) establishes the correspondence between clusters and taxa, (4) constructs from the taxa a new type of taxon, the genetic community (GC), and (5) classifies the GCs: Archaea–Eukaryotes contrastingly different from the six others, all bacterial. The GCs would be the broadest frame to carry out the phylogenies. PMID:27346943

  9. New culturing studies of various haptophyte algae: The role of phylogeny on the alkenone paleothermometer

    NASA Astrophysics Data System (ADS)

    Walker Karega, I. I.; D'Andrea, W. J.; Juhl, A. R.

    2015-12-01

    Alkenone paleothermometry (via the Uk37and UK'37 indices) is widely used to reconstruct sea surface temperature and, more recently, lake water temperature. Genetic analyses indicate that there is a diversity of different alkenone-producing lacustrine haptophytes, and differences among UK37-temperature calibrations suggest that unique calibrations might be required to quantify past temperature variation from individual lakes. The only term needed to quantify UK37-inferred temperature relative to a reference period (e.g., modern temperature, or 20th Century mean temperature) is the slope of the calibration regression: UK37-temperature sensitivity (i.e., the change in UK37 per °C temperature change). Here, we present new data developed by culturing four different species of alkenone-producing haptophyte algae across a range of temperatures (6-30 °C) and light levels (20-200 mE). The simultaneous culture of four distinct species allows direct comparison of the absolute quantities of alkenones and alkenoates, as well as other lipids, produced by different species of haptophytes under identical environmental conditions. Our results indicate that algal growth rate, when controlled by light intensity, has no impact on values. As expected, we find that growth temperature controls both the degree of alkenone unsaturation and the relative production of alkenones vs. alkenoates in all four species. Importantly, comparison of the four UK37-temperature calibrations resulting from our experiments with preexisting calibrations supports the hypothesis that UK37-temperature sensitivity is controlled by phylogeny. Therefore, even in the absence of a site-specific calibration, this term can be used to quantify past temperature variation from lake sediments if the genetic identity of the lake's alkenone-producer is known.

  10. Archaebacterial phylogeny: perspectives on the urkingdoms

    NASA Technical Reports Server (NTRS)

    Woese, C. R.; Olsen, G. J.

    1986-01-01

    Comparisons of complete 16S ribosomal RNA sequences have been used to confirm, refine and extend earlier concepts of archaebacterial phylogeny. The archaebacteria fall naturally into two major branches or divisions, I--the sulfur-dependent thermophilic archaebacteria, and II--the methanogenic archaebacteria and their relatives. Division I comprises a relatively closely related and phenotypically homogeneous collection of thermophilic sulfur-dependent species--encompassing the genera Sulfolobus, Thermoproteus, Pyrodictium and Desulfurococcus. The organisms of Division II, however, form a less compact grouping phylogenetically, and are also more diverse in phenotype. All three of the (major) methanogen groups are found in Division II, as are the extreme halophiles and two types of thermoacidophiles, Thermoplasma acidophilum and Thermococcus celer. This last species branches sufficiently deeply in the Division II line that it might be considered to represent a separate, third Division. However, both the extreme halophiles and Tp. acidophilum branch within the cluster of methanogens. The extreme halophiles are specifically related to the Methanomicrobiales, to the exclusion of both the Methanococcales and the Methanobacteriales. Tp. acidophilum is peripherally related to the halophile-Methanomicrobiales group. By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Alternative proposals for archaebacterial phylogeny, not based upon sequence evidence, are discussed and evaluated. In particular, proposals to rename (reclassify) various subgroups of the archaebacteria as new kingdoms are found wanting, for both their lack of proper experimental support and the taxonomic confusion they introduce.

  11. Phylogeny and forelimb disparity in waterbirds.

    PubMed

    Wang, Xia; Clarke, Julia A

    2014-10-01

    Previous work has shown that the relative proportions of wing components (i.e., humerus, ulna, carpometacarpus) in birds are related to function and ecology, but these have rarely been investigated in a phylogenetic context. Waterbirds including "Pelecaniformes," Ciconiiformes, Procellariiformes, Sphenisciformes, and Gaviiformes form a highly supported clade and developed a great diversity of wing forms and foraging ecologies. In this study, forelimb disparity in the waterbird clade was assessed in a phylogenetic context. Phylogenetic signal was assessed via Pagel's lambda, Blomberg's K, and permutation tests. We find that different waterbird clades are clearly separated based on forelimb component proportions, which are significantly correlated with phylogeny but not with flight style. Most of the traditional contents of "Pelecaniformes" (e.g., pelicans, cormorants, and boobies) cluster with Ciconiiformes (herons and storks) and occupy a reduced morphospace. These taxa are closely related phylogenetically but exhibit a wide range of ecologies and flight styles. Procellariiformes (e.g., petrels, albatross, and shearwaters) occupy a wide range of morphospace, characterized primarily by variation in the relative length of carpometacarpus and ulna. Gaviiformes (loons) surprisingly occupy a wing morphospace closest to diving petrels and penguins. Whether this result may reflect wing proportions plesiomorphic for the waterbird clade or a functional signal is unclear. A Bayesian approach detecting significant rate shifts across phylogeny recovered two such shifts. At the base of the two sister clades Sphenisciformes + Procellariiformes, a shift to an increase evolutionary rate of change is inferred for the ulna and carpometacarpus. Thus, changes in wing shape begin prior to the loss of flight in the wing-propelled diving clade. Several shifts to slower rate of change are recovered within stem penguins. PMID:24989899

  12. Homology and phylogeny and their automated inference

    NASA Astrophysics Data System (ADS)

    Fuellen, Georg

    2008-06-01

    The analysis of the ever-increasing amount of biological and biomedical data can be pushed forward by comparing the data within and among species. For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts. Here, I review the foundations and advantages of this “historical” approach and evaluate recent attempts at automating such analyses. Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene. If the family has relatives in other species, we can assume that the ancestral gene was present in the ancestral species from which all the other species evolved. In particular, describing the relationships among the duplicated biological sequences found in the various species is often possible by a phylogeny, which is more informative than homology statements. Detecting and elaborating on common origins may answer how certain biological sequences developed, and predict what sequences are in a particular species and what their function is. Such knowledge transfer from sequences in one species to the homologous sequences of the other is based on the principle of ‘my closest relative looks and behaves like I do’, often referred to as ‘guilt by association’. To enable knowledge transfer on a large scale, several automated ‘phylogenomics pipelines’ have been developed in recent years, and seven of these will be described and compared. Overall, the examples in this review demonstrate that homology and phylogeny analyses, done on a large (and automated) scale, can give insights into function in biology and biomedicine.

  13. A MOLECULAR PHYLOGENY FOR THE PROTOSTRONGYLIDAE (NEMATODA: METASTRONGYLINA)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Protostrongylids, a putative monophyletic group among the lungworms (Metastrongylina: Metastrongyloidea), are economically important pathogens infecting domestic and free-ranging ungulate and leporid hosts throughout the world. Here, we reconstruct a molecular phylogeny based on ribosomal DNA (28S) ...

  14. Target recognitions in multiple-camera closed-circuit television using color constancy

    NASA Astrophysics Data System (ADS)

    Soori, Umair; Yuen, Peter; Han, Ji Wen; Ibrahim, Izzati; Chen, Wentao; Hong, Kan; Merfort, Christian; James, David; Richardson, Mark

    2013-04-01

    People tracking in crowded scenes from closed-circuit television (CCTV) footage has been a popular and challenging task in computer vision. Due to the limited spatial resolution in the CCTV footage, the color of people's dress may offer an alternative feature for their recognition and tracking. However, there are many factors, such as variable illumination conditions, viewing angles, and camera calibration, that may induce illusive modification of intrinsic color signatures of the target. Our objective is to recognize and track targets in multiple camera views using color as the detection feature, and to understand if a color constancy (CC) approach may help to reduce these color illusions due to illumination and camera artifacts and thereby improve target recognition performance. We have tested a number of CC algorithms using various color descriptors to assess the efficiency of target recognition from a real multicamera Imagery Library for Intelligent Detection Systems (i-LIDS) data set. Various classifiers have been used for target detection, and the figure of merit to assess the efficiency of target recognition is achieved through the area under the receiver operating characteristics (AUROC). We have proposed two modifications of luminance-based CC algorithms: one with a color transfer mechanism and the other using a pixel-wise sigmoid function for an adaptive dynamic range compression, a method termed enhanced luminance reflectance CC (ELRCC). We found that both algorithms improve the efficiency of target recognitions substantially better than that of the raw data without CC treatment, and in some cases the ELRCC improves target tracking by over 100% within the AUROC assessment metric. The performance of the ELRCC has been assessed over 10 selected targets from three different camera views of the i-LIDS footage, and the averaged target recognition efficiency over all these targets is found to be improved by about 54% in AUROC after the data are processed by

  15. Inferring the Origin of Metastases from Cancer Phylogenies.

    PubMed

    Hong, Woo Suk; Shpak, Max; Townsend, Jeffrey P

    2015-10-01

    Determining the evolutionary history of metastases is a key problem in cancer biology. Several recent studies have presented inferences regarding the origin of metastases based on phylogenies of cancer lineages. Many of these studies have concluded that the observed monophyly of metastatic subclones favored metastasis-to-metastasis spread ("a metastatic cascade" rather than parallel metastases from the primary tumor). In this article, we argue that identifying a monophyletic clade of metastatic subclones does not provide sufficient evidence to unequivocally establish a history of metastatic cascades. In the absence of a complete phylogeny of the subclones within the primary tumor, a scenario of parallel metastatic events from the primary tumor is an equally plausible interpretation. Future phylogenetic studies on the origin of metastases should obtain a complete phylogeny of subclones within the primary tumor. This complete phylogeny may be obtainable by ultra-deep sequencing and phasing of large sections or by targeted sequencing of many small, spatially heterogeneous sections, followed by phylogenetic reconstruction using well-established molecular evolutionary models. In addition to resolving the evolutionary history of metastases, a complete phylogeny of subclones within the primary tumor facilitates the identification of driver mutations by application of phylogeny-based tests of natural selection. PMID:26260528

  16. The shape of mammalian phylogeny: patterns, processes and scales

    PubMed Central

    Purvis, Andy; Fritz, Susanne A.; Rodríguez, Jesús; Harvey, Paul H.; Grenyer, Richard

    2011-01-01

    Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of ‘regime changes’—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be ‘downshifts’. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of ‘rules’. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space. PMID:21807729

  17. Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida).

    PubMed

    Cornils, Astrid; Blanco-Bercial, Leocadio

    2013-12-01

    The Paracalanidae are ecologically-important marine planktonic copepods that occur in the epipelagic zone in temperate and tropical waters. They are often the dominant taxon - in terms of biomass and abundance - in continental shelf regions. As primary consumers, they form a vital link in the pelagic food web between primary producers and higher trophic levels. Despite the ecological importance of the taxon, evolutionary and systematic relationships within the family remain largely unknown. A multigene phylogeny including 24 species, including representatives for all seven genera, was determined based on two nuclear genes, small-subunit (18S) ribosomal RNA and Histone 3 (H3) and one mitochondrial gene, cytochrome c oxidase subunit I (COI). The molecular phylogeny was well supported by Maximum likelihood and Bayesian inference analysis; all genera were found to be monophyletic, except for Paracalanus, which was separated into two distinct clades: the Paracalanus aculeatus group and Paracalanus parvus group. The molecular phylogeny also confirmed previous findings that Mecynocera and Calocalanus are genera of the family Paracalanidae. For comparison, a morphological phylogeny was created for 35 paracalanid species based on 54 morphological characters derived from published descriptions. The morphological phylogeny did not resolve all genera as monophyletic and bootstrap support was not strong. Molecular and morphological phylogenies were not congruent in the positioning of Bestiolina and the Paracalanus species groups, possibly due to the lack of sufficient phylogenetically-informative morphological characters. PMID:23831457

  18. Conquest of the deep, old and cold: an exceptional limpet radiation in Lake Baikal.

    PubMed

    Stelbrink, Björn; Shirokaya, Alena A; Clewing, Catharina; Sitnikova, Tatiana Y; Prozorova, Larisa A; Albrecht, Christian

    2015-07-01

    Lake Baikal is the deepest, oldest and most speciose ancient lake in the world. The lake is characterized by high levels of molluscan species richness and endemicity, including the limpet family Acroloxidae with 25 endemic species. Members of this group generally inhabit the littoral zone, but have been recently found in the abyssal zone at hydrothermal vents and oil-seeps. Here, we use mitochondrial and nuclear data to provide a first molecular phylogeny of the Lake Baikal limpet radiation, and to date the beginning of intra-lacustrine diversification. Divergence time estimates suggest a considerably younger age for the species flock compared with lake age estimates, and the beginning of extensive diversification is possibly related to rapid deepening and cooling during rifting. Phylogenetic relationships and divergence time estimates do not clearly indicate when exactly the abyssal was colonized but suggest a timeframe coincident with the formation of the abyssal in the northern basin (Middle to Late Pleistocene). PMID:26202427

  19. Conquest of the deep, old and cold: an exceptional limpet radiation in Lake Baikal

    PubMed Central

    Stelbrink, Björn; Shirokaya, Alena A.; Clewing, Catharina; Sitnikova, Tatiana Y.; Prozorova, Larisa A.; Albrecht, Christian

    2015-01-01

    Lake Baikal is the deepest, oldest and most speciose ancient lake in the world. The lake is characterized by high levels of molluscan species richness and endemicity, including the limpet family Acroloxidae with 25 endemic species. Members of this group generally inhabit the littoral zone, but have been recently found in the abyssal zone at hydrothermal vents and oil-seeps. Here, we use mitochondrial and nuclear data to provide a first molecular phylogeny of the Lake Baikal limpet radiation, and to date the beginning of intra-lacustrine diversification. Divergence time estimates suggest a considerably younger age for the species flock compared with lake age estimates, and the beginning of extensive diversification is possibly related to rapid deepening and cooling during rifting. Phylogenetic relationships and divergence time estimates do not clearly indicate when exactly the abyssal was colonized but suggest a timeframe coincident with the formation of the abyssal in the northern basin (Middle to Late Pleistocene). PMID:26202427

  20. Visual discrimination of rotated 3D objects in Malawi cichlids (Pseudotropheus sp.): a first indication for form constancy in fishes.

    PubMed

    Schluessel, V; Kraniotakes, H; Bleckmann, H

    2014-03-01

    Fish move in a three-dimensional environment in which it is important to discriminate between stimuli varying in colour, size, and shape. It is also advantageous to be able to recognize the same structures or individuals when presented from different angles, such as back to front or front to side. This study assessed visual discrimination abilities of rotated three-dimensional objects in eight individuals of Pseudotropheus sp. using various plastic animal models. All models were displayed in two choice experiments. After successful training, fish were presented in a range of transfer tests with objects rotated in the same plane and in space by 45° and 90° to the side or to the front. In one experiment, models were additionally rotated by 180°, i.e., shown back to front. Fish showed quick associative learning and with only one exception successfully solved and finished all experimental tasks. These results provide first evidence for form constancy in this species and in fish in general. Furthermore, Pseudotropheus seemed to be able to categorize stimuli; a range of turtle and frog models were recognized independently of colour and minor shape variations. Form constancy and categorization abilities may be important for behaviours such as foraging, recognition of predators, and conspecifics as well as for orienting within habitats or territories. PMID:23982620

  1. Illuminant estimation for color constancy: why spatial-domain methods work and the role of the color distribution.

    PubMed

    Cheng, Dongliang; Prasad, Dilip K; Brown, Michael S

    2014-05-01

    Color constancy is a well-studied topic in color vision. Methods are generally categorized as (1) low-level statistical methods, (2) gamut-based methods, and (3) learning-based methods. In this work, we distinguish methods depending on whether they work directly from color values (i.e., color domain) or from values obtained from the image's spatial information (e.g., image gradients/frequencies). We show that spatial information does not provide any additional information that cannot be obtained directly from the color distribution and that the indirect aim of spatial-domain methods is to obtain large color differences for estimating the illumination direction. This finding allows us to develop a simple and efficient illumination estimation method that chooses bright and dark pixels using a projection distance in the color distribution and then applies principal component analysis to estimate the illumination direction. Our method gives state-of-the-art results on existing public color constancy datasets as well as on our newly collected dataset (NUS dataset) containing 1736 images from eight different high-end consumer cameras. PMID:24979637

  2. Biomass Size Spectra and Plankton Diversity in a Shallow Eutrophic Lake

    NASA Astrophysics Data System (ADS)

    Gaedke, Ursula; Seifried, Angelika; Adrian, Rita

    2004-01-01

    Biomass size spectra collate structural and functional attributes of plankton communities enabling standardised temporal and cross-system comparisons and may be rapidly obtained by automated particle counters. To examine how differences in plankton communities from highly eutrophic and more oligotrophic lakes are reflected in size spectra, a three-year time series of biomass size spectra was established for polymictic, eutrophic Lake Müggelsee, based on approximately weekly sampling and microscopic enumeration. The continuous but often bumpy size spectra reflected appropriately the seasonal and trophy-related variations in the plankton composition and growth conditions and the potential impact of daphnids on smaller plankton. We tested the hypothesis that more diverse plankton communities have smoother size spectra than impoverished ones. The spectra of Lake Müggelsee and other more or less eutrophic lakes covaried roughly with the functional diversity in total plankton composition but were unrelated to taxonomical diversity within the phyto- or mesozooplankton. The slopes of the normalised size spectra of Lake Müggelsee were generally more negative than -1, exhibited a recurrent seasonal pattern and were strongly correlated with crustacean biomass. In contrast to less eutrophic systems, slopes could not be used to quantify energy fluxes within the food web due to highly variable algal P/B ratios and frequently bumpy size distributions. The latter indicated stronger deviations from the ideal concept of a steady energy flow along the size gradient than found in e.g. large, mesotrophic Lake Constance. (

  3. Evolutionary History of Lake Tanganyika's Predatory Deepwater Cichlids

    PubMed Central

    Kirchberger, Paul C.; Sefc, Kristina M.; Sturmbauer, Christian; Koblmüller, Stephan

    2012-01-01

    Hybridization among littoral cichlid species in Lake Tanganyika was inferred in several molecular phylogenetic studies. The phenomenon is generally attributed to the lake level-induced shoreline and habitat changes. These allow for allopatric divergence of geographically fragmented populations alternating with locally restricted secondary contact and introgression between incompletely isolated taxa. In contrast, the deepwater habitat is characterized by weak geographic structure and a high potential for gene flow, which may explain the lower species richness of deepwater than littoral lineages. For the same reason, divergent deepwater lineages should have evolved strong intrinsic reproductive isolation already in the incipient stages of diversification, and, consequently, hybridization among established lineages should have been less frequent than in littoral lineages. We test this hypothesis in the endemic Lake Tanganyika deepwater cichlid tribe Bathybatini by comparing phylogenetic trees of Hemibates and Bathybates species obtained with nuclear multilocus AFLP data with a phylogeny based on mitochondrial sequences. Consistent with our hypothesis, largely congruent tree topologies and negative tests for introgression provided no evidence for introgressive hybridization between the deepwater taxa. Together, the nuclear and mitochondrial data established a well-supported phylogeny and suggested ecological segregation during speciation. PMID:22675652

  4. Molecular phylogeny of euthyneura (mollusca: gastropoda).

    PubMed

    Grande, Cristina; Templado, José; Cervera, J Lucas; Zardoya, Rafael

    2004-02-01

    A new phylogenetic hypothesis for Euthyneura is proposed based on the analysis of primary sequence data (mitochondrial cox1, trnV, rrnL, trnL(cun), trnA, trnP, nad6, and nad5 genes) and the phylogenetic utility of two rare genomic changes (the relative position of the mitochondrial trnP gene, and an insertion/deletion event in a conserved region of the mitochondrial Cox1 protein) is addressed. Both sources of phylogenetic information clearly rejected the monophyly of pulmonates, a group of gastropods well supported so far by morphological evidence. The marine basommatophoran pulmonate Siphonaria was placed within opisthobranchs and shared with them the insertion of a Glycine in the Cox 1 protein. The marine systellommatophoran pulmonate Onchidella was recovered at the base of the opisthobranch + Siphonaria clade. Opisthobranchs, Siphonaria, and Onchidella shared the relative position of the mitochondrial trnP gene between the mitochondrial trnA and nad6 genes. The land snails and slugs (stylommatophoran pulmonates) were recovered as an early split in the phylogeny of advanced gastropods. The monophyly of the Euthyneura (Opisthobranchia + Pulmonata) was rejected by the inclusion of the heterostrophan Pyramidella. PMID:14660702

  5. Molecular phylogeny of Triatomini (Hemiptera: Reduviidae: Triatominae)

    PubMed Central

    2014-01-01

    Background The Triatomini and Rhodniini (Hemiptera: Reduviidae) tribes include the most diverse Chagas disease vectors; however, the phylogenetic relationships within the tribes remain obscure. This study provides the most comprehensive phylogeny of Triatomini reported to date. Methods The relationships between all of the Triatomini genera and representatives of the three Rhodniini species groups were examined in a novel molecular phylogenetic analysis based on the following six molecular markers: the mitochondrial 16S; Cytochrome Oxidase I and II (COI and COII) and Cytochrome B (Cyt B); and the nuclear 18S and 28S. Results Our results show that the Rhodnius prolixus and R. pictipes groups are more closely related to each other than to the R. pallescens group. For Triatomini, we demonstrate that the large complexes within the paraphyletic Triatoma genus are closely associated with their geographical distribution. Additionally, we observe that the divergence within the spinolai and flavida complex clades are higher than in the other Triatoma complexes. Conclusions We propose that the spinolai and flavida complexes should be ranked under the genera Mepraia and Nesotriatoma. Finally, we conclude that a thorough morphological investigation of the paraphyletic genera Triatoma and Panstrongylus is required to accurately assign queries to natural genera. PMID:24685273

  6. A Framework for Studying Emotions Across Phylogeny

    PubMed Central

    Anderson, David J.; Adolphs, Ralph

    2014-01-01

    Since the 19th century, there has been disagreement over the fundamental question of whether “emotions” are cause or consequence of their associated behaviors. This question of causation is most directly addressable in genetically tractable model organisms, including invertebrates such as Drosophila. Yet there is ongoing debate about whether such species even have “emotions,” since emotions are typically defined with reference to human behavior and neuroanatomy. Here we argue that emotional behaviors are a class of behaviors that express internal emotion states. These emotion states exhibit certain general functional and adaptive properties that apply across any specific human emotions like fear or anger, as well as across phylogeny. These general properties, which can be thought of as “emotion primitives”, can be modeled and studied in evolutionarily distant model organisms, allowing functional dissection of their mechanistic bases, and tests of their causal relationships to behavior. More generally, our approach aims not only at better integration of such studies in model organisms with studies of emotion in humans, but also suggests a revision of how emotion should be operationalized within psychology and psychiatry. PMID:24679535

  7. Bacterial phylogeny structures soil resistomes across habitats

    NASA Astrophysics Data System (ADS)

    Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

    2014-05-01

    Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.

  8. A transcriptome approach to ecdysozoan phylogeny.

    PubMed

    Borner, Janus; Rehm, Peter; Schill, Ralph O; Ebersberger, Ingo; Burmester, Thorsten

    2014-11-01

    The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns. PMID:25124096

  9. Molecular epidemiology, phylogeny and evolution of Legionella.

    PubMed

    Khodr, A; Kay, E; Gomez-Valero, L; Ginevra, C; Doublet, P; Buchrieser, C; Jarraud, S

    2016-09-01

    Legionella are opportunistic pathogens that develop in aquatic environments where they multiply in protozoa. When infected aerosols reach the human respiratory tract they may accidentally infect the alveolar macrophages leading to a severe pneumonia called Legionnaires' disease (LD). The ability of Legionella to survive within host-cells is strictly dependent on the Dot/Icm Type 4 Secretion System that translocates a large repertoire of effectors into the host cell cytosol. Although Legionella is a large genus comprising nearly 60 species that are worldwide distributed, only about half of them have been involved in LD cases. Strikingly, the species Legionella pneumophila alone is responsible for 90% of all LD cases. The present review summarizes the molecular approaches that are used for L. pneumophila genotyping with a major focus on the contribution of whole genome sequencing (WGS) to the investigation of local L. pneumophila outbreaks and global epidemiology studies. We report the newest knowledge regarding the phylogeny and the evolution of Legionella and then focus on virulence evolution of those Legionella species that are known to have the capacity to infect humans. Finally, we discuss the evolutionary forces and adaptation mechanisms acting on the Dot/Icm system itself as well as the role of mobile genetic elements (MGE) encoding T4ASSs and of gene duplications in the evolution of Legionella and its adaptation to different hosts and lifestyles. PMID:27180896

  10. A retroposon analysis of Afrotherian phylogeny.

    PubMed

    Nishihara, Hidenori; Satta, Yoko; Nikaido, Masato; Thewissen, J G M; Stanhope, Michael J; Okada, Norihiro

    2005-09-01

    Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed. PMID:15930154

  11. Alu insertion loci and platyrrhine primate phylogeny.

    PubMed

    Ray, David A; Xing, Jinchuan; Hedges, Dale J; Hall, Michael A; Laborde, Meredith E; Anders, Bridget A; White, Brittany R; Stoilova, Nadica; Fowlkes, Justin D; Landry, Kate E; Chemnick, Leona G; Ryder, Oliver A; Batzer, Mark A

    2005-04-01

    Short INterspersed Elements (SINEs) make very useful phylogenetic markers because the integration of a particular element at a location in the genome is irreversible and of known polarity. These attributes make analysis of SINEs as phylogenetic characters an essentially homoplasy-free affair. Alu elements are primate-specific SINEs that make up a large portion of the human genome and are also widespread in other primates. Using a combination wet-bench and computational approach we recovered 190 Alu insertions, 183 of which are specific to the genomes of nine New World primates. We used these loci to investigate branching order and have produced a cladogram that supports a sister relationship between Atelidae (spider, woolly, and howler monkeys) and Cebidae (marmosets, tamarins, and owl monkeys) and then the joining of this two family clade to Pitheciidae (titi and saki monkeys). The data support these relationships with a homoplasy index of 0.00. In this study, we report one of the largest applications of SINE elements to phylogenetic analysis to date, and the results provide a robust molecular phylogeny for platyrrhine primates. PMID:15737586

  12. Primate jumping genes elucidate strepsirrhine phylogeny

    PubMed Central

    Roos, Christian; Schmitz, Jürgen; Zischler, Hans

    2004-01-01

    Transposable elements provide a highly informative marker system for analyzing evolutionary histories. To solve controversially discussed topics in strepsirrhine phylogeny, we characterized 61 loci containing short interspersed elements (SINEs) and determined the SINE presence–absence pattern at orthologous loci in a representative strepsirrhine panel. This SINE monolocus study was complemented by a Southern blot analysis tracing multiple loci of two different strepsirrhine specific SINEs. The results thereof were combined with phylogenetic trees reconstructed on the basis of complete mitochondrial cytochrome b sequences from all recognized strepsirrhine genera. Here we present evidence for (i) a sister group relationship of Malagasy Chiromyiformes and Lemuriformes, (ii) Lorisidae being a monophyletic sister clade to the Galagidae, and (iii) common ancestry of African and Asian lorisids. Based on these findings, we conclude that strepsirrhines originated in Africa and that Madagascar and Asia were colonized by respective single immigration events. In agreement with paleocontinental data, the molecular analyses suggest a crossing of the Mozambique channel by rafting between the late Cretaceous and the middle Eocene, whereas Asia was most likely colonized between the early Eocene and the middle Oligocene on a continental route. Furthermore, one SINE integration links the two Lemuriformes families, Lemuridae and Indriidae, indicating a common origin of diurnality or cathemerality and a later reversal to nocturnality by the indriid genus Avahi. PMID:15249661

  13. Dobrava-Belgrade virus: phylogeny, epidemiology, disease.

    PubMed

    Papa, Anna

    2012-08-01

    Dobrava-Belgrade virus (DOBV) is an Old World hantavirus that causes hemorrhagic fever with renal syndrome in humans. With a case fatality rate up to 12%, DOBV infection is the most life-threatening hantavirus disease in Europe. The virus was initially identified in the Balkans, but the discovery of new endemic foci have expanded its recognized geographic range. The recent description of novel genetic variants with different degrees of pathogenicity have complicated its taxonomic analysis. The original rodent host of DOBV is Apodemus flavicollis, however additional Apodemus species, such Apodemus agrarius and Apodemus ponticus, have been found to serve as hosts of the various DOBV genotypes. The complex evolution and genetic diversity of the virus are still under investigation. The present review aims to provide an update on the phylogeny of DOBV and the epidemiology of infection in rodents and humans; to describe the clinical characteristics of the disease; to present current knowledge about laboratory diagnosis, treatment and prevention; discuss the current state of the art in antiviral drug and vaccine development. PMID:22659378

  14. Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae).

    PubMed

    Tang, Kevin L; Agnew, Mary K; Chen, Wei-Jen; Vincent Hirt, M; Raley, Morgan E; Sado, Tetsuya; Schneider, Leah M; Yang, Lei; Bart, Henry L; He, Shunping; Liu, Huanzhang; Miya, Masaki; Saitoh, Kenji; Simons, Andrew M; Wood, Robert M; Mayden, Richard L

    2011-10-01

    The members of the cyprinid subfamily Gobioninae, commonly called gudgeons, form one of the most well-established assemblages in the family Cyprinidae. The subfamily is a species-rich group of fishes, these fishes display diverse life histories, appearances, and behavior. The phylogenetic relationships of Gobioninae are examined using sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. This investigation produced a data matrix of 4114 bp for 162 taxa that was analyzed using parsimony, maximum likelihood, and Bayesian inference methods. The phylogenies our analyses recovered corroborate recent studies on the group. The subfamily Gobioninae is monophyletic and composed of three major lineages. We find evidence for a Hemibarbus-Squalidus group, and the tribes Gobionini and Sarcocheilichthyini, with the Hemibarbus-Squalidus group sister to a clade of Gobionini-Sarcocheilichthyini. The Hemibarbus-Squalidus group includes those two genera; the tribe Sarcocheilichthyini includes Coreius, Coreoleuciscus, Gnathopogon, Gobiocypris, Ladislavia, Paracanthobrama, Pseudorasbora, Pseudopungtungia, Pungtungia, Rhinogobio, and Sarcocheilichthys; the tribe Gobionini includes Abbottina, Biwia, Gobio, Gobiobotia, Huigobio, Microphysogobio, Platysmacheilus, Pseudogobio, Romanogobio, Saurogobio, and Xenophysogobio. The monotypic Acanthogobio is placed into the synonymy of Gobio. We tentatively assign Belligobio to the Hemibarbus-Squalidus group and Mesogobio to Gobionini; Paraleucogobio and Parasqualidus remain incertae sedis. Based on the topologies presented, the evolution of swim bladder specializations, a distinctive feature among cyprinids, has occurred more than once within the subfamily. PMID:21672635

  15. Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa).

    PubMed

    Kretzschmar, Martin; Kuhnt, Andreas; Bonkowski, Michael; Fiore-Donno, Anna Maria

    2016-07-01

    Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update. PMID:26663217

  16. Dating Phylogenies with Hybrid Local Molecular Clocks

    PubMed Central

    Aris-Brosou, Stéphane

    2007-01-01

    Background Because rates of evolution and species divergence times cannot be estimated directly from molecular data, all current dating methods require that specific assumptions be made before inferring any divergence time. These assumptions typically bear either on rates of molecular evolution (molecular clock hypothesis, local clocks models) or on both rates and times (penalized likelihood, Bayesian methods). However, most of these assumptions can affect estimated dates, oftentimes because they underestimate large amounts of rate change. Principal Findings A significant modification to a recently proposed ad hoc rate-smoothing algorithm is described, in which local molecular clocks are automatically placed on a phylogeny. This modification makes use of hybrid approaches that borrow from recent theoretical developments in microarray data analysis. An ad hoc integration of phylogenetic uncertainty under these local clock models is also described. The performance and accuracy of the new methods are evaluated by reanalyzing three published data sets. Conclusions It is shown that the new maximum likelihood hybrid methods can perform better than penalized likelihood and almost as well as uncorrelated Bayesian models. However, the new methods still tend to underestimate the actual amount of rate change. This work demonstrates the difficulty of estimating divergence times using local molecular clocks. PMID:17849008

  17. Migration of 137Cs in tributaries, lake water and sediment of Lago Maggiore (Italy, Switzerland) - analysis and comparison with Lago di Lugano and other lakes.

    PubMed

    Putyrskaya, Victoria; Klemt, Eckehard; Röllin, Stefan

    2009-01-01

    This paper describes the behaviour of 137Cs in Lago Maggiore and other pre-alpine lakes as a consequence of atmospheric nuclear weapons testing fallout and the fallout from the nuclear accident in Chernobyl. It presents data on the 137Cs distribution in tributaries, lake water, bottom sediments and reveals the role of (137)Cs as a marker of the sedimentation processes. The run-off of 137Cs from the watershed to the lake is described with a simple compartment model. Measurements of the activity concentration of (137)Cs in sediments are compared with the output of a model (diffusion-convection type) which describes the input of 137Cs into and its vertical distribution within the sediment. Varying sedimentation rates (0.05-0.90g(cm2y)(-1)) in Lago Maggiore are compared with data of other authors. Sedimentation rates and total distribution coefficients (of about 10(5) Lkg(-1)) in Lago Maggiore are discussed and compared with those of Lago di Lugano, Lake Constance, and Lake Vorsee. PMID:19019505

  18. Phylogeny of Cirsium spp. in North America: Host Specificity Does Not Follow Phylogeny

    PubMed Central

    Slotta, Tracey A. Bodo; Horvath, David P.; Foley, Michael E.

    2012-01-01

    Weedy invasive Cirsium spp. are widespread in temperate regions of North America and some of their biological control agents have attacked native Cirsium spp. A phylogenetic tree was developed from DNA sequences for the internal transcribed spacer and external transcribed spacer regions from native and non-native Great Plains Cirsium spp. and other thistles to determine if host specificity follows phylogeny. The monophyly of Cirsium spp. and Carduus within the tribe Cardinae was confirmed with native North American and European lineages of the Cirsium spp. examined. We did not detect interspecific hybridization between the introduced invasive and the native North American Cirsium spp. Selected host-biological control agent interactions were mapped onto the phylogenic tree derived by maximum likelihood analysis to examine the co-occurrence of known hosts with biological control agents. Within Cirsium-Cardueae, the insect biological control agents do not associate with host phylogenetic lines. Thus, more comprehensive testing of species in host-specificity trials, rather than relying on a single representative of a given clade may be necessary; because the assumption that host-specificity follows phylogeny does not necessarily hold. Since the assumption does not always hold, it will also be important to evaluate ecological factors to provide better cues for host specificity. PMID:27137640

  19. Investigation of Color Constancy in 4.5-Month-Old Infants under a Strict Control of Luminance Contrast for Individual Participants

    ERIC Educational Resources Information Center

    Yang, Jiale; Kanazawa, So; Yamaguchi, Masami K.; Kuriki, Ichiro

    2013-01-01

    The current study examined color constancy in infants using a familiarization paradigm. We first obtained isoluminance in each infant as defined by the minimum motion paradigm and used these data to control the luminance of stimuli in the main experiments. In the familiarization phase of the main experiment, two identical smiling face patterns…

  20. Interracial Contact and Racial Constancy: A Multi-Site Study of Racial Intergroup Bias in 3-5 Year Old Anglo-British Children

    ERIC Educational Resources Information Center

    Rutland, Adam; Cameron, Lindsey; Bennett, Laura; Ferrell, Jennifer

    2005-01-01

    This paper examined the influence of interracial contact and racial constancy on the racial intergroup bias of young Anglo-British children. This multi-site study was conducted in areas of Great Britain that varied in terms of racial diversity. The study also investigated whether preschool children express bias on positive, but not negative,…

  1. On simulated annealing phase transitions in phylogeny reconstruction.

    PubMed

    Strobl, Maximilian A R; Barker, Daniel

    2016-08-01

    Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. PMID:27150349

  2. Phylogeny of Porphyromonas gingivalis by Ribosomal Intergenic Spacer Region Analysis

    PubMed Central

    Rumpf, Robert W.; Griffen, Ann L.; Leys, Eugene J.

