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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. 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.

  5. ["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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. Binaural Loudness Constancy.

    PubMed

    Culling, John F; Dare, Helen

    2016-01-01

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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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)

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  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. 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)

  16. 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.

  17. 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

  18. White constancy method for mobile displays

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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…

  6. 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

  7. 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.

  8. Lake

    ERIC Educational Resources Information Center

    Wien, Carol Anne

    2008-01-01

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

  9. 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

  10. 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.

  11. 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.

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

    PubMed

    Vazquez-Corral, Javier; Bertalmío, Marcelo

    2014-02-26

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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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…

  19. 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…

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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…

  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. 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…

  8. 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.

  9. 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.

  10. 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.

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

    PubMed

    Olsson, Peter; Wilby, David; Kelber, Almut

    2016-05-11

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

  12. Building a Twig Phylogeny

    ERIC Educational Resources Information Center

    Flinn, Kathryn M.

    2015-01-01

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

  13. 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

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

    PubMed

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

    2014-01-01

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

  15. 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

  16. The effect of exposure on MaxRGB color constancy

    NASA Astrophysics Data System (ADS)

    Funt, Brian; Shi, Lilong

    2010-02-01

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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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…

  8. 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.

  9. 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...

  10. 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…

  11. 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.

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

    ERIC Educational Resources Information Center

    Dupagne, Michel; Green, R. Jeffery

    1996-01-01

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

  13. 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)

  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. 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

  16. 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…

  17. 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…

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. Molecular phylogeny of Daucus (Apiaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  6. 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.

  7. 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.

  8. 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.

  9. [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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  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. 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…

  17. 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.

  18. 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.

  19. 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)…

  20. 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…

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. [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

  7. 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.

  8. 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.

  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. 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

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  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. 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.

  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. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  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. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  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 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.

  2. 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…

  3. Lake acidification

    SciTech Connect

    Dobson, J.E.; Peplies, R.W.; Rush, R.M.

    1987-06-01

    This paper examined a National Research Council (NRC) report called Acid Deposition: Long-Term Trends. The report has been the final word on acid deposition as the cause of acidification of lakes. The authors considered it important that the tentative nature of this report be kept in perspective so that the work of the NRC would promote rather than inhibit scientific inquiry on the lake acidification issue. In this spirit, this report proposed that degradation of storm damaged trees could increase the acidity of the forest humus and as a result the ground water which would fed local streams and lakes. They proposed that extensive forest blowdown could be a factor in acidification of surface waters.

  4. 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.

  5. 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.

  6. 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.

  7. 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).

  8. 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.

  9. [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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Archaebacterial phylogeny: perspectives on the urkingdoms

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  11. Phylogeny and forelimb disparity in waterbirds.

    PubMed

    Wang, Xia; Clarke, Julia A

    2014-10-01

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

  12. 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

  13. 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.

  14. 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.

  15. 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).

  16. 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.

  17. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  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. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. Bacterial phylogeny structures soil resistomes across habitats

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. [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.

  14. 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.

  15. 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.

  16. 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.

  17. 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 ...

  18. 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.

  19. 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

  20. Utah: Salt Lake Region

    Atmospheric Science Data Center

    2014-05-15

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. [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.

  7. 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.…

  8. 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…

  9. 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…

  10. 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)

  11. 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…

  12. 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.

  13. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Phylogeny and life histories of the 'Insectivora': controversies and consequences.

    PubMed

    Symonds, Matthew R E

    2005-02-01

    The evolutionary relationships of the eutherian order Insectivora (Lipotyphla sensu stricto) are the subject of considerable debate. The difficulties in establishing insectivore phylogeny stem from their lack of many shared derived characteristics. The grouping is therefore something of a 'wastebasket' taxon. Most of the older estimates of phylogeny, based on morphological evidence, assumed insectivore monophyly. More recently, molecular phylogenies argue strongly against monophyly, although they differ in the extent of polyphyly inferred for the order. I review the history of insectivore phylogenetics and systematics, focussing on the relationships between the six extant families (Erinaceidae--hedgehogs and moonrats, Talpidae - moles and desmans, Soricidae - shrews, Solenodontidae--solenodons, Tenrecidae--tenrecs and otter-shrews and Chrysochloridae--golden moles). I then examine how these various phylogenetic hypotheses influence the results of comparative analyses and our interpretation of insectivore life-history evolution. I assess which particular controversies have the greatest effect on results, and discuss the implications for comparative analyses where the phylogeny is controversial. I also explore and suggest explanations for certain insectivore life-history trends: increased gestation length and litter size in tenrecs, increased encephalization in moles, and the mixed fast and slow life-history strategies in solenodons. Finally, I consider the implications for comparative analyses of the recent strongly supported phylogenetic hypothesis of an endemic African clade of mammals that includes the insectivore families of tenrecs and golden moles.

  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. 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

  3. 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.

  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. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Mitochondrial phylogeny of the Chrysisignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction.

    PubMed

    Soon, Villu; Saarma, Urmas

    2011-07-01

    The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute

  11. 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

  12. 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)

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. David Morrison on Lake Vostok

    NASA Video Gallery

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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

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

    PubMed Central

    Wang, Aisuo; Ash, Gavin J.

    2015-01-01

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

  5. 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

  6. 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.

  7. The Aplacophora: History, Taxonomy, Phylogeny, Biogeography, and Ecology

    DTIC Science & Technology

    1992-02-01

    871-882. Field, K. G., G. J. Olsen, D. J. Lane, S. J. Giovannoni, M. T. Ghiselin, E. C. Raff, N. R. Pace and R. A. Raff. 1988. Molecular phylogeny of...Laboratory, Beaufort, North Carolina. 9. Harbor Branch Laboratory, FL Pierce, Florida. 10. Dives 492. 563, 752-754, 849, 1072. 11. Intituto de Biologia ...University (1965) Stns 351, 2361, 2732. and 3417 (14 specimens): and from the Inslituto de Biologia . Universidade Federal do Rio de Janeiro (9 specimens). 52

  8. 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.

  9. 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

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

    PubMed

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

    2007-12-01

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

  11. Phylogeny and evolution of apicoplasts and apicomplexan parasites.

    PubMed

    Arisue, Nobuko; Hashimoto, Tetsuo

    2015-06-01

    The phylum Apicomplexa includes many parasitic genera of medical and veterinary importance including Plasmodium (causative agent of malaria), Toxoplasma (toxoplasmosis), and Babesia (babesiosis). Most of the apicomplexan parasites possess a unique, essential organelle, the apicoplast, which is a plastid without photosynthetic ability. Although the apicoplast is considered to have evolved through secondary endosymbiosis of a red alga into the common ancestral cell of apicomplexans, its evolutionary history has been under debate until recently. The apicoplast has a genome around 30-40 kb in length. Repertoire and arrangement of the apicoplast genome-encoded genes differ among apicomplexan genera, although within the genus Plasmodium these are almost conserved. Genes in the apicoplast genome may be useful markers for Plasmodium phylogeny, because these are single copy (except for the inverted repeat region) and may have more phylogenetic signal than the mitochondrial genome that have been most commonly used for Plasmodium phylogeny. This review describes recent studies concerning the evolutionary origin of the apicoplast, presents evolutionary comparison of the primary structures of apicoplast genomes from apicomplexan parasites, and summarizes recent findings of malaria phylogeny based on apicoplast genome-encoded genes.

