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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. Bacteria associated with benthic diatoms from Lake Constance: phylogeny and influences on diatom growth and secretion of extracellular polymeric substances.

    PubMed

    Bruckner, Christian G; Bahulikar, Rahul; Rahalkar, Monali; Schink, Bernhard; Kroth, Peter G

    2008-12-01

    The composition of diatom-associated bacterial communities was studied with 14 different unialgal xenic diatom cultures isolated from freshwater epilithic biofilms of Lake Constance, Germany. A clear dominance of Alphaproteobacteria was observed, followed by Betaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia. Pure cultures of the diatom Cymbella microcephala, which was found to be dominant in epilithic biofilms in Lake Constance, were cocultivated with six associated bacterial strains. All these bacterial strains were able to grow in C. microcephala cultures in the absence of organic cosubstrates. Diatom growth was generally enhanced in the presence of bacteria, and polysaccharide secretion was generally increased in the presence of Proteobacteria. The monomer composition of extracellular polysaccharides of C. microcephala changed in relation to the presence of different bacteria, but the dominant monomers were less affected. Our results indicate that these changes were caused by the diatom itself rather than by specific bacterial degradation. One Bacteroidetes strain strongly influenced carbohydrate secretion by the alga via extracellular soluble compounds. Biofilms were formed only in the presence of bacteria. Phylogenetic analysis and coculture studies indicate an adaptation of Proteobacteria and Bacteroidetes to the microenvironment created by the diatom biofilm.

  3. [On sinusitis in swimmers in Lake Constance (author's transl)].

    PubMed

    Waggershauser, C P

    1980-04-01

    Since the expansion of water-cleaning plants at Lake Constance, the rate of diseases in swimmers, like the sinusitis and otitis in swimmers gradually declined. These sickness almost only occur in teenagers by diving at water temperatures of some 20 degrees centigrade. The rhinogene complications of orbita develop fulminantly.

  4. Epilimnetic scavenging of Chernoobyl radionuclides in Lake Constance

    NASA Astrophysics Data System (ADS)

    Robbins, J. A.; Lindner, G.; Pfeiffer, W.; Kleiner, J.; Stabel, H. H.; Frenzel, P.

    1992-06-01

    Radioactive debris from the Chernobyl reactor accident entered Lake Constance in southwestern Germany mainly through one rainfall episode on April 30, 1986. Nuclides scavenged by particles in a newly established epilimnion accumulated in traps deployed weekly (20 m depth) at a site in the Überlinger See, a northwestern bight of the lake. Activities of 137Cs and 103Ru (plus 106Ru, 125Sb, 110mAg, and 144Ce) in trapped material collected during the subsequent 21 weeks is here described by a two-stage scavenging model involving (1) nuclide transfer to "reactive particles" with negligible mean settling rate. (2) their entrainment by large, rapidly settling particles dominated by chemically passive calcite formed seasonally in the epilimnion. The model employs first-order kinetics where forward rate coefficients depend on time-dependent concentrations of candidate "reactive phases" such as total suspended matter (TSM), paniculate inorganic matter (PIM), paniculate organic matter (POM), and paniculate aluminum (PAL). First-order, irreversible nuclide transfer to nonexchangeable portions of reactive phases is also included. Vertical transport is described by a time-dependent rate of particle settling through a vertically and horizontally well-mixed epilimnion of increasing depth. Model calculations reproduced observations well with PAL as the "reactive phase" for 137Cs and POM for 103Ru. Calculated reaction rates for all nuclides were sufficiently high that activity changes were dominated by temporal variations in pertinent state variables. Selective chemical extraction of Chernobyl 137Cs from sediments and study of uptake kinetics by addition of radiocesium to fresh sediment suspensions supported model results indicating its negligible affinity for calcite, probable transfer to clay minerals (for which PAL is a surrogate), particle concentration-independent distribution coefficient, and significant transfer to nonexchangeable sites. For 103Ru, model calculations implied

  5. Old fish in a young lake: stone loach (Pisces: Barbatula barbatula) populations in Lake Constance are genetically isolated by distance.

    PubMed

    Barluenga, Marta; Meyer, Axel

    2005-04-01

    The genetic structure of 10 populations (453 individuals) of stone loach (Barbatula barbatula L.), a small bottom-dwelling cyprinid fish, in the littoral zone of Lake Constance, central Europe, was investigated by analysing the mitochondrial control region sequences and five microsatellite loci. An unexpectedly high degree of genetic diversity (up to 0.36%) and old estimated age of these populations (> 150 000 years) based on mitochondrial DNA (mtDNA) was found. These findings contrast with the relatively young age of the lake, which could be colonized by fish only after the last ice age around 15 000 bp. Stone loach appears to be an old species in a young lake. Both types of molecular markers showed population genetic structure pronounced in mtDNA (overall F(ST) = 0.15) but moderate in microsatellites (F(ST) = 0.03). As predicted by its life history, philopatry, and limited capacity for dispersal, stone loach populations of Lake Constance show a clear pattern of isolation by distance. Geographic distances along the shores are the best explanation for the observed geographical distribution of genetic differentiation (r = 0.88), indicating that open water represents a barrier for the dispersal of the stone loach. The colonization of Lake Constance might have occurred initially at one location and then populations spread throughout the lake in a stepwise manner following the shoreline, and subsequently remained largely genetically isolated as suggested by the large observed differences among them.

  6. ["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.

  7. Long-term development of hypolimnetic oxygen depletion rates in the large Lake Constance.

    PubMed

    Rhodes, Justin; Hetzenauer, Harald; Frassl, Marieke A; Rothhaupt, Karl-Otto; Rinke, Karsten

    2017-01-30

    This study investigates over 30 years of dissolved oxygen dynamics in the deep interior of Lake Constance (max. depth: 250 m). This lake supplies approximately four million people with drinking water and has undergone strong re-oligotrophication over the past decades. We calculated depth-specific annual oxygen depletion rates (ODRs) during the period of stratification and found that 50% of the observed variability in ODR was already explained by a simple separation into a sediment- and volume-related oxygen consumption. Adding a linear factor for water depth further improved the model indicating that oxygen depletion increased substantially along the depth. Two other factors turned out to significantly influence ODR: total phosphorus as a proxy for the lake's trophic state and mean oxygen concentration in the respective depth layer. Our analysis points to the importance of nutrient reductions as effective management measures to improve and protect the oxygen status of such large and deep lakes.

  8. 3D simulation of the influence of internal mixing dynamics on the propagation of river plumes in Lake Constance

    NASA Astrophysics Data System (ADS)

    Pflugbeil, Thomas; Pöschke, Franziska; Noffke, Anna; Winde, Vera; Wolf, Thomas

    2017-04-01

    Lake Constance is one of most important drinking water resources in southern Germany. Furthermore, the lake and its catchment is a meaningful natural habitat as well as economical and cultural area. In this context, sustainable development and conservation of the lake ecosystem and drinking water quality is of high importance. However, anthropogenic pressures (e.g. waste water, land use, industry in catchment area) on the lake itself and its external inflows are high. The project "SeeZeichen" (ReWaM-project cluster by BMBF, funding number 02WRM1365) is investigating different immission pathways (groundwater, river, superficial inputs) and their impact on the water quality of Lake Constance. The investigation includes the direct inflow areas as well as the lake-wide context. The present simulation study investigates the mixing dynamics of Lake Constance and its impacts on river inflows and vice versa. It considers different seasonal (mixing and stratification periods), hydrological (flood events, average and low discharge) and transport conditions (sediment loads). The simulations are focused on two rivers: The River Alpenrhein delivers about 60 % of water and material input into Lake Constance. The River Schussen was chosen since it is highly anthropogenic influenced. For this purpose, a high-resolution three-dimensional hydrodynamic model of the Lake Constance is set up with Delft3D-Flow model system. The model is calibrated and validated with long term data sets of water levels, discharges and temperatures. The model results will be analysed for residence times of river water within the lake and particle distributions to evaluate potential impacts of river plume water constituents on the general water quality of the lake.

  9. Remote sensing techniques and in situ fluorometry as alternative methods for the determination of algae pigments in lakes - application to Lake Constance and small lakes

    NASA Astrophysics Data System (ADS)

    Wolf, Thomas; Heege, Thomas; Schenk, Karin; Stark, Markus; Stich, Hans-Bernd

    2014-05-01

    Satellite based remote sensing techniques were used in order to assess the variability of Chlorophyll-a distributions in Lake Constance and additionally within some smaller lakes in the South of Germany. For Lake Constance we used for most investigations spatially medium resolved satellite scanners with a higher spectral resolution whereas in the case of smaller lakes having a size of 1 … 10 km spatially highly resolved satellite scanners were used having a lower spectral resolution. The satellite imagery allowed for a higher spatial as well temporal resolution of information about Chlorophyll-a distribution in these lakes compared to classical methodologies as water sampling and subsequent species analysis using microscopes and/or HPLC analysis for accessory algae pigments. We found - depending on weather and hydrodynamic conditions - highly variable Chlorophyll-a distributions under some circumstances whereas there are as well time periods when almost perfectly homogeneous distributions of Chlorophyll-a where detected in Lake Constance. Additionally we used HPLC analysis in order to validate the satellite remote sensing results showing good agreement between in situ measured and remote sensing values for Chlorophyll-a. During some measurement campaigns in Lake Constance we used an in situ fluorometer probe (BBE FluoroProbe) in order to determine the spatial fluctuations of Chlorophyll-a and additional accessory algae pigments. These algae pigments were measured along horizontal transects using a temporal sampling interval of about dt=2 … 10 seconds giving a high spatial sampling frequency in the order O[10 … 50]m. Based on these horizontal records we can get further insight into the spatial fluctuations of algae pigments and their spatial patterns in Lake Constance. Characteristics of these patterns can be quantified using some patchiness state vector (psv) summarizing different specific features of the algae distribution into some vector quantity. Special

  10. 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

  11. 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.

  12. An iodine mass-balance for Lake Constance, Germany: Insights into iodine speciation changes and fluxes

    NASA Astrophysics Data System (ADS)

    Gilfedder, B. S.; Petri, M.; Wessels, M.; Biester, H.

    2010-06-01

    Lake Constance is one of Europe's largest oligotrophic lakes and provides a water source for more than 4.5 million people in Germany and Switzerland. We present here a 12 month study on iodine concentrations, speciation and fluxes to and from the lake to gain a quantitative understanding of the limnic iodine cycle. Monthly water samples were obtained from all major tributaries (14) and the outflow to construct a mass-balance model. Sediment traps were also deployed in the lake for two years at two different stations. Total soluble iodine (TSI) in aqueous samples were analysed by ICP-MS and speciation (iodide, iodate and soluble organically bound iodine, SOI) by ion chromatography-ICP-MS. Iodine concentrations in the Alpine tributaries (1-2 μg l -1) decreased over the summer months due to increasing proportions of snow and glacial melt water from the Alps, while iodine levels in the lowland rivers (˜2-10 μg l -1) increased over the summer. Deposition of TSI to the catchment (16,340 kg I yr -1) was similar to the TSI out-flux by rivers (16,000 kg I yr -1). By also including the particulate riverine iodine flux out of the catchment (˜12,350 kg I yr -1) it is shown that the catchment is a net source of iodine, with the highest particulate fluxes coming from the Alpine rivers. The total TSI flux to the lake was 16,770 kg I yr -1, the largest proportion coming from the Alpenrhein (43%), followed by the Schussen (8%) and Bregenzer Ach (7.7%). Overall the mass-balance for TSI in the lake was negative, with more iodine flowing out of the lake than in (-2050 kg I yr -1; 12% of TSI in-flux). To maintain mass-balance, 8.8 μg I m -2 d -1 from the Obersee and 23 μg I m -2 d -1 from the Untersee must be released from the sediments into the water column. Thus, in comparison with the total iodine flux to the sediments measured by the sediment traps (4762-8075 kg I yr -1), up to 39% of the deposited iodine may be mobilised back into the lake. SOI was the dominant iodine

  13. Anaerobic Oxidation of Methane in Sediments of Lake Constance, an Oligotrophic Freshwater Lake▿

    PubMed Central

    Deutzmann, Jörg S.; Schink, Bernhard

    2011-01-01

    Anaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor has been reported for various environments, including freshwater habitats, and also, nitrate and nitrite were recently shown to act as electron acceptors for methane oxidation in eutrophic freshwater habitats. Radiotracer experiments with sediment material of Lake Constance, an oligotrophic freshwater lake, were performed to follow 14CO2 formation from 14CH4 in sediment incubations in the presence of different electron acceptors, namely, nitrate, nitrite, sulfate, or oxygen. Whereas 14CO2 formation without and with sulfate addition was negligible, addition of nitrate increased 14CO2 formation significantly, suggesting that AOM could be coupled to denitrification. Nonetheless, denitrification-dependent AOM rates remained at least 1 order of magnitude lower than rates of aerobic methane oxidation. Using molecular techniques, putative denitrifying methanotrophs belonging to the NC10 phylum were detected on the basis of the pmoA and 16S rRNA gene sequences. These findings show that sulfate-dependent AOM was insignificant in Lake constant sediments. However, AOM can also be coupled to denitrification in this oligotrophic freshwater habitat, providing first indications that this might be a widespread process that plays an important role in mitigating methane emissions. PMID:21551281

  14. Pelagic Ciliates in a Large Mesotrophic Lake: Seasonal Succession and Taxon-Specific Bacterivory in Lake Constance

    NASA Astrophysics Data System (ADS)

    Cleven, Ernst-Josef

    2004-07-01

    The taxonomic composition of the ciliate assemblage and their taxon-specific bacterial grazing rates in Lake Constance were investigated over the course of one year. Bacterial grazing rates were measured using natural fluorescently labelled bacteria (FLB) and compared to bacterial production. Small species such as Balanion planctonicum/Urotricha furcata and Rimostrombidium spp./Halteria sp. were the most numerous ciliates on the annual average. Larger ciliates such as Rimostrombidium lacustris and Limnostrombidium spp. contributed significantly to total ciliate biomass, but were relatively unimportant as bacterial grazers. Per capita ingestion rates ranged from 0-194 bacteria ciliate-1 h-1 and changed seasonally up to a hundredfold within a given taxon. Approximately 1% of the bacterial production were removed by the ciliate community on the annual average. (

  15. Elstera litoralis gen. nov., sp. nov., isolated from stone biofilms of Lake Constance, Germany.

    PubMed

    Rahalkar, Monali; Bahulikar, Rahul A; Deutzmann, Jörg S; Kroth, Peter G; Schink, Bernhard

    2012-08-01

    An alphaproteobacterium, strain Dia-1(T), was isolated from algae-dominated biofilms on stones from the littoral zone of Lake Constance, Germany. This bacterium was isolated after initial enrichment in spent medium obtained after growth of a diatom culture. Numerous sugars and some organic acids and alcohols served as growth substrates. The bacterium grew slowly, was strictly aerobic but microaerophilic, and did not grow in cultures shaken under air. 16S rRNA gene sequence analysis indicated that strain Dia-1(T) was distantly related to representatives of the genera Azospirillum (90-91% sequence similarity), Skermanella (88-89%), Rhodocista (87-88%) and Dongia (88-89% sequence similarity). Based on this sequence comparison, on phenotypic characterization including substrate utilization patterns, and comparison of cellular fatty acids, quinones, polar lipids and polyamines, this isolate was found to be substantially different from the genera mentioned above. On the basis of these results, a novel genus and species is proposed for this strain. The name Elstera litoralis gen. nov., sp. nov. is suggested, with strain Dia-1(T) ( = DSM 19532(T) = LMG 24234(T)) as the type strain of the type species.

  16. 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

  17. 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

  18. Assessment of the spatio-temporal structure of chlorophyll pigments and the characterization of algae patchiness in Lake Constance

    NASA Astrophysics Data System (ADS)

    Wolf, Thomas; Heege, Thomas; Kempken, Ludger; Schwenk, Karin; Stich, Hans-Bernd

    2013-04-01

    The determination of the chlorophyll- a content by water sampling and subsequent liquid chromatography (HPLC) as well as algae species analysis using microscopy form the basis for many limnological studies and the assessment according to the EU WFD. Because of the sampling and analysis effort which is associated with these methods, for routine monitoring purposes only a limited number of points can be sampled and investigated within a lake. On the other hand it is well known, that the spatial distribution of algae in aquatic environments is often nonhomogeneous and spatially highly variable making it sometimes difficult to determine the algae stock content by using only a few water samples. In order to bridge the gap between the stochastically distributed algae pattern on one hand and the sampling methodologies which allow only for a limited number of samples (HPLC, microscopy) we tested the applicability of additional alternative algae monitoring techniques - the in-situ fluorometry and satellite remote sensing techniques - for Lake Constance. The usage of these alternative methodologies enables us to get information about the spatial structure of the algae pigment distribution in a lake with higher temporal and spatial resolution. Thus we can get a more detailed picture about the structure and the statistical properties of algae pigment distribution and thus about the distribution of algae in the lake. In order to make use of this additional information about the spatial distribution of algae pigments we use some conceptual approach which describes some of the characteristics of the algae pattern more quantitatively. Therefore we apply some statistical and geostatistical methods and we derive parameters which describe different aspects of the patchiness phenomenon. By combining these parameters into some patchiness state vector we have a possibility to describe and classify the patchiness we are faced with. Using this set of parameters we then can investigate

  19. 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.

  20. 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.

  1. 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

    2013-07-02

    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%).

  2. 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. PMID:27873774

  3. The first decade of oligotrophication in Lake Constance : I. The response of phytoplankton biomass and cell size.

    PubMed

    Gaedke, Ursula; Schweizer, Anette

    1993-03-01

    Phytoplankton biomass and species composition were measured with a relatively high temporal resolution (once or twice a week during the growing season) from 1979 to 1989 in Lake Constance/Überlingersee. Over this period soluble reactive phosphorus (SRP) concentrations during winter mixing were reduced by ca. 50% from 104 to 47 μg 1(-1), which caused a prolongation and amplification of the epilimnetic P depletion during the growth period. Seasonal dynamics of phytoplankton reacted to the decrease of SRP in the following ways: (1) Algal biomass decreased at least proportionally to the winter SRP concentrations in summer, but not in spring and autumn when biomass fluctuated irregularly. (2) The peak of biomass concentration changed from summer to spring. (3) The earlier onset of epilimnetic P depletion during the season in recent years promoted a stronger growth of some pennate diatoms in spring. It caused an amplification of the silicon depletion in summer, which may cause still greater reduction of diatoms and total algal biomass in summer. (4) Reduction of algal biomass during the clear-water phase proper became shorter and less pronounced. (5) The temporal variability of algal biomass decreased in summer and autumn but not in spring. (6) Average cell sizes remained unchanged in summer and autumn but increased in spring during the beginning of oligotrophication. These results are largely in agreement with other studies on lake restoration and expectations derived from the PEG (Plankton Ecology Group) model (Sommer et al. 1986). They show that a 50% reduction of SRP concentrations during homothermy may have pronounced effects on seasonal dynamics of algal biomass in a large and deep lake. The algal response to the external change of SRP concentrations can be described by the Le Chatelier principle, implying that the internal structure of the system (e.g. species composition) changes in order to minimize the effect of the external pressure (e.g. reduction of total

  4. Genetic diversity of upper Lake Constance whitefish Coregonus spp. under the influence of fisheries: a DNA study based on archived scale samples from 1932, 1975 and 2006.

    PubMed

    Gum, B; Geist, J; Eckenfels, S; Brinker, A

    2014-06-01

    This investigation examined changes in the genetic diversity of pelagic upper Lake Constance (ULC) whitefish Coregonus wartmanni population before and after the alteration of fishery methods and management from 1932 to 2006. The study spans a period of pronounced changes in trophic status of the lake and transitions from traditional relatively unselective pelagic seine (Klusgarn) fishing to highly size-selective nylon gillnet techniques. In addition, supportive breeding and stocking became most popular during the phase of eutrophication in the 1970s. The main hypothesis is that size-selective fisheries and breeding lead to an overall decrease in genetic variability over time. A total of 215 archived C. wartmanni scale samples from 1932, 1975 and 2006 were analysed by genotyping 11 microsatellite loci. A comparison of population genetic parameters, including allelic richness, observed and expected heterozygosities, and estimates of effective population sizes, suggests that the genetic diversity of C. wartmanni population has not decreased. The appearance of new alleles in the gene pool in 1975 and 2006 may be indicative of admixture with other forms in the lake or with stocked allochthonous forms. Overall, the fisheries management practice in ULC, including the effects of size-selective fisheries, supportive breeding and stocking, have not significantly altered the genetic diversity of Coregonus spp. over an 80 year period.

  5. 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. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Depth-specific and spatiotemporal variation of δ13C and δ15N in Charophytes of Lake Constance: implications for food web studies.

    PubMed

    Matuszak, Anja; Voigt, Christian C; Storch, Ilse; Bauer, Hans-Günther; Quillfeldt, Petra

    2011-07-30

    Macrophytes are at the base of many lake food webs providing essential food resources for animals at higher trophic level, such as invertebrates, fish and waterbirds. However, data regarding the spatiotemporal variation in isotopic composition of macrophytes are generally missing. We measured the carbon and nitrogen stable isotope ratios of Charophytes at Lake Constance, where they constitute a major food source for waterbirds. Our data reveal seasonal and site-specific differences as well as depth-specific variations in isotopic carbon values within the littoral zone. Charophytes were enriched in (13)C at sites of higher productivity: the δ(13)C values were high in summer, at shallow and at relatively nutrient-rich sites, and comparatively low in winter, and in deeper and nutrient-poorer sites. In contrast, no temporal or spatial trend was found to explain the variability in the isotopic nitrogen values. These results imply that the seasonal timing of food intake (relative to turnover rates of consumers tissue) and the potential depth of foraging need to be taken into account when calculating the relative contribution of energy sources to diets of consumers such as waterbirds.

  7. Spatial and temporal constancy of seismic strain release along the Death Valley-Fish Lake Valley fault and Pacific-North America plate boundary strain distribution

    NASA Astrophysics Data System (ADS)

    Frankel, K. L.; Dolan, J. F.; Ganev, P.; Finkel, R. C.

    2008-12-01

    The Death Valley-Fish Lake Valley fault (DV-FLVF) is the most active fault system along the Pacific-North America plate boundary east of the San Andreas fault. Recent work in the region suggests the late Pleistocene slip rate decreases from approximately 4.5 mm/yr along the central part of the DV-FLVF in northern Death Valley to approximately 2.5 mm/yr at the northern end of the DV-FLVF in Fish Lake Valley. This decrease in slip rate is at odds with observations at the latitude of northern Death Valley, which show late Pleistocene rates of deformation across the eastern California shear zone are coincident with short- terms rates of dextral shear determined from GPS data. Here, we report on alluvial fan offsets from three additional sites along the DV-FLVF to help determine the distribution of strain and the temporal and spatial constancy of deformation in the northern eastern California shear zone. From south to north these sites are: Cucomongo Canyon, Leidy Creek, and Indian Creek. We generated digital elevation models with 1 m horizontal resolution and decimeter vertical accuracy of the offsets from an airborne laser swath mapping (ALSM) survey along the fault zone. Right lateral displacements in offset late Pleistocene alluvial fans at Cucomongo Canyon and Leidy Creek are approximately 190 m and 50 m, respectively. A Holocene fan deposit at Indian Creek displays a dextral offset of approximately 15 m. Sixteen surface boulder samples were collected from the Leidy Creek and Indian Creek alluvial fans and five samples were collected from a depth profile at the Cucomongo Canyon fan for cosmogenic Beryllium-10 geochronology. These samples will help establish the age of the alluvial fans and when combined with the measured offsets from the ALSM data will provide slip rates over a variety of temporal and spatial scales. Ultimately, these rates will add to a growing number of such data, which are helping to elucidate how strain is distributed along this important

  8. 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.

  9. 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

  10. 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.

  11. 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'. © 2016 The Authors.

  12. 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

  13. 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.

  14. Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika--the result of repeated introgressive hybridization.

    PubMed

    Koblmüller, Stephan; Duftner, Nina; Sefc, Kristina M; Aibara, Mitsuto; Stipacek, Martina; Blanc, Michel; Egger, Bernd; Sturmbauer, Christian

    2007-01-25

    The tribe Lamprologini is the major substrate breeding lineage of Lake Tanganyika's cichlid species flock. Among several different life history strategies found in lamprologines, the adaptation to live and breed in empty gastropod shells is probably the most peculiar. Although shell-breeding arose several times in the evolutionary history of the lamprologines, all obligatory and most facultative shell-breeders belong to the so called "ossified group", a monophyletic lineage within the lamprologine cichlids. Since their distinctive life style enables these species to live and breed in closest vicinity, we hypothesized that these cichlids might be particularly prone to accidental hybridization, and that introgression might have affected the evolutionary history of this cichlid lineage. Our analyses revealed discrepancies between phylogenetic hypotheses based on mitochondrial and nuclear (AFLP) data. While the nuclear phylogeny was congruent with morphological, behavioral and ecological characteristics, several species--usually highly specialized shell-breeders--were placed at contradicting positions in the mitochondrial phylogeny. The discordant phylogenies strongly suggest repeated incidents of introgressive hybridization between several distantly related shell-breeding species, which reticulated the phylogeny of this group of cichlids. Long interior branches and high bootstrap support for many interior nodes in the mitochondrial phylogeny argue against a major effect of ancient incomplete lineage sorting on the phylogenetic reconstruction. Moreover, we provide morphological and genetic (mtDNA and microsatellites) evidence for ongoing hybridization among distantly related shell-breeders. In these cases, the territorial males of the inferred paternal species are too large to enter the shells of their mate, such that they have to release their sperm over the entrance of the shell to fertilize the eggs. With sperm dispersal by water currents and wave action, trans

  15. 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.

  16. Development of Phonological Constancy

    PubMed Central

    Best, Catherine T.; Tyler, Michael D.; Gooding, Tiffany N.; Orlando, Corey B.; Quann, Chelsea A.

    2009-01-01

    Efficient word recognition depends on detecting critical phonetic differences among similar-sounding words, or sensitivity to phonological distinctiveness, an ability evident at 19 months of age but unreliable at 14 to 15 months of age. However, little is known about phonological constancy, the equally crucial ability to recognize a word's identity across natural phonetic variations, such as those in cross-dialect pronunciation differences. We show that 15- and 19-month-old children recognize familiar words spoken in their native dialect, but that only the older children recognize familiar words in a dissimilar nonnative dialect, providing evidence for emergence of phonological constancy by 19 months. These results are compatible with a perceptual-attunement account of developmental change in early word recognition, but not with statistical-learning or phonological accounts. Thus, the complementary skills of phonological constancy and distinctiveness both appear at around 19 months of age, together providing the child with a fundamental insight that permits rapid vocabulary growth and later reading acquisition. PMID:19368700

  17. 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. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  18. 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

  19. 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.

  20. An Interview with Constance Reid.

    ERIC Educational Resources Information Center

    Alexanderson, G. L.

    1980-01-01

    Constance Reid, a well-known author of books on mathematics and mathematicians, is interviewed at her home in San Francisco in July, 1979. She discusses her studies of the lives of Hilbert, Courant and other mathematicians. (MP)

  1. Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection.

    PubMed

    Naumenko, Sergey A; Logacheva, Maria D; Popova, Nina V; Klepikova, Anna V; Penin, Aleksey A; Bazykin, Georgii A; Etingova, Anna E; Mugue, Nikolai S; Kondrashov, Alexey S; Yampolsky, Lev Y

    2017-01-01

    Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two nonendemic outgroups, we report a revised phylogeny of this species flock and analyse evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armour and reduction in appendages and sensory organs, evolved in several lineages in parallel. Radiation of Baikal amphipods has been characterized by short phylogenetic branches and frequent episodes of positive selection which tended to be more frequent in the early phase of the second invasion of amphipods into Baikal when the most intensive diversification occurred. Notably, signatures of positive selection are frequent in genes encoding mitochondrial membrane proteins with electron transfer chain and ATP synthesis functionality. In particular, subunits of both the membrane and substrate-level ATP synthases show evidence of positive selection in the plankton species Macrohectopus branickii, possibly indicating adaptation to active plankton lifestyle and to survival under conditions of low temperature and high hydrostatic pressures known to affect membranes functioning. Other functional categories represented among genes likely to be under positive selection include Ca-binding muscle-related proteins, possibly indicating adaptation to Ca-deficient low mineralization Baikal waters. © 2016 John Wiley & Sons Ltd.

  2. The inconstant "principle of constancy".

    PubMed

    Kanzer, M

    1983-01-01

    A review of the principle of constancy, as it appeared in Freud's writings, shows that it was inspired by his clinical observations, first with Breuer in the field of cathartic therapy and then through experiences in the early usage of psychoanalysis. The recognition that memories repressed in the unconscious created increasing tension, and that this was relieved with dischargelike phenomena when the unconscious was made conscious, was the basis for his claim to originality in this area. The two principles of "neuronic inertia" Freud expounded in the Project (1895), are found to offer the key to the ambiguous definition of the principle of constancy he was to offer in later years. The "original" principle, which sought the complete discharge of energy (or elimination of stimuli), became the forerunner of the death drive; the "extended" principle achieved balances that were relatively constant, but succumbed in the end to complete discharge. This was the predecessor of the life drives. The relation between the constancy and pleasure-unpleasure principles was maintained for twenty-five years largely on an empirical basis which invoked the concept of psychophysical parallelism between "quantity" and "quality." As the links between the two principles were weakened by clinical experiences attendant upon the growth of ego psychology, a revision of the principle of constancy was suggested, and it was renamed the Nirvana principle. Actually it was shifted from alignment with the "extended" principle of inertia to the original, so that "constancy" was incongruously identified with self-extinction. The former basis for the constancy principle, the extended principle of inertia, became identified with Eros. Only a few commentators seem aware of this radical transformation, which has been overlooked in the Standard Edition of Freud's writings. Physiological biases in the history and conception of the principle of constancy are noted in the Standard Edition. The historical

  3. 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

  4. Microbial activity and phylogeny in ice cores retrieved from Lake Paula, a newly detected freshwater lake in Antarctica

    NASA Astrophysics Data System (ADS)

    Sattler, Birgit I.; Waldhuber, Sebastian; Fischer, Helgard; Semmler, Hans; Sipiera, Paul P.; Psenner, Roland

    2004-11-01

    A permanent ice covered water body, called Lake Paula, was detected in Patriot Hills in the West Antarctic and sampled for the first time ever for microbial life. The ice sheet measured approximately 2,5m thickness and the water body has a depth of about 10m. The lake is situated near a moraine which partly ablates from snow and provides meltwater from the slopes to the lake during austral summer. These running waters which are kept liquid by the heating up of the dark soil are penetrating the lower ice cover and thus softening up the lakeside part if the ice core. It is inoculated by nutrients, active microbes and diatoms of terrestrial origin. A distinct gradient concerning bacterial numbers, biomass and production which is 10 fold at the ice-water interface compared to the exposed part is observable. Temperature sensitivity of the embedded microbes reflect the gradient as well: Bacteria isolated from the upper part showed growth optima at 10°C, the lower part at 25°C, phylogenetic properties done by 16s rDNA reveal distinct communities depending on their vertical position, some clones are similar to those retrieved in Lake Vostok ice cores. These results offer the conclusion that even in this harsh environment like the Antarctic continent a dynamic system like microbial ice aggregates can be sustained as long as the supply of liquid water which is essential for an active bacterial metabolism is provided at least for a small time frame.

  5. Mitochondrial phylogeny of the endemic mouthbrooding lineages of cichlid fishes from Lake Tanganyika in eastern Africa.

    PubMed

    Sturmbauer, C; Meyer, A

    1993-07-01

    Of the three cichlid species flocks in eastern Africa, Lake Tanganyika harbors the oldest species assemblage, which is also the most diverse morphologically and behaviorally. For 12 species (20 individuals) of 12 genera of the tribe Ectodini, 852 bp from two segments (cytochrome b and control region) of the mitochondrial genome were sequenced. In addition, orthologous sequences were obtained from eight species (11 individuals) representing other mouthbrooding lineages from Lake Tanganyika. Comparisons of sequence divergences revealed that the single Tanganyikan tribe Ectodini appears to be approximately five times older than the whole Lake Malawi cichlid species flock, suggesting that the radiation of the Tanganyikan mouthbrooding lineages took place long before the species flocks of Lakes Malawi and Victoria evolved. Seven of nine surveyed tribes of Tanganyikan cichlids appear to be approximately equally divergent, and this seems to corroborate the hypothesis of a rapid simultaneous formation of lineages at an early stage in the history of the Lake Tanganyika species flock. The close genetic relationship between the endemic Tropheus lineage and a nonendemic "Haplochromine," Astatotilapia burtoni, indicates that members of the tribe Tropheini may be the sister group of the cichlid flocks of Lakes Malawi and Victoria. The phylogenetic analyses demonstrate the monophyly of the Ectodini and identify the Cyprichromini as their sister group among the Tanganyikan cichlids. Within the tribe Ectodini the molecular data suggest both a branching pattern different than that previously proposed and a subdivision of the Ectodini into four clades, instead of the two originally described. The previously postulated model of morphological transformations believed to be responsible for the drastically different types of ecological specialization found among the Ectodini might therefore be in need of reinterpretation. Characters immediately related to foraging and nutrition seem to

  6. Time constancy in human perception.

    PubMed

    Lisi, Matteo; Gorea, Andrei

    2016-11-01

    Estimated time contracts or dilates depending on many visual-stimulation attributes (size, speed, etc.). Here we show that when such attributes are jointly modulated so as to respect the rules of perspective, their effect on the perceived duration of moving objects depends on the presence of contextual information about viewing distance. We show that perceived duration contracts and dilates with changes in the retinal input associated with increasing distance from the observer only when the moving objects are presented in the absence of information about the viewing distance. When this information (in the form of linear perspective cues) is present, the time-contraction/dilation effect is eliminated and time constancy is preserved. This is the first demonstration of a perceptual time constancy, analogous to size constancy but in the time domain. It points to a normalization of time computation operated by the visual brain when stimulated within a quasi-ecological environment.

  7. 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.

  8. Lightness Constancy in Surface Visualization

    PubMed Central

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

    2016-01-01

    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

  9. Color constancy at a pixel.

    PubMed

    Finlayson, G D; Hordley, S D

    2001-02-01

    In computational terms we can solve the color constancy problem if device red, green, and blue sensor responses, or RGB's, for surfaces seen under an unknown illuminant can be mapped to corresponding RGB's under a known reference light. In recent years almost all authors have argued that this three-dimensional problem is too hard. It is argued that because a bright light striking a dark surface results in the same physical spectra as those of a dim light incident on a light surface, the magnitude of RGB's cannot be recovered. Consequently, modern color constancy algorithms attempt only to recover image chromaticities under the reference light: They solve a two-dimensional problem. While significant progress has been made toward achieving chromaticity constancy, recent work has shown that the most advanced algorithms are unable to render chromaticity stable enough so that it can be used as a cue for object recognition [B. V. Funt, K. Bernard, and L. Martin, in Proceedings of the Fifth European Conference on Computer Vision (European Vision Society, Springer-Verlag, Berlin, 1998), Vol. II, p. 445.] We take this reductionist approach a little further and look at the one-dimensional color constancy problem. We ask, Is there a single color coordinate, a function of image chromaticities, for which the color constancy problem can be solved? Our answer is an emphatic yes. We show that there exists a single invariant color coordinate, a function of R, G, and B, that depends only on surface reflectance. Two corollaries follow. First, given an RGB image of a scene viewed under any illuminant, we can trivially synthesize the same gray-scale image (we simply code the invariant coordinate as a gray scale). Second, this result implies that we can solve the one-dimensional color constancy problem at a pixel (in scenes with no color diversity whatsoever). We present experiments that show that invariant gray-scale histograms are a stable feature for object recognition. Indexing on

  10. Ancient divergence in bathypelagic lake tanganyika deepwater cichlids: mitochondrial phylogeny of the tribe bathybatini.