    2000-01-01

    Periodontitis has been associated with the presence of Porphyromonas gingivalis, and previous studies have shown phenotypic differences in the pathogenicities of strains of P. gingivalis. An accurate and comprehensive phylogeny of strains of P. gingivalis would be useful in determining if there is an evolutionary basis to pathogenicity in this species. Previous phylogenies of P. gingivalis strains based on random amplified polymorphic DNA (RAPD) analysis and multilocus enzyme electrophoresis (MLEE) show little agreement. While the 16S ribosomal gene is the standard for phylogenetic reconstruction among bacterial species, it is insufficiently variable for this purpose. In the present study, the phylogeny of P. gingivalis was constructed on the basis of the sequence of the most variable region of the ribosomal operon, the intergenic spacer region (ISR). Heteroduplex analysis of the ISR has been used to study the variability of P. gingivalis strains in periodontitis. In the present study, typing by heteroduplex analysis was compared to ISR sequence-based phylogeny and close agreement was observed. The two strains of P. gingivalis whose heteroduplex types are strongly associated with periodontitis were found to be closely related and were well separated from strains whose heteroduplex types are less strongly associated with disease, suggesting a relationship between pathogenicity and phylogeny. PMID:10790104

  3. Partitioning the Relative Importance of Phylogeny and Environmental Conditions on Phytoplankton Fatty Acids.

    PubMed

    Galloway, Aaron W E; Winder, Monika

    2015-01-01

    Essential fatty acids (EFA), which are primarily generated by phytoplankton, limit growth and reproduction in diverse heterotrophs. The biochemical composition of phytoplankton is well-known to be governed both by phylogeny and environmental conditions. Nutrients, light, salinity, and temperature all affect both phytoplankton growth and fatty acid composition. However, the relative importance of taxonomy and environment on algal fatty acid content has yet to be comparatively quantified, thus inhibiting predictions of changes to phytoplankton food quality in response to global environmental change. We compiled 1145 published marine and freshwater phytoplankton fatty acid profiles, consisting of 208 species from six major taxonomic groups, cultured in a wide range of environmental conditions, and used a multivariate distance-based linear model to quantify the total variation explained by each variable. Our results show that taxonomic group accounts for 3-4 times more variation in phytoplankton fatty acids than the most important growth condition variables. The results underscore that environmental conditions clearly affect phytoplankton fatty acid profiles, but also show that conditions account for relatively low variation compared to phylogeny. This suggests that the underlying mechanism determining basal food quality in aquatic habitats is primarily phytoplankton community composition, and allows for prediction of environmental-scale EFA dynamics based on phytoplankton community data. We used the compiled dataset to calculate seasonal dynamics of long-chain EFA (LCEFA; ≥C20 ɷ-3 and ɷ-6 polyunsaturated fatty acid) concentrations and ɷ-3:ɷ-6 EFA ratios in Lake Washington using a multi-decadal phytoplankton community time series. These analyses quantify temporal dynamics of algal-derived LCEFA and food quality in a freshwater ecosystem that has undergone large community changes as a result of shifting resource management practices, highlighting diatoms

  4. Partitioning the Relative Importance of Phylogeny and Environmental Conditions on Phytoplankton Fatty Acids

    PubMed Central

    Galloway, Aaron W. E.; Winder, Monika

    2015-01-01

    Essential fatty acids (EFA), which are primarily generated by phytoplankton, limit growth and reproduction in diverse heterotrophs. The biochemical composition of phytoplankton is well-known to be governed both by phylogeny and environmental conditions. Nutrients, light, salinity, and temperature all affect both phytoplankton growth and fatty acid composition. However, the relative importance of taxonomy and environment on algal fatty acid content has yet to be comparatively quantified, thus inhibiting predictions of changes to phytoplankton food quality in response to global environmental change. We compiled 1145 published marine and freshwater phytoplankton fatty acid profiles, consisting of 208 species from six major taxonomic groups, cultured in a wide range of environmental conditions, and used a multivariate distance-based linear model to quantify the total variation explained by each variable. Our results show that taxonomic group accounts for 3-4 times more variation in phytoplankton fatty acids than the most important growth condition variables. The results underscore that environmental conditions clearly affect phytoplankton fatty acid profiles, but also show that conditions account for relatively low variation compared to phylogeny. This suggests that the underlying mechanism determining basal food quality in aquatic habitats is primarily phytoplankton community composition, and allows for prediction of environmental-scale EFA dynamics based on phytoplankton community data. We used the compiled dataset to calculate seasonal dynamics of long-chain EFA (LCEFA; ≥C20 ɷ-3 and ɷ-6 polyunsaturated fatty acid) concentrations and ɷ-3:ɷ-6 EFA ratios in Lake Washington using a multi-decadal phytoplankton community time series. These analyses quantify temporal dynamics of algal-derived LCEFA and food quality in a freshwater ecosystem that has undergone large community changes as a result of shifting resource management practices, highlighting diatoms

  5. Local to regional scale industrial heavy metal pollution recorded in sediments of large freshwater lakes in central Europe (lakes Geneva and Lucerne) over the last centuries.

    PubMed

    Thevenon, Florian; Graham, Neil D; Chiaradia, Massimo; Arpagaus, Philippe; Wildi, Walter; Poté, John

    2011-12-15

    This research first focuses on the spatial and temporal patterns of heavy metals from contrasting environments (highly polluted to deepwater sites) of Lake Geneva. The mercury (Hg) and lead (Pb) records from two deepwater sites show that the heavy metal variations before the industrial period are primarily linked to natural weathering input of trace elements. By opposition, the discharge of industrial treated wastewaters into Vidy Bay of Lake Geneva during the second part of the 20th century, involved the sedimentation of highly metal-contaminated sediments in the area surrounding the WWTP outlet pipe discharge. Eventually, a new Pb isotope record of sediments from Lake Lucerne identifies the long-term increasing anthropogenic lead pollution after ca. 1500, probably due to the development of metallurgical activities during the High Middle Ages. These data furthermore allows to compare the recent anthropogenic sources of water pollution from three of the largest freshwater lakes of Western Europe (lakes Geneva, Lucerne, and Constance). High increases in Pb and Hg highlight the regional impact of industrial pollution after ca. 1750-1850, and the decrease of metal pollution in the 1980s due to the effects of remediation strategies such as the implementation of wastewater treatment plants (WWTPs). However, at all the studied sites, the recent metal concentrations remain higher than pre-industrial levels. Moreover, the local scale pollution data reveal two highly contaminated sites (>100 μg Pb/g dry weight sediment) by industrial activities, during the late-19th and early-20th centuries (Lake Lucerne) and during the second part of the 20th century (Vidy Bay of Lake Geneva). Overall, the regional scale pollution history inferred from the three large and deep perialpine lakes points out at the pollution of water systems by heavy metals during the last two centuries due to the discharge of industrial effluents. PMID:22047737

  6. Cosmic ray exposure ages of iron meteorites, complex irradiation and the constancy of cosmic ray flux in the past

    NASA Technical Reports Server (NTRS)

    Marti, K.; Lavielle, B.; Regnier, S.

    1984-01-01

    While previous calculations of potassium ages assumed a constant cosmic ray flux and a single stage (no change in size) exposure of iron meteorites, present calculations relaxed these constancy assumptions and the results reveal multistage irradiations for some 25% of the meteorites studied, implying multiple breakup in space. The distribution of exposure ages suggests several major collisions (based on chemical composition and structure), although the calibration of age scales is not yet complete. It is concluded that shielding-corrected (corrections which depend on size and position of sample) production rates are consistent for the age bracket of 300 to 900 years. These production rates differ in a systematic way from those calculated for present day fluxes of cosmic rays (such as obtained for the last few million years).

  7. Molecular phylogeny and a taxonomic proposal for the genus Streptococcus.

    PubMed

    Póntigo, F; Moraga, M; Flores, S V

    2015-01-01

    Alternative phylogenies for the genus Streptococcus have been proposed due to uncertainty about the among-species group relationships. Here, we performed a phylogenetic analysis of the genus Streptococcus, considering all the species groups and also the genomic data accumulated by other studies. Seventy-five species were subjected to a Bayesian phylogenetic analysis using sequences from eight genes (16S rRNA, rpoB, sodA, tuf, rnpB, gyrB, dnaJ, and recN). On the basis of our results, we propose a new Phylogeny for the genus, with special emphasis on the inter-species group level. This new phylogeny differs from those suggested previously. From topological and evolutionary distance criteria, we propose that gordonii, pluranimalium, and sobrinus should be considered as new species groups, in addition to the currently recognized groups of mutans, bovis, pyogenic, suis, mitis, and salivarius. PMID:26400318

  8. Diversity dynamics: molecular phylogenies need the fossil record.

    PubMed

    Quental, Tiago B; Marshall, Charles R

    2010-08-01

    Over the last two decades, new tools in the analysis of molecular phylogenies have enabled study of the diversification dynamics of living clades in the absence of information about extinct lineages. However, computer simulations and the fossil record show that the inability to access extinct lineages severely limits the inferences that can be drawn from molecular phylogenies. It appears that molecular phylogenies can tell us only when there have been changes in diversification rates, but are blind to the true diversity trajectories and rates of origination and extinction that have led to the species that are alive today. We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota. PMID:20646780

  9. Ontogeny tends to recapitulate phylogeny in digital organisms.

    PubMed

    Clune, Jeff; Pennock, Robert T; Ofria, Charles; Lenski, Richard E

    2012-09-01

    Biologists have long debated whether ontogeny recapitulates phylogeny and, if so, why. Two plausible explanations are that (i) changes to early developmental stages are selected against because they tend to disrupt later development and (ii) simpler structures often precede more complex ones in both ontogeny and phylogeny if the former serve as building blocks for the latter. It is difficult to test these hypotheses experimentally in natural systems, so we used a computational system that exhibits evolutionary dynamics. We observed that ontogeny does indeed recapitulate phylogeny; traits that arose earlier in a lineage's history also tended to be expressed earlier in the development of individuals. The relative complexity of traits contributed substantially to this correlation, but a significant tendency toward recapitulation remained even after accounting for trait complexity. This additional effect provides evidence that selection against developmental disruption also contributed to the conservation of early stages in development. PMID:22854085

  10. Are most species small? Not within species-level phylogenies.

    PubMed Central

    Orme, C David L; Isaac, Nick J B; Purvis, Andy

    2002-01-01

    The robust macro-ecological observation that there are more small-bodied species implies that small-bodied organisms have experienced elevated net rates of diversification. We investigate the role of body size in creating non-random differences in rates of cladogenesis using a set of 38 species-level phylogenies drawn from a range of animal groups. We use independent contrasts to explore the relationship between body size and species richness within individual phylogenies and across related sets of phylogenies. We also carry out a meta-analysis looking for associations between body size and species richness across the taxa. We find little evidence for increased cladogenesis among small-bodied organisms within taxa, and no evidence for any consistent differences between taxa. We explore possible explanations for the inconsistency of our findings with macro-ecological patterns. PMID:12065045

  11. [Summary of phylogeny in family Felidae of Carnivora].

    PubMed

    Wang, Jin-Feng; Zhang, Ya-Ping; Yu, Li

    2012-11-01

    Felidae (cats) is one of the strict carnivorous groups in the order Carnivora, many of which are most familiar and spectacular to us. They are the top predators in the world. Thirty-six of 37 living cat species are considered as either "endangered" or "threatened". The relationships among species of the family Felidae, which evolved recently and rapidly, are difficult to resolve, and have been the subject of debate. Construction of a reliable Felidae phylogeny will be of evolutionarily significance and conservation value. In this paper, we summarized phylogeny of Felidae, including cytological, morphological and molecular evidence, and pointed out the existing phylogenetic problems. This review is expected to guide future researches of Felidae phylogeny, and to lay a theoretic foundation for the protection of this animal group. PMID:23208134

  12. Feedback from horizontal cells to cones mediates color induction and may facilitate color constancy in rainbow trout.

    PubMed

    Sabbah, Shai; Zhu, Changhai; Hornsby, Mark A W; Kamermans, Maarten; Hawryshyn, Craig W

    2013-01-01

    Color vision is most beneficial when the visual system is color constant and can correct the excitations of photoreceptors for differences in environmental irradiance. A phenomenon related to color constancy is color induction, where the color of an object shifts away from the color of its surroundings. These two phenomena depend on chromatic spatial integration, which was suggested to originate at the feedback synapse from horizontal cells (HC) to cones. However, the exact retinal site was never determined. Using the electroretinogram and compound action potential recordings, we estimated the spectral sensitivity of the photoresponse of cones, the output of cones, and the optic nerve in rainbow trout. Recordings were performed before and following pharmacological inhibition of HC-cone feedback, and were repeated under two colored backgrounds to estimate the efficiency of color induction. No color induction could be detected in the photoresponse of cones. However, the efficiency of color induction in the cone output and optic nerve was substantial, with the efficiency in the optic nerve being significantly higher than in the cone output. We found that the efficiency of color induction in the cone output and optic nerve decreased significantly with the inhibition of HC-cone feedback. Therefore, our findings suggest not only that color induction originates as a result of HC-cone feedback, but also that this effect of HC-cone feedback is further amplified at downstream retinal elements, possibly through feedback mechanisms at the inner plexiform layer. This study provides evidence for an important role of HC-cone feedback in mediating color induction, and therefore, likely also in mediating color constancy. PMID:23750282

  13. The evolutionary phylogeny of the oomycete "fungi".

    PubMed

    Beakes, Gordon W; Glockling, Sally L; Sekimoto, Satoshi

    2012-01-01

    Molecular sequencing has helped resolve the phylogenetic relationships amongst the diverse groups of algal, fungal-like and protist organisms that constitute the Chromalveolate "superkingdom" clade. It is thought that the whole clade evolved from a photosynthetic ancestor and that there have been at least three independent plastid losses during their evolutionary history. The fungal-like oomycetes and hyphochytrids, together with the marine flagellates Pirsonia and Developayella, form part of the clade defined by Cavalier-Smith and Chao (2006) as the phylum "Pseudofungi", which is a sister to the photosynthetic chromistan algae (phylum Ochrophyta). Within the oomycetes, a number of predominantly marine holocarpic genera appear to diverge before the main "saprolegnian" and "peronosporalean" lines, into which all oomycetes had been traditionally placed. It is now clear that oomycetes have their evolutionary roots in the sea. The earliest diverging oomycete genera so far documented, Eurychasma and Haptoglossa, are both obligate parasites that show a high degree of complexity and sophistication in their host parasite interactions and infection structures. Key morphological and cytological features of the oomycetes will be reviewed in the context of our revised understanding of their likely phylogeny. Recent genomic studies have revealed a number of intriguing similarities in host-pathogen interactions between the oomycetes with their distant apicocomplexan cousins. Therefore, the earlier view that oomycetes evolved from the largely saprotrophic "saprolegnian line" is not supported and current evidence shows these organisms evolved from simple holocarpic marine parasites. Both the hyphal-like pattern of growth and the acquisition of oogamous sexual reproduction probably developed largely after the migration of these organisms from the sea to land. PMID:21424613

  14. THE RETICULATING PHYLOGENY OF ISLAND BIOGEOGRAPHY THEORY

    PubMed Central

    Lomolino, Mark V.; Brown, James H.

    2010-01-01

    Biogeographers study all patterns in the geographic variation of life, from the spatial variation in genetic and physiological characteristics of cells and individuals, to the diversity and dynamics of biological communities among continental biotas or across oceanic archipelagoes. The field of island biogeography, in particular, has provided some genuinely transformative insights for the biological sciences, especially ecology and evolutionary biology. Our purpose here is to review the historical development of island biogeography theory during the 20th century by identifying the common threads that run through four sets of contributions made during this period, including those by Eugene Gordon Munroe (1948, 1953), Edward O. Wilson (1959, 1961), Frank W. Preston (1962a,b), and the seminal collaborations between Wilson and Robert H. MacArthur (1963, 1967), which revolutionized the field and served as its paradigm for nearly four decades. This epistemological account not only reviews the intriguing history of island theory, but it also includes fundamental lessons for advancing science through transformative integrations. Indeed, as is likely the case with many disciplines, island theory advanced not as a simple accumulation of facts and an orderly succession of theories and paradigms, but rather in fits and starts through a reticulating phylogeny of ideas and alternating periods of specialization and reintegration. We conclude this review with a summary of the salient features of this scientific revolution in the context of Kuhn’s structure, which strongly influenced theoretical advances during this period, and we then describe some of the fundamental assumptions and tenets of an emerging reintegration of island biogeography theory. PMID:20039528

  15. A Mitogenomic Phylogeny of Living Primates

    PubMed Central

    Finstermeier, Knut; Zinner, Dietmar; Brameier, Markus; Meyer, Matthias; Kreuz, Eva; Hofreiter, Michael; Roos, Christian

    2013-01-01

    Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels. PMID:23874967

  16. The reticulating phylogeny of island biogeography theory.

    PubMed

    Lomolino, Mark V; Brown, James H

    2009-12-01

    Biogeographers study all patterns in the geographic variation of life, from the spatial variation in genetic and physiological characteristics of cells and individuals, to the diversity and dynamics of biological communities among continental biotas or across oceanic archipelagoes. The field of island biogeography, in particular, has provided some genuinely transformative insights for the biological sciences, especially ecology and evolutionary biology. Our purpose here is to review the historical development of island biogeography theory during the 20th century by identifying the common threads that run through four sets of contributions made during this period, including those by Eugene Gordon Munroe (1948, 1953), Edward O. Wilson (1959, 1961), Frank W. Preston (1962a,b), and the seminal collaborations between Wilson and Robert H. MacArthur (1963, 1967), which revolutionized the field and served as its paradigm for nearly four decades. This epistemological account not only reviews the intriguing history of island theory, but it also includes fundamental lessons for advancing science through transformative integrations. Indeed, as is likely the case with many disciplines, island theory advanced not as a simple accumulation of facts and an orderly succession of theories and paradigms, but rather in fits and starts through a reticulating phylogeny of ideas and alternating periods of specialization and reintegration. We conclude this review with a summary of the salient features of this scientific revolution in the contest of Kuhn's structure, which strongly influenced theoretical advances during this period, and we then describe some of the fundamental assumptions and tenets of an emerging reintegration of island biogeography theory. PMID:20039528

  17. Phylogeny of culturable cyanobacteria from Brazilian mangroves.

    PubMed

    Silva, Caroline Souza Pamplona; Genuário, Diego Bonaldo; Vaz, Marcelo Gomes Marçal Vieira; Fiore, Marli Fátima

    2014-03-01

    The cyanobacterial community from Brazilian mangrove ecosystems was examined using a culture-dependent method. Fifty cyanobacterial strains were isolated from soil, water and periphytic samples collected from Cardoso Island and Bertioga mangroves using specific cyanobacterial culture media. Unicellular, homocytous and heterocytous morphotypes were recovered, representing five orders, seven families and eight genera (Synechococcus, Cyanobium, Cyanobacterium, Chlorogloea, Leptolyngbya, Phormidium, Nostoc and Microchaete). All of these novel mangrove strains had their 16S rRNA gene sequenced and BLAST analysis revealed sequence identities ranging from 92.5 to 99.7% when they were compared with other strains available in GenBank. The results showed a high variability of the 16S rRNA gene sequences among the genotypes that was not associated with the morphologies observed. Phylogenetic analyses showed several branches formed exclusively by some of these novel 16S rRNA gene sequences. BLAST and phylogeny analyses allowed for the identification of Nodosilinea and Oxynema strains, genera already known to exhibit poor morphological diacritic traits. In addition, several Nostoc and Leptolyngbya morphotypes of the mangrove strains may represent new generic entities, as they were distantly affiliated with true genera clades. The presence of non-ribosomal peptide synthetase, polyketide synthase, microcystin and saxitoxin genes were detected in 20.5%, 100%, 37.5% and 33.3%, respectively, of the 44 tested isolates. A total of 134 organic extracts obtained from 44 strains were tested against microorganisms, and 26% of the extracts showed some antimicrobial activity. This is the first polyphasic study of cultured cyanobacteria from Brazilian mangrove ecosystems using morphological, genetic and biological approaches. PMID:24461713

  18. Efficient Recycled Algorithms for Quantitative Trait Models on Phylogenies

    PubMed Central

    Hiscott, Gordon; Fox, Colin; Parry, Matthew; Bryant, David

    2016-01-01

    We present an efficient and flexible method for computing likelihoods for phenotypic traits on a phylogeny. The method does not resort to Monte Carlo computation but instead blends Felsenstein’s discrete character pruning algorithm with methods for numerical quadrature. It is not limited to Gaussian models and adapts readily to model uncertainty in the observed trait values. We demonstrate the framework by developing efficient algorithms for likelihood calculation and ancestral state reconstruction under Wright’s threshold model, applying our methods to a data set of trait data for extrafloral nectaries across a phylogeny of 839 Fabales species. PMID:27056412

  19. Efficient Recycled Algorithms for Quantitative Trait Models on Phylogenies.

    PubMed

    Hiscott, Gordon; Fox, Colin; Parry, Matthew; Bryant, David

    2016-01-01

    We present an efficient and flexible method for computing likelihoods for phenotypic traits on a phylogeny. The method does not resort to Monte Carlo computation but instead blends Felsenstein's discrete character pruning algorithm with methods for numerical quadrature. It is not limited to Gaussian models and adapts readily to model uncertainty in the observed trait values. We demonstrate the framework by developing efficient algorithms for likelihood calculation and ancestral state reconstruction under Wright's threshold model, applying our methods to a data set of trait data for extrafloral nectaries across a phylogeny of 839 Fabales species. PMID:27056412

  20. A molecular phylogeny of aquatic gastropods provides a new perspective on biogeographic history of the Snake River Region.

    PubMed

    Hershler, Robert; Liu, Hsiu-Ping

    2004-09-01

    Mitochondrial DNA sequences of aquatic gastropods of the subgenus Pyrgulopsis (Natricola) were analyzed to test a commonly accepted hypothesis concerning the early history of the Snake River in the northwestern US. Distributions of Natricola and other regional biota were previously used to infer that the Snake River flowed to the Pacific through southeastern Oregon and northern California during the Neogene prior to its capture by the Columbia River in the late Pliocene (2 Ma). A molecular phylogeny based on partial sequences of COI and NDI (1149 bp) indicates that the Natricola clade is restricted to the modern Snake-Columbia River Basin and the Oregon Lakes region whereas northern California populations previously assigned to this subgenus belong to other lineages. The Natricola clade is not deeply subdivided into Oregon Lakes and Snake River Basin units consistent with late Pliocene fragmentation of the hypothesized paleodrainage, but instead is shallowly structured and contains multiple transitions among these two geographic areas. The strongly supported sister relationship between Natricola and a species from northwest Nevada (P. imperialis) is consistent with a recent proposal that the ancestral Snake River did not flow through southeast Oregon but instead flowed south to the Humboldt River. Within the context of this hypothesis, the multiple transitions between the Snake River Basin and the Oregon Lakes region that occurred within Natricola may be attributed to a late Pleistocene connection between these areas that was unrelated to the early course of the Snake River. PMID:15288067

  1. Longevity of Lake Superior lake trout

    USGS Publications Warehouse

    Schram, Stephen T.; Fabrizio, Mary C.

    1998-01-01

    The age structure of mature lake trout Salvelinus namaycush from the Wisconsin waters of Lake Superior increased following a population recovery that has taken place since the 1960s. As the population aged, it became apparent that scales were unreliable aging structures. Beginning in 1986, we examined both scale and sagittal otolith ages from tagged fish with a known period at liberty. We found large discrepancies in scale and sagittal otolith ages of mature fish, such that scale ages were biased low. We estimated lake trout living up to 42 years, which is greater than previously reported from Lake Superior. Investigators studying lake trout population dynamics in the Great Lakes should be aware that lake trout can live longer than previously thought.

  2. Lake Volta, Ghana

    NASA Technical Reports Server (NTRS)

    2002-01-01

    This true-color image of Lake Volta in Ghana was acquired March 31, 2002 by the Moderate Resolution Imaging Spectroradiometer (MODIS). Lake Volta is one of the world's largest artificially created lakes. Lake Volta is actually a reservoir formed from the damming of the Volta River, and extends 250 miles north of the Akosombo Dam. The lake covers an area of 8,482 square km. Credit: Jacques Descloitres, MODIS Land Rapid Response Team, NASA/GSFC

  3. Use of Whole Genome Sequence Data To Infer Baculovirus Phylogeny

    PubMed Central

    Herniou, Elisabeth A.; Luque, Teresa; Chen, Xinwen; Vlak, Just M.; Winstanley, Doreen; Cory, Jennifer S.; O'Reilly, David R.

    2001-01-01

    Several phylogenetic methods based on whole genome sequence data were evaluated using data from nine complete baculovirus genomes. The utility of three independent character sets was assessed. The first data set comprised the sequences of the 63 genes common to these viruses. The second set of characters was based on gene order, and phylogenies were inferred using both breakpoint distance analysis and a novel method developed here, termed neighbor pair analysis. The third set recorded gene content by scoring gene presence or absence in each genome. All three data sets yielded phylogenies supporting the separation of the Nucleopolyhedrovirus (NPV) and Granulovirus (GV) genera, the division of the NPVs into groups I and II, and species relationships within group I NPVs. Generation of phylogenies based on the combined sequences of all 63 shared genes proved to be the most effective approach to resolving the relationships among the group II NPVs and the GVs. The history of gene acquisitions and losses that have accompanied baculovirus diversification was visualized by mapping the gene content data onto the phylogenetic tree. This analysis highlighted the fluid nature of baculovirus genomes, with evidence of frequent genome rearrangements and multiple gene content changes during their evolution. Of more than 416 genes identified in the genomes analyzed, only 63 are present in all nine genomes, and 200 genes are found only in a single genome. Despite this fluidity, the whole genome-based methods we describe are sufficiently powerful to recover the underlying phylogeny of the viruses. PMID:11483757

  4. Phylogeny and classification of tribe Aedini (Diptera: Culicidae).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylogeny and classification of tribe Aedini are delineated based on a cladistic analysis of 336 characters from eggs, fourth-instar larvae, pupae, adult females and males, and immature stage habitat coded for 270 exemplar species, including an outgroup of four species from different non-aedine ...

  5. Phylogeny and adaptation shape the teeth of insular mice.

    PubMed

    Ledevin, Ronan; Chevret, Pascale; Ganem, Guila; Britton-Davidian, Janice; Hardouin, Emilie A; Chapuis, Jean-Louis; Pisanu, Benoit; da Luz Mathias, Maria; Schlager, Stefan; Auffray, Jean-Christophe; Renaud, Sabrina

    2016-02-10

    By accompanying human travels since prehistorical times, the house mouse dispersed widely throughout the world, and colonized many islands. The origin of the travellers determined the phylogenetic source of the insular mice, which encountered diverse ecological and environmental conditions on the various islands. Insular mice are thus an exceptional model to disentangle the relative role of phylogeny, ecology and climate in evolution. Molar shape is known to vary according to phylogeny and to respond to adaptation. Using for the first time a three-dimensional geometric morphometric approach, compared with a classical two-dimensional quantification, the relative effects of size variation, phylogeny, climate and ecology were investigated on molar shape diversity across a variety of islands. Phylogeny emerged as the factor of prime importance in shaping the molar. Changes in competition level, mostly driven by the presence or absence of the wood mouse on the different islands, appeared as the second most important effect. Climate and size differences accounted for slight shape variation. This evidences a balanced role of random differentiation related to history of colonization, and of adaptation possibly related to resource exploitation. PMID:26842576

  6. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Next generation sequencing is helping to solve the data insufficiency problem hindering well-resolved dominant gene phylogenies. We used Roche 454 technology to obtain DNA sequences from 93 nuclear orthologs, dispersed throughout all linkage groups of Daucus. Of these 93 orthologs, ten were designed...

  7. Ecological interaction and phylogeny, studying functionality on composed networks

    NASA Astrophysics Data System (ADS)

    Cruz, Claudia P. T.; Fonseca, Carlos Roberto; Corso, Gilberto

    2012-02-01

    We study a class of composed networks that are formed by two tree networks, TP and TA, whose end points touch each other through a bipartite network BPA. We explore this network using a functional approach. We are interested in how much the topology, or the structure, of TX (X=A or P) determines the links of BPA. This composed structure is a useful model in evolutionary biology, where TP and TA are the phylogenetic trees of plants and animals that interact in an ecological community. We make use of ecological networks of dispersion of fruits, which are formed by frugivorous animals and plants with fruits; the animals, usually birds, eat fruits and disperse their seeds. We analyse how the phylogeny of TX determines or is correlated with BPA using a Monte Carlo approach. We use the phylogenetic distance among elements that interact with a given species to construct an index κ that quantifies the influence of TX over BPA. The algorithm is based on the assumption that interaction matrices that follows a phylogeny of TX have a total phylogenetic distance smaller than the average distance of an ensemble of Monte Carlo realisations. We find that the effect of phylogeny of animal species is more pronounced in the ecological matrix than plant phylogeny.

  8. Ontogeny and Phylogeny from an Epigenetic Point of View.

    ERIC Educational Resources Information Center

    Lovtrup, Soren

    1984-01-01

    The correlation between ontogeny and phylogeny is analyzed through the discussion of four theories on the reality, history, epigenetic, and ecological aspects of the mechanism of evolution. Also discussed are historical and creative aspects of evolution and three epigenetic mechanisms instantiated in the case of the amphibian embryo. (Author/RH)

  9. Multiple Nuclear Ortholog (COSII) Phylogeny of Wild Potatoes and Tomatoes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined more than 80 c...

  10. Cytochrome b and Bayesian inference of whale phylogeny.

    PubMed

    May-Collado, Laura; Agnarsson, Ingi

    2006-02-01

    In the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many novel and provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and the collection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now become benchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditional views. That major conflicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim specifically to resolve higher-level conflicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecular study to date has included more than 33 cetaceans. More detailed molecular phylogenies will provide better tools for evolutionary studies. Until more genes are available for a high number of taxa, can we rely on readily available single gene mitochondrial data? Here, we estimate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based on the recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the first time supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly of all but one family level taxa within Cetacea, and most recently proposed super- and subfamilies. In contrast, parsimony never recovered all benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea to date and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggest that dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction. PMID:16325433

  11. Influence of climate variability on whitefish (Coregonus lavaretus) year-class strength in a deep, warm monomictic lake.

    PubMed

    Straile, Dietmar; Eckmann, Reiner; Jüngling, Tobias; Thomas, Gregor; Löffler, Herbert

    2007-03-01

    The year-class strength (YCS) of Blaufelchen (Coregonus lavaretus) in deep Upper Lake Constance was analysed for a 52-year period, from 1947 to 1998. Despite strong anthropogenic influences on the species' population dynamics due to cultural eutrophication and oligotrophication, intense fishing, and large-scale stocking, the influence of climate variability associated with the North Atlantic Oscillation (NAO) is apparent in the data set. This influence is significant although large-scale stocking of cold-bred larvae was performed to avoid a mismatch of larvae with their food. The importance of stocking on YCS, however, is unclear and was only detectable when analysing a subset of the data. In addition to climate variability a yet unidentified factor related to zooplankton suitability as food for fish larvae, and density-dependent mortality probably related to cannibalism do significantly influence YCS. The NAO seemed to influence YCS twofold, through temperature effects on egg development time and on larval growth rate. The first of these two mechanisms is related to the NAO via a time lag of 1 year due to the specific mixing dynamics of warm monomictic Lake Constance. Hence, a warm winter in the year before spawning results in earlier hatching of larvae, that is, hatching is decoupled from the actual meteorological conditions. This should make the larvae very prone to mismatch the dynamics of their food. However, we found no evidence for such a mismatch in this 52-year data set. PMID:17109176

  12. Investigation of color constancy in 4.5-month-old infants under a strict control of luminance contrast for individual participants.

    PubMed

    Yang, Jiale; Kanazawa, So; Yamaguchi, Masami K; Kuriki, Ichiro

    2013-05-01

    The current study examined color constancy in infants using a familiarization paradigm. We first obtained isoluminance in each infant as defined by the minimum motion paradigm and used these data to control the luminance of stimuli in the main experiments. In the familiarization phase of the main experiment, two identical smiling face patterns were presented side by side in surrounding patches of various colors, presented on a computer-controlled display. The colors in the stimuli simulated the chromaticity of color chips (OSA uniform color scale) under a certain illuminant. The chromaticity of the whole pattern was changed to simulate illuminant color changes in the test phase except for one of the smiling face patterns that preserved its chromaticity and luminance. If infants had color constancy, they would perceive the face without any change in the chromaticity and luminance as a novel object surface and would show preference for it. Two types of illuminant changes were applied, from 6500 to 10,000 K and from 6500 to 4500 K, in correlated color temperature. The luminance contrast between the background and the face patterns remained constant across the illuminant changes. Our results showed that 4.5-month-old infants preferred the pattern that did not change its chromaticity under both types of illuminant color changes. This finding suggests that 4.5-month-olds may have color constancy under the strict control of luminance contrast. PMID:23419408

  13. Lake Nasser and Toshka Lakes, Egypt

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Lake Nasser (center) and the Toshka Lakes (center left) glow emerald green and black in this MODIS true-color image acquired March 8, 2002. Located on and near the border of Egypt and Norther Sudan, these lakes are an oasis of water in between the Nubian (lower right) and Libyan Deserts (upper left). Also visible are the Red Sea (in the upper right) and the Nile River (running north from Lake Nasser). Credit: Jacques Descloitres, MODIS Land Rapid Response Team, NASA/GSFC

  14. Guide for establishing and maintaining a calibration-constancy intercomparison system for microwave-oven-compliance survey instruments (revised)

    SciTech Connect

    Not Available

    1988-03-01

    Public Law 90-602, the Radiation Control for Health and Safety Act of 1968 (the Act), directs the Department of Health and Human Services to evaluate production-testing and quality-control programs carried out by the industry to assure adequacy of safeguards against hazardous electronic-product radiation and to assure that the products comply with performance standards. Under the Act, manufacturers of microwave ovens, a product listed under 21 CFR 1002.61, are required to certify that their microwave ovens are in compliance with all of the applicable provisions of the Federal Performance Standard for Microwave Ovens, 21 CFR 1030.10. In order to comply with microwave-emission-level provisions of the performance standard, manufacturers must use properly calibrated microwave-leakage measurement instruments in their production and quality control testing programs. This document was prepared in order to assist the microwave oven manufacturers in establishing and maintaining a calibration-constancy intercomparison system for compliance survey instruments and replaces guidance previously issued by the Center for Devices and Radiological Health (the Center).

  15. On the constancy of solar particle fluxes from track, thermoluminescence and solar wind measurements in lunar rocks

    NASA Technical Reports Server (NTRS)

    Zinner, E.

    1980-01-01

    Evidence contained within lunar rocks concerning possible variations in solar activity over the last 1 to 2 million years is reviewed. The effects of solar wind particles, which are implanted at shallow depths, solar flare protons, which produce thermoluminescence as well as stable and radionuclides, and solar flare heavy nuclei, which produce tracks, are considered, and the quality and limitations of nuclear tracks measurements as indicators of solar flare flux histories are discussed. Methods used for the determination of the solar flare track production rate, which must be known in order to measure lunar rock surface exposure times, are compared, and it is concluded that most of the evidence favors the rate obtained by Blanford et al. (1975). Information on the constancy of the solar flare particle flux obtained by comparison of the effects of different surface phenomena with solar particle effects is then illustrated for the cases of comparisons between solar flare tracks and microcrater densities, solar flare particle fluxes measured over different periods, and comparisons of the solar flare track production rate with the solar wind flux and microcratering rate. It is noted that these studies provide no evidence for a change in solar particle flux by more than a factor of two over the last 10,000 to 1 million years, or for a change in the solar flare Fe/H ratio in the last 2 million years.

  16. Constancy of local spread rates for buffelgrass (Pennisetum ciliare L.) in the Arizona Upland of the Sonoran Desert

    USGS Publications Warehouse

    Olsson, Aaryn D.; Betancourt, Julio L.; Crimmins, Michael A.; Marsh, Stuart E.

    2012-01-01

    In North American deserts, grass invasions threaten native vegetation via competition and altered fire regimes. Accurate prediction and successful mitigation of these invasions hinge on estimation of spread rates and their degree of constancy in time and space. We used high-resolution aerial photographs from 11 sites in the Santa Catalina Mountains, southern Arizona to reconstruct the spread of buffelgrass (Pennisetum ciliare), a C4 perennial bunchgrass, since 1980. The total area infested was fit to a logistic model and residuals of the model were compared to climatic factors of the corresponding and lagged time periods. Infestations grew from small colonizing patches in the 1980s to 66 ha in 2008, doubling every 2.26–7.04 years since 1988. Although buffelgrass germination, establishment and distribution are favored by wet summers and warm winters, climate variables did not predict spread rates. Buffelgrass has grown at a constant rate, at least since 1988, when much of its expansion took place. In the study area, minimum requirements are met almost every year for germination and reproduction, establishing a consistent baseline for spread that manifests as a constant spread rate.