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

    PubMed

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

    2013-03-01

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

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

    PubMed

    Deyasi, Krishanu; Banerjee, Anirban; Deb, Bony

    2015-10-01

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

  14. Correcting for sequencing error in maximum likelihood phylogeny inference.

    PubMed

    Kuhner, Mary K; McGill, James

    2014-11-04

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

  15. Higher-level crustacean phylogeny: consensus and conflicting hypotheses.

    PubMed

    Jenner, Ronald A

    2010-01-01

    This paper presents an overview of current hypotheses of higher-level crustacean phylogeny in order to assist and help focus further research. It concentrates on hypotheses proposed or debated in the recent literature based on morphological, molecular and combined evidence phylogenetic analyses. It can be concluded that crustacean phylogeny remains essentially unresolved. Conflict is rife, irrespective of whether one compares different morphological studies, molecular studies, or both. Using the number of recently proposed alternative sister group hypotheses for each of the major tetraconatan taxa as a rough estimate of phylogenetic uncertainty, it can be concluded that the phylogenetic position of Malacostraca remains the most problematic, closely followed by Branchiopoda, Cephalocarida, Remipedia, Ostracoda, Branchiura, Copepoda and Hexapoda. Future progress will depend upon a broader taxon sampling in molecular analyses, and the further exploration of new molecular phylogenetic markers. However, the need for continued revision and expansion of morphological datasets remains undiminished given the conspicuous lack of agreement between molecules and morphology for positioning several taxa. In view of the unparalleled morphological diversity of Crustacea, and the likely nesting of Hexapoda somewhere within Crustacea, working out a detailed phylogeny of Tetraconata is a crucial step towards understanding arthropod body plan evolution.

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

    PubMed Central

    Goswami, Anjali

    2007-01-01

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

  17. Taxonomic and phytogeographic implications from ITS phylogeny in Berberis (Berberidaceae).

    PubMed

    Kim, Young-Dong; Kim, Sung-Hee; Landrum, Leslie R

    2004-06-01

    A phylogeny based on the internal transcribed spacer (ITS) sequences from 79 taxa representing much of the diversity of Berberis L. (four major groups and 22 sections) was constructed for the first time. The phylogeny was basically congruent with the previous classification schemes at higher taxonomic levels, such as groups and subgroups. A notable exception is the non-monophyly of the group Occidentales of compound-leaved Berberis (previously separated as Mahonia). At lower levels, however, most of previous sections and subsections were not evident especially in simple-leaved Berberis. Possible relationship between section Horridae (group Occidentales) and the simple-leaved Berberis clade implies paraphyly of the compound-leaved Berberis. A well-known South America-Old World (mainly Asia) disjunctive distribution pattern of the simple-leaved Berberis is explained by a vicariance event occurring in the Cretaceous period. The ITS phylogeny also suggests that a possible connection between the Asian and South American groups through the North American species ( Berberis canadensis or B. fendleri) is highly unlikely.

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

    PubMed

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

    2005-06-01

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

  19. 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

  20. 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.

  1. 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.

  2. 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…

  3. 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.

  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. Lake Wobegon Dice

    ERIC Educational Resources Information Center

    Moraleda, Jorge; Stork, David G.

    2012-01-01

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

  6. 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)…

  7. 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…

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Hindcast Wave Information for the Great Lakes. Lake Michigan

    DTIC Science & Technology

    1991-10-01

    has three major bathymetric regions, a southern, central, and northern basin. Depths over the lake are generally greater than 100 m with the...AD-A243 784 w,,v,,,,l,,,IWAVE INFORMATION STUDIES L OF US COASTLINES US AmWIS REPORT 24 HINDCAST WAVE INFORMATION FOR THE GREAT LAKES : LAKE MICHIGAN...October 1991 Final report 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Hindcast Wave Information for the Great Lakes : Lake Michigan 6. AUTHOR(S) Jon M

  14. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

    PubMed Central

    Smith, Stephen A; Beaulieu, Jeremy M; Donoghue, Michael J

    2009-01-01

    Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Results Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae) with 13,533 species and 1,401 sites. Conclusion By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes

  15. 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.

  16. Ecology under lake ice.

    PubMed

    Hampton, Stephanie E; Galloway, Aaron W E; Powers, Stephen M; Ozersky, Ted; Woo, Kara H; Batt, Ryan D; Labou, Stephanie G; O'Reilly, Catherine M; Sharma, Sapna; Lottig, Noah R; Stanley, Emily H; North, Rebecca L; Stockwell, Jason D; Adrian, Rita; Weyhenmeyer, Gesa A; Arvola, Lauri; Baulch, Helen M; Bertani, Isabella; Bowman, Larry L; Carey, Cayelan C; Catalan, Jordi; Colom-Montero, William; Domine, Leah M; Felip, Marisol; Granados, Ignacio; Gries, Corinna; Grossart, Hans-Peter; Haberman, Juta; Haldna, Marina; Hayden, Brian; Higgins, Scott N; Jolley, Jeff C; Kahilainen, Kimmo K; Kaup, Enn; Kehoe, Michael J; MacIntyre, Sally; Mackay, Anson W; Mariash, Heather L; McKay, Robert M; Nixdorf, Brigitte; Nõges, Peeter; Nõges, Tiina; Palmer, Michelle; Pierson, Don C; Post, David M; Pruett, Matthew J; Rautio, Milla; Read, Jordan S; Roberts, Sarah L; Rücker, Jacqueline; Sadro, Steven; Silow, Eugene A; Smith, Derek E; Sterner, Robert W; Swann, George E A; Timofeyev, Maxim A; Toro, Manuel; Twiss, Michael R; Vogt, Richard J; Watson, Susan B; Whiteford, Erika J; Xenopoulos, Marguerite A

    2017-01-01

    Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer 'growing seasons'. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.

  17. 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

  18. 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.

  19. Ecology of playa lakes

    USGS Publications Warehouse

    Haukos, David A.; Smith, Loren M.