    PubMed

    Koblmüller, Stephan; Duftner, Nina; Katongo, Cyprian; Phiri, Harris; Sturmbauer, Christian

    2005-03-01

    The cichlid species flock of Lake Tanganyika represents a polyphyletic assemblage of eight ancestral lineages, which colonized the emerging lake independently. Our study is focused on one of these lineages, the Bathybatini, a tribe of specialized piscivorous cichlids of the deep pelagic zone. By analyzing three mtDNA gene segments of all eight species of the tribe and two species of the closely related Trematocarini, we propose on the basis of a linearized tree analysis that the Bathybatini comprise two distinct lineages, the genera Hemibates and Bathybates, that seeded the primary lacustrine Tanganyika radiation independently. The genus Hemibates is likely to represent a distinct lineage that emerged simultaneously with the tribe Trematocarini and the genus Bathybates and should be therefore treated as a distinct tribe. Within the genus Bathybates, B. minor clearly represents the most ancestral split and is likely to have diverged from the remaining species in the course of the "primary lacustrine Tanganyika radiation" during which also the radiations of the Lamprologini and the H-lineage took place. The remaining "large" Bathybates species also diversified almost simultaneously and in step with the diversification of other Tanganyikan lineages-the Limnochromini and Cyprichromini-with B. graueri occupying the most ancestral branch, suggesting that these were induced by the same environmental changes. The lack of geographic color morphs suggests that competition and resource partitioning, rather than allopatric speciation, promoted speciation within the genus Bathybates.

  11. 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

    2016-08-15

    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.

  12. Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the Central and East African haplochromine cichlid fish faunas.

    PubMed

    Salzburger, Walter; Meyer, Axel; Baric, Sanja; Verheyen, Erik; Sturmbauer, Christian

    2002-02-01

    Lake Tanganyika, the oldest of the East African Great Lakes, harbors the ecologically, morphologically, and behaviorally most complex of all assemblages of cichlid fishes, consisting of about 200 described species. The evolutionary old age of the cichlid assemblage, its extreme degree of morphological differentiation, the lack of species with intermediate morphologies, and the rapidity of lineage formation have made evolutionary reconstruction difficult. The number and origin of seeding lineages, particularly the possible contribution of riverine haplochromine cichlids to endemic lacustrine lineages, remains unclear. Our phylogenetic analyses, based on mitochondrial DNA sequences of three gene segments of 49 species (25% of all described species, up to 2,400 bp each), yield robust phylogenies that provide new insights into the Lake Tanganyika adaptive radiation as well as into the origin of the Central- and East-African haplochromine faunas. Our data suggest that eight ancient African lineages may have seeded the Tanganyikan cichlid radiation. One of these seeding lineages, probably comprising substrate spawning Lamprologus-like species, diversified into six lineages that evolved mouthbrooding during the initial stage of the radiation. All analyzed haplochromines from surrounding rivers and lakes seem to have evolved within the radiating Tanganyikan lineages. Thus, our findings contradict the current hypothesis that ancestral riverine haplochromines colonized Lake Tanganyika to give rise to at least part of its spectacular endemic cichlid species assemblage. Instead, the early phases of the Tanganyikan radiation affected Central and East African rivers and lakes. The haplochromines may have evolved in the Tanganyikan basin before the lake became a hydrologically and ecologically closed system and then secondarily colonized surrounding rivers. Apparently, therefore, the current diversity of Central and East African haplochromines represents a relatively young and

  13. Color Constancy: Phenomenal or Projective?

    PubMed Central

    REEVES, ADAM J.; AMANO, KINJIRO; FOSTER, DAVID H.

    2008-01-01

    Naive observers viewed a sequence of colored Mondrian patterns, simulated on a color monitor. Each pattern was presented twice in succession, first under one daylight illuminant with a correlated color temperature of either 16,000 or 4,000 K and then under the other, to test for color-constancy. The observers compared the central square of the pattern across illuminants, either rating it for sameness of material-appearance or sameness of hue and saturation or judging an objective property—that is, whether its change of color originated from a change in material or only from a change in illumination. Average color constancy indices were high for material-appearance ratings and binary judgments of origin and low for hue–saturation ratings. Individuals' performance varied, but judgments of material and of hue and saturation remained demarcated. Observers seem able to separate phenomenal percepts from their ontological projections of mental appearance onto physical phenomena; thus, even when a chromatic change alters perceived hue and saturation, observers can reliably infer the cause, the constancy of the underlying surface spectral reflectance. PMID:18372745

  14. Molecular phylogeny and diversification of freshwater shrimps (Decapoda, Atyidae, Caridina) from ancient Lake Poso (Sulawesi, Indonesia)--the importance of being colourful.

    PubMed

    von Rintelen, Kristina; von Rintelen, Thomas; Glaubrecht, Matthias

    2007-12-01

    Ancient Lake Poso on the Indonesian island Sulawesi hosts a highly diverse endemic fauna, including a small species flock of atyid Caridina shrimps, which are characterized by conspicuous colour patterns. We used a mtDNA based molecular phylogeny to test the assumption of a monophyletic origin and intralacustrine radiation of the species flock and to assess the species specificity of some colour morphs. Our data reveal a rapid radiation of Caridina in the entire Poso drainage system, but provide no strong evidence for a monophyletic radiation of the lake species. Nevertheless each lacustrine species shows a varying degree of substrate or trophic specialization, usually considered a hallmark of adaptive radiation. Two distinct colour forms previously attributed to a single species, C. ensifera, lack distinguishing qualitative morphological characters, but are shown to be two different species. In contrast, morphologically rather distinct lake species lacking specific colour patterns may be hybridizing with riverine taxa. These results suggest that colour may play a similar role in species recognition and possibly speciation in ancient lake Caridina as hypothesized, e.g. for some African cichlids.

  15. 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.

  16. 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.

  17. 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)

  18. 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)

  19. Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan.

    PubMed

    Tabata, Ryoichi; Kakioka, Ryo; Tominaga, Koji; Komiya, Takefumi; Watanabe, Katsutoshi

    2016-04-01

    To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mtDNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3-13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan.

  20. Spatial constancy mechanisms in motor control

    PubMed Central

    Medendorp, W. Pieter

    2011-01-01

    The success of the human species in interacting with the environment depends on the ability to maintain spatial stability despite the continuous changes in sensory and motor inputs owing to movements of eyes, head and body. In this paper, I will review recent advances in the understanding of how the brain deals with the dynamic flow of sensory and motor information in order to maintain spatial constancy of movement goals. The first part summarizes studies in the saccadic system, showing that spatial constancy is governed by a dynamic feed-forward process, by gaze-centred remapping of target representations in anticipation of and across eye movements. The subsequent sections relate to other oculomotor behaviour, such as eye–head gaze shifts, smooth pursuit and vergence eye movements, and their implications for feed-forward mechanisms for spatial constancy. Work that studied the geometric complexities in spatial constancy and saccadic guidance across head and body movements, distinguishing between self-generated and passively induced motion, indicates that both feed-forward and sensory feedback processing play a role in spatial updating of movement goals. The paper ends with a discussion of the behavioural mechanisms of spatial constancy for arm motor control and their physiological implications for the brain. Taken together, the emerging picture is that the brain computes an evolving representation of three-dimensional action space, whose internal metric is updated in a nonlinear way, by optimally integrating noisy and ambiguous afferent and efferent signals. PMID:21242137

  1. 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

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

    PubMed Central

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

    2015-01-01

    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 18 kb. 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

  3. 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.

  4. Bayesian model of human color constancy

    PubMed Central

    Brainard, David H.; Longère, Philippe; Delahunt, Peter B.; Freeman, William T.; Kraft, James M.; Xiao, Bei

    2008-01-01

    Vision is difficult because images are ambiguous about the structure of the world. For object color, the ambiguity arises because the same object reflects a different spectrum to the eye under different illuminations. Human vision typically does a good job of resolving this ambiguity—an ability known as color constancy. The past 20 years have seen an explosion of work on color constancy, with advances in both experimental methods and computational algorithms. Here, we connect these two lines of research by developing a quantitative model of human color constancy. The model includes an explicit link between psychophysical data and illuminant estimates obtained via a Bayesian algorithm. The model is fit to the data through a parameterization of the prior distribution of illuminant spectral properties. The fit to the data is good, and the derived prior provides a succinct description of human performance. PMID:17209734

  5. 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.

  6. 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

  7. Rhizamoeba neglecta n. sp. (Amoebozoa, Tubulinea) from the bottom sediments of freshwater Lake Leshevoe (Valamo Island, North-Western Russia), with notes on the phylogeny of the order Leptomyxida.

    PubMed

    Smirnov, Alexey; Nassonova, Elena; Fahrni, Jose; Pawlowski, Jan

    2009-11-01

    A new species of Leptomyxida, named Rhizamoeba neglecta was found during studies of the amoeba fauna of the inner Lake Leshevoe located at Valamo archipelago (The Lake Ladoga, North-Western Russia). Light-microscopical and ultrastructural studies indicated that it represents a new species of Leptomyxida. The partial 18S rDNA sequence of this amoeba is very similar to that of Leptomyxa reticulata.. These organisms, however, are very different in LM morphology and biology. Organisms assigned to the genus Rhizamoeba do not form a single clade in the 18S rDNA tree. This may indicate that the genus is an artificial grouping or that a number of studied strains were misidentified. The phylogeny and the systematics of leptomyxids require further investigation.

  8. Limitations of surface-color and apparent-color constancy.

    PubMed

    Kuriki, I; Uchikawa, K

    1996-08-01

    Color-constancy mechanisms have been studied and discussed in a number of investigations. However, there has been little attempt to reveal how color constancy deteriorates as the conditions for it become less than optimal. We carried out a series of asymmetric color-matching experiments, using two criteria: surface-color match and apparent-color match. With brief adaptation the degree of color constancy increased as chromatic cues were added in the surround. In the condition of black surround, the test stimuli appeared self-luminous, and chromaticities of the chosen matching stimuli were the same as the physical chromaticities of the test stimulus, indicating a total deficiency of color constancy. With 15 min of preadaptation to the illuminant, the surface-color matches showed almost perfect color constancy under illuminant change. In both adaptation conditions, the chromatic-shift of matches from what would be expected for perfect color constancy increased gradually between 1,700- and 30,000-K illuminant, as chromaticity of the illuminant departed from 6,500-K illuminant. Under 1,000-K illuminant the surface-color appearance became totally achromatic, and color constancy was completely lost. Our results show that, even with brief adaptation to the illuminant, the contribution of the surrounding stimulus is large enough to achieve a fair degree of color constancy, but complete adaptation to the illuminant helps to achieve almost perfect color constancy.

  9. CONSTANCY OF CHARACTERISTICS IN THE STREPTOMYCETES1

    PubMed Central

    Sanchez-Marroquin, A.

    1962-01-01

    Sanchez-Marroquin, A. (University of Mexico, México D.F.). Constancy of characteristics in the streptomycetes. J. Bacteriol. 83:1183–1192. 1962.—A total of 150 Streptomyces strains isolated from soil was studied during a 3-year period in regard to constancy and variation of the following characteristics: sporophore micromorphology, color of the aerial and substrate mycelium, surface configuration of the spores, assimilation of carbon compounds, production of H2S and melanoid pigment, and reduction of nitrates. A remarkable constancy in the following characteristics was found: (i) sporophore micromorphology when only three of the seven morphological series of Pridham et al. were developed on tomato paste-oatmeal agar or yeast extract-malt extract agar; (ii) color of the aerial mycelium if only four fundamental colors are distinguished (white to cream or buff shades; yellow to orange or brown; pink to cinnamon, red or pinkish tan to lavender; and green to gray or blue); (iii) surface configuration of the spores divided in two types (smooth and warty to spinous or hairy); (iv) assimilation of five carbon compounds (arabinose, xylose, rhamnose, raffinose, and mannitol); (v) production of H2S on Difco peptone-iron agar supplemented with 0.1% Difco yeast extract; and (vi) production of melanoid pigment on peptone agar, giving similar results to those of the H2S test. Color of the substrate mycelium, size and shape of the spores, and reduction of nitrates should be used only as complementary data in the species descriptions, owing to their inconsistency and unreliability. Images PMID:14496763

  10. Constancy of characteristics in the streptomycetes.

    PubMed

    SANCHEZ-MARROQUIN, A

    1962-06-01

    Sanchez-Marroquin, A. (University of Mexico, México D.F.). Constancy of characteristics in the streptomycetes. J. Bacteriol. 83:1183-1192. 1962.-A total of 150 Streptomyces strains isolated from soil was studied during a 3-year period in regard to constancy and variation of the following characteristics: sporophore micromorphology, color of the aerial and substrate mycelium, surface configuration of the spores, assimilation of carbon compounds, production of H(2)S and melanoid pigment, and reduction of nitrates. A remarkable constancy in the following characteristics was found: (i) sporophore micromorphology when only three of the seven morphological series of Pridham et al. were developed on tomato paste-oatmeal agar or yeast extract-malt extract agar; (ii) color of the aerial mycelium if only four fundamental colors are distinguished (white to cream or buff shades; yellow to orange or brown; pink to cinnamon, red or pinkish tan to lavender; and green to gray or blue); (iii) surface configuration of the spores divided in two types (smooth and warty to spinous or hairy); (iv) assimilation of five carbon compounds (arabinose, xylose, rhamnose, raffinose, and mannitol); (v) production of H(2)S on Difco peptone-iron agar supplemented with 0.1% Difco yeast extract; and (vi) production of melanoid pigment on peptone agar, giving similar results to those of the H(2)S test. Color of the substrate mycelium, size and shape of the spores, and reduction of nitrates should be used only as complementary data in the species descriptions, owing to their inconsistency and unreliability.

  11. 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…

  12. The Role of Gender Constancy in Early Gender Development

    ERIC Educational Resources Information Center

    Ruble, Diane N.; Taylor, Lisa J.; Cyphers, Lisa; Greulich, Faith K.; Lurye, Leah E.; Shrout, Patrick E.

    2007-01-01

    Kohlberg's (1966) hypothesis that the attainment of gender constancy motivates children to attend to gender norms was reevaluated by examining these links in relation to age. Ninety-four 3- to 7-year-old children were interviewed to assess whether and how constancy mediates age-related changes in gender-related beliefs. As expected, results…

  13. 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.

  14. 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

  15. 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. © 2011 Optical Society of America

  16. Computational color constancy using chromagenic filters in color filter arrays

    NASA Astrophysics Data System (ADS)

    Shrestha, Raju; Hardeberg, Jon Yngve

    2012-03-01

    We have proposed, in this paper, a new color constancy technique, an extension to the chromagenic color constancy. Chromagenic based illuminant estimation methods take two shots of a scene, one without and one with a specially chosen color filter in front of the camera lens. Here, we introduce chromagenic filters into the color filter array itself by placing them on top of R, G or B filters and replacing one of the two green filters in the Bayer's pattern with them. This allows obtaining two images of the same scene via demosaicking: a normal RGB image, and a chromagenic image, equivalent of RGB image with a chromagenic filter. The illuminant can then be estimated using chromagenic based illumination estimation algorithms. The method, we named as CFA based chromagenic color constancy (or 4C in short), therefore, does not require two shots and no registration issues involved unlike as in the other chromagenic based color constancy algorithms, making it more practical and useful computational color constancy method in many applications. Experiments show that the proposed color filter array based chromagenic color constancy method produces comparable results with the chromagenic color constancy without interpolation.

  17. 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

  18. 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.

  19. Can illumination estimates provide the basis for color constancy?

    PubMed

    Granzier, Jeroen J M; Brenner, Eli; Smeets, Jeroen B J

    2009-03-24

    Objects hardly appear to change color when the spectral distribution of the illumination changes: a phenomenon known as color constancy. Color constancy could either be achieved by relying on properties that are insensitive to changes in the illumination (such as spatial color contrast) or by compensating for the estimated chromaticity of the illuminant. We examined whether subjects can judge the illuminant's color well enough to account for their own color constancy. We found that subjects were very poor at judging the color of a lamp from the light reflected by the scene it illuminated. They were much better at judging the color of a surface within the scene. We conclude that color constancy must be achieved by relying on relationships that are insensitive to the illumination rather than by explicitly judging the color of the illumination.

  20. Relative colour cues improve colour constancy in birds.

    PubMed

    Olsson, Peter; Kelber, Almut

    2017-05-15

    A ripe strawberry looks red to our eyes in sunlight and in the green light of a forest, although the spectrum of light reflected from its surface differs dramatically. This is caused by two effects: colour constancy and our ability to learn relative colour cues - the ripe strawberry remains relatively 'redder' than an unripe green strawberry. While colour constancy - the ability to recognize colours in shifted illumination - has been studied in many animals, the use of relative colour cues is investigated more rarely. In a previous study on chickens, we measured how large a shift in illumination their colour constancy mechanisms tolerate without reliable relative colour cues. Here, we show that chickens remain colour constant over larger illumination shifts, if they can use such relative colour cues. As relative colour cues are readily available in natural environments, we suggest that their use contributes strongly to colour constancy performance in nature. © 2017. Published by The Company of Biologists Ltd.

  1. A theory of shape constancy based on perspective invariants.

    PubMed

    Pizlo, Z

    1994-06-01

    Shape constancy refers to the phenomenon in which the percept of the shape of a given object remains constant despite changes in the shape of the object's retinal image. The phenomenon of shape constancy is considered from historical, theoretical and empirical perspectives in this paper. First, four prior theories are discussed; specifically, (1) Helmholtzian theory, which assumes that shape constancy is achieved by taking an object's orientation into account, (2) Gestalt theory, which assumes that shape constancy involves a relationship between the perceived shape and perceived orientation of an object, (3) Gibsonian theory, which assumes that shape constancy is based on projective invariants and (4) multiple view theory, which assumes that shape constancy is achieved by memorizing a large set of different views of the object. It is shown, by an analysis of the prior literature, that none of these theories can actually explain the phenomenon of shape constancy. A new theory, which is based on new perspective invariants of a flat shape, is then proposed. The new Perspective Invariants Theory can account for all prior shape constancy experiments. New experiments, testing predictions of the Perspective Invariants Theory are then described. These experiments showed that: (1) a novel shape can be matched with its single perspective image in the absence of depth cues, (2) perceptual processing of shape is impaired when the range of possible values of tilt is wide, (3) perceptual processing of shape is not affected by the width of the range of possible values of slant. These results support predictions of Perspective Invariants Theory.

  2. Representation or context as a cognitive strategy in colour constancy?

    PubMed

    Lin, Ta-Wei; Sun, Chun-Wang

    2008-01-01

    If an identification task with colour constancy as its objective is carried out under drastically changing illumination, do people rely mainly on colour information or do they rely on other sources of information? This question suggested two hypotheses for testing: (i) context hypothesis: people rely mainly on colour information (spectral reflectance or illumination chromaticity) to achieve colour constancy; (ii) representation hypothesis: people rely mainly on all other clues associated with colour to achieve colour constancy, including form information (any shape elements) and space information (spatial coordinates or spatial correlation). Experiment 1 showed that form information was readily associated with colour information to produce implicit representation. This gave the best colour-constancy performance (95.72%) and the fastest processing speed, so it probably used a top-down process. However, it was also prone to error owing to assumptions. Space information was not readily associated with colour information so colour-constancy performance was halved (48.73%) and processing time doubled. When the subject was deprived of both information sources and only given colour information, this resulted in the longest reaction times and the worst colour-constancy performance (41.38%). These results clearly support the representation hypothesis rather than the context hypothesis. When all three clues were available at the same time, the order of preference was: symbol, location, then colour. Experiment 2 showed that when form information was the main clue, colour-constancy performance was conceptually driven and processed more quickly; this supports the representation hypothesis. However, when form information was not used, colour constancy was data-driven, processed more slowly, and achieved an inferior identification rate overall; this supports the context hypothesis.

  3. The CONSTANCES cohort: an open epidemiological laboratory

    PubMed Central

    2010-01-01

    Background Prospective cohorts represent an essential design for epidemiological studies and allow for the study of the combined effects of lifestyle, environment, genetic predisposition, and other risk factors on a large variety of disease endpoints. The CONSTANCES cohort is intended to provide public health information and to serve as an "open epidemiologic laboratory" accessible to the epidemiologic research community. Although designed as a "general-purpose" cohort with very broad coverage, it will particularly focus on occupational and social determinants of health, and on aging. Methods/Design The CONSTANCES cohort is designed as a randomly selected representative sample of French adults aged 18-69 years at inception; 200,000 subjects will be included over a five-year period. At inclusion, the selected subjects will be invited to fill a questionnaire and to attend a Health Screening Center (HSC) for a comprehensive health examination: weight, height, blood pressure, electrocardiogram, vision, auditory, spirometry, and biological parameters; for those aged 45 years and older, a specific work-up of functional, physical, and cognitive capacities will be performed. A biobank will be set up. The follow-up includes a yearly self-administered questionnaire, and a periodic visit to an HSC. Social and work-related events and health data will be collected from the French national retirement, health and death databases. The data that will be collected include social and demographic characteristics, socioeconomic status, life events, behaviors, and occupational factors. The health data will cover a wide spectrum: self-reported health scales, reported prevalent and incident diseases, long-term chronic diseases and hospitalizations, sick-leaves, handicaps, limitations, disabilities and injuries, healthcare utilization and services provided, and causes of death. To take into account non-participation at inclusion and attrition throughout the longitudinal follow-up, a cohort

  4. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. An experimental test of the effects of gender constancy on sex typing.

    PubMed

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

    2009-12-01

    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 (anti-constancy condition). Posttests revealed that the lessons were effective; children in the pro-constancy condition showed higher gender constancy and appearance-reality distinction scores than did children in the anti-constancy condition. Sex typing did not, however, differ between treatment conditions at immediate and 3-month posttesting.

  6. Chromatic settings and the structural color constancy index.

    PubMed

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

    2013-03-11

    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.

  7. Perceptual constancy of texture roughness in the tactile system.

    PubMed

    Yoshioka, Takashi; Craig, James C; Beck, Graham C; Hsiao, Steven S

    2011-11-30

    Our tactual perception of roughness is independent of the manner in which we touch the surface. A brick surface feels rough no matter how slowly or how rapidly we move our fingers, despite the fluctuating sensory inputs that are transmitted to the finger. Current theories of roughness perception rely solely on inputs from the cutaneous afferents, which are highly affected by scan velocity and force. The question then is: how is roughness constancy achieved? To this end, we characterized the subject's perceived roughness in six scanning conditions. These included two modes of touch: direct touch, where the finger is in contact with the surface, and indirect touch, where the surface is scanned with a hand-held probe; and three scanning modes: active (moving the hand across a stationary surface), passive (moving the surface across a stationary hand), and pseudo-passive (subject's hand is moved by the experimenter across a stationary surface). Here, we show that roughness constancy is preserved during active but not passive scanning, indicating that the hand movement is necessary for roughness constancy in both direct and indirect touch. Roughness constancy is also preserved during pseudo-passive scanning, which stresses the importance of proprioceptive input. The results show that cutaneous input provides the signals necessary for roughness perception and that proprioceptive input resulting from hand movement-rather than a motor efference copy-is necessary to achieve roughness constancy. These findings have important implications in providing realistic sensory feedback for prosthetic-hand users.

  8. Color constancy of red-green dichromats and anomalous trichromats.

    PubMed

    Baraas, Rigmor C; Foster, David H; Amano, Kinjiro; Nascimento, Sérgio M C

    2010-04-01

    Purpose. Color-vision deficiency is associated with abnormalities in color matching and color discrimination, but its impact on the ability of people to judge the constancy of surface colors under different lights (color constancy) is less clear. This work had two aims: first, to quantify the degree of color constancy in subjects with congenital red-green color deficiency; second, to test whether the degree of color constancy in anomalous trichromats can be predicted from their Rayleigh anomaloscope matches. Methods. Color constancy of red-green color-deficient subjects was tested in a task requiring the discrimination of illuminant changes from surface-reflectance changes. Mondrian-like colored patterns, generated on the screen of a computer monitor, were used as stimuli to avoid the spatial cues provided by natural objects and scenes. Spectral reflectances were taken from the Munsell Book of Color and from natural scenes. Illuminants were taken from the daylight locus. Results. Protanopes and deuteranopes performed more poorly than normal trichromats with Munsell spectral reflectances but were less impaired with natural spectral reflectances. Protanomalous and deuteranomalous trichromats performed as well as, or almost as well as, normal trichromats, independent of the type of reflectance. Individual differences were not correlated with Rayleigh anomaloscope matches. Conclusions. Despite the evidence of clinical color-vision tests, red-green color-deficient persons are less disadvantaged than might be expected in their judgments of surface colors under different lights.

  9. The role of gender constancy in early gender development.

    PubMed

    Ruble, Diane N; Taylor, Lisa J; Cyphers, Lisa; Greulich, Faith K; Lurye, Leah E; Shrout, Patrick E

    2007-01-01

    Kohlberg's (1966) hypothesis that the attainment of gender constancy motivates children to attend to gender norms was reevaluated by examining these links in relation to age. Ninety-four 3- to 7-year-old children were interviewed to assess whether and how constancy mediates age-related changes in gender-related beliefs. As expected, results indicated a general pattern of an increase in stereotype knowledge, the importance and positive evaluation of one's own gender category, and rigidity of beliefs between the ages of 3 and 5. Moreover, the stability phase, rather than full constancy, mediated some of these relations. After age 5, rigidity generally decreased with age, with relations primarily mediated by consistency.

  10. Underwater color constancy: enhancement of automatic live fish recognition

    NASA Astrophysics Data System (ADS)

    Chambah, Majed; Semani, Dahbia; Renouf, Arnaud; Courtellemont, Pierre; Rizzi, Alessandro

    2003-12-01

    We present in this paper some advances in color restoration of underwater images, especially with regard to the strong and non uniform color cast which is typical of underwater images. The proposed color correction method is based on ACE model, an unsupervised color equalization algorithm. ACE is a perceptual approach inspired by some adaptation mechanisms of the human visual system, in particular lightness constancy and color constancy. A perceptual approach presents a lot of advantages: it is unsupervised, robust and has local filtering properties, that lead to more effective results. The restored images give better results when displayed or processed (fish segmentation and feature extraction). The presented preliminary results are satisfying and promising.

  11. Retroposition of the AFC family of SINEs (short interspersed repetitive elements) before and during the adaptive radiation of cichlid fishes in Lake Malawi and related inferences about phylogeny.

    PubMed

    Takahashi, K; Nishida, M; Yuma, M; Okada, N

    2001-01-01

    Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis.

  12. 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…

  13. 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…

  14. 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

  15. The Music of the Amish: Constancy Amidst Early Turmoil.

    ERIC Educational Resources Information Center

    Hardy, Donna Dee

    Amish music has its roots in Mennonite history and music. To study a selected piece of Amish music, one should first understand the heritage of the music that demonstrates the constancy of the Amish traditions. With that in mind, a brief history of the Mennonites and Amish is offered including information about their music. The Mennonite hymn…

  16. 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…

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

    PubMed

    Qian, Jiehui; Petrov, Yury

    2013-09-10

    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.

  18. Robust colour constancy in red-green dichromats.

    PubMed

    Álvaro, Leticia; Linhares, João M M; Moreira, Humberto; Lillo, Julio; Nascimento, Sérgio M C

    2017-01-01

    Colour discrimination has been widely studied in red-green (R-G) dichromats but the extent to which their colour constancy is affected remains unclear. This work estimated the extent of colour constancy for four normal trichromatic observers and seven R-G dichromats when viewing natural scenes under simulated daylight illuminants. Hyperspectral imaging data from natural scenes were used to generate the stimuli on a calibrated CRT display. In experiment 1, observers viewed a reference scene illuminated by daylight with a correlated colour temperature (CCT) of 6700K; observers then viewed sequentially two versions of the same scene, one illuminated by either a higher or lower CCT (condition 1, pure CCT change with constant luminance) or a higher or lower average luminance (condition 2, pure luminance change with a constant CCT). The observers' task was to identify the version of the scene that looked different from the reference scene. Thresholds for detecting a pure CCT change or a pure luminance change were estimated, and it was found that those for R-G dichromats were marginally higher than for normal trichromats regarding CCT. In experiment 2, observers viewed sequentially a reference scene and a comparison scene with a CCT change or a luminance change above threshold for each observer. The observers' task was to identify whether or not the change was an intensity change. No significant differences were found between the responses of normal trichromats and dichromats. These data suggest robust colour constancy mechanisms along daylight locus in R-G dichromacy.

  19. Robust colour constancy in red-green dichromats

    PubMed Central

    Linhares, João M. M.; Moreira, Humberto; Lillo, Julio; Nascimento, Sérgio M. C.

    2017-01-01

    Colour discrimination has been widely studied in red-green (R-G) dichromats but the extent to which their colour constancy is affected remains unclear. This work estimated the extent of colour constancy for four normal trichromatic observers and seven R-G dichromats when viewing natural scenes under simulated daylight illuminants. Hyperspectral imaging data from natural scenes were used to generate the stimuli on a calibrated CRT display. In experiment 1, observers viewed a reference scene illuminated by daylight with a correlated colour temperature (CCT) of 6700K; observers then viewed sequentially two versions of the same scene, one illuminated by either a higher or lower CCT (condition 1, pure CCT change with constant luminance) or a higher or lower average luminance (condition 2, pure luminance change with a constant CCT). The observers’ task was to identify the version of the scene that looked different from the reference scene. Thresholds for detecting a pure CCT change or a pure luminance change were estimated, and it was found that those for R-G dichromats were marginally higher than for normal trichromats regarding CCT. In experiment 2, observers viewed sequentially a reference scene and a comparison scene with a CCT change or a luminance change above threshold for each observer. The observers’ task was to identify whether or not the change was an intensity change. No significant differences were found between the responses of normal trichromats and dichromats. These data suggest robust colour constancy mechanisms along daylight locus in R-G dichromacy. PMID:28662218

  20. Analysis of higher-primate phylogeny from transversion differences in nuclear and mitochondrial DNA by Lake's methods of evolutionary parsimony and operator metrics.

    PubMed

    Holmquist, R; Miyamoto, M M; Goodman, M

    1988-05-01

    In the companion paper (Holmquist et al. 1988), we concluded that there is no agreement on either the correct branching order or differential rates of evolution among the higher primates, and we examined in depth why this uncertainty in the evolutionary understanding of our closest living relatives persists. Recently, Lake developed two novel methods, based on group properties of transition and transversion operators, that (a) permit, in principle, objective resolution of problems of the above type and (b) attach a statistical significance level to the conclusions drawn. In the present paper, we develop formulas for using these two methods in tandem and apply them to study transversion differences in (1) nuclear DNA for a 7-kb segment of the psi eta-globin locus and a 3-kb intergenic region between the psi beta- and delta-globin loci and (2) mitochondrial DNA for the 896-bp fragment of Brown et al. Although each of these nucleotide sequence regions has its characteristic tempo and mode of evolution, the nuclear and mitochondrial data together, comprising a total of 10,939 base positions, support a Homo/Pan clade at the 97% confidence level. If we calibrate the divergence point for humans and chimpanzees at 5 Myr, consideration of the transversion branch lengths for the combined nuclear data indicates that the gorilla lineage branched off 600,000-900,000 years prior to that, although the 2 sigma sampling errors do not preclude either a temporal trifurcation for the three species or a considerably more ancient branch point for the gorilla. To resolve the length of this central branch to a relative accuracy of 25% and 30% will require a factor of 16 and nine times more data, respectively--i.e., in excess of 100,000 homologous nucleotides for each of the four primates. For the nuclear genes, heterogeneity in evolutionary rates between different parts of the genome is mostly restricted to the human lineage for these two segments. The lineage leading to chimpanzees has

  1. Color constancy in natural scenes explained by global image statistics.

    PubMed

    Foster, David H; Amano, Kinjiro; Nascimento, Sérgio M C

    2006-01-01

    To what extent do observers' judgments of surface color with natural scenes depend on global image statistics? To address this question, a psychophysical experiment was performed in which images of natural scenes under two successive daylights were presented on a computer-controlled high-resolution color monitor. Observers reported whether there was a change in reflectance of a test surface in the scene. The scenes were obtained with a hyperspectral imaging system and included variously trees, shrubs, grasses, ferns, flowers, rocks, and buildings. Discrimination performance, quantified on a scale of 0 to 1 with a color-constancy index, varied from 0.69 to 0.97 over 21 scenes and two illuminant changes, from a correlated color temperature of 25,000 K to 6700 K and from 4000 K to 6700 K. The best account of these effects was provided by receptor-based rather than colorimetric properties of the images. Thus, in a linear regression, 43% of the variance in constancy index was explained by the log of the mean relative deviation in spatial cone-excitation ratios evaluated globally across the two images of a scene. A further 20% was explained by including the mean chroma of the first image and its difference from that of the second image and a further 7% by the mean difference in hue. Together, all four global color properties accounted for 70% of the variance and provided a good fit to the effects of scene and of illuminant change on color constancy, and, additionally, of changing test-surface position. By contrast, a spatial-frequency analysis of the images showed that the gradient of the luminance amplitude spectrum accounted for only 5% of the variance.

  2. 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.

  3. Colour constancy and conscious perception of changes of illuminant.

    PubMed

    Barbur, John L; Spang, Karoline

    2008-02-12

    A sudden change in illuminant (e.g., the outcome of turning on a tungsten light in a room illuminated with dim, natural daylight) causes a "global" change in perceived colour which subjects often recognise as a change of illuminant. In spite of this distinct, global change in the perceptual appearance of the scene caused by significant changes in the wavelength composition of the light reflected from different objects under the new illuminant, the perceived colour of the objects remains largely unchanged and this cornerstone property of human vision is often described as instantaneous colour constancy (ICC). ICC mechanisms are often difficult to study. The generation of appropriate stimuli to isolate ICC mechanisms remains a difficult task since the extraction of colour signals is also confounded in the processing of spatial chromatic context that leads to ICC. The extraction of differences in chromaticity that describe spatial changes in the wavelength composition of the light on the retina is a necessary operation that must precede colour constancy computations. A change of illuminant or changes in the spectral reflectance of the elements that make up the scene under a constant illuminant cause spatial changes in chromatic context and are likely to drive colour constancy mechanisms, but not exclusively. The same stimulus changes also cause differences in local luminance contrast and overall light flux changes, stimulus attributes that can activate different areas of the visual cortex. In order to address this problem we carried out a series of dichoptic experiments designed to investigate how the colour signals from the two eyes are combined in dichoptically viewed Mondrians and the extent to which the processing of chromatic context in monocularly driven neurons contributes to ICC. The psychophysical findings show that normal levels of ICC can be achieved in dichoptic experiments, even when the subject remains unaware of any changes of illuminant. Functional MRI

  4. 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…

  5. 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…

  6. 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…

  7. Spatial filtering, color constancy, and the color-changing dress.

    PubMed

    Dixon, Erica L; Shapiro, Arthur G

    2017-03-01

    The color-changing dress is a 2015 Internet phenomenon in which the colors in a picture of a dress are reported as blue-black by some observers and white-gold by others. The standard explanation is that observers make different inferences about the lighting (is the dress in shadow or bright yellow light?); based on these inferences, observers make a best guess about the reflectance of the dress. The assumption underlying this explanation is that reflectance is the key to color constancy because reflectance alone remains invariant under changes in lighting conditions. Here, we demonstrate an alternative type of invariance across illumination conditions: An object that appears to vary in color under blue, white, or yellow illumination does not change color in the high spatial frequency region. A first approximation to color constancy can therefore be accomplished by a high-pass filter that retains enough low spatial frequency content so as to not to completely desaturate the object. We demonstrate the implications of this idea on the Rubik's cube illusion; on a shirt placed under white, yellow, and blue illuminants; and on spatially filtered images of the dress. We hypothesize that observer perceptions of the dress's color vary because of individual differences in how the visual system extracts high and low spatial frequency color content from the environment, and we demonstrate cross-group differences in average sensitivity to low spatial frequency patterns.