  17. Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters

    PubMed Central

    Comeau, André M.; Harding, Tommy; Galand, Pierre E.; Vincent, Warwick F.; Lovejoy, Connie

    2012-01-01

    Meromictic lakes are useful biogeochemical models because of their stratified chemical gradients and separation of redox reactions down the water column. Perennially ice-covered meromictic lakes are particularly stable, with long term constancy in their density profiles. Here we sampled Lake A, a deep meromictic lake at latitude 83°N in High Arctic Canada. Sampling was before (May) and after (August) an unusual ice-out event during the warm 2008 summer. We determined the bacterial and archaeal community composition by high-throughput 16S rRNA gene tag-pyrosequencing. Both prokaryote communities were stratified by depth and the Bacteria differed between dates, indicating locally driven selection processes. We matched taxa to known taxon-specific biogeochemical functions and found a close correspondence between the depth of functional specialists and chemical gradients. These results indicate a rich microbial diversity despite the extreme location, with pronounced vertical structure in taxonomic and potential functional composition, and with community shifts during ice-out. PMID:22930670

  18. Lakes Ecosystem Services Online

    EPA Science Inventory

    Northeastern lakes provide valuable ecosystem services that benefit residents and visitors and are increasingly important for provisioning of recreational opportunities and amenities. Concurrently, however, population growth threatens lakes by, for instance, increasing nutrient ...

  19. Utah: Salt Lake Region

    Atmospheric Science Data Center

    2014-05-15

    article title:  Winter and Summer Views of the Salt Lake Region     View Larger Image Magnificent views of the region surrounding Salt Lake City, Utah are captured in these winter and summer images from the ...

  20. Lake trout rehabilitation in Lake Ontario

    USGS Publications Warehouse

    Elrod, Joseph H.; O'Gorman, Robert; Schneider, Clifford P.; Eckert, Thomas H.; Schaner, Ted; Bowlby, James N.; Schleen, Larry P.

    1995-01-01

    Attempts to maintain the native lake trout (Salvelinus namaycush) population in Lake Ontario by stocking fry failed and the species was extirpated by the 1950s. Hatchery fish stocked in the 1960s did not live to maturity because of sea lamprey (Petromyzon marinus) predation and incidental commercial harvest. Suppression of sea lampreys began with larvicide treatments of Lake Ontario tributaries in 1971 and was enhanced when the tributaries of Oneida Lake and Lake Erie were treated in the 1980s. Annual stocking of hatchery fish was resumed with the 1972 year class and peaked at about 1.8 million yearlings and 0.3 million fingerlings from the 1985–1990 year classes. Survival of stocked yearlings declined over 50% in the 1980 s and was negatively correlated with the abundance of lake trout > 550 mm long (r = −0.91, P < 0.01, n = 12). A slot length limit imposed by the State of New York for the 1988 fishing season reduced angler harvest. Angler harvest in Canadian waters was 3 times higher in eastern Lake Ontario than in western Lake Ontario. For the 1977–1984 year classes, mean annual survival rate of lake trout age 6 and older was 0.45 (range: 0.35–0.56). In U.S. waters during 1985–1992, the total number of lake trout harvested by anglers was about 2.4 times greater than that killed by sea lampreys. The number of unmarked lake trout < 250 mm long in trawl catches in 1978–1992 was not different from that expected due to loss of marks and failure to apply marks at the hatchery, and suggested that recruitment of naturally-produced fish was nil. However, many of the obstacles which may have impeded lake trout rehabilitation in Lake Ontario during the 1980s are slowly being removed, and there are signs of a general ecosystem recovery. Significant recruitment of naturally produced lake trout by the year 2000, one interim objective of the rehabilitation plan for the Lake, may be achieved.

  1. Toward image phylogeny forests: automatically recovering semantically similar image relationships.

    PubMed

    Dias, Zanoni; Goldenstein, Siome; Rocha, Anderson

    2013-09-10

    In the past few years, several near-duplicate detection methods appeared in the literature to identify the cohabiting versions of a given document online. Following this trend, there are some initial attempts to go beyond the detection task, and look into the structure of evolution within a set of related images overtime. In this paper, we aim at automatically identify the structure of relationships underlying the images, correctly reconstruct their past history and ancestry information, and group them in distinct trees of processing history. We introduce a new algorithm that automatically handles sets of images comprising different related images, and outputs the phylogeny trees (also known as a forest) associated with them. Image phylogeny algorithms have many applications such as finding the first image within a set posted online (useful for tracking copyright infringement perpetrators), hint at child pornography content creators, and narrowing down a list of suspects for online harassment using photographs. PMID:23890634

  2. Congruence of morphologically-defined genera with molecular phylogenies

    PubMed Central

    Jablonski, David; Finarelli, John A.

    2009-01-01

    Morphologically-defined mammalian and molluscan genera (herein “morphogenera”) are significantly more likely to be monophyletic relative to molecular phylogenies than random, under 3 different models of expected monophyly rates: ≈63% of 425 surveyed morphogenera are monophyletic and 19% are polyphyletic, although certain groups appear to be problematic (e.g., nonmarine, unionoid bivalves). Compiled nonmonophyly rates are probably extreme values, because molecular analyses have focused on “problem” taxa, and molecular topologies (treated herein as error-free) contain contradictory groupings across analyses for 10% of molluscan morphogenera and 37% of mammalian morphogenera. Both body size and geographic range, 2 key macroevolutionary and macroecological variables, show significant rank correlations between values for morphogenera and molecularly-defined clades, even when strictly monophyletic morphogenera are excluded from analyses. Thus, although morphogenera can be imperfect reflections of phylogeny, large-scale statistical treatments of diversity dynamics or macroevolutionary variables in time and space are unlikely to be misleading. PMID:19416868

  3. Phylogeny and biogeography of hogfishes and allies (Bodianus, Labridae).

    PubMed

    Santini, Francesco; Sorenson, Laurie; Alfaro, Michael E

    2016-06-01

    Bodianus wrasses comprise one of the most diverse genera of labrids. Also known as hogfishes due to the presence of a large pig-like snout, Bodianus species are found in warm waters across the Pacific, Atlantic and Indian Oceans. To this date no densely sampled molecular phylogeny is available for this group, and a single morphological study did not include two genera (Clepticus and Semicossyphus) that have been shown to belong within hogfishes by molecular studies. Our study produced the first multi-locus molecular phylogeny of Bodianus species, and corroborated the non-monophyly of this group without the inclusion of the Creole wrasse (Clepticus) and the sheepheads (Semicossyphus). We further showed that hogfishes and allies started to radiate during the Early Miocene, ∼20Ma, and that while this group originated in the Indo-western and South-western Pacific, it experienced multiple episodes during which it successfully invaded different geographic regions and/or ocean basins. PMID:26944013

  4. Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)

    PubMed Central

    Wang, Aisuo; Ash, Gavin J.

    2015-01-01

    Fifty complete Bacillus genome sequences and associated plasmids were compared using the “feature frequency profile” (FFP) method. The resulting whole-genome phylogeny supports the placement of three Bacillus species (B. thuringiensis, B. anthracis and B. cereus) as a single clade. The monophyletic status of B. anthracis was strongly supported by the analysis. FFP proved to be more effective in inferring the phylogeny of Bacillus than methods based on single gene sequences [16s rRNA gene, GryB (gyrase subunit B) and AroE (shikimate-5-dehydrogenase)] analyses. The findings of FFP analysis were verified using kSNP v2 (alignment-free sequence analysis method) and Harvest suite (core genome sequence alignment method).

  5. Lake Layers: Stratification.

    ERIC Educational Resources Information Center

    Brothers, Chris; And Others

    This teacher guide and student workbook set contains two learning activities, designed for fifth through ninth grade students, that concentrate on lake stratification and water quality. In the activities students model the seasonal temperature changes that occur in temperate lakes and observe the resulting stratification of lake waters. Students…

  6. Great Lakes: Chemical Monitoring

    ERIC Educational Resources Information Center

    Delfino, Joseph J.

    1976-01-01

    The Tenth Great Lakes Regional Meeting of the American Chemical Society met to assess current Chemical Research activity in the Great Lakes Basin, and addressed to the various aspects of the theme, Chemistry of the Great Lakes. Research areas reviewed included watershed studies, atmospheric and aquatic studies, and sediment studies. (BT)

  7. Great Minds? Great Lakes!

    ERIC Educational Resources Information Center

    Environmental Protection Agency, Chicago, IL. Great Lakes National Program Office.

    This book contains lesson plans that provide an integrated approach to incorporating Great Lakes environmental issues into elementary subjects. The book is divided into three subject areas: (1) History, which includes the origins of the Great Lakes, Great Lakes people, and shipwrecks; (2) Social Studies, which covers government, acid rain as a…

  8. A Killer Lake

    ERIC Educational Resources Information Center

    Horvath, Thomas

    2005-01-01

    In 1986, Lake Nyos, a volcanic lake in Cameroon, released a huge amount of carbon dioxide gas, killing over 1,700 people in the surrounding area. This case study, developed for use in a limnology or aquatic biology course, explores that event, introducing students to concepts relating to lake formation, thermal stratification, and dissolved gases.…

  9. Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification.

    PubMed

    Gundersen, D E; Lee, I M; Rehner, S A; Davis, R E; Kingsbury, D T

    1994-09-01

    A global phylogenetic analysis using parsimony of 16S rRNA gene sequences from 46 mollicutes, 19 mycoplasmalike organisms (MLOs) (new trivial name, phytoplasmas), and several related bacteria placed the MLOs definitively among the members of the class Mollicutes and revealed that MLOs form a large discrete monophyletic clade, paraphyletic to the Acholeplasma species, within the Anaeroplasma clade. Within the MLO clade resolved in the global mollicutes phylogeny and a comprehensive MLO phylogeny derived by parsimony analyses of 16S rRNA gene sequences from 30 diverse MLOs representative of nearly all known distinct MLO groups, five major phylogenetic groups with a total of 11 distinct subclades (monophyletic groups or taxa) could be recognized. These MLO subclades (roman numerals) and designated type strains were as follows: i, Maryland aster yellows AY1; ii, apple proliferation AP-A; iii, peanut witches'-broom PnWB; iv, Canada peach X CX; v, rice yellow dwarf RYD; vi, pigeon pea witches'-broom PPWB; vii, palm lethal yellowing LY; viii, ash yellows AshY; ix, clover proliferation CP; x, elm yellows EY; and xi, loofah witches'-broom LfWB. The designations of subclades and their phylogenetic positions within the MLO clade were supported by a congruent phylogeny derived by parsimony analyses of ribosomal protein L22 gene sequences from most representative MLOs. On the basis of the phylogenies inferred in the present study, we propose that MLOs should be represented taxonomically at the minimal level of genus and that each phylogenetically distinct MLO subclade identified should represent at least a distinct species under this new genus. PMID:8071198

  10. Multigene phylogeny of the red algal subclass Nemaliophycidae.

    PubMed

    Lam, Daryl W; Verbruggen, Heroen; Saunders, Gary W; Vis, Morgan L

    2016-01-01

    The red algae (Rhodophyta) are a lineage of primary endosymbionts whose ancestors represent some of the first photosynthetic eukaryotes on the planet. They primarily inhabit marine ecosystems, with only ∼5% of species found in freshwater systems. The subclass Nemaliophycidae is very diverse in ecological and life history features and therefore a useful model to study these traits, but the phylogenetic relationships among the orders are, for the most part, poorly resolved. To elucidate the phylogeny of the Nemaliophycidae, we constructed a nine-gene dataset comprised of nuclear, plastid, and mitochondrial markers for 67 red algal specimens. The resulting maximum likelihood (ML) phylogeny confirmed the monophyly of all orders. The sister relationship of the Acrochaetiales and Palmariales received high support and the relationship of the Balliales with Balbianiales and Entwisleiales with Colaconematales was moderately supported. The Nemaliales, Entwisleiales, Colaconematales, Palmariales and Acrochaetiales formed a highly supported clade. Unfortunately, all other relationships among the orders had low bootstrap support. Although the ML analysis did not resolve many of the relationships, further analyses suggested that a resolution is possible. A Phycas analysis supported a dichotomously branching tree and Bayesian analysis showed a similar topology with all relationships highly supported. Simulations extrapolating the number of nucleotide characters beyond the current size of the dataset suggested that most nodes in the phylogeny would be resolved if more data become available. Phylogenomic approaches will be necessary to provide a well-supported phylogeny of this subclass with all relationships resolved such that the evolution of freshwater species from marine ancestors as well as reproductive traits can be explored. PMID:26518739

  11. Prokaryotic Phylogeny Based on Complete Genomes Without Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Hao, Bailin; Qi, Ji; Wang, Bin

    We present a brief review of a series of on-going work on bacterial phylogeny. We propose a new method to infer relatedness of prokaryotes from their complete genome data without using sequence alignment, leading to results comparable with the bacteriologist's systematics as reflected in the latest 2001 edition of Bergey's Manual of Systematic Bacteriology.1 We only touch on the mathematical aspects of the method. The biological implications of our results will be published elsewhere.

  12. Deep phylogeny and evolution of sponges (phylum Porifera).

    PubMed

    Wörheide, G; Dohrmann, M; Erpenbeck, D; Larroux, C; Maldonado, M; Voigt, O; Borchiellini, C; Lavrov, D V

    2012-01-01

    Sponges (phylum Porifera) are a diverse taxon of benthic aquatic animals of great ecological, commercial, and biopharmaceutical importance. They are arguably the earliest-branching metazoan taxon, and therefore, they have great significance in the reconstruction of early metazoan evolution. Yet, the phylogeny and systematics of sponges are to some extent still unresolved, and there is an on-going debate about the exact branching pattern of their main clades and their relationships to the other non-bilaterian animals. Here, we review the current state of the deep phylogeny of sponges. Several studies have suggested that sponges are paraphyletic. However, based on recent phylogenomic analyses, we suggest that the phylum Porifera could well be monophyletic, in accordance with cladistic analyses based on morphology. This finding has many implications for the evolutionary interpretation of early animal traits and sponge development. We further review the contribution that mitochondrial genes and genomes have made to sponge phylogenetics and explore the current state of the molecular phylogenies of the four main sponge lineages (Classes), that is, Demospongiae, Hexactinellida, Calcarea, and Homoscleromorpha, in detail. While classical systematic systems are largely congruent with molecular phylogenies in the class Hexactinellida and in certain parts of Demospongiae and Homoscleromorpha, the high degree of incongruence in the class Calcarea still represents a challenge. We highlight future areas of research to fill existing gaps in our knowledge. By reviewing sponge development in an evolutionary and phylogenetic context, we support previous suggestions that sponge larvae share traits and complexity with eumetazoans and that the simple sedentary adult lifestyle of sponges probably reflects some degree of secondary simplification. In summary, while deep sponge phylogenetics has made many advances in the past years, considerable efforts are still required to achieve a

  13. Lake Effects: The Lake Superior Curriculum Guide.

    ERIC Educational Resources Information Center

    Beery, Tom; And Others

    This curriculum guide was launched in response to a need for Lake Superior-specific educational materials and contains lessons and activities that can be used to teach about Lake Superior. The lessons in this book are divided into four sections. Each of the first three sections has a background section that provides basic information about Lake…

  14. Phylogeny versus body size as determinants of food web structure

    PubMed Central

    Naisbit, Russell E.; Rohr, Rudolf P.; Rossberg, Axel G.; Kehrli, Patrik; Bersier, Louis-Félix

    2012-01-01

    Food webs are the complex networks of trophic interactions that stoke the metabolic fires of life. To understand what structures these interactions in natural communities, ecologists have developed simple models to capture their main architectural features. However, apparently realistic food webs can be generated by models invoking either predator–prey body-size hierarchies or evolutionary constraints as structuring mechanisms. As a result, this approach has not conclusively revealed which factors are the most important. Here we cut to the heart of this debate by directly comparing the influence of phylogeny and body size on food web architecture. Using data from 13 food webs compiled by direct observation, we confirm the importance of both factors. Nevertheless, phylogeny dominates in most networks. Moreover, path analysis reveals that the size-independent direct effect of phylogeny on trophic structure typically outweighs the indirect effect that could be captured by considering body size alone. Furthermore, the phylogenetic signal is asymmetric: closely related species overlap in their set of consumers far more than in their set of resources. This is at odds with several food web models, which take only the view-point of consumers when assigning interactions. The echo of evolutionary history clearly resonates through current food webs, with implications for our theoretical models and conservation priorities. PMID:22628467

  15. Heavy metal resistant strains are widespread along Streptomyces phylogeny.

    PubMed

    Alvarez, Analía; Catalano, Santiago A; Amoroso, María Julia

    2013-03-01

    The genus Streptomyces comprises a group of bacteria species with high economic importance. Several of these species are employed at industrial scale for the production of useful compounds. Other characteristic found in different strains within this genus is their capability to tolerate high level of substances toxic for humans, heavy metals among them. Although several studies have been conducted in different species of the genus in order to disentangle the mechanisms associated to heavy metal resistance, little is known about how they have evolved along Streptomyces phylogeny. In this study we built the largest Streptomyces phylogeny generated up to date comprising six genes, 113 species of Streptomyces and 27 outgroups. The parsimony-based phylogenetic analysis indicated that (i) Streptomyces is monophyletic and (ii) it appears as sister clade of a group formed by Kitasatospora and Streptacidiphilus species, both genera also monophyletic. Streptomyces strains resistant to heavy metals are not confined to a single lineage but widespread along Streptomyces phylogeny. Our result in combination with genomic, physiological and biochemical data suggest that the resistance to heavy metals originated several times and by different mechanisms in Streptomyces history. PMID:23247041

  16. Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus).

    PubMed

    Herron, Matthew D; Castoe, Todd A; Parkinson, Christopher L

    2004-06-01

    The squirrel family, Sciuridae, is one of the largest and most widely dispersed families of mammals. In spite of the wide distribution and conspicuousness of this group, phylogenetic relationships remain poorly understood. We used DNA sequence data from the mitochondrial cytochrome b gene of 114 species in 21 genera to infer phylogenetic relationships among sciurids based on maximum parsimony and Bayesian phylogenetic methods. Although we evaluated more complex alternative models of nucleotide substitution to reconstruct Bayesian phylogenies, none provided a better fit to the data than the GTR+G+I model. We used the reconstructed phylogenies to evaluate the current taxonomy of the Sciuridae. At essentially all levels of relationships, we found the phylogeny of squirrels to be in substantial conflict with the current taxonomy. At the highest level, the flying squirrels do not represent a basal divergence, and the current division of Sciuridae into two subfamilies is therefore not phylogenetically informative. At the tribal level, the Neotropical pygmy squirrel, Sciurillus, represents a basal divergence and is not closely related to the other members of the tribe Sciurini. At the genus level, the sciurine genus Sciurus is paraphyletic with respect to the dwarf squirrels (Microsciurus), and the Holarctic ground squirrels (Spermophilus) are paraphyletic with respect to antelope squirrels (Ammospermophilus), prairie dogs (Cynomys), and marmots (Marmota). Finally, several species of chipmunks and Holarctic ground squirrels do not appear monophyletic, indicating a need for reevaluation of alpha taxonomy. PMID:15120398

  17. Phylogeny of metabolic networks: a spectral graph theoretical approach.

    PubMed

    Deyasi, Krishanu; Banerjee, Anirban; Deb, Bony

    2015-10-01

    Many methods have been developed for finding the commonalities between different organisms in order to study their phylogeny. The structure of metabolic networks also reveals valuable insights into metabolic capacity of species as well as into the habitats where they have evolved. We constructed metabolic networks of 79 fully sequenced organisms and compared their architectures. We used spectral density of normalized Laplacian matrix for comparing the structure of networks. The eigenvalues of this matrix reflect not only the global architecture of a network but also the local topologies that are produced by different graph evolutionary processes like motif duplication or joining. A divergence measure on spectral densities is used to quantify the distances between various metabolic networks, and a split network is constructed to analyse the phylogeny from these distances. In our analysis, we focused on the species that belong to different classes, but appear more related to each other in the phylogeny. We tried to explore whether they have evolved under similar environmental conditions or have similar life histories. With this focus, we have obtained interesting insights into the phylogenetic commonality between different organisms. PMID:26564980

  18. Phylogeny, Diet, and Cranial Integration in Australodelphian Marsupials

    PubMed Central

    Goswami, Anjali

    2007-01-01

    Studies of morphological integration provide valuable information on the correlated evolution of traits and its relationship to long-term patterns of morphological evolution. Thus far, studies of morphological integration in mammals have focused on placentals and have demonstrated that similarity in integration is broadly correlated with phylogenetic distance and dietary similarity. Detailed studies have also demonstrated a significant correlation between developmental relationships among structures and adult morphological integration. However, these studies have not yet been applied to marsupial taxa, which differ greatly from placentals in reproductive strategy and cranial development and could provide the diversity necessary to assess the relationships among phylogeny, ecology, development, and cranial integration. This study presents analyses of morphological integration in 20 species of australodelphian marsupials, and shows that phylogeny is significantly correlated with similarity of morphological integration in most clades. Size-related correlations have a significant affect on results, particularly in Peramelia, which shows a striking decrease in similarity of integration among species when size is removed. Diet is not significantly correlated with similarity of integration in any marsupial clade. These results show that marsupials differ markedly from placental mammals in the relationships of cranial integration, phylogeny, and diet, which may be related to the accelerated development of the masticatory apparatus in marsupials. PMID:17912372

  19. Mitogenomic perspectives on the origin and phylogeny of living amphibians.

    PubMed

    Zhang, Peng; Zhou, Hui; Chen, Yue-Qin; Liu, Yi-Fei; Qu, Liang-Hu

    2005-06-01

    Establishing the relationships among modern amphibians (lissamphibians) and their ancient relatives is necessary for our understanding of early tetrapod evolution. However, the phylogeny is still intractable because of the highly specialized anatomy and poor fossil record of lissamphibians. Paleobiologists are still not sure whether lissamphibians are monophyletic or polyphyletic, and which ancient group (temnospondyls or lepospondyls) is most closely related to them. In an attempt to address these problems, eight mitochondrial genomes of living amphibians were determined and compared with previously published amphibian sequences. A comprehensive molecular phylogenetic analysis of nucleotide sequences yields a highly resolved tree congruent with the traditional hypotheses (Batrachia). By using a molecular clock-independent approach for inferring dating information from molecular phylogenies, we present here the first molecular timescale for lissamphibian evolution, which suggests that lissamphibians first emerged about 330 million years ago. By observing the fit between molecular and fossil times, we suggest that the temnospondyl-origin hypothesis for lissamphibians is more credible than other hypotheses. Moreover, under this timescale, the potential geographic origins of the main living amphibian groups are discussed: (i) advanced frogs (neobatrachians) may possess an Africa-India origin; (ii) salamanders may have originated in east Asia; (iii) the tropic forest of the Triassic Pangaea may be the place of origin for the ancient caecilians. An accurate phylogeny with divergence times can be also helpful to direct the search for "missing" fossils, and can benefit comparative studies of amphibian evolution. PMID:16012106

  20. Correcting for Sequencing Error in Maximum Likelihood Phylogeny Inference

    PubMed Central

    Kuhner, Mary K.; McGill, James

    2014-01-01

    Accurate phylogenies are critical to taxonomy as well as studies of speciation processes and other evolutionary patterns. Accurate branch lengths in phylogenies are critical for dating and rate measurements. Such accuracy may be jeopardized by unacknowledged sequencing error. We use simulated data to test a correction for DNA sequencing error in maximum likelihood phylogeny inference. Over a wide range of data polymorphism and true error rate, we found that correcting for sequencing error improves recovery of the branch lengths, even if the assumed error rate is up to twice the true error rate. Low error rates have little effect on recovery of the topology. When error is high, correction improves topological inference; however, when error is extremely high, using an assumed error rate greater than the true error rate leads to poor recovery of both topology and branch lengths. The error correction approach tested here was proposed in 2004 but has not been widely used, perhaps because researchers do not want to commit to an estimate of the error rate. This study shows that correction with an approximate error rate is generally preferable to ignoring the issue. PMID:25378476

  1. Food of lake trout in Lake Superior

    USGS Publications Warehouse

    Dryer, William R.; Erkkila, Leo F.; Tetzloff, Clifford L.

    1965-01-01

    Stomachs were examined from 1,492 lake trout and 83 siscowets collected from Lake Superior. Data are given on the food of lake trout of legal size (17 inches or longer) by year, season, and depth of water, and on the relation between food and size among smaller lake trout. Fish contributed 96.7 to 99.9 per cent of the total volume of food in the annual samples. Ciscoes (Coregonus spp.) were most common (52.2 to 87.5 per cent of the volume) in 1950 to 1953 and American smelt ranked first (65.6 per cent of the volume) in 1963. Cottids were in 8.9 to 12.3 per cent of the stomachs in 1950 to 1953 but in only 4.3 per cent in 1963. Insects ranked second to fish in occurrence (9.6 per cent for the combined samples) and crustaceans followed at 3.9 per cent. The greatest seasonal changes in the food of lake trout were among fish caught at 35 fathoms and shallower. The occurrence of Coregonus increased from 34.6 per cent in February-March to 71.1 per cent in October-December. Smelt were in 76.9 per cent of the stomachs in February-March but in only 2.2 per cent in October-December. Cottids, Mysis relicta, and insects were most common in the July-September collections. Lake trout taken at depths greater than 35 fathoms had eaten a higher percentage of Cottidae and Coregonus than had those captured in shallower water. Smelt, ninespine sticklebacks, Mysis, and insects were more frequent in stomachs of lake trout from less than 35 fathoms. Crustaceans comprised more than 70 per cent of the total volume of food for 4.0- to 7.9-inch lake trout but their importance decreased as the lake trout grew larger. Pontoporeia affinis was the most common in the stomachs of 4.0- to 6.9-inch lake trout and Mysis held first rank at 7.0 to 12.9 inches. Ostracods were important only to 4.0- to 4.9-inch lake trout. As the lake trout became larger, the importance of fish grew from 4.4-per cent occurrence at 5.0 to 5.9 inches to 93.9 per cent at 16.0 to 16.9 inches. Smelt were most commonly eaten by

  2. Top-down modulation of visual processing and knowledge after 250 ms supports object constancy of category decisions

    PubMed Central

    Schendan, Haline E.; Ganis, Giorgio

    2015-01-01

    People categorize objects more slowly when visual input is highly impoverished instead of optimal. While bottom-up models may explain a decision with optimal input, perceptual hypothesis testing (PHT) theories implicate top-down processes with impoverished input. Brain mechanisms and the time course of PHT are largely unknown. This event-related potential study used a neuroimaging paradigm that implicated prefrontal cortex in top-down modulation of occipitotemporal cortex. Subjects categorized more impoverished and less impoverished real and pseudo objects. PHT theories predict larger impoverishment effects for real than pseudo objects because top-down processes modulate knowledge only for real objects, but different PHT variants predict different timing. Consistent with parietal-prefrontal PHT variants, around 250 ms, the earliest impoverished real object interaction started on an N3 complex, which reflects interactive cortical activity for object cognition. N3 impoverishment effects localized to both prefrontal and occipitotemporal cortex for real objects only. The N3 also showed knowledge effects by 230 ms that localized to occipitotemporal cortex. Later effects reflected (a) word meaning in temporal cortex during the N400, (b) internal evaluation of prior decision and memory processes and secondary higher-order memory involving anterotemporal parts of a default mode network during posterior positivity (P600), and (c) response related activity in posterior cingulate during an anterior slow wave (SW) after 700 ms. Finally, response activity in supplementary motor area during a posterior SW after 900 ms showed impoverishment effects that correlated with RTs. Convergent evidence from studies of vision, memory, and mental imagery which reflects purely top-down inputs, indicates that the N3 reflects the critical top-down processes of PHT. A hybrid multiple-state interactive, PHT and decision theory best explains the visual constancy of object cognition. PMID:26441701

  3. Water quality of Lake Austin and Town Lake, Austin, Texas

    SciTech Connect

    Andrews, F.L.; Wells, F.C.; Shelby, W.J.; McPherson, E.M.

    1988-01-01

    Lake Austin and Town Lake are impoundments on the Colorado River in Travis County, central Texas, and are a source of water for municipal industrial water supplies, electrical-power generation, and recreation for more than 500,000 people in the Austin metropolitan area. Small vertical temperature variations in both lakes were attributed to shallow depths in the lakes and short retention times of water in the lakes during the summer months. The largest areal variations in dissolved oxygen generally occur in Lake Austin during the summer as a result of releases of water from below the thermocline in Lake Travis. Except for iron, manganese, and mercury, dissolved concentrations of trace elements in water collected from Lake Austin and Town Lake did not exceed the primary or secondary drinking water standards set by the US Environmental Protection Agency. Little or no effect of stormwater runoff on temperature, dissolved oxygen, or minor elements could be detected in either Lake Austin or Town Lake. Little seasonal or areal variation was noted in nitrogen concentrations in Lake Austin or Town lake. Total phosphorus concentrations generally were small in both lakes. Increased concentrations of nitrogen and phosphorus were detected after storm runoff inflow in Town Lake, but not in Lake Austin; densities of fecal-coliform bacteria increased in Lake Austin and Town Lake, but were substantially greater in Town Lake than in Lake Austin. 18 refs., 38 figs., 59 tabs.

  4. Lake trout rehabilitation in Lake Huron

    USGS Publications Warehouse

    Eshenroder, Randy L.; Payne, N. Robert; Johnson, James E.; Bowen, Charles, II; Ebener, Mark P.

    1995-01-01

    Efforts to restore lake trout (Salvelinus namaycush) in Lake Huron after their collapse in the 1940s were underway in the early 1970s with completion of the first round of lampricide applications in tributary streams and the stocking of several genotypes. We assess results of rehabilitation and establish a historical basis for comparison by quantifying the catch of spawning lake trout from Michigan waters in 1929-1932. Sixty-eight percent of this catch occurred in northern waters (MH-1) and most of the rest (15%) was from remote reefs in the middle of the main basin. Sea lampreys (Petromyzon marinus) increased in the early 1980s in the main basin and depressed spawning populations of lake trout. This increase was especially severe in northern waters and appeared to be associated with untreated populations in the St. Marys River. Excessive commercial fishing stemming from unresolved treaty rights also contributed to loss of spawning fish in northern Michigan waters. Seneca-strain lake trout did not appear to be attacked by sea lampreys until they reached a size > 532 mm. At sizes > 632 mm, Seneca trout were 40-fold more abundant than the Marquette strain in matched-planting experiments. Natural reproduction past the fry stage has occurred in Thunder Bay and South Bay, but prospects for self-sustaining populations of lake trout in the main basin are poor because sea lampreys are too abundant, only one side of the basin is stocked, and stocking is deferred to allow commercial gillnetting in areas where most of the spawning occurred historically. Backcross lake trout, a lake trout x splake (s. Fontinalis x s. Namaycush) hybrid, did not reproduce in Georgian Bay, but this genotype is being replaced with pure-strain lake trout, whose early performance appears promising.

  5. Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow).

    PubMed Central

    Weiss, P; Schweitzer, B; Amann, R; Simon, M

    1996-01-01

    Microbial assemblages on large organic aggregates (lake snow) of Lake Constance, Germany, were analyzed with rRNA-directed fluorescent oligonucleotide probes specific for the domain Bacteria and the alpha-, beta-, and gamma-subclasses of the class Proteobacteria. Lake snow aggregates were either collected in situ by SCUBA diving or in a sediment trap at 50 m or formed of natural lake water incubated in rolling cylinders under simulated in situ conditions. For the latter aggregates, the time course of the microbial colonization was also examined. The natural aggregates and those made in rolling cylinders were composed of the particulate organic material present in the lake and thus reflected the composition of the ambient plankton community. All types of lake snow aggregates examined were heavily colonized by microbial cells and harbored between 0.5 x 10(6) and > 2 x 10(6) cells aggregate -1. Between 55 and 100% of the microbial cells stained with 4', 6-diamidino-2-phenylindole (DAPI) could be visualized with the domain Bacteria-specific probe. In most samples, beta-subclass proteobacteria dominated the microbial community, constituting 27 to 42% of total cells as counted by DAPI staining, irrespective of the composition of the aggregates. During the time course experiments with the laboratory-made aggregates, the fraction of beta-subclass proteobacteria usually increased over time. Except for a few samples, alpha- and gamma-subclass proteobacteria were far less abundant than beta-subclass proteobacteria, constituting 11 to 25 and 9 to 33% of total cells, respectively. Therefore, we assume that a specific aggregate-adapted microbial community was established on the aggregates. Because the compositions of the microbial assemblages on natural and laboratory-made aggregates were similar, we conclude that aggregates made in rolling cylinders are good model system with which to examine the formation and microbial colonization of macroscopic organic aggregates. PMID

  6. View of Lake Sabrina Dam and Lake Sabrina from east ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View of Lake Sabrina Dam and Lake Sabrina from east ridge showing spillway at photo center, view southwest - Bishop Creek Hydroelectric System, Plant 2, Lake Sabrina Dam, Bishop Creek, Bishop, Inyo County, CA

  7. Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika

    PubMed Central

    Rüber, Lukas; Verheyen, Erik; Meyer, Axel

    1999-01-01

    The current phylogenetic hypothesis for the endemic Lake Tanganyika cichlid fishes of the tribe Eretmodini is based solely on morphology and suggests that more complex trophic morphologies derived only once from a less specialized ancestral condition. A molecular phylogeny of eretmodine cichlids based on partial mitochondrial DNA cytochrome b and control-region sequences was used to reconstruct the evolutionary sequence of trophic adaptations and to test alternative models of morphological divergence. The six mitochondrial lineages found disagree with the current taxonomy and the morphology-based phylogeny. Mitochondrial lineages with similar trophic morphologies are not grouped monophyletically but are typically more closely related to lineages with different trophic phenotypes currently assigned to other genera. Our results indicate multiple independent origins of similar trophic specializations in these cichlids. A pattern of repeated divergent morphological evolution becomes apparent when the phylogeography of the mitochondrial haplotypes is analyzed in the context of the geological and paleoclimatological history of Lake Tanganyika. In more than one instance within Lake Tanganyika, similar morphological divergence of dentitional traits occurred in sympatric species pairs. Possibly, resource-based divergent selective regimes led to resource partitioning and brought about similar trophic morphologies independently and repeatedly. PMID:10468591

  8. Industrial applications of high-performance computing for phylogeny reconstruction

    NASA Astrophysics Data System (ADS)

    Bader, David A.; Moret, Bernard M.; Vawter, Lisa

    2001-07-01

    Phylogenies (that is, tree-of-life relationships) derived from gene order data may prove crucial in answering some fundamental open questions in biomolecular evolution. Real-world interest is strong in determining these relationships. For example, pharmaceutical companies may use phylogeny reconstruction in drug discovery for discovering synthetic pathways unique to organisms that they wish to target. Health organizations study the phylogenies of organisms such as HIV in order to understand their epidemiologies and to aid in predicting the behaviors of future outbreaks. And governments are interested in aiding the production of such foodstuffs as rice, wheat and potatoes via genetics through understanding of the phylogenetic distribution of genetic variation in wild populations. Yet few techniques are available for difficult phylogenetic reconstruction problems. Appropriate tools for analysis of such data may aid in resolving some of the phylogenetic problems that have been analyzed without much resolution for decades. With the rapid accumulation of whole genome sequences for a wide diversity of taxa, especially microbial taxa, phylogenetic reconstruction based on changes in gene order and gene content is showing promise, particularly for resolving deep (i.e., ancient) branch splits. However, reconstruction from gene-order data is even more computationally expensive than reconstruction from sequence data, particularly in groups with large numbers of genes and highly-rearranged genomes. We have developed a software suite, GRAPPA, that extends the breakpoint analysis (BPAnalysis) method of Sankoff and Blanchette while running much faster: in a recent analysis of chloroplast genome data for species of Campanulaceae on a 512-processor Linux supercluster with Myrinet, we achieved a one-million-fold speedup over BPAnalysis. GRAPPA can use either breakpoint or inversion distance (computed exactly) for its computation and runs on single-processor machines as well as

  9. Origins of rainbow smelt in Lake Ontario

    USGS Publications Warehouse

    Bergstedt, Roger A.

    1983-01-01

    The first rainbow smelt (Osmerus mordax) to enter Lake Ontario were probably migrants from an anadromous strain introduced into New York's Finger Lakes. Since the upper Great Lakes were originally stocked with a landlocked strain from Green Lake, Maine, subsequent migration to Lake Ontario from Lake Erie makes Lake Ontario unique among the Great Lakes in probably having received introductions from two distinct populations.

  10. Phylogeny of the Ants: Diversification in the Age of Angiosperms

    NASA Astrophysics Data System (ADS)

    Moreau, Corrie S.; Bell, Charles D.; Vila, Roger; Archibald, S. Bruce; Pierce, Naomi E.