    1992-01-01

    Between 25,000 and 30,000 playa lakes are in the playa lakes region of the southern high plains (Fig. 1). Most playas are in west Texas (about 20,000), and fewer, in New Mexico, Oklahoma, Kansas, and Colorado. The playa lakes region is one of the most intensively cultivated areas of North America. Dominant crops range from cotton in southern areas to cereal grains in the north. Therefore, most of the native short-grass prairie is gone, replaced by crops and, recently, grasses of the Conservation Reserve Program. Playas are the predominant wetlands and major wildlife habitat of the region.More than 115 bird species, including 20 species of waterfowl, and 10 mammal species have been documented in playas. Waterfowl nest in the area, producing up to 250,000 ducklings in wetter years. Dominant breeding and nesting species are mallards and blue-winged teals. During the very protracted breeding season, birds hatch from April through August. Several million shorebirds and waterfowl migrate through the area each spring and fall. More than 400,000 sandhill cranes migrate through and winter in the region, concentrating primarily on the larger saline lakes in the southern portion of the playa lakes region.The primary importance of the playa lakes region to waterfowl is as a wintering area. Wintering waterfowl populations in the playa lakes region range from 1 to 3 million birds, depending on fall precipitation patterns that determine the number of flooded playas. The most common wintering ducks are mallards, northern pintails, green-winged teals, and American wigeons. About 500,000 Canada geese and 100,000 lesser snow geese winter in the playa lakes region, and numbers of geese have increased annually since the early 1980’s. This chapter describes the physiography and ecology of playa lakes and their attributes that benefit waterfowl.

  20. The Great Salt Lake

    USGS Publications Warehouse

    Hassibe, W.R.; Keck, W.G.

    1991-01-01

    The western part of the conterminous United States is often thought of as being a desert without any large bodies of water. In the desert area of western Utah, however, lies Great Salt Lake, which in 1986 covered approximately 2,300 square miles and contained 30 million acre-feet of water (an acre-foot is the amount of water necessary to cover 1 acre of land with water 1 foot in depth or about 326,000 gallons). To emphasize its size, the Great Salt Lake is the largest lake west of the Mississippi River, larger than the states of Rhode Island and Delaware.

  1. National Lakes Assessment Data

    EPA Pesticide Factsheets

    The National Lakes Assessment (NLA) is a first-ever statistically-valid survey of the biological condition of lakes and reservoirs throughout the U.S. The U.S. Environmental Protection Agency (EPA) worked with states and tribes to conduct the assessment in 2007. Data for each parameter sampled in the National Lakes Assessment (NLA) are available for downloading in a series of files as comma separated values (*.csv). Each *.csv data file has a companion text file (*.txt) that lists a dataset label and individual descriptions for each variable. Users should view the *.txt files first to help guide their understanding and use of the data.

  2. Can lake sensitivity to desiccation be predicted from lake geometry?

    NASA Astrophysics Data System (ADS)

    Torabi Haghighi, Ali; Menberu, Meseret Walle; Aminnezhad, Mousa; Marttila, Hannu; Kløve, Bjørn

    2016-08-01

    Declining lake levels (Aral Sea syndrome) can be caused by changes in climate, increased water use or changed regulation patterns. This paper introduces a novel lake geometry index (LGI) to quantify lake hydrological characteristics. The index was developed using a large representative dataset of lake hypsographic characteristics from 152 lakes and man-made reservoirs. Using the LGI index, lakes can be classified into five groups: groups 1-4 when LGI is 0.5-2.5, 2.5-4.5, 4.5-6.5 and 6.5-8.5, respectively, and group 5 when LGI is >8.5. Naturally shallow and vast lakes and wetlands fall into the first group and deep man-made reservoirs in narrow valleys are in group 5. The response of three different lake systems (LGI 0.75, 2.75 and 6.5) to different water flow scenarios was then simulated using the water balance equation. From this, the index 'potential lake area' (Apot) was developed to show lake responses to changed hydro-climatological conditions. Apot and LGI can be used to classify lakes into open or closed systems. Simulations showed that lakes with low LGI have a shorter response time to flow and climate changes. As a result, the impact of water balance restoration is faster for lakes with low LGI than for lakes with high LGI. The latter are also more vulnerable to climate variation and change.

  3. Phylogeny and evolution of glass sponges (porifera, hexactinellida).

    PubMed

    Dohrmann, Martin; Janussen, Dorte; Reitner, Joachim; Collins, Allen G; Worheide, Gert

    2008-06-01

    Reconstructing the phylogeny of sponges (Porifera) is one of the remaining challenges to resolve the metazoan Tree of Life and is a prerequisite for understanding early animal evolution. Molecular phylogenetic analyses for two of the three extant classes of the phylum, Demospongiae and Calcarea, are largely incongruent with traditional classifications, most likely because of a paucity of informative morphological characters and high levels of homoplasy. For the third class, Hexactinellida (glass sponges)--predominantly deep-sea inhabitants with unusual morphology and biology--we present the first molecular phylogeny, along with a cladistic analysis of morphological characters. We collected 18S, 28S, and mitochondrial 16S ribosomal DNA sequences of 34 glass sponge species from 27 genera, 9 families, and 3 orders and conducted partitioned Bayesian analyses using RNA secondary structure-specific substitution models (paired-sites models) for stem regions. Bayes factor comparisons of different paired-sites models against each other and conventional (independent-sites) models revealed a significantly better fit of the former but, contrary to previous predictions, the least parameter-rich of the tested paired-sites models provided the best fit to our data. In contrast to Demospongiae and Calcarea, our rDNA phylogeny agrees well with the traditional classification and a previously proposed phylogenetic system, which we ascribe to a more informative morphology in Hexactinellida. We find high support for a close relationship of glass sponges and Demospongiae sensu stricto, though the latter may be paraphyletic with respect to Hexactinellida. Homoscleromorpha appears to be the sister group of Calcarea. Contrary to most previous findings from rDNA, we recover Porifera as monophyletic, although support for this clade is low under paired-sites models.

  4. Recapitulating phylogenies using k-mers: from trees to networks

    PubMed Central

    Bernard, Guillaume; Ragan, Mark A.; Chan, Cheong Xin

    2016-01-01

    Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k-mers (subsequences at fixed length k). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel’s idea of ontogeny, we argue that genome phylogenies can be inferred using k-mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner. PMID:28105314

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

    NASA Astrophysics Data System (ADS)

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

    2001-07-01

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

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

    PubMed

    Takahashi, Tetsumi; Moreno, Edmundo

    2015-12-01

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

  7. Phylogeny of Vibrio cholerae Based on recA Sequence

    PubMed Central

    Stine, O. Colin; Sozhamannan, Shanmuga; Gou, Qing; Zheng, Siqen; Morris, J. Glenn; Johnson, Judith A.

    2000-01-01

    We sequenced a 705-bp fragment of the recA gene from 113 Vibrio cholerae strains and closely related species. One hundred eighty-seven nucleotides were phylogenetically informative, 55 were phylogenetically uninformative, and 463 were invariant. Not unexpectedly, Vibrio parahaemolyticus and Vibrio vulnificus strains formed out-groups; we also identified isolates which resembled V. cholerae biochemically but which did not cluster with V. cholerae. In many instances, V. cholerae serogroup designations did not correlate with phylogeny, as reflected by recA sequence divergence. This observation is consistent with the idea that there is horizontal transfer of O-antigen biosynthesis genes among V. cholerae strains. PMID:11083852

  8. The phylogeny of invertebrates and the evolution of myelin.

    PubMed

    Roots, Betty I

    2008-05-01

    Current concepts of invertebrate phylogeny are reviewed. Annelida and Arthropoda, previously regarded as closely related, are now placed in separate clades. Myelin, a sheath of multiple layers of membranes around nerve axons, is found in members of the Annelida, Arthropoda and Chordata. The structure, composition and function of the sheaths in Annelida and Arthropoda are examined and evidence for the separate evolutionary origins of myelin in the three clades is presented. That myelin has arisen independently at least three times, namely in Annelids, Arthropodas and Chordates, provides a remarkable example of convergent evolution.