  8. 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…

  9. 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…

  10. Concurrent performances: rate constancies without changeover delays1

    PubMed Central

    Catania, A. Charles

    1976-01-01

    Pigeons' pecks on two keys were maintained, without changeover delays, by independent variable-interval schedules of food reinforcement. Four regularly cycling 2-min components scheduled reinforcement respectively for both keys, left key only, both keys, and right key only. Initially, reinforcement scheduled for one key alone produced more responding on that key than reinforcement scheduled concurrently for both keys. Continued sessions reduced this difference; response rate on a given key approached constancy, or invariance with respect to the performance on and schedule for the other key. When extinction replaced the reinforcement schedule on either key, responding on that key decreased more during components that scheduled reinforcement for the other key than during those that did not. This demonstration that responses on one key were not supported by reinforcers on the other key suggested that the alternation of concurrent responding and either-key-alone responding prevented concurrent superstitions from developing. PMID:16811922

  11. 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.

  12. 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.

  13. Baculovirus phylogeny and evolution.

    PubMed

    Herniou, Elisabeth A; Jehle, Johannes A

    2007-10-01

    The family Baculoviridae represents one of the largest and most diverse groups of viruses and a unique model for studying the forces driving the evolution and biodiversity of double-stranded DNA viruses with large genomes. With the advent of comparative genomics, the phylogenetic relationships of baculoviruses have been put on solid bases. This, as well as improved bioinformatic approaches, has provided a detailed picture of baculovirus phylogeny and evolution. According to the present knowledge, baculoviruses can be classified into at least four evolutionary lineages: the most ancestral dipteran nucleopolyhedroviruses, the hymenopteran nucleopolyhedroviruses and the lepidopteran nucleopolyhedroviruses and granuloviruses. Despite the growing understanding of baculovirus phylogeny and macro-evolution, our knowledge of the micro-evolutionary processes within baculovirus species and virus populations is still limited. Here we present the state of the art on baculovirus phylogeny and evolution.

  14. 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.

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

    PubMed Central

    2016-01-01

    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

  16. Summary of Surface-Water Quality, Ground-Water Quality, and Water Withdrawals for the Spirit Lake Reservation, North Dakota

    DTIC Science & Technology

    2006-01-01

    Spirit Lake Nation (North Dakota Indian Affairs Commission, 2005). Thanks are given to Silas Ironheart, Jr., Constance Baker, Oliver Gourd , Jr...David Azure, Jr., Frank Black Cloud, Sean Gourd , and Lorna Walking Eagle from the Spirit Lake Tribal EPA office and to Dave Cavanaugh and R. J

  17. 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…

  18. 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…

  19. Consumer Spending on the Mass Media: The Principle of Relative Constancy Reconsidered.

    ERIC Educational Resources Information Center

    Wood, William C.

    1986-01-01

    Argues that the major studies supporting the Principle of Relative Constancy in consumption of mass communication products were statistically defective. Presents updated tests of data suggesting that the principle is actually of doubtful predictive value. (MS)

  20. 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.

  1. 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

  2. Pedestrian Detection Inspired by Appearance Constancy and Shape Symmetry

    NASA Astrophysics Data System (ADS)

    Cao, Jiale; Pang, Yanwei; Li, Xuelong

    2016-12-01

    The discrimination and simplicity of features are very important for effective and efficient pedestrian detection. However, most state-of-the-art methods are unable to achieve good tradeoff between accuracy and efficiency. Inspired by some simple inherent attributes of pedestrians (i.e., appearance constancy and shape symmetry), we propose two new types of non-neighboring features (NNF): side-inner difference features (SIDF) and symmetrical similarity features (SSF). SIDF can characterize the difference between the background and pedestrian and the difference between the pedestrian contour and its inner part. SSF can capture the symmetrical similarity of pedestrian shape. However, it's difficult for neighboring features to have such above characterization abilities. Finally, we propose to combine both non-neighboring and neighboring features for pedestrian detection. It's found that non-neighboring features can further decrease the average miss rate by 4.44%. Experimental results on INRIA and Caltech pedestrian datasets demonstrate the effectiveness and efficiency of the proposed method. Compared to the state-of-the-art methods without using CNN, our method achieves the best detection performance on Caltech, outperforming the second best method (i.e., Checkboards) by 1.63%.

  3. Pedestrian Detection Inspired by Appearance Constancy and Shape Symmetry.

    PubMed

    Cao, Jiale; Pang, Yanwei; Li, Xuelong

    2016-12-01

    Most state-of-the-art methods in pedestrian detection are unable to achieve a good trade-off between accuracy and efficiency. For example, ACF has a fast speed but a relatively low detection rate, while checkerboards have a high detection rate but a slow speed. Inspired by some simple inherent attributes of pedestrians (i.e., appearance constancy and shape symmetry), we propose two new types of non-neighboring features: side-inner difference features (SIDF) and symmetrical similarity features (SSFs). SIDF can characterize the difference between the background and pedestrian and the difference between the pedestrian contour and its inner part. SSF can capture the symmetrical similarity of pedestrian shape. However, it is difficult for neighboring features to have such above characterization abilities. Finally, we propose to combine both non-neighboring features and neighboring features for pedestrian detection. It is found that non-neighboring features can further decrease the log-average miss rate by 4.44%. The relationship between our proposed method and some state-of-the-art methods is also given. Experimental results on INRIA, Caltech, and KITTI data sets demonstrate the effectiveness and efficiency of the proposed method. Compared with the state-of-the-art methods without using CNN, our method achieves the best detection performance on Caltech, outperforming the second best method (i.e., checkerboards) by 2.27%. Using the new annotations of Caltech, it can achieve 11.87% miss rate, which outperforms other methods.

  4. 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.

  5. 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.

  6. Testing the Constancy of the Velocity of Light

    NASA Astrophysics Data System (ADS)

    Wu, Jingshown; Chang, Shenq-Tsong; Tsao, Hen-Wai; Huang, Yen-Ru; Lee, San-Liang; Lin, Wei-Cheng; Tsay, Ho-Lin; Tsai, Din Ping

    2012-03-01

    The constancy of the velocity of light, which is one of the most important postulates of modern physics, assumes that the speed of light is independent of the choice of observer regardless the relative motion between the light source and the observer. However, this postulate has never been directly experimentally tested. We present a measurement system which can directly test this postulate. This system consists of a transmitter and a distant receiver. The transmitter modulates the terrestrial 635 nm, 1550 nm lights and the starlights emitted from Capella, Betelgeuse, and Vega, which have large radial velocities with respect to the earth around the spring Equinox, into pulses simultaneously. These pulses are received by the distant receiver. We employ a terrestrial white light which travels along the exact path of the starlights to calibrate the system. We compare the arrival times of these pulses at the receiver, in which the startlight pulses have different degrees of delays with respect to the terrestrial pulses. The results indicate that the observed speeds of startlights are related to the radial velocities of the stars with respect to the earth.

  7. Perceptual constancy in auditory perception of distance to railway tracks.

    PubMed

    De Coensel, Bert; Nilsson, Mats E; Berglund, Birgitta; Brown, A L

    2013-07-01

    Distance to a sound source can be accurately estimated solely from auditory information. With a sound source such as a train that is passing by at a relatively large distance, the most important auditory information for the listener for estimating its distance consists of the intensity of the sound, spectral changes in the sound caused by air absorption, and the motion-induced rate of change of intensity. However, these cues are relative because prior information/experience of the sound source-its source power, its spectrum and the typical speed at which it moves-is required for such distance estimates. This paper describes two listening experiments that allow investigation of further prior contextual information taken into account by listeners-viz., whether they are indoors or outdoors. Asked to estimate the distance to the track of a railway, it is shown that listeners assessing sounds heard inside the dwelling based their distance estimates on the expected train passby sound level outdoors rather than on the passby sound level actually experienced indoors. This form of perceptual constancy may have consequences for the assessment of annoyance caused by railway noise.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

    2014-02-21

    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.

  13. 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.

  14. Rate constancy of globin gene evolution in placental mammals.

    PubMed Central

    Easteal, S

    1988-01-01

    The molecular clock hypothesis is investigated by comparison of the rates of nucleotide substitution in globin genes of mice, cows and goats, humans, and rabbits, using the relative rate test. These comparisons are based on a branching order of genes and species established by cladistic analysis of nucleotide sequences. The species branching order is shown to be mouse, cow/goat, human, and rabbit. Relative rate tests involving paralogous and orthologous genes provide no evidence of heterogeneity, among species, in the rate of evolution of the genes. This result is discrepant with the conclusions of most other recent, similar studies. By comparison with previous studies, the present study is based on a sound phylogeny and involves a larger sample of species, genes, and genic regions. The result provides strong support for the neutral theory of molecular evolution and demonstrates that molecular evolutionary rate does not depend on generation time. PMID:3174656

  15. 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.

  16. 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.

  17. 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.

  18. Improved color constancy in honey bees enabled by parallel visual projections from dorsal ocelli

    PubMed Central

    Garcia, Jair E.; Hung, Yu-Shan; Greentree, Andrew D.; Rosa, Marcello G. P.; Endler, John A.

    2017-01-01

    How can a pollinator, like the honey bee, perceive the same colors on visited flowers, despite continuous and rapid changes in ambient illumination and background color? A hundred years ago, von Kries proposed an elegant solution to this problem, color constancy, which is currently incorporated in many imaging and technological applications. However, empirical evidence on how this method can operate on animal brains remains tenuous. Our mathematical modeling proposes that the observed spectral tuning of simple ocellar photoreceptors in the honey bee allows for the necessary input for an optimal color constancy solution to most natural light environments. The model is fully supported by our detailed description of a neural pathway allowing for the integration of signals originating from the ocellar photoreceptors to the information processing regions in the bee brain. These findings reveal a neural implementation to the classic color constancy problem that can be easily translated into artificial color imaging systems. PMID:28673984

  19. [Physician from Constance doctor of medicine Georg Vogelin (1508-1542), an early follower of Copernicus].

    PubMed

    Burmeister, K H

    1999-01-01

    Georg Vogelin was born in Constance as the son of the town clerk. He studied the artes liberales and medicine at Wittenberg (since 1523) and Montpellier (since 1527). From 1531 onwards he practiced as a medical doctor in Constance. In 1542 Vogelin died of the plague in Constance. Vogelin was very close friends with the medical doctor Achilles Pirmin Gasser (1505-1577) and Georg Joachim Rheticus (1514-1574), a well known pupil of Copernicus. He was amongst the first supporters of the teachings of Copernicus. Gasser, who published the second edition of Rheticus' "Narratio prima" (Basle 1541), dedicated this edition to Georg Vogelin. In this book Vogelin published a poem in Latin. In the poem he described the teachings of Copernicus ("Terraque iam currit, credita stare prius") and recommended the academic community to approve Copernicus' theory.

  20. Phylogeny of gammaproteobacteria.

    PubMed

    Williams, Kelly P; Gillespie, Joseph J; Sobral, Bruno W S; Nordberg, Eric K; Snyder, Eric E; Shallom, Joshua M; Dickerman, Allan W

    2010-05-01

    The phylogeny of the large bacterial class Gammaproteobacteria has been difficult to resolve. Here we apply a telescoping multiprotein approach to the problem for 104 diverse gammaproteobacterial genomes, based on a set of 356 protein families for the whole class and even larger sets for each of four cohesive subregions of the tree. Although the deepest divergences were resistant to full resolution, some surprising patterns were strongly supported. A representative of the Acidithiobacillales routinely appeared among the outgroup members, suggesting that in conflict with rRNA-based phylogenies this order does not belong to Gammaproteobacteria; instead, it (and, independently, "Mariprofundus") diverged after the establishment of the Alphaproteobacteria yet before the betaproteobacteria/gammaproteobacteria split. None of the orders Alteromonadales, Pseudomonadales, or Oceanospirillales were monophyletic; we obtained strong support for clades that contain some but exclude other members of all three orders. Extreme amino acid bias in the highly A+T-rich genome of Candidatus Carsonella prevented its reliable placement within Gammaproteobacteria, and high bias caused artifacts that limited the resolution of the relationships of other insect endosymbionts, which appear to have had multiple origins, although the unbiased genome of the endosymbiont Sodalis acted as an attractor for them. Instability was observed for the root of the Enterobacteriales, with nearly equal subsets of the protein families favoring one or the other of two alternative root positions; the nematode symbiont Photorhabdus was identified as a disruptor whose omission helped stabilize the Enterobacteriales root.

  1. Phylogeny of Gammaproteobacteria▿ §

    PubMed Central

    Williams, Kelly P.; Gillespie, Joseph J.; Sobral, Bruno W. S.; Nordberg, Eric K.; Snyder, Eric E.; Shallom, Joshua M.; Dickerman, Allan W.

    2010-01-01

    The phylogeny of the large bacterial class Gammaproteobacteria has been difficult to resolve. Here we apply a telescoping multiprotein approach to the problem for 104 diverse gammaproteobacterial genomes, based on a set of 356 protein families for the whole class and even larger sets for each of four cohesive subregions of the tree. Although the deepest divergences were resistant to full resolution, some surprising patterns were strongly supported. A representative of the Acidithiobacillales routinely appeared among the outgroup members, suggesting that in conflict with rRNA-based phylogenies this order does not belong to Gammaproteobacteria; instead, it (and, independently, “Mariprofundus”) diverged after the establishment of the Alphaproteobacteria yet before the betaproteobacteria/gammaproteobacteria split. None of the orders Alteromonadales, Pseudomonadales, or Oceanospirillales were monophyletic; we obtained strong support for clades that contain some but exclude other members of all three orders. Extreme amino acid bias in the highly A+T-rich genome of Candidatus Carsonella prevented its reliable placement within Gammaproteobacteria, and high bias caused artifacts that limited the resolution of the relationships of other insect endosymbionts, which appear to have had multiple origins, although the unbiased genome of the endosymbiont Sodalis acted as an attractor for them. Instability was observed for the root of the Enterobacteriales, with nearly equal subsets of the protein families favoring one or the other of two alternative root positions; the nematode symbiont Photorhabdus was identified as a disruptor whose omission helped stabilize the Enterobacteriales root. PMID:20207755

  2. Size Constancy Is Preserved but Afterimages Are Prolonged in Typical Individuals with Higher Degrees of Self-Reported Autistic Traits

    ERIC Educational Resources Information Center

    Sperandio, Irene; Unwin, Katy L.; Landry, Oriane; Chouinard, Philippe A.

    2017-01-01

    Deficits in perceptual constancies from early infancy have been proposed to contribute to autism and exacerbate its symptoms (Hellendoorn et al., "Frontiers in Psychology" 6:1-16, 2015). Here, we examined size constancy in adults from the general population (N = 106) with different levels of self-reported autistic traits using an…

  3. Size Constancy Is Preserved but Afterimages Are Prolonged in Typical Individuals with Higher Degrees of Self-Reported Autistic Traits

    ERIC Educational Resources Information Center

    Sperandio, Irene; Unwin, Katy L.; Landry, Oriane; Chouinard, Philippe A.

    2017-01-01

    Deficits in perceptual constancies from early infancy have been proposed to contribute to autism and exacerbate its symptoms (Hellendoorn et al., "Frontiers in Psychology" 6:1-16, 2015). Here, we examined size constancy in adults from the general population (N = 106) with different levels of self-reported autistic traits using an…

  4. The Significance of the Appearance-Reality Distinction for the Development of Gender Constancy. Nr. 7, 1985/1.

    ERIC Educational Resources Information Center

    Trautner, Hanns Martin

    Attainment of gender constancy is commonly asserted if gender is judged invariant despite superficial opposite-sex transformations, such as in hairstyle, clothing, or behavior. This notion suggests that the distinction between appearance and reality is crucial for gender constancy understanding. Four tasks requiring differentiation between…

  5. Discrimination of cone contrast changes as evidence for colour constancy in cerebral achromatopsia.

    PubMed

    Hurlbert, A C; Bramwell, D I; Heywood, C; Cowey, A

    1998-11-01

    One proposed mechanism for underpinning colour constancy is computation of the relative activity of cones within one class--cone ratios, or cone contrasts--between surfaces in a fixed scene undergoing a change in illuminant. Although there is evidence that cone ratios do determine colour appearance under many conditions, the site or sites of their computation is unknown. Here, we report that a cerebrally achromatopsic observer, MS, displayed evidence of colour constancy in asymmetric colour matching tasks and was able to discriminate changes in cone ratios for simple, but not complex scenes. We hypothesise that the site of local cone-ratio computation is therefore early in the visual system, probably retinal.

  6. A depth illusion supports the model of General Object Constancy: Size and depth constancies related by a same distance-scaling factor.

    PubMed

    Qian, Jiehui; Petrov, Yury

    2016-12-01

    Perceptual constancy refers to the ability to stabilize the representation of an object even though the retinal image of the object undergoes variations. In previous studies, we proposed a General Object Constancy (GOC) hypothesis to demonstrate a common stabilization mechanism for perception of an object's features, such as size, contrast and depth, as the perceived distance varies. In the present study, we report another depth illusion supporting the GOC model. The stimuli comprised pairs of disks moving in a pattern of radial optic flow. Each pair consisted of a white disk positioned upper left to a dark disk, creating a percept of the white disk casting a shadow. As the pairs contracted towards the center of the screen in accordance with motion away from the observer, the two disks in each pair appeared to increase in contrast and separate farther away from each other both in the fronto-parallel plane (angular separation illusion) and in depth (depth separation illusion). While the contrast illusion and the angular separation illusion, which is a variant of the size illusion, replicated our previous findings, the illusion of depth separation revealed a depth constancy phenomenon. We further confirmed that the size and depth perception were related, e.g., the depth separation and the angular separation illusions were highly correlated across observers. Whereas the illusory increase in the angular separation between a disk and its 'shadow' could not be canceled by modulation of depth, decreasing the angular separation could offset the illusory increase in depth separation. The results can be explained by the GOC hypothesis: the visual system uses the same scaling factor to account for contrast, size (angular separation), and depth variations with distance; additionally, the perceived size of the object is used to scale its depth and contrast signals in order to achieve constancy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. 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.

  8. The contribution of the outer retina to color constancy: a general model for color constancy synthesized from primate and fish data.

    PubMed

    Vanleeuwen, M T; Joselevitch, C; Fahrenfort, I; Kamermans, M

    2007-01-01

    Color constancy is one of the most impressive features of color vision systems. Although the phenomenon has been studied for decades, its underlying neuronal mechanism remains unresolved. Literature indicates an early, possibly retinal mechanism and a late, possibly cortical mechanism. The early mechanism seems to involve chromatic spatial integration and performs the critical calculations for color constancy. The late mechanism seems to make the color manifest. We briefly review the current evidence for each mechanism. We discuss in more detail a model for the early mechanism that is based on direct measurements of goldfish outer retinal processing and induces color constancy and color contrast. In this study we extrapolate this model to primate retina, illustrating that it is highly likely that a similar mechanism is also present in primates. The logical consequence of our experimental work in goldfish and our model is that the wiring of the cone/horizontal cell system sets the reference point for color vision (i.e., it sets the white point for that animal).

  9. Molecular phylogeny of kinorhynchs.

    PubMed

    Yamasaki, Hiroshi; Hiruta, Shimpei F; Kajihara, Hiroshi

    2013-05-01

    We reconstructed kinorhynch phylogeny using maximum-likelihood and Bayesian analyses of nuclear 18S and 28S rRNA gene sequences from 30 species in 13 genera (18S) and 23 species in 12 genera (28S), representing eight families and both orders (Cyclorhagida and Homalorhagida) currently recognized in the phylum. We analyzed the two genes individually (18S and 28S datasets) and in combination (18S+28S dataset). We detected four main clades (I-IV). Clade I consisted of family Echinoderidae. Clade II contained representatives of Zelinkaderidae, Antygomonidae, Semnoderidae, Centroderes, and Condyloderes, the latter two currently classified in Centroderidae; within Clade II, Zelinkaderidae, Antygomonidae, and Semnoderidae comprised a clade with strong nodal support. Clade III contained only two species in Campyloderes, also currently classified in the Centroderidae, indicating polyphyly for this family. Clades I-III, containing all representatives of Cyclorhagida included in the analysis except for Dracoderes abei, formed a clade with high nodal support in the 28S and 18S+28S trees. Clade IV, resolved in the 18S and 18S+28S trees with high nodal support, contained only species in order Homalorhagida, with the exception of the cyclorhagid Dracoderes abei. Order Cyclorhagida as it currently stands is thus polyphyletic, and order Homalorhagida paraphyletic. Our results indicate that Dracoderidae has been misplaced in Cyclorhagida based on homoplasious characters. Our analyses did not resolve the relationships among Clades I-III within Cyclorhagida. Neither gene alone nor the combined dataset resolved all nodes in trees, indicating that additional markers will be needed to reconstruct kinorhynch phylogeny. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. 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.

  11. 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

  12. Gender Constancy and the Effects of Sex-typed Televised Toy Commercials.

    ERIC Educational Resources Information Center

    Ruble, Diane N.; And Others

    1981-01-01

    Presents a cognitive-developmental analysis of the effects of televised, sex-stereotypic information on children's behavior and attitudes towards toy play. Subjects were 100 children, ages four to six divided into groups exhibiting high and low gender-constancy. (Author/CM)

  13. 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...

  14. 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.…

  15. 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…

  16. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. 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.…

  18. 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…

  19. Development of Gender Constancy and Children's Sex-Typed Free Play Behavior.

    ERIC Educational Resources Information Center

    Smetana, Judith G.; Letourneau, Karen J.

    1984-01-01

    Examines relationships among gender constancy, preferences for same- or opposite-sex playmates, and sex-typed activities in preschool children. Findings suggest that, at least for females, gender concepts may have an organizing role in sex-role development by motivating children to seek social contexts in which to acquire and practice…

  20. 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.

  1. 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.

  2. 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…

  3. 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…

  4. 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…

  5. On Robustness of Non-Inferiority Clinical Trial Designs against Bias, Variability, and Non-Constancy

    PubMed Central

    Liu, Qing; Li, Yulan; Odem-Davis, Katherine

    2014-01-01

    The regulatory guidelines on non-inferiority trials emphasize constancy not only in the treatment effect over time but also in the trial design, clinical practice, and quality of the trial conduct and execution. In practice, the constancy assumption is generally impossible to justify; often there are clear reasons to expect a loss of efficacy over time. There are also concerns about the inherent and publication bias in the historical data, and various sources of selection bias in the non-inferiority trial design. Thus, a conservative non-inferiority margin is often considered. However, different non-inferiority margin approaches are largely evaluated under the assumption of constancy and absence of bias, and therefore, controversies arise and are unresolved on the necessary degree of conservativeness. We develop a framework to quantify the robustness of any non-inferiority margin approach against inherent and publication bias in historical data, selection bias in trial design, non-constancy in reference effects. We introduce a consistency principle to address variability in the historical data. We control across-trial conditional error rates given a final non-inferiority trial design over a design specific robust range for reference effects. Following a conditionality principle, we provide a theoretical justification of the framework and the conditions for controlling across-trial unconditional type 1 error rates. We raise the issue of inherent bias in historical data with an illustrative example. PMID:24918326

  6. 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...

  7. Global Lakes Sentinel Services: Evaluation of Chl-a Trends in Deep Clear Lakes

    NASA Astrophysics Data System (ADS)

    Cazzaniga, Ilaria; Giardino, Claudia; Bresciani, Mariano; Poser, Kathrin; Peters, Steef; Hommersom, Annelies; Schenk, Karin; Heege, Thomas; Philipson, Petra; Ruescas, Ana; Bottcher, Martin; Stelzer, Kerstin

    2016-08-01

    The aim of this study is the analysis of trend in the trophic level evolution in clear deep lakes which, being characterised by good quality state, are important socio- economic resources for their regions. The selected lakes are situated in Europe (Garda, Maggiore, Constance and Vättern), North America (Michigan) and Africa (Malawi and Tanganyika) and cover a range of eco- regions (continental, perialpine, boreal, rift valley) distributed globally.To evaluate trophic level tendency we mainly focused on chlorophyll-a concentrations (chl-a) which is a direct proxy of trophic status. The chl-a concentrations were obtained from 5216 cloud-free MERIS imagery from 2002 to 2012.The 'GLaSS RoIStats tool' available within the GLaSS project was used to extract chl-a in a number of region of interests (ROI) located in pelagic waters as well as some few other stations depending on lakes morphology. For producing the time-series trend, these extracted data were analysed with the Seasonal Kendall test.The results overall show almost stable conditions with a slight increase in concentration for lakes Maggiore, Constance, and the Green Bay of Lake Michigan; a slight decrease for lakes Garda and Tanganyika and absolutely stable conditions for lakes Vättern and Malawi.The results presented in this work show the great capability of MERIS to perform trend tests analysis on trophic status with focus on chl-a concentration. Being chl-a also a key parameter in water quality monitoring plans, this study also supports the managing practices implemented worldwide for using the water of the lakes.

  8. 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.

  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. The constancy myth, the vocabulary of color perception, and the ATD04 model

    NASA Astrophysics Data System (ADS)

    Guth, S. Lee

    2004-06-01

    Evidence is presented that colar constancy does not exist as a special phenomenon of human color vision. It is argued that results of experiments, as well as casual observations, which seem to illustrate color constancy, can be easily understood from basic facts about chromatic adaptation and simultaneous contrast. The argument is supported by (i) a critique of the famous Mondrian studies, (ii) the ATD model's predictions of the Mondrian data, and (iii) a summary of a demonstration experiment regarding Mondrian patterns. Concerning definitions of color concepts, it is noted that, in any field of science, definitions change according to theoretical advances, but the vocabulary of color vision has not. In particular, the ATD models of the past ten years or so suggest that some of the universally accepted and seemingly essential terms of color require re-examination.

  11. Phylogeny and Evolution of Lepidoptera.

    PubMed

    Mitter, Charles; Davis, Donald R; Cummings, Michael P

    2017-01-31

    Until recently, deep-level phylogeny in Lepidoptera, the largest single radiation of plant-feeding insects, was very poorly understood. Over the past two decades, building on a preceding era of morphological cladistic studies, molecular data have yielded robust initial estimates of relationships both within and among the ∼43 superfamilies, with unsolved problems now yielding to much larger data sets from high-throughput sequencing. Here we summarize progress on lepidopteran phylogeny since 1975, emphasizing the superfamily level, and discuss some resulting advances in our understanding of lepidopteran evolution.

  12. [Constancy or change in personality in the elderly? Findings and discussion of a controversy].

    PubMed

    Olbrich, E

    1994-01-01

    Research on personality development in the second half of life is reviewed, making a distinction between studies following a trait-oriented and studies using a process-oriented approach. A methodological and theoretical discussion of results not only explains differences in results, it also allows to conclude that the two approaches describe and explain complementary facets of the field. A synthesis between approaches is proposed in order to understand part of the controversy on constancy and change of personality development.

  13. 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.

  14. Depth Constancy in Stereoscopic Afterimages: Effects of Viewing Distance and Measurement Method.

    DTIC Science & Technology

    1982-08-01

    AREA A WORK UNIT NUMBERS Vanderbilt University 61153N 42; RR0420902; Nashville, Tennessee 37240 o4209-020; NR 197-067 11. CONTROLLING OFFICE NAME AND...19. KEY WORDS (Continue an rovers* side It necesseary eid ident’ify by block number) Stereopsi s Depth Depth constancy Afterimages 20. AD0RACT...distances greater than 20 meters, observa- tions were made outdoors with familiar objects as fixation points. The results show that stereopsis can provide

  15. 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.

  16. An optical flow algorithm based on gradient constancy assumption for PIV image processing

    NASA Astrophysics Data System (ADS)

    Zhong, Qianglong; Yang, Hua; Yin, Zhouping

    2017-05-01

    Particle image velocimetry (PIV) has matured as a flow measurement technique. It enables the description of the instantaneous velocity field of the flow by analyzing the particle motion obtained from digitally recorded images. Correlation based PIV evaluation technique is widely used because of its good accuracy and robustness. Although very successful, correlation PIV technique has some weakness which can be avoided by optical flow based PIV algorithms. At present, most of the optical flow methods applied to PIV are based on brightness constancy assumption. However, some factors of flow imaging technology and the nature property of the fluids make the brightness constancy assumption less appropriate in real PIV cases. In this paper, an implementation of a 2D optical flow algorithm (GCOF) based on gradient constancy assumption is introduced. The proposed GCOF assumes the edges of the illuminated PIV particles are constant during motion. It comprises two terms: a combined local-global gradient data term and a first-order divergence and vorticity smooth term. The approach can provide accurate dense motion fields. The approach are tested on synthetic images and on two experimental flows. The comparison of GCOF with other optical flow algorithms indicates the proposed method is more accurate especially in conditions of illumination variation. The comparison of GCOF with correlation PIV technique shows that the proposed GCOF has advantages on preserving small divergence and vorticity structures of the motion field and getting less outliers. As a consequence, the GCOF acquire a more accurate and better topological description of the turbulent flow.

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

    PubMed

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

    2014-06-26

    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.

  18. 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

  19. Obesity in primary care: evidence for advising weight constancy rather than weight loss in unsuccessful dieters

    PubMed Central

    Pryke, Rachel; Docherty, Andrea

    2008-01-01

    In view of the limited success rates of all weight-loss strategies to date, this article hypothesises that in situations where previous dieting attempts have failed, better outcomes and health improvements will arise from advocating weight-stability goals. This means the promotion of weight maintenance (to ensure any reduction in weight is maintained) and weight constancy (where steps are taken to maintain existing weight without attempting weight loss), rather than advocating existing 5–10% weight-loss targets for these patients. The majority of approaches to obesity focus on weight reduction despite poor evidence of effectiveness. Primary care remains reluctant to engage in ineffective approaches, yet is well placed to give advice, and would undoubtedly adopt effective obesity-management approaches if they were developed. Despite guidance for overweight or obese people to aim for a 5–10% weight reduction, current trends demonstrate escalation of average weights and obesity. A literature review found little information about evaluation of weight-stability approaches (either weight maintenance or weight constancy), despite theoretical support for them. Yet taking steps to protect weight reduction where it is achieved, and to promote weight constancy (without weight loss) where further dieting is predicted to fail, would have a beneficial effect on preventing further growth of obesity-related morbidity in the population. Some evidence exists to support simple behavioural approaches to improve weight stability, but these measures do not feature in current advice and hence are not widely advocated. PMID:18307855

  20. 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.

  1. Obesity in primary care: evidence for advising weight constancy rather than weight loss in unsuccessful dieters.

    PubMed

    Pryke, Rachel; Docherty, Andrea

    2008-02-01

    In view of the limited success rates of all weight-loss strategies to date, this article hypothesises that in situations where previous dieting attempts have failed, better outcomes and health improvements will arise from advocating weight-stability goals. This means the promotion of weight maintenance (to ensure any reduction in weight is maintained) and weight constancy (where steps are taken to maintain existing weight without attempting weight loss), rather than advocating existing 5-10% weight-loss targets for these patients. The majority of approaches to obesity focus on weight reduction despite poor evidence of effectiveness. Primary care remains reluctant to engage in ineffective approaches, yet is well placed to give advice, and would undoubtedly adopt effective obesity-management approaches if they were developed. Despite guidance for overweight or obese people to aim for a 5-10% weight reduction, current trends demonstrate escalation of average weights and obesity. A literature review found little information about evaluation of weight-stability approaches (either weight maintenance or weight constancy), despite theoretical support for them. Yet taking steps to protect weight reduction where it is achieved, and to promote weight constancy (without weight loss) where further dieting is predicted to fail, would have a beneficial effect on preventing further growth of obesity-related morbidity in the population. Some evidence exists to support simple behavioural approaches to improve weight stability, but these measures do not feature in current advice and hence are not widely advocated.

  2. Pollen Load and Flower Constancy of Three Species of Stingless Bees (Hymenoptera, Apidae, Meliponinae).

    PubMed

    Pangestika, Norita Widya; Atmowidi, Tri; Kahono, Sih

    2017-07-01

    The genera of stingless bees play an important role as pollinators of plants. These bees are actively involved in the pollination of agricultural crops and known to have preferences in selecting flowers to pollinate. The aims of this study were to analyse the pollen load and flower constancy in Tetragonula laeviceps, Lepidotrigona terminata, and Heterotrigona itama. Each individual of species stingless bees collected and was put in a 1.5 mL micro-tube contain 0.5 mL 70% ethanol:glycerol (4:1). Pollen loads on each individual of stingless bees was counted by hemocytometer. Flower constancy of stingless bees was measured based on percentage of pollen type loaded on the body. Results showed that the pollen loads of H. itama was the highest (31392 pollen grains) followed by L. terminata (23017 pollen grains) and T. laeviceps (8015 pollen grains). These species also demonstrated different flower constancy, T. laeviceps on Poaceae flowers (76.49%), L. terminata on Euphorbiaceae flowers (80.46%), and H. itama on Solanaceae flowers (83.33%).

  3. Neural Correlates underlying Size Constancy in Virtual Three-Dimensional Space.

    PubMed

    Xia, Jing; Wang, Pengfei; Chen, Qi

    2017-06-12

    The perceived size of an object remains relatively constant although its retinal size keeps decreasing as the object moves away along the depth dimension of the 3D space, i.e. size constancy. Neural mechanisms generating size constancy in virtual 3D space, however, remain poorly understood. By constructing a virtual 3D world in the MR scanner, we positioned the same 3D objects either near or far from the observers so that the near and far objects were perceived as having the same physical size despite their differences in retinal size. To control for the effect of differential retinal size, an additional 2D condition was introduced: a large and a small object, with matched retinal images as the near and far objects in the 3D condition, respectively, were presented on a 2D screen. Differences in retinal size activated overlapped areas in bilateral inferior occipital gyrus (IOG) in both experiments. The overlapped areas in IOG, however, showed different patterns of functional connectivity with different neural networks, depending on the perceived size of objects. In particular, IOG showed enhanced connectivity with bilateral superior parietal cortex in the 2D condition, but with inferior temporal and prefrontal cortex in the virtual 3D condition, i.e., size constancy.

  4. Molecular phylogeny of Daucus (Apiaceae)

    USDA-ARS?s Scientific Manuscript database

    We studied the phylogeny of 22 accessions of Daucus: D. broteri, D. capillifolius, D. carota, D. carota subsp. carota, D. carota subsp. commutatus, D. carota subsp. commutatus, D. carota subsp. drepanensis, D. carota subsp. gadecaei, D. carota subsp. gummifer, D. carota subsp. halophilius, D. carota...

  5. Phylogeny, genomics, and symbiosis of Photobacterium.

    PubMed

    Urbanczyk, Henryk; Ast, Jennifer C; Dunlap, Paul V

    2011-03-01

    Photobacterium comprises several species in Vibrionaceae, a large family of Gram-negative, facultatively aerobic, bacteria that commonly associate with marine animals. Members of the genus are widely distributed in the marine environment and occur in seawater, surfaces, and intestines of marine animals, marine sediments and saline lake water, and light organs of fish. Seven Photobacterium species are luminous via the activity of the lux genes, luxCDABEG. Much recent progress has been made on the phylogeny, genomics, and symbiosis of Photobacterium. Phylogenetic analysis demonstrates a robust separation between Photobacterium and its close relatives, Aliivibrio and Vibrio, and reveals the presence of two well-supported clades. Clade 1 contains luminous and symbiotic species and one species with no luminous members, and Clade 2 contains mostly nonluminous species. The genomes of Photobacterium are similar in size, structure, and organization to other members of Vibrionaceae, with two chromosomes of unequal size and multiple rrn operons. Many species of marine fish form bioluminescent symbioses with three Photobacterium species: Photobacterium kishitanii, Photobacterium leiognathi, and Photobacterium mandapamensis. These associations are highly, but not strictly species specific, and they do not exhibit symbiont-host codivergence. Environmental congruence instead of host selection might explain the patterns of symbiont-host affiliation observed from nature.

  6. 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

  7. [Practical dosimetry and constancy check at introduction of intraoperative radiotherapy with Intrabeam (Zeiss)].