    2006-04-01

    We present a large-scale molecular phylogeny of the ants (Hymenoptera: Formicidae), based on 4.5 kilobases of sequence data from six gene regions extracted from 139 of the 288 described extant genera, representing 19 of the 20 subfamilies. All but two subfamilies are recovered as monophyletic. Divergence time estimates calibrated by minimum age constraints from 43 fossils indicate that most of the subfamilies representing extant ants arose much earlier than previously proposed but only began to diversify during the Late Cretaceous to Early Eocene. This period also witnessed the rise of angiosperms and most herbivorous insects.

  11. Probing protistan phylogenies with an anti-tubulin antibody.

    PubMed

    Brugerolle, G; Adoutte, A

    1988-01-01

    Representatives from most of the protist phyla were probed by immunofluorescence or by immunoblotting with an anti-tubulin antibody of sharp specificity previously raised against Paramecium axonemal tubulin. Excellent intra-phylum homogeneity of results was recorded except for chlorophytes. All ciliates, dinoflagellates and cryptomonads tested were strongly positive while actinopods, Euglenozoa and parabasalids were negative. All representatives of the broad chromophyte assemblage were positive while all rhizopods were negative. This simple binary immunological character was superimposed on a number of published protist phylogenies and seen to fit very well with some of them. Other immunological approaches to protist taxonomy and evolution are briefly reviewed. PMID:2456108

  12. Prokaryotic Phylogeny Based on Complete Genomes Without Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Hao, Bailin; Qi, Ji; Wang, Bin

    2003-04-01

    This is a brief review of a series of on-going work on bacterial phylogeny. We have proposed a new method to infer relatedness of prokaryotes from their complete genome data without using sequence alignment. It has led to results comparable with the bacteriologists' systematics as reflected in the latest 2001 edition of the Bergey's Manual of Systematic Bacteriology1. In what follows we only touch on the mathematical aspects of the method. The biological implications of our results will be published elsewhere.

  13. The phylogeny of yeasts—A cladistic analysis

    NASA Astrophysics Data System (ADS)

    Sun, Xiuqin; Wu, Baoling

    1992-12-01

    Cladistic analysis was used to clarify the phylogeny of 16 genera of yeasts whose great morphological differences and inclusion in different classification systems resulted in controversies over the taxonomy of seven genera such as Crypeococcus. etc. Some scholars suggest that they belong to Ascomycetes, but others think they belong to fungi imperfecti. After comprehensive cladistic analysis of many genetic characters, the authors consider that the above-mentioned seven genera of yeasts developed in parallel with Ascomycetes so that they should belong to one and the same developmental system.

  14. Population dynamics of flaviviruses revealed by molecular phylogenies.

    PubMed Central

    Zanotto, P M; Gould, E A; Gao, G F; Harvey, P H; Holmes, E C

    1996-01-01

    The phylogeny of 123 complete envelope gene sequences was reconstructed in order to understand the evolution of tick- and mosquito-borne flaviviruses. An analysis of phylogenetic tree structure reveals a continual and asymmetric branching process in the tick-borne flaviviruses, compared with an explosive radiation in the last 200 years in viruses transmitted by mosquitoes. The distinction between these two viral groups probably reflects differences in modes of dispersal, propagation, and changes in the size of host populations. The most serious implication of this work is that growing human populations are being exposed to an expanding range of increasingly diverse viral strains. PMID:8570593

  15. David Morrison on Lake Vostok

    NASA Video Gallery

    Dr. David Morrison discusses the implications of research possibilities at Lake Vostok, one of the largest subglacial lakes located over two miles beneath the ice in Antarctica. The lake has been c...

  16. Lake Mead, NV

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Lake Mead, Nevada, (36.0N, 114.5E) where the water from the Colorado River empties after it's 273 mile journey through the Grand Canyon of Arizona is the subject of this photo. Other features of interest are Hoover Dam on the south shore of Lake Mead where cheap hydroelectric power is secondary to the water resources made available in this northern desert region and the resort city of Las Vegas, just to the west of Lake Mead.

  17. Great Lakes Literacy Principles

    NASA Astrophysics Data System (ADS)

    Fortner, Rosanne W.; Manzo, Lyndsey

    2011-03-01

    Lakes Superior, Huron, Michigan, Ontario, and Erie together form North America's Great Lakes, a region that contains 20% of the world's fresh surface water and is home to roughly one quarter of the U.S. population (Figure 1). Supporting a $4 billion sport fishing industry, plus $16 billion annually in boating, 1.5 million U.S. jobs, and $62 billion in annual wages directly, the Great Lakes form the backbone of a regional economy that is vital to the United States as a whole (see http://www.miseagrant.umich.edu/downloads/economy/11-708-Great-Lakes-Jobs.pdf). Yet the grandeur and importance of this freshwater resource are little understood, not only by people in the rest of the country but also by many in the region itself. To help address this lack of knowledge, the Centers for Ocean Sciences Education Excellence (COSEE) Great Lakes, supported by the U.S. National Science Foundation and the National Oceanic and Atmospheric Administration, developed literacy principles for the Great Lakes to serve as a guide for education of students and the public. These “Great Lakes Literacy Principles” represent an understanding of the Great Lakes' influences on society and society's influences on the Great Lakes.

  18. Chitinase genes in lake sediments of Ardley Island, Antarctica.

    PubMed

    Xiao, Xiang; Yin, Xuebin; Lin, Jian; Sun, Liguang; You, Ziyong; Wang, Peng; Wang, Fengping

    2005-12-01

    A sediment core spanning approximately 1,600 years was collected from a lake on Ardley Island, Antarctica. The sediment core had been greatly influenced by penguin guano. Using molecular methods, the chitinolytic bacterial community along the sediment core was studied over its entire length. Primers targeting conserved sequences of the catalytic domains of family 18 subgroup A chitinases detected group A chitinases from a wide taxonomic range of bacteria. Using quantitative competitive PCR (QC-PCR), chitinase gene copies in each 1-cm section of the whole sediment column were quantified. QC-PCR determination of the chitinase gene copies indicated significant correlation with phosphorus and total organic carbon concentration, suggesting a historical connection between chitinase gene copies and the amount of penguin guano input into the lake sediment. Most of the chitinase genes cloned from the historic sediment core were novel. Analysis of the chitinase gene diversity in selected sediment layers and in the fresh penguin deposits indicated frequent shifts in the chitinolytic bacterial community over time. Sequence analysis of the 16S rRNA genes of chitinolytic bacteria isolated from the lake sediment revealed that the isolates belonged to Janthinobacterium species, Stenotrophomonas species of gamma-Proteobacteria, Cytophaga species of the Cytophaga-Flexibacter-Bacteroides group, and Streptomyces and Norcardiopsis species of Actinobacteria. Chitinase gene fragments were cloned and sequenced from these cultivated chitinolytic bacteria. The phylogeny of the chitinase genes obtained from the isolates did not correspond well to that of the isolates, suggesting acquisition via horizontal gene transfer. PMID:16332766

  19. Phylogeny and taxonomy of sculpins, sandfishes, and snailfishes (Perciformes: Cottoidei) with comments on the phylogenetic significance of their early-life-history specializations.

    PubMed

    Smith, W Leo; Busby, Morgan S

    2014-10-01

    Despite recent progress on the higher-level relationships of the Cottoidei and its familial components, phylogenetic conflict and uncertainty remain within the Cottoidea. We analyzed a dataset composed of 4518 molecular (mitochondrial 12S, tRNA-Val, 16S, and cytochrome b and nuclear TMO-4c4, Histone H3, and 28S) and 72 morphological characters for 69 terminals to address cottoid intrarelationships. The resulting well-resolved phylogeny was used to produce a revised taxonomy that is consistent with the available molecular and morphological data and recognizes six families: Agonidae, Cottidae, Jordaniidae, Psychrolutidae, Rhamphocottidae, and Scorpaenichthyidae. The traditional Agonidae was expanded to include traditional hemitripterids and Hemilepidotus. The traditional Cottidae was restricted to Leptocottus, Trachidermus, and the riverine, lacustrine, and Lake Baikal freshwater cottoids. Jordaniidae (Jordania and Paricelinus) was separated from the traditional cottids; Psychrolutidae was expanded from the traditional grouping to include nearly all traditional marine cottids and the single species of bathylutichthyid. Rhamphocottidae was expanded to include the traditional ereuniids, and Scorpaenichthyidae separated Scorpaenichthys from the traditional cottids. The importance of early-life-history characters to the resulting phylogeny and taxonomy were highlighted. PMID:25014569

  20. Lakes, Lagerstaetten, and Evolution

    NASA Astrophysics Data System (ADS)

    Kordesch, E. G.; Park, L. E.

    2001-12-01

    The diversity of terrestrial systems is estimated to be greater than in the marine realm. However no hard data yet exists to substantiate this claim. Ancient lacustrine deposits may preserve an exceptionally diverse fossil fauna and aid in determining continental faunal diversities. Fossils preserved in lake deposits, especially those with exceptional preservation (i.e. Konservat Lagerstaetten), may represent a dependable method for determining species diversity changes in the terrestrial environment because of their faunal completeness. Important Konservat Lagerstaetten, such as the Green River Formation (US) and Messel (Germany), both Eocene in age, are found in lake sediments and show a remarkable faunal diversity for both vertebrates and invertebrates. To date information from nearly 25 lake lagerstaetten derived from different types of lake basins from the Carboniferous to the Miocene have been collected and described. Carboniferous sites derive from the cyclothems of Midcontinent of the US while many Cenozoic sites have been described from North and South America as well as Europe and Australia. Asian sites contain fossils from the Mesozoic and Cenozoic. With this data, insight into the evolutionary processes associated with lake systems can be examined. Do lakes act as unique evolutionary crucibles in contrast to marine systems? The speciation of cichlid fishes in present-day African lakes appears to be very high and is attributed to the diversity of environments found in large rift lakes. Is this true of all ancient lakes or just large rift lakes? The longevity of a lake system may be an important factor in allowing speciation and evolutionary processes to occur; marine systems are limited only in the existence of environments as controlled by tectonics and sea level changes, on the order of tens of millions of years. Rift lakes are normally the longest lived in the millions of years. Perhaps there are only certain types of lakes in which speciation of

  1. The geological record and phylogeny of the Myriapoda.

    PubMed

    Shear, William A; Edgecombe, Gregory D

    2010-01-01

    We review issues of myriapod phylogeny, from the position of the Myriapoda amongst arthropods to the relationships of the orders of the classes Chilopoda and Diplopoda. The fossil record of each myriapod class is reviewed, with an emphasis on developments since 1997. We accept as working hypotheses that Myriapoda is monophyletic and belongs in Mandibulata, that the classes of Myriapoda are monophyletic, and that they are related as (Chilopoda (Symphyla (Diplopoda+Pauropoda))). The most pressing challenges to these hypotheses are some molecular and developmental evidence for an alliance between myriapods and chelicerates, and the attraction of symphylans to pauropods in some molecular analyses. While the phylogeny of the orders of Chilopoda appears settled, the relationships within Diplopoda remain unclear at several levels. Chilopoda and Diplopoda have a relatively sparse representation as fossils, and Symphyla and Pauropoda fossils are known only from Tertiary ambers. Fossils are difficult to place in trees based on living forms because many morphological characters are not very likely to be preserved in the fossils; as a consequence, most diplopod fossils have been placed in extinct higher taxa. Nevertheless, important information from diplopod fossils includes the first documented occurrence of air-breathing, and the first evidence for the use of a chemical defense. Stem-group myriapods are unknown, but evidence suggests the group must have arisen in the Early Cambrian, with a major period of cladogenesis in the Late Ordovician and early Silurian. Large terrestrial myriapods were on land at least by mid-Silurian. PMID:19944188

  2. Molecular phylogeny of choanoflagellates, the sister group to Metazoa

    PubMed Central

    Carr, M.; Leadbeater, B. S. C.; Hassan, R.; Nelson, M.; Baldauf, S. L.

    2008-01-01

    Choanoflagellates are single-celled aquatic flagellates with a unique morphology consisting of a cell with a single flagellum surrounded by a “collar” of microvilli. They have long interested evolutionary biologists because of their striking resemblance to the collared cells (choanocytes) of sponges. Molecular phylogeny has confirmed a close relationship between choanoflagellates and Metazoa, and the first choanoflagellate genome sequence has recently been published. However, molecular phylogenetic studies within choanoflagellates are still extremely limited. Thus, little is known about choanoflagellate evolution or the exact nature of the relationship between choanoflagellates and Metazoa. We have sequenced four genes from a broad sampling of the morphological diversity of choanoflagellates including most species currently available in culture. Phylogenetic analyses of these sequences, alone and in combination, reject much of the traditional taxonomy of the group. The molecular data also strongly support choanoflagellate monophyly rejecting proposals that Metazoa were derived from a true choanoflagellate ancestor. Mapping of a complementary matrix of morphological and ecological traits onto the phylogeny allows a reinterpretation of choanoflagellate character evolution and predicts the nature of their last common ancestor. PMID:18922774

  3. Phylogeny of bovine species based on AFLP fingerprinting.

    PubMed

    Buntjer, J B; Otsen, M; Nijman, I J; Kuiper, M T R; Lenstra, J A

    2002-01-01

    The Bovini species comprise both domestic and wild cattle species. Published phylogenies of this tribe based on mitochondrial DNA contain anomalies, while nuclear sequences show only low variation. We have used amplified fragment length polymorphism (AFLP) fingerprinting in order to detect variation in loci distributed over the nuclear genome. Computer-assisted scoring of electrophoretic fingerprinting patterns yielded 361 markers, which provided sufficient redundancy to suppress stochastic effects of intraspecies polymorphisms and length homoplasies (comigration of non-homologous fragments). Tree reconstructions reveal three clusters: African buffalo with water buffalo, ox with zebu, and bison with wisent. Similarity values suggest a clustering of gaur and banteng, but bifurcating clustering algorithms did not assign consistent positions to these species and yak. We propose that because of shared polymorphisms and reticulations, tree topologies are only partially adequate to represent the phylogeny of the Bovini. Principal-coordinate analysis positions zebu between a gaur/banteng cluster and taurine cattle. This correlates with the region of origin of these species and suggests that genomic distances between the cattle species have been influenced by genetic exchange between neighbouring ancestral populations. PMID:11813106

  4. A synthetic phylogeny of freshwater crayfish: insights for conservation.

    PubMed

    Owen, Christopher L; Bracken-Grissom, Heather; Stern, David; Crandall, Keith A

    2015-02-19

    Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts. PMID:25561670

  5. Refining the Y chromosome phylogeny with southern African sequences.

    PubMed

    Barbieri, Chiara; Hübner, Alexander; Macholdt, Enrico; Ni, Shengyu; Lippold, Sebastian; Schröder, Roland; Mpoloka, Sununguko Wata; Purps, Josephine; Roewer, Lutz; Stoneking, Mark; Pakendorf, Brigitte

    2016-05-01

    The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species. PMID:27043341

  6. A novel methodology for large-scale phylogeny partition.

    PubMed

    Prosperi, Mattia C F; Ciccozzi, Massimo; Fanti, Iuri; Saladini, Francesco; Pecorari, Monica; Borghi, Vanni; Di Giambenedetto, Simona; Bruzzone, Bianca; Capetti, Amedeo; Vivarelli, Angela; Rusconi, Stefano; Re, Maria Carla; Gismondo, Maria Rita; Sighinolfi, Laura; Gray, Rebecca R; Salemi, Marco; Zazzi, Maurizio; De Luca, Andrea

    2011-01-01

    Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. The method has been applied to identify transmission clusters of a phylogeny of 11,541 human immunodeficiency virus-1 subtype B pol gene sequences from a large Italian cohort. Molecular transmission chains were characterized by means of different clinical/demographic factors, such as the interaction between male homosexuals and male heterosexuals. Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics. PMID:21610724

  7. Deep metazoan phylogeny: when different genes tell different stories.

    PubMed

    Nosenko, Tetyana; Schreiber, Fabian; Adamska, Maja; Adamski, Marcin; Eitel, Michael; Hammel, Jörg; Maldonado, Manuel; Müller, Werner E G; Nickel, Michael; Schierwater, Bernd; Vacelet, Jean; Wiens, Matthias; Wörheide, Gert

    2013-04-01

    Molecular phylogenetic analyses have produced a plethora of controversial hypotheses regarding the patterns of diversification of non-bilaterian animals. To unravel the causes for the patterns of extreme inconsistencies at the base of the metazoan tree of life, we constructed a novel supermatrix containing 122 genes, enriched with non-bilaterian taxa. Comparative analyses of this supermatrix and its two non-overlapping multi-gene partitions (including ribosomal and non-ribosomal genes) revealed conflicting phylogenetic signals. We show that the levels of saturation and long branch attraction artifacts in the two partitions correlate with gene sampling. The ribosomal gene partition exhibits significantly lower saturation levels than the non-ribosomal one. Additional systematic errors derive from significant variations in amino acid substitution patterns among the metazoan lineages that violate the stationarity assumption of evolutionary models frequently used to reconstruct phylogenies. By modifying gene sampling and the taxonomic composition of the outgroup, we were able to construct three different yet well-supported phylogenies. These results show that the accuracy of phylogenetic inference may be substantially improved by selecting genes that evolve slowly across the Metazoa and applying more realistic substitution models. Additional sequence-independent genomic markers are also necessary to assess the validity of the phylogenetic hypotheses. PMID:23353073

  8. A synthetic phylogeny of freshwater crayfish: insights for conservation

    PubMed Central

    Owen, Christopher L.; Bracken-Grissom, Heather; Stern, David; Crandall, Keith A.

    2015-01-01

    Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts. PMID:25561670

  9. Molecular Phylogeny of the Bamboo Sharks (Chiloscyllium spp.)

    PubMed Central

    Masstor, Noor Haslina; Samat, Abdullah; Nor, Shukor Md; Md-Zain, Badrul Munir

    2014-01-01

    Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN) Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences' lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate) that can clearly be used to differentiate each species. PMID:25013766

  10. Neocortical Expansion: An Attempt toward Relating Phylogeny and Ontogeny.

    PubMed

    Killackey, H P

    1990-01-01

    The neocortex is the most characteristic feature of the human brain. On gross inspection, its convoluted surfaces can be seen to have overgrown and covered most other brain structures. In the functional sphere, it is to the neocortex that we attribute those behaviors assumed to be most uniquely human such as cognition and linguistic behavior. This essay is an attempt to understand how this structure expanded during the course of mammalian evolution. At present, any attempt must be more speculative than definitive, but it is offered in the hope that it will generate more discussion on a topic that is central to all neurobiology, as well as a number of allied disciplines. I will proceed by outlining current views on the evolution of the brain, briefly review the organization of the somatosensory cortex in several mammalian forms, and then discuss in some detail ontogenetic mechanisms that may have some bearing on neocortical phylogeny. The primary proposition put forth is that the mammalian neocortex is relatively unspecified by strict genetic means, and that this allowed the neocortex to expand and adapt to a variety of circumstances during the course of phylogeny. PMID:23964719

  11. A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences

    PubMed Central

    Song, Nan; Liang, Ai-Ping; Bu, Cui-Ping

    2012-01-01

    Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses. PMID:23144967

  12. Phylogeny congruence analysis and isozyme classification: the pyruvate kinase system.

    PubMed

    Guderley, H; Fournier, P; Auclair, J C

    1989-09-22

    As the isozymes of pyruvate kinase (PK) are best known in rats, the characteristics of the rat isozymes are generally used to classify the PK isozymes in other species. Given the discrepancies generated by this classification by analogy, we evaluated a classification using a phylogeny congruence analysis of the compositional relatedness of vertebrate PK's. While our phylogenetic analysis confirmed the well established separation of the L and R isozymes from the K and M isozymes, its power became most evident in the identification of non-orthologous (or variant) forms of PK. Our analysis emphasized the uniqueness of chicken liver PK which cannot be classified either as a K or an L isozyme, confirmed that tumors express a variety of forms of PK, and indicated that lungs systematically express PK's which are not orthologous with PK's from other tissues. The determination of orthology by the phylogeny congruence analysis assumes that the structural data from different sources are subject to similar methodological error. However, we cannot reject the possibility that an apparent lack of orthology be due to artifacts during purification and analysis. PMID:2615396

  13. Phylogeny of the Gondwanan beetle family Ulodidae (Tenebrionoidea).

    PubMed

    Leschen, Richard A B; Escalona, Hermes E; Elgueta, Mario

    2016-01-01

    Ulodidae is a small family of saproxylic and fungus feeding beetles restricted to New Zealand, Australia, Chile and New Caledonia. The phylogeny of this family is presented for the first time, based on a cladistic analysis of 53 adult characters from 16 ulodid genera, rooted with Parahelops Waterhouse (Promecheilidae). The topology shows Arthopus Sharp at the base of the tree and confirms the placement of Meryx Latreille as a member of Ulodidae and closely related to the Chilean genus Trachyderas Philippi & Philippi. The extinct New Zealand genus Waitomophylax Leschen & Rhode was placed among a clade consisting of Brouniphylax Strand, Exohadrus Broun, and Pteroderes Germain. Two new genera and two new species are described: Ulobostrichus gen. n. (type species: Ulobostrichus monteithi sp. n.) and Ulocyphaleus gen. n. (type species: Cyphaleus valdivianus Philippi & Philippi, 1864, now U. valdivianus (Philippi & Philippi) n. comb.; U. laetus sp. n.). Dipsaconia pyritosa Pascoe is designated as the type species of Dipsaconia Pascoe and a lectotype was designated for C. valdivianus. A fully illustrated key to the genera and a checklist of the 16 genera and 42 species is included. Based on the phylogeny, the following characters are derived in the family: tuberculate body surface and the presence of scales and /or encrustations. The presence of pore-fields in the abdominal cuticle has evolved at least three times in Meryx Latreille (Australia), Syrphetodes Pascoe (New Zealand) and Trachyderastes Kaszab (New Caledonia). PMID:27470774

  14. Phylogeny of Basal Iguanodonts (Dinosauria: Ornithischia): An Update

    PubMed Central

    McDonald, Andrew T.

    2012-01-01

    The precise phylogenetic relationships of many non-hadrosaurid members of Iguanodontia, i.e., basal iguanodonts, have been unclear. Therefore, to investigate the global phylogeny of basal iguanodonts a comprehensive data matrix was assembled, including nearly every valid taxon of basal iguanodont. The matrix was analyzed in the program TNT, and the maximum agreement subtree of the resulting most parsimonious trees was then calculated in PAUP. Ordering certain multistate characters and omitting taxa through safe taxonomic reduction did not markedly improve resolution. The results provide some new information on the phylogeny of basal iguanodonts, pertaining especially to obscure or recently described taxa, and support some recent taxonomic revisions, such as the splitting of traditional “Camptosaurus” and “Iguanodon”. The maximum agreement subtree also shows a close relationship between the Asian Probactrosaurus gobiensis and the North American Eolambia, supporting the previous hypothesis of faunal interchange between Asia and North America in the early Late Cretaceous. Nevertheless, the phylogenetic relationships of many basal iguanodonts remain ambiguous due to the high number of taxa removed from the maximum agreement subtree and poor resolution of consensus trees. PMID:22629328

  15. Heat flux modifications related to climate-induced warming of large European lakes

    NASA Astrophysics Data System (ADS)

    Fink, Gabriel; Schmid, Martin; Wahl, Bernd; Wolf, Thomas; Wüest, Alfred

    2014-03-01

    Within the last decades, the water temperature of several European lakes has risen. It is assumed that these temperature increases are due to a reconfiguration of the heat-balance components. This study explores the dominant modifications of heat exchange with the atmosphere and their temporal evolutions. The objective is to identify the primary changes in heat fluxes and the sequence of events of the reconfiguration for the period 1984-2011. For this purpose, a model was applied to Lake Constance to estimate the contributions of the individual heat fluxes to the total heat balance. The results show that increasing absorption of solar radiation (+0.21 ± 0.13 W m-2 yr-1) and of longwave radiation (+0.25 ± 0.11 W m-2 yr-1) was responsible for the lake surface warming of 0.046 ± 0.011°C yr-1. Heat losses to the atmosphere by longwave emission (-0.24 ± 0.06 W m-2 yr-1) and by latent heat flux (-0.27 ± 0.12 W m-2 yr-1) have intensified in parallel due to higher lake surface temperatures. The heat budget is in a quasi-steady state, whereas incoming solar radiation and the warmer atmosphere increased the lake surface temperature; the warmer surface emits more longwave radiation and more water is evaporated. At each level of the slowly increasing water temperature, the heat fluxes are balanced. The overall change of the total heat content, however, is relatively little. Although the cooling effect of inflowing rivers decreased, this contribution is also small.

  16. Lessons from a Lake.

    ERIC Educational Resources Information Center

    Goethals, Susan

    1997-01-01

    Describes a study that included classroom lessons on hydroelectric power, the history and construction of a nearby lake, data recording, the use of field guides, and methods of counting natural populations. The study culminated in a field trip to the lake. (JRH)

  17. Great Lakes: Great Gardening.

    ERIC Educational Resources Information Center

    New York Sea Grant Inst., Albany, NY.

    This folder contains 12 fact sheets designed to improve the quality of gardens near the Great Lakes. The titles are: (1) "Your Garden and the Great Lakes"; (2) "Organic Gardening"; (3) "Fruit and Vegetable Gardening"; (4) "Composting Yard Wastes"; (5) "Herbicides and Water Quality"; (6) "Watering"; (7) "Soil Erosion by Water"; (8) "Soil…

  18. Venezuela: Lake Maracaibo

    Atmospheric Science Data Center

    2013-04-18

    article title:  Oil Slicks on Lake Maracaibo, Venezuela     View Larger Image Several oil slicks occurred on Lake Maracaibo in northwestern Venezuela between ... wave facets divert reflected rays into many directions. An oil film dampens the presence of small wind-driven "capillary" waves, resulting ...

  19. Lake Effect Clouds

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The lake effect is particularly clear in this Sea-viewing Wide field-of-view Sensor (SeaWiFS) true-color image of the North American Great Lakes region, acquired December 5, 2000. Lakes Nipigon, Superior, and Michigan show striking contrasts between clear and cloudy air as the wind blows from the northwest across the lakes. As it flows across the relatively warm lakes, the cold dry air gathers heat and moisture from the surface. The warm moist air rises into the atmosphere and mixes vigorously with the cold dry air above. The layer of warm moist air deepens as it travels across the lake. Some of the evaporated water from the lake condenses into streamers of fog rising from the surface, while much of the moisture condenses to form a stratocumulus cloud in the upper half of the mixed layer. The cloud-forming water droplets may freeze into ice crystals and, due to accumulated water deposition over time, grow into snowflakes. This process can generate snowstorms that produce significant amounts of snowfall downwind. It is not uncommon for lake effect snowstorms to produce as much as two feet of snow within a 24-hour period in northwestern parts of New York and Pennsylvania. Image provided by the SeaWiFS Project, NASA/Goddard Space Flight Center, and ORBIMAGE

  20. GREAT LAKES LIMNOLOGY MONITORING

    EPA Science Inventory

    The Great Lakes National Program Office (GLNPO) of the United States Environmental Protection Agency (USEPA) has primary responsibility within the U.S. for conducting surveillance monitoring of the offshore waters of the Great Lakes. This monitoring is intended to fulfill provis...

  1. The Great Lakes.

    ERIC Educational Resources Information Center

    Seasons, 1987

    1987-01-01

    The Great Lakes are one of the world's greatest reserviors of fresh water, the foundation of Ontario's economic development, a primary force in ecological systems, and a base for pleasure and recreation. These lakes and their relationship with people of Canada and the United States can be useful as a subject for teaching the impact of human…

  2. The lakes of Titan

    USGS Publications Warehouse

    Stofan, E.R.; Elachi, C.; Lunine, J.I.; Lorenz, R.D.; Stiles, B.; Mitchell, K.L.; Ostro, S.; Soderblom, L.; Wood, C.; Zebker, H.; Wall, S.; Janssen, M.; Kirk, R.; Lopes, R.; Paganelli, F.; Radebaugh, J.; Wye, L.; Anderson, Y.; Allison, M.; Boehmer, R.; Callahan, P.; Encrenaz, P.; Flamini, E.; Francescetti, G.; Gim, Y.; Hamilton, G.; Hensley, S.; Johnson, W.T.K.; Kelleher, K.; Muhleman, D.; Paillou, P.; Picardi, G.; Posa, F.; Roth, L.; Seu, R.; Shaffer, S.; Vetrella, S.; West, R.

    2007-01-01

    The surface of Saturn's haze-shrouded moon Titan has long been proposed to have oceans or lakes, on the basis of the stability of liquid methane at the surface. Initial visible and radar imaging failed to find any evidence of an ocean, although abundant evidence was found that flowing liquids have existed on the surface. Here we provide definitive evidence for the presence of lakes on the surface of Titan, obtained during the Cassini Radar flyby of Titan on 22 July 2006 (T16). The radar imaging polewards of 70?? north shows more than 75 circular to irregular radar-dark patches, in a region where liquid methane and ethane are expected to be abundant and stable on the surface. The radar-dark patches are interpreted as lakes on the basis of their very low radar reflectivity and morphological similarities to lakes, including associated channels and location in topographic depressions. Some of the lakes do not completely fill the depressions in which they lie, and apparently dry depressions are present. We interpret this to indicate that lakes are present in a number of states, including partly dry and liquid-filled. These northern-hemisphere lakes constitute the strongest evidence yet that a condensable-liquid hydrological cycle is active in Titan's surface and atmosphere, in which the lakes are filled through rainfall and/or intersection with the subsurface 'liquid methane' table. ??2007 Nature Publishing Group.

  3. Great Lakes Teacher's Guide.

    ERIC Educational Resources Information Center

    Reid, Ron

    The Great Lakes are one of the world's greatest reservoirs of fresh water, the foundation of Ontario's economic development, a primary force in ecological systems, and a base for pleasure and recreation. They are also a magnificent resource for the teachers of Ontario. Study of the Great Lakes can bring to life the factors that shape the ecology…

  4. Lake trophic applications: Wisconsin

    NASA Technical Reports Server (NTRS)

    Scarpace, F.

    1981-01-01

    Efforts to classify the water quality characteristics of lakes using LANDSAT imagery are reported. Image processing and registration techniques are described. A lake classification scheme which involves the assignment of a trophic class number was used in the data analysis. The resulting values were compared to the corresponding rank assignment derived from field measurements.

  5. Lake Wobegon Dice

    ERIC Educational Resources Information Center

    Moraleda, Jorge; Stork, David G.

    2012-01-01

    We introduce Lake Wobegon dice, where each die is "better than the set average." Specifically, these dice have the paradoxical property that on every roll, each die is more likely to roll greater than the set average on the roll, than less than this set average. We also show how to construct minimal optimal Lake Wobegon sets for all "n" [greater…

  6. Lakes and reservoirs

    SciTech Connect

    Taub, F.B.

    1984-01-01

    This volume in the Ecosystems of the World series studies lakes and reservoirs. The book opens with a discussion of the ecosystem processes that are common to all lakes and reservoirs and then proceeds to a description of mathematical models of these processes. The chapters concentrate on lakes and reservoirs in different parts of the world, ranging from polar to tropical lakes, and in many of the chapters the effects of human activities such as dam construction, increased nutrient inputs, toxic contaminants and fish introduction, are also considered. The book concludes with a summary of the efforts at lake restoration that are being undertaken in many communities in an attempt to undo the damage that has resulted from some of these activities.

  7. Lake trout in northern Lake Huron spawn on submerged drumlins

    USGS Publications Warehouse

    Riley, Stephen C.; Binder, Thomas; Wattrus, Nigel J.; Faust, Matthew D.; Janssen, John; Menzies, John; Marsden, J. Ellen; Ebener, Mark P.; Bronte, Charles R.; He, Ji X.; Tucker, Taaja R.; Hansen, Michael J.; Thompson, Henry T.; Muir, Andrew M.; Krueger, Charles C.

    2014-01-01

    Recent observations of spawning lake trout Salvelinus namaycush near Drummond Island in northern Lake Huron indicate that lake trout use drumlins, landforms created in subglacial environments by the action of ice sheets, as a primary spawning habitat. From these observations, we generated a hypothesis that may in part explain locations chosen by lake trout for spawning. Most salmonines spawn in streams where they rely on streamflows to sort and clean sediments to create good spawning habitat. Flows sufficient to sort larger sediment sizes are generally lacking in lakes, but some glacial bedforms contain large pockets of sorted sediments that can provide the interstitial spaces necessary for lake trout egg incubation, particularly if these bedforms are situated such that lake currents can penetrate these sediments. We hypothesize that sediment inclusions from glacial scavenging and sediment sorting that occurred during the creation of bedforms such as drumlins, end moraines, and eskers create suitable conditions for lake trout egg incubation, particularly where these bedforms interact with lake currents to remove fine sediments. Further, these bedforms may provide high-quality lake trout spawning habitat at many locations in the Great Lakes and may be especially important along the southern edge of the range of the species. A better understanding of the role of glacially-derived bedforms in the creation of lake trout spawning habitat may help develop powerful predictors of lake trout spawning locations, provide insight into the evolution of unique spawning behaviors by lake trout, and aid in lake trout restoration in the Great Lakes.

  8. Spatial patterns in PCB concentrations of Lake Michigan lake trout

    USGS Publications Warehouse

    Madenjian, Charles P.; DeSorcie, Timothy J.; Stedman, Ralph M.; Brown, Edward H., Jr.; Eck, Gary W.; Schmidt, Larry J.; Hesselberg, Robert J.; Chernyak, Sergei M.; Passino-Reader, Dora R.

    1999-01-01

    Most of the PCB body burden in lake trout (Salvelinus namaycush) of the Great Lakes is from their food. PCB concentrations were determined in lake trout from three different locations in Lake Michigan during 1994–1995, and lake trout diets were analyzed at all three locations. The PCB concentrations were also determined in alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax), bloater (Coregonus hoyi), slimy sculpin (Cottus cognatus), and deepwater sculpin (Myoxocephalus thompsoni), five species of prey fish eaten by lake trout in Lake Michigan, at three nearshore sites in the lake. Despite the lack of significant differences in the PCB concentrations of alewife, rainbow smelt, bloater, slimy sculpin, and deepwater sculpin from the southeastern nearshore site near Saugatuck (Michigan) compared with the corresponding PCB concentrations from the northwestern nearshore site near Sturgeon Bay (Wisconsin), PCB concentrations in lake trout at Saugatuck were significantly higher than those at Sturgeon Bay. The difference in the lake trout PCB concentrations between Saugatuck and Sturgeon Bay could be explained by diet differences. The diet of lake trout at Saugatuck was more concentrated in PCBs than the diet of Sturgeon Bay lake trout, and therefore lake trout at Saugatuck were more contaminated in PCBs than Sturgeon Bay lake trout. These findings were useful in interpreting the long-term monitoring series for contaminants in lake trout at both Saugatuck and the Wisconsin side of the lake.

  9. Evidence of offshore lake trout reproduction in Lake Huron

    USGS Publications Warehouse

    DeSorcie, Timothy J.; Bowen, Charles A., II

    2003-01-01

    Six Fathom Bank-Yankee Reef, an offshore reef complex, was an historically important spawning area believed to represent some of the best habitat for the rehabilitation of lake trout Salvelinus namaycush in Lake Huron. Since 1986, lake trout have been stocked on these offshore reefs to reestablish self-sustaining populations. We sampled with beam trawls to determine the abundance of naturally reproduced age-0 lake trout on these offshore reefs during May-July in 1994-1998 and 2000-2002. In total, 123 naturally reproduced lake trout fry were caught at Six Fathom Bank, and 2 naturally reproduced lake trout fry were caught at nearby Yankee Reef. Our findings suggest that this region of Lake Huron contains suitable habitat for lake trout spawning and offers hope that lake trout rehabilitation can be achieved in the main basin of Lake Huron.

  10. Lake whitefish and lake herring population structure and niche in ten south-central Ontario lakes

    USGS Publications Warehouse

    Carl, Leon M.; McGuiness, Fiona

    2006-01-01

    This study compares simple fish communities of ten oligotrophic lakes in south-central Ontario. Species densities and population size structure vary significantly among these lake communities depending on fish species present beyond the littoral zone. Lake whitefish are fewer and larger in the presence of lake herring than in their absence. Diet analysis indicates that lake whitefish shift from feeding on both plankton and benthic prey when lake herring are absent to a primarily benthic feeding niche in the presence of lake herring. When benthic round whitefish are present, lake whitefish size and density decline and they move lower in the lake compared to round whitefish. Burbot are also fewer and larger in lakes with lake herring than in lakes without herring. Burbot, in turn, appear to influence the population structure of benthic coregonine species. Lower densities of benthic lake whitefish and round whitefish are found in lakes containing large benthic burbot than in lakes with either small burbot or where burbot are absent. Predation on the pelagic larvae of burbot and lake whitefish by planktivorous lake herring alters the size and age structure of these populations. As life history theory predicts, those species with poor larval survival appear to adopt a bet-hedging life history strategy of long-lived individuals as a reproductive reserve.