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

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

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

  10. The phylogeny of yeasts—A cladistic analysis

    NASA Astrophysics Data System (ADS)

    Sun, Xiuqin; Wu, Baoling

    1992-12-01

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

  11. Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

    PubMed

    Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

    2017-04-01

    Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era.

  12. Challenges to the Lake

    EPA Science Inventory

    During the past decade we have extensively studied coastal ecosystems in the Great Lakes. Some research efforts have linked coastal receiving systems to conditions in their contributing watersheds; others have focused on developing invasive species detection and monitoring strat...

  13. About Deer Lake AOC

    EPA Pesticide Factsheets

    Named an Area of Concern under the Great Lakes Water Quality Agreement of 1987, due to beneficial use impairments caused by mercury contamination: consumption restrictions, deformities or reproductive problems, eutrophication.

  14. Estimating shifts in diversification rates based on higher-level phylogenies

    PubMed Central

    Smrckova, Jana

    2016-01-01

    Macroevolutionary studies recently shifted from only reconstructing the past state, i.e. the species phylogeny, to also infer the past speciation and extinction dynamics that gave rise to the phylogeny. Methods for estimating diversification dynamics are sensitive towards incomplete species sampling. We introduce a method to estimate time-dependent diversification rates from phylogenies where clades of a particular age are represented by only one sampled species. A popular example of this type of data is phylogenies on the genus- or family-level, i.e. phylogenies where one species per genus or family is included. We conduct a simulation study to validate our method in a maximum-likelihood framework. Further, this method has already been introduced into the Bayesian package MrBayes, which led to new insights into the evolution of Hymenoptera. PMID:27703054

  15. Is Lake Tahoe Terminal?

    NASA Astrophysics Data System (ADS)

    Coats, R. N.; Reuter, J.; Heyvaert, A.; Lewis, J.; Sahoo, G. B.; Schladow, G.; Thorne, J. H.

    2014-12-01

    Lake Tahoe, an iconic ultra-oligotrophic lake in the central Sierra Nevada, has been studied intensively since 1968, with the goal of understanding and ultimately controlling its eutrophication and loss of clarity. Research on the lake has included a) periodic profiles of primary productivity, nutrients, temperature, and plankton; b) Secchi depth; c) nutrient limitation experiments; d) analysis of sediment cores; e) radiocarbon dating of underwater in-place tree stumps; g) analysis of long-term temperature trends. Work in its watershed has included a) monitoring of stream discharge, sediment and nutrients at up to 20 stream gaging stations; b) monitoring of urban runoff water quality at selected sites; c) development of a GIS data base, including soils, vegetation, and land use. Based on these studies, we know that a) primary productivity in the lake is limited by phosphorus, and continues to increase; b) the loss of clarity continues, but at a declining rate; c) the lake has been warming since 1970, and its resistance to deep mixing is increasing; d) historically the lake level drops below the outlet elevation about one year in seven; e) 6300 to 4300 yrs BP lake level was below the present outlet elevation long enough for large trees to grow; f) the date of the peak snowmelt runoff is shifting toward earlier dates; g) after accounting for annual runoff, loads of nutrients and suspended sediment have declined significantly in some basin streams since 1980. Downscaled outputs from GCM climatic models have recently been used to drive hydrologic models and a lake clarity model, projecting future trends in the lake and watersheds. Results show a) the temperature and thermal stability will likely continue to increase, with deep mixing shutting down in the latter half of this century; b) the lake may drop below the outlet for an extended period beginning about 2085; c) the annual snowpack will continue to decline, with earlier snowmelt and shift from snowfall to rain; d

  16. Stratification of lakes

    NASA Astrophysics Data System (ADS)

    Boehrer, Bertram; Schultze, Martin

    2008-06-01

    Many lakes show vertical stratification of their water masses, at least for some extended time periods. Density differences in water bodies facilitate an evolution of chemical differences with many consequences for living organisms in lakes. Temperature and dissolved substances contribute to density differences in water. The atmosphere imposes a temperature signal on the lake surface. As a result, thermal stratification can be established during the warm season if a lake is sufficiently deep. On the contrary, during the cold period, surface cooling forces vertical circulation of water masses and removal of gradients of water properties. However, gradients of dissolved substances may be sustained for periods much longer than one annual cycle. Such lakes do not experience full overturns. Gradients may be a consequence of external inflows or groundwater seepage. In addition, photosynthesis at the lake surface and subsequent decomposition of organic material in the deeper layers of a lake can sustain a gradient of dissolved substances. Three more geochemical cycles, namely, calcite precipitation, iron cycle, and manganese cycle, are known for sustaining meromixis. A limited number of lakes do not experience a complete overturn because of pressure dependence of temperature of maximum density. Such lakes must be sufficiently deep and lie in the appropriate climate zone. Although these lakes are permanently stratified, deep waters are well ventilated, and chemical differences are small. Turbulent mixing and convective deep water renewal must be very effective. As a consequence, these lakes usually are not termed meromictic. Permanent stratification may also be created by episodic partial recharging of the deep water layer. This mechanism resembles the cycling of the ocean: horizontal gradients result from gradients at the surface, such as differential cooling or enhanced evaporation in adjacent shallow side bays. Dense water parcels can be formed which intrude the deep

  17. Lake Chad, Chad, Africa

    NASA Technical Reports Server (NTRS)

    1988-01-01

    The fluctuating water levels of Lake Chad, (13.0N, 15.0E) at the intersection of the borders of Chad, Niger and Cameroon in the Sahara Desert, is an index of the drought in Africa. The lake level continues to decrease as indicated by the growing number and extent of emerging islands as previously submerged ancient sand dunes become visible. The water impounded between the dunes is probably because of local rainfall rather than a reversal of desertification.

  18. Antarctic subglacial lake discharges

    NASA Astrophysics Data System (ADS)

    Pattyn, Frank

    Antarctic subglacial lakes were long time supposed to be relatively closed and stable environments with long residence times and slow circulations. This view has recently been challenged with evidence of active subglacial lake discharge underneath the Antarctic ice sheet. Satellite altimetry observations witnessed rapid changes in surface elevation across subglacial lakes over periods ranging from several months to more than a year, which were interpreted as subglacial lake discharge and subsequent lake filling, and which seem to be a common and widespread feature. Such discharges are comparable to jökulhlaups and can be modeled that way using the Nye-Röthlisberger theory. Considering the ice at the base of the ice sheet at pressure melting point, subglacial conduits are sustainable over periods of more than a year and over distances of several hundreds of kilometers. Coupling of an ice sheet model to a subglacial lake system demonstrated that small changes in surface slope are sufficient to start and sustain episodic subglacial drainage events on decadal time scales. Therefore, lake discharge may well be a common feature of the subglacial hydrological system, influencing the behavior of large ice sheets, especially when subglacial lakes are perched at or near the onset of large outlet glaciers and ice streams. While most of the observed discharge events are relatively small (101-102 m3 s-1), evidence for larger subglacial discharges is found in ice free areas bordering Antarctica, and witnessing subglacial floods of more than 106 m3 s-1 that occurred during the middle Miocene.