    PubMed

    Härtl, Petra Maria; Dobler, Barbara; Kölbl, Oliver; Treutwein, Marius

    2009-01-01

    The check of dosimetry of the intraoperative radiotherapy system Intrabeam is predefined by the manufacture (Zeiss). The purpose of the study was to develop and implement a method to verify the internal dosimetry of Intrabeam (Zeiss). Additionally the long-term stability of Intrabeam was checked for dose and isotropy. For dose to water measurements an Unidos was combined with a soft jet chamber (TM 23342) which was calibrated in water absorbed dose and as a phantom the type 2962 (PTW Freiburg) was used. RW1 plates were inserted as build up material. The applicators were placed in a bag filled with water to consider the side-scattering. At the surface of the applicator there was a mean difference of 3 percent between the dose to water measurement and the internal dosimetry. The constancy of the dose rate showed a mean deviation of 0.3% at the reference point. The analysis of the dose distribution perpendicular to the applicator axis z (reference z-axis) resulted in a mean deviation of -2.7% (x-direction) and -7,1% (-x-direction) for the x-axis and, respectively -4.1% (y-direction) and -5.3% (-y-direction) for the y-axis. The proposed method is suitable to verify the absolute dose of Intrabeam. The dose values measured by this method were congruent to the dosimetry of the manufacture (Zeiss). From our point of view it is sufficient to verify the absolute dosimetry only at time of commissioning of the system or in the case of changing the applicator. For the daily routine the check of constancy specified by the manufacture is adequate, because the dose rate is checked on a daily basis. Additionally the test of constancy showed a high long-term stability in terms of dose rate and symmetry.

  8. Molecular phylogeny of Arthrotardigrada (Tardigrada).

    PubMed

    Jørgensen, Aslak; Faurby, Søren; Hansen, Jesper G; Møbjerg, Nadja; Kristensen, Reinhardt M

    2010-03-01

    Tardigrades are microscopic ecdysozoans with a worldwide distribution covering marine, limnic and terrestrial habitats. They are regarded as a neglected phylum with regard to studies of their phylogeny. During the last decade molecular data have been included in the investigation of tardigrades. However, the marine arthrotardigrades are still poorly sampled due to their relative rarity, difficult identification and minute size even for tardigrades. In the present study, we have sampled various arthrotardigrades and sequenced the 18S and partial 28S ribosomal subunits. The phylogenetic analyses based on Bayesian inference and maximum parsimony inferred Heterotardigrada (Arthrotardigrada+Echiniscoidea) and Eutardigrada to be monophyletic. Arthrotardigrada was inferred to be paraphyletic as the monophyletic Echiniscoidea is included within the arthrotardigrades. The phylogenetic positions of Stygarctidae and Batillipedidae are poorly resolved with low branch support. The Halechiniscidae is inferred to be polyphyletic as the currently recognized Styraconyxinae is not part of the family. Archechiniscus is the sister-group to the Halechiniscidae and Orzeliscus is placed as one of the basal halechiniscids. The phylogeny of the included eutardigrade taxa resembles the current molecular phylogenies. The genetic diversity within Arthrotardigrada is much larger (18S 15.1-26.5%, 28S 7.2-20.7%) than within Eutardigrada (18S 1.0-12.6%, 28S 1.3-8.2%). This can be explained by higher substitution rates in the arthrotardigrades or by a much younger evolutionary age of the sampled eutardigrades.

  9. 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.

  10. [Population-based cohorts. Example of the Gazel and Constances cohorts].

    PubMed

    Goldberg, Marcel; Zins, Marie

    2013-02-01

    Population-based cohorts focus on the causes of diseases, especially multifactorial diseases. Some are very large, and prospectively collect personal, lifestyle, occupational and environmental data over several decades. All include biobanks. "Generalist" cohorts cover a large field of diseases and risk factors. Two examples are presented here The Gazel cohort was composed of 20,000 subjects aged 35-50 at enrolment andfollowed-up for 25 years, resulting in about 200 publications. The Constances cohort, created in 2012, aims to include a representative sample of 200,000 adults aged 18-69 at enrolment.

  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.

  12. The development of time sense--from birth to object constancy.

    PubMed

    Colarusso, C A

    1979-01-01

    This paper represents an attempt to delineate the developmental line of time sense from birth to object constancy, concentrating on those maturational and environmental factors which determine psychotemporal adaptation in infancy and early childhood. Observational data and clinical vignettes are used to support theoretical formulations. Time sense is understood as a subjective, dynamic emergence which evolves throughout the life cycle. Psychoanalysis has paid little attention to the theory of time, and much needs to be accomplished to formulate the developmental line of time for the remainder of the life cycle.

  13. Constance Pascal's Chagrins d'amour et psychoses (1935): a French psychiatrist's views on psychoanalysis.

    PubMed

    Gordon, Felicia

    2015-03-01

    In 1935 Constance Pascal (1877-1937), France's first woman psychiatrist, published Chagrins d'amour et psychoses (The Sorrows of Love and Psychosis). My analysis of her monograph will consider: her major article leading up to Chagrins; Pascal's debts to her predecessors, particularly Morel and Kretschmer; her relationship to the French psychoanalytic movement; her co-option of psychoanalysis as a tool in her own therapeutic work with patients in the state psychiatric system; and her social/cultural interpretations of her woman patients. The literary and philosophic aspects of her work are emphasized as well as her contribution to French psychiatry. © The Author(s) 2014.

  14. 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)…

  15. 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…

  16. 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…

  17. 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…

  18. 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…

  19. 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

  20. The constancy of ζ in single-clock Inflation at all loops

    NASA Astrophysics Data System (ADS)

    Senatore, Leonardo; Zaldarriaga, Matias

    2013-09-01

    Studying loop corrections to inflationary perturbations, with particular emphasis on infrared factors, is important to understand the consistency of the inflationary theory, its predictivity and to establish the existence of the slow-roll eternal inflation phenomena and its recently found volume bound. In this paper we show that ζ-correlators are time-independent at large distances at all-loop level in single clock inflation. We write the n-th order correlators of ζ as the time-integral of Green's functions times the correlators of local sources that are function of the lower order fluctuations. The Green's functions are such that only non-vanishing correlators of the sources at late times can lead to non- vanishing correlators for ζ at long distances. When the sources are connected by high wavenumber modes, the correlator is peaked at short distances, and these diagrams cannot lead to a time-dependence by simple diff. invariance arguments. When the sources are connected by long wavenumber modes one can use similar arguments once the constancy of ζ at lower orders was established. Therefore the conservation of ζ at a given order follows from the conservation of ζ at the lower orders. Since at tree-level ζ is constant, this implies constancy at all-loops by induction.

  1. Effects of gender constancy and figure's height and sex on young children's gender-typed attributions.

    PubMed

    Levy, G D

    1998-01-01

    Young children's attributions of gender-typed activities to figures/models differing in height and/or sex were examined over three experiments. The influence of gender constancy understanding on children's gender-typed attributions was also examined. In Experiment 1, young children attributed significantly more masculine activities to male than female figures and significantly more feminine activities to female than male figures. Experiment 2 confirmed the results demonstrated in Experiment 1. In Experiment 2, additional line-drawn stimuli and figure comparisons were incorporated; participants attributed significantly more masculine activities to taller than shorter male figures and taller than shorter female figures. In addition, children attributed significantly more feminine activities to taller than shorter female figures. In Experiment 3, participants viewed pictures of taller and shorter male and female models. Results confirmed those of Experiment 1, as well as most of those of Experiment 2. No consistent patterns of children's gender-typed attributions as a function of gender constancy understanding emerged in the three experiments. Results are discussed as they apply to unexplored tenets from Kohlberg's cognitive-developmental model, as well as those of gender schema models, of early gender role development.

  2. Measuring Asymmetry in Time-Stamped Phylogenies.

    PubMed

    Dearlove, Bethany L; Frost, Simon D W

    2015-07-01

    Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of 'core groups' with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However, current tests of phylogenetic asymmetry (a) suffer from false positives when the tips of the phylogeny are sampled at different times and (b) only test for global asymmetry, and hence suffer from false negatives when asymmetry is localised to part of a phylogeny. We present a simple permutation-based approach for testing for asymmetry in a phylogeny, where we compare the observed phylogeny with random phylogenies with the same sampling and coalescence times, to reduce the false positive rate. We also demonstrate how profiles of measures of asymmetry calculated over a range of evolutionary times in the phylogeny can be used to identify local asymmetry. In combination with different metrics of asymmetry, this combined approach offers detailed insights of how phylogenies reconstructed from real viral datasets may deviate from the simplistic assumptions of commonly used coalescent and birth-death process models.

  3. RECONSTRUCTING IMMUNE PHYLOGENY: NEW PERSPECTIVES

    PubMed Central

    Litman, Gary W.; Cannon, John P.; Dishaw, Larry J.

    2013-01-01

    Numerous studies of the mammalian immune system have begun to uncover profound interrelationships, as well as fundamental differences, between the adaptive and innate systems of immune recognition. Coincident with these investigations, the increasing experimental accessibility of non-mammalian jawed vertebrates, jawless vertebrates, protochordates and invertebrates has provided intriguing new information regarding the likely patterns of emergence of immune-related molecules during metazoan phylogeny, as well as the evolution of alternative mechanisms for receptor diversification. Such findings blur traditional distinctions between adaptive and innate immunity and emphasize that, throughout evolution, the immune system has used a remarkably extensive variety of solutions to meet fundamentally similar requirements for host protection. PMID:16261174

  4. Approximating subtree distances between phylogenies.

    PubMed

    Bonet, Maria Luisa; St John, Katherine; Mahindru, Ruchi; Amenta, Nina

    2006-10-01

    We give a 5-approximation algorithm to the rooted Subtree-Prune-and-Regraft (rSPR) distance between two phylogenies, which was recently shown to be NP-complete. This paper presents the first approximation result for this important tree distance. The algorithm follows a standard format for tree distances. The novel ideas are in the analysis. In the analysis, the cost of the algorithm uses a "cascading" scheme that accounts for possible wrong moves. This accounting is missing from previous analysis of tree distance approximation algorithms. Further, we show how all algorithms of this type can be implemented in linear time and give experimental results.

  5. 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

  6. An even "newer" animal phylogeny.

    PubMed

    DeSalle, Rob; Schierwater, Bernd

    2008-11-01

    Metazoa are one of the great monophyletic groups of organisms. They comprise several major groups of organisms readily recognizable based on their anatomy. These major groups include the Bilateria (animals with bilateral symmetry), Cnidaria (jellyfish, corals and other closely related animals), Porifera (sponges), Ctenophores (comb jellies) and a phylum currently made up of a single species, the Placozoa. Attempts to systematize the relationships of these major groups as well as to determine relationships within the groups have been made for nearly two centuries. Many of the attempts have led to frustration, because of a lack of resolution between and within groups. Other attempts have led to "a new animal phylogeny". Now, a study by Dunn et al., using the expresssed sequence tag (EST) approach to obtaining high-throughput large phylogenetic matrices, presents an "even newer" animal phylogeny. There are two major aspects of this study that should be of interest to the general biological community. First, the methods used by the authors to generate their phylogenetic hypotheses call for close examination. Second, the relationships of animal taxa in their resultant trees also prompt further discussion.

  7. 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…

  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. Lake Tahoe

    EPA Pesticide Factsheets

    Information on the Lake Tahoe watershed, EPA's protection efforts, water quality issues, effects of climate change, Lake Tahoe Total Maximum Daily Load (TMDL), EPA-sponsored projects, list of partner agencies.

  10. 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.

  11. French psychiatry and the new woman: the case of Dr Constance Pascal, 1877-1937.

    PubMed

    Gordon, Felicia

    2006-06-01

    This article traces the connections between the public career and private life of Constance Pascal (1877-1937), the first woman psychiatrist in France, in the social context of the Belle Epoque. Pascal, of Romanian origin, attained professional success at the cost of suppressing her personal life. Best known for her work on dementia praecox, she researched the social as well as the biological causes of mental illness. She founded one of the first 'medical-pedagogic' institutes in France. Her monograph, Chagrins d'amour et psychoses (1935) reflects her wide cultural interests. Until recently, Pascal has been neglected by historians of psychiatry and of French women's history. Her life exemplified many of the conflicts experienced by women entering hitherto all-male professions.

  12. Image enhancement and color constancy for a vehicle-mounted change detection system

    NASA Astrophysics Data System (ADS)

    Tektonidis, Marco; Monnin, David

    2016-10-01

    Vehicle-mounted change detection systems allow to improve situational awareness on outdoor itineraries of inter- est. Since the visibility of acquired images is often affected by illumination effects (e.g., shadows) it is important to enhance local contrast. For the analysis and comparison of color images depicting the same scene at different time points it is required to compensate color and lightness inconsistencies caused by the different illumination conditions. We have developed an approach for image enhancement and color constancy based on the center/surround Retinex model and the Gray World hypothesis. The combination of the two methods using a color processing function improves color rendition, compared to both methods. The use of stacked integral images (SII) allows to efficiently perform local image processing. Our combined Retinex/Gray World approach has been successfully applied to image sequences acquired on outdoor itineraries at different time points and a comparison with previous Retinex-based approaches has been carried out.

  13. Poster - Thur Eve - 04: Online review of beam output and profile constancy using statistical process control.

    PubMed

    Chmielewski, R; Abbas, A; Yeung, I

    2012-07-01

    The objective of this work was to create a comprehensive online tool to evaluate and review the performance of quality assurance measurements that assess beam output and profile constancy as soon as they are acquired using statistical process control. As part of routine quality assurance: output, flatness and symmetry measurements are acquired daily and weekly with DQA3 and the Matrix and symmetry and flatness are acquired on a monthly basis with Profiler2. An individuals control chart and a moving range control chart was plotted for each set of data. Upper and lower control limits were calculated using measurements acquired during a several month period when the linear accelerators were operating optimally. The existing action levels, established according to TG142 and CAPCA guidelines were compared with the calculated statistical control limits. Tighter tolerance limits were recommended for output, symmetry and flatness Matrix measurements and DQA3 flatness measurements. © 2012 American Association of Physicists in Medicine.

  14. 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.

  15. 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

  16. Objective criteria for acceptability and constancy tests of digital subtraction angiography.

    PubMed

    de las Heras, Hugo; Torres, Ricardo; Fernández-Soto, José Miguel; Vañó, Eliseo

    2016-01-01

    Demonstrate an objective procedure to quantify image quality in digital subtraction angiography (DSA) and suggest thresholds for acceptability and constancy tests. Series of images were obtained in a DSA system simulating a small (paediatric) and a large patient using the dynamic phantom described in the IEC and DIN standards for acceptance tests of DSA equipment. Image quality was quantified using measurements of contrast-to-noise ratio (CNR). Overall scores combining the CNR of 10-100 mg/ml Iodine at a vascular diameter of 1-4 mm in a homogeneous background were defined. Phantom entrance surface air kerma (Ka,e) was measured with an ionisation chamber. The visibility of a low-contrast vessel in DSA images has been identified with a CNR value of 0.50 ± 0.03. Despite using 14 times more Ka,e (8.85 vs 0.63 mGy/image), the protocol for large patients showed a decrease in the overall score CNRsum of 67% (4.21 ± 0.06 vs 2.10 ± 0.05). The uncertainty in the results of the objective method was below 5%. Objective evaluation of DSA images using CNR is feasible with dedicated phantom measurements. An objective methodology has been suggested for acceptance tests compliant with the IEC/DIN standards. The defined overall scores can serve to fix a reproducible baseline for constancy tests, as well as to study the device stability within one acquisition series and compare different imaging protocols. This work provides aspects that have not been included in the recent European guidelines on Criteria for Acceptability of Medical Radiological Equipment. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  17. [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

  18. CONSTANCES: a general prospective population-based cohort for occupational and environmental epidemiology: cohort profile.

    PubMed

    Goldberg, Marcel; Carton, Matthieu; Descatha, Alexis; Leclerc, Annette; Roquelaure, Yves; Santin, Gaëlle; Zins, Marie

    2017-01-01

    WHY THE COHORT WAS SET UP?: CONSTANCES is a general-purpose cohort with a focus on occupational and environmental factors. CONSTANCES was designed as a randomly selected sample of French adults aged 18-69 years at inception; 200 000 participants will be included. At enrolment, the participants are invited to complete questionnaires and to attend a health screening centre (HSC) for a health examination. A biobank will be set up. The follow-up includes an yearly self-administered questionnaire, a periodic visit to an HSC and linkage to social and national health administrative databases. Data collected for participants include social and demographic characteristics, socioeconomic status, life events and behaviours. Regarding occupational and environmental factors, a wealth of data on organisational, chemical, biological, biomechanical and psychosocial lifelong exposure, as well as residential characteristics, are collected at enrolment and during follow-up. The health data cover a wide spectrum: self-reported health scales, reported prevalent and incident diseases, long-term chronic diseases and hospitalisations, sick-leaves, handicaps, limitations, disabilities and injuries, healthcare usage and services provided, and causes of death. To take into account non-participation and attrition, a random cohort of non-participants was set up and will be followed through the same national databases as participants. Inclusions begun at the end of 2012 and more than 110 000 participants were already included by September 2016. Several projects on occupational and environmental risks already applied to a public call for nested research projects. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  19. CONSTANCES: a general prospective population-based cohort for occupational and environmental epidemiology: cohort profile

    PubMed Central

    Goldberg, Marcel; Carton, Matthieu; Descatha, Alexis; Leclerc, Annette; Roquelaure, Yves; Santin, Gaëlle; Zins, Marie

    2017-01-01

    Why the cohort was set up? CONSTANCES is a general-purpose cohort with a focus on occupational and environmental factors. Cohort participants CONSTANCES was designed as a randomly selected sample of French adults aged 18–69 years at inception; 200 000 participants will be included. Data collection phases At enrolment, the participants are invited to complete questionnaires and to attend a health screening centre (HSC) for a health examination. A biobank will be set up. The follow-up includes an yearly self-administered questionnaire, a periodic visit to an HSC and linkage to social and national health administrative databases. Main types of data collected Data collected for participants include social and demographic characteristics, socioeconomic status, life events and behaviours. Regarding occupational and environmental factors, a wealth of data on organisational, chemical, biological, biomechanical and psychosocial lifelong exposure, as well as residential characteristics, are collected at enrolment and during follow-up. The health data cover a wide spectrum: self-reported health scales, reported prevalent and incident diseases, long-term chronic diseases and hospitalisations, sick-leaves, handicaps, limitations, disabilities and injuries, healthcare usage and services provided, and causes of death. Control of selection effects To take into account non-participation and attrition, a random cohort of non-participants was set up and will be followed through the same national databases as participants. Data access Inclusions begun at the end of 2012 and more than 110 000 participants were already included by September 2016. Several projects on occupational and environmental risks already applied to a public call for nested research projects. PMID:27884936

  20. Lake Powell

    Atmospheric Science Data Center

    2014-05-15

    article title:  Lake Powell     View Larger Image ... format (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 ...

  1. Animating and exploring phylogenies with fibre plots

    PubMed Central

    Pearse, William D.

    2017-01-01

    Despite the progress that has been made in many other aspects of data visualisation, phylogenies are still represented in much the same way as they first were by Darwin. In this brief essay, I give a short review of what I consider to be some recent major advances, and outline a new kind of phylogenetic visualisation. This new graphic, the fibre plot, uses the metaphor of sections through a tree to describe change in a phylogeny. I suggest it is a useful tool in gaining an rapid overview of the timing and scale of diversification in large phylogenies. PMID:28413610

  2. Towards a molecular systematics of the Lake Baikal/Lake Tuva sponges.

    PubMed

    Wiens, Matthias; Wrede, Petra; Grebenjuk, Vladislav A; Kaluzhnaya, Oxana V; Belikov, Sergey I; Schröder, Heinz C; Müller, Werner E G

    2009-01-01

    Lake Baikal is famous for its extensive biodiversity that is equaled only by few other lakes. Fascinatingly, about 80% of all the animals the lake hosts are endemic. Sponges (Porifera) that live in symbiosis with photosynthetic algae are the most abundant animal taxon found in the littoral zone of Lake Baikal and have been grouped to the family Lubomirskiidae. In recent years, several attempts to determine the phylogenetic relationship between Lubomirskiidae and cosmopolitan freshwater sponges have been undertaken. Yet the results obtained remain inconclusive. Here, we strive to determine the phylogeny of freshwater sponges with the focus on endemic Lake Baikal species, also taking into account two poriferan species that were collected during an expedition in 2006 in two other isolated Siberian lakes, Lake Chagytai and Lake Tore-Khol. Since its discovery at the beginning of the twentieth century, the Lake Chagytai species was grouped to the Lubomirskiidae and called Baikalospongia dzhegatajensis. However, analyses of molecular sequence data [internal transcribed spacer 2 (ITS2), ribosomal DNA (rDNA)] and morphological markers (spicules, habitus) inferred a close relationship to the cosmopolitan genus Ephydatia and also to the Lake Tore-Khol species that had not so far been described. Thus, both species were tentatively termed Ephydatia tuva (Lake Chagytai) and E. altaiensis (Lake Tore-Khol). We hypothesize that these new species might have evolved from Ephydatia-like ancestors through adaptation to the unique environmental conditions of both lakes. To test the ITS data, an unlinked genetic locus was chosen for further phylogenetic analyses, the protein-coding gene silicatein. These analyses provided not only a more robust resolution between the Lubomirskiidae, but also corroborated the grouping of the Lake Chagytai and Lake Tore-Khol species to the genus Ephydatia. In addition, the phylogenetic analyses suggest a Spongilla-like founder generation of poriferan

  3. 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

  4. Eumetazoan cryptochrome phylogeny and evolution.

    PubMed

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

    2015-01-18

    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. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. The undirected incomplete perfect phylogeny problem.

    PubMed

    Satya, Ravi Vijaya; Mukherjee, Amar

    2008-01-01

    The incomplete perfect phylogeny (IPP) problem and the incomplete perfect phylogeny haplotyping (IPPH) problem deal with constructing a phylogeny for a given set of haplotypes or genotypes with missing entries. The earlier approaches for both of these problems dealt with restricted versions of the problems, where the root is either available or can be trivially re-constructed from the data, or certain assumptions were made about the data. In this paper, we deal with the unrestricted versions of the problems, where the root of the phylogeny is neither available nor trivially recoverable from the data. Both IPP and IPPH problems have previously been proven to be NP-complete. Here, we present efficient enumerative algorithms that can handle practical instances of the problem. Empirical analysis on simulated data shows that the algorithms perform very well both in terms of speed and in terms accuracy of the recovered data.

  6. 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

  7. Radiographic film dosimetry of proton beams for depth-dose constancy check and beam profile measurement.

    PubMed

    Yeo, Inhwan J; Teran, Anthony; Ghebremedhin, Abiel; Johnson, Matt; Patyal, Baldev

    2015-05-08

    Radiographic film dosimetry suffers from its energy dependence in proton dosimetry. This study sought to develop a method of measuring proton beams by the film and to evaluate film response to proton beams for the constancy check of depth dose (DD). It also evaluated the film for profile measurements. To achieve this goal, from DDs measured by film and ion chamber (IC), calibration factors (ratios of dose measured by IC to film responses) as a function of depth in a phantom were obtained. These factors imply variable slopes (with proton energy and depth) of linear characteristic curves that relate film response to dose. We derived a calibration method that enables utilization of the factors for acquisition of dose from film density measured at later dates by adapting to a potentially altered processor condition. To test this model, the characteristic curve was obtained by using EDR2 film and in-phantom film dosimetry in parallel with a 149.65 MeV proton beam, using the method. An additional validation of the model was performed by concurrent film and IC measurement perpendicular to the beam at various depths. Beam profile measurements by the film were also evaluated at the center of beam modulation. In order to interpret and ascertain the film dosimetry, Monte Carlos simulation of the beam was performed, calculating the proton fluence spectrum along depths and off-axis distances. By multiplying respective stopping powers to the spectrum, doses to film and water were calculated. The ratio of film dose to water dose was evaluated. Results are as follows. The characteristic curve proved the assumed linearity. The measured DD approached that of IC, but near the end of the spread-out Bragg peak (SOBP), a spurious peak was observed due to the mismatch of distal edge between the calibration and measurement films. The width of SOBP and the proximal edge were both reproducible within a maximum of 5mm; the distal edge was reproducible within 1 mm. At 5 cm depth, the dose was

  8. 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

  9. 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.

  10. Phylogeny and taxonomy of Chlorobiaceae.

    PubMed

    Imhoff, Johannes F; Thiel, Vera

    2010-06-01

    Based on phylogenetic relationships found according to gene sequences of the 16S rRNA and the FMO (Fenna-Matthews-Olson protein) genes, and supported by the G + C content of the DNA and sequence signatures, the strains and species of green sulfur bacteria have been grouped into a phylogenetic system. Since properties used previously for classification such as cell morphology, photosynthetic pigments and substrate utilization do not conform with their phylogeny, a reassignment of strains to species, and a rearrangement among the species were necessary. The comparison of the traditional classification system of these bacteria with their phylogenetic relationship yielded a confusing picture. As a consequence of this rearrangement, species of the green sulfur bacteria were classified into the genera Chlorobium, Chlorobaculum, Prosthecochloris, and Chloroherpeton. Strains were assigned to the species according to their phylogenetic similarity and a number of new combinations, and new species were defined. New isolates and also environmental gene sequences fit very well into the established groups or may form new species, some of which have been described and others are awaiting their description. New strains and available gene sequences are included into the phylogenetic system, and a taxonomic classification on the species level is proposed.

  11. 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.

  12. Remarks on non-Gaussian fluctuations of the inflaton and constancy of {zeta} outside the horizon

    SciTech Connect

    Mahajan, Namit; Rangarajan, Raghavan

    2011-02-15

    We point out that the non-Gaussianity arising from cubic self-interactions of the inflaton field is proportional to {xi}N{sub e} where {xi}{approx}V{sup '''} and N{sub e} is the number of e-foldings from horizon exit till the end of inflation. For scales of interest N{sub e}=60, and for models of inflation such as new inflation, natural inflation, and running mass inflation {xi} is large compared to the slow-roll parameter {epsilon}{approx}V{sup '2}. Therefore, the contribution from self-interactions should not be outrightly ignored while retaining other terms in the non-Gaussianity parameter f{sub NL}. However, the N{sub e}-dependent term seems to imply the growth of non-Gaussianities outside the horizon. Therefore, we briefly discuss the issue of the constancy of correlations of the curvature perturbation {zeta} outside the horizon. We then calculate the 3-point function of the inflaton fluctuations using the canonical formalism and further obtain the 3-point function of {zeta}{sub k}. We find that the N{sub e}-dependent contribution to f{sub NL} from self-interactions of the inflaton field is canceled by contributions from other terms associated with nonlinearities in cosmological perturbation theory.

  13. Where vision meets memory: prefrontal-posterior networks for visual object constancy during categorization and recognition.

    PubMed

    Schendan, Haline E; Stern, Chantal E

    2008-07-01

    Objects seen from unusual relative to more canonical views require more time to categorize and recognize, and, according to object model verification theories, additionally recruit prefrontal processes for cognitive control that interact with parietal processes for mental rotation. To test this using functional magnetic resonance imaging, people categorized and recognized known objects from unusual and canonical views. Canonical views activated some components of a default network more on categorization than recognition. Activation to unusual views showed that both ventral and dorsal visual pathways, and prefrontal cortex, have key roles in visual object constancy. Unusual views activated object-sensitive and mental rotation (and not saccade) regions in ventrocaudal intraparietal, transverse occipital, and inferotemporal sulci, and ventral premotor cortex for verification processes of model testing on any task. A collateral-lingual sulci "place" area activated for mental rotation, working memory, and unusual views on correct recognition and categorization trials to accomplish detailed spatial matching. Ventrolateral prefrontal cortex and object-sensitive lateral occipital sulcus activated for mental rotation and unusual views on categorization more than recognition, supporting verification processes of model prediction. This visual knowledge framework integrates vision and memory theories to explain how distinct prefrontal-posterior networks enable meaningful interactions with objects in diverse situations.

  14. Gender constancy and the effects of sex-typed televised toy commercials.

    PubMed

    Ruble, D N; Balaban, T; Cooper, J

    1981-06-01

    The present study represented a cognitive-developmental analysis of the effects of televised, sex-stereotypic information on children's behavior and attitudes toward toy play. The subjects were 50 male and 50 female 4-6-year-olds divided into high and low gender-constancy levels. As the children watched a cartoon, they either saw a commercial of a gender-neutral toy that showed 2 boys or 2 girls playing with the toy, or they saw no commercial (control). As predicted, only the high gender-constant children were differentially affected by the sex-role information in the different commercial conditions. Children at this stage who saw opposite-sex children playing with the toy avoided spending time with the toy and stated verbally that the toy was more appropriate for an opposite-sex sibling, relative to children in the 2 other conditions. The results are discussed in terms of their implications for theories of sex-role development and in terms of the role that television may play in maintaining sex stereotypes and sex-typed behavior.

  15. Artist's colour rendering of HDR scenes in 3D Mondrian colour-constancy experiments

    NASA Astrophysics Data System (ADS)

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

    2010-01-01

    The presentation provides an update on ongoing research using three-dimensional Colour Mondrians. Two still life arrangements comprising hand-painted coloured blocks of 11 different colours were subjected to two different lighting conditions of a nearly uniform light and directed spotlights. The three-dimensional nature of these test targets adds shadows and multiple reflections, not found in flat Mondrian targets. Working from exactly the same pair of scenes, an author painted them using watercolour inks and paints to recreate both LDR and HDR Mondrians on paper. This provided us with a second set of appearance measurements of both scenes. Here we measured appearances by measuring reflectances of the artist's rendering. Land's Colour Mondrian extended colour constancy from a pixel to a complex scene. Since it used a planar array in uniform illumination, it did not measure the appearances of real life 3-D scenes in non-uniform illumination. The experiments in this paper, by simultaneously studying LDR and HDR renditions of the same array of reflectances, extend Land's Mondrian towards real scenes in non-uniform illumination. The results show that the appearances of many areas in complex scenes do not correlate with reflectance.

  16. 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.

  17. Investigation of a scabies outbreak in a kindergarten in Constance, Germany.

    PubMed

    Ariza, L; Walter, B; Worth, C; Brockmann, S; Weber, M-L; Feldmeier, H

    2013-03-01

    In industrialized countries, scabies occurs sporadically or in the form of protracted epidemics, typically in nursing homes for elderly people. Outbreaks of scabies in a kindergarten are very rare. The main goal of our study was to investigate an outbreak of scabies in a kindergarten and to identify risk factors for the infestation with the ectoparasitosis. We investigated an outbreak of scabies in a kindergarten in the City of Constance, southern Germany, with a particular pedagogical concept. Risk factors indicating a transmission of Sarcoptes mites through body contact or via fomites were assessed using questionnaires and by following the daily routine in the kindergarten. A total of 16 cases were identified. The attack rate was significantly higher in nursery teachers (risk ratio 42.1) compared to children (risk ratio 10.5). In all cases, scabies had developed rather recently, with minimal clinical manifestations. In nursery teachers, the probability of scabies was 4.4 times higher in those teachers who hugged children regularly. Children who preferably played with their own soft toys had a lower probability of developing scabies [risk ratio 0.14, 95 % confidence interval (CI) 0.05-0.42; p = 0.04]. It seems conceivable that the particular pedagogical concept of the kindergarten favored the spread of Sarcoptes mites. We were unable to show whether transmission had preferably occurred through body contact or via fomites.

  18. Perfect Phylogeny Problems with Missing Values.

    PubMed

    Kirkpatrick, Bonnie; Stevens, Kristian

    2014-01-01

    The perfect phylogeny problem is of central importance to both evolutionary biology and population genetics. Missing values are a common occurrence in both sequence and genotype data, but they make the problem of finding a perfect phylogeny NPhard even for binary characters. We introduce new and efficient perfect phylogeny algorithms for broad classes of binary and multistate data with missing values. Specifically, we address binary missing data consistent with the rich data hypothesis (RDH) introduced by Halperin and Karp and give an efficient algorithm for enumerating phylogenies. This algorithm is useful for computing the probability of data with missing values under the coalescent model. In addition, we use the partition intersection (PI) graph and chordal graph theory to generalize the RDH to multi-state characters with missing values. For a bounded number of states, we provide a fixed parameter tractable algorithm for the perfect phylogeny problem with missing data. Utilizing the PI graph, we are able to show that under multiple biologically motivated models for character data, our generalized RDH holds with high probability, and we evaluate our results with extensive empirical analysis.

  19. [Ontogeny and phylogeny: a quantitative theory of heterochrony].

    PubMed

    Demetrius, L; Goux, J M

    1985-01-01

    Developmental variability in organisms underlies the relationship between ontogeny and phylogeny. The concept entropy permits a quantitative characterization of this variability and provides a basis for interpreting the phylogeny of heterochrony in evolution.

  20. Lake Powell

    NASA Image and Video Library

    2007-09-20

    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. This image from NASA Terra satellite. http://photojournal.jpl.nasa.gov/catalog/PIA10614

  1. Treelength Optimization for Phylogeny Estimation

    PubMed Central

    Liu, Kevin; Warnow, Tandy

    2012-01-01

    The standard approach to phylogeny estimation uses two phases, in which the first phase produces an alignment on a set of homologous sequences, and the second phase estimates a tree on the multiple sequence alignment. POY, a method which seeks a tree/alignment pair minimizing the total treelength, is the most widely used alternative to this two-phase approach. The topological accuracy of trees computed under treelength optimization is, however, controversial. In particular, one study showed that treelength optimization using simple gap penalties produced poor trees and alignments, and suggested the possibility that if POY were used with an affine gap penalty, it might be able to be competitive with the best two-phase methods. In this paper we report on a study addressing this possibility. We present a new heuristic for treelength, called BeeTLe (Better Treelength), that is guaranteed to produce trees at least as short as POY. We then use this heuristic to analyze a large number of simulated and biological datasets, and compare the resultant trees and alignments to those produced using POY and also maximum likelihood (ML) and maximum parsimony (MP) trees computed on a number of alignments. In general, we find that trees produced by BeeTLe are shorter and more topologically accurate than POY trees, but that neither POY nor BeeTLe produces trees as topologically accurate as ML trees produced on standard alignments. These findings, taken as a whole, suggest that treelength optimization is not as good an approach to phylogenetic tree estimation as maximum likelihood based upon good alignment methods. PMID:22442677

  2. Molecular phylogeny: reconstructing the forest.

    PubMed

    Lopez, Philippe; Bapteste, Eric

    2009-01-01

    Phylogeny, be it morphological or molecular, has long tried to explain the extant biodiversity by the Tree of Species, which is a logical consequence of strict Darwinian evolutionary principles. Through constant improvement of both methods and data sets, some parts of this diversity have actually been demonstrated to be the result of a tree-like process. For some other parts, and especially for prokaryotes, different molecular markers have, however, produced different evolutionary trees, preventing the reconstruction of such a Tree. While technical artifacts could be blamed for these discrepancies, Lateral Gene Transfers are now largely held for responsible, and their existence requires an extension of the Darwinian framework, since genetic material is not always vertically inherited from parents to offspring. Through a variety of biological processes, sometimes large parts of DNA are exchanged between phylogenetically distant contemporary organisms, especially between those sharing the same environment. While mainly concerning prokaryotes, Lateral Gene Transfers have been also demonstrated to affect eukaryotes, and even multicellular ones, like plants or animals. Most of the time, these transfers allow important adaptations and the colonisation of new niches. The quantitative and qualitative importance of genetic transfers has thus severely challenged the very existence of a universal Tree of Species, since genetic connections, at least for microbes, seem more reticulated than tree-like. Even traditional biological concepts, like the concept of species, need to be re-evaluated in the light of recent discoveries. In short, instead of focusing on a elusive universal tree, biologists are now considering the whole forest corresponding to the multiple processes of inheritance, both vertical and horizontal. This constitutes the major challenge of evolutionary biology for the years to come.