  11. Contribution of genosystematics to current concepts of phylogeny and classification of bryophytes.

    PubMed

    Troitsky, A V; Ignatov, M S; Bobrova, V K; Milyutina, I A

    2007-12-01

    This paper is a survey of the current state of molecular studies on bryophyte phylogeny. Molecular data have greatly contributed to developing a phylogeny and classification of bryophytes. The previous traditional systems of classification based on morphological data are being significantly revised. New data of the authors are presented on phylogeny of Hypnales pleurocarpous mosses inferred from nucleotide sequence data of the nuclear DNA internal transcribed spacers ITS1-2 and the trnL-F region of the chloroplast genome. PMID:18205621

  12. Echinothurioid phylogeny and the phylogenetic significance of Kamptosoma (Echinoidea: Echinodermata)

    NASA Astrophysics Data System (ADS)

    Mooi, Rich; Constable, Heather; Lockhart, Susanne; Pearse, John

    2004-07-01

    The Echinothurioida is an unusual group of regular sea urchins that are characterized by soft, flexible tests and in some cases, hoof-shaped spines used for locomotion across soft, deep-sea sediments. As far as is known, all species are armed with venom-bearing spines that have been known to cause serious injury in humans. There are 50 species of echinothurioids arranged in 11 extant genera. Their fossil record is very poor, being limited to two additional fossil taxa (one of which is only tentatively considered an echinothurioid), two assigned to extant taxa, and three of more dubious affinity. With very few exceptions, only disjointed plates are preserved—and those very rarely. Today, echinothurioids are found around the globe from as far north as the Arctic Circle and as far south as Antarctica, with a bathymetric distribution ranging from inshore on coral reefs to depths of almost 5000 m. The majority of species are characteristic of the deep sea, and consequently little is known about these urchins. Many are known only from type and associated material. Their fragile tests, deep benthic habitat, and rarity make it difficult to develop a complete picture of their morphology, and as we demonstrate, breakage of the test can lead to misinterpretations of plate architecture in some taxa. The sole Antarctic species, Kamptosoma asterias, is usually considered an echinothurioid, but its unusual morphology has made its position difficult to ascertain. In addition, previous genus-level phylogenies do not test the monophyly of the genera, and some studies even suggest that the echinothurioids themselves do not constitute a monophyletic group. This study focuses on finding a species level phylogeny of the echinothurioids in order to perform these tests, and to place the enigmatic Kamptosoma in a phylogenetic context that determines whether it is indeed an echinothurioid, and if so, to which clade it is most closely related. The present analysis surveys ambulacral

  13. Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)

    PubMed Central

    2011-01-01

    Background Introgressive events (e.g., hybridization, gene flow, horizontal gene transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene trees. Previous phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. Therefore, obtaining a resolved picture of relationships among genera and species of this tribe has been a challenging task. Here, we obtain the most comprehensive molecular dataset to date in Triticeae, including one chloroplastic and 26 nuclear genes. We aim to test whether it is possible to infer phylogenetic relationships in the face of (potentially) large-scale introgressive events and/or incomplete lineage sorting; to identify parts of the evolutionary history that have not evolved in a tree-like manner; and to decipher the biological causes of gene-tree conflicts in this tribe. Results We obtain resolved phylogenetic hypotheses using the supermatrix and Bayesian Concordance Factors (BCF) approaches despite numerous incongruences among gene trees. These phylogenies suggest the existence of 4-5 major clades within Triticeae, with Psathyrostachys and Hordeum being the deepest genera. In addition, we construct a multigenic network that highlights parts of the Triticeae history that have not evolved in a tree-like manner. Dasypyrum, Heteranthelium and genera of clade V, grouping Secale, Taeniatherum, Triticum and Aegilops, have evolved in a reticulated manner. Their relationships are thus better represented by the multigenic network than by the supermatrix or BCF trees. Noteworthy, we demonstrate that gene-tree incongruences increase with genetic distance and are greater in telomeric than centromeric genes. Together, our results suggest that recombination is the main factor decoupling gene trees from

  14. A RAD-based phylogenetics for Orestias fishes from Lake Titicaca.

    PubMed

    Takahashi, Tetsumi; Moreno, Edmundo

    2015-12-01

    The fish genus Orestias is endemic to the Andes highlands, and Lake Titicaca is the centre of the species diversity of the genus. Previous phylogenetic studies based on a single locus of mitochondrial and nuclear DNA strongly support the monophyly of a group composed of many of species endemic to the Lake Titicaca basin (the Lake Titicaca radiation), but the relationships among the species in the radiation remain unclear. Recently, restriction site-associated DNA (RAD) sequencing, which can produce a vast number of short sequences from various loci of nuclear DNA, has emerged as a useful way to resolve complex phylogenetic problems. To propose a new phylogenetic hypothesis of Orestias fishes of the Lake Titicaca radiation, we conducted a cluster analysis based on morphological similarities among fish samples and a molecular phylogenetic analysis based on RAD sequencing. From a morphological cluster analysis, we recognised four species groups in the radiation, and three of the four groups were resolved as monophyletic groups in maximum-likelihood trees based on RAD sequencing data. The other morphology-based group was not resolved as a monophyletic group in molecular phylogenies, and some members of the group were diverged from its sister group close to the root of the Lake Titicaca radiation. The evolution of these fishes is discussed from the phylogenetic relationships. PMID:26291568

  15. Lake sturgeon population characteristics in Rainy Lake, Minnesota and Ontario

    USGS Publications Warehouse

    Adams, W.E., Jr.; Kallemeyn, L.W.; Willis, D.W.

    2006-01-01

    Rainy Lake contains a native population of lake sturgeon Acipenser fulvescens that has been largely unstudied. The aims of this study were to document the population characteristics of lake sturgeon in Rainy Lake and to relate environmental factors to year-class strength for this population. Gill-netting efforts throughout the study resulted in the capture of 322 lake sturgeon, including 50 recaptures. Lake sturgeon in Rainy Lake was relatively plump and fast growing compared with a 32-population summary. Population samples were dominated by lake sturgeon between 110 and 150 cm total length. Age–structure analysis of the samples indicated few younger (<10 years) lake sturgeon, but the smallest gill net mesh size used for sampling was 102 mm (bar measure) and would not retain small sturgeon. Few lake sturgeon older than age 50 years were captured, and maximum age of sampled fish was 59 years. Few correlations existed between lake sturgeon year-class indices and both annual and monthly climate variables, except that mean June air temperature was positively correlated with year-class strength. Analysis of Rainy Lake water elevation and resulting lake sturgeon year-class strength indices across years yielded consistent but weak negative correlations between late April and early June, when spawning of lake sturgeon occurs. The baseline data collected in this study should allow Rainy Lake biologists to establish more specific research questions in the future.

  16. Whiting in Lake Michigan

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Satellites provide a view from space of changes on the Earth's surface. This series of images from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) aboard the Orbview-2 satellite shows the dramatic change in the color of Lake Michigan during the summer. The bright color that appears in late summer is probably caused by calcium carbonate-chalk-in the water. Lake Michigan always has a lot of calcium carbonate in it because the floor of the lake is limestone. During most of the year the calcium carbonate remains dissolved in the cold water, but at the end of summer the lake warms up, lowering the solubility of calcium carbonate. As a result, the calcium carbonate precipitates out of the water, forming clouds of very small solid particles that appear as bright swirls from above. The phenomenon is appropriately called a whiting event. A similar event occured in 1999, but appears to have started later and subsided earlier. It is also possible that a bloom of the algae Microcystis is responsible for the color change, but unlikely because of Lake Michigan's depth and size. Microcystis blooms have occured in other lakes in the region, however. On the shore of the lake it is possible to see the cities of Chicago, Illinois, and Milwaukee, Wisconsin. Both appear as clusters of gray-brown pixels. Image courtesy the SeaWiFS Project, NASA/Goddard Space Flight Center, and ORBIMAGE

  17. Yellowstone Lake Nanoarchaeota

    PubMed Central

    Clingenpeel, Scott; Kan, Jinjun; Macur, Richard E.; Woyke, Tanja; Lovalvo, Dave; Varley, John; Inskeep, William P.; Nealson, Kenneth; McDermott, Timothy R.

    2013-01-01

    Considerable Nanoarchaeota novelty and diversity were encountered in Yellowstone Lake, Yellowstone National Park (YNP), where sampling targeted lake floor hydrothermal vent fluids, streamers and sediments associated with these vents, and in planktonic photic zones in three different regions of the lake. Significant homonucleotide repeats (HR) were observed in pyrosequence reads and in near full-length Sanger sequences, averaging 112 HR per 1349 bp clone and could confound diversity estimates derived from pyrosequencing, resulting in false nucleotide insertions or deletions (indels). However, Sanger sequencing of two different sets of PCR clones (110 bp, 1349 bp) demonstrated that at least some of these indels are real. The majority of the Nanoarchaeota PCR amplicons were vent associated; however, curiously, one relatively small Nanoarchaeota OTU (71 pyrosequencing reads) was only found in photic zone water samples obtained from a region of the lake furthest removed from the hydrothermal regions of the lake. Extensive pyrosequencing failed to demonstrate the presence of an Ignicoccus lineage in this lake, suggesting the Nanoarchaeota in this environment are associated with novel Archaea hosts. Defined phylogroups based on near full-length PCR clones document the significant Nanoarchaeota 16S rRNA gene diversity in this lake and firmly establish a terrestrial clade distinct from the marine Nanoarcheota as well as from other geographical locations. PMID:24062731

  18. LAKE RESTORATION BY DILUTION: MOSES LAKE, WASHINGTON

    EPA Science Inventory

    Dilution water, low in macronutrients, was added to Moses Lake on three occasions in 1977 and once in 1978 during the spring-summer period. The addition resulted in reducing the annual average inflow concentration of phosphorus from about 130-140 micrograms/l to 100 micrograms/l....

  19. Phylogeny and comparative genome analysis of a Basidiomycete fungi

    SciTech Connect

    Riley, Robert W.; Salamov, Asaf; Grigoriev, Igor; Hibbett, David

    2011-03-14

    Fungi of the phylum Basidiomycota, make up some 37percent of the described fungi, and are important from the perspectives of forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, plant pathogenic rusts and smuts, and some human pathogens. To better understand these important fungi, we have undertaken a comparative genomic analysis of the Basidiomycetes with available sequenced genomes. We report a phylogeny that sheds light on previously unclear evolutionary relationships among the Basidiomycetes. We also define a `core proteome? based on protein families conserved in all Basidiomycetes. We identify key expansions and contractions in protein families that may be responsible for the degradation of plant biomass such as cellulose, hemicellulose, and lignin. Finally, we speculate as to the genomic changes that drove such expansions and contractions.

  20. Reconstructing phylogeny from the multifractal spectrum of mitochondrial DNA

    NASA Astrophysics Data System (ADS)

    Glazier, James A.; Raghavachari, Sridhar; Berthelsen, Cheryl L.; Skolnick, Mark H.

    1995-03-01

    Conventional methods of phylogenetic reconstruction from DNA sequences require simplified models of evolutionary dynamics. We present a method based on fractal analysis to reconstruct the evolutionary history of organisms from mitochondrial DNA sequences. We map animal mtDNA into four-dimensional random walks and estimate their long range correlations using multifractal spectra. We see systematic changes in correlations in mtDNA sequences across taxonomic lines, which translate into changes in the scaling of the random walks. We use cluster analysis to group the multifractal spectra and obtain the phylogeny of the organisms. Though our method uses no a priori assumptions and is independent of gene order, it yields phylogenetic relationships broadly consistent with established results. Several recent papers have analyzed DNA using fractal analysis and have found long range correlations. However, no one has succeeded in using them to deduce biologically significant relationships.

  1. A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

    PubMed Central

    Challis, Christopher J.; Schmidler, Scott C.

    2012-01-01

    We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

  2. Regeneration across metazoan phylogeny: lessons from model organisms.

    PubMed

    Li, Qiao; Yang, Hao; Zhong, Tao P

    2015-02-20

    Comprehending the diversity of the regenerative potential across metazoan phylogeny represents a fundamental challenge in biology. Invertebrates like Hydra and planarians exhibit amazing feats of regeneration, in which an entire organism can be restored from minute body segments. Vertebrates like teleost fish and amphibians can also regrow large sections of the body. While this regenerative capacity is greatly attenuated in mammals, there are portions of major organs that remain regenerative. Regardless of the extent, there are common basic strategies to regeneration, including activation of adult stem cells and proliferation of differentiated cells. Here, we discuss the cellular features and molecular mechanisms that are involved in regeneration in different model organisms, including Hydra, planarians, zebrafish and newts as well as in several mammalian organs. PMID:25697100

  3. Hemiplasy and homoplasy in the karyotypic phylogenies of mammals.

    PubMed

    Robinson, Terence J; Ruiz-Herrera, Aurora; Avise, John C

    2008-09-23

    Phylogenetic reconstructions are often plagued by difficulties in distinguishing phylogenetic signal (due to shared ancestry) from phylogenetic noise or homoplasy (due to character-state convergences or reversals). We use a new interpretive hypothesis, termed hemiplasy, to show how random lineage sorting might account for specific instances of seeming "phylogenetic discordance" among different chromosomal traits, or between karyotypic features and probable species phylogenies. We posit that hemiplasy is generally less likely for underdominant chromosomal polymorphisms (i.e., those with heterozygous disadvantage) than for neutral polymorphisms or especially for overdominant rearrangements (which should tend to be longer-lived), and we illustrate this concept by using examples from chiropterans and afrotherians. Chromosomal states are especially powerful in phylogenetic reconstructions because they offer strong signatures of common ancestry, but their evolutionary interpretations remain fully subject to the principles of cladistics and the potential complications of hemiplasy. PMID:18787123

  4. Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates).

    PubMed

    Singer, Silke S; Schmitz, Jürgen; Schwiegk, Claudia; Zischler, Hans

    2003-03-01

    Transpositions of primate-specific Alu elements were applied as molecular cladistic markers in a phylogenetic analysis of South American primates. Seventy-four human and platyrrhine loci containing intronic Alu elements were PCR screened in various New World monkeys and the human outgroup to detect the presence of orthologous retrotransposons informative of New World monkey phylogeny. Six loci revealed size polymorphism in the amplification pattern, indicating a shared derived character state due to the presence of orthologous Alu elements confirmed by subsequent sequencing. Three markers corroborate (1) New World monkey monophyly and one marker supports each of the following callitrichine relationships: (2) Callithrix and Cebuella are more closely related to each other than to any other callitrichine, (3) the callitrichines form a monophyletic clade including Callimico, and (4) the next living relatives to the callitrichines are Cebus, Saimiri, and Aotus. PMID:12644406

  5. Quantifying Age-dependent Extinction from Species Phylogenies.

    PubMed

    Alexander, Helen K; Lambert, Amaury; Stadler, Tanja

    2016-01-01

    Several ecological factors that could play into species extinction are expected to correlate with species age, i.e., time elapsed since the species arose by speciation. To date, however, statistical tools to incorporate species age into likelihood-based phylogenetic inference have been lacking. We present here a computational framework to quantify age-dependent extinction through maximum likelihood parameter estimation based on phylogenetic trees, assuming species lifetimes are gamma distributed. Testing on simulated trees shows that neglecting age dependence can lead to biased estimates of key macroevolutionary parameters. We then apply this method to two real data sets, namely a complete phylogeny of birds (class Aves) and a clade of self-compatible and -incompatible nightshades (Solanaceae), gaining initial insights into the extent to which age-dependent extinction may help explain macroevolutionary patterns. Our methods have been added to the R package TreePar. PMID:26405218

  6. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

    PubMed Central

    Spielman, Stephanie J.; Wilke, Claus O.

    2015-01-01

    We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve. PMID:26397960

  7. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.

    PubMed

    Spielman, Stephanie J; Wilke, Claus O

    2015-01-01

    We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve. PMID:26397960

  8. Lake Mead, NV

    NASA Technical Reports Server (NTRS)

    1973-01-01

    Lake Mead, Nevada, (36.0N, 114.5E) where the water from the Colorado River empties after it's 273 mile journey through the Grand Canyon of Arizona is the subject of this photo. Other features of interest are Hoover Dam on the south shore of Lake Mead where cheap hydroelectric power is secondary to the water resources made available in this northern desert region and the resort city of Las Vegas, just to the west of Lake Mead. In this harsh desert environment, color infrared photography readily penetrates haze, detects and portrays vegetation as shades of red.

  9. Estimating divergence dates and substitution rates in the Drosophila phylogeny.

    PubMed

    Obbard, Darren J; Maclennan, John; Kim, Kang-Wook; Rambaut, Andrew; O'Grady, Patrick M; Jiggins, Francis M

    2012-11-01

    An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25-40 Ma) is closer to being compatible with independent fossil-derived dates (20-50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will

  10. Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

    PubMed Central

    Obbard, Darren J.; Maclennan, John; Kim, Kang-Wook; Rambaut, Andrew; O’Grady, Patrick M.; Jiggins, Francis M.

    2012-01-01

    An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25–40 Ma) is closer to being compatible with independent fossil-derived dates (20–50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will

  11. Phylogeny and biogeography of the carnivorous plant family Sarraceniaceae.

    PubMed

    Ellison, Aaron M; Butler, Elena D; Hicks, Emily Jean; Naczi, Robert F C; Calie, Patrick J; Bell, Charles D; Davis, Charles C

    2012-01-01

    The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family's phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44-53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25-44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14-32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2-7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, <3 Mya

  12. COI barcodes and phylogeny of doves (Columbidae family).

    PubMed

    Khan, Haseeb Ahmad; Arif, Ibrahim Abdulwahid

    2013-12-01

    Cytochrome oxidase subunit I (COI) gene has been recognized as an authentic tool for species identification. Besides its potential barcoding capacity, COI sequences have also been used for inferring the phylogeny. Phylogenetic relationships among genera of Columbidae (pigeons and doves family) have not been fully resolved because of scarce sampling of taxa and limited availability of sequence data. In this study, we have evaluated the efficiency of COI barcodes for species identification and phylogenetic analysis of various doves. We sequenced the 693 bp region of COI gene of three species of doves including Oena capensis, Streptopelia decaocto, and Streptopelia senegalensis. After retrieving the relevant sequences from the GenBank, the entire data-set of 85 sequences represented 25 dove species from 11 different genera of the family Columbidae. The COI sequences of four species including Chalcophaps indica (two specimens), Columbina inca (five specimens), Geopelia striata (three specimens), and Macropygia phasianella (three specimens) were identical. The mean intraspecific base differences ranged from 0 to 37 while the P-distances ranged between 0 and 0.058. For most of the species, the P-distances were ≤ 0.008. Phylogenetic analysis differentiated the taxa into three major clusters. One of the clusters grouped five genera including Claravis, Columbina, Gallicolumba, Geopelia, and Geotrygon. The remaining two clusters grouped three genera each including Chalcophaps, Oena, and Turtur in one cluster and Macropygia, Streptopelia, and Zenaida in another cluster. Further sub-clustering clearly separated all the genera into individual clusters except two discrepancies for the genera Streptopelia and Turtur. Species-level cladistics clearly separated all the species into distinctive clades. In conclusion, COI barcoding is a powerful tool for species identification with added information on phylogenetic inference. The finding of this study will help to understand the

  13. An Alu-Based Phylogeny of Lemurs (Infraorder: Lemuriformes)

    PubMed Central

    McLain, Adam T.; Meyer, Thomas J.; Faulk, Christopher; Herke, Scott W.; Oldenburg, J. Michael; Bourgeois, Matthew G.; Abshire, Camille F.

    2012-01-01

    Lemurs (infraorder: Lemuriformes) are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ∼55–60 million years ago (mya). Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs), to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus) was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction) verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the exclusion of

  14. An alu-based phylogeny of lemurs (infraorder: Lemuriformes).

    PubMed

    McLain, Adam T; Meyer, Thomas J; Faulk, Christopher; Herke, Scott W; Oldenburg, J Michael; Bourgeois, Matthew G; Abshire, Camille F; Roos, Christian; Batzer, Mark A

    2012-01-01

    LEMURS (INFRAORDER: Lemuriformes) are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ∼55-60 million years ago (mya). Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs), to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus) was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction) verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the exclusion of

  15. Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae

    PubMed Central

    Ellison, Aaron M.; Butler, Elena D.; Hicks, Emily Jean; Naczi, Robert F. C.; Calie, Patrick J.; Bell, Charles D.; Davis, Charles C.

    2012-01-01

    The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family's phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44–53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25–44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14–32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2–7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene

  16. Constructing perfect phylogenies and proper triangulations for three-state characters

    PubMed Central

    2012-01-01

    In this paper, we study the problem of constructing perfect phylogenies for three-state characters. Our work builds on two recent results. The first result states that for three-state characters, the local condition of examining all subsets of three characters is sufficient to determine the global property of admitting a perfect phylogeny. The second result applies tools from minimal triangulation theory to the partition intersection graph to determine if a perfect phylogeny exists. Despite the wealth of combinatorial tools and algorithms stemming from the chordal graph and minimal triangulation literature, it is unclear how to use such approaches to efficiently construct a perfect phylogeny for three-state characters when the data admits one. We utilize structural properties of both the partition intersection graph and the original data in order to achieve a competitive time bound. PMID:23006612

  17. A phylogeny of cockroaches and related insects based on DNA sequence of mitochondrial ribosomal RNA genes.

    PubMed Central

    Kambhampati, S

    1995-01-01

    Cockroaches are among the most ancient winged insects, the earliest fossils dating back to about 400 million years. Several conflicting phylogenies for cockroach families, subfamilies, and genera have been proposed in the past. In addition, the relationship of Cryptocercidae to other cockroach families and the relationship between the cockroach, Cryptocercus punctulatus, and the termite, Mastotermes darwiniensis, have generated debate. In this paper, a phylogeny for cockroaches, mantids, and termites based on DNA sequence of the mitochondrial ribosomal RNA genes is presented. The results indicated that cockroaches are a monophyletic group, whose sister group is Mantoidea. The inferred relationship among cockroach families was in agreement with the presently accepted phylogeny. However, there was only partial congruence at the subfamily and the generic levels. The phylogeny inferred here does not support a close relationship between C. punctulatus and M. darwiniensis. The apparent synapomorphies of these two species are likely a manifestation of convergent evolution because there are similarities in biology and habitat. PMID:7534409

  18. Abundance and Diversity of Ammonia-Oxidizing Archaea and Bacteria in Sediments of Trophic End Members of the Laurentian Great Lakes, Erie and Superior

    PubMed Central

    Bollmann, Annette; Bullerjahn, George S.; McKay, Robert Michael

    2014-01-01

    Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes. PMID:24819357

  19. Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior.

    PubMed

    Bollmann, Annette; Bullerjahn, George S; McKay, Robert Michael

    2014-01-01

    Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes. PMID:24819357

  20. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach.

    PubMed

    Erickson, David L; Jones, Frank A; Swenson, Nathan G; Pei, Nancai; Bourg, Norman A; Chen, Wenna; Davies, Stuart J; Ge, Xue-Jun; Hao, Zhanqing; Howe, Robert W; Huang, Chun-Lin; Larson, Andrew J; Lum, Shawn K Y; Lutz, James A; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D; Fang-Sun, I; Wright, S Joseph; Wolf, Amy T; Ye, W; Xing, Dingliang; Zimmerman, Jess K; Kress, W John

    2014-01-01

    Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

  1. Can lake sensitivity to desiccation be predicted from lake geometry?

    NASA Astrophysics Data System (ADS)

    Torabi Haghighi, Ali; Menberu, Meseret Walle; Aminnezhad, Mousa; Marttila, Hannu; Kløve, Bjørn

    2016-08-01

    Declining lake levels (Aral Sea syndrome) can be caused by changes in climate, increased water use or changed regulation patterns. This paper introduces a novel lake geometry index (LGI) to quantify lake hydrological characteristics. The index was developed using a large representative dataset of lake hypsographic characteristics from 152 lakes and man-made reservoirs. Using the LGI index, lakes can be classified into five groups: groups 1-4 when LGI is 0.5-2.5, 2.5-4.5, 4.5-6.5 and 6.5-8.5, respectively, and group 5 when LGI is >8.5. Naturally shallow and vast lakes and wetlands fall into the first group and deep man-made reservoirs in narrow valleys are in group 5. The response of three different lake systems (LGI 0.75, 2.75 and 6.5) to different water flow scenarios was then simulated using the water balance equation. From this, the index 'potential lake area' (Apot) was developed to show lake responses to changed hydro-climatological conditions. Apot and LGI can be used to classify lakes into open or closed systems. Simulations showed that lakes with low LGI have a shorter response time to flow and climate changes. As a result, the impact of water balance restoration is faster for lakes with low LGI than for lakes with high LGI. The latter are also more vulnerable to climate variation and change.

  2. Next-Generation Anchor Based Phylogeny (NexABP): Constructing phylogeny from Next-generation sequencing data

    PubMed Central

    Roychowdhury, Tanmoy; Vishnoi, Anchal; Bhattacharya, Alok

    2013-01-01

    Whole genome sequences are ideally suited for deriving evolutionary relationship among organisms. With the availability of Next Generation sequencing (NGS) datasets in an unprecedented scale, it will be highly desirable if phylogenetic analysis can be carried out using short read NGS data. We described here an anchor based approach NexABP for phylogenetic construction of closely related strains/isolates from NGS data. This approach can be used even in the absence of a fully assembled reference genome and works by reducing the complexity of the datasets without compromising results. NexABP was used for constructing phylogeny of different strains of some of the common pathogens, such as Mycobacterium tuberculosis, Vibrio cholera and Escherichia coli. In addition to classification into distinct lineages, NexABP could resolve inner branches and also allow statistical testing using bootstrap analysis. We believe that there are some clear advantages of using NexABP based phylogenetic analysis as compared to other methods. PMID:24022334

  3. GREAT LAKES PLANKTON PROGRAM

    EPA Science Inventory

    Phytoplankton, which have short carbon turnover rates, are sensitive to water quality conditions and grazing by zooplankton, and thus respond rapidly to perturbations of the lake ecosystem. The determination of phytoplankton abundance and species composition is one method to tra...

  4. Is Lake Tahoe Terminal?

    NASA Astrophysics Data System (ADS)

    Coats, R. N.; Reuter, J.; Heyvaert, A.; Lewis, J.; Sahoo, G. B.; Schladow, G.; Thorne, J. H.

    2014-12-01

    Lake Tahoe, an iconic ultra-oligotrophic lake in the central Sierra Nevada, has been studied intensively since 1968, with the goal of understanding and ultimately controlling its eutrophication and loss of clarity. Research on the lake has included a) periodic profiles of primary productivity, nutrients, temperature, and plankton; b) Secchi depth; c) nutrient limitation experiments; d) analysis of sediment cores; e) radiocarbon dating of underwater in-place tree stumps; g) analysis of long-term temperature trends. Work in its watershed has included a) monitoring of stream discharge, sediment and nutrients at up to 20 stream gaging stations; b) monitoring of urban runoff water quality at selected sites; c) development of a GIS data base, including soils, vegetation, and land use. Based on these studies, we know that a) primary productivity in the lake is limited by phosphorus, and continues to increase; b) the loss of clarity continues, but at a declining rate; c) the lake has been warming since 1970, and its resistance to deep mixing is increasing; d) historically the lake level drops below the outlet elevation about one year in seven; e) 6300 to 4300 yrs BP lake level was below the present outlet elevation long enough for large trees to grow; f) the date of the peak snowmelt runoff is shifting toward earlier dates; g) after accounting for annual runoff, loads of nutrients and suspended sediment have declined significantly in some basin streams since 1980. Downscaled outputs from GCM climatic models have recently been used to drive hydrologic models and a lake clarity model, projecting future trends in the lake and watersheds. Results show a) the temperature and thermal stability will likely continue to increase, with deep mixing shutting down in the latter half of this century; b) the lake may drop below the outlet for an extended period beginning about 2085; c) the annual snowpack will continue to decline, with earlier snowmelt and shift from snowfall to rain; d

  5. Lake Superior, Duluth, MN

    NASA Technical Reports Server (NTRS)

    1973-01-01

    This view shows the west end of Lake Superior and Duluth, MN (47.0N, 91.0W). Portions of Minnesota, Michigan and Ontario, Canada are in the scene. The Duluth metropolitan area is at the west end of the lake. The discoloration plume in the water at Duluth is the result of tailings from the iron ore smelters that process the iron ore from the nearby open pit mines seen near the upper left corner of the photo.

  6. Lake Chad, Chad, Africa

    NASA Technical Reports Server (NTRS)

    1988-01-01

    The fluctuating water levels of Lake Chad, (13.0N, 15.0E) at the intersection of the borders of Chad, Niger and Cameroon in the Sahara Desert, is an index of the drought in Africa. The lake level continues to decrease as indicated by the growing number and extent of emerging islands as previously submerged ancient sand dunes become visible. The water impounded between the dunes is probably because of local rainfall rather than a reversal of desertification.

  7. WHISKER LAKE WILDERNESS, WISCONSIN.

    USGS Publications Warehouse

    Schulz, Klaus J.

    1984-01-01

    The mineral-resource potential of the Whisker Lake Wilderness in northeastern Wisconsin was evaluated. Only a strip along the southwest corner of the wilderness is assessed as having probable mineral-resource potential. If mineral deposits exist, they probably are of the massive sulfide type. The geologic terrain precludes the presence of fossil fuel resources. Sand and gravel and peat in swampy lowlands are the only resources of the Whisker lake Wilderness.

  8. Dragon Lake, Siberia

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Nicknamed 'Dragon Lake,' this body of water is formed by the Bratskove Reservoir, built along the Angara river in southern Siberia, near the city of Bratsk. This image was acquired in winter, when the lake is frozen. This image was acquired by Landsat 7's Enhanced Thematic Mapper plus (ETM+) sensor on December 19, 1999. This is a natural color composite image made using blue, green, and red wavelengths. Image provided by the USGS EROS Data Center Satellite Systems Branch

  9. Salt Lake City, Utah

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Salt Lake City, Utah, will host the 2002 Winter Olympic Games. The city is located on the southeastern shore of the Great Salt Lake and sits to the west of the Wasatch Mountains, which rise more than 3,500 meters (10,000 feet) above sea level. The city was first settled in 1847 by pioneers seeking relief from religious persecution. Today Salt Lake City, the capital of Utah, is home to more than 170,000 residents. This true-color image of Salt Lake City was acquired by the Enhanced Thematic Mapper Plus (ETM+), flying aboard Landsat 7, on May 26, 2000. The southeastern tip of the Great Salt Lake is visible in the upper left of the image. The furrowed green and brown landscape running north-south is a portion of the Wasatch Mountains, some of which are snow-capped (white pixels). The greyish pixels in the center of the image show the developed areas of the city. A number of water reservoirs can be seen east of the mountain range. Salt Lake City International Airport is visible on the northwestern edge of the city. About 20 miles south of the airport is the Bingham Canyon Copper Mine (tan pixels), the world's largest open pit excavation. See also this MODIS image of Utah. Image courtesy NASA Landsat7 Science Team and USGS Eros Data Center

  10. Is Lake Chabot Eutrophic?

    NASA Astrophysics Data System (ADS)

    Pellegrini, K.; Logan, J.; Esterlis, P.; Lew, A.; Nguyen, M.

    2013-12-01

    Introduction/Abstract: Lake Chabot is an integral part of the East Bay watershed that provides habitats for animals and recreation for humans year-round. Lake Chabot has been in danger of eutrophication due to excessive dumping of phosphorous and nitrogen into the water from the fertilizers of nearby golf courses and neighboring houses. If the lake turned out to be eutrophified, it could seriously impact what is currently the standby emergency water supply for many Castro Valley residents. Eutrophication is the excessive richness of nutrients such as nitrogen and phosphorus in a lake, usually as a result of runoff. This buildup of nutrients causes algal blooms. The algae uses up most of the oxygen in the water, and when it dies, it causes the lake to hypoxify. The fish in the lake can't breathe, and consequently suffocate. Other oxygen-dependant aquatic creatures die off as well. Needless to say, the eutrophication of a lake is bad news for the wildlife that lives in or around it. The level of eutrophication in our area in Northern California tends to increase during the late spring/early summer months, so our crew went out and took samples of Lake Chabot on June 2. We focused on the area of the lake where the water enters, known on the map as Honker Bay. We also took readings a ways down in deeper water for comparison's sake. Visually, the lake looked in bad shape. The water was a murky green that glimmered with particulate matter that swirled around the boat as we went by. In the Honker Bay region where we focused our testing, there were reeds bathed in algae that coated the surface of the lake in thick, swirling patterns. Surprisingly enough, however, our test results didn't reveal any extreme levels of phosphorous or nitrogen. They were slightly higher than usual, but not by any significant amount. The levels we found were high enough to stimulate plant and algae growth and promote eutrophication, but not enough to do any severe damage. After a briefing with a

  11. Availability of lake trout reproductive habitat in the Great Lakes

    USGS Publications Warehouse

    Edsall, Thomas A.; Kennedy, Gregory W.

    1995-01-01

    A decades-long program to reestablish self-sustaining stocks of lake trout (Salvelinus namaycush) in the four lower Great Lakes produced excellent fisheries supported by stocked fish. These fish spawned widely and small numbers of their offspring were collected intermittently from Lakes Michigan, Huron, and Ontario, but no self-sustaining stocks were established. Irt this paper we address habitat sufficiency as a factor in the failure of stocked lake trout to established self-sustaining populations in the four lower Great Lakes. We present the previously unpublished results of lake trout spawning habitat surveys conducted at seven sites in the Great Lakes since 1987 and we compare them with the published results of similar surveys conducted at 24 other sites in the four lower lakes since 1981. Our evaluation indicates all but two of these sites can support the production of viable fry from spawnings by the shallow-water strains of lake trout that are stocked in the Great Lakes. However, some of the best spawning, egg, and fry habitat in the lower Great Lakes seems to be at deeper offshore sites that may be unattractive to these shallow-water strains. Thus, we suggest also stocking the lower four lakes with strains from Lake Superior that might more fully exploit the best spawning habitat at these deeper, offshore sites.

  12. Contaminants in American alligator eggs from Lake Apopka, Lake Griffin, and Lake Okeechobee, Florida

    USGS Publications Warehouse

    Heinz, G.H.; Percival, H.F.; Jennings, Michael L.

    1991-01-01

    Residues of organochlorine pesticides, polychlorinated biphenyls (PCBs), and 16 elements were measured in American alligator (Alligator mississippiensis) eggs collected in 1984 from Lakes Apopka, Griffin, and Okeechobee in central and south Florida. Organochlorine pesticides were highest in eggs from Lake Apopka. None of the elements appeared to be present at harmful concentrations in eggs from any of the lakes. A larger sample of eggs was collected in 1985, but only from Lakes Griffin, a lake where eggs were relatively clean, and Apopka, where eggs were most contaminated. In 1985, hatching success of artificially incubated eggs was lower for Lake Apopka, and several organochlorine pesticides were higher than in eggs from Lake Griffin. However, within Lake Apopka, higher levels of pesticides in chemically analyzed eggs were not associated with reduced hatching success of the remaining eggs in the clutch. Therefore, it did not appear that any of the pesticides we measured were responsible for the reduced hatching of Lake Apopka eggs.

  13. Big lake records preserved in a little lake's sediment: An example from Silver Lake, Michigan, USA

    USGS Publications Warehouse

    Fisher, T.G.; Loope, W.L.; Pierce, W.; Jol, H.M.

    2007-01-01

    We reconstruct postglacial lake-level history within the Lake Michigan basin using soil stratigraphy, ground-penetrating radar (GPR), sedimentology and 14C data from the Silver Lake basin, which lies adjacent to Lake Michigan. Stratigraphy in nine vibracores recovered from the floor of Silver Lake appears to reflect fluctuation of water levels in the Lake Michigan basin. Aeolian activity within the study area from 3,000 years (cal yr. B.P.) to the present was inferred from analysis of buried soils, an aerial photograph sequence, and GPR. Sediments in and around Silver Lake appear to contain a paleoenvironmental record that spans the entire post-glacial history of the Lake Michigan basin. We suggest that (1) a pre-Nipissing rather than a Nipissing barrier separated Silver Lake basin from the Lake Michigan basin, (2) that the Nipissing transgression elevated the water table in the Silver Lake basin about 6,500 cal yr. B.P., resulting in reestablishment of a lake within the basin, and (3) that recent dune migration into Silver Lake is associated with levels of Lake Michigan.

  14. Evidence of Lake Trout reproduction at Lake Michigan's mid-lake reef complex

    USGS Publications Warehouse

    Janssen, J.; Jude, D.J.; Edsall, T.A.; Paddock, R.W.; Wattrus, N.; Toneys, M.; McKee, P.