  19. Dragon Lake, Siberia

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Nicknamed 'Dragon Lake,' this body of water is formed by the Bratskove Reservoir, built along the Angara river in southern Siberia, near the city of Bratsk. This image was acquired in winter, when the lake is frozen. This image was acquired by Landsat 7's Enhanced Thematic Mapper plus (ETM+) sensor on December 19, 1999. This is a natural color composite image made using blue, green, and red wavelengths. Image provided by the USGS EROS Data Center Satellite Systems Branch

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

    PubMed

    Smith, W Leo; Busby, Morgan S

    2014-10-01

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

  1. Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.

    PubMed

    Meinel, Thomas; Krause, Antje

    2012-01-01

    In the last two decades, a large number of whole-genome phylogenies have been inferred to reconstruct the Tree of Life (ToL). Underlying data models range from gene or functionality content in species to phylogenetic gene family trees and multiple sequence alignments of concatenated protein sequences. Diversity in data models together with the use of different tree reconstruction techniques, disruptive biological effects and the steadily increasing number of genomes have led to a huge diversity in published phylogenies. Comparison of those and, moreover, identification of the impact of inference properties (underlying data model, inference technique) on particular reconstructions is almost impossible. In this work, we introduce tree topology profiling as a method to compare already published whole-genome phylogenies. This method requires visual determination of the particular topology in a drawn whole-genome phylogeny for a set of particular bacterial clans. For each clan, neighborhoods to other bacteria are collected into a catalogue of generalized alternative topologies. Particular topology alternatives found for an ordered list of bacterial clans reveal a topology profile that represents the analyzed phylogeny. To simulate the inhomogeneity of published gene content phylogenies we generate a set of seven phylogenies using different inference techniques and the SYSTERS-PhyloMatrix data model. After tree topology profiling on in total 54 selected published and newly inferred phylogenies, we separate artefactual from biologically meaningful phylogenies and associate particular inference results (phylogenies) with inference background (inference techniques as well as data models). Topological relationships of particular bacterial species groups are presented. With this work we introduce tree topology profiling into the scientific field of comparative phylogenomics.

  2. Lake retention of manufactured nanoparticles.

    PubMed

    Koelmans, A A; Quik, J T K; Velzeboer, I

    2015-01-01

    For twenty-five world lakes and three engineered nanoparticles (ENP), lake retention was calculated using a uniformly mixed lake mass balance model. This follows similar approaches traditionally used in water quality management. Lakes were selected such that lake residence times, depths and areal hydraulic loadings covered the widest possible range among existing lakes. Sedimentation accounted for natural colloid as well as suspended solid settling regimes. An ENP-specific mixed sedimentation regime is proposed. This regime combines ENP sedimentation through slow settling with natural colloids from the water column, with faster settling with suspended solids from a selected part of the water column. Although sedimentation data and hydrodynamic concepts as such were not new, their first time combination or application to ENPs shows in which cases lake retention is important for these particles. In combination with ENP emission data, lake retention translates directly into potential risks of ENPs for lake benthic communities.

  3. Schistosomiasis in Lake Malawi.

    PubMed

    Cetron, M S; Chitsulo, L; Sullivan, J J; Pilcher, J; Wilson, M; Noh, J; Tsang, V C; Hightower, A W; Addiss, D G

    1996-11-09

    Schistosomiasis is a parasitic infection caused by trematodes. Humans are infected through skin contact with free-swimming cercariae which develop in freshwater snails. Schistosomiasis has been endemic to Malawi for several decades, but the open waters and shores of Lake Malawi have long been thought to be risk-free with regard to schistosomiasis transmission. However, in 1992, two US Peace Corps volunteers developed central nervous system schistosomiasis due to infection with Schistosoma haematobium following recreational water exposure at Cape Maclear on Lake Malawi. In light of these infections, a cross-sectional survey of resident expatriates and visitors to Malawi was subsequently conducted during March-April 1993 to determine the transmission potential and risk for acquiring schistosomiasis in the lake. 305 US citizens and 650 non-US foreign nationals participated in the study. Serological evidence of current or past schistosome infection was identified in 303 subjects. Indeed, seroprevalence was 32% among expatriates whose freshwater exposure was limited to Lake Malawi; S. haematobium antibodies were found in 135 of 141 seropositive specimens. The risk of seropositivity increased with the number of freshwater exposures at Lake Malawi resorts. While many resort areas in the southwestern lake region posed a significant risk, Cape Maclear was the location most strongly associated with seropositivity. Schistosome-infected Bulinus globosus, the snail vector of S. haematobium in Malawi, were found at Cape Maclear and other locations along the lakeshore.

  4. Salt Lake City, Utah

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Salt Lake City, Utah, will host the 2002 Winter Olympic Games. The city is located on the southeastern shore of the Great Salt Lake and sits to the west of the Wasatch Mountains, which rise more than 3,500 meters (10,000 feet) above sea level. The city was first settled in 1847 by pioneers seeking relief from religious persecution. Today Salt Lake City, the capital of Utah, is home to more than 170,000 residents. This true-color image of Salt Lake City was acquired by the Enhanced Thematic Mapper Plus (ETM+), flying aboard Landsat 7, on May 26, 2000. The southeastern tip of the Great Salt Lake is visible in the upper left of the image. The furrowed green and brown landscape running north-south is a portion of the Wasatch Mountains, some of which are snow-capped (white pixels). The greyish pixels in the center of the image show the developed areas of the city. A number of water reservoirs can be seen east of the mountain range. Salt Lake City International Airport is visible on the northwestern edge of the city. About 20 miles south of the airport is the Bingham Canyon Copper Mine (tan pixels), the world's largest open pit excavation. See also this MODIS image of Utah. Image courtesy NASA Landsat7 Science Team and USGS Eros Data Center

  5. Red Lake and Clearwater Rivers, Red Lake County, Minnesota. Reconnaissance Report for Red Lake and Clearwater Rivers

    DTIC Science & Technology

    1991-08-01

    the -stbbasin. These are the result of efforts by the U.S. Fish and Wildlife Service (e.g., Agassiz Lake Project and Goose Lake Project), U.S. Soil...by glacial Lake Agassiz . Upper and Lower Red Lakes are remnants of this glacial lake. The topography of the subbasin ranges from 800 feet above mean...glacial Lake Agassiz and together comprise thelargest lake area wholly contained in Minnesota. The watershed drained by the Red Lake River lies within

  6. Is Lake Chabot Eutrophic?

    NASA Astrophysics Data System (ADS)

    Pellegrini, K.; Logan, J.; Esterlis, P.; Lew, A.; Nguyen, M.