  3. Flood frequency matters: Why climate change degrades deep-water quality of peri-alpine lakes

    NASA Astrophysics Data System (ADS)

    Fink, Gabriel; Wessels, Martin; Wüest, Alfred

    2016-09-01

    Sediment-laden riverine floods transport large quantities of dissolved oxygen into the receiving deep layers of lakes. Hence, the water quality of deep lakes is strongly influenced by the frequency of riverine floods. Although flood frequency reflects climate conditions, the effects of climate variability on the water quality of deep lakes is largely unknown. We quantified the effects of climate variability on the potential shifts in the flood regime of the Alpine Rhine, the main catchment of Lake Constance, and determined the intrusion depths of riverine density-driven underflows and the subsequent effects on water exchange rates in the lake. A simplified hydrodynamic underflow model was developed and validated with observed river inflow and underflow events. The model was implemented to estimate underflow statistics for different river inflow scenarios. Using this approach, we integrated present and possible future flood frequencies to underflow occurrences and intrusion depths in Lake Constance. The results indicate that more floods will increase the number of underflows and the intensity of deep-water renewal - and consequently will cause higher deep-water dissolved oxygen concentrations. Vice versa, fewer floods weaken deep-water renewal and lead to lower deep-water dissolved oxygen concentrations. Meanwhile, a change from glacial nival regime (present) to a nival pluvial regime (future) is expected to decrease deep-water renewal. While flood frequencies are not expected to change noticeably for the next decades, it is most likely that increased winter discharge and decreased summer discharge will reduce the number of deep density-driven underflows by 10% and favour shallower riverine interflows in the upper hypolimnion. The renewal in the deepest layers is expected to be reduced by nearly 27%. This study underlines potential consequences of climate change on the occurrence of deep river underflows and water residence times in deep lakes.

  4. Juvenile morphology in baleen whale phylogeny.

    PubMed

    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.

  5. 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.

  6. 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.

  7. Ribosomal RNA: a key to phylogeny.

    PubMed

    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.

  8. Cestode systematics and phylogeny move forward.

    PubMed

    Caira, Janine N; Scholz, Tomás; Georgiev, Boyko B

    2006-10-01

    This paper represents a meeting report for the Fifth International Workshop on Cestode Systematics and Phylogeny held at the Institute of Parasitology, Academy of Sciences of the Czech Republic, Ceské Budejovice, 18-22 July 2005. The major topics discussed included (i) the progress in cestode systematics during 2002-2005, (ii) the use of the life-cycle data in phylogenetic studies, (iii) the utilisation of new morphological and molecular characters in cestode systematics and phylogeny, and (iv) the ongoing work on the completion of the Global Cestode Database.

  9. 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.

  10. Great Lakes

    NASA Image and Video Library

    2017-09-28

    Bands of lake effect snow drift eastward from the western Great Lakes in this true-color image captured by the NOAA/NASA Suomi NPP satellite's Visible Infrared Imaging Radiometer Suite (VIIRS) instrument on January 5, 2017. National Weather Service forecasters expect light to moderate lake effect snow showers to continue throughout the day today and into Saturday (1/7). Lake-effect snow forms when cold air passes over the warmer waters of a lake. This causes some lake water to evaporate into the air and warm it. This warmer, wetter air rises and cools as it moves away from the lake. When it cools, it releases that moisture and, if it’s cold enough, that moisture turns into snow. Although true-color images like this may appear to be photographs of Earth, they aren't. They are created by combining data from the three color channels on the VIIRS instrument sensitive to the red, green and blue (or RGB) wavelengths of light into one composite image. In addition, data from several other channels are often also included to cancel out or correct atmospheric interference that may blur parts of the image. Credit: NOAA/NASA/Suomi NPP via NOAA's Environmental Visualization Laboratory

  11. 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.

  12. [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. Copyright © 2015. Published by Elsevier GmbH.

  13. 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

  14. Monitoring Daily QA 3 constancy for routine quality assurance on linear accelerators.

    PubMed

    Binny, Diana; Lancaster, Craig M; Kairn, Tanya; Trapp, Jamie V; Crowe, Scott B

    2016-11-01

    The purpose of this study was to evaluate the suitability of the Daily QA 3 (Sun Nuclear Corporation, Melbourne, USA) device as a safe quality assurance device for control of machine specific parameters, such as linear accelerator output, beam quality and beam flatness and symmetry. Measurements were performed using three Varian 2300iX linear accelerators. The suitability of Daily QA 3 as a device for quality control of linear accelerator parameters was investigated for both 6 and 10MV photons and 6, 9, 12, 15 and 18MeV electrons. Measurements of machine specific using the Daily QA 3 device were compared to corresponding measurements using a simpler constancy meter, Farmer chamber and plane parallel ionisation chamber in a water tank. The Daily QA 3 device showed a linear dose response making it a suitable device for detection of output variations during routine measurements. It was noted that over estimations of variations compared with Farmer chamber readings were seen if the Daily QA 3 wasn't calibrated for output and sensitivity on a regular eight to ten monthly basis. Temperature-pressure correction factors calculated by Daily QA 3 also contributed towards larger short term variations seen in output measurements. Energy, symmetry and flatness variations detected by Daily QA 3 were consistent with measurements performed in water tank using a parallel plate chamber. It was concluded that the Daily QA 3 device is suitable for routine daily and fortnightly quality assurance of linear accelerator beam parameters however a regular eight-ten monthly dose and detector array calibration will improve error detection capabilities of the device.

  15. Exploiting object constancy: effects of active exploration and shape morphing on similarity judgments of novel objects.

    PubMed

    Lee, Haemy; Wallraven, Christian

    2013-03-01

    Humans are experts at shape processing. This expertise has been learned and fine tuned by actively manipulating and perceiving thousands of objects during development. Therefore, shape processing possesses an active component and a perceptual component. Here, we investigate both components in six experiments in which participants view and/or interact with novel, parametrically defined 3D objects using a touch-screen interface. For probing shape processing, we use a similarity rating task. In Experiments 1-3, we show that active manipulation leads to a better perceptual reconstruction of the physical parameter space than judging rotating objects, or passively viewing someone else's exploration pattern. In Experiment 4, we exploit object constancy-the fact that the visual system assumes that objects do not change their identity during manipulation. We show that slow morphing of an object during active manipulation systematically biases similarity ratings-despite the participants being unaware of the morphing. Experiments 5 and 6 investigate the time course of integrating shape information by restricting the morphing to the first and second half of the trial only. Interestingly, the results indicate that participants do not seem to integrate shape information beyond 5 s of exploration time. Finally, Experiment 7 uses a secondary task that suggests that the previous results are not simply due to lack of attention during the later parts of the trial. In summary, our results demonstrate the advantage of active manipulation for shape processing and indicate a continued, perceptual integration of complex shape information within a time window of a few seconds during object interactions.

  16. Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known.

    PubMed

    Housworth, E A; Martins, E P

    2001-01-01

    Statistical randomization tests in evolutionary biology often require a set of random, computer-generated trees. For example, earlier studies have shown how large numbers of computer-generated trees can be used to conduct phylogenetic comparative analyses even when the phylogeny is uncertain or unknown. These methods were limited, however, in that (in the absence of molecular sequence or other data) they allowed users to assume that no phylogenetic information was available or that all possible trees were known. Intermediate situations where only a taxonomy or other limited phylogenetic information (e.g., polytomies) are available are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., four taxa belong together in a subclade). The procedure can be used to conduct comparative analyses when the phylogeny is only partially resolved or can be used in other randomization tests in which large numbers of possible phylogenies are needed.

  17. Molecular phylogeny of the Notostraca.

    PubMed

    Korn, Michael; Rabet, Nicolas; Ghate, Hemant V; Marrone, Federico; Hundsdoerfer, Anna K

    2013-12-01

    We used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the genera Triops and Lepidurus in the Mesozoic, most likely at a minimum age of 152.3-233.5 Ma, i.e., in the Triassic or Jurassic. Implications for the interpretation of fossils and the evolution of notostracan morphology are discussed. We further use the divergence date estimates to formulate a biogeographic hypothesis that explains distributions of extant lineages predominantly by overland dispersal routes. We identified an additional hitherto unrecognised highly diverged lineage within Lepidurus apus lubbocki and three additional previously unknown major lineages within Triops. Within T. granarius we found deep differentiation, with representatives distributed among three major phylogenetic lineages. One of these major lineages comprises T. cancriformis, the T. mauritanicus species group and two hitherto unrecognised T. granarius lineages. Samples that were morphologically identified as T. granarius diverged from the most basal nodes within this major lineage, and divergence dates suggested an approximate age of 23.7-49.6 Ma for T. cancriformis, indicating the need for a taxonomic revision of Triassic and Permian fossils that are currently attributed to the extant T. cancriformis. We thus elevate T. cancriformis minor to full species status as Triops minorTrusheim, 1938 and include in this

  18. Plastome phylogeny and early diversification of Brassicaceae.

    PubMed

    Guo, Xinyi; Liu, Jianquan; Hao, Guoqian; Zhang, Lei; Mao, Kangshan; Wang, Xiaojuan; Zhang, Dan; Ma, Tao; Hu, Quanjun; Al-Shehbaz, Ihsan A; Koch, Marcus A

    2017-02-16

    The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

  19. Primate diversification inferred from phylogenies and fossils.

    PubMed

    Herrera, James P

    2017-09-14

    Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: 1) diversification rates increased through time; 2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies consistently supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  20. Estimating the duration of speciation from phylogenies.

    PubMed

    Etienne, Rampal S; Morlon, Hélène; Lambert, Amaury

    2014-08-01

    Speciation is not instantaneous but takes time. The protracted birth-death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. ). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation.

  1. Context-dependent judgments of color that might allow color constancy in scenes with multiple regions of illumination

    PubMed Central

    Lee, R. J.; Smithson, H. E.

    2012-01-01

    For a color-constant observer, a change in the spectral composition of the illumination is accompanied by a corresponding change in the chromaticity associated with an achromatic percept. However, maintaining color constancy for different regions of illumination within a scene implies the maintenance of multiple perceptual references. We investigated the features of a scene that enable the maintenance of separate perceptual references for two displaced but overlapping chromaticity distributions. The time-averaged, retinotopically localized stimulus was the primary determinant of color appearance judgments. However, spatial separation of test samples additionally served as a symbolic cue that allowed observers to maintain two separate perceptual references. PMID:22330386

  2. Context-dependent judgments of color that might allow color constancy in scenes with multiple regions of illumination.

    PubMed

    Lee, R J; Smithson, H E

    2012-02-01

    For a color-constant observer, a change in the spectral composition of the illumination is accompanied by a corresponding change in the chromaticity associated with an achromatic percept. However, maintaining color constancy for different regions of illumination within a scene implies the maintenance of multiple perceptual references. We investigated the features of a scene that enable the maintenance of separate perceptual references for two displaced but overlapping chromaticity distributions. The time-averaged, retinotopically localized stimulus was the primary determinant of color appearance judgments. However, spatial separation of test samples additionally served as a symbolic cue that allowed observers to maintain two separate perceptual references.

  3. White Lake AOC

    EPA Pesticide Factsheets

    White Lake is in Muskegon County along the eastern shore of Lake Michigan. It was named an Area of Concern on the Great Lakes under the Great Lakes Water Quality Agreement of 1987 and delisted in 2014.

  4. Principles of lake sedimentology

    SciTech Connect

    Janasson, L.

    1983-01-01

    This book presents a comprehensive outline on the basic sedimentological principles for lakes, and focuses on environmental aspects and matters related to lake management and control-on lake ecology rather than lake geology. This is a guide for those who plan, perform and evaluate lake sedimentological investigations. Contents abridged: Lake types and sediment types. Sedimentation in lakes and water dynamics. Lake bottom dynamics. Sediment dynamics and sediment age. Sediments in aquatic pollution control programmes. Subject index.

  5. 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

  6. Sexual isolation promotes divergence between parapatric lake and stream stickleback.

    PubMed

    Berner, D; Ammann, M; Spencer, E; Rüegg, A; Lüscher, D; Moser, D

    2017-02-01

    Speciation can be initiated by adaptive divergence between populations in ecologically different habitats, but how sexually based reproductive barriers contribute to this process is less well understood. We here test for sexual isolation between ecotypes of threespine stickleback fish residing in adjacent lake and stream habitats in the Lake Constance basin, Central Europe. Mating trials exposing females to pairings of territorial lake and stream males in outdoor mesocosms allowing for natural reproductive behaviour reveal that mating occurs preferentially between partners of the same ecotype. Compared to random mating, this sexual barrier reduces gene flow between the ecotypes by some 36%. This relatively modest strength of sexual isolation is surprising because comparing the males between the two ecotypes shows striking differentiation in traits generally considered relevant to reproductive behaviour (body size, breeding coloration, nest size). Analysing size differences among the individuals in the mating trials further indicates that assortative mating is not related to ecotype differences in body size. Overall, we demonstrate that sexually based reproductive isolation promotes divergence in lake-stream stickleback along with other known reproductive barriers, but we also caution against inferring strong sexual isolation from the observation of strong population divergence in sexually relevant traits.

  7. Uniform Temperature Dependency in the Phenology of a Keystone Herbivore in Lakes of the Northern Hemisphere

    PubMed Central

    Straile, Dietmar; Adrian, Rita; Schindler, Daniel E.

    2012-01-01

    Spring phenologies are advancing in many ecosystems associated with climate warming causing unpredictable changes in ecosystem functioning. Here we establish a phenological model for Daphnia, an aquatic keystone herbivore based on decadal data on water temperatures and the timing of Daphnia population maxima from Lake Constance, a large European lake. We tested this model with long-term time-series data from two lakes (Müggelsee, Germany; Lake Washington, USA), and with observations from a diverse set of 49 lakes/sites distributed widely across the Northern Hemisphere (NH). The model successfully captured the observed temporal variation of Daphnia phenology in the two case study sites (r2 = 0.25 and 0.39 for Müggelsee and Lake Washington, respectively) and large-scale spatial variation in the NH (R2 = 0.57). These results suggest that Daphnia phenology follows a uniform temperature dependency in NH lakes. Our approach – based on temperature phenologies – has large potential to study and predict phenologies of animal and plant populations across large latitudinal gradients in other ecosystems. PMID:23071520

  8. 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.

  9. Optical angular constancy is maintained as a navigational control strategy when pursuing robots moving along complex pathways.

    PubMed

    Wang, Wei; McBeath, Michael K; Sugar, Thomas G

    2015-03-24

    The optical navigational control strategy used to intercept moving targets was explored using a real-world object that travels along complex, evasive pathways. Fielders ran across a gymnasium attempting to catch a moving robot that varied in speed and direction, while ongoing position was measured using an infrared motion-capture system. Fielder running paths were compared with the predictions of three lateral control models, each based on maintaining a particular optical angle relative to the robotic target: (a) constant alignment angle (CAA), (b) constant eccentricity angle (CEA), and (c) linear optical trajectory (LOT). Findings reveal that running pathways were most consistent with maintenance of LOT and least consistent with CEA. This supports that fielders use the same optical control strategy of maintaining angular constancy using a LOT when navigating toward targets moving along complex pathways as when intercepting simple ballistic trajectories. In those cases in which a target dramatically deviates from its optical path, fielders appear to simply reset LOT parameters using a new constant angle value. Maintenance of such optical angular constancy has now been shown to work well with ballistic, complex, and evasive moving targets, confirming the LOT strategy as a robust, general-purpose optical control mechanism for navigating to intercept catchable targets, both airborne and ground based. © 2015 ARVO.

  10. Physiological responses of a rodent to heliox reveal constancy of evaporative water loss under perturbing environmental conditions.

    PubMed

    Cooper, Christine Elizabeth; Withers, Philip Carew

    2014-10-15

    Total evaporative water loss of endotherms is assumed to be determined essentially by biophysics, at least at temperatures below thermoneutrality, with evaporative water loss determined by the water vapor deficit between the animal and the ambient air. We present here evidence, based on the first measurements of evaporative water loss for a small mammal in heliox, that mammals may have a previously unappreciated ability to maintain acute constancy of total evaporative water loss under perturbing environmental conditions. Thermoregulatory responses of ash-grey mice (Pseudomys albocinereus) to heliox were as expected, with changes in metabolic rate, conductance, and respiratory ventilation consistent with maintaining constancy of body temperature under conditions of enhanced heat loss. However, evaporative water loss did not increase in heliox. This is despite our confirmation of the physical effect that heliox augments evaporation from nonliving surfaces, which should increase cutaneous water loss, and increases minute volume of live ash-grey mice in heliox to accommodate their elevated metabolic rate, which should increase respiratory water loss. Therefore, mice had not only a thermoregulatory but also a hygroregulatory response to heliox. We interpret these results as evidence that ash-grey mice can acutely control their evaporative water loss under perturbing environmental conditions and suggest that hygroregulation at and below thermoneutrality is an important aspect of the physiology of at least some small mammals.

  11. 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

  12. 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

  13. Explaining evolution via constrained persistent perfect phylogeny.

    PubMed

    Bonizzoni, Paola; Carrieri, Anna Paola; Della Vedova, Gianluca; Trucco, Gabriella

    2014-01-01

    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. 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. A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to explain efficiently data that do not

  14. Tempo and mode of diversification of lake Tanganyika cichlid fishes.

    PubMed

    Day, Julia J; Cotton, James A; Barraclough, Timothy G

    2008-03-05

    Understanding the causes of disparities in species diversity across taxonomic groups and regions is a fundamental aim in evolutionary biology. Addressing these questions is difficult because of the need for densely sampled phylogenies and suitable empirical systems. Here we investigate the cichlid fish radiation of Lake Tanganyika and show that per lineage diversification rates have been more than six times slower than in the species flocks of Lakes Victoria and Malawi. The result holds even at peak periods of diversification in Lake Tanganyika, ruling out the age of the lake as an explanation for slow average rates, and is robust to uncertainties over the calibration of cichlid radiations in geological time. Moreover, Lake Tanganyika lineages, irrespective of different biological characteristics (e.g. sexually dichromatic versus sexually monochromatic clades), have diversified at similar rates, falling within typical estimates across a range of plant and animal clades. For example, the mostly sexually dichromatic haplochromines, which have speciated explosively in Lakes Victoria and Malawi, have displayed modest rates in Lake Tanganyika (where they are called Tropheini). Our results show that either the Lake Tanganyika environment is less conducive for cichlid speciation or the remarkable diversifying abilities of the haplochromines were inhibited by the prior occupancy of older radiations. Although the results indicate a dominant role for the environment in shaping cichlid diversification, differences in the timing of diversification among the Tanganyikan tribes indicate that biological differences were still important for the dynamics of species build-up in the lake. While we cannot resolve the timing of the radiation relative to the origin of the lake, because of the lack of robust geological date calibrations for cichlids, our results are consistent with a scenario that the different clades reflect independent adaptive radiations into different broad niches in

  15. Tempo and Mode of Diversification of Lake Tanganyika Cichlid Fishes

    PubMed Central

    Day, Julia J.; Cotton, James A.; Barraclough, Timothy G.

    2008-01-01

    Background Understanding the causes of disparities in species diversity across taxonomic groups and regions is a fundamental aim in evolutionary biology. Addressing these questions is difficult because of the need for densely sampled phylogenies and suitable empirical systems. Methodology/Principal Findings Here we investigate the cichlid fish radiation of Lake Tanganyika and show that per lineage diversification rates have been more than six times slower than in the species flocks of Lakes Victoria and Malawi. The result holds even at peak periods of diversification in Lake Tanganyika, ruling out the age of the lake as an explanation for slow average rates, and is robust to uncertainties over the calibration of cichlid radiations in geological time. Moreover, Lake Tanganyika lineages, irrespective of different biological characteristics (e.g. sexually dichromatic versus sexually monochromatic clades), have diversified at similar rates, falling within typical estimates across a range of plant and animal clades. For example, the mostly sexually dichromatic haplochromines, which have speciated explosively in Lakes Victoria and Malawi, have displayed modest rates in Lake Tanganyika (where they are called Tropheini). Conclusion/Significance Our results show that either the Lake Tanganyika environment is less conducive for cichlid speciation or the remarkable diversifying abilities of the haplochromines were inhibited by the prior occupancy of older radiations. Although the results indicate a dominant role for the environment in shaping cichlid diversification, differences in the timing of diversification among the Tanganyikan tribes indicate that biological differences were still important for the dynamics of species build-up in the lake. While we cannot resolve the timing of the radiation relative to the origin of the lake, because of the lack of robust geological date calibrations for cichlids, our results are consistent with a scenario that the different clades

  16. 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.

  17. Joint Bayesian estimation of alignment and phylogeny.

    PubMed

    Redelings, Benjamin D; Suchard, Marc A

    2005-06-01

    We describe a novel model and algorithm for simultaneously estimating multiple molecular sequence alignments and the phylogenetic trees that relate the sequences. Unlike current techniques that base phylogeny estimates on a single estimate of the alignment, we take alignment uncertainty into account by considering all possible alignments. Furthermore, because the alignment and phylogeny are constructed simultaneously, a guide tree is not needed. This sidesteps the problem in which alignments created by progressive alignment are biased toward the guide tree used to generate them. Joint estimation also allows us to model rate variation between sites when estimating the alignment and to use the evidence in shared insertion/deletions (indels) to group sister taxa in the phylogeny. Our indel model makes use of affine gap penalties and considers indels of multiple letters. We make the simplifying assumption that the indel process is identical on all branches. As a result, the probability of a gap is independent of branch length. We use a Markov chain Monte Carlo (MCMC) method to sample from the posterior of the joint model, estimating the most probable alignment and tree and their support simultaneously. We describe a new MCMC transition kernel that improves our algorithm's mixing efficiency, allowing the MCMC chains to converge even when started from arbitrary alignments. Our software implementation can estimate alignment uncertainty and we describe a method for summarizing this uncertainty in a single plot.

  18. Phylogeny mandalas for illustrating the Tree of Life.

    PubMed

    Hasegawa, Masami

    2016-11-02

    A circular phylogeny with photos or drawings of species is named a phylogeny mandala. This is one of the ways for illustrating the Tree of Life, and is suitable to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. To demonstrate the recent progress of molecular phylogenetics, six phylogeny mandalas for various taxonomic groups of life were presented; i.e., (1) Eukaryota, (2) Metazoa, (3) Hexapoda, (4) Tetrapoda, (5) Eutheria, and (6) Primates.

  19. Great Lakes

    USGS Publications Warehouse

    Edsall, Thomas A.; Mac, Michael J.; Opler, Paul A.; Puckett Haecker, Catherine E.; Doran, Peter D.

    1998-01-01

    The Great Lakes region, as defined here, includes the Great Lakes and their drainage basins in Minnesota, Wisconsin, Illinois, Indiana, Ohio, Pennsylvania, and New York. The region also includes the portions of Minnesota, Wisconsin, and the 21 northernmost counties of Illinois that lie in the Mississippi River drainage basin, outside the floodplain of the river. The region spans about 9º of latitude and 20º of longitude and lies roughly halfway between the equator and the North Pole in a lowland corridor that extends from the Gulf of Mexico to the Arctic Ocean.The Great Lakes are the most prominent natural feature of the region (Fig. 1). They have a combined surface area of about 245,000 square kilometers and are among the largest, deepest lakes in the world. They are the largest single aggregation of fresh water on the planet (excluding the polar ice caps) and are the only glacial feature on Earth visible from the surface of the moon (The Nature Conservancy 1994a).The Great Lakes moderate the region’s climate, which presently ranges from subarctic in the north to humid continental warm in the south (Fig. 2), reflecting the movement of major weather masses from the north and south (U.S. Department of the Interior 1970; Eichenlaub 1979). The lakes act as heat sinks in summer and heat sources in winter and are major reservoirs that help humidify much of the region. They also create local precipitation belts in areas where air masses are pushed across the lakes by prevailing winds, pick up moisture from the lake surface, and then drop that moisture over land on the other side of the lake. The mean annual frost-free period—a general measure of the growing-season length for plants and some cold-blooded animals—varies from 60 days at higher elevations in the north to 160 days in lakeshore areas in the south. The climate influences the general distribution of wild plants and animals in the region and also influences the activities and distribution of the human

  20. Characterization and phylogeny of a novel methanotroph, Methyloglobulus morosus gen. nov., spec. nov.

    PubMed

    Deutzmann, J S; Hoppert, M; Schink, B

    2014-05-01

    A novel methanotrophic gammaproteobacterium, strain KoM1, was isolated from the profundal sediment of Lake Constance after initial enrichment in opposing gradients of methane and oxygen. Strain KoM1 grows on methane or methanol as its sole source of carbon and energy. It is a Gram-negative methanotroph, often expressing red pigmentation. Cells are short rods and occur sometimes in pairs or short chains. Strain KoM1 grows preferably at reduced oxygen concentrations (pO2=0.05-0.1bar). It can fix nitrogen, and grows at neutral pH and at temperatures between 4 and 30°C. Phylogenetically, the closest relatives are Methylovulum miyakonense and Methylosoma difficile showing 91% 16S rRNA gene sequence identity. The only respiratory quinone is ubiquinone Q8; the main polar lipids are phosphatidyl ethanolamine and phosphatidyl glycerol. The major cellular fatty acids are summed feature 3 (presumably C16:1ω7c) and C16:1ω5c, and the G+C content of the DNA is 47.7mol%. Strain KoM1 is described as the type strain of a novel species within a new genus, Methyloglobulus morosus gen. nov., sp. nov.

  1. Lake Bonneville

    USGS Publications Warehouse

    Gilbert, Grove Karl

    1890-01-01

    This volume is a contribution to the later physical history of the Great Basin. As a geographic province the Great Basin is characterized by a dry climate, changes of drainage, volcanic eruption, and crustal displacement. Lake Bonneville, the special theme of the volume, was a phenomenon of climate and drainage, but its complete history includes an account of contemporaneous eruption and displacement.

  2. A guide to the natural history of freshwater lake bacteria.

    PubMed

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

    2011-03-01

    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.

  3. 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

  4. 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…

  5. 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…

  6. Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera).

    PubMed

    Gómez, Africa; Serra, Manuel; Carvalho, Gary R; Lunt, David H

    2002-07-01

    Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

  7. Evidence of pheromonal constancy among sexual and asexual females in a population of fall cankerworm,Alsophila pometaria (Lepidoptera: Geometridae).

    PubMed

    Mitter, C; Klun, J A

    1987-08-01

    The compounds (Z,Z,Z)-3,6,9-nonadecatriene (I), (Z,Z,Z,E)-(II), and (Z,Z,Z,Z)-3,6,9,11-nonadecatetraene (III) have been implicated as components of the female sex pheromone of the fall cankerworm. Chromatographie determination of the proportions of these compounds in individual females of sympatric asexual and sexual reproductive forms of the species, with concurrent analysis of the electrophoretic profiles of the same females, showed that the I: II: III proportion of compounds was constant across electrophoretically differing asexual genotypes and between these and the sexual form. Life-history characters, in contrast, typically show great variation among these genetic groups. The results indicate that pheromonal constancy is maintained in a reproductive system that is theoretically vulnerable to selective pressures that would lead to heterogeneity in the species' pheromonal communication channel.

  8. 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).

  9. Energy constancy checking for electron beams using a wedge-shaped solid phantom combined with a beam profile scanner.

    PubMed

    Rosenow, U F; Islam, M K; Gaballa, H; Rashid, H

    1991-01-01

    An energy constancy checking method is presented which involves a specially designed wedge-shaped solid phantom in combination with a multiple channel ionization chamber array known as the Thebes device. Once the phantom/beam scanner combination is set up, measurements for all electron energies can be made and evaluated without re-entering the treatment room. This is also valid for the readjustment of beam energies which are found to deviate from required settings. The immediate presentation of the measurements is in the form of crossplots which resemble depth dose profiles. The evaluation of the measured data can be performed using a hand-held calculator, but processing of the measured signals through a PC-type computer is advisable. The method is insensitive to usual fluctuations in beam flatness. The sensitivity and reproducibility of the method are more than adequate. The method may also be used in modified form for photon beams.

  10. Cosmic ray exposure ages of chondrites, pre-irradiation and constancy of cosmic ray flux in the past

    NASA Technical Reports Server (NTRS)

    Nishizumi, K.; Regnier, S.; Marti, K.

    1980-01-01

    Calibration of the production rate of the Ne-21 nuclide was accomplished by 4 methods based on (Al-26)-age, (Mn-53)-age, Kr-81/Kr-83, and Na-22/Ne-22. These production rates are normalized to a shielding parameter ratio Ne-22/Ne-21 = 1.11 and to the chemical composition of L chondrites; a value of P(21)(1.11) = 0.31 is suggested, and a production rate equation derived in terms of the 'F' parameters for L, LL, and H chondrites. The Al-26 half-life measurements are considered to evaluate the effects resulting from preirradiation of meteorites and to examine the data on the constancy of the cosmic ray flux in the light of current astronomical observations.

  11. [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.

  12. Feedback from Horizontal Cells to Cones Mediates Color Induction and May Facilitate Color Constancy in Rainbow Trout

    PubMed Central

    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. From constancy and polyfunctionality in perception to the transcendental psychology approach: historical overview of a novel psychological paradigm.

    PubMed

    Artemenkov, Sergey L; Harris, Mike G

    2005-12-01

    This paper presents an overview of a novel approach called Transcendental Psychology Methodology (TPM), largely inspired by Bach-y-Rita's work and developed by A.I. Mirakyan (1929-1995) and his associates. Beginning with the perceptual constancy problem, in which stimuli do not change perceptually despite variations in their physical characteristics, Mirakyan recognized that contemporary accounts of constancy included both theoretical contradictions and empirical discrepancies. This led him to propose TPM as an alternative to the traditional Product Basis Paradigm (PBP). Whilst PBP focuses upon perceptual phenomena, TPM focuses upon the underlying processes and upon the principles that support the flexibility needed to create complex, coherent representations under different stimulus conditions. The central idea that generative perceptual processes may be universal is grounded in Bach-y-Rita's famous experiments and has important parallels with present day conceptions of the construction of meaning in neurophysiological process. TPM inspired studies of a wide range of perceptual phenomena have so far suggested basic principles that can be applied to all perceptual processes, regardless of their modality. Its new conception of the perception of spatial extent can contribute to our understanding of the visual effects that Bach-y-Rita's blind subjects experience and it may provide a useful general tool for uncovering the psychological principles behind Bach-y-Rita's findings. Because of its axiomatic approach and its focus upon universal, generative processes, TPM may also be useful in other disciplines, e.g., in providing a line between neurophysiological and psychological levels of investigation. It may ultimately serve as a general theory of how sensory experience is created.

  14. 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.

  15. Lake Mackay, Australia

    NASA Image and Video Library

    2014-10-27

    This image from NASA Terra spacecraft shows Lake Mackay, the largest of hundreds of ephemeral lakes scattered throughout Western Australia and the Northern Territory, and is the second largest lake in Australia.

  16. 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

  17. Bayesian coestimation of phylogeny and sequence alignment.

    PubMed

    Lunter, Gerton; Miklós, István; Drummond, Alexei; Jensen, Jens Ledet; Hein, Jotun

    2005-04-01

    Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to first build a multiple alignment of these sequences, followed by a phylogenetic reconstruction step based on this multiple alignment. However, alignment and phylogenetic inference are fundamentally interdependent, and ignoring this fact leads to biased and overconfident estimations. Whether the main interest be in sequence alignment or phylogeny, a major goal of computational biology is the co-estimation of both. We developed a fully Bayesian Markov chain Monte Carlo method for coestimating phylogeny and sequence alignment, under the Thorne-Kishino-Felsenstein model of substitution and single nucleotide insertion-deletion (indel) events. In our earlier work, we introduced a novel and efficient algorithm, termed the "indel peeling algorithm", which includes indels as phylogenetically informative evolutionary events, and resembles Felsenstein's peeling algorithm for substitutions on a phylogenetic tree. For a fixed alignment, our extension analytically integrates out both substitution and indel events within a proper statistical model, without the need for data augmentation at internal tree nodes, allowing for efficient sampling of tree topologies and edge lengths. To additionally sample multiple alignments, we here introduce an efficient partial Metropolized independence sampler for alignments, and combine these two algorithms into a fully Bayesian co-estimation procedure for the alignment and phylogeny problem. Our approach results in estimates for the posterior distribution of evolutionary rate parameters, for the maximum a-posteriori (MAP) phylogenetic tree, and for the posterior decoding alignment. Estimates for the evolutionary tree and multiple alignment are augmented with confidence estimates for each node height and alignment column. Our results indicate that the patterns in

  18. 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. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. A supertree approach to shorebird phylogeny

    PubMed Central

    Thomas, Gavin H; Wills, Matthew A; Székely, Tamás

    2004-01-01

    Background Order Charadriiformes (shorebirds) is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have been presented for subsets of the Charadriiformes none to date include all recognised species. Here we use the matrix representation with parsimony method to produce the first fully inclusive supertree of Charadriiformes. We also provide preliminary estimates of ages for all nodes in the tree. Results Three main lineages are revealed: i) the plovers and allies; ii) the gulls and allies; and iii) the sandpipers and allies. The relative position of these clades is unresolved in the strict consensus tree but a 50% majority-rule consensus tree indicates that the sandpiper clade is sister group to the gulls and allies whilst the plover group is placed at the base of the tree. The overall topology is highly consistent with recent molecular hypotheses of shorebird phylogeny. Conclusion The supertree hypothesis presented herein is (to our knowledge) the only complete phylogenetic hypothesis of all extant shorebirds. Despite concerns over the robustness of supertrees (see Discussion), we believe that it provides a valuable framework for testing numerous evolutionary hypotheses relating to the diversity of behaviour, ecology and life-history of the Charadriiformes. PMID:15329156

  20. A molecular phylogeny of two extinct sloths.

    PubMed

    Greenwood, A D; Castresana, J; Feldmaier-Fuchs, G; Pääbo, S

    2001-01-01

    Xenarthra (Edentata) is an extremely diverse mammalian order whose modern representatives are the armadillos, anteaters, and sloths. The phylogeny of these groups is poorly resolved. This is particularly true for the sloths (phyllophagans), originally a large and diverse group now reduced to two genera in two different families. Both morphological analyses and molecular analyses of rDNA genes of living and extinct sloths have been used with limited success to elucidate their phylogeny. In an attempt to clarify relationships among the sloths, DNA was extracted and mitochondrial cytochrome b gene sequences were determined from representatives of two extinct groups of sloths (Mylodontidae and Megatheriidae), their two living relatives (two-toed sloths [Megalonychidae], three-toed sloths [Bradypodidae]), anteaters and armadillos. A consistent feature of the latter two species was the nuclear copies of cytochrome b gene sequences. Several methods of phylogenetic reconstruction were applied to the sequences determined, and the results were compared with 12S rDNA sequences obtained in previous studies. The cytochrome b gene exhibited a phylogenetic resolving power similar to that of the 12S rDNA sequences. When both data sets were combined, they tended to support the grouping of two-toed sloths with mylodontids and three-toed sloths with megatheriids. The results strengthen the view that the two families of living sloths adapted independently to an arboreal life-style.

  1. 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.

  2. Molecular phylogeny of the Siphonocladales (Chlorophyta: Cladophorophyceae).

    PubMed

    Leliaert, Frederik; De Clerck, Olivier; Verbruggen, Heroen; Boedeker, Christian; Coppejans, Eric

    2007-09-01

    The Siphonocladales are tropical to warm-temperate, marine green macro-algae characterized by a wide variety of thallus morphologies, ranging from branched filaments to pseudo-parenchymatous plants. Phylogenetic analyses of partial large subunit (LSU) rDNA sequences sampled from 166 isolates revealed nine well-supported siphonocladalean clades. Analyses of a concatenated dataset of small subunit (SSU) and partial LSU rDNA sequences greatly clarified the phylogeny of the Siphonocladales. However, the position of the root of the Siphonocladales could not be determined unambiguously, as outgroup rooting and molecular clock rooting resulted in a different root placement. Different phylogenetic methods (likelihood, parsimony and distance) yielded similar tree topologies with comparable internal node resolution. Likewise, analyses under more realistic models of sequence evolution, taking into account differences in evolution between stem and loop regions of rRNA, did not differ markedly from analyses using standard four-state models. The molecular phylogeny revealed that all siphonocladalean architectures may be derived from a single Cladophora-like ancestor. Parallel and convergent evolution of various morphological characters (including those traditionally employed to circumscribe the families and genera) have occurred in the Siphonocladales. Consequently, incongruence with traditional classifications, including non-monophyly in all families and most genera, was shown.