    2006-01-01

    The Mid-Lake Reef Complex (MLRC), a large area of deep (> 40 m) reefs, was a major site where indigenous lake trout (Salvelinus namaycush) in Lake Michigan aggregated during spawning. As part of an effort to restore Lake Michigan's lake trout, which were extirpated in the 1950s, yearling lake trout have been released over the MLRC since the mid-1980s and fall gill net censuses began to show large numbers of lake trout in spawning condition beginning about 1999. We report the first evidence of viable egg deposition and successful lake trout fry production at these deep reefs. Because the area's existing bathymetry and habitat were too poorly known for a priori selection of sampling sites, we used hydroacoustics to locate concentrations of large fish in the fall; fish were congregating around slopes and ridges. Subsequent observations via unmanned submersible confirmed the large fish to be lake trout. Our technological objectives were driven by biological objectives of locating where lake trout spawn, where lake trout fry were produced, and what fishes ate lake trout eggs and fry. The unmanned submersibles were equipped with a suction sampler and electroshocker to sample eggs deposited on the reef, draw out and occasionally catch emergent fry, and collect egg predators (slimy sculpin Cottus cognatus). We observed slimy sculpin to eat unusually high numbers of lake trout eggs. Our qualitative approaches are a first step toward quantitative assessments of the importance of lake trout spawning on the MLRC.

  15. Winter Lake Breezes near the Great Salt Lake

    NASA Astrophysics Data System (ADS)

    Crosman, Erik T.; Horel, John D.

    2016-05-01

    Case studies of lake breezes during wintertime cold air pools in Utah's Salt Lake Valley are examined. While summer breezes originating from the Great Salt Lake are typically deeper, of longer duration, and have higher wind speeds than winter breezes, the rate of inland penetration and cross-frontal temperature differences can be higher during the winter. The characteristics of winter breezes and the forcing mechanisms controlling them (e.g., snow cover, background flow, vertical stability profile, clouds, lake temperature, lake sheltering, and drainage pooling) are more complex and variable than those evident in summer. During the afternoon in the Salt Lake Valley, these lake breezes can lead to elevated pollution levels due to the transport of fine particle pollutants from over the Great Salt Lake, decreased vertical mixing depth, and increased vertical stability.

  16. Crater Lake revealed

    USGS Publications Warehouse

    Ramsey, David W.; Dartnell, Peter; Bacon, Charles R.; Robinson, Joel E.; Gardner, James V.

    2003-01-01

    Around 500,000 people each year visit Crater Lake National Park in the Cascade Range of southern Oregon. Volcanic peaks, evergreen forests, and Crater Lake’s incredibly blue water are the park’s main attractions. Crater Lake partially fills the caldera that formed approximately 7,700 years ago by the eruption and subsequent collapse of a 12,000-foot volcano called Mount Mazama. The caldera-forming or climactic eruption of Mount Mazama drastically changed the landscape all around the volcano and spread a blanket of volcanic ash at least as far away as southern Canada. Prior to the climactic event, Mount Mazama had a 400,000 year history of cone building activity like that of other Cascade volcanoes such as Mount Shasta. Since the climactic eruption, there have been several less violent, smaller postcaldera eruptions within the caldera itself. However, relatively little was known about the specifics of these eruptions because their products were obscured beneath Crater Lake’s surface. As the Crater Lake region is still potentially volcanically active, understanding past eruptive events is important to understanding future eruptions, which could threaten facilities and people at Crater Lake National Park and the major transportation corridor east of the Cascades. Recently, the lake bottom was mapped with a high-resolution multibeam echo sounder. The new bathymetric survey provides a 2m/pixel view of the lake floor from its deepest basins virtually to the shoreline. Using Geographic Information Systems (GIS) applications, the bathymetry data can be visualized and analyzed to shed light on the geology, geomorphology, and geologic history of Crater Lake.

  17. The Wandering Lake

    NASA Technical Reports Server (NTRS)

    2002-01-01

    In the area at the very far eastern corner of China's Taklimakan Desert, Lop Nor Lake was located up until some years ago. Lop Nor, also called the 'the heart of the heart' of Asia, was the place where the waters of the largest inner basin (i.e., not flowing into the sea) of the world-including the Tarim and Kum-daria Rivers-were collected. Depending on the balance between rainfall water yield and evaporation, both position and size of the lake were strongly variable, thus giving rise to the legend of the Wandering Lake. 'Lop City' was the place where Marco Polo took his last rest before facing the one-year long crossing of the Gobi Desert. Starting from the end of the 19th century, several explorers tried to find the legendary place. One such explorer was Sven Hedin, who was commissioned by the Governor of Nanjing to lead an expedition to find the lake. In 1937, the Swedish explorer published his book entitled The Wandering Lake. Comparing this very precise map from Sven Hedin's book with the above Moderate-resolution Imaging Spectroradiometer (MODIS) false-color image (acquired on October 28, 2001), one can find a faint sign on the soil where the Lop Nor was located. This image, derived using a combination of MODIS' near-infrared and red channels (vegetation in red), shows where the Tarim River waters currently end their flow. The Wandering Lake does not exist anymore. The combination of climate change and human exploitation of water resources for agriculture caused the disappearance of the lake. This image was processed by Telespazio, Earth Observation division, new products development facility in Rome, Italy. The MODIS sensor flies aboard NASA's Terra spacecraft, launched in December 1999. Caption and image courtesy Luca Pietranera, Telespazio, Rome, Italy, based on data from the MODIS Science Team

  18. Lake Sarez, Tajikistan

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Lake Sarez (top), deep in the Pamir mountains of Tajikistan, was created 90 years ago when a strong earthquake triggered a massive landslide that, in turn, became a huge dam along the Murghob River, now called the Usoi Dam. The resulting lake is perched above surrounding drainages at an elevation greater than 3000m, and is part of the watershed that drains the towering Akademi Nauk Range (see the regional image, lower). The lake is 61 km long and as deep as 500 m, and holds an estimated 17 cubic km of water. The area experiences considerable seismic activity, and scientists fear that part of the right bank may slump into the lake, creating a huge wave that will top over and possibly breach the natural dam. Such a wave would create a catastrophic flood downstream along the Bartang, Panj and Amu Darya Rivers, perhaps reaching all the way to the Aral Sea. Currently, central Asian governments, as well as the World Bank and the UN are monitoring the dam closely, and have proposed gradually lowering the lake level as a preventive measure. More information about the lake is available at the following web sites: Lake Sarez Study group, UN Report, Reliefweb Digital photograph numbers ISS002-E-7771 and ISS002-E-7479 were taken in the spring of 2001 from Space Station Alpha and are provided by the Earth Sciences and Image Analysis Laboratory at Johnson Space Center. Additional images taken by astronauts and cosmonauts can be viewed at the NASA-JSC Gateway to Astronaut Photography of Earth.

  19. Examining indirect effects of lake trout recovery

    EPA Science Inventory

    With the recovery of lake trout populations in Lake Superior, there are indications of decreased forage fish abundance and density-dependence in lake trout. In Lake Superior, lean lake trout historically occupied depths < 60 m, and siscowet lake trout occupied depths > 60 m...

  20. Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites

    PubMed Central

    Vanhove, Maarten P. M.; Pariselle, Antoine; Van Steenberge, Maarten; Raeymaekers, Joost A. M.; Hablützel, Pascal I.; Gillardin, Céline; Hellemans, Bart; Breman, Floris C.; Koblmüller, Stephan; Sturmbauer, Christian; Snoeks, Jos; Volckaert, Filip A. M.; Huyse, Tine

    2015-01-01

    The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebrate radiation, we study monogenean parasites infecting tropheine cichlids from Lake Tanganyika. Monogeneans are flatworms usually infecting the body surface and gills of fishes. In contrast to many other parasites, they depend only on a single host species to complete their lifecycle. Our spatially comprehensive combined nuclear-mitochondrial DNA dataset of the parasites covering almost all tropheine host species (N = 18), reveals species-rich parasite assemblages and shows consistent host-specificity. Statistical comparisons of host and parasite phylogenies based on distance and topology-based tests demonstrate significant congruence and suggest that host-switching is rare. Molecular rate evaluation indicates that species of Cichlidogyrus probably diverged synchronically with the initial radiation of the tropheines. They further diversified through within-host speciation into an overlooked species radiation. The unique life history and specialisation of certain parasite groups has profound evolutionary consequences. Hence, evolutionary parasitology adds a new dimension to the study of biodiversity hotspots like Lake Tanganyika. PMID:26335652

  1. Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites.

    PubMed

    Vanhove, Maarten P M; Pariselle, Antoine; Van Steenberge, Maarten; Raeymaekers, Joost A M; Hablützel, Pascal I; Gillardin, Céline; Hellemans, Bart; Breman, Floris C; Koblmüller, Stephan; Sturmbauer, Christian; Snoeks, Jos; Volckaert, Filip A M; Huyse, Tine

    2015-01-01

    The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebrate radiation, we study monogenean parasites infecting tropheine cichlids from Lake Tanganyika. Monogeneans are flatworms usually infecting the body surface and gills of fishes. In contrast to many other parasites, they depend only on a single host species to complete their lifecycle. Our spatially comprehensive combined nuclear-mitochondrial DNA dataset of the parasites covering almost all tropheine host species (N = 18), reveals species-rich parasite assemblages and shows consistent host-specificity. Statistical comparisons of host and parasite phylogenies based on distance and topology-based tests demonstrate significant congruence and suggest that host-switching is rare. Molecular rate evaluation indicates that species of Cichlidogyrus probably diverged synchronically with the initial radiation of the tropheines. They further diversified through within-host speciation into an overlooked species radiation. The unique life history and specialisation of certain parasite groups has profound evolutionary consequences. Hence, evolutionary parasitology adds a new dimension to the study of biodiversity hotspots like Lake Tanganyika. PMID:26335652

  2. View of Lake Sabrina Dam and dry Lake Sabrina Basin ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View of Lake Sabrina Dam and dry Lake Sabrina Basin with the upstream side of the outlet structure visible at photo center, view to north-northwest - Bishop Creek Hydroelectric System, Plant 2, Lake Sabrina Dam, Bishop Creek, Bishop, Inyo County, CA

  3. 42. Peaks of Otter, Abbott Lake. View across lake to ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    42. Peaks of Otter, Abbott Lake. View across lake to peaks of Outter Lodge, completed in 1964. Construction of the lake got underway in 1964. Looking east-northeast. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  4. Lake Michigan lake trout PCB model forecast post audit

    EPA Science Inventory

    Scenario forecasts for total PCBs in Lake Michigan (LM) lake trout were conducted using the linked LM2-Toxics and LM Food Chain models, supported by a suite of additional LM models. Efforts were conducted under the Lake Michigan Mass Balance Study and the post audit represents th...

  5. Mono Lake Excursion Reviewed

    NASA Astrophysics Data System (ADS)

    Liddicoat, J. C.; Coe, R. S.

    2007-05-01

    The Mono Lake Excursion as recorded in the Mono Basin, CA, has an older part that is about negative 30 degrees inclination and about 300 degrees declination during low relative field intensity. Those paleomagnetic directions are closely followed by greater than 80 degrees positive inclination and east declination of about 100 degrees during higher relative field intensity. A path of the Virtual Geomagnetic Poles (VGPs) for the older part followed from old to young forms a large clockwise loop that reaches 35 degrees N latitude and is centered at about 35 degrees E longitude. That loop is followed by a smaller one that is counterclockwise and centered at about 70 degrees N latitude and 270 degrees E longitude (Denham & Cox, 1971; Denham, 1974; Liddicoat & Coe, 1979). The Mono Lake Excursion outside the Mono Basin in western North America is recorded as nearly the full excursion at Summer Lake, OR (Negrini et al., 1984), and as the younger portion of steep positive inclination/east declination in the Lahontan Basin, NV. The overall relative field intensity during the Mono Lake Excursion in the Lahontan Basin mirrors very closely the relative field intensity in the Mono Basin (Liddicoat, 1992, 1996; Coe & Liddicoat, 1994). Using 14C and 40Ar/39Ar dates (Kent et al., 2002) and paleoclimate and relative paleointensity records (Zimmerman et al., 2006) for the Mono Lake Excursion in the Mono Basin, it has been proposed that the Mono Lake Excursion might be older than originally believed and instead be the Laschamp Excursion at about 40,000 yrs B.P. (Guillou et al., 2004). On the contrary, we favor a younger age for the Mono Lake Excursion, about 32,000 yrs B.P., using the relative paleointensity in the Mono Basin and Lahontan Basin and 14C dates from the Lahontan Basin (Benson et al., 2002). The age of about 32,000 yrs B.P. is also in accord with the age (32,000- 34,000 yrs B.P.) reported by Channell (2006) for the Mono Lake Excursion at ODP Site 919 in the Irminger Basin

  6. Phylogeny.fr: robust phylogenetic analysis for the non-specialist

    PubMed Central

    Dereeper, A.; Guignon, V.; Blanc, G.; Audic, S.; Buffet, S.; Chevenet, F.; Dufayard, J.-F.; Guindon, S.; Lefort, V.; Lescot, M.; Gascuel, O.

    2008-01-01

    Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The ‘One Click’ mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The ‘Advanced’ mode uses the same pipeline but allows the parameters of each program to be customized by users. The ‘A la Carte’ mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/ PMID:18424797

  7. Molecular Phylogeny and Biogeography of Percocypris (Cyprinidae, Teleostei)

    PubMed Central

    Wang, Mo; Yang, Jun-Xing; Chen, Xiao-Yong

    2013-01-01

    Fierce predatory freshwater fishes, the species of Percocypris (Cyprinidae, Teleostei) inhabit large rivers or lakes, and have a specific distribution pattern. Only a single species or subspecies occurs in each large-scale drainage basin of the Southeastern Tibetan Plateau. In this study, the molecular phylogenetic relationships for all but one of the described subspecies/species of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results of Maximum Likelihood and Bayesian Inference analyses show that Percocypris is a strongly supported monophyletic group and that it is the sister group of Schizothorax. Combined with analyses of morphological characters, our results suggest that Percocypris needs to be reclassified, and we propose that six species be recognized, with corresponding distributions in five main drainages (including one lake). In addition, based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance (due to the uplift of the Tibetan Plateau modifying the large-scale morphologies of drainage basins in the Southeastern Tibetan Plateau) has played an important role in the speciation of the genus. Furthermore, external morphological characters (such as the length of the fins) and an internal trait (the position of pterygiophore) appear to be correlated with different habitats in rivers and the lake. PMID:23750199

  8. Old fossils–young species: evolutionary history of an endemic gastropod assemblage in Lake Malawi

    PubMed Central

    Schultheiß, Roland; Van Bocxlaer, Bert; Wilke, Thomas; Albrecht, Christian

    2009-01-01

    Studies on environmental changes provide important insights into modes of speciation, into the (adaptive) reoccupation of ecological niches and into species turnover. Against this background, we here examine the history of the gastropod genus Lanistes in the African Rift Lake Malawi, guided by four general evolutionary scenarios, and compare it with patterns reported from other endemic Malawian rift taxa. Based on an integrated approach using a mitochondrial DNA phylogeny and a trait-specific molecular clock in combination with insights from the fossil record and palaeoenvironmental data, we demonstrate that the accumulation of extant molecular diversity in the endemic group did not start before approximately 600 000 years ago from a single lineage. Fossils of the genus from the Malawi Rift, however, are over one million years older. We argue that severe drops in the lake level of Lake Malawi in the Pleistocene offer a potential explanation for this pattern. Our results also challenge previously established phylogenetic relationships within the genus by revealing parallel evolution and providing evidence that the endemic Lanistes species are not restricted to the lake proper but are present throughout the Malawi Rift. PMID:19439440

  9. Microplastic pollution in lakes and lake shoreline sediments - A case study on Lake Bolsena and Lake Chiusi (central Italy).

    PubMed

    Fischer, Elke Kerstin; Paglialonga, Lisa; Czech, Elisa; Tamminga, Matthias

    2016-06-01

    Rivers and effluents have been identified as major pathways for microplastics of terrestrial sources. Moreover, lakes of different dimensions and even in remote locations contain microplastics in striking abundances. This study investigates concentrations of microplastic particles at two lakes in central Italy (Lake Bolsena, Lake Chiusi). A total number of six Manta Trawls have been carried out, two of them one day after heavy winds occurred on Lake Bolsena showing effects on particle distribution of fragments and fibers of varying size categories. Additionally, 36 sediment samples from lakeshores were analyzed for microplastic content. In the surface waters 2.68 to 3.36 particles/m(3) (Lake Chiusi) and 0.82 to 4.42 particles/m(3) (Lake Bolsena) were detected, respectively. Main differences between the lakes are attributed to lake characteristics such as surface and catchment area, depth and the presence of local wind patterns and tide range at Lake Bolsena. An event of heavy winds and moderate rainfall prior to one sampling led to an increase of concentrations at Lake Bolsena which is most probable related to lateral land-based and sewage effluent inputs. The abundances of microplastic particles in sediments vary from mean values of 112 (Lake Bolsena) to 234 particles/kg dry weight (Lake Chiusi). Lake Chiusi results reveal elevated fiber concentrations compared to those of Lake Bolsena what might be a result of higher organic content and a shift in grain size distribution towards the silt and clay fraction at the shallow and highly eutrophic Lake Chiusi. The distribution of particles along different beach levels revealed no significant differences. PMID:27104923

  10. The origin of the cancer cell: oncogeny reverses phylogeny.

    PubMed

    Johnston, R N; Pai, S B; Pai, R B

    1992-01-01

    The formulation in 1874 of the biogenetic law by Ernst Haeckel as "ontogeny recapitulates phylogeny" emphasized the structural similarities detected in metazoans between their developmental and ancestral forms. More recently, many workers have independently commented on the similarities observed between the behaviours displayed by dedifferentiated cancer cells and their embryonic precursors. This review will explore a possible linkage between these disparate observations and will suggest that cancer cells behave in ways that are reminiscent of primitive eukaryotic cells. In particular, we suggest that the acquisition of a multicellular level of organization during early metazoan evolution required a critical and difficult change in growth strategy as germ line and somatic cells became distinct. Whereas unicellular free living eukaryotes follow a simple strategy of rapid division as long as conditions permit, the elaboration of powerful growth inhibitory pathways must have been necessary in primitive multicellular organisms to enable some but not all sister cells to stop dividing, even under conditions of nutrient abundance. This limitation on cellular growth would than have permitted the appearance of tissues and organs with differentiated characteristics, ultimately enabling the enhanced survival of the meiotic lineage. Cancer cells might therefore be considered to represent, with their loss of tumor suppressor inhibitory activity and elevation of oncogene stimulatory activity, a reversion to a more primitive evolutionary state capable of indeterminate growth at the expense of the host. By this analogy, the growth phenotypes displayed by cancer cells, embryonic cells, and free-living eukaryotes are fundamentally similar. PMID:1297348

  11. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials.

    PubMed

    Mitchell, Kieren J; Pratt, Renae C; Watson, Laura N; Gibb, Gillian C; Llamas, Bastien; Kasper, Marta; Edson, Janette; Hopwood, Blair; Male, Dean; Armstrong, Kyle N; Meyer, Matthias; Hofreiter, Michael; Austin, Jeremy; Donnellan, Stephen C; Lee, Michael S Y; Phillips, Matthew J; Cooper, Alan

    2014-09-01

    Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation. PMID:24881050

  12. The rRNA evolution and procaryotic phylogeny

    NASA Technical Reports Server (NTRS)

    Fox, G. E.

    1986-01-01

    Studies of ribosomal RNA primary structure allow reconstruction of phylogenetic trees for prokaryotic organisms. Such studies reveal major dichotomy among the bacteria that separates them into eubacteria and archaebacteria. Both groupings are further segmented into several major divisions. The results obtained from 5S rRNA sequences are essentially the same as those obtained with the 16S rRNA data. In the case of Gram negative bacteria the ribosomal RNA sequencing results can also be directly compared with hybridization studies and cytochrome c sequencing studies. There is again excellent agreement among the several methods. It seems likely then that the overall picture of microbial phylogeny that is emerging from the RNA sequence studies is a good approximation of the true history of these organisms. The RNA data allow examination of the evolutionary process in a semi-quantitative way. The secondary structures of these RNAs are largely established. As a result it is possible to recognize examples of local structural evolution. Evolutionary pathways accounting for these events can be proposed and their probability can be assessed.

  13. Phylogeny and phylogeography of the Tuber brumale aggr.

    PubMed

    Merényi, Zsolt; Varga, Torda; Geml, József; Orczán, Ákos Kund; Chevalier, Gerard; Bratek, Zoltán

    2014-04-01

    The Tuber brumale (winter truffle) is a black truffle reported from most European countries, belonging to the Melanosporum group. Its significance in the economy is ambivalent as the winter truffle has been shown to be a frequent contaminant species in the orchards of the Perigord truffle and occasionally in those of the summer truffle, yet owing to its delicate fragrance, its trade is worthy of note. The phylogeny and phylogeography of economically important truffles are relatively well-explored; however, no thorough research has been published on these aspects of the winter truffle. Therefore, here, we report the first phylogeographic analyses based on samples representing the entire distribution of the species. ITS sequences were used in this survey for haplotype and coalescent analyses, while phylogenetic analyses were based on the ITS, LSU and PKC loci. According to all loci, the samples clustered into two big clades imply the existence of two phylogenetic species. Based on our results, one of these appears to be endemic to the Carpathian Basin. In the other more widespread species, two main phylogeographic groups can be distinguished that show east-west separation with a zone of overlap in the Carpathian Basin, suggesting that they survived the latest glacial period in separate refugia. PMID:24604084

  14. Phylogeny and biology of neotropical orchid bees (Euglossini).

    PubMed

    Cameron, Sydney A

    2004-01-01

    Orchid bees (Euglossini), noted for their brilliant iridescence, are elusive pollinators throughout the American tropics. Males are especially important in the pollination of some orchids, from which they collect aromatic fragrances thought to play a role in territorial display and courtship. The tribe contains approximately 190 described species divided among five genera, distributed from Mexico to central Argentina. Relatively intense study of their biology in the 1960s through the mid-1980s shed light on their nesting biology, chemical ecology, and classification. Vigorous taxonomic research led to the naming of many new species, revisions, and checklists, but phylogenetic studies were scarce. In the two decades following the last comprehensive review, phylogenetic research has resulted in new hypotheses of generic relationships, and further examination of male display has led to additional interpretations. Females in natural and artificial nesting cavities have revealed social interactions and additional details of parasitism within the nest. This review emphasizes areas in need of more study, particularly phylogeny, phylogeography, chemosensory ecology, and comparative behavior, and highlights how historical context can guide future research. PMID:14651469

  15. A mitogenomic phylogeny and genetic history of sable (Martes zibellina).

    PubMed

    Malyarchuk, Boris; Derenko, Miroslava; Denisova, Galina

    2014-10-15

    We assessed phylogeny of sable (Martes zibellina, Linnaeus, 1758) by sequence analysis of nearly complete, new mitochondrial genomes in 36 specimens from different localities in northern Eurasia (Primorye, Khabarovsk and Krasnoyarsk regions, the Kamchatka Peninsula, the Kuril Islands and the Urals). Phylogenetic analysis of mtDNA sequences demonstrates that two clades, A and BC, radiated about 200-300 thousandyears ago (kya) according to results of Bayesian molecular clock and RelTime analyses of different mitogenome alignments (nearly complete mtDNA sequences, protein-coding region, and synonymous sites), while the age estimates of clades A, B and C fall within the Late Pleistocene (~50-140 kya). Bayesian skyline plots (BSPs) of sable population size change based on analysis of nearly complete mtDNAs show an expansion around 40 kya in the warm Karganian time, without a decline of population size around the Last Glacial Maximum (21 kya). The BSPs based on synonymous clock rate indicate that M. zibellina experienced demographic expansions later, approximately 22 kya. The A2a clade that colonized Kamchatka ~23-50 kya (depending on the mutation rate used) survived the last glaciation there as demonstrated by the BSP analysis. In addition, we have found evidence of positive selection acting at ND4 and cytochrome b genes, thereby suggesting adaptive evolution of the A2a clade in Kamchatka. PMID:25110108

  16. Phylogeny-aware identification and correction of taxonomically mislabeled sequences

    PubMed Central

    Kozlov, Alexey M.; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros

    2016-01-01

    Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences (‘mislabels’) using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa. PMID:27166378

  17. Phylogeny and systematics of the anamorphic, entomopathogenic genus Beauveria.

    PubMed

    Rehner, Stephen A; Minnis, Andrew M; Sung, Gi-Ho; Luangsa-ard, J Jennifer; Devotto, Luis; Humber, Richard A

    2011-01-01

    Beauveria is a cosmopolitan anamorphic genus of arthropod pathogens that includes the agronomically important species, B. bassiana and B. brongniartii, which are used as mycoinsecticides for the biological control of pest insects. Recent phylogenetic evidence demonstrates that Beauveria is monophyletic within the Cordycipitaceae (Hypocreales), and both B. bassiana and B. brongniartii have been linked developmentally and phylogenetically to Cordyceps species. Despite recent interest in the genetic diversity and molecular ecology of Beauveria, particularly as it relates to their role as pathogens of insects in natural and agricultural environments, the genus has not received critical taxonomic review for several decades. A multilocus phylogeny of Beauveria based on partial sequences of RPB1, RPB2, TEF and the nuclear intergenic region, Bloc, is presented and used to assess diversity within the genus and to evaluate species concepts and their taxonomic status. B. bassiana and B. brongniartii, both which represent species complexes and which heretofore have lacked type specimens, are redescribed and types are proposed. In addition six new species are described including B. varroae and B. kipukae, which form a biphyletic, morphologically cryptic sister lineage to B. bassiana, B. pseudobassiana, which also is morphologically similar to but phylogenetically distant from B. bassiana, B. asiatica and B. australis, which are sister lineages to B. brongniartii, and B. sungii, an Asian species that is linked to an undetermined species of Cordyceps. The combination B. amorpha is validly published and an epitype is designated. PMID:21482632

  18. Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

    PubMed Central

    Moreira, Cristiana; Vasconcelos, Vitor; Antunes, Agostinho

    2013-01-01

    Phylogeny is an evolutionary reconstruction of the past relationships of DNA or protein sequences and it can further be used as a tool to assess population structuring, genetic diversity and biogeographic patterns. In the microbial world, the concept that everything is everywhere is widely accepted. However, it is much debated whether microbes are easily dispersed globally or whether they, like many macro-organisms, have historical biogeographies. Biogeography can be defined as the science that documents the spatial and temporal distribution of a given taxa in the environment at local, regional and continental scales. Speciation, extinction and dispersal are proposed to explain the generation of biogeographic patterns. Cyanobacteria are a diverse group of microorganisms that inhabit a wide range of ecological niches and are well known for their toxic secondary metabolite production. Knowledge of the evolution and dispersal of these microorganisms is still limited, and further research to understand such topics is imperative. Here, we provide a compilation of the most relevant information regarding these issues to better understand the present state of the art as a platform for future studies, and we highlight examples of both phylogenetic and biogeographic studies in non-symbiotic cyanobacteria and cyanotoxins. PMID:24189276

  19. Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

    PubMed Central

    Chan, Yi-Chiao; Roos, Christian; Inoue-Murayama, Miho; Inoue, Eiji; Shih, Chih-Chin; Pei, Kurtis Jai-Chyi; Vigilant, Linda

    2010-01-01

    Background Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. Methodology/Principal Findings We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. Conclusions/Significance Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species. PMID:21203450

  20. Morphology, epidemiology, and phylogeny of Babesia: An overview

    PubMed Central

    Laha, Ramgopal; Das, M; Sen, A

    2015-01-01

    Babesiosis is a tick-borne hemoprotozoan disease of domestic and wild animals. The disease is caused by various species of Babesia and some species of Babesia have also zoonotic significance. The parasite in vertebrate hosts’ remains in erythrocytes and the morphology of Babesia spp. is not uniform in all vertebrate hosts. With the advancement of science, particularly the use of molecular techniques made it easy to study the evolution of parasites and thereby reclassifying Babesia spp. as per their phylogeny and to establish the relation of one isolate of Babesia spp. with isolates throughout the world. An attempt also made in this communication to enlighten the readers regarding relationship of one isolate of Babesia spp. of a particular area to another isolate of Babesia spp. of that area or other parts of the world and phylogenetic classification of Babesia spp. was also discussed. It has been concluded that as the study on Babesia is complex in nature so monitoring of the infection with the use of modern techniques is very much needed to control the infection. Second, more research work on phylogenetic relationship of Babesia spp. isolated from different hosts is needed, particularly in India to know the evolution of Babesia spp. of a particular area, as it has great importance to study the trans boundary diseases of animals. PMID:26629451

  1. Multigene phylogeny reveals eusociality evolved twice in vespid wasps

    PubMed Central

    Hines, Heather M.; Hunt, James H.; O'Connor, Timothy K.; Gillespie, Joseph J.; Cameron, Sydney A.

    2007-01-01

    Eusocial wasps of the family Vespidae are thought to have derived their social behavior from a common ancestor that had a rudimentary caste-containing social system. In support of this behavioral scenario, the leading phylogenetic hypothesis of Vespidae places the eusocial wasps (subfamilies Stenogastrinae, Polistinae, and Vespinae) as a derived monophyletic clade, thus implying a single origin of eusocial behavior. This perspective has shaped the investigation and interpretation of vespid social evolution for more than two decades. Here we report a phylogeny of Vespidae based on data from four nuclear gene fragments (18S and 28S ribosomal DNA, abdominal-A and RNA polymerase II) and representatives from all six extant subfamilies. In contrast to the current phylogenetic perspective, our results indicate two independent origins of vespid eusociality, once in the clade Polistinae+Vespinae and once in the Stenogastrinae. The stenogastrines appear as an early diverging clade distantly related to the vespines and polistines and thus evolved their distinctive form of social behavior from a different ancestor than that of Polistinae+Vespinae. These results support earlier views based on life history and behavior and have important implications for interpreting transitional stages in vespid social evolution. PMID:17360641

  2. Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited

    PubMed Central

    Hess, Sebastian; Sausen, Nicole; Melkonian, Michael

    2012-01-01

    With the advent of molecular phylogenetic techniques the polyphyly of naked filose amoebae has been proven. They are interspersed in several supergroups of eukaryotes and most of them already found their place within the tree of life. Although the ‘vampire amoebae’ have attracted interest since the middle of the 19th century, the phylogenetic position and even the monophyly of this traditional group are still uncertain. In this study clonal co-cultures of eight algivorous vampyrellid amoebae and the respective food algae were established. Culture material was characterized morphologically and a molecular phylogeny was inferred using SSU rDNA sequence comparisons. We found that the limnetic, algivorous vampyrellid amoebae investigated in this study belong to a major clade within the Endomyxa Cavalier-Smith, 2002 (Cercozoa), grouping together with a few soil-dwelling taxa. They split into two robust clades, one containing species of the genus Vampyrella Cienkowski, 1865, the other containing the genus Leptophrys Hertwig & Lesser, 1874, together with terrestrial members. Supported by morphological data these clades are designated as the two families Vampyrellidae Zopf, 1885, and Leptophryidae fam. nov. Furthermore the order Vampyrellida West, 1901 was revised and now corresponds to the major vampyrellid clade within the Endomyxa, comprising the Vampyrellidae and Leptophryidae as well as several environmental sequences. In the light of the presented phylogenetic analyses morphological and ecological aspects, the feeding strategy and nutritional specialization within the vampyrellid amoebae are discussed. PMID:22355342

  3. Genomes-based phylogeny of the genus Xanthomonas

    PubMed Central

    2012-01-01

    Background The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus. Results Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines. Conclusions Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters. PMID:22443110

  4. Molecular phylogeny and ultrastructure of Aphelidium aff. melosirae (Aphelida, Opisthosporidia)

    PubMed Central

    Karpov, Sergey A.; Mamkaeva, Maria A.; Benzerara, Karim; Moreira, David; López-García, Purificación

    2014-01-01

    Aphelids are a poorly known group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position. Together with Cryptomycota and the highly derived Microsporidia, they have been recently re-classified as Opisthosporidia, being the sister group to fungi. Despite their huge diversity, as revealed by molecular environmental studies, and their phylogenetic interest, only three genera have been described (Aphelidium, Amoeboaphelidium, and Pseudaphelidium), from which 18S rRNA gene sequences exist only for Amoeboaphelidium species. Here, we describe the life cycle and ultrastructure of Aphelidium aff. melosirae, and provide the first 18S rRNA gene sequence obtained for this genus. Molecular phylogeny analysis indicates that Aphelidium is very distantly related to Amoebaphelidium, highlighting the wide genetic diversity of the aphelids. The parasitoid encysts and penetrates the host alga, Tribonema gayanum through an infection tube. Cyst germination leads to a young trophont that phagocytes the algal cell content and progressively develops a plasmodium, which becomes a zoospore-producing sporangium. Aphelidium aff. melosirae has amoeboflagellate zoospores, tubular/lamellar mitochondrial cristae, a metazoan type of centrosome, and closed orthomitosis with intranuclear spindle. These features together with trophont phagocytosis distinguish Aphelidium from fungi and support the erection of the new superphylum Opisthosporidia as sister to fungi. PMID:24995586

  5. Molecular phylogeny of the forensically important genus Cochliomyia (Diptera: Calliphoridae).

    PubMed

    Yusseff-Vanegas, Sohath; Agnarsson, Ingi

    2016-01-01

    Cochliomyia Townsend includes several abundant and one of the most broadly distributed, blow flies in the Americas, and is of significant economic and forensic importance. For decades, Cochliomyia hominivorax (Coquerel) and Cochliomyia macellaria (Fabricius) have received attention as livestock parasites and primary indicator species in forensic entomology. However, Cochliomyia minima Shannon and Cochliomyia aldrichi Del Ponte have only been subject to basic taxonomy and faunistic studies. Here we present the first complete phylogeny of Cochliomyia including numerous specimens per species, collected from 13 localities in the Caribbean. Four genes, the mitochondrial COI and the nuclear EF-1α, 28S rRNA, and ITS2, were analyzed. While we found some differences among gene trees, a concatenated gene matrix recovered a robustly supported monophyletic Cochliomyia with Compsomyiops Townsend as its sister group and recovered the monophyly of Cochliomyia hominivorax, Cochliomyia macellaria and Cochliomyia minima. Our results support a close relationship between Cochliomyia minima and Cochliomyia aldrichi. However, we found Cochliomyia aldrichi containing Cochliomyia minima, indicating recent speciation, or issues with the taxonomy of the group. We provide basic information on habitat preference, distribution and feeding habits of Cochliomyia minima and Cochliomyia aldrichi that will be useful for future forensic studies in the Caribbean. PMID:27563274

  6. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

    PubMed Central

    Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Pukall, Rüdiger; Dalin, Eileen; Ivanova, Natalia N.; Kunin, Victor; Goodwin, Lynne; Wu, Martin; Tindall, Brian J.; Hooper, Sean D.; Pati, Amrita; Lykidis, Athanasios; Spring, Stefan; Anderson, Iain J.; D’haeseleer, Patrik; Zemla, Adam; Singer, Mitchell; Lapidus, Alla; Nolan, Matt; Copeland, Alex; Han, Cliff; Chen, Feng; Cheng, Jan-Fang; Lucas, Susan; Kerfeld, Cheryl; Lang, Elke; Gronow, Sabine; Chain, Patrick; Bruce, David; Rubin, Edward M.; Kyrpides, Nikos C.; Klenk, Hans-Peter; Eisen, Jonathan A.

    2011-01-01

    Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms1. There are now nearly 1,000 completed bacterial and archaeal genomes available2, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution3–5. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. PMID:20033048

  7. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana.