    2013-12-01

    Introduction/Abstract: Lake Chabot is an integral part of the East Bay watershed that provides habitats for animals and recreation for humans year-round. Lake Chabot has been in danger of eutrophication due to excessive dumping of phosphorous and nitrogen into the water from the fertilizers of nearby golf courses and neighboring houses. If the lake turned out to be eutrophified, it could seriously impact what is currently the standby emergency water supply for many Castro Valley residents. Eutrophication is the excessive richness of nutrients such as nitrogen and phosphorus in a lake, usually as a result of runoff. This buildup of nutrients causes algal blooms. The algae uses up most of the oxygen in the water, and when it dies, it causes the lake to hypoxify. The fish in the lake can't breathe, and consequently suffocate. Other oxygen-dependant aquatic creatures die off as well. Needless to say, the eutrophication of a lake is bad news for the wildlife that lives in or around it. The level of eutrophication in our area in Northern California tends to increase during the late spring/early summer months, so our crew went out and took samples of Lake Chabot on June 2. We focused on the area of the lake where the water enters, known on the map as Honker Bay. We also took readings a ways down in deeper water for comparison's sake. Visually, the lake looked in bad shape. The water was a murky green that glimmered with particulate matter that swirled around the boat as we went by. In the Honker Bay region where we focused our testing, there were reeds bathed in algae that coated the surface of the lake in thick, swirling patterns. Surprisingly enough, however, our test results didn't reveal any extreme levels of phosphorous or nitrogen. They were slightly higher than usual, but not by any significant amount. The levels we found were high enough to stimulate plant and algae growth and promote eutrophication, but not enough to do any severe damage. After a briefing with a

  7. TOXAPHENE STUDY OF GREAT LAKES TRIBUTARY SEDIMENTS

    EPA Science Inventory

    The Product is the paper "Pulp and Paper Mills as Sources of Toxaphene to Lake Superior and Northern Lake Michigan" published in the Journal of Great Lakes Research, 25(2):383-394 International Association of Great Lakes 1999.

  8. Glacial lake inventory and lake outburst potential in Uzbekistan.

    PubMed

    Petrov, Maxim A; Sabitov, Timur Y; Tomashevskaya, Irina G; Glazirin, Gleb E; Chernomorets, Sergey S; Savernyuk, Elena A; Tutubalina, Olga V; Petrakov, Dmitriy A; Sokolov, Leonid S; Dokukin, Mikhail D; Mountrakis, Giorgos; Ruiz-Villanueva, Virginia; Stoffel, Markus

    2017-03-16

    Climate change has been shown to increase the number of mountain lakes across various mountain ranges in the World. In Central Asia, and in particular on the territory of Uzbekistan, a detailed assessment of glacier lakes and their evolution over time is, however lacking. For this reason we created the first detailed inventory of mountain lakes of Uzbekistan based on recent (2002-2014) satellite observations using WorldView-2, SPOT5, and IKONOS imagery with a spatial resolution from 2 to 10m. This record was complemented with data from field studies of the last 50years. The previous data were mostly in the form of inventories of lakes, available in Soviet archives, and primarily included localized in-situ data. The inventory of mountain lakes presented here, by contrast, includes an overview of all lakes of the territory of Uzbekistan. Lakes were considered if they were located at altitudes above 1500m and if lakes had an area exceeding 100m(2). As in other mountain regions of the World, the ongoing increase of air temperatures has led to an increase in lake number and area. Moreover, the frequency and overall number of lake outburst events have been on the rise as well. Therefore, we also present the first outburst assessment with an updated version of well-known approaches considering local climate features and event histories. As a result, out of the 242 lakes identified on the territory of Uzbekistan, 15% are considered prone to outburst, 10% of these lakes have been assigned low outburst potential and the remainder of the lakes have an average level of outburst potential. We conclude that the distribution of lakes by elevation shows a significant influence on lake area and hazard potential. No significant differences, by contrast, exist between the distribution of lake area, outburst potential, and lake location with respect to glaciers by regions.

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

    PubMed Central

    Bollmann, Annette; Bullerjahn, George S.; McKay, Robert Michael

    2014-01-01

    Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes. PMID:24819357

  10. Adipokinetic hormones provide inference for the phylogeny of odonata.

    PubMed

    Gäde, Gerd; Simek, Petr; Fescemyer, Howard W

    2011-01-01

    Adipokinetic neuropeptides from the corpora cardiaca of 17 species of Odonata encompassing mainly the families Corduliidae and Libellulidae were isolated and structurally elucidated using liquid chromatography coupled with ion trap electrospray ionization mass spectrometry. It became evident that all species of the family Corduliidae studied express the peptide code-named Libau-AKH (pGlu-Val-Asn-Phe-Thr-Pro-Ser-Trp amide), which is also present in all but one libellulid species, Erythemis simplicicollis which expresses Erysi-AKH (pGlu-Leu-Asn-Phe-Thr-Pro-Ser-Trp amide). This divergence from all other Libellulids is due to a nonsynonymous missense single nucleotide polymorphism (SNP) in the nucleotide coding sequence (CDS) of prepro-AKH CDS and supports the polyphyletic nature of Sympetrinae and other subfamilies of libellulids. Despite this exception, these findings then support the hypothesis that Corduliidae and Libellulidae are closely related as stated in most phylogenies. The presence of Anaim-AKH (pGlu-Val-Asn-Phe-Ser-Pro-Ser-Trp amide) in Macromiidae likely distinguishes species in this family from Corduliidae. Current molecular genetic phylogenies and our AKH findings suggest that Syncordulia gracilis, which expresses Anaim-AKH, does not belong in Corduliidae. Evolution of AKHs in anisopteran Odonata are likely due to nucleotide substitution involving nonsynonymous missense SNPs in the CDS of prepro-AKH.

  11. Mixed integer linear programming for maximum-parsimony phylogeny inference.

    PubMed

    Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell

    2008-01-01

    Reconstruction of phylogenetic trees is a fundamental problem in computational biology. While excellent heuristic methods are available for many variants of this problem, new advances in phylogeny inference will be required if we are to be able to continue to make effective use of the rapidly growing stores of variation data now being gathered. In this paper, we present two integer linear programming (ILP) formulations to find the most parsimonious phylogenetic tree from a set of binary variation data. One method uses a flow-based formulation that can produce exponential numbers of variables and constraints in the worst case. The method has, however, proven extremely efficient in practice on datasets that are well beyond the reach of the available provably efficient methods, solving several large mtDNA and Y-chromosome instances within a few seconds and giving provably optimal results in times competitive with fast heuristics than cannot guarantee optimality. An alternative formulation establishes that the problem can be solved with a polynomial-sized ILP. We further present a web server developed based on the exponential-sized ILP that performs fast maximum parsimony inferences and serves as a front end to a database of precomputed phylogenies spanning the human genome.