  3. Towards a mitogenomic phylogeny of Lepidoptera.

    PubMed

    Timmermans, Martijn J T N; Lees, David C; Simonsen, Thomas J

    2014-10-01

    The backbone phylogeny of Lepidoptera remains unresolved, despite strenuous recent morphological and molecular efforts. Molecular studies have focused on nuclear protein coding genes, sometimes adding a single mitochondrial gene. Recent advances in sequencing technology have, however, made acquisition of entire mitochondrial genomes both practical and economically viable. Prior phylogenetic studies utilised just eight of 43 currently recognised lepidopteran superfamilies. Here, we add 23 full and six partial mitochondrial genomes (comprising 22 superfamilies of which 16 are newly represented) to those publically available for a total of 24 superfamilies and ask whether such a sample can resolve deeper lepidopteran phylogeny. Using recoded datasets we obtain topologies that are highly congruent with prior nuclear and/or morphological studies. Our study shows support for an expanded Obtectomera including Gelechioidea, Thyridoidea, plume moths (Alucitoidea and Pterophoroidea; possibly along with Epermenioidea), Papilionoidea, Pyraloidea, Mimallonoidea and Macroheterocera. Regarding other controversially positioned higher taxa, Doidae is supported within the new concept of Drepanoidea and Mimallonidae sister to (or part of) Macroheterocera, while among Nymphalidae butterflies, Danainae and not Libytheinae are sister to the remainder of the family. At the deepest level, we suggest that a tRNA rearrangement occurred at a node between Adeloidea and Ditrysia+Palaephatidae+Tischeriidae.

  4. The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes).

    PubMed

    Amaral, Cesar R L; Pereira, Filipe; Silva, Dayse A; Amorim, António; de Carvalho, Elizeu F

    2017-09-20

    Here we present a mitogenomic perspective on the evolution of sharks and rays, being a first glance on the complete mitochondrial history of such an old and diversified group of vertebrates. The Elasmobranchii is a diverse subclass of Chondrichthyes, or cartilaginous fish, with about 1200 species of ocean- and freshwater-dwelling fishes spread all over the world's seas, including some of the ocean's largest fishes. The group dates back about 400 million years near the Devonian-Silurian boundary, being nowadays represented by several derivative lineages, mainly related to Mesozoic forms. Although considered of ecological, commercial and conservation importance, the phylogeny of this old group is poorly studied and still under debate. Here we apply a molecular systematic approach on 82 complete mitochondrial genomes to investigate the phylogeny of the Elasmobranchii. By using maximum likelihood (ML) and Bayesian analyses, we found a clear separation within the shark clade between the Galeomorphii and the Squalomorphii, as well as sister taxa relationships between the Carcharhiniformes and the Lamniformes. Moreover, we found that Pristoidei clusters within the Rhinobatoidei, having been recovered as the sister taxon of the Rhinobatos genus in a clade which also includes the basal Zapteryx. Our results also reject the Hypnosqualea hypothesis, which proposes that the Batoidea should be placed within the Selachii.

  5. 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

  6. Evolution and phylogeny of old world deer.

    PubMed

    Pitra, Christian; Fickel, Joerns; Meijaard, Erik; Groves, P Colin

    2004-12-01

    The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with muntjacs as sister group as well as for the divergence of at least three distinct genera: Rucervus, Dama, and Cervus. The latter clade comprises what have previously been regarded as the genera or subgenera Panolia, Rusa, Cervus, Sika, and probably Przewalskium. Our data also consistently confirmed paraphyly of nominate C. elaphus and did not support the monophyly of Axis. We used these molecular phylogenies to assess the homoplastic evolution of morphological, geographical, ecological, and selected behavioural character state differences within the Cervinae. Reliable fossil calibrations, large molecular data sets, and improved dating methods are shaping a molecular time scale for the evolutionary radiation of Old World deer that occurred at the Miocene/Pliocene transition and is largely compatible with existing palaeontological evidence. Using node ages estimated from sequence data, we estimated an average per-lineage diversification rate of 0.51+/-0.1 species per million years (my) over roughly the last 6 mya.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    Alkenone paleothermometry (via the UK37 and 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 µE). 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 UK37 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.

  9. The roots of phylogeny: how did Haeckel build his trees?

    PubMed

    Dayrat, Benoît

    2003-08-01

    Haeckel created much of our current vocabulary in evolutionary biology, such as the term phylogeny, which is currently used to designate trees. Assuming that Haeckel gave the same meaning to this term, one often reproduces Haeckel's trees as the first illustrations of phylogenetic trees. A detailed analysis of Haeckel's own evolutionary vocabulary and theory revealed that Haeckel's trees were genealogical trees and that Haeckel's phylogeny was a morphological concept. However, phylogeny was actually the core of Haeckel's tree reconstruction, and understanding the exact meaning Haeckel gave to phylogeny is crucial to understanding the information Haeckel wanted to convey in his famous trees. Haeckel's phylogeny was a linear series of main morphological stages along the line of descent of a given species. The phylogeny of a single species would provide a trunk around which lateral branches were added as mere ornament; the phylogeny selected for drawing a tree of a given group was considered the most complete line of progress from lower to higher forms of this group, such as the phylogeny of Man for the genealogical tree of Vertebrates. Haeckel's phylogeny was mainly inspired by the idea of the scala naturae, or scale of being. Therefore, Haeckel's genealogical trees, which were only branched on the surface, mainly represented the old idea of scale of being. Even though Haeckel decided to draw genealogical trees after reading On the Origin of Species and was called the German Darwin, he did not draw Darwinian branching diagrams. Although Haeckel always saw Lamarck, Goethe, and Darwin as the three fathers of the theory of evolution, he was mainly influenced by Lamarck and Goethe in his approach to tree reconstruction.

  10. Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies.

    PubMed

    Steiner, Cynthia C; Mitelberg, Anna; Tursi, Rosanna; Ryder, Oliver A

    2012-11-01

    Short divergence times and processes such as incomplete lineage sorting and species hybridization are known to hinder the inference of species-level phylogenies due to the lack of sufficient informative genetic variation or the presence of shared but incongruent polymorphism among taxa. Extant equids (horses, zebras, and asses) are an example of a recently evolved group of mammals with an unresolved phylogeny, despite a large number of molecular studies. Previous surveys have proposed trees with rather poorly supported nodes, and the bias caused by genetic introgression or ancestral polymorphism has not been assessed. Here we studied the phylogenetic relationships of all extant species of Equidae by analyzing 22 partial mitochondrial and nuclear genes using maximum likelihood and Bayesian inferences that account for heterogeneous gene histories. We also examined genetic signatures of lineage sorting and/or genetic introgression in zebras by evaluating patterns of intraspecific genetic variation. Our study improved the resolution and support of the Equus phylogeny and in particular the controversial positions of the African wild ass (E. asinus) and mountain zebra (E. zebra): the African wild ass is placed as a sister species of the Asiatic asses and the mountain zebra as the sister taxon of Grevy's and Burchell's zebras. A shared polymorphism (indel) detected among zebra species in the Estrogen receptor 1 gene was likely due to incomplete lineage sorting and not genetic introgression as also indicated by other mitochondrial (Cytochrome b) and nuclear (Y chromosome and microsatellites) markers. Ancestral polymorphism in equids might have contributed to the long-standing lack of clarity in the phylogeny of this highly threatened group of mammals.

  11. Okanagan Lake, British Columbia

    NASA Image and Video Library

    1994-10-01

    STS068-155-011 (30 September-11 October 1994) --- (Okanagan Lake, British Columbia) View southward down the lake; Vernon is in the foreground, Kelowna just before the bend in the lake, and Penticton at the far end of the lake. Green crops are still vigorous despite the season (early October); clear-cuts dot the forested hillsides.

  12. Rediscovery of lake balls in Lake Michigan

    USGS Publications Warehouse

    Schloesser, Donald W.; Hiltunen, Jarl K.; Owens, Randall W.

    1983-01-01

    For the first time in 70 years, the occurrence of a 'lake ball' in Lake Michigan is here reported in the literature. According to a published system of classification, the object we collected in 1978 was a 'false' lake ball. Dissection revealed that it was colonized by 5 chironomid larvae and 162 oligochaetes. The species and numerical proportions of the oligochaetes indicated that it was formed in or near the mouth of a eutrophic tributary rather than in the open waters of Lake Michigan where it was found. Because of their mobility, false lake balls may be ecologically important, serving as natural vehicles for the dispersal of invertebrates.

  13. Partitional Classification: A Complement to Phylogeny.

    PubMed

    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.

  14. Haplotyping as perfect phylogeny: a direct approach.

    PubMed

    Bafna, Vineet; Gusfield, Dan; Lancia, Giuseppe; Yooseph, Shibu

    2003-01-01

    A full haplotype map of the human genome will prove extremely valuable as it will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A haplotype map project has been announced by NIH. The biological key to that project is the surprising fact that some human genomic DNA can be partitioned into long blocks where genetic recombination has been rare, leading to strikingly fewer distinct haplotypes in the population than previously expected (Helmuth, 2001; Daly et al., 2001; Stephens et al., 2001; Friss et al., 2001). In this paper we explore the algorithmic implications of the no-recombination in long blocks observation, for the problem of inferring haplotypes in populations. This assumption, together with the standard population-genetic assumption of infinite sites, motivates a model of haplotype evolution where the haplotypes in a population are assumed to evolve along a coalescent, which as a rooted tree is a perfect phylogeny. We consider the following algorithmic problem, called the perfect phylogeny haplotyping problem (PPH), which was introduced by Gusfield (2002) - given n genotypes of length m each, does there exist a set of at most 2n haplotypes such that each genotype is generated by a pair of haplotypes from this set, and such that this set can be derived on a perfect phylogeny? The approach taken by Gusfield (2002) to solve this problem reduces it to established, deep results and algorithms from matroid and graph theory. Although that reduction is quite simple and the resulting algorithm nearly optimal in speed, taken as a whole that approach is quite involved, and in particular, challenging to program. Moreover, anyone wishing to fully establish, by reading existing literature, the correctness of the entire algorithm would need to read several deep and difficult papers in graph and matroid theory. However, as stated by Gusfield (2002), many simplifications are possible and the

  15. 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

  16. Future of phylogeny in HIV prevention.

    PubMed

    Brenner, Bluma G; Wainberg, Mark A

    2013-07-01

    The success of the HIV Prevention Trials Network 052 trial has led to revisions in HIV-1 treatment guidelines. Antiretroviral therapy may reduce the risk of HIV-1 transmissions at the population level. The design of successful treatment as prevention interventions will be predicated on a comprehensive understanding of the spatial, temporal, and biological dynamics of heterosexual men who have sex with men and intravenous drug user epidemics. Viral phylogenetics can capture the underlying structure of transmission networks based on the genetic interrelatedness of viral sequences and cluster networks that could not be otherwise identified. This article describes the phylogenetic expansion of the Montreal men who have sex with men epidemic over the last decade. High rates of coclustering of primary infections are associated with 1 infection leading to 13 onward transmissions. Phylogeny substantiates the role of primary and recent stage infection in transmission dynamics, underlying the importance of timely diagnosis and immediate antiretroviral therapy initiation to avert transmission cascades.

  17. Metazoan phylogeny and the Cambrian radiation.

    PubMed

    Erwin, D H

    1991-04-01

    Sequence analysis of small-subunit ribosomal RNA (18S rRNA) has provided important new pieces for the great puzzle of metazoan phylogeny and has generated new perspectives on the Precambrian-Cambrian fossil record of the metazoan radiation. While the puzzle is far from resolved and the early results are plagued by difficulties in data analysis, intriguing insights have appeared. Early results suggest that molluscs and lophophorates are protostomes, and that deuterostomes may be derived from protostomes. More speculatively, annelids and molluscs may be derived from arthropods or an arthropod ancestor. The molecular evidence further strengthens paleontological arguments for an explosive metazoan radiation near the Vendian-Cambrian boundary, rather than a lengthy, but hidden, period of Precambrian diversification. Copyright © 1991. Published by Elsevier Ltd.

  18. Molecular epidemiology, phylogeny and evolution of dermatophytes.

    PubMed

    Cafarchia, Claudia; Iatta, Roberta; Latrofa, Maria Stefania; Gräser, Yvonne; Otranto, Domenico

    2013-12-01

    Dermatophytes are fungi that invade and propagate in the keratinized skin of mammals, including humans, often causing contagious infections. The species of medical concern belong to the genera Microsporum, Trichophyton, Epidermophyton (in their anamorphic state) and Arthroderma (in their telomorphic state), which were traditionally identified based on their morphology and biochemical characters. Nonetheless, limitations linked to the differentiation of closely related agents at species and strains level have been recently overcome by molecular studies. Indeed, an accurate identification of dermatophytes is pivotal for the establishment of effective control and prevention programs as well as for determining the most appropriate and effective antifungal therapies to be applied. This article reviews the DNA techniques and the molecular markers used to identify and to characterize dermatophyte species, as well as aspects of their phylogeny and evolution. The applications of typing molecular strain to both basic and applied research (e.g., taxonomy, ecology, typing of infection, antifungal susceptibility) have also been discussed.

  19. Coloration mechanisms and phylogeny of Morpho butterflies.

    PubMed

    Giraldo, M A; Yoshioka, S; Liu, C; Stavenga, D G

    2016-12-15

    Morpho butterflies are universally admired for their iridescent blue coloration, which is due to nanostructured wing scales. We performed a comparative study on the coloration of 16 Morpho species, investigating the morphological, spectral and spatial scattering properties of the differently organized wing scales. In numerous previous studies, the bright blue Morpho coloration has been fully attributed to the multi-layered ridges of the cover scales' upper laminae, but we found that the lower laminae of the cover and ground scales play an important additional role, by acting as optical thin film reflectors. We conclude that Morpho coloration is a subtle combination of overlapping pigmented and/or unpigmented scales, multilayer systems, optical thin films and sometimes undulated scale surfaces. Based on the scales' architecture and their organization, five main groups can be distinguished within the genus Morpho, largely agreeing with the accepted phylogeny.

  20. 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

  1. Lake Chad, Chad, Africa

    NASA Image and Video Library

    1990-04-29

    Africa's Lake Chad where the borders of Chad, Niger, Nigeria and Cameroon merge (13.0N, 14.0E) has been undergoing change for the past 25 to 30 years when it was first noticed that the lake is drying up. Since then, astronauts have been photographing it on a regular basis to record the diminishing lake bed. This lake was once the aproximate size of Lake Erie but is now only about half that size and is still receeding.

  2. Reconstructing contact network parameters from viral phylogenies.

    PubMed

    McCloskey, Rosemary M; Liang, Richard H; Poon, Art F Y

    2016-07-01

    Models of the spread of disease in a population often make the simplifying assumption that the population is homogeneously mixed, or is divided into homogeneously mixed compartments. However, human populations have complex structures formed by social contacts, which can have a significant influence on the rate of epidemic spread. Contact network models capture this structure by explicitly representing each contact which could possibly lead to a transmission. We developed a method based on approximate Bayesian computation (ABC), a likelihood-free inference strategy, for estimating structural parameters of the contact network underlying an observed viral phylogeny. The method combines adaptive sequential Monte Carlo for ABC, Gillespie simulation for propagating epidemics though networks, and a kernel-based tree similarity score. We used the method to fit the Barabási-Albert network model to simulated transmission trees, and also applied it to viral phylogenies estimated from ten published HIV sequence datasets. This model incorporates a feature called preferential attachment (PA), whereby individuals with more existing contacts accumulate new contacts at a higher rate. On simulated data, we found that the strength of PA and the number of infected nodes in the network can often be accurately estimated. On the other hand, the mean degree of the network, as well as the total number of nodes, was not estimable with ABC. We observed sub-linear PA power in all datasets, as well as higher PA power in networks of injection drug users. These results underscore the importance of considering contact structures when performing phylodynamic inference. Our method offers the potential to quantitatively investigate the contact network structure underlying viral epidemics.

  3. 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.

  4. 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.

  5. Evolution, phylogeny, and molecular epidemiology of Chlamydia.

    PubMed

    Nunes, Alexandra; Gomes, João P

    2014-04-01

    The Chlamydiaceae are a family of obligate intracellular bacteria characterized by a unique biphasic developmental cycle. It encompasses the single genus Chlamydia, which involves nine species that affect a wide range of vertebral hosts, causing infections with serious impact on human health (mainly due to Chlamydia trachomatis infections) and on farming and veterinary industries. It is believed that Chlamydiales originated ∼700mya, whereas C. trachomatis likely split from the other Chlamydiaceae during the last 6mya. This corresponds to the emergence of modern human lineages, with the first descriptions of chlamydial infections as ancient as four millennia. Chlamydiaceae have undergone a massive genome reduction, on behalf of the deletional bias "use it or lose it", stabilizing at 1-1.2Mb and keeping a striking genome synteny. Their phylogeny reveals species segregation according to biological properties, with huge differences in terms of host range, tissue tropism, and disease outcomes. Genome differences rely on the occurrence of mutations in the >700 orthologous genes, as well as on events of recombination, gene loss, inversion, and paralogous expansion, affecting both a hypervariable region named the plasticity zone, and genes essentially encoding polymorphic and transmembrane head membrane proteins, type III secretion effectors and some metabolic pathways. Procedures for molecular typing are still not consensual but have allowed the knowledge of molecular epidemiology patterns for some species as well as the identification of outbreaks and emergence of successful clones for C. trachomatis. This manuscript intends to provide a comprehensive review on the evolution, phylogeny, and molecular epidemiology of Chlamydia. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. 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. © 2014 The Author(s). Evolution © 2014 The Society for the Study of

  7. Reconstructing contact network parameters from viral phylogenies

    PubMed Central

    McCloskey, Rosemary M.; Liang, Richard H.; Poon, Art F.Y.

    2016-01-01

    Models of the spread of disease in a population often make the simplifying assumption that the population is homogeneously mixed, or is divided into homogeneously mixed compartments. However, human populations have complex structures formed by social contacts, which can have a significant influence on the rate of epidemic spread. Contact network models capture this structure by explicitly representing each contact which could possibly lead to a transmission. We developed a method based on approximate Bayesian computation (ABC), a likelihood-free inference strategy, for estimating structural parameters of the contact network underlying an observed viral phylogeny. The method combines adaptive sequential Monte Carlo for ABC, Gillespie simulation for propagating epidemics though networks, and a kernel-based tree similarity score. We used the method to fit the Barabási-Albert network model to simulated transmission trees, and also applied it to viral phylogenies estimated from ten published HIV sequence datasets. This model incorporates a feature called preferential attachment (PA), whereby individuals with more existing contacts accumulate new contacts at a higher rate. On simulated data, we found that the strength of PA and the number of infected nodes in the network can often be accurately estimated. On the other hand, the mean degree of the network, as well as the total number of nodes, was not estimable with ABC. We observed sub-linear PA power in all datasets, as well as higher PA power in networks of injection drug users. These results underscore the importance of considering contact structures when performing phylodynamic inference. Our method offers the potential to quantitatively investigate the contact network structure underlying viral epidemics. PMID:27818787

  8. Molecular phylogeny of extant Holothuroidea (Echinodermata).

    PubMed

    Miller, Allison K; Kerr, Alexander M; Paulay, Gustav; Reich, Mike; Wilson, Nerida G; Carvajal, Jose I; Rouse, Greg W

    2017-06-01

    Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown

  9. Inferring Phylogenies from RAD Sequence Data

    PubMed Central

    Rubin, Benjamin E. R.; Ree, Richard H.; Moreau, Corrie S.

    2012-01-01

    Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD) to sequence restriction-site associated DNA (RAD) – the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts) and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct “known” phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for “total evidence” phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively). RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in which

  10. Inferring phylogenies from RAD sequence data.

    PubMed

    Rubin, Benjamin E R; Ree, Richard H; Moreau, Corrie S

    2012-01-01

    Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD) to sequence restriction-site associated DNA (RAD)--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts) and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct "known" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for "total evidence" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively). RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in which sufficient

  11. [Constancy check of system linearity for dose calibrators. Effect of molybdenum impurities at high start activities of 99mTc].

    PubMed

    Schütze, Christian; Knoop, Bernd O; Vehrenkamp, Iris; Rudolf, Frank; Geworski, Lilli

    2016-08-05

    Dose calibrators are one of the most important and most frequently used instruments for the determination of activities in nuclear medicine. For guaranteeing a constant quality of the dose calibrators' measurements, constancy checks including the examination of the system linearity have to be performed regularly, usually measured using 99mTc. The 99mTc eluate extracted from a 99Mo/99mTc generator is contaminated with molybdenum. Not accounting for the molybdenum impurity might lead to an exceed of the tolerance limit of 5% deviation to the reference value for this constancy check. The reason for this effect is the contamination of the 99mTc eluate with 99Mo, whose impact depends on both the amount of the impurity and on the total measurement time (high start activities). In this work, the influence of the molybdenum impurity on the results of the constancy check of the system linearity was investigated and maximum start activities for certain impurities were determined providing that the deviation to the reference values is below 5%. Provided that certain boundary conditions are observed, a correction of the results with respect to the molybdenum contamination is not necessary.

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

    USDA-ARS?s Scientific Manuscript database

    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) ...

  13. 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.

  14. [The opening of the French national health database: Opportunities and difficulties. The experience of the Gazel and Constances cohorts].

    PubMed

    Goldberg, M; Carton, M; Gourmelen, J; Genreau, M; Montourcy, M; Le Got, S; Zins, M

    2016-09-01

    In France, the national health database (SNIIRAM) is an administrative health database that collects data on hospitalizations and healthcare consumption for more than 60 million people. Although it does not record behavioral and environmental data, these data have a major interest for epidemiology, surveillance and public health. One of the most interesting uses of SNIIRAM is its linkage with surveys collecting data directly from persons. Access to the SNIIRAM data is currently relatively limited, but in the near future changes in regulations will largely facilitate open access. However, it is a huge and complex database and there are some important methodological and technical difficulties for using it due to its volume and architecture. We are developing tools for facilitating the linkage of the Gazel and Constances cohorts to the SNIIRAM: interactive documentation on the SNIIRAM database, software for the verification of the completeness and validity of the data received from the SNIIRAM, methods for constructing indicators from the raw data in order to flag the presence of certain events (specific diagnosis, procedure, drug…), standard queries for producing a set of variables on a specific area (drugs, diagnoses during a hospital stay…). Moreover, the REDSIAM network recently set up aims to develop, evaluate and make available algorithms to identify pathologies in SNIIRAM. In order to fully benefit from the exceptional potential of the SNIIRAM database, it is essential to develop tools to facilitate its use. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  15. Colour identification and colour constancy are impaired in a patient with incomplete achromatopsia associated with prestriate cortical lesions.

    PubMed

    Kennard, C; Lawden, M; Morland, A B; Ruddock, K H

    1995-05-22

    We have examined visual functions, including colour vision, in a patient with bilateral cortical lesions involving mainly the fusiform and lingual gyri, areas known to be involved in the central processing of chromatic stimuli. The patient has near normal (6/9) acuity, and his responses to tests of binocular function and spatial vision are normal, as are his discrimination of changes in target speed and surface lightness. He does, however, exhibit minor losses in the upper visual field, mild prosopagnosia and topographical agnosia, all conditions commonly associated with cerebral achromatopsia. Colour matches and spectral response data establish that his cone photoreceptors have normal spectral characteristics and his spectral sensitivity measured against a white background reveals normal postreceptoral chromatic function. The patient's colour discrimination for differences in wavelength, hue or saturation is, however, impaired and his colour naming is significantly disturbed, particularly for blues and greens. We have determined the areas of the chromaticity chart that correspond to his naming categories for surface colours, and show that changes in illuminant cause him to alter the names of surface colours in a manner consistent with the changes in their chromaticities. Other subjects with normal or congenital red-green deficient colour vision make many fewer name changes under changes in illuminant. We conclude that the patient's colour constancy is impaired as a consequence of abnormal central processing of colour vision.

  16. 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).

  17. ION KINETIC ENERGY CONSERVATION AND MAGNETIC FIELD STRENGTH CONSTANCY IN MULTI-FLUID SOLAR WIND ALFVÉNIC TURBULENCE

    SciTech Connect

    Matteini, L.; Horbury, T. S.; Schwartz, S. J.; Pantellini, F.; Velli, M.

    2015-03-20

    We investigate the properties of plasma fluid motion in the large-amplitude, low-frequency fluctuations of highly Alfvénic fast solar wind. We show that protons locally conserve total kinetic energy when observed from an effective frame of reference comoving with the fluctuations. For typical properties of the fast wind, this frame can be reasonably identified by alpha particles which, due to their drift with respect to protons at about the Alfvén speed along the magnetic field, do not partake in the fluid low-frequency fluctuations. Using their velocity to transform the proton velocity into the frame of Alfvénic turbulence, we demonstrate that the resulting plasma motion is characterized by a constant absolute value of the velocity, zero electric fields, and aligned velocity and magnetic field vectors as expected for unidirectional Alfvénic fluctuations in equilibrium. We propose that this constraint, via the correlation between velocity and magnetic field in Alfvénic turbulence, is the origin of the observed constancy of the magnetic field; while the constant velocity corresponding to constant energy can only be observed in the frame of the fluctuations, the corresponding constant total magnetic field, invariant for Galilean transformations, remains the observational signature in the spacecraft frame of the constant total energy in the Alfvén turbulence frame.

  18. 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.

  19. Phylogeny and Species Diversity of Gulf of California Oysters

    EPA Pesticide Factsheets

    Dataset of DNA sequence data from two mitochondrial loci (COI and 16S) used to infer the phylogeny of oysters in the genus Ostrea along the Pacific coast of North America.This dataset is associated with the following publication:Raith, M., D. Zacherl, E. Pilgrim , and D. Eernisse. Phylogeny and species diversity of Gulf of California oysters (Ostreidae) inferred from mitochondrial DNA. American Malacological Bulletin. American Malacological Society, Arlington, VA, USA, 33(2): 263-283, (2016).

  20. Inferring the origin of metastases from cancer phylogenies

    PubMed Central

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

    2015-01-01

    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

  1. 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. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. 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

  3. Phylogeny of suckermouth catfishes (Mochokidae: Chiloglanis) from Kenya: the utility of Growth Hormone introns in species level phylogenies.

    PubMed

    Schmidt, Ray C; Bart, Henry L; Nyingi, Dorothy Wanja; Gichuki, Nathan Ndegwa

    2014-10-01

    African suckermouth catfishes (Mochokidae: Chiloglanis) occur in freshwater throughout tropical Africa. Specimens from all major drainages across Kenya were collected over three field seasons. Here we present a phylogeny inferred from both mitochondrial cytochrome b (cyt b) and introns of the nuclear Growth Hormone gene (GH). The phylogeny inferred from introns is largely congruent with the results from an analysis of cyt b. The length and variability of GH introns make them ideal species level nuclear markers without the problem of introgression commonly encountered with mitochondrial genes. This analysis confirmed the presence of two previously known undescribed Chiloglanis species and also suggests the presence of previously unknown diversity within the Athi River system. The resulting phylogeny also indicates the presence of two separate lineages within C. brevibarbis. The historical biogeography of Chiloglanis within Kenya is discussed. The utility of GH intron for species level phylogenies of Siluriformes is compared to that in other groups. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. A novel phylogenetic clade of picocyanobacteria from the Mazurian lakes (Poland) reflects the early ontogeny of glacial lakes.

    PubMed

    Jasser, Iwona; Królicka, Adriana; Karnkowska-Ishikawa, Anna

    2011-01-01

    The community of picocyanobacteria inhabiting the Great Mazurian Lakes system (comprising lakes ranging from mesotrophic to hypertrophic) is dominated by phycoerythrin-rich cells, which outnumber phycocyanin-rich cells, even in hypertrophic lakes. The genetic diversity and phylogeny of 43 strains of picocyanobacteria isolated from four Mazurian lakes were studied by analyzing the nucleotide sequences of the 16S rRNA gene and cpcBA-IGS operon. Phylogenetic analyses assigned some of the strains to several previously described clusters (Groups A, B, C, E and I) and revealed the existence of a novel clade, Group M (Mazurian), which exhibited a low level of similarity to the other clusters. Both phycocyanin and phycoerythrin picocyanobacteria were assigned to this clade based on an analysis of the 16S rRNA gene. The cpcBA sequence analysis assigned only phycocyanin strains to Group M, whereas the phycoerythrin strains from the M ribogroup were assigned to Groups B and E. We hypothesize that Group M originally contained only phycocyanin picocyanobacteria. The phycoerythrin found in strains belonging to ribogroup M seems to have been acquired through horizontal gene transfer as an adaptation to the changing environment early in the ontogeny of these glacial lakes.

  5. Multiple colonisations of the Lake Malawi catchment by the genus Opsaridium (Teleostei: Cyprinidae).

    PubMed

    Sungani, Harold; Ngatunga, Benjamin P; Koblmüller, Stephan; Mäkinen, Tuuli; Skelton, Paul H; Genner, Martin J

    2017-02-01

    It has been proposed that the fish faunas of African rivers assemble through multiple colonisation events, while lake faunas form additionally through intralacustine speciation. While this pattern has been established for many lineages, most notably cichlids, there are opportunities to further investigate the concept using phylogenies of congeneric endemic species within ancient lake catchments. The Lake Malawi catchment contains three river-spawning cyprinids of the genus Opsaridium, two of which are endemic. These species differ in body size, migratory behaviour and habitat use, but it has never previously been tested if these represent a monophyletic radiation, or have instead colonised the lake independently. We placed these species in a broader phylogeny of Opsaridium and the related genus Raiamas, including all known species from the river systems surrounding Lake Malawi. Our results suggest that each of the species has independently colonised the lake catchment, with all three taxa having well-defined sister taxa outside of the lake, and all sharing a common ancestor ∼14.9million years ago, before the Lake Malawi basin started to form ∼8.6million years ago. Additionally, the results strongly support previous observations that Opsaridium is not a monophyletic group, but instead contains Raiamas from the Congo drainage. Together these results are supportive of the concept that river fish faunas within African catchments are primarily assembled through a process of accumulation from independent origins, rather than within-catchment speciation and adaptive radiation. In light of these results we also suggest there is scope for a re-evaluation of systematics of both Opsaridium and Raiamas.

  6. Sedimentary DNA Reveals Cyanobacterial Community Diversity over 200 Years in Two Perialpine Lakes.

    PubMed

    Monchamp, Marie-Eve; Walser, Jean-Claude; Pomati, Francesco; Spaak, Piet

    2016-11-01

    We reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years of lake history in the perialpine lakes Greifensee and Lake Zurich (Switzerland). Community analysis based on amplification and sequencing of a 400-nucleotide (nt)-long 16S rRNA fragment specific to Cyanobacteria revealed operational taxonomic units (OTUs) capturing the whole phylum, including representatives of a newly characterized clade termed Melainabacteria, which shares common ancestry with Cyanobacteria and has not been previously described in lakes. The reconstruction of cyanobacterial richness and phylogenetic structure was validated using a data set consisting of 40 years of pelagic microscopic counts from each lake. We identified the OTUs assigned to common taxa known to be present in Greifensee and Lake Zurich and found a strong and significant relationship (adjusted R(2) = 0.89; P < 0.001) between pelagic species richness in water and OTU richness in the sediments. The water-sediment richness relationship varied between cyanobacterial orders, indicating that the richness of Chroococcales and Synechococcales may be underestimated by microscopy. PCR detection of the microcystin synthetase gene mcyA confirmed the presence of potentially toxic cyanobacterial taxa over recent years in Greifensee and throughout the last century in Lake Zurich. The approach presented in this study demonstrates that it is possible to reconstruct past pelagic cyanobacterial communities in lakes where the integrity of the sedimentary archive is well preserved and to explore changes in phylogenetic and functional diversity over decade-to-century timescales.

  7. 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

  8. ESTimating plant phylogeny: lessons from partitioning

    PubMed Central

    de la Torre, Jose EB; Egan, Mary G; Katari, Manpreet S; Brenner, Eric D; Stevenson, Dennis W; Coruzzi, Gloria M; DeSalle, Rob

    2006-01-01

    Background While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. Results A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. Conclusion Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In

  9. Molecular phylogeny of thorny catfishes (Siluriformes: Doradidae).

    PubMed

    Arce H, Mariangeles; Reis, Roberto E; Geneva, Anthony J; Sabaj Pérez, Mark H

    2013-06-01

    Doradidae is a monophyletic catfish family endemic to continental South America, and composed of 93 valid species here placed in 31 genera. Existing phylogenetic hypotheses for Doradidae are derived from comprehensive analyses of morphological data, and a single molecular-based study on a limited subset of taxa. To provide a robust molecular phylogeny commensurate with those based on morphology, we gathered original and published sequence data for 86 species-level taxa (at least 70 valid species plus 16 new or questionably nominal species) and all genera of Doradidae, as well as 10 species (nine genera) of Auchenipteridae and three species and genera of Aspredinidae as outgroups. 3011 base pairs were aligned for two mitochondrial genes (cytochrome c oxidase subunit 1, and 16S ribosomal RNA) and one nuclear gene (recombination activating gene 1), and analyzed for a total of 143 specimens (130 doradids, 10 auchenipterids and three aspredinids). Tree topologies generated by Maximum Parsimony, Maximum Likelihood, and Bayesian analyses were largely congruent, and are compared to existing phylogenies based on morphology and molecules. Although many of the relationships supported by our molecular analyses corroborated those based on morphology, others are newly hypothesized or remain in conflict. The monotypic Wertheimeria, Franciscodoras and Kalyptodoras, for example, form a newly proposed clade, and the subfamily Astrodoradinae is placed at the base of the doradid tree. The monotypic Doraops and Centrochir, endemic to Caribbean drainages north and west of the Andes, are sister to Pterodoras and Platydoras, respectively, two genera that are widely distributed in Atlantic drainages. Additional biogeographic implications are discussed for hypothesized relationships among doradids. Molecular evidence strongly supports synonymization of monotypic Merodoras with Amblydoras, and transfer of Amblydoras bolivarensis to genus Scorpiodoras. Furthermore, we consider Opsodoras

  10. 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

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

    PubMed

    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.

  12. Comparing chromosomal and mitochondrial phylogenies of the Indriidae (Primates, Lemuriformes).

    PubMed

    Rumpler, Yves; Hauwy, Marcel; Fausser, Jean-Luc; Roos, Christian; Zaramody, Alphonse; Andriaholinirina, Nicole; Zinner, Dietmar

    2011-02-01

    The Malagasy primate family Indriidae comprises three genera with up to 19 species. Cytogenetic and molecular phylogenies of the Indriidae have been performed with special attention to the genus Propithecus. Comparative R-banding and FISH with human paints were applied to karyotypes of representatives of all three genera and confirmed most of the earlier R-banding results. However, additional chromosomal rearrangements were detected. A reticulated and a cladistic phylogeny, the latter including hemiplasies, have been performed. Cladistic analysis of cytogenetic data resulted in a phylogenetic tree revealing (1) monophyly of the family Indriidae, (2) monophyly of the genus Avahi, (3) sister-group relationships between Propithecus diadema and Propithecus edwardsi, and (4) the grouping of the latter with Indri indri, Propithecus verreauxi, and Propithecus tattersalli, and thus suggesting paraphyly of the genus Propithecus. A molecular phylogeny based on complete mitochondrial cytochrome b sequences of 16 species indicated some identical relationships, such as the monophyly of Avahi and the sister-group relationships of the eastern (P. diadema and P. edwardsi) to the western Propithecus species (P. verreauxi, Propithecus coquereli, and P. tattersalli). However, the main difference between the molecular and cytogenetic phylogenies consists in an early divergence of Indri in the molecular phylogeny while in the chromosomal phylogeny it is nested within Propithecus. The similarities and differences between molecular and cytogenetic phylogenies in relation to data on the species' geographic distributions and mating systems allow us to propose a scenario of the evolution of Indriidae. Chromosomal and molecular processes alone or in combination created a reproductive barrier that was then followed by further speciation processes.