    PubMed

    Beilstein, Mark A; Nagalingum, Nathalie S; Clements, Mark D; Manchester, Steven R; Mathews, Sarah

    2010-10-26

    Dated molecular phylogenies are the basis for understanding species diversity and for linking changes in rates of diversification with historical events such as restructuring in developmental pathways, genome doubling, or dispersal onto a new continent. Valid fossil calibration points are essential to the accurate estimation of divergence dates, but for many groups of flowering plants fossil evidence is unavailable or limited. Arabidopsis thaliana, the primary genetic model in plant biology and the first plant to have its entire genome sequenced, belongs to one such group, the plant family Brassicaceae. Thus, the timing of A. thaliana evolution and the history of its genome have been controversial. We bring previously overlooked fossil evidence to bear on these questions and find the split between A. thaliana and Arabidopsis lyrata occurred about 13 Mya, and that the split between Arabidopsis and the Brassica complex (broccoli, cabbage, canola) occurred about 43 Mya. These estimates, which are two- to threefold older than previous estimates, indicate that gene, genomic, and developmental evolution occurred much more slowly than previously hypothesized and that Arabidopsis evolved during a period of warming rather than of cooling. We detected a 2- to 10-fold shift in species diversification rates on the branch uniting Brassicaceae with its sister families. The timing of this shift suggests a possible impact of the Cretaceous-Paleogene mass extinction on their radiation and that Brassicales codiversified with pierid butterflies that specialize on mustard-oil-producing plants. PMID:20921408

  8. Deep phylogeny, ancestral groups and the four ages of life.

    PubMed

    Cavalier-Smith, Thomas

    2010-01-12

    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution. PMID:20008390

  9. Phylogeny and disjunct distribution: evolution of Saintpaulia (Gesneriaceae).

    PubMed

    Möller, M; Cronk, Q C

    1997-12-22

    The molecular phylogeny of African violets (Saintpaulia H. Wendl.), based on ribosomal DNA internal transcribed spacer (ITS) sequences, follows the disjunct biogeography of the genus. Sequence analysis by parsimony of 19 accessions, representing 17 currently recognized Saintpaulia species, resulted in four trees of 182 steps. The first major division is between S. goetzeana, from the Uluguru Mts, Tanzania, and the rest of the genus. The basal position of S. goetzeana, and its putative primitive characters, may indicate an Uluguru origin for Saintpaulia and subsequent colonization of the more northerly mountains. Of the remainder, S. teitensis, from the Teita Hills of Kenya, is sister taxon to the other species (which occur mainly in the Usambara Mts of north-east Tanzania). A group of nine Usambaran species that we call the 'ionantha complex' show minimal ITS genetic differentiation and are also taxonomically critical. Species diversity in the Usambara Mts appears to be the result of rapid, recent (possibly Pleistocene) radiation. This study reveals the limitations of ITS sequences for elucidating the radiation of poorly differentiated species (the ionantha complex). However, the molecular data strongly suggest that conservation of the Uluguru and Teita populations is essential for the protection of the full range of diversity within the genus. PMID:9447739

  10. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

    PubMed Central

    Wen, Dingqiao; Yu, Yun; Nakhleh, Luay

    2016-01-01

    The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. PMID:27144273

  11. Molecular phylogeny of the forensically important genus Cochliomyia (Diptera: Calliphoridae)

    PubMed Central

    Yusseff-Vanegas, Sohath; Agnarsson, Ingi

    2016-01-01

    Abstract Cochliomyia Townsend includes several abundant and one of the most broadly distributed, blow flies in the Americas, and is of significant economic and forensic importance. For decades, Cochliomyia hominivorax (Coquerel) and Cochliomyia macellaria (Fabricius) have received attention as livestock parasites and primary indicator species in forensic entomology. However, Cochliomyia minima Shannon and Cochliomyia aldrichi Del Ponte have only been subject to basic taxonomy and faunistic studies. Here we present the first complete phylogeny of Cochliomyia including numerous specimens per species, collected from 13 localities in the Caribbean. Four genes, the mitochondrial COI and the nuclear EF-1α, 28S rRNA, and ITS2, were analyzed. While we found some differences among gene trees, a concatenated gene matrix recovered a robustly supported monophyletic Cochliomyia with Compsomyiops Townsend as its sister group and recovered the monophyly of Cochliomyia hominivorax, Cochliomyia macellaria and Cochliomyia minima. Our results support a close relationship between Cochliomyia minima and Cochliomyia aldrichi. However, we found Cochliomyia aldrichi containing Cochliomyia minima, indicating recent speciation, or issues with the taxonomy of the group. We provide basic information on habitat preference, distribution and feeding habits of Cochliomyia minima and Cochliomyia aldrichi that will be useful for future forensic studies in the Caribbean. PMID:27563274

  12. Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers.

    PubMed

    Pavan-Kumar, A; Gireesh-Babu, P; Babu, P P Suresh; Jaiswar, A K; Hari Krishna, V; Prasasd, K Pani; Chaudhari, Aparna; Raje, S G; Chakraborty, S K; Krishna, Gopal; Lakra, W S

    2014-01-01

    The elasmobranchs (sharks, rays and skates) being the extant survivors of one of the earliest offshoots of the vertebrate evolutionary tree are good model organisms to study the primitive vertebrate conditions. They play a significant role in maintaining the ecological balance and have high economic value. Due to over-exploitation and illegal fishing worldwide, the elasmobranch stocks are being decimated at an alarming rate. Appropriate management measures are necessary for restoring depleted elasmobranch stocks. One approach for restoring stocks is implementation of conservation measures and these measures can be formulated effectively by knowing the evolutionary relationship among the elasmobranchs. In this study, a total of 30 species were chosen for molecular phylogeny studies using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA gene and nuclear Internal Transcribed Spacer 2. Among different genes, the combined dataset of COI and 12S rRNA resulted in a well resolved tree topology with significant bootstrap/posterior probabilities values. The results supported the reciprocal monophyly of sharks and batoids. Within Galeomorphii, Heterodontiformes (bullhead sharks) formed as a sister group to Lamniformes (mackerel sharks): Orectolobiformes (carpet sharks) and to Carcharhiniformes (ground sharks). Within batoids, the Myliobatiformes formed a monophyly group while Pristiformes (sawfishes) and Rhinobatiformes (guitar fishes) formed a sister group to all other batoids. PMID:24293104

  13. Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny.

    PubMed

    Egan, Ashley N; Vatanparast, Mohammad; Cagle, William

    2016-11-01

    Several taxonomic and phylogenetic studies have hypothesized polyphyly within Pueraria DC., a genus comprising 19 species (24 with varieties) including the highly invasive Pueraria montana var. lobata (Kudzu) introduced to the U.S.A. about 150years ago. Previous efforts to investigate monophyly of the genus have been hampered by limited taxon sampling or a lack of comprehensive evolutionary context that would enable definitive taxonomic associations. This work presents a comprehensive phylogenetic investigation of Pueraria within the context of tribe Phaseoleae (Leguminosae). Polyphyly was found to be more extensive than previously thought, with five distinct lineages spread across the tribe and spanning over 25mya of divergence strongly supported by two chloroplast and one nuclear marker, AS2, presented here as a phylogenetic marker for the first time. Our phylogenies support taxonomic revisions to rectify polyphyly within Pueraria, including the resurrection of Neustanthus, moving one species to Teyleria, and the creation of two new genera, Haymondia and Toxicopueraria (taxonomic revisions published elsewhere). PMID:27495827

  14. Phylogeny of marine Bacillus isolates from the Gulf of Mexico

    NASA Technical Reports Server (NTRS)

    Siefert, J. L.; Larios-Sanz, M.; Nakamura, L. K.; Slepecky, R. A.; Paul, J. H.; Moore, E. R.; Fox, G. E.; Jurtshuk, P. Jr

    2000-01-01

    The phylogeny of 11 pigmented, aerobic, spore-forming isolates from marine sources was studied. Forty-two biochemical characteristics were examined, and a 16S rDNA sequence was obtained for each isolate. In a phylogenetic tree based on 16S sequencing, four isolates (NRRL B-14850, NRRL B-14904, NRRL B-14907, and NRRL B-14908) clustered with B. subtilis and related organisms; NRRL B-14907 was closely related to B. amyloliquefaciens. NRRL B-14907 and NRRL B-14908 were phenotypically similar to B. amyloliquefaciens and B. pumilus, respectively. Three strains (NRRL B-14906, NRRL B-14910, and NRRL B-14911) clustered in a clade that included B. firmus, B. lentus, and B. megaterium. NRRL B-14910 was closely related phenotypically and phylogenetically to B. megaterium. NRRL B-14905 clustered with the mesophilic round spore-producing species, B. fusiformis and B. sphaericus; the isolate was more closely related to B. fusiformis. NRRL B-14905 displayed characteristics typical of the B. sphaericus-like organisms. NRRL B-14909 and NRRL B-14912 clustered with the Paenibacillus species and displayed characteristics typical of the genus. Only NRRL B-14851, an unusually thin rod that forms very small spores, may represent a new Bacillus species.

  15. The phylogeny and evolutionary history of tyrannosauroid dinosaurs

    NASA Astrophysics Data System (ADS)

    Brusatte, Stephen L.; Carr, Thomas D.

    2016-02-01

    Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work.

  16. Phylogeny and radiation of pollination systems in DISA (Orchidaceae).

    PubMed

    Johnson, S; Linder, H; Steiner, K

    1998-03-01

    We studied the patterns of adaptive radiation in Disa, a large orchid genus in southern Africa. A cladogram for 27 species was constructed using 44 morphological characters. Pollination systems were then mapped onto the phylogeny in order to analyze pathways of floral evolution. Shifts from one pollination system to another have been a major feature of the evolutionary diversification of Disa. Unlike many plant genera that are pollinated mainly by a single group of insects, radiation in Disa has encompassed nearly all major groups of pollinating insects; in all, 19 different specialized pollination systems have been found in the 27 species included in this analysis. Another striking pattern is the repeated evolution of broadly similar pollination systems in unrelated clades. For example, butterfly-pollinated flowers have evolved twice; showy deceptive flowers pollinated by carpenter bees, twice; long-spurred flowers pollinated by long-tongued flies, four times; night-scented flowers pollinated by moths, three times; and self-pollination, three times. This suggests that a few dominant pollinator species in a region may be sufficient to generate diversification in plants through repeated floral shifts that never retrace the same pathways. PMID:21684924

  17. Phylogeny, evolution, and biogeography of Asiatic Salamanders (Hynobiidae)

    PubMed Central

    Zhang, Peng; Chen, Yue-Qin; Zhou, Hui; Liu, Yi-Fei; Wang, Xiu-Ling; Papenfuss, Theodore J.; Wake, David B.; Qu, Liang-Hu

    2006-01-01

    We sequenced 15 complete mitochondrial genomes and performed comprehensive molecular phylogenetic analyses to study the origin and phylogeny of the Hynobiidae, an ancient lineage of living salamanders. Our phylogenetic analyses show that the Hynobiidae is a clade with well resolved relationships, and our results contrast with a morphology-based phylogenetic hypothesis. These salamanders have low vagility and are limited in their distribution primarily by deserts, mountains, and oceans. Our analysis suggests that the relationships among living hynobiids have been shaped primarily by geography. We show that four-toed species assigned to Batrachuperus do not form a monophyletic group, and those that occur in Afghanistan and Iran are transferred to the resurrected Paradactylodon. Convergent morphological characters in different hynobiid lineages are likely produced by similar environmental selective pressures. Clock-independent molecular dating suggests that hynobiids originated in the Middle Cretaceous [≈110 million years ago (Mya)]. We propose an “out of North China” hypothesis for hynobiid origins and hypothesize an ancestral stream-adapted form. Given the particular distributional patterns and our molecular dating estimates, we hypothesize that: (i) the interior desertification from Mongolia to Western Asia began ≈50 Mya; (ii) the Tibetan plateau (at least on the eastern fringe) experienced rapid uplift ≈40 Mya and reached an altitude of at least 2,500 m; and (iii) the Ailao–Red River shear zone underwent the most intense orogenic movement ≈24 Mya. PMID:16648252

  18. Shedding light on vampires: the phylogeny of vampyrellid amoebae revisited.

    PubMed

    Hess, Sebastian; Sausen, Nicole; Melkonian, Michael

    2012-01-01

    With the advent of molecular phylogenetic techniques the polyphyly of naked filose amoebae has been proven. They are interspersed in several supergroups of eukaryotes and most of them already found their place within the tree of life. Although the 'vampire amoebae' have attracted interest since the middle of the 19th century, the phylogenetic position and even the monophyly of this traditional group are still uncertain. In this study clonal co-cultures of eight algivorous vampyrellid amoebae and the respective food algae were established. Culture material was characterized morphologically and a molecular phylogeny was inferred using SSU rDNA sequence comparisons. We found that the limnetic, algivorous vampyrellid amoebae investigated in this study belong to a major clade within the Endomyxa Cavalier-Smith, 2002 (Cercozoa), grouping together with a few soil-dwelling taxa. They split into two robust clades, one containing species of the genus Vampyrella Cienkowski, 1865, the other containing the genus Leptophrys Hertwig & Lesser, 1874, together with terrestrial members. Supported by morphological data these clades are designated as the two families Vampyrellidae Zopf, 1885, and Leptophryidae fam. nov. Furthermore the order Vampyrellida West, 1901 was revised and now corresponds to the major vampyrellid clade within the Endomyxa, comprising the Vampyrellidae and Leptophryidae as well as several environmental sequences. In the light of the presented phylogenetic analyses morphological and ecological aspects, the feeding strategy and nutritional specialization within the vampyrellid amoebae are discussed. PMID:22355342

  19. A phylogeny of the land snails (Gastropoda: Pulmonata).

    PubMed Central

    Wade, C. M.; Mordan, P. B.; Clarke, B.

    2001-01-01

    We have undertaken the first large-scale molecular phylogenetic analysis of the Stylommatophora. Sequences of the ribosomal RNA gene-cluster were examined in 104 species of snails and slugs from 50 families, encompassing all the currently recognized major groups. It allows an independent test of the present classification based on morphology. At the level of families our molecular phylogeny closely supports the current taxonomy, but the deep branches within the tree do not. Surprisingly, a single assemblage including the families Achatinidae, Subulinidae and Streptaxidae lies near the base of the tree, forming a sister group to all remaining stylommatophorans. This primary division into 'achatinoid' and 'non-achatinoid' taxa is unexpected, and demands a radical reinterpretation of early stylommatophoran evolution. In particular, the Orthurethra appear to be relatively advanced within the 'non-achatinoid clade', and broadly equivalent to other super-familial clusters. This indicates that supposedly primitive features such as the orthurethran kidney are derived. The molecular tree also suggests that the origin of the Stylommatophora is much earlier than the main period of their diversification. PMID:11270439

  20. Deep phylogeny, ancestral groups and the four ages of life

    PubMed Central

    Cavalier-Smith, Thomas

    2010-01-01

    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria—the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution. PMID:20008390

  1. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.

    PubMed

    Wen, Dingqiao; Yu, Yun; Nakhleh, Luay

    2016-05-01

    The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. PMID:27144273

  2. Complete, accurate, mammalian phylogenies aid conservation planning, but not much

    PubMed Central

    Rodrigues, Ana S. L.; Grenyer, Richard; Baillie, Jonathan E. M.; Bininda-Emonds, Olaf R. P.; Gittlemann, John L.; Hoffmann, Michael; Safi, Kamran; Schipper, Jan; Stuart, Simon N.; Brooks, Thomas

    2011-01-01

    In the face of unprecedented global biodiversity loss, conservation planning must balance between refining and deepening knowledge versus acting on current information to preserve species and communities. Phylogenetic diversity (PD), a biodiversity measure that takes into account the evolutionary relationships between species, is arguably a more meaningful measure of biodiversity than species diversity, but cannot yet be applied to conservation planning for the majority of taxa for which phylogenetic trees have not yet been developed. Here, we investigate how the quality of data on the taxonomy and/or phylogeny of species affects the results of spatial conservation planning in terms of the representation of overall mammalian PD. The results show that the better the quality of the biodiversity data the better they can serve as a basis for conservation planning. However, decisions based on incomplete data are remarkably robust across different levels of degrading quality concerning the description of new species and the availability of phylogenetic information. Thus, given the level of urgency and the need for action, conservation planning can safely make use of the best available systematic data, limited as these data may be. PMID:21844044

  3. Molecular phylogeny and ultrastructure of Aphelidium aff. melosirae (Aphelida, Opisthosporidia).

    PubMed

    Karpov, Sergey A; Mamkaeva, Maria A; Benzerara, Karim; Moreira, David; López-García, Purificación

    2014-08-01

    Aphelids are a poorly known group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position. Together with Cryptomycota and the highly derived Microsporidia, they have been recently re-classified as Opisthosporidia, being the sister group to fungi. Despite their huge diversity, as revealed by molecular environmental studies, and their phylogenetic interest, only three genera have been described (Aphelidium, Amoeboaphelidium, and Pseudaphelidium), from which 18S rRNA gene sequences exist only for Amoeboaphelidium species. Here, we describe the life cycle and ultrastructure of Aphelidium aff. melosirae, and provide the first 18S rRNA gene sequence obtained for this genus. Molecular phylogeny analysis indicates that Aphelidium is very distantly related to Amoebaphelidium, highlighting the wide genetic diversity of the aphelids. The parasitoid encysts and penetrates the host alga, Tribonema gayanum through an infection tube. Cyst germination leads to a young trophont that phagocytes the algal cell content and progressively develops a plasmodium, which becomes a zoospore-producing sporangium. Aphelidium aff. melosirae has amoeboflagellate zoospores, tubular/lamellar mitochondrial cristae, a metazoan type of centrosome, and closed orthomitosis with an intranuclear spindle. These features together with trophont phagocytosis distinguish Aphelidium from fungi and support the erection of the new superphylum Opisthosporidia as sister to fungi. PMID:24995586

  4. [Skin derivatives in ontogeny and phylogeny of vertebrates].

    PubMed

    Chernova, O F

    2009-01-01

    The skin of vertebrates has numerous and diverse derivatives, either located within the epithelial sheet itself (glands) or extending above its surface (teeth, scales, feathers, hairs, etc.). Many of them have a modular structure and constitute structural-functional units. Ontogenetically, all skin derivatives are of ectomesodermal origin, and their morphogenesis is subject to metabolic control, heterochronies (divergence in the timing of origination and development), and regulation by means of tissue interactions and molecular signaling via similar pathways. The diversification (origination of morphological diversity) of skin derivatives within the same morphological type is explained by the development of new generations of ectomesodermal structures separated be heterochronies and regulated by changes in the gradients of molecular signaling pathways under the influence of environmental factors. Evolutionary relationships between the majority of skin derivatives are obscure, except for teeth and glands associated with sensory organs, which evolved together with the latter. Apparently, many vertebrate skin derivatives (scales, feathers, hairs, and glands) originated as innovations at nodal stages of phylogeny and subsequently evolved convergently or in parallel. PMID:19391480

  5. The chaos prevails: molecular phylogeny of the Haptoria (Ciliophora, Litostomatea).

    PubMed

    Vďačný, Peter; Breiner, Hans-Werner; Yashchenko, Varvara; Dunthorn, Micah; Stoeck, Thorsten; Foissner, Wilhelm

    2014-01-01

    The Haptoria are free-living predatory ciliates living in terrestrial and aquatic habitats all around the world. They belong to a highly diverse class, Litostomatea, whose morphological and molecular classifications harmonize poorly since both approaches produce rather different frameworks. In the present study, we analyzed the genealogy of the litostomateans, including eight new haptorian 18S rRNA gene sequences. Apart from traditional tree-building methods, we also applied phylogenetic networks, split spectrum analysis and quartet likelihood mapping to assess the information content of alignments. These analyses show that: (1) there are several strongly supported monophyletic litostomatean lineages--Rhynchostomatia, Trichostomatia, Haptorida, Lacrymariida, Pleurostomatida, and Didiniida; (2) the Rhynchostomatia are the best candidates for a basal litostomatean group; (3) sister relationship of the Trichostomatia and Haptoria is very likely, which well corroborates the traditional morphology-based classifications; (4) molecular phylogeny of the order Spathidiida is only poorly resolved very likely due to one or several rapid radiation events or due to the incomplete lineage sorting at the rRNA locus; and (5) the basal position of the genera Chaenea and Trachelotractus in molecular trees and phylogenetic networks is very likely a result of class III long-branch effects. PMID:24524973

  6. The phylogeny and evolutionary history of tyrannosauroid dinosaurs

    PubMed Central

    Brusatte, Stephen L.; Carr, Thomas D.

    2016-01-01

    Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work. PMID:26830019

  7. Moss Phylogeny Reconstruction Using Nucleotide Pangenome of Complete Mitogenome Sequences.

    PubMed

    Goryunov, D V; Nagaev, B E; Nikolaev, M Yu; Alexeevski, A V; Troitsky, A V

    2015-11-01

    Stability of composition and sequence of genes was shown earlier in 13 mitochondrial genomes of mosses (Rensing, S. A., et al. (2008) Science, 319, 64-69). It is of interest to study the evolution of mitochondrial genomes not only at the gene level, but also on the level of nucleotide sequences. To do this, we have constructed a "nucleotide pangenome" for mitochondrial genomes of 24 moss species. The nucleotide pangenome is a set of aligned nucleotide sequences of orthologous genome fragments covering the totality of all genomes. The nucleotide pangenome was constructed using specially developed new software, NPG-explorer (NPGe). The stable part of the mitochondrial genome (232 stable blocks) is shown to be, on average, 45% of its length. In the joint alignment of stable blocks, 82% of positions are conserved. The phylogenetic tree constructed with the NPGe program is in good correlation with other phylogenetic reconstructions. With the NPGe program, 30 blocks have been identified with repeats no shorter than 50 bp. The maximal length of a block with repeats is 140 bp. Duplications in the mitochondrial genomes of mosses are rare. On average, the genome contains about 500 bp in large duplications. The total length of insertions and deletions was determined in each genome. The losses and gains of DNA regions are rather active in mitochondrial genomes of mosses, and such rearrangements presumably can be used as additional markers in the reconstruction of phylogeny. PMID:26615445

  8. A molecular phylogeny of bullfinches Pyrrhula Brisson, 1760 (Aves: Fringillidae).

    PubMed

    Töpfer, T; Haring, E; Birkhead, T R; Lopes, R J; Severinghaus, L Liu; Martens, J; Päckert, M

    2011-02-01

    We present a molecular phylogeny of bullfinches (Pyrrhula Brisson, 1760) based on 2357bp DNA sequence information of mitochondrial genes (cyt-b, 16S rRNA) and nuclear introns (fib-7, GAPDH-11). The genus is clearly a monophyletic group. Within the limits of Pyrrhula, molecular methods support the subdivision of three main groups: (1) "Southeast-Asian bullfinches" (P. nipalensis and P. leucogenis), (2) "Himalayan bullfinches" (P. aurantiaca, P. erythaca, P. erythrocephala), and (3) "Eurasian bullfinches" (P. pyrrhula s.l.). Within the last group there are four different subgroups: (3a) P. (p.) murina, (3b) P. (p.) cineracea, (3c) P. (p.) griseiventris, and (3d) P. pyrrhula s.str. The centre of origin of the genus Pyrrhula was most probably Southeast Asia. Incomplete lineage sorting of both mitochondrial and nuclear genes is observed among two apparently good species (P. erythaca and P. erythrocephala) indicating a very recent speciation event within the Himalayan Mountain chain. According to our estimates, the Pyrrhula ancestors split from the Pinicola ancestors before the Pleistocene. Apart from the subsequent Pre-Pleistocene splits of the three ancestral main groups, most of the diversification of today's representatives probably took place during the past 600,000 years, possibly in interaction with Pleistocene refugia and successive colonization movements after the last glaciation. Thus our work confirms the traditional delimitation of the bullfinches towards the other members of the finch family Fringillidae and corroborates most of the classic intra-generic subdivisions. PMID:21044888

  9. Evaluating topological conflict in centipede phylogeny using transcriptomic data sets.

    PubMed

    Fernández, Rosa; Laumer, Christopher E; Vahtera, Varpu; Libro, Silvia; Kaluziak, Stefan; Sharma, Prashant P; Pérez-Porro, Alicia R; Edgecombe, Gregory D; Giribet, Gonzalo

    2014-06-01

    Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record. PMID:24674821

  10. Reconstructing Histories of Complex Gene Clusters on a Phylogeny

    NASA Astrophysics Data System (ADS)

    Vinař, Tomáš; Brejová, Broňa; Song, Giltae; Siepel, Adam

    Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. These clusters are one of the major sources of evolutionary innovation, and they are linked to multiple diseases, including HIV and a variety of cancers. Understanding their evolutionary histories is a key to the application of comparative genomics methods in these regions of the genome. We propose a probabilistic model of gene cluster evolution on a phylogeny, and an MCMC algorithm for reconstruction of duplication histories from genomic sequences in multiple species. Several projects are underway to obtain high quality BAC-based assemblies of duplicated clusters in multiple species, and we anticipate use of our methods in their analysis. Supplementary materials are located at http://compbio.fmph.uniba.sk/suppl/09recombcg/

  11. Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

    PubMed

    Kozlov, Alexey M; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros

    2016-06-20

    Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences ('mislabels') using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa. PMID:27166378

  12. The phylogeny and evolutionary history of tyrannosauroid dinosaurs.

    PubMed

    Brusatte, Stephen L; Carr, Thomas D

    2016-01-01

    Tyrannosauroids--the group of carnivores including Tyrannosaurs rex--are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work. PMID:26830019

  13. Evolution of consciousness: Phylogeny, ontogeny, and emergence from general anesthesia

    PubMed Central

    Mashour, George A.; Alkire, Michael T.

    2013-01-01

    Are animals conscious? If so, when did consciousness evolve? We address these long-standing and essential questions using a modern neuroscientific approach that draws on diverse fields such as consciousness studies, evolutionary neurobiology, animal psychology, and anesthesiology. We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution. Thus, in agreement with Darwin’s insight and the recent “Cambridge Declaration on Consciousness in Non-Human Animals,” a review of modern scientific data suggests that the differences between species in terms of the ability to experience the world is one of degree and not kind. PMID:23754370

  14. Molecular and morphological evidence on the phylogeny of the Elephantidae.

    PubMed Central

    Thomas, M G; Hagelberg, E; Jone, H B; Yang, Z; Lister, A M

    2000-01-01

    The African and Asian elephants and the mammoth diverged ca. 4-6 million years ago and their phylogenetic relationship has been controversial. Morphological studies have suggested a mammoth Asian elephant relationship, while molecular studies have produced conflicting results. We obtained cytochrome b sequences of up to 545 base pairs from five mammoths, 14 Asian and eight African elephants. A high degree of polymorphism is detected within species. With a dugong sequence used as the outgroup, parsimony and maximum-likelihood analyses support a mammoth African elephant clade. As the dugong is a very distant outgroup, we employ likelihood analysis to root the tree with a molecular clock, and use bootstrap and Bayesian analyses to quantify the relative support for different topologies. The analyses support the mammoth African elephant relationship, although other trees cannot be rejected. Ancestral polymorphisms may have resulted in gene trees differing from the species phylogeny Examination of morphological data, especially from primitive fossil members, indicates that some supposed synapomorphies between the mammoth and Asian elephant are variable, others convergent or autapomorphous. A mammoth African elephant relationship is not excluded. Our results highlight the need, in both morphological and molecular phylogenetics, for multiple markers and close attention to within-taxon variation and outgroup selection. PMID:11197124

  15. A multilocus phylogeny of the Sulidae (Aves: Pelecaniformes).

    PubMed

    Patterson, S A; Morris-Pocock, J A; Friesen, V L

    2011-02-01

    Gene trees will often differ from the true species history, the species tree, as a result of processes such as incomplete lineage sorting. New methods such as Bayesian Estimation of the Species Tree (BEST) use the multispecies coalescent to model lineage sorting, and directly infer the species tree from multilocus DNA sequence data. The Sulidae (Aves: Pelecaniformes) is a family of ten booby and gannet species with a global distribution. We sequenced five nuclear intron loci and one mitochondrial locus to estimate a species tree for the Sulidae using both BEST and by concatenating nuclear loci. We also used fossil calibrated strict and relaxed molecular clocks in BEAST to estimate divergence times for major nodes in the sulid phylogeny. Individual gene trees showed little phylogenetic conflict but varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. On the other hand, both the BEST and concatenated species trees were highly resolved, strongly supported, and topologically consistent with each other. The three sulid genera (Morus, Sula, Papasula) were monophyletic and the relationships within genera were mostly consistent with both a previously estimated mtDNA gene tree and the mtDNA gene tree estimated here. However, our species trees conflicted with the mtDNA gene trees in the relationships among the three genera. Most notably, we find that the endemic and endangered Abbott's booby (Papasula abbotti) is likely basal to all other members of the Sulidae and diverged from them approximately 22 million years ago. PMID:21144905

  16. Arthropod phylogeny based on eight molecular loci and morphology

    NASA Technical Reports Server (NTRS)

    Giribet, G.; Edgecombe, G. D.; Wheeler, W. C.

    2001-01-01

    The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

  17. Michigan: The Great Lakes State

    ERIC Educational Resources Information Center

    McKay, Sandra Lee; La Luzerne-Oi, Sally

    2009-01-01

    Although Michigan is often called the "Wolverine State," its more common nickname is the "Great Lakes State." This name comes from the fact that Michigan is the only state in the United States that borders four of the five Great Lakes. Also referred to as the "Water Wonderland," Michigan has 11,000 additional lakes, 36,000 miles of streams, and…

  18. Viruses in Antarctic lakes

    NASA Technical Reports Server (NTRS)

    Kepner, R. L. Jr; Wharton, R. A. Jr; Suttle, C. A.; Wharton RA, J. r. (Principal Investigator)

    1998-01-01

    Water samples collected from four perennially ice-covered Antarctic lakes during the austral summer of 1996-1997 contained high densities of extracellular viruses. Many of these viruses were found to be morphologically similar to double-stranded DNA viruses that are known to infect algae and protozoa. These constitute the first observations of viruses in perennially ice-covered polar lakes. The abundance of planktonic viruses and data suggesting substantial production potential (relative to bacteria] secondary and photosynthetic primary production) indicate that viral lysis may be a major factor in the regulation of microbial populations in these extreme environments. Furthermore, we suggest that Antarctic lakes may be a reservoir of previously undescribed viruses that possess novel biological and biochemical characteristics.

  19. Transient Tsunamis in Lakes

    NASA Astrophysics Data System (ADS)

    Couston, L.; Mei, C.; Alam, M.

    2013-12-01

    A large number of lakes are surrounded by steep and unstable mountains with slopes prone to failure. As a result, landslides are likely to occur and impact water sitting in closed reservoirs. These rare geological phenomena pose serious threats to dam reservoirs and nearshore facilities because they can generate unexpectedly large tsunami waves. In fact, the tallest wave experienced by contemporary humans occurred because of a landslide in the narrow bay of Lituya in 1958, and five years later, a deadly landslide tsunami overtopped Lake Vajont's dam, flooding and damaging villages along the lakefront and in the Piave valley. If unstable slopes and potential slides are detected ahead of time, inundation maps can be drawn to help people know the risks, and mitigate the destructive power of the ensuing waves. These maps give the maximum wave runup height along the lake's vertical and sloping boundaries, and can be obtained by numerical simulations. Keeping track of the moving shorelines along beaches is challenging in classical Eulerian formulations because the horizontal extent of the fluid domain can change over time. As a result, assuming a solid slide and nonbreaking waves, here we develop a nonlinear shallow-water model equation in the Lagrangian framework to address the problem of transient landslide-tsunamis. In this manner, the shorelines' three-dimensional motion is part of the solution. The model equation is hyperbolic and can be solved numerically by finite differences. Here, a 4th order Runge-Kutta method and a compact finite-difference scheme are implemented to integrate in time and spatially discretize the forced shallow-water equation in Lagrangian coordinates. The formulation is applied to different lake and slide geometries to better understand the effects of the lake's finite lengths and slide's forcing mechanism on the generated wavefield. Specifically, for a slide moving down a plane beach, we show that edge-waves trapped by the shoreline and free

  20. A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny

    PubMed Central

    Mithani, Aziz; Preston, Gail M.; Hein, Jotun

    2010-01-01

    The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions) or complex (incorporating dependencies among reactions) stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks. PMID:20700467

  1. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record.

    PubMed

    Etienne, Rampal S; Haegeman, Bart; Stadler, Tanja; Aze, Tracy; Pearson, Paul N; Purvis, Andy; Phillimore, Albert B

    2012-04-01

    The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility. PMID:21993508

  2. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.

    PubMed

    FitzJohn, Richard G; Maddison, Wayne P; Otto, Sarah P

    2009-12-01

    Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies. PMID:20525612

  3. Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae

    PubMed Central

    2012-01-01

    Background During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer a predictive approach enabling more efficient selection of plants for the development of traditional medicine and lead discovery. However, this relationship has rarely been rigorously tested and the potential predictive power is consequently unknown. Results We produced a phylogenetic hypothesis for the medicinally important plant subfamily Amaryllidoideae (Amaryllidaceae) based on parsimony and Bayesian analysis of nuclear, plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloid diversity and activity in bioassays related to the central nervous system are significantly correlated with phylogeny and found evidence for a significant phylogenetic signal in these traits, although the effect is not strong. Conclusions Several genera are non-monophyletic emphasizing the importance of using phylogeny for interpretation of character distribution. Alkaloid diversity and in vitro inhibition of acetylcholinesterase (AChE) and binding to the serotonin reuptake transporter (SERT) are significantly correlated with phylogeny. This has implications for the use of phylogenies to interpret chemical evolution and biosynthetic pathways, to select candidate taxa for lead discovery, and to make recommendations for policies regarding traditional use and conservation priorities. PMID:22978363

  4. Reevaluation of lake trout and lake whitefish bioenergetics models

    USGS Publications Warehouse

    Madenjian, Charles P.; Pothoven, Steve A.; Kao, Yu-Chun

    2013-01-01

    Using a corrected algorithm for balancing the energy budget, we reevaluated the Wisconsin bioenergetics model for lake trout (Salvelinus namaycush) in the laboratory and for lake whitefish (Coregonus clupeaformis) in the laboratory and in the field. For lake trout, results showed that the bioenergetics model slightly overestimated food consumption by the lake trout when they were fed low and intermediate rations, whereas the model predicted food consumption by lake trout fed ad libitum without any detectable bias. The slight bias in model predictions for lake trout on restricted rations may have been an artifact of the feeding schedule for these fish, and we would therefore recommend application of the Wisconsin lake trout bioenergetics model to lake trout populations in the field without any revisions to the model. Use of the Wisconsin bioenergetics model for coregonids resulted in overestimation of food consumption by lake whitefish both in the laboratory and in the field by between 20 and 30%, on average. This overestimation of food consumption was most likely due to overestimation of respiration rate. We therefore adjusted the respiration component of the bioenergetics model to obtain a good fit to the observed consumption in our laboratory tanks. The adjusted model predicted the consumption in the laboratory and the field without any detectable bias. Until a detailed lake whitefish respiration study can be conducted, we recommend application of our adjusted version of the Wisconsin generalized coregonid bioenergetics model to lake whitefish populations in the field.

  5. Maturity schedules of lake trout in Lake Michigan

    USGS Publications Warehouse

    Madenjian, Charles P.; DeSorcie, Timothy J.; Stedman, Ralph M.

    1998-01-01

    We determined maturity schedules of male and female lake trout (Salvelinus namaycush) in Lake Michigan from nearshore populations and from an offshore population on Sheboygan Reef, which is located in midlake. Gill nets and bottom trawls were used to catch lake trout in fall 1994 and 1995 from two nearshore sites and Sheboygan Reef. Each lake trout was judged immature or mature, based on visual examination of gonads. Probit analysis, coupled with relative potency testing, revealed that age-at-maturity and length-at-maturity were similar at the two nearshore sites, but that lake trout from the nearshore sites matured at a significantly earlier age than lake trout from Sheboygan Reef. However, length at maturity for the nearshore populations was nearly identical to that for the offshore population, suggesting that rate of lake trout maturation in Lake Michigan was governed by growth rather than age. Half of the lake trout males reached maturity at a total length of 580 mm, whereas half of the females were mature at a length of 640 mm. Over half of nearshore males were mature by age 5, and over half the nearshore females matured by age 6. Due to a slower growth rate, maturity was delayed by 2 years on Sheboygan Reef compared with the nearshore populations. Documentation of this delay in maturation may be useful in deciding stocking allocations for lake trout rehabilitation in Lake Michigan.

  6. Gas exchange on Mono Lake and Crowley Lake, California

    NASA Technical Reports Server (NTRS)

    Wanninkhof, Rik; Ledwell, James R.; Broecker, Wallace S.

    1987-01-01

    Gas exchange coefficients (k) have been determined for freshwater Crowley Lake and saline Mono Lake through the use of a man-made purposefully injected gas, SF6. The concentration decreased from an initial value of 40 to 4 pmol/L for Mono Lake and from 20 to 1 pmol/L for Crowley lake over a period of 6 wks. Wind-speed (u) records from anemometers on the shore of each lake made it possible to determine the relationship between k and u. The average u and k values for the experiment were identical for the two lakes, despite the large chemical differences. It is estimated that, for the u values observed over Mono Lake from July to December 1984, the exchange of CO2 occurred 2.5 times faster than without chemical enhancement. This is a factor of 4 lower than needed to explain the high invasion rate of C-14 produced by nuclear bomb tests.

  7. Bilaterian phylogeny: a broad sampling of 13 nuclear genes provides a new Lophotrochozoa phylogeny and supports a paraphyletic basal acoelomorpha.