  12. Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida).

    PubMed

    Smirnov, Alexey; Nassonova, Elena; Geisen, Stefan; Bonkowski, Michael; Kudryavtsev, Alexander; Berney, Cedric; Glotova, Anna; Bondarenko, Natalya; Dyková, Iva; Mrva, Martin; Fahrni, Jose; Pawlowski, Jan

    2016-10-26

    We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other.

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

    PubMed

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

    2015-02-19

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

  14. Phylogeny Explains Variation in The Root Chemistry of Eucalyptus Species.

    PubMed

    Senior, John K; Potts, Brad M; Davies, Noel W; Wooliver, Rachel C; Schweitzer, Jennifer A; Bailey, Joseph K; O'Reilly-Wapstra, Julianne M

    2016-10-01

    Plants are dependent on their root systems for survival, and thus are defended from belowground enemies by a range of strategies, including plant secondary metabolites (PSMs). These compounds vary among species, and an understanding of this variation may provide generality in predicting the susceptibility of forest trees to belowground enemies and the quality of their organic matter input to soil. Here, we investigated phylogenetic patterns in the root chemistry of species within the genus Eucalyptus. Given the known diversity of PSMs in eucalypt foliage, we hypothesized that (i) the range and concentrations of PSMs and carbohydrates in roots vary among Eucalyptus species, and (ii) that phylogenetic relationships explain a significant component of this variation. To test for interspecific variation in root chemistry and the influence of tree phylogeny, we grew 24 Eucalyptus species representing two subgenera (Eucalyptus and Symphyomyrtus) in a common garden for two years. Fine root samples were collected from each species and analyzed for total phenolics, condensed tannins, carbohydrates, terpenes, and formylated phloroglucinol compounds. Compounds displaying significant interspecific variation were mapped onto a molecular phylogeny and tested for phylogenetic signal. Although all targeted groups of compounds were present, we found that phenolics dominated root defenses and that all phenolic traits displayed significant interspecific variation. Further, these compounds displayed a significant phylogenetic signal. Overall, our results suggest that within these representatives of genus Eucalyptus, more closely related species have more similar root chemistry, which may influence their susceptibility to belowground enemies and soil organic matter accrual.

  15. Phylogeny and biogeography of the fruit doves (Aves: Columbidae).

    PubMed

    Cibois, Alice; Thibault, Jean-Claude; Bonillo, Céline; Filardi, Christopher E; Watling, Dick; Pasquet, Eric

    2014-01-01

    We reconstruct the phylogeny of fruit doves (genus Ptilinopus) and allies with a dense sampling that includes almost all species, based on mitochondrial and nuclear sequence data. We evaluate the most likely biogeographic scenario for the evolution of this group that colonized many islands of the Pacific Ocean. We also investigate the evolution of one of the main plumage character of fruit doves (the color of the crown), and we propose several revisions of the group's systematics. All Ptilinopus taxa formed a monophyletic group that includes two morphologically distinct genera, Alectroenas and Drepanoptila, confirming a previous result found with less species and genes. The divergence time analysis suggests that the basal divergences within Ptilinopus dated to the Early Oligocene, and the biogeographic analysis indicates that fruit doves originated most probably from the proto New Guinea region. The earliest dispersals from the New Guinea region to Oceania occurred with the colonization of New Caledonia and Fiji. A large group of Polynesian species (Central and Eastern), as well as the three taxa found in Micronesia and four species from the Guinean-Moluccan region, form the "purpuratus" clade, the largest diversification of fruit doves within Oceania, which also has a New Guinean origin. However, the eastbound colonization of fruit doves was not associated with a significant increase of their diversification rate. Overall, the Melanesian region did not act as a cradle for fruit doves, in contrast to the New Guinea region which is found as the ancestral area for several nodes within the phylogeny.

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

    PubMed

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

    2016-07-18

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

  17. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.

    PubMed

    Bernt, Matthias; Bleidorn, Christoph; Braband, Anke; Dambach, Johannes; Donath, Alexander; Fritzsch, Guido; Golombek, Anja; Hadrys, Heike; Jühling, Frank; Meusemann, Karen; Middendorf, Martin; Misof, Bernhard; Perseke, Marleen; Podsiadlowski, Lars; von Reumont, Björn; Schierwater, Bernd; Schlegel, Martin; Schrödl, Michael; Simon, Sabrina; Stadler, Peter F; Stöger, Isabella; Struck, Torsten H

    2013-11-01

    About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.

  18. A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences.

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-05-01

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

  1. An experimental phylogeny to benchmark ancestral sequence reconstruction

    PubMed Central

    Randall, Ryan N.; Radford, Caelan E.; Roof, Kelsey A.; Natarajan, Divya K.; Gaucher, Eric A.

    2016-01-01

    Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as ‘modern' sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences. PMID:27628687

  2. Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and character evolution.

    PubMed

    Justo, Alfredo; Vizzini, Alfredo; Minnis, Andrew M; Menolli, Nelson; Capelari, Marina; Rodríguez, Olivia; Malysheva, Ekaterina; Contu, Marco; Ghignone, Stefano; Hibbett, David S

    2011-01-01

    The phylogeny of the genera traditionally classified in the family Pluteaceae (Agaricales, Basidiomycota) was investigated using molecular data from nuclear ribosomal genes (nSSU, ITS, nLSU) and consequences for taxonomy and character evolution were evaluated. The genus Volvariella is polyphyletic, as most of its representatives fall outside the Pluteoid clade and shows affinities to some hygrophoroid genera (Camarophyllus, Cantharocybe). Volvariella gloiocephala and allies are placed in a different clade, which represents the sister group of Pluteus, and a new generic name, Volvopluteus, is proposed to accommodate these taxa. Characters such as basidiospore size and pileipellis structure can be used to separate Pluteus, Volvariella and Volvopluteus. The genus Pluteus is monophyletic and includes species with partial veil traditionally classified in the genus Chamaeota. The evolution of morphological features used in the infrageneric taxonomy of the genus, such as metuloid cystidia and pileipellis structure, was analyzed. Agreement between the molecular phylogeny and morphological subdivision of Pluteus is, generally speaking, good, though some rearrangements are necessary: (i) species with non-metuloid pleurocystidia and pileipellis as a cutis are placed either in sect. Celluloderma, together with the species characterized by a hymenidermal pipeipellis, or in sect. Pluteus, with the metuloid bearing species; (ii) subdivision of sect. Celluloderma according to the presence/absence of cystidioid elements in the pileipellis is not supported by molecular data.

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

    PubMed

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

    2013-04-01

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

  4. Single-cell mutational profiling and clonal phylogeny in cancer

    PubMed Central

    Potter, Nicola E.; Ermini, Luca; Papaemmanuil, Elli; Cazzaniga, Giovanni; Vijayaraghavan, Gowri; Titley, Ian; Ford, Anthony; Campbell, Peter; Kearney, Lyndal; Greaves, Mel

    2013-01-01

    The development of cancer is a dynamic evolutionary process in which intraclonal, genetic diversity provides a substrate for clonal selection and a source of therapeutic escape. The complexity and topography of intraclonal genetic architectures have major implications for biopsy-based prognosis and for targeted therapy. High-depth, next-generation sequencing (NGS) efficiently captures the mutational load of individual tumors or biopsies. But, being a snapshot portrait of total DNA, it disguises the fundamental features of subclonal variegation of genetic lesions and of clonal phylogeny. Single-cell genetic profiling provides a potential resolution to this problem, but methods developed to date all have limitations. We present a novel solution to this challenge using leukemic cells with known mutational spectra as a tractable model. DNA from flow-sorted single cells is screened using multiplex targeted Q-PCR within a microfluidic platform allowing unbiased single-cell selection, high-throughput, and comprehensive analysis for all main varieties of genetic abnormalities: chimeric gene fusions, copy number alterations, and single-nucleotide variants. We show, in this proof-of-principle study, that the method has a low error rate and can provide detailed subclonal genetic architectures and phylogenies. PMID:24056532

  5. The geological record and phylogeny of the Myriapoda.

    PubMed

    Shear, William A; Edgecombe, Gregory D

    2010-01-01

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

  6. A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes).

    PubMed

    Santini, Francesco; Sorenson, Laurie; Marcroft, Tina; Dornburg, Alex; Alfaro, Michael E

    2013-01-01

    Boxfishes (superfamily Ostracioidea, order Tetraodontiformes) are comprised of 37 species within the families Aracanidae (13 sp.) and Ostracidae (24 sp.). These species are characterized by several dramatic reductive trends in their axial and appendicular skeleton, and by the presence of a carapace formed by enlarged and thickened scale plates. While strong support exists for the monophyly of both families, interspecific relationships remain unclear as no species-level molecular phylogeny currently exists for either of these two clades, and the only hypotheses of relationships are based on morphological studies that were mostly restricted to generic-level relationships. Here we present the results of a new phylogenetic study of a dataset composed of 9 loci for 26 species of boxfishes using both likelihood and Bayesian methods. Our topology strongly supports the monophyly of both groups, and additionally provides strongly supported resolution for the vast majority of species-level interrelationships. Based on this new phylogeny, we suggest changing the taxonomic status of the species Lactoria fornasini to Tetrasomus fornasini, and Rhynchostracion nasus to Ostracion nasus. Using a Bayesian approach to divergence time estimation we inferred a Paleocene origin of the Ostracioidea, with an estimated origin of the reef-associated ostraciids spanning the Eocene and Oligocene, and a Miocene/Pliocene origin of the aracanids.

  7. Phylogeny and development of marine model species: strongylocentrotid sea urchins.

    PubMed

    Biermann, Christiane H; Kessing, Bailey D; Palumbi, Stephen R

    2003-01-01

    The phylogenetic relationships of ten strongy-locentrotid sea urchin species were determined using mitochondrial DNA sequences. This phylogeny provides a backdrop for the evolutionary history of one of the most studied groups of sea urchins. Our phylogeny indicates that a major revision of this group is in order. All else remaining unchanged, it supports the inclusion of three additional species into the genus Strongylocentrotus (Hemicentrotus pulcherrimus, Allocentrotus fragilis, and Pseudocentrotus depressus). All were once thought to be closely related to this genus, but subsequent revisions separated them into other taxonomic groupings. Most strongylocentrotid species are the result of a recent burst of speciation in the North Pacific that resulted in an ecological diversification. There has been a steady reduction in the complexity of larval skeletons during the expansion of this group. Gamete attributes like egg size, on the other hand, are not correlated with phylogenetic position. In addition, our results indicate that the rate of replacement substitutions is highly variable among phylogenetic lineages. The branches leading to S. purpuratus and S. franciscanus were three to six times longer than those leading to closely related species.

  8. First insights into fern matK phylogeny.

    PubMed

    Kuo, Li-Yaung; Li, Fay-Wei; Chiou, Wen-Liang; Wang, Chun-Neng

    2011-06-01

    MatK, the only maturase gene in the land plant plastid genome, is a very popular phylogenetic marker that has been extensively applied in reconstructing angiosperm phylogeny. However, the use of matK in fern phylogeny is largely unknown, due to difficulties with amplification: ferns have lost the flanking trnK exons, typically the region used for designing stable priming sites. We developed primers that are either universal or lineage-specific that successfully amplify matK across all fern families. To evaluate whether matK is as powerful a phylogenetic marker in ferns as in angiosperms, we compared its sequence characteristics and phylogenetic performance to those of rbcL and atpA. Among these three genes, matK has the highest variability and substitution evenness, yet shows the least homoplasy. Most importantly, applying matK in fern phylogenetics better resolved relationships among families, especially within eupolypods I and II. Here we demonstrate the power of matK for fern phylogenetic reconstruction, as well as provide primers and extensive sequence data that will greatly facilitate future evolutionary studies of ferns.

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

    PubMed Central

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

    2014-01-01

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

  10. Quorum sensing by N-acylhomoserine lactones is not required for Aeromonas hydrophila during growth with organic particles in lake water microcosms.

    PubMed

    Styp von Rekowski, Katharina; Hempel, Melanie; Philipp, Bodo

    2008-05-01

    It was investigated whether quorum sensing (QS) mediated by N-acylhomoserine lactones (AHLs) was important for heterotrophic bacteria from the littoral zone of the oligotrophic Lake Constance for growth with organic particles. More than 900 colonies from lake water microcosms with artificial organic aggregates consisting of autoclaved unicellular algae embedded in agarose beads were screened for AHL-production. AHL-producing bacteria of the genus Aeromonas enriched in the microcosms but AHLs could not be detected in any microcosm. To test for a potential function of AHL-mediated QS, growth experiments with the wild type and an AHL-deficient mutant of Aeromonas hydrophila in lake water microcosms were performed. Growth of both strains did not differ in single cultures and showed no mutual influence in co-cultures. In co-cultures with a competitor bacterium belonging to the Cytophaga-Flavobacterium group, growth of both A. hydrophila strains was reduced while growth of the competitor bacterium was not affected. Exogenous AHL-addition did not influence growth of the Aeromonas strains in any microcosm experiment. These results showed that AHL-mediated QS was not required for A. hydrophila during colonization and degradation of organic particles in lake water microcosms, suggesting that cell-cell signalling of heterotrophic bacteria in oligotrophic waters relies on novel signal molecules.

  11. Contaminants in American alligator eggs from Lake Apopka, Lake Griffin, and Lake Okeechobee, Florida

    USGS Publications Warehouse

    Heinz, G.H.; Percival, H.F.; Jennings, Michael L.

    1991-01-01

    Residues of organochlorine pesticides, polychlorinated biphenyls (