  13. Lake Huron LAMPs

    EPA Pesticide Factsheets

    The approach in Lake Huron differs from the Lakewide Management Plans of the other Great Lakes: no formal binational designation of lakewide beneficial use impairments, nor extensive lakewide modeling of chemical loadings

  14. Lake Tahoe Projects

    EPA Pesticide Factsheets

    Information on the Lake Tahoe watershed, EPA's protection efforts, water quality issues, effects of climate, change, Lake Tahoe Total Maximum Daily Load TMDL), EPA-sponsored projects, list of partner agencies.

  15. The Great Lakes

    EPA Pesticide Factsheets

    The Great Lakes form the largest surface freshwater system on Earth. The U.S. and Canada work together to restore and protect the environment in the Great Lakes Basin. Top issues include contaminated sediments, water quality and invasive species.

  16. Lakes on Titan

    NASA Image and Video Library

    2006-07-24

    The Cassini spacecraft, using its radar system, has discovered very strong evidence for hydrocarbon lakes on Titan. Dark patches, which resemble terrestrial lakes, seem to be sprinkled all over the high latitudes surrounding Titan north pole

  17. Looking Down on Lakes

    NASA Image and Video Library

    2014-04-07

    NASA Cassini spacecraft peers down though layers of haze to glimpse the lakes of Titan northern regions. Titan has a hydrological cycle similar to Earth, but instead of water, Titan lakes and seas are filled with liquid methane and ethane.

  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. National Lakes Assessment

    EPA Pesticide Factsheets

    The National Lakes Assessment is a collaborative, statistical survey of the nation's lakes. It is one of four national surveys that EPA and its partners conduct to assess the condition and health of the nation's water resources.

  20. About Lake Tahoe

    EPA Pesticide Factsheets

    Information on the Lake Tahoe watershed, EPA's protection efforts, water quality issues, effects of climate, change, Lake Tahoe Total Maximum Daily Load TMDL), EPA-sponsored projects, list of partner agencies.

  1. 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 ...

  2. Evolution of the ribosomal RNA internal transcribed spacer one (ITS-1) in cichlid fishes of the Lake Victoria region.

    PubMed

    Booton, G C; Kaufman, L; Chandler, M; Oguto-Ohwayo, R; Duan, W; Fuerst, P A

    1999-03-01

    The nucleotide sequences of the first internal transcribed spacer (ITS-1) of the ribosomal RNA gene cluster have been determined for 11 species of closely related endemic cichlid fishes of the Lake Victoria region (LVR) and 6 related East African cichlids. The ITS-1 sequences confirmed independently derived basal phylogenies, but provide limited insight within this species flock. The line leading to Pseudocrenilabrus multicolor arose early, close to the divergence event that separated the tilapiine and haplochromine tribes of the "African Group" of the family Cichlidae. In this phylogeny, Astatoreochromis alluaudi and the riverine Astatotilapia burtoni are sister taxa, which together are a sister group to a monophyletic assemblage including both Lake Victoria and Lake Edward taxa. The ITS-1 data support the monophyly of haplochromine genera across lakes. Since Lake Victoria is believed to have been dry between 14, 500 and 12,400 BPE, the modern assemblage must have been derived from reinvasion by the products of earlier cladogenesis events. Thus, although the regional superflock is monophyletic, the haplochromines of Lake Victoria itself did not evolve in situ from a single ancestor.

  3. 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

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

    PubMed

    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.

  5. Shape constancy and depth-order violations in structure from motion: A look at non-frontoparallel axes of rotation

    PubMed Central

    Fernandez, Julian M.; Farell, Bart

    2007-01-01

    Humans can recover the structure of a 3D object from motion cues alone. Recovery of structure from motion (SFM) from the projected 2D motion field of a rotating object has been studied almost exclusively in one particular condition, that in which the axis of rotation lies in the frontoparallel plane. Here, we assess the ability of humans to recover SFM in the general case, where the axis of rotation may be slanted out of the frontoparallel plane. Using elliptical cylinders whose cross section was constant along the axis of rotation, we find that, across a range of parameters, subjects accurately matched the simulated shape of the cylinder regardless of how much the axis of rotation is inclined away from the frontoparallel plane. Yet, we also find that subjects do not perceive the inclination of the axis of rotation veridically. This combination of results violates a relationship between perceived angle of inclination and perceived shape that must hold if SFM is to be recovered from the instantaneous velocity field. The contradiction can be resolved if the angular speed of rotation is not consistently estimated from the instantaneous velocity field. This, in turn, predicts that variation in object size along the axis of rotation can cause depth-order violations along the line of sight. This prediction was verified using rotating circular cones as stimuli. Thus, as the axis of rotation changes its inclination, shape constancy is maintained through a trade-off. Humans perceive the structure of the object relative to a changing axis of rotation as unchanging by introducing an inconsistency between the perceived speed of rotation and the first-order optic flow. The observed depth-order violations are the cost of the trade-off. PMID:17685799

  6. Constancy, Distribution, and Frequency of Lepidoptera Defoliators of Eucalyptus grandis and Eucalyptus urophylla (Myrtaceae) in Four Brazilian Regions.

    PubMed

    Ribeiro, G T; Zanuncio, J C; de S Tavares, W; de S Ramalho, F; Serrão, J E

    2016-12-01

    The growth of the Brazilian forest sector with monocultures favors the adaptation of Arthropoda pests. The Lepidoptera order includes major pests of Eucalyptus spp. (Myrtaceae). The aim of this work is to study the population constancy, distribution, and frequency of Lepidoptera primary pests of Eucalyptus spp. Lepidoptera pests in Eucalyptus spp. plantations were collected in Três Marias and Guanhães (state of Minas Gerais), Niquelândia (state of Goiás), and Monte Dourado (state of Pará), Brazil, for a period of 5 years, with light traps and captures, every 15 days, for every region. The number of primary pest species (12) has been similar in the four regions, and even with 1.5 to 2.4% of the total species collected, this group has shown a high frequency, especially in Três Marias, Niquelândia, and Monte Dourado, with 66.3, 54.2, and 40.0% of the individuals collected, respectively, for 5 years. The primary pest species have been constant and frequent in all the regions, with population peaks from February to September in Três Marias, February and May in Niquelândia, and from July to September in Monte Dourado. The highest population peaks of these species have been recorded when the Eucalyptus spp. plants are 3 to 6 years old. The Guanhães region is more stable and, therefore, has a lower possibility of outbreaks of the Lepidoptera primary pest species.

  7. 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.

  8. Phylogeny and diversification patterns among vesicomyid bivalves.

    PubMed

    Decker, Carole; Olu, Karine; Cunha, Regina L; Arnaud-Haond, Sophie

    2012-01-01

    Vesicomyid bivalves are among the most abundant and diverse symbiotic taxa in chemosynthetic-based ecosystems: more than 100 different vesicomyid species have been described so far. In the present study, we investigated the phylogenetic positioning of recently described vesicomyid species from the Gulf of Guinea and their western Atlantic and Pacific counterparts using mitochondrial DNA sequence data. The maximum-likelihood (ML) tree provided limited support for the recent taxonomic revision of vesicomyids based on morphological criteria; nevertheless, most of the newly sequenced specimens did not cluster with their morphological conspecifics. Moreover, the observed lack of geographic clustering suggests the occurrence of independent radiations followed by worldwide dispersal. Ancestral character state reconstruction showed a significant correlation between the characters "depth" and "habitat" and the reconstructed ML phylogeny suggesting possible recurrent events of 'stepwise speciation' from shallow to deep waters in different ocean basins. This is consistent with genus or species bathymetric segregation observed from recent taxonomic studies. Altogether, our results highlight the need for ongoing re-evaluation of the morphological characters used to identify vesicomyid bivalves.

  9. 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

  10. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. 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.

  12. 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. © 2015 The Author(s) Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

  13. Multigene phylogeny resolves deep branching of Amoebozoa.

    PubMed

    Cavalier-Smith, Thomas; Fiore-Donno, Anna Maria; Chao, Ema; Kudryavtsev, Alexander; Berney, Cédric; Snell, Elizabeth A; Lewis, Rhodri

    2015-02-01

    Amoebozoa is a key phylum for eukaryote phylogeny and evolutionary history, but its phylogenetic validity has been questioned since included species are very diverse: amoebo-flagellate slime-moulds, naked and testate amoebae, and some flagellates. 18S rRNA gene trees have not firmly established its internal topology. To rectify this we sequenced cDNA libraries for seven diverse Amoebozoa and conducted phylogenetic analyses for 109 eukaryotes (17-18 Amoebozoa) using 60-188 genes. We conducted Bayesian inferences with the evolutionarily most realistic site-heterogeneous CAT-GTR-Γ model and maximum likelihood analyses. These unequivocally establish the monophyly of Amoebozoa, showing a primary dichotomy between the previously contested subphyla Lobosa and Conosa. Lobosa, the entirely non-flagellate lobose amoebae, are robustly partitioned into the monophyletic classes Tubulinea, with predominantly tube-shaped pseudopodia, and Discosea with flattened cells and different locomotion. Within Conosa 60/70-gene trees with very little missing data show a primary dichotomy between the aerobic infraphylum Semiconosia (Mycetozoa and Variosea) and secondarily anaerobic Archamoebae. These phylogenetic features are entirely congruent with the most recent major amoebozoan classification emphasising locomotion modes, pseudopodial morphology, and ultrastructure. However, 188-gene trees where proportionally more taxa have sparser gene-representation weakly place Archamoebae as sister to Macromycetozoa instead, possibly a tree reconstruction artefact of differentially missing data.

  14. Higher classification and phylogeny of Euglenozoa.

    PubMed

    Cavalier-Smith, Thomas

    2016-10-01

    Discoveries of numerous new taxa and advances in ultrastructure and sequence phylogeny (including here the first site-heterogeneous 18S rDNA trees) require major improvements to euglenozoan higher-level taxonomy. I therefore divide Euglenozoa into three subphyla of substantially different body plans: Euglenoida with pellicular strips; anaerobic Postgaardia (class Postgaardea) dependent on surface bacteria and with uniquely modified feeding apparatuses; and new subphylum Glycomonada characterised by glycosomes (Kinetoplastea, Diplonemea). Euglenoida comprise two new infraphyla: Entosiphona with three feeding rods and Dipilida ancestrally with two. Dipilida comprise basal superclass Rigimonada with longitudinal rigid strips [i.e. new classes Stavomonadea (Petalomonadida, Decastavida and new order Heterostavida) and Ploeotarea (Ploeotiida) with contrasting oral cytoskeletons] and derived superclass Spirocuta with more numerous spirally arranged, often slideable, strips (clade Peranemea/Euglenophyceae) and a different, highly conserved microtubule pattern at strip joints. Peranemea comprise four orders: Peranemida (anterior gliding, protrusible rods), and three new, Anisonemida (posterior gliders), Natomonadida (swimmers including phagotrophic new suborder Metanemina and osmotrophic suborder Rhabdomonadina), and Acroglissida (anterior gliders with cytoproct). I establish orders Entosiphonida, Rapazida, Bihospitida; and seven new euglenoid families (Entosiphonidae, peranemean Neometanemidae, Rapazidae, two stavomonad, two ploeotiid) and three new postgaardian, and three kinetoplastid families (Neobodonidae, Rhynchomonadidae, Parabodonidae), plus new diplonemid family Hemistasiidae for Hemistasia.

  15. 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

  16. Phylogeny and Diversification Patterns among Vesicomyid Bivalves

    PubMed Central

    Decker, Carole; Olu, Karine; Cunha, Regina L.; Arnaud-Haond, Sophie

    2012-01-01

    Vesicomyid bivalves are among the most abundant and diverse symbiotic taxa in chemosynthetic-based ecosystems: more than 100 different vesicomyid species have been described so far. In the present study, we investigated the phylogenetic positioning of recently described vesicomyid species from the Gulf of Guinea and their western Atlantic and Pacific counterparts using mitochondrial DNA sequence data. The maximum-likelihood (ML) tree provided limited support for the recent taxonomic revision of vesicomyids based on morphological criteria; nevertheless, most of the newly sequenced specimens did not cluster with their morphological conspecifics. Moreover, the observed lack of geographic clustering suggests the occurrence of independent radiations followed by worldwide dispersal. Ancestral character state reconstruction showed a significant correlation between the characters “depth” and “habitat” and the reconstructed ML phylogeny suggesting possible recurrent events of ‘stepwise speciation’ from shallow to deep waters in different ocean basins. This is consistent with genus or species bathymetric segregation observed from recent taxonomic studies. Altogether, our results highlight the need for ongoing re-evaluation of the morphological characters used to identify vesicomyid bivalves. PMID:22511920

  17. Bacterial phylogeny structures soil resistomes across habitats.

    PubMed

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

    2014-05-29

    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.

  18. A mitogenomic phylogeny of living primates.

    PubMed

    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.

  19. Babesia ovata: Taxonomy, phylogeny and epidemiology.

    PubMed

    Sivakumar, Thillaiampalam; Igarashi, Ikuo; Yokoyama, Naoaki

    2016-10-15

    Babesia ovata, which is transmitted by Haemaphysalis longicornis, is an intraerythrocytic protozoan parasite of cattle. Based on its morphology, B. ovata is classified as a large-type Babesia. The developmental stages of B. ovata have been described both in cattle and the tick vector. In infected adult female ticks, the parasite is transovarially transmitted to the tick eggs. The sexual reproduction of B. ovata has been demonstrated in the tick midgut. The diagnostic tools that are currently available for the specific detection of B. ovata in cattle include microscopy and polymerase chain reaction assays. The development of improved molecular and serological diagnostic tools has been constrained by the limited availability of genetic data. B. ovata has been reported in cattle populations in Japan, Korea, China, Mongolia and Thailand. B. ovata was thought to be a benign parasite; however, infections in immuno compromised or Theileria orientalis-infected animals are clinically significant. Thus, control strategies aimed at minimizing the prevalence of B. ovata are vital. The taxonomy of B. ovata is unclear, and the phylogenetic position has not been well defined. Consequently, non-B. ovata species have sometimes been classified as B. ovata. In this review, we provide an outline of the lifecycle, geographical distribution, and control of B. ovata, and critically discuss the taxonomy and phylogeny of this bovine Babesia. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. 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

  1. 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.

  2. Ontogenetic Data Analyzed As Such in Phylogenies.

    PubMed

    Bardin, Jérémie; Rouget, Isabelle; Cecca, Fabrizio

    2016-06-16

    Ontogeny is rarely included in phylogenetic analyses of morphological data. When used, the ontogenetic information is reduced to one character for two or three different ontogenetic stages. Several examples show that current methods miss a major part of the information. We here propose a new method for including the ontogenetic dimension in coding schemes of phylogenetic analyses. Our goal was to maximize the phylogenetic information extracted from ontogenetic trajectories. For discrete features, we recommend including precise timings of transformation(s) from one state to another in the ontogenetic trajectories. For continuously varying features, growth laws are modeled on raw data using least-square regressions. Then, parameters of models are included in the coding scheme as continuous characters. This method is employed to reconstruct phylogenetic relationships using the ammonite family Amaltheidae as a test subject. Based on the same data set, a second analysis has been performed only for characters of the adult stage. Comparisons of retention index, bootstrap support, and stratigraphic congruence between the two analyses show that the inclusion of ontogeny yields better phylogenetic reconstruction. Morphological traits in ammonites which are usually the most homoplastic show a better fit to most parsimonious trees by including the ontogenetic dimension. In several cases, growth rates and patterns of growth have better fit to phylogeny than adult shapes, implying that paths of ontogeny can be more relevant than its products.

  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. 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.…

  6. 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…

  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. 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)

  9. 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.…

  10. Great Lakes in January

    NASA Image and Video Library

    2017-09-28

    This image taken on January 13, 2015 from the Suomi NPP satellite's VIIRS instrument shows the Great Lakes and surrounding areas. The latest Great Lakes Surface Environmental Analysis (GLSEA) from the NOAA Great Lakes Environmental Research Laboratory shows total ice cover of 29.3% as of January 13th. Credit: NOAA/NASA/NPP Via NOAA Environmental Visualization Laboratory

  11. 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)

  12. 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…

  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. 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.

  15. When integration fails: Prokaryote phylogeny and the tree of life.

    PubMed

    O'Malley, Maureen A

    2013-12-01

    Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today's literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history (often called 'universal phylogeny'). Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a 'meta-heuristic' in the normative commitments guiding scientific practice. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. Trees of trees: an approach to comparing multiple alternative phylogenies.

    PubMed

    Nye, Tom M W

    2008-10-01

    Phylogenetic analysis very commonly produces several alternative trees for a given fixed set of taxa. For example, different sets of orthologous genes may be analyzed, or the analysis may sample from a distribution of probable trees. This article describes an approach to comparing and visualizing multiple alternative phylogenies via the idea of a "tree of trees" or "meta-tree." A meta-tree clusters phylogenies with similar topologies together in the same way that a phylogeny clusters species with similar DNA sequences. Leaf nodes on a meta-tree correspond to the original set of phylogenies given by some analysis, whereas interior nodes correspond to certain consensus topologies. The construction of meta-trees is motivated by analogy with construction of a most parsimonious tree for DNA data, but instead of using DNA letters, in a meta-tree the characters are partitions or splits of the set of taxa. An efficient algorithm for meta-tree construction is described that makes use of a known relationship between the majority consensus and parsimony in terms of gain and loss of splits. To illustrate these ideas meta-trees are constructed for two datasets: a set of gene trees for species of yeast and trees from a bootstrap analysis of a set of gene trees in ray-finned fish. A software tool for constructing meta-trees and comparing alternative phylogenies is available online, and the source code can be obtained from the author.

  17. Stream, Lake, and Reservoir Management.

    PubMed

    Dai, Jingjing; Mei, Ying; Chang, Chein-Chi

    2017-10-01

    This review on stream, lake, and reservoir management covers selected 2016 publications on the focus of the following sections: Stream, lake, and reservoir management • Water quality of stream, lake, and reservoir • Reservoir operations • Models of stream, lake, and reservoir • Remediation and restoration of stream, lake, and reservoir • Biota of stream, lake, and reservoir • Climate effect of stream, lake, and reservoir.

  18. Time-calibrated molecular phylogeny of pteropods.

    PubMed

    Burridge, Alice K; Hörnlein, Christine; Janssen, Arie W; Hughes, Martin; Bush, Stephanie L; Marlétaz, Ferdinand; Gasca, Rebeca; Pierrot-Bults, Annelies C; Michel, Ellinor; Todd, Jonathan A; Young, Jeremy R; Osborn, Karen J; Menken, Steph B J; Peijnenburg, Katja T C A

    2017-01-01

    Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and examine the evolutionary history of pteropods based on combined analyses of Cytochrome Oxidase I, 28S, and 18S ribosomal rRNA sequences and a molecular clock calibrated using fossils and the estimated timing of the formation of the Isthmus of Panama. Euthecosomes with uncoiled shells were monophyletic with Creseis as the earliest diverging lineage, estimated at 41-38 million years ago (mya). The coiled euthecosomes (Limacina, Heliconoides, Thielea) were not monophyletic contrary to the accepted morphology-based taxonomy; however, due to their high rate heterogeneity no firm conclusions can be drawn. We found strong support for monophyly of most euthecosome genera, but Clio appeared as a polyphyletic group, and Diacavolinia grouped within Cavolinia, making the latter genus paraphyletic. The highest evolutionary rates were observed in Heliconoides inflatus and Limacina bulimoides for both 28S and 18S partitions. Using a fossil-calibrated phylogeny that sets the first occurrence of coiled euthecosomes at 79-66 mya, we estimate that uncoiled euthecosomes evolved 51-42 mya and that most extant uncoiled genera originated 40-15 mya. These findings are congruent with a molecular clock analysis using the Isthmus of Panama formation as an independent calibration. Although not all phylogenetic relationships could be resolved based on three molecular markers, this study provides a useful resource to study pteropod diversity and provides general insight into the

  19. Time-calibrated molecular phylogeny of pteropods

    PubMed Central

    Hörnlein, Christine; Janssen, Arie W.; Hughes, Martin; Bush, Stephanie L.; Marlétaz, Ferdinand; Gasca, Rebeca; Pierrot-Bults, Annelies C.; Michel, Ellinor; Todd, Jonathan A.; Young, Jeremy R.; Osborn, Karen J.; Menken, Steph B. J.

    2017-01-01

    Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and examine the evolutionary history of pteropods based on combined analyses of Cytochrome Oxidase I, 28S, and 18S ribosomal rRNA sequences and a molecular clock calibrated using fossils and the estimated timing of the formation of the Isthmus of Panama. Euthecosomes with uncoiled shells were monophyletic with Creseis as the earliest diverging lineage, estimated at 41–38 million years ago (mya). The coiled euthecosomes (Limacina, Heliconoides, Thielea) were not monophyletic contrary to the accepted morphology-based taxonomy; however, due to their high rate heterogeneity no firm conclusions can be drawn. We found strong support for monophyly of most euthecosome genera, but Clio appeared as a polyphyletic group, and Diacavolinia grouped within Cavolinia, making the latter genus paraphyletic. The highest evolutionary rates were observed in Heliconoides inflatus and Limacina bulimoides for both 28S and 18S partitions. Using a fossil-calibrated phylogeny that sets the first occurrence of coiled euthecosomes at 79–66 mya, we estimate that uncoiled euthecosomes evolved 51–42 mya and that most extant uncoiled genera originated 40–15 mya. These findings are congruent with a molecular clock analysis using the Isthmus of Panama formation as an independent calibration. Although not all phylogenetic relationships could be resolved based on three molecular markers, this study provides a useful resource to study pteropod diversity and provides general insight

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Phylogeny of a neural cell adhesion molecule.

    PubMed

    Hall, A K; Rutishauser, U

    1985-07-01

    The phylogeny of adhesion among cells derived from neural tissue has been examined using a combination of functional and immunological analyses. The presence of the neural cell adhesion molecule (NCAM) was evaluated with respect to NCAM-specific antigenic determinants attached to a polypeptide chain with appropriate electrophoretic properties. By these criteria, NCAM-like molecules were detected in all embryonic and adult vertebrates tested, and an adult mollusc, but not in an adult insect, crustacean, or nematode. The functional assays measured adhesiveness by simple aggregation of neural membrane vesicles, as well as by NCAM-specific binding between membranes from different species. The presence of the NCAM antigen in vertebrate membranes correlated with binding activity in both the NCAM-specific and general adhesion assays, implying that the adhesiveness of these membranes largely reflects NCAM-mediated binding. The results also indicate that NCAM function has been conserved during the evolution of vertebrates, and supports the possibility that mechanisms of nerve-nerve, nerve-muscle, and nerve-glial interaction, which have been demonstrated previously to involve NCAM, may be similar for many chordates. Whereas NCAM was not detected in adult fly and worm, these species did express NCAM-like antigens transiently during early development. These results are consistent with the hypothesis that NCAM is required during several periods of development, and that the functions of this molecule in nematodes and insects may be distinct from or a subset of those that occur in vertebrates. The expanded role of the molecule represented by its expression during later stages of vertebrate development may thus have been an important contribution to the evolution of chordates.

  6. DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae).

    PubMed

    Huang, Zuhao; Tu, Feiyun

    2017-07-01

    The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.

  7. Bayesian phylogeny analysis via stochastic approximation Monte Carlo.

    PubMed

    Cheon, Sooyoung; Liang, Faming

    2009-11-01

    Monte Carlo methods have received much attention in the recent literature of phylogeny analysis. However, the conventional Markov chain Monte Carlo algorithms, such as the Metropolis-Hastings algorithm, tend to get trapped in a local mode in simulating from the posterior distribution of phylogenetic trees, rendering the inference ineffective. In this paper, we apply an advanced Monte Carlo algorithm, the stochastic approximation Monte Carlo algorithm, to Bayesian phylogeny analysis. Our method is compared with two popular Bayesian phylogeny software, BAMBE and MrBayes, on simulated and real datasets. The numerical results indicate that our method outperforms BAMBE and MrBayes. Among the three methods, SAMC produces the consensus trees which have the highest similarity to the true trees, and the model parameter estimates which have the smallest mean square errors, but costs the least CPU time.

  8. [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.

  9. pHMM-tree: phylogeny of profile hidden Markov models.

    PubMed

    Huo, Luyang; Zhang, Han; Huo, Xueting; Yang, Yasong; Li, Xueqiong; Yin, Yanbin

    2017-01-05

    Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file. The output will be a pHMM phylogeny of different protein families delineating their relationships. We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phylogenetic representation of the evolutionary relationship among distant protein families.

  10. Arthropod fossil data increase congruence of morphological and molecular phylogenies.

    PubMed

    Legg, David A; Sutton, Mark D; Edgecombe, Gregory D

    2013-01-01

    The relationships of major arthropod clades have long been contentious, but refinements in molecular phylogenetics underpin an emerging consensus. Nevertheless, molecular phylogenies have recovered topologies that morphological phylogenies have not, including the placement of hexapods within a paraphyletic Crustacea, and an alliance between myriapods and chelicerates. Here we show enhanced congruence between molecular and morphological phylogenies based on 753 morphological characters for 309 fossil and Recent panarthropods. We resolve hexapods within Crustacea, with remipedes as their closest extant relatives, and show that the traditionally close relationship between myriapods and hexapods is an artefact of convergent character acquisition during terrestrialisation. The inclusion of fossil morphology mitigates long-branch artefacts as exemplified by pycnogonids: when fossils are included, they resolve with euchelicerates rather than as a sister taxon to all other euarthropods.

  11. Gene order phylogeny and the evolution of methanogens.

    PubMed

    Luo, Haiwei; Sun, Zhiyi; Arndt, William; Shi, Jian; Friedman, Robert; Tang, Jijun

    2009-06-29

    Methanogens are a phylogenetically diverse group belonging to Euryarchaeota. Previously, phylogenetic approaches using large datasets revealed that methanogens can be grouped into two classes, "Class I" and "Class II". However, some deep relationships were not resolved. For instance, the monophyly of "Class I" methanogens, which consist of Methanopyrales, Methanobacteriales and Methanococcales, is disputable due to weak statistical support. In this study, we use MSOAR to identify common orthologous genes from eight methanogen species and a Thermococcale species (outgroup), and apply GRAPPA and FastME to compute distance-based gene order phylogeny. The gene order phylogeny supports two classes of methanogens, but it differs from the original classification of methanogens by placing Methanopyrales and Methanobacteriales together with Methanosarcinales in Class II rather than with Methanococcales. This study suggests a new classification scheme for methanogens. In addition, it indicates that gene order phylogeny can complement traditional sequence-based methods in addressing taxonomic questions for deep relationships.

  12. 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.

  13. Hazardous crater lakes studied

    NASA Astrophysics Data System (ADS)

    Kusakabe, Minoru

    Crater lakes usually sit on top of volcanic conduits and act as condensers of magmatic vapor. Studies of crater lakes can therefore provide information on both deep magmatic activity and variations in the degassing state of a shallow magmatic body. The Lake Nyos gas disaster of August 1986 and a similar event in August 1984 at Lake Monoun, both in Cameroon, resulted from the accumulation of magmatic CO2 in the bottom layers of the lakes. Geochemical monitoring of crater lakes is a promising tool for forecasting not only limnic but also volcanic eruptions. Acid-mineralized waters formed by condensation of hot magmatic volatiles in crater lakes are thought to bear some resemblance to hydrothermal fluids acting in the genesis of acid-sulfate alteration and Au-Cu-Ag mineralization of volcanic-hosted precious metal deposits.

  14. Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea).

    PubMed

    Puillandre, N; Bouchet, P; Duda, T F; Kauferstein, S; Kohn, A J; Olivera, B M; Watkins, M; Meyer, C

    2014-09-01

    We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using molecular data. About 85% of the species cluster in the single Large Major Clade; the others are divided between the Small Major Clade (∼12%), the Conus californicus lineage (one species), and a newly defined clade (∼3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the molecular phylogeny, is published in an accompanying paper. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. 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.

  16. Lake trout rehabilitation in Lake Huron

    USGS Publications Warehouse

    Eshenroder, Randy L.; Payne, N. Robert; Johnson, James E.; Bowen, Charles; 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.

  17. Phylogeny, culturing, and metagenomics of the human gut microbiota.

    PubMed

    Walker, Alan W; Duncan, Sylvia H; Louis, Petra; Flint, Harry J

    2014-05-01

    The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics. Copyright © 2014. Published by Elsevier Ltd.

  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. [Genosystematics and new insight on phylogeny and taxonomy of liverworts].

    PubMed

    Vil'net, A A; Konstantinova, N A; Troitskiĭ, A V

    2009-01-01

    The paper covers a current state of molecular studies of liverworts including new data from authors. The traditional conceptions of liverwort phylogeny and systematics were changed greatly in a result of recent molecular researches. The phylogenetic inferences from studies of different DNA loci and species sampling are mainly congruent. The phylogeny and systematics of one of the largest and taxonomically difficult suborder Jungermaniineae was discussed based on analyses of internal transcribed spacer ITS1-2 of nuclear rDNA and chloroplast trnL-F of large species number.

  20. Stage fluctuations of Wisconsin lakes

    USGS Publications Warehouse

    House, Leo B.

    1985-01-01

    This report describes lake-stage fluctuations of 83 gaged lakes in Wisconsin and presents techniques for estimating stage fluctuation at ungaged lakes. Included are stage information at 83 lakes and stage-frequency data for 32 of these lakes that had sufficient record for analysis. Lakes are classified by a hydrologic-topographic lake classification scheme as ground-water flowthrough (GWF) lakes, surface-water drainage (SWD) lakes, and surface-water flow-through (SWF) lakes. Lakes within the same class were found to have similar water-level fluctuations. The lake-stage records indicate that most annual maximums occur during the months of May and June for all three classes. Annual minimum lake levels generally occur in September for surface-water drainage lakes, in March for surface-water flowthrough lakes, and in November for ground-water flow-through lakes. Data for each lake include location, period of water-level record, hydrologic classification, drainage area, surface area, lake volume, maximum depth, long-term mean stage and its standard deviation, maximum and minimum observed lake stage, and the average annual lake-stage fluctuation.

  1. Salting our freshwater lakes.

    PubMed

    Dugan, Hilary A; Bartlett, Sarah L; Burke, Samantha M; Doubek, Jonathan P; Krivak-Tetley, Flora E; Skaff, Nicholas K; Summers, Jamie C; Farrell, Kaitlin J; McCullough, Ian M; Morales-Williams, Ana M; Roberts, Derek C; Ouyang, Zutao; Scordo, Facundo; Hanson, Paul C; Weathers, Kathleen C

    2017-04-10

    The highest densities of lakes on Earth are in north temperate ecosystems, where increasing urbanization and associated chloride runoff can salinize freshwaters and threaten lake water quality and the many ecosystem services lakes provide. However, the extent to which lake salinity may be changing at broad spatial scales remains unknown, leading us to first identify spatial patterns and then investigate the drivers of these patterns. Significant decadal trends in lake salinization were identified using a dataset of long-term chloride concentrations from 371 North American lakes. Landscape and climate metrics calculated for each site demonstrated that impervious land cover was a strong predictor of chloride trends in Northeast and Midwest North American lakes. As little as 1% impervious land cover surrounding a lake increased the likelihood of long-term salinization. Considering that 27% of large lakes in the United States have >1% impervious land cover around their perimeters, the potential for steady and long-term salinization of these aquatic systems is high. This study predicts that many lakes will exceed the aquatic life threshold criterion for chronic chloride exposure (230 mg L(-1)), stipulated by the US Environmental Protection Agency (EPA), in the next 50 y if current trends continue.

  2. Lake Balkhash, Kazakhstan

    NASA Technical Reports Server (NTRS)

    2002-01-01

    This image of crescent-shaped Lake Balkhash was taken by the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) on April 27, 2000. Lake Balkhash is located in eastern Kazakhstan, north of the Tian-Shan mountains. The Ili River flows into the western end of the lake, filling it with bright sediment. This sediment highlights the difference between the freshwater western side of the lake and the saline eastern side. A sandbar prevents mixing between the lake's two sections.Other features in this image include Lake Sayram in the lower right (southeast) corner, which is surrounded by the Borohoro Shan mountain range. At center right, just north of the Borohoro Shan, are lakes Sasykkol (left) and Alakol (right). The Karatal River flows northward through an arid and sandy landscape into the center of Lake Balkhash. The full-size image compares the region on April 27th image with one from the 18th. In that time sediments in lakes Balkhash and Sasykol increased noticeably, probably due to snowmelt-note the decrease in snowcover on the region's mountains. Also, the ice on Lake Sayram melted. These images were retrieved by the SeaWiFS high-resolution ground station in Mongolia, which recently began sending data to Goddard Space Flight Center. Image provided by the SeaWiFS Project, NASA/Goddard Space Flight Center, and ORBIMAGE

  3. Salting our freshwater lakes

    PubMed Central

    Bartlett, Sarah L.; Burke, Samantha M.; Doubek, Jonathan P.; Krivak-Tetley, Flora E.; Skaff, Nicholas K.; Summers, Jamie C.; Farrell, Kaitlin J.; McCullough, Ian M.; Morales-Williams, Ana M.; Roberts, Derek C.; Ouyang, Zutao; Scordo, Facundo; Hanson, Paul C.; Weathers, Kathleen C.

    2017-01-01

    The highest densities of lakes on Earth are in north temperate ecosystems, where increasing urbanization and associated chloride runoff can salinize freshwaters and threaten lake water quality and the many ecosystem services lakes provide. However, the extent to which lake salinity may be changing at broad spatial scales remains unknown, leading us to first identify spatial patterns and then investigate the drivers of these patterns. Significant decadal trends in lake salinization were identified using a dataset of long-term chloride concentrations from 371 North American lakes. Landscape and climate metrics calculated for each site demonstrated that impervious land cover was a strong predictor of chloride trends in Northeast and Midwest North American lakes. As little as 1% impervious land cover surrounding a lake increased the likelihood of long-term salinization. Considering that 27% of large lakes in the United States have >1% impervious land cover around their perimeters, the potential for steady and long-term salinization of these aquatic systems is high. This study predicts that many lakes will exceed the aquatic life threshold criterion for chronic chloride exposure (230 mg L−1), stipulated by the US Environmental Protection Agency (EPA), in the next 50 y if current trends continue. PMID:28396392

  4. A proposed protocol for acceptance and constancy control of computed tomography systems: a Nordic Association for Clinical Physics (NACP) work group report.

    PubMed

    Kuttner, Samuel; Bujila, Robert; Kortesniemi, Mika; Andersson, Henrik; Kull, Love; Østerås, Bjørn Helge; Thygesen, Jesper; Tarp, Ivanka Sojat

    2013-03-01

    Quality assurance (QA) of computed tomography (CT) systems is one of the routine tasks for medical physicists in the Nordic countries. However, standardized QA protocols do not yet exist and the QA methods, as well as the applied tolerance levels, vary in scope and extent at different hospitals. To propose a standardized protocol for acceptance and constancy testing of CT scanners in the Nordic Region. Following a Nordic Association for Clinical Physics (NACP) initiative, a group of medical physicists, with representatives from four Nordic countries, was formed. Based on international literature and practical experience within the group, a comprehensive standardized test protocol was developed. The proposed protocol includes tests related to the mechanical functionality, X-ray tube, detector, and image quality for CT scanners. For each test, recommendations regarding the purpose, equipment needed, an outline of the test method, the measured parameter, tolerance levels, and the testing frequency are stated. In addition, a number of optional tests are briefly discussed that may provide further information about the CT system. Based on international references and medical physicists' practical experiences, a comprehensive QA protocol for CT systems is proposed, including both acceptance and constancy tests. The protocol may serve as a reference for medical physicists in the Nordic countries.

  5. A molecular phylogeny of thermophilic fungi.

    PubMed

    Morgenstern, Ingo; Powlowski, Justin; Ishmael, Nadeeza; Darmond, Corinne; Marqueteau, Sandrine; Moisan, Marie-Claude; Quenneville, Geneviève; Tsang, Adrian

    2012-04-01

    Sequences from 86 fungal genomes and from the two outgroup genomes Arabidopsis thaliana and Drosophila melanogaster were analyzed to construct a robust molecular phylogeny of thermophilic fungi, which are potentially rich sources of industrial enzymes. To provide experimental reference points, growth characteristics of 22 reported thermophilic or thermotolerant fungi, together with eight mesophilic species, were examined at four temperatures: 22 °C, 34 °C, 45 °C, and 55 °C. Based on the relative growth performances, species with a faster growth rate at 45 °C than at 34 °C were classified as thermophilic, and species with better or equally good growth at 34 °C compared to 45 °C as thermotolerant. We examined the phylogenetic relationships of a diverse range of fungi, including thermophilic and thermotolerant species, using concatenated amino acid sequences of marker genes mcm7, rpb1, and rpb2 obtained from genome sequencing projects. To further elucidate the phylogenetic relationships in the thermophile-rich orders Sordariales and Eurotiales, we used nucleotide sequences from the nuclear ribosomal small subunit (SSU), the 5.8S gene with internal transcribed spacers 1 and 2 (ITS 1 and 2), and the ribosomal large subunit (LSU) to include additional species for analysis. These phylogenetic analyses clarified the position of several thermophilic taxa. Thus, Myriococcum thermophilum and Scytalidium thermophilum fall into the Sordariales as members of the Chaetomiaceae, Thermomyces lanuginosus belongs to the Eurotiales, Malbranchea cinnamomea is a member of the Onygenales, and Calcarisporiella thermophila is assigned to the basal fungi close to the Mucorales. The mesophilic alkalophile Acremonium alcalophilum clusters with Verticillium albo-atrum and Verticillium dahliae, placing them in the recently established order Glomerellales. Taken together, these data indicate that the known thermophilic fungi are limited to the Sordariales, Eurotiales, and

  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. In-lake Modeling Recommendation Report for Lake Champlain TMDL

    EPA Pesticide Factsheets

    This report describes the recommended modeling approach for the in-lake modeling component of the Lake Champlain TMDL project. The report was prepared by Tetra Tech, with input from the Lake Champlain modeling workgroup. (TetraTech, 2012b)

  8. 9. GRANT LAKE AND MONO LAKE IN DISTANCE, LOOKING NORTHEAST ...

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

    9. GRANT LAKE AND MONO LAKE IN DISTANCE, LOOKING NORTHEAST - Los Angeles Aqueduct, From Lee Vining Intake (Mammoth Lakes) to Van Norman Reservoir Complex (San Fernando Valley), Los Angeles, Los Angeles County, CA

  9. 2016 Lake Michigan Lake Trout Working Group Report

    USGS Publications Warehouse

    Madenjian, Charles P.; Breidert, Brian; Boyarski, David; Bronte, Charles R.; Dickinson, Ben; Donner, Kevin; Ebener, Mark P.; Gordon, Roger; Hanson, Dale; Holey, Mark; Janssen, John; Jonas, Jory; Kornis, Matthew; Olsen, Erik; Robillard, Steve; Treska, Ted; Weldon, Barry; Wright, Greg D.

    2017-01-01

    This report provides a review on the progression of lake trout rehabilitation towards meeting the Salmonine Fish Community Objectives (FCOs) for Lake Michigan (Eshenroder et. al. 1995) and the interim goal and evaluation objectives articulated in A Fisheries Management Implementation Strategy for the Rehabilitation of Lake Trout in Lake Michigan (Dexter et al. 2011); we also include data describing lake trout stocking and mortality to portray the present state of progress towards lake trout rehabilitation.

  10. 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.

  11. Hydrology of Indiana lakes

    USGS Publications Warehouse

    Perrey, Joseph Irving; Corbett, Don Melvin

    1956-01-01

    The stabilization of lake levels often requires the construction of outlet control structures. A detailed study of past lake-level elevations and other hydologic date is necessary to establish a level that can be maintained and to determine the means necessary for maintaining the established level. Detailed lake-level records for 28 lakes are included in the report, and records for over 100 other lakes data are available in the U.S. Geological Survey Office, Indianapolis, Ind. Evaporation data from the four Class A evaporation station of the U. S. Weather Bureau have been compiled in this report. A table showing the established legal lake level and related data is included.

  12. Mono Lake, California

    NASA Image and Video Library

    2017-03-24

    In eastern California, along the western edge of the Great Basin, sits Mono Lake. This is a salty remnant of a wetter era. Estimates are that the lake existed for at least 760,000 years. Now surrounded by mountain ranges, however, Mono Lake has no outlet; water entering the lake can only evaporate away, so Mono Lake is saltier than the ocean. South of the lake appear some of the geologic features known as Mono Craters. Geologists estimate that the Mono Craters last erupted about 650 years ago. The image was acquired July 7, 2016, covers an area of 22.6 by 34 km, and is located at 37.9 degrees north, 119 degrees west. http://photojournal.jpl.nasa.gov/catalog/PIA21518

  13. Lake Enriquillo, Dominican Republic

    NASA Image and Video Library

    2017-08-15

    Lake Enriquillo is a hypersaline lake in the Dominican Republic. In 2004, the lake covered an area of 164 square kilometers; by 2011, it had doubled in size and grown to 350 km2, inundating farmland and homes. Various reasons for the flooding include increases in rainfall; increase of sediments going into the lake, raising the lakebed; and milder temperatures, reducing surface evaporation. The lake is home to the largest population of American crocodiles in the Caribbean. The images were acquired October 26, 2003 and June 10, 2017, cover an area of 22.7 by 45.4 km, and are located at 18.5 degrees north, 71.6 degrees west. An image of Lake Enriquillo taken in 2003 is available at https://photojournal.jpl.nasa.gov/catalog/PIA21815

  14. Speciation in ancient lakes.

    PubMed

    Martens, K

    1997-05-01

    About a dozen lakes in the world are up to three orders of magnitude older than most others. Lakes Tanganyika (East Africa) and Baikal (Siberia) have probably existed in some form for 12-20 million years, maybe more. Such lakes can have different origins, sizes, shapes, depths and limnologies, but, in contrast to short-lived (mostly post-glacial) lakes, they have exceptionally high faunal diversity and levels of endemicity. A multitude of and processes accounting for these explosive radiations have recently been documented, most of them based on particular groups in certain lakes, but comparative research can detect repeated patterns. No special speciafion mechanism, exclusive to ancient lakes has been demonstrated, although cases of ultra-rapid speciation have been documented. Extant diversity results not by simple accumulation, but by a complex process of immigration, speciation and extinction.

  15. Phylogeny predicts future habitat shifts due to climate change.

    PubMed

    Kuntner, Matjaž; Năpăruş, Magdalena; Li, Daiqin; Coddington, Jonathan A

    2014-01-01

    Taxa may respond differently to climatic changes, depending on phylogenetic or ecological effects, but studies that discern among these alternatives are scarce. Here, we use two species pairs from globally distributed spider clades, each pair representing two lifestyles (generalist, specialist) to test the relative importance of phylogeny versus ecology in predicted responses to climate change. We used a recent phylogenetic hypothesis for nephilid spiders to select four species from two genera (Nephilingis and Nephilengys) that match the above criteria, are fully allopatric but combined occupy all subtropical-tropical regions. Based on their records, we modeled each species niche spaces and predicted their ecological shifts 20, 40, 60, and 80 years into the future using customized GIS tools and projected climatic changes. Phylogeny better predicts the species current ecological preferences than do lifestyles. By 2080 all species face dramatic reductions in suitable habitat (54.8-77.1%) and adapt by moving towards higher altitudes and latitudes, although at different tempos. Phylogeny and life style explain simulated habitat shifts in altitude, but phylogeny is the sole best predictor of latitudinal shifts. Models incorporating phylogenetic relatedness are an important additional tool to predict accurately biotic responses to global change.

  16. 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. © 2016 The Author(s).

  17. 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)

  18. The imbalanced supertree of flowering-plant phylogeny

    PubMed Central

    Graham, Sean W; Cronk, Quentin CB

    2004-01-01

    Two contrasting approaches have been used to construct the overall tree of life from molecular data: one involves the analysis of single large datasets, while the other involves joining many independent smaller analyses into a supertree. A recent study uses the latter approach to produce the most complete phylogeny yet of flowering plant families. PMID:15287967

  19. A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides).

    PubMed

    Jønsson, Knud Andreas; Fabre, Pierre-Henri; Kennedy, Jonathan D; Holt, Ben G; Borregaard, Michael K; Rahbek, Carsten; Fjeldså, Jon

    2016-01-01

    The Corvides (previously referred to as the core Corvoidea) are a morphologically diverse clade of passerine birds comprising nearly 800 species. The group originated some 30 million years ago in the proto-Papuan archipelago, to the north of Australia, from where lineages have dispersed and colonized all of the world's major continental and insular landmasses (except Antarctica). During the last decade multiple species-level phylogenies have been generated for individual corvoid families and more recently the inter-familial relationships have been resolved, based on phylogenetic analyses using multiple nuclear loci. In the current study we analyse eight nuclear and four mitochondrial loci to generate a dated phylogeny for the majority of corvoid species. This phylogeny includes 667 out of 780 species (85.5%), 141 out of 143 genera (98.6%) and all 31 currently recognized families, thus providing a baseline for comprehensive macroecological, macroevolutionary and biogeographical analyses. Using this phylogeny we assess the temporal consistency of the current taxonomic classification of families and genera. By adopting an approach that enforces temporal consistency by causing the fewest possible taxonomic changes to currently recognized families and genera, we find the current familial classification to be largely temporally consistent, whereas that of genera is not. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. 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)

  1. The effects of island ontogeny on species diversity and phylogeny.

    PubMed

    Valente, Luis M; Etienne, Rampal S; Phillimore, Albert B

    2014-06-07

    A major goal of island biogeography is to understand how island communities are assembled over time. However, we know little about the influence of variable area and ecological opportunity on island biotas over geological timescales. Islands have limited life spans, and it has been posited that insular diversity patterns should rise and fall with an island's ontogeny. The potential of phylogenies to inform us of island ontogenetic stage remains unclear, as we lack a phylogenetic framework that focuses on islands rather than clades. Here, we present a parsimonious island-centric model that integrates phylogeny and ontogeny into island biogeography and can incorporate a negative feedback of diversity on species origination. This framework allows us to generate predictions about species richness and phylogenies on islands of different ages. We find that peak richness lags behind peak island area, and that endemic species age increases with island age on volcanic islands. When diversity negatively affects rates of immigration and cladogenesis, our model predicts speciation slowdowns on old islands. Importantly, we find that branching times of in situ radiations can be informative of an island's ontogenetic stage. This novel framework provides a quantitative means of uncovering processes responsible for island biogeography patterns using phylogenies.

  2. 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

  3. Ethnobotany, Phylogeny, and 'Omics' for Human Health and Food Security.

    PubMed

    Garnatje, Teresa; Peñuelas, Josep; Vallès, Joan

    2017-03-01

    Here, we propose a new term, 'ethnobotanical convergence', to refer to the similar uses for plants included in the same node of a phylogeny. This phylogenetic approach, together with the 'omics' revolution, shows how combining modern technologies with traditional ethnobotanical knowledge could be used to identify potential new applications of plants.

  4. Phylogeny, phylogenetic inference, and cranial evolution in pitheciids and Aotus.

    PubMed

    Bjarnason, Alexander; Soligo, Christophe; Elton, Sarah

    2017-03-01

    Pitheciids, one of the major radiations of New World monkeys endemic to South and Central America, are distributed in the Amazon and Orinoco basins, and include Callicebus, Cacajao, Chiropotes, and Pithecia. Molecular phylogenetics strongly support pitheciid monophyly, whereas morphological analyses infer a range of phylogenies including a sister relationship between Aotus and Callicebus. We collected geometric morphometric cranial data from pitheciids and Aotus, and used cranial data for distance-based phylogenetic analysis and tests of phylogenetic signal. Phylogenetic analyses of pitheciids were repeated with Lagothrix, Callimico, and Saimiri outgroups for Procrustes shape with and without Aotus based on the whole cranium and six anatomical regions. All phylogenetic signal tests were significant, and tree lengths were shortest and had the least morphological change over the phylogeny for Procrustes residuals from the cranial base and palate. The majority of phylogenetic analyses of Procrustes shape for pitheciids without Aotus supported the molecular phylogeny, and with Aotus included the majority inferred an Aotus-Callicebus clade, although three analyses with Callimico as outgroup supported the molecular phylogeny. The morphological similarity of Aotus and Callicebus is likely a mix of plesiomorphy, allometry, and homoplasy, and future phylogenetic inference of living and extinct platyrrhine taxa should consider the impact of these factors alongside outgroup selection and cranial region.

  5. Phylogeny and adaptation shape the teeth of insular mice

    PubMed Central

    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

    2016-01-01

    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. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data.

    PubMed

    Aze, Tracy; Ezard, Thomas H G; Purvis, Andy; Coxall, Helen K; Stewart, Duncan R M; Wade, Bridget S; Pearson, Paul N

    2011-11-01

    We present a complete phylogeny of macroperforate planktonic foraminifer species of the Cenozoic Era (∼65 million years ago to present). The phylogeny is developed from a large body of palaeontological work that details the evolutionary relationships and stratigraphic (time) distributions of species-level taxa identified from morphology ('morphospecies'). Morphospecies are assigned to morphogroups and ecogroups depending on test morphology and inferred habitat, respectively. Because gradual evolution is well documented in this clade, we have identified many instances of morphospecies intergrading over time, allowing us to eliminate 'pseudospeciation' and 'pseudoextinction' from the record and thereby permit the construction of a more natural phylogeny based on inferred biological lineages. Each cladogenetic event is determined as either budding or bifurcating depending on the pattern of morphological change at the time of branching. This lineage phylogeny provides palaeontologically calibrated ages for each divergence that are entirely independent of molecular data. The tree provides a model system for macroevolutionary studies in the fossil record addressing questions of speciation, extinction, and rates and patterns of evolution. © 2011 The Authors. Biological Reviews © 2011 Cambridge Philosophical Society.

  7. Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

    Treesearch

    D. Jean Lodge; Mahajabeen Padamsee; P. Brandon Matheny; M. Catherine Aime; Sharon A. Cantrell; David Boertmann; Alexander Kovalenko; Alfredo Vizzini; Bryn T.M. Dentinger; Paul M. Kirk; A. Martin Ainsworth; Jean-Marc Moncalvo; Rytas Vilgalys; Ellen Larsson; Robert Lucking; Gareth W. Griffith; Matthew E. Smith; Lorilei L. Norvell; Dennis E. Desjardin; Scott A. Redhead; Clark L. Ovrebo; Edgar B. Lickey; Enrico Ercole; Karen W. Hughes; Regis Courtecuisse; Anthony Young; Manfred Binder; Andrew M. Minnis; Daniel L. Lindner; Beatriz Ortiz-Santana; John Haight; Thomas Laessoe; Timothy J. Baroni; Jozsef Geml; Tsutomu Hattori

    2013-01-01

    Molecular phylogenies using 1–4 gene regions and information on ecology, morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae. The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are: Acantholichen, Ampulloclitocybe, Arrhenia, Cantharellula, Cantharocybe,...

  8. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    USDA-ARS?s Scientific Manuscript database

    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...

  9. Phylogeny Predicts Future Habitat Shifts Due to Climate Change

    PubMed Central

    Kuntner, Matjaž; Năpăruş, Magdalena; Li, Daiqin; Coddington, Jonathan A.

    2014-01-01

    Background Taxa may respond differently to climatic changes, depending on phylogenetic or ecological effects, but studies that discern among these alternatives are scarce. Here, we use two species pairs from globally distributed spider clades, each pair representing two lifestyles (generalist, specialist) to test the relative importance of phylogeny versus ecology in predicted responses to climate change. Methodology We used a recent phylogenetic hypothesis for nephilid spiders to select four species from two genera (Nephilingis and Nephilengys) that match the above criteria, are fully allopatric but combined occupy all subtropical-tropical regions. Based on their records, we modeled each species niche spaces and predicted their ecological shifts 20, 40, 60, and 80 years into the future using customized GIS tools and projected climatic changes. Conclusions Phylogeny better predicts the species current ecological preferences than do lifestyles. By 2080 all species face dramatic reductions in suitable habitat (54.8–77.1%) and adapt by moving towards higher altitudes and latitudes, although at different tempos. Phylogeny and life style explain simulated habitat shifts in altitude, but phylogeny is the sole best predictor of latitudinal shifts. Models incorporating phylogenetic relatedness are an important additional tool to predict accurately biotic responses to global change. PMID:24892737

  10. Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts.

    PubMed

    Burki, Fabien; Pawlowski, Jan

    2006-10-01

    Reconstructing a global phylogeny of eukaryotes is an ongoing challenge of molecular phylogenetics. The availability of genomic data from a broad range of eukaryotic phyla helped in resolving the eukaryotic tree into a topology with a rather small number of large assemblages, but the relationships between these "supergroups" are yet to be confirmed. Rhizaria is the most recently recognized "supergroup," but, in spite of this important position within the tree of life, their representatives are still missing in global phylogenies of eukaryotes. Here, we report the first large-scale analysis of eukaryote phylogeny including data for 2 rhizarian species, the foraminiferan Reticulomyxa filosa and the chlorarachniophyte Bigelowiella natans. Our results confirm the monophyly of Rhizaria (Foraminifera + Cercozoa), with very high bootstrap supports in all analyses. The overall topology of our trees is in agreement with the current view of eukaryote phylogeny with basal division into "unikonts" (Opisthokonts and Ameobozoa) and "bikonts" (Plantae, alveolates, stramenopiles, and excavates). As expected, Rhizaria branch among bikonts; however, their phylogenetic position is uncertain. Depending on the data set and the type of analysis, Rhizaria branch as sister group to either stramenopiles or excavates. Overall, the relationships between the major groups of unicellular bikonts are poorly resolved, despite the use of 85 proteins and the largest taxonomic sampling for this part of the tree available to date. This may be due to an acceleration of evolutionary rates in some bikont phyla or be related to their rapid diversification in the early evolution of eukaryotes.

  11. Mitochondrial data are not suitable for resolving placental mammal phylogeny.

    PubMed

    Morgan, Claire C; Creevey, Christopher J; O'Connell, Mary J

    2014-12-01

    Mitochondrial data have traditionally been used in reconstructing a variety of species phylogenies. The low rates of recombination and thorough characterization of mitochondrial data across vertebrate species make it a particularly attractive phylogenetic marker. The relatively low number of fully sequenced mammal genomes and the lack of extensive sampling within Superorders have posed a serious problem for reaching agreement on the placement mammal species. The use of mitochondrial data sequences from large numbers of mammals could serve to circumvent the taxon-sampling deficit. Here we assess the suitability of mitochondrial data as a phylogenetic marker in mammal phylogenetics. MtDNA datasets of mammal origin have been filtered as follows: (i) we have sampled sparsely across the phylogenetic tree, (ii) we have constrained our sampling to genes with high taxon coverage, (iii) we have categorised rates across sites in a phylogeny independent manner and have removed fast evolving sites, and (iv), we have sampled from very shallow divergence times to reduce phylogenetic conflict. However, topologies obtained using these filters are not consistent with previous studies and are discordant across different genes. Individual mitochondrial genes, and indeed all mitochondrial genes analysed as a supermatrix, resulted in poor resolution of the species phylogeny. Overall, our study highlights the limitations of mitochondrial data, not only for resolving deep divergences and but also for shallow divergences in the mammal phylogeny.

  12. David Morrison on Lake Vostok

    NASA Image and Video Library

    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...

  13. Aquatic biogeochemistry: Cleaner Chinese lakes

    NASA Astrophysics Data System (ADS)

    Corman, Jessica

    2017-07-01

    Phosphorus loading can cause eutrophication of lakes. Analyses of lake chemistry in China reveal that policies have led to lower phosphorus levels overall, but increasing trends in some lakes suggest that expanded policies may be needed.

  14. 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.

  15. Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes.

    PubMed

    McCarthy, Charley G P; Fitzpatrick, David A

    2017-01-01

    The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus. Genome-scale phylogenetic studies have successfully resolved many eukaryotic relationships by using supertree methods, which combine large numbers of potentially disparate trees to determine evolutionary relationships that cannot be inferred from individual phylogenies alone. With a sufficient amount of genomic data now available, we have undertaken the first whole-genome phylogenetic analysis of the oomycetes using data from 37 oomycete species and 6 SAR species. In our analysis, we used established supertree methods to generate phylogenies from 8,355 homologous oomycete and SAR gene families and have complemented those analyses with both phylogenomic network and concatenated supermatrix analyses. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and individual clades within the problematic Phytophthora genus. Support for the resolution of the inferred relationships between individual Phytophthora clades varies depending on the methodology used. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes. IMPORTANCE The oomycetes are a class of eukaryotes and include ecologically significant animal and plant pathogens. Single-gene and multigene phylogenetic studies of individual oomycete genera and of members of the larger classes have resulted in conflicting conclusions concerning interspecies relationships among these species, particularly for the

  16. Ribosomal ITS sequences allow resolution of freshwater sponge phylogeny with alignments guided by secondary structure prediction.

    PubMed

    Itskovich, Valeria; Gontcharov, Andrey; Masuda, Yoshiki; Nohno, Tsutomu; Belikov, Sergey; Efremova, Sofia; Meixner, Martin; Janussen, Dorte

    2008-12-01

    Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges.

  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. Community composition of nirS-type denitrifier in a shallow eutrophic lake.

    PubMed

    Yang, Jiang-Ke; Cheng, Zhan-Bing; Li, Jia; Miao, Li-Hong

    2013-11-01

    Denitrification is a major biological process to reduce nitrate to molecular nitrogen (N2). In shallow eutrophic lakes, this process can remove the largest portion of fixed nitrogen and plays an important role in self-purification of this ecosystem. To understand the structure of denitrifying communities in a shallow eutrophic lake, denitrifier communities in four sub-lakes of East Lake in Wuhan, China, were explored by restriction fragment length polymorphisms (RFLP) analysis and sequencing of nirS gene clone libraries. nirS is a functional marker gene for denitrification encoding cytochrome cd 1-containing nitrite reductase, which catalyzes the reduction of nitrite to nitric oxide. Both RFLP fingerprints clustering analysis and phylogeny analysis based on the amino acid sequences of NirS revealed that NirS-type communities in East Lake sediment could be roughly divided into three clusters. Cluster I accounted for 74-82 % of clones from the moderately eutrophic sub-lakes Tuan, Tang Ling, and Guo Zheng. Cluster II accounted for 76 % of the communities in hypertrophic sub-lake Miao Lake and cluster III as a minor group (7 % of the total), mainly presented in Miao Lake. Phylogenetic analysis revealed that cluster I was related to the reference clones from a broad range of ecological environments, and clusters II and III were more phylogenetically related to the reference clones from entrophic environments. Canonical correspondence analysis indicated that total nitrogen, total phosphate, total organic carbon, and NH4-N and NO2-N were important environmental factors affecting the dispersion of NirS-type denitrifier in the sediments. Cluster I showed a weak relationship with the nutrient content, while cluster II and III were positively related with the nutrient content. Principal coordinates analysis indicated that NirS-type communities from Tuan Lake, Tang Ling Lake, and Guo Zheng Lake sediments were divergent from those found in river, estuary sediment, and forest

  19. The ontogeny and phylogeny of copepod antennules

    PubMed Central

    Boxshall, G. A.

    1998-01-01

    Comparative analysis of the development of antennulary segmentation and setation patterns across six orders of copepods revealed numerous common features. These features are combined to produce a hypothetical general model for antennulary development in the Copepoda as a whole. In this model most compound segments result from the failure of expression of articulations separating ancestral segments. In adult males, however, compound segments either side of the neocopepodan geniculation are typically formed by secondary fusion at the last moult from CoV (stage 5). The array of segments distal to the articulation separating segments XX and XXI is highly conserved both in ontogeny and phylogeny: typically the distal segmentation of the adult female is already present in the CoI. A maximum of three setae is added to the distal array during the entire copepodid phase. This morphological conservatism is interpreted as evidence of the functional continuity of the distal setal array as a mechanosensory system providing early warning of approaching predators. Sexual dimorphism typically appears late in development; the male undergoing modifications especially at the final moult to sexual maturity. These modifications include the formation of the neocopepodan geniculation at the XX to XXI articulation and, in some orders, the formation of a proximal geniculation at the XV to XVI articulation. A proximal geniculation is reported here from the Calanoida for the first time. The geniculations allow the male to grasp the female during any mate guarding and during spermatophore transfer. Particular setae on segments either side of the neocopepodan geniculation are modified as basally fused spines in at least some representatives of the Calanoida, Misophrioida, Cyclopoida, Harpacticoida and Siphonostomatoida. The antennulary chemosensory system, comprising primarily the aesthetascs, is enhanced at the final moult in many male copepods. In planktonic copepods this enhancement may

  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. Intrinsic breaking of internal solitary waves in a deep lake.

    PubMed

    Preusse, Martina; Stastna, Marek; Freistühler, Heinrich; Peeters, Frank

    2012-01-01

    Based on simulations with the Dubreil-Jacotin-Long (DJL) equation, the limiting amplitude and the breaking mechanisms of internal solitary waves of depression (ISWs) are predicted for different background stratifications. These theoretical predictions are compared to the amplitude and the stability of the leading internal solitary waves of more than 200 trains of ISWs observed in the centre of a sub-basin of Lake Constance. The comparison of the model results with the field observations indicates that the simulated limiting amplitude of the ISWs provides an excellent prediction of the critical wave height above which ISWs break in the field. Shear instabilities and convective instabilities are each responsible for about half of the predicted wave breaking events. The data suggest the presence of core-like structures within the convectively unstable waves, but fully developed and stable cores were not observed. The lack of stable trapped cores in the field can be explained by the results from dynamic simulations of ISWs with trapped cores which demonstrate that even slight disturbances of the background stratification cause trapped cores to become unstable.

  2. 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)…

  3. Utah: Salt Lake Region

    Atmospheric Science Data Center

    2014-05-15

    ... mountains including the Wasatch Range to the east, and the temperature difference between the Great Salt Lake and the overlying atmosphere ... snow cover between the winter and summer views, water color changes in parts of the Great Salt Lake are apparent in these images. The ...

  4. 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)

  5. 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…

  6. 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…

  7. The lakes of Titan.

    PubMed

    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

    2007-01-04

    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 degrees 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.

  8. 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.

  9. 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…

  10. 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)

  11. 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…

  12. 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…

  13. Great Salt Lake, Utah

    USGS Publications Warehouse

    Stephens, Doyle W.; Gardner, Joe F.

    1999-01-01

    This document is intended as a source of general information and facts about Great Salt Lake, Utah. This U.S. Geological Survey information sheet answers frequently asked questions about Great Salt Lake. Topics include: History, salinity, brine shrimp, brine flies, migratory birds, and recreation. Great Salt Lake, the shrunken remnant of prehistoric Lake Bonneville, has no outlet. Dissolved salts accumulate in the lake by evaporation. Salinity south of the causeway has ranged from 6 percent to 27 percent over a period of 22 years (2 to 7 times saltier than the ocean). The high salinity supports a mineral industry that extracts about 2 million tons of salt from the lake each year. The aquatic ecosystem consists of more than 30 species of organisms. Harvest of its best-known species, the brine shrimp, annually supplies millions of pounds of food for the aquaculture industry worldwide. The lake is used extensively by millions of migratory and nesting birds and is a place of solitude for people. All this occurs in a lake that is located at the bottom of a 35,000-square-mile drainage basin that has a human population of more than 1.5 million.

  14. Evaporation From Lake Superior

    NASA Astrophysics Data System (ADS)

    Spence, C.; Blanken, P.; Hedstrom, N.; Leshkevich, G.; Fortin, V.; Charpentier, D.; Haywood, H.

    2009-05-01

    Evaporation is a critical component of the water balance of each of the Laurentian Great Lakes, and understanding the magnitude and physical controls of evaporative water losses are important for several reasons. Recently, low water levels in Lakes Superior and Michigan/Huron have had socioeconomic, ecological, and even meteorological impacts (e.g. water quality and quantity, transportation, invasive species, recreation, etc.). The recent low water levels may be due to increased evaporation, but this is not known as operational evaporation estimates are currently calculated as the residual of water or heat budgets. Perhaps surprisingly, almost nothing is known about evaporation dynamics from Lake Superior and few direct measurements of evaporation have been made from any of the Laurentian Great Lakes. This research is the first to attempt to directly measure evaporation from Lake Superior by deploying eddy covariance instrumentation. Results of evaporation rates, their patterns and controlling mechanisms will be presented. The direct measurements of evaporation are used with concurrent satellite and climate model data to extrapolate evaporation measurements across the entire lake. This knowledge could improve predictions of how climate change may impact the lake's water budget and subsequently how the water in the lake is managed.

  15. 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…

  16. RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.

    PubMed

    Lyu, Ming-Ju Amy; Gowik, Udo; Kelly, Steve; Covshoff, Sarah; Mallmann, Julia; Westhoff, Peter; Hibberd, Julian M; Stata, Matt; Sage, Rowan F; Lu, Haorong; Wei, Xiaofeng; Wong, Gane Ka-Shu; Zhu, Xin-Guang

    2015-06-18

    The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F). Here we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a "F. pringlei" genotype recently used in a number of labs may be a hybrid between F. pringlei (C3) and F. angustifolia (C3-C4). We propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C4 photosynthesis in the Flavaria clade.

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

    USGS Publications Warehouse

    Andrews, Freeman L.; Wells, Frank C.; Shelby, Wanda J.; McPherson, Emma

    1988-01-01

    Water-quality data collected from Lake Austin and Town Lake, following runoff, generally were not adequate to fully determine the effects of runoff on the lakes. Data collection should not to be limited to fixed-station sampling following runoff, and both lakes need to be sampled simultaneously as soon as possible following significant precipitation.

  18. 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.

  19. Lake Superior revisited 1984

    USGS Publications Warehouse

    MacCallum, Wayne R.; Selgeby, James H.

    1987-01-01

    The Lake Superior fish community has changed substantially since the early 1960s, when control of the sea lamprey (Petromyzon marinus) became effective. Self-reproducing stocks of lake trout (Salvelinus namaycush) have been reestablished in many inshore areas, although they have not yet reached pre-sea lamprey abundance; offshore lake trout are probably at or near pre-sea lamprey abundance. Stocks of lake whitefish (Coregonus clupeaformis) appear to have fully recovered; commercial catches are at or above historical levels. Lake herring (Coregonus artedii) are recovering rapidly in U.S. waters and are abundant in western Canadian waters. The population of rainbow smelt (Osmerus mordax), which declined in the 1970s, is recovering. Pacific salmon (Oncorhynchus) are becoming more abundant as a result of increased stocking in U.S. waters and are reproducing in most suitable tributaries; they have become significant in anglers' creels.

  20. Lake Morphometry for NHD Lakes in California Region 18 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  1. Lake Morphometry for NHD Lakes in Tennessee Region 6 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  2. Lake Morphometry for NHD Lakes in Ohio Region 5 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  3. Evidence of offshore lake trout reproduction in Lake Huron

    USGS Publications Warehouse

    DeSorcie, Timothy J.; Bowen, Charles A.

    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.

  4. 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

  5. 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.

  6. Extrapolating demography with climate, proximity and phylogeny: approach with caution.

    PubMed

    Coutts, Shaun R; Salguero-Gómez, Roberto; Csergő, Anna M; Buckley, Yvonne M

    2016-12-01

    Plant population responses are key to understanding the effects of threats such as climate change and invasions. However, we lack demographic data for most species, and the data we have are often geographically aggregated. We determined to what extent existing data can be extrapolated to predict population performance across larger sets of species and spatial areas. We used 550 matrix models, across 210 species, sourced from the COMPADRE Plant Matrix Database, to model how climate, geographic proximity and phylogeny predicted population performance. Models including only geographic proximity and phylogeny explained 5-40% of the variation in four key metrics of population performance. However, there was poor extrapolation between species and extrapolation was limited to geographic scales smaller than those at which landscape scale threats typically occur. Thus, demographic information should only be extrapolated with caution. Capturing demography at scales relevant to landscape level threats will require more geographically extensive sampling. © 2016 John Wiley & Sons Ltd/CNRS.

  7. Understanding tissue expression evolution: from expression phylogeny to phylogenetic network.

    PubMed

    Gu, Xun

    2016-03-01

    Our understanding of tissue expression evolution in multi-cellular model organisms has been considerably advanced with the help of high-throughput technologies from EST, microarray to RNA-seq. Yet, many controversies remained unsolved, ranging from the evolutionary patterns of tissue expressions to expression phylogenetic analysis. Moreover, despite numerous reports published, it is desirable to have a general framework for study of tissue expression evolution. In this article, we first provide an up-to-date and concise review for the study of tissue expression evolution in multi-cellular organisms. While the expression phylogeny of the same tissues sampled from closely or intermediately related species largely reflects the species phylogeny, we demonstrate that phylogenetic network approach may shed some lights for our understanding of the developmental similarity and evolutionary relatedness during the multi-tissue evolution. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  8. 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).

  9. Phylogenies support out-of-equilibrium models of biodiversity.

    PubMed

    Manceau, Marc; Lambert, Amaury; Morlon, Hélène

    2015-04-01

    There is a long tradition in ecology of studying models of biodiversity at equilibrium. These models, including the influential Neutral Theory of Biodiversity, have been successful at predicting major macroecological patterns, such as species abundance distributions. But they have failed to predict macroevolutionary patterns, such as those captured in phylogenetic trees. Here, we develop a model of biodiversity in which all individuals have identical demographic rates, metacommunity size is allowed to vary stochastically according to population dynamics, and speciation arises naturally from the accumulation of point mutations. We show that this model generates phylogenies matching those observed in nature if the metacommunity is out of equilibrium. We develop a likelihood inference framework that allows fitting our model to empirical phylogenies, and apply this framework to various mammalian families. Our results corroborate the hypothesis that biodiversity dynamics are out of equilibrium.

  10. 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. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  11. Robust Dinoflagellata phylogeny inferred from public transcriptome databases.

    PubMed

    Price, Dana C; Bhattacharya, Debashish

    2017-03-08

    Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number. To address this issue, we used recently generated public sequencing data, including from the Moore Microbial Eukaryote Transcriptome Sequencing Project, to identify dinoflagellate-specific ortholog groups. These orthologs were combined to create a broadly sampled and highly resolved phylogeny of dinoflagellates. Our results emphasize the scope and utility of public sequencing databases in creating broad and robust phylogenies for large and complex taxonomic lineages, while also providing unique insights into the evolution of thecate dinoflagellates.

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

    USGS Publications Warehouse

    Adams, W.E.; 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.

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

    USGS Publications Warehouse

    Adams, W.E.; 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.

  14. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Taxonomy and phylogeny of papillomaviruses: an overview and recent developments.

    PubMed

    Bernard, Hans-Ulrich

    2013-08-01

    For more than 30 years, papillomaviruses are standing in the center of medical and molecular interest as they cause several important cancers in humans. Research of the sheer unlimited number of different papillomavirus genomes, their host specificity and slow mutation rate is an important a branch of these efforts and has led to fascinating insight into the phylogeny of a virus family that can be traced back for several 100 million years.

  16. 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

  17. 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.

  18. 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

  19. Yellowstone lake nanoarchaeota.

    PubMed

    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.

  20. 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