    PubMed

    Paps, Jordi; Baguñà, Jaume; Riutort, Marta

    2009-10-01

    During the past decade, great progress has been made in clarifying the relationships among bilaterian animals. Studies based on a limited number of markers established new hypotheses such as the existence of three superclades (Deuterostomia, Ecdysozoa, and Lophotrochozoa) but left major questions unresolved. The data sets used to the present either bear few characters for many taxa (i.e., the ribosomal genes) or present many characters but lack many phyla (such as recent phylogenomic approaches) failing to provide definitive answers for all the regions of the bilaterian tree. We performed phylogenetic analyses using a molecular matrix with a high number of characters and bilaterian phyla. This data set is built from 13 genes (8,880 bp) belonging to 90 taxa from 27 bilaterian phyla. Probabilistic analyses robustly support the three superclades, the monophyly of Chordata, a spiralian clade including Brachiozoa, the basal position of a paraphyletic Acoelomorpha, and point to an ecdysozoan affiliation for Chaetognatha. This new phylogeny not only agrees with most classical molecular results but also provides new insights into the relationships between lophotrochozoans and challenges the results obtained using high-throughput strategies, highlighting the problems associated with the current trend to increase gene number rather than taxa. PMID:19602542

  8. Lake whitefish diet, condition, and energy density in Lake Champlain and the lower four Great Lakes following dreissenid invasions

    USGS Publications Warehouse

    Herbst, Seth J.; Marsden, J. Ellen; Lantry, Brian F.

    2013-01-01

    Lake Whitefish Coregonus clupeaformis support some of the most valuable commercial freshwater fisheries in North America. Recent growth and condition decreases in Lake Whitefish populations in the Great Lakes have been attributed to the invasion of the dreissenid mussels, zebra mussels Dreissena polymorpha and quagga mussels D. bugensis, and the subsequent collapse of the amphipod, Diporeia, a once-abundant high energy prey source. Since 1993, Lake Champlain has also experienced the invasion and proliferation of zebra mussels, but in contrast to the Great Lakes, Diporeia were not historically abundant. We compared the diet, condition, and energy density of Lake Whitefish from Lake Champlain after the dreissenid mussel invasion to values for those of Lake Whitefish from Lakes Michigan, Huron, Erie, and Ontario. Lake Whitefish were collected using gill nets and bottom trawls, and their diets were quantified seasonally. Condition was estimated using Fulton's condition factor (K) and by determining energy density. In contrast to Lake Whitefish from some of the Great Lakes, those from Lake Champlain Lake Whitefish did not show a dietary shift towards dreissenid mussels, but instead fed primarily on fish eggs in spring, Mysis diluviana in summer, and gastropods and sphaeriids in fall and winter. Along with these dietary differences, the condition and energy density of Lake Whitefish from Lake Champlain were high compared with those of Lake Whitefish from Lakes Michigan, Huron, and Ontario after the dreissenid invasion, and were similar to Lake Whitefish from Lake Erie; fish from Lakes Michigan, Huron, and Ontario consumed dreissenids, whereas fish from Lake Erie did not. Our comparisons of Lake Whitefish populations in Lake Champlain to those in the Great Lakes indicate that diet and condition of Lake Champlain Lake Whitefish were not negatively affected by the dreissenid mussel invasion.

  9. Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America.

    PubMed

    Perez, Manolo F; Carstens, Bryan C; Rodrigues, Gustavo L; Moraes, Evandro M

    2016-03-01

    Supportive data related to the article "Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America" (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny. PMID:26900589

  10. Rapid evolution of sessility in an endemic species flock of the freshwater bivalve Corbicula from ancient lakes on Sulawesi, Indonesia

    PubMed Central

    von Rintelen, Thomas; Glaubrecht, Matthias

    2005-01-01

    The fauna of ancient lakes frequently contains taxa with highly derived morphologies that resulted from in situ radiation of lacustrine lineages with high antiquity. We employed a molecular mtDNA phylogeny to investigate this claim for corbiculid freshwater bivalves in two ancient lake systems on the Indonesian island Sulawesi. Among the otherwise mobile corbiculid species flock, only one taxon, Posostrea anomioides, in the ancient Lake Poso exhibits a unique habit, i.e. cementing one valve to the substrate. Our data show that Corbicula on Sulawesi is polyphyletic, with the endemic riverine taxa in terminal position, and the lacustrine species flock being paraphyletic. Surprisingly, Posostrea is not confirmed as a genus distinct from Corbicula and genetic distances suggest a rather recent origin from the only other corbiculid species endemic to Lake Poso, the non-cementing Corbicula possoensis. While the cementing anomioides, despite its unique behavioural and morphological characteristics, clusters together with non-sessile Corbicula species, the latter exhibit strong genetic distances in the absence of morphological disparity and fall into several genetically rather distinct clades. These findings suggest that developmental plasticity of animals in ancient lakes rather than the antiquity of lineages might account for the unique morphology of some species. PMID:17148330

  11. Temperature Trends in Montane Lakes

    NASA Astrophysics Data System (ADS)

    Melack, J. M.; Sadro, S.; Jellison, R.

    2014-12-01

    Long-term temperature trends in lakes integrate hydrological and meteorological factors. We examine temperature trends in a small montane lake with prolonged ice-cover and large seasonal snowfall and in a large saline lake. Emerald Lake, located in the Sierra Nevada (California), is representative of high-elevation lakes throughout the region. No significant trend in outflow temperature was apparent from 1991to 2012. Snowfall in the watershed accounted for 93% of the variability in average summer lake temperatures. Mono Lake (California) lies in a closed, montane basin and is hypersaline and monomictic or meromictic. Temperature profiles have been collected from 1982 to 2010. In the upper water column, the July-August-September water temperatures increased 0.8-1.0°C over the 29 years. This rate of warming is less than published estimates based on satellite-derived skin temperatures and will discussed in the context of general limnological interpretation of temperature trends.

  12. Institutional aspects of lake management

    NASA Astrophysics Data System (ADS)

    Born, Stephen M.; Rumery, Carolyn

    1989-01-01

    The major barriers to successful lake management are institutional. However, in contrast to the technical and limnological dimensions of lake management, the institutional aspects of managing lakes have received little attention. The institutional factors that are important for successful lake management outcomes are: overlapping areal jurisdiction among governmental units, fragmented functional program responsibilities, ineffective coordination, limited authority, financial constraints, private sector roles, and inadequate public awareness and consensus. The range of typical institutional problems confronting lake management are well illustrated through experiences from the state of Wisconsin, USA. Because lake management programs with institutional shortcomings rarely realize their goals, it is critical to assimilate, evaluate, and apply our experience to date with the institutional arrangements necessary to effectively manage lake resources.

  13. CONTOURITES IN LAKE SUPERIOR

    EPA Science Inventory

    Contour currents influence sedimentation in an area 15 km wide and 65 km long at the base of the slope off the Keweenaw Peninsula in Lake Superior, northwestern Michigan. Seismic-reflection profiles (3.5 kHz) from this area show distinct wavy reflectors in a scoured trough at a d...

  14. Utah: Salt Lake City

    Atmospheric Science Data Center

    2014-05-15

    ... mountains surrounding Salt Lake City are renowned for the dry, powdery snow that results from the arid climate and location at the ... should be used with the red filter placed over your left eye. The canyons and peaks of the Uinta and Wasatch Mountains are ...

  15. Quebec: Lake Manicouagan

    Atmospheric Science Data Center

    2013-04-17

    ... and other erosional processes have reduced the extent of the crater, with the original diameter estimated at about 100 kilometers. This ... metamorphic effects are abundant in the target rocks of the crater floor. Today Lake Manicouagan serves as a reservoir and is one of ...

  16. The People's Lake

    ERIC Educational Resources Information Center

    Carlson, Karen Townsend

    1975-01-01

    Citizen action to stop the disposal of taconite tailings into Lake Superior was unsuccessful when the courts settled in the favor of industry. Although citizen research revealed a form of asbestos, as well as other toxic chemicals in the discharged wastes, company representatives stated that there were no health hazards. (MA)

  17. Great Minds? Great Lakes!

    ERIC Educational Resources Information Center

    Environmental Protection Agency, Chicago, IL. Great Lakes National Program Office.

    This booklet introduces an environmental curriculum for use in a variety of elementary subjects. The lesson plans provide an integrated approach to incorporating Great Lakes environmental issues into the subjects of history, social studies, and environmental sciences. Each of these sections contains background information, discussion points, and a…

  18. Echoes of Bark Lake.

    ERIC Educational Resources Information Center

    Duenkel, Nicky; Hemstreet, Jeff

    1997-01-01

    Two former staff members reflect on their feelings about the August 1995 closing of Bark Lake Leadership Centre (Ontario, Canada), which for 49 years had offered outdoor adventure and environmental education courses to youth and adults. They discuss their experiences as both students and teachers at the center, which helped shape their careers in…

  19. Upwellings in Lake Baikal

    NASA Astrophysics Data System (ADS)

    Shimaraev, M. N.; Troitskaya, E. S.; Blinov, V. V.; Ivanov, V. G.; Gnatovskii, R. Yu.

    2012-02-01

    Based on shipboard and satellite observations, the characteristics of upwelling in Lake Baikal in the period of direct temperature stratification have been determined for the first time. Coastal upwellings appear annually under the effect of run-down and alongshore winds and are traced along the coast to a distance of up to 60-100 km and up to 250 km in North Baikal. Analogous to the way it occurs in seas, water rises from the depths of 100-200 m (350 m as a maximum) at the velocity of 0.1 × 10-2-6.5 × 10-2 cm/s. Divergence in the field of intràbasin cyclonic macrovortices produces upwelling in the Baikal pelagic zone and downwelling in the vicinity of shores; this lasts from 7 to 88 days and covers the depth interval of 80-300 m in August and up to 400-800 m in early-mid November. The area of upwellings occupies up to 20-60% of the separate basins of the lake. Vertical circulation of water in the field of pelagic upwellings leads to intensification of coastal currents and to formation of the thermobar with a heat inert zone in the central part of the lake in November, and this thermobar is not observed in other lakes, at that.

  20. LAKE TAHOE VISIBILITY STUDY

    EPA Science Inventory

    Visibility monitoring and airborne particulate sampling in the Lake Tahoe Basin were used to document visual air quality levels and to assess the relative impacts of major contributing emission source categories. Visibility data were obtained by long path contrast and particle sc...

  1. Lake Ontario: Nearshore Variability

    EPA Science Inventory

    We conducted a high-resolution survey with towed electronic instrumentation along the Lake Ontario nearshore (720 km) at a 20 meter contour. The survey was conducted September 6-10, 2008 with a shorter 300 km survey conducted August 14-15 for comparing of temporal variability. ...

  2. Lake Michigan: Nearshore Variability

    EPA Science Inventory

    We conducted a high-resolution survey in the nearshore of Lake Michigan at a 20 meter contour using towed electronic instrumentation. The nearly 1200 km survey was conducted Sep 8-15, 2010. We also conducted six cross-contour tows. Along the survey tracks we sampled fixed stat...

  3. Does behavior reflect phylogeny in swiftlets (Aves: Apodidae)? A test using cytochrome b mitochondrial DNA sequences.

    PubMed Central

    Lee, P L; Clayton, D H; Griffiths, R; Page, R D

    1996-01-01

    Swiftlets are small insectivorous birds, many of which nest in caves and are known to echolocate. Due to a lack of distinguishing morphological characters, the taxonomy of swiftlets is primarily based on the presence or absence of echolocating ability, together with nest characters. To test the reliability of these behavioral characters, we constructed an independent phylogeny using cytochrome b mitochondrial DNA sequences from swiftlets and their relatives. This phylogeny is broadly consistent with the higher classification of swifts but does not support the monophyly of swiftlets. Echolocating swiftlets (Aerodramus) and the nonecholocating "giant swiftlet" (Hydrochous gigas) group together, but the remaining nonecholocating swiftlets belonging to Collocalia are not sister taxa to these swiftlets. While echolocation may be a synapomorphy of Aerodramus (perhaps secondarily lost in Hydrochous), no character of Aerodramus nests showed a statistically significant fit to the molecular phylogeny, indicating that nest characters are not phylogenetically reliable in this group. Images Fig. 1 PMID:8692950

  4. RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas.

    PubMed

    Díaz-Arce, Natalia; Arrizabalaga, Haritz; Murua, Hilario; Irigoien, Xabier; Rodríguez-Ezpeleta, Naiara

    2016-09-01

    Although species from the genus Thunnus include some of the most commercially important and most severely overexploited fishes, the phylogeny of this genus is still unresolved, hampering evolutionary and traceability studies that could help improve conservation and management strategies for these species. Previous attempts based on mitochondrial and nuclear markers were unsuccessful in inferring a congruent and reliable phylogeny, probably due to mitochondrial introgression events and lack of enough phylogenetically informative markers. Here we infer the first genome-wide nuclear marker-based phylogeny of tunas using restriction site associated DNA sequencing (RAD-seq) data. Our results, derived from phylogenomic inferences obtained from 128 nucleotide matrices constructed using alternative data assembly procedures, support a single Thunnus evolutionary history that challenges previous assumptions based on morphological and molecular data. PMID:27286653

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

    PubMed

    Gao, Yang; Luo, Liaofu

    2012-01-15

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

  6. Lake level variability in Silver Lake, Michigan: a response to fluctuations in lake levels of Lake Michigan

    USGS Publications Warehouse

    Fisher, Timothy G.; Loope, Walter L.

    2004-01-01

    Sediment from Silver Lake, Michigan, can be used to constrain the timing and elevation of Lake Michigan during the Nipissing transgression. Silver Lake is separated from Lake Michigan by a barrier/dune complex and the Nipissing, Calumet, and Glenwood shorelines of Lake Michigan are expressed landward of this barrier. Two Vibracores were taken from the lake in February 2000 and contain pebbly sand, sand, buried soils, marl, peat, and sandy muck. It is suggested here that fluctuations in the level of Lake Michigan are reflected in Silver Lake since the Chippewa low phase, and possibly at the end of the Algonquin phase. An age of 12,490 B.P. (10,460±50 14C yrs B.P.) on wood from a buried Entisol may record the falling Algonquin phase as the North Bay outlet opened. A local perched water table is indicated by marl deposited before 7,800 B.P. and peat between 7,760-7,000 B.P. when Lake Michigan was at the low elevation Chippewa phase. Continued deepening of the lake is recorded by the transition from peat to sandy muck at 7,000 B.P. in the deeper core, and with the drowning of an Inceptisol nearly 3 m higher at 6,410 B.P. in the shallower core. A rising groundwater table responding to a rising Lake Michigan base level during the Nipissing transgression, rather than a response to mid-Holocene climate change, explains deepening of Silver Lake. Sandy muck was deposited continually in Silver Lake between Nipissing and modern time. Sand lenses within the muck are presumed to be eolian in origin, derived from sand dunes advancing into the lake on the western side of the basin.

  7. Temperate Lakes Discovered on Titan

    NASA Astrophysics Data System (ADS)

    Vixie, Graham; Barnes, Jason W.; Jackson, Brian; Wilson, Paul

    2012-04-01

    We have discovered two temperate lakes on Titan using Cassini's Visual and Infrared Mapping Spectrometer (VIMS). Three key features help to identify these surface features as lakes: morphology, albedo, and specular reflection. The presence of lakes at the mid-latitudes mean liquid can accumulate and remain stable outside of the poles. We first identify a lake surface by looking for possible shorelines with a lacustrine morphology. Then, we apply a simple atmospheric correction that produces an approximate surface albedo. Next, we prepare cylindrical projection maps of the brightness of the sky as seen from any points on the surface to identify specular reflections. Our techniques can then be applied to other areas, such as Arrakis Planitia, to test for liquid. Currently, all the known lakes on Titan are concentrated at the poles. Lakes have been suggested in the tropic zone by Griffith et al. Our discovery of non-transient, temperate lakes has important implications for Titan's hydrologic cycle. Clouds have been recorded accumulating in the mid-latitudes and areas have been darkened by rainfall but later brightened after evaporation (Turtle et al. 2011). Stable temperate lakes would affect total rainfall, liquid accumulation, evaporation rates, and infiltration. Polaznik Macula (Figure 1) is a great candidate for lake filling, evaporation rates, and stability. References: Griffith, C., et al.: "Evidence for Lakes on Titan's Tropical Surface". AAS/Division for Planetary Sciences Meeting Abstracts #42, Vol. 42, pp. 1077, 2010. Turtle, E. P., et al.: "Rapid and Extensive Surface Changes Near Titan's Equator: Evidence of April Showers". Science, Vol. 331, pp. 1414-, 2011. Figure 1: Polaznik Macula is the large, dark area central to the figure. The encircled dark blue areas represent positively identified lake regions in the T66 flyby. The light blue areas represent lake candidates still under analysis. The green circle marks a non-lake surface feature enclosed by a

  8. A multilocus molecular phylogeny of Fasciolariidae (Neogastropoda: Buccinoidea).

    PubMed

    Couto, Diogo R; Bouchet, Philippe; Kantor, Yuri I; Simone, Luiz R L; Giribet, Gonzalo

    2016-06-01

    The neogastropod family Fasciolariidae Gray, 1853 - tulips, horse-conchs, spindles, etc., comprises important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae Gray, 1853, Fusininae Wrigley, 1927 and Peristerniinae Tryon, 1880. Fasciolariids have had a rather complicated taxonomical history, with several genus names for a long time used as waste baskets to group many unrelated species; based on shell characters, recent taxonomic revisions have, however, began to set some order in its taxonomy. The present work is the first molecular approach to the phylogeny of Fasciolariidae based on a multigene dataset, which provides support for fasciolariids, an old group with a fossil record dating back to the Cretaceous. Molecular markers used were the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I, and the nuclear genes 18S rRNA, 28S rRNA and histone H3, sequenced for up to 116 ingroup taxa and 17 outgroups. Phylogenetic analyses revealed monophyly of Dolicholatirus Bellardi, 1884 and Teralatirus Coomans, 1965, however it was not possible to discern if the group is the sister clade to the remaining fasciolariids; the latter, on the other hand, proved monophyletic and contained highly supported groups. A first split grouped fusinines and Pseudolatirus Bellardi, 1884; a second split grouped the peristerniine genera Peristernia Mörch, 1852 and Fusolatirus Kuroda and Habe, 1971, while the last group comprised fasciolariines and the remaining peristerniines. None of these clades correspond to the present-day accepted circumscription of the three recognized subfamilies. PMID:27033950

  9. Reproductive Rates in Australian Rodents Are Related to Phylogeny

    PubMed Central

    Geffen, Eli; Rowe, Kevin C.; Yom-Tov, Yoram

    2011-01-01

    Background The native rodents of Australia are commonly divided into two groups based on the time of their colonization of the Sahulian continent, which encompasses Australia, New Guinea, and the adjacent islands. The first group, the “old endemics,” is a diverse assemblage of 34 genera that are descended from a single colonization of the continent during the Pliocene. A second group, the “new endemics,” is composed of several native Rattus species that are descended from a single colonization during the Pleistocene. Finally, a third group is composed of three non-native species of Rattus and Mus introduced into Australia by humans over the last 200 years. Previous studies have claimed that the three groups differ in their reproductive rates and that this variation in rates is associated with the unique environmental conditions across Australia. We examined these hypotheses using phylogenetically controlled methods. Methodology and Results We examined the relationship between the reproductive rates of the Australian rodents and the environmental variations across the continent, as well as the epoch of their colonization of the continent. Our results revealed no significant correlation with environmental variables but a significant association between colonization age and all the reproductive parameters examined. Discussion Based on a larger phylogeny of the subfamily Murinae, we showed that significant differences in reproductive rates among colonization groups are shared with their closest relatives outside Sahul. Therefore, the lower reproductive rates in the old endemics are more likely to be the result of phylogenetic history and conservation of traits than an adaptation to the Australian environment. In the new endemics, we found a trend of increasing reproductive rates with diversification. We suggest that the differences in reproductive rates of the old endemic rodents and the native Rattus represent alternative adaptive strategies that have allowed

  10. Functional traits, the phylogeny of function, and ecosystem service vulnerability

    PubMed Central

    Díaz, Sandra; Purvis, Andy; Cornelissen, Johannes H C; Mace, Georgina M; Donoghue, Michael J; Ewers, Robert M; Jordano, Pedro; Pearse, William D

    2013-01-01

    People depend on benefits provided by ecological systems. Understanding how these ecosystem services – and the ecosystem properties underpinning them – respond to drivers of change is therefore an urgent priority. We address this challenge through developing a novel risk-assessment framework that integrates ecological and evolutionary perspectives on functional traits to determine species’ effects on ecosystems and their tolerance of environmental changes. We define Specific Effect Function (SEF) as the per-gram or per capita capacity of a species to affect an ecosystem property, and Specific Response Function (SRF) as the ability of a species to maintain or enhance its population as the environment changes. Our risk assessment is based on the idea that the security of ecosystem services depends on how effects (SEFs) and tolerances (SRFs) of organisms – which both depend on combinations of functional traits – correlate across species and how they are arranged on the species’ phylogeny. Four extreme situations are theoretically possible, from minimum concern when SEF and SRF are neither correlated nor show a phylogenetic signal, to maximum concern when they are negatively correlated (i.e., the most important species are the least tolerant) and phylogenetically patterned (lacking independent backup). We illustrate the assessment with five case studies, involving both plant and animal examples. However, the extent to which the frequency of the four plausible outcomes, or their intermediates, apply more widely in real-world ecological systems is an open question that needs empirical evidence, and suggests a research agenda at the interface of evolutionary biology and ecosystem ecology. PMID:24101986

  11. Hylid frog phylogeny and sampling strategies for speciose clades.

    PubMed

    Wiens, John J; Fetzner, James W; Parkinson, Christopher L; Reeder, Tod W

    2005-10-01

    How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships. We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S). Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being > 90% incomplete. Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree. Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis. The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family. They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera. A new classification of hylid frogs is proposed. Several potentially misleading signals in the morphological data are discussed. PMID:16243760

  12. Global Diversity and Phylogeny of the Asteroidea (Echinodermata)

    PubMed Central

    Mah, Christopher L.; Blake, Daniel B.

    2012-01-01

    Members of the Asteroidea (phylum Echinodermata), popularly known as starfish or sea stars, are ecologically important and diverse members of marine ecosystems in all of the world's oceans. We present a comprehensive overview of diversity and phylogeny as they have figured into the evolution of the Asteroidea from Paleozoic to the living fauna. Living post-Paleozoic asteroids, the Neoasteroidea, are morphologically separate from those in the Paleozoic. Early Paleozoic asteroid faunas were diverse and displayed morphology that foreshadowed later living taxa. Preservation presents significant difficulties, but fossil occurrence and current accounts suggests a diverse Paleozoic fauna, which underwent extinction around the Permian-Triassic interval was followed by re-diversification of at least one surviving lineage. Ongoing phylogenetic classification debates include the status of the Paxillosida and the Concentricycloidea. Fossil and molecular evidence has been and continues to be part of the ongoing evolution of asteroid phylogenetic research. The modern lineages of asteroids include the Valvatacea, the Forcipulatacea, the Spinlosida, and the Velatida. We present an overview of diversity in these taxa, as well as brief notes on broader significance, ecology, and functional morphology of each. Although much asteroid taxonomy is stable, many new taxa remain to be discovered with many new species currently awaiting description. The Goniasteridae is currently one of the most diverse families within the Asteroidea. New data from molecular phylogenetics and the advent of global biodiversity databases, such as the World Asteroidea Database (http://www.marinespecies.org/Asteroidea/) present important new springboards for understanding the global biodiversity and evolution of asteroids. PMID:22563389

  13. A revised dated phylogeny of the arachnid order Opiliones.

    PubMed

    Sharma, Prashant P; Giribet, Gonzalo

    2014-01-01

    Dating the Opiliones tree of life has become an important enterprise for this group of arthropods, due to their ancient origins and important biogeographic implications. To incorporate both methodological innovations in molecular dating as well as new systematic discoveries of harvestman diversity, we conducted total evidence dating on a data set uniting morphological and/or molecular sequence data for 47 Opiliones species, including all four well-known Palaeozoic fossils, to test the placement of both fossils and newly discovered lineages in a single analysis. Furthermore, we investigated node dating with a phylogenomic data set of 24,202 amino acid sites for 14 species of Opiliones, sampling all extant suborders. In this way, we approached molecular dating of basal harvestman phylogeny using different data sets and approaches to assess congruence of divergence time estimates. In spite of the markedly different composition of data sets, our results show congruence across all analyses for age estimates of basal nodes that are well constrained with respect to fossil calibrations (e.g., Opiliones, Palpatores). By contrast, derived nodes that lack fossil calibrations (e.g., the suborders Cyphophthalmi, and Laniatores) have large uncertainty intervals in diversification times, particularly in the total evidence dating analysis, reflecting the dearth of calibration points and undersampling of derived lineages. Total evidence dating consistently produced older median ages than node dating for ingroup nodes, due to the nested placement of multiple Palaeozoic fossils. Our analyses support basal diversification of Opiliones in the Ordovician-Devonian period, corroborating the inferred ancient origins of this arthropod order, and underscore the importance of diversity discovery-both paleontological and neontological-in evolutionary inference. PMID:25120562

  14. Ballooning dispersal using silk: world fauna, phylogenies, genetics and models.

    PubMed

    Bell, J R; Bohan, D A; Shaw, E M; Weyman, G S

    2005-04-01

    Aerial dispersal using silk ('ballooning') has evolved in spiders (Araneae), spider mites (Acari) and in the larvae of moths (Lepidoptera). Since the 17th century, over 500 observations of ballooning behaviours have been published, yet there is an absence of any evolutionary synthesis of these data. In this paper the literature is reviewed, extensively documenting the known world fauna that balloon and the principal behaviours involved. This knowledge is then incorporated into the current evolutionary phylogenies to examine how ballooning might have arisen. Whilst it is possible that ballooning co-evolved with silk and emerged as early as the Devonian (410-355 mya), it is arguably more likely that ballooning evolved in parallel with deciduous trees, herbaceous annuals and grasses in the Cretaceous (135-65 mya). During this period, temporal (e.g. bud burst, chlorophyll thresholds) and spatial (e.g. herbivory, trampling) heterogeneities in habitat structuring predominated and intensified into the Cenozoic (65 mya to the present). It is hypothesized that from the ancestral launch mechanism known as 'suspended ballooning', widely used by individuals in plant canopies, 'tip-toe' and 'rearing' take-off behaviours were strongly selected for as habitats changed. It is contended that ballooning behaviour in all three orders can be described as a mixed Evolutionary Stable Strategy. This comprises individual bet-hedging due to habitat unpredictability, giving an underlying randomness to individual ballooning, with adjustments to the individual ballooning probability being conferred by more predictable habitat changes or colonization strategies. Finally, current methods used to study ballooning, including modelling and genetic research, are illustrated and an indication of future prospects given. PMID:15877859

  15. A fully resolved genus level phylogeny of neotropical primates (Platyrrhini).

    PubMed

    Wildman, Derek E; Jameson, Natalie M; Opazo, Juan C; Yi, Soojin V

    2009-12-01

    There are more than 125 species of extant New World monkeys (Primates: Platyrrhini) found in approximately 15 genera. The phylogenetic relationships of these neotropical primates have been extensively studied from a molecular perspective. While these studies have been successful at inferring many of the relationships within the platyrrhines, key questions remain. The current study provides a framework for using non-genic, non-coding markers in comparative primate phylogenomic studies in species whose genomes are not yet scheduled for complete sequencing. A random genomic shotgun library was generated from the nocturnal Owl monkey Aotus lemurinus. Eleven unlinked, non-coding, non-genic, non-repetitive, nuclear DNA markers derived from this library were sequenced in at least one representative species of every platyrrhine genus. The combined sequence from these markers yielded a 7.7 kb multiple sequence alignment of 22 taxa. We analyzed these markers independently and combined with a 10 kb dataset consisting of "traditional," previously published markers located within or directly adjacent to genes. Parsimony, maximum likelihood, and Bayesian analysis converged on a single topology for the platyrrhine generic relationships. Notably, we confidently inferred that Pitheciidae is the sister taxon to the other two platyrrhine families (Cebidae, Atelidae). This relationship is supported by high values of branch support as well as topology tests. Additionally, Aotus formed a sister taxon to a clade comprising Cebus and Saimiri. With a fully resolved platyrrhine phylogeny in place it is now possible to design and test hypotheses regarding the evolution and diversification of platyrrhine phenotypes and life histories. PMID:19632342

  16. FROM MOLECULAR PHYLOGENY TOWARDS DIFFERENTIATING PHARMACOLOGY FOR NMDA RECEPTOR SUBTYPES

    PubMed Central

    Platt, Randall J.; Curtice, Kigen J.; Twede, Vernon D.; Watkins, Maren; Gruszczyński, Paweł; Bulaj, Grzegorz; Horvath, Martin P.; Olivera, Baldomero M.

    2014-01-01

    In order to decode the roles that N-methyl-D-aspartate (NMDA) receptors play in excitatory neurotransmission, synaptic plasticity, and neuropathologies, there is need for ligands that differ in their subtype selectivity. The conantokin family of Conus peptides is the only group of peptidic natural products known to target NMDA receptors. Using a search that was guided by phylogeny, we identified new conantokins from the marine snail Conus bocki that complement the current repertoire of NMDA receptor pharmacology. Channel currents measured in Xenopus oocytes demonstrate conantokins conBk-A, conBk-B, and conBk-C have highest potencies for NR2D containing receptors, in contrast to previously characterized conantokins that preferentially block NR2B containing NMDA receptors. Conantokins are rich in γ-carboxyglutamate, typically 17–34 residues, and adopt helical structure in a calcium-dependent manner. As judged by CD spectroscopy, conBk-C adopts significant helical structure in a calcium ion-dependent manner, while calcium, on its own, appears insufficient to stabilize helical conformations of conBk-A or conBk-B. Molecular dynamics simulations help explain the differences in calcium-stabilized structures. Two-dimensional NMR spectroscopy shows that the 9-residue conBk-B is relatively unstructured but forms a helix in the presence of TFE and calcium ions that is similar to other conantokin structures. These newly discovered conantokins hold promise that further exploration of small peptidic antagonists will lead to a set of pharmacological tools that can be used to characterize the role of NMDA receptors in nervous system function and disease. PMID:24508768

  17. Arthropod phylogeny revisited, with a focus on crustacean relationships.

    PubMed

    Koenemann, Stefan; Jenner, Ronald A; Hoenemann, Mario; Stemme, Torben; von Reumont, Björn M

    2010-01-01

    Higher-level arthropod phylogenetics is an intensely active field of research, not least as a result of the hegemony of molecular data. However, not all areas of arthropod phylogenetics have so far received equal attention. The application of molecular data to infer a comprehensive phylogeny of Crustacea is still in its infancy, and several emerging results are conspicuously at odds with morphology-based studies. In this study, we present a series of molecular phylogenetic analyses of 88 arthropods, including 57 crustaceans, representing all the major lineages, with Onychophora and Tardigrada as outgroups. Our analyses are based on published and new sequences for two mitochondrial markers, 16S rDNA and cytochrome c oxidase subunit I (COI), and the nuclear ribosomal gene 18S rDNA. We designed our phylogenetic analyses to assess the effects of different strategies of sequence alignment, alignment masking, nucleotide coding, and model settings. Our comparisons show that alignment optimization of ribosomal markers based on secondary structure information can have a radical impact on phylogenetic reconstruction. Trees based on optimized alignments recover monophyletic Arthropoda (excluding Onychophora), Pancrustacea, Malacostraca, Insecta, Myriapoda and Chelicerata, while Maxillopoda and Hexapoda emerge as paraphyletic groups. Our results are unable to resolve the highest-level relationships within Arthropoda, and none of our trees supports the monophyly of Myriochelata or Mandibulata. We discuss our results in the context of both the methodological variations between different analyses, and of recently proposed phylogenetic hypotheses. This article offers a preliminary attempt to incorporate the large diversity of crustaceans into a single molecular phylogenetic analysis, assessing the robustness of phylogenetic relationships under varying analysis parameters. It throws into sharp relief the relative strengths and shortcomings of the combined molecular data for

  18. Mitochondrial DNA phylogeny in Eastern and Western Slavs.

    PubMed

    Malyarchuk, B; Grzybowski, T; Derenko, M; Perkova, M; Vanecek, T; Lazur, J; Gomolcak, P; Tsybovsky, I

    2008-08-01

    To resolve the phylogeny of certain mitochondrial DNA (mtDNA) haplogroups in eastern Europe and estimate their evolutionary age, a total of 73 samples representing mitochondrial haplogroups U4, HV*, and R1 were selected for complete mitochondrial genome sequencing from a collection of about 2,000 control region sequences sampled in eastern (Russians, Belorussians, and Ukrainians) and western (Poles, Czechs, and Slovaks) Slavs. On the basis of whole-genome resolution, we fully characterized a number of haplogroups (HV3, HV4, U4a1, U4a2, U4a3, U4b, U4c, U4d, and R1a) that were previously described only partially. Our findings demonstrate that haplogroups HV3, HV4, and U4a1 could be traced back to the pre-Neolithic times ( approximately 12,000-19,000 years before present [YBP]) in eastern Europe. In addition, an ancient connection between the Caucasus/Europe and India has been revealed by analysis of haplogroup R1 diversity, with a split between the Indian and Caucasus/European R1a lineages occurring about 16,500 years ago. Meanwhile, some mtDNA subgroups detected in Slavs (such as U4a2a, U4a2*, HV3a, and R1a1) are definitely younger being dated between 6,400 and 8,200 YBP. However, robust age estimations appear to be problematic due to the high ratios of nonsynonymous to synonymous substitutions found in young mtDNA subclusters. PMID:18477584

  19. Detection of nonneutral substitution rates on mammalian phylogenies

    PubMed Central

    Pollard, Katherine S.; Hubisz, Melissa J.; Rosenbloom, Kate R.; Siepel, Adam

    2010-01-01

    Methods for detecting nucleotide substitution rates that are faster or slower than expected under neutral drift are widely used to identify candidate functional elements in genomic sequences. However, most existing methods consider either reductions (conservation) or increases (acceleration) in rate but not both, or assume that selection acts uniformly across the branches of a phylogeny. Here we examine the more general problem of detecting departures from the neutral rate of substitution in either direction, possibly in a clade-specific manner. We consider four statistical, phylogenetic tests for addressing this problem: a likelihood ratio test, a score test, a test based on exact distributions of numbers of substitutions, and the genomic evolutionary rate profiling (GERP) test. All four tests have been implemented in a freely available program called phyloP. Based on extensive simulation experiments, these tests are remarkably similar in statistical power. With 36 mammalian species, they all appear to be capable of fairly good sensitivity with low false-positive rates in detecting strong selection at individual nucleotides, moderate selection in 3-bp elements, and weaker or clade-specific selection in longer elements. By applying phyloP to mammalian multiple alignments from the ENCODE project, we shed light on patterns of conservation/acceleration in known and predicted functional elements, approximate fractions of sites subject to constraint, and differences in clade-specific selection in the primate and glires clades. We also describe new “Conservation” tracks in the UCSC Genome Browser that display both phyloP and phastCons scores for genome-wide alignments of 44 vertebrate species. PMID:19858363

  20. Multi-level human evolution: ecological patterns in hominin phylogeny.

    PubMed

    Parravicini, Andrea; Pievani, Telmo

    2016-06-20

    Evolution is a process that occurs at many different levels, from genes to ecosystems. Genetic variations and ecological pressures are hence two sides of the same coin; but due both to fragmentary evidence and to the influence of a gene-centered and gradualistic approach to evolutionary phenomena, the field of paleoanthropology has been slow to take the role of macro-evolutionary patterns (i.e. ecological and biogeographical at large scale) seriously. However, several very recent findings in paleoanthropology stress both climate instability and ecological disturbance as key factors affecting the highly branching hominin phylogeny, from the earliest hominins to the appearance of cognitively modern humans. Allopatric speciation due to geographic displacement, turnover-pulses of species, adaptive radiation, mosaic evolution of traits in several coeval species, bursts of behavioral innovation, serial dispersals out of Africa, are just some of the macro-evolutionary patterns emerging from the field. The multilevel approach to evolution proposed by paleontologist Niles Eldredge is adopted here as interpretative tool, and has yielded a larger picture of human evolution that integrates different levels of evolutionary change, from local adaptations in limited ecological niches to dispersal phenotypes able to colonize an unprecedented range of ecosystems. Changes in global climate and Earth's surface most greatly affected human evolution. Precisely because it is cognitively hard for us to appreciate the long-term common destiny we share with the whole biosphere, it is particularly valuable to highlight the accumulating evidence that human evolution has been deeply affected by global ecological changes that transformed our African continent of origin. PMID:26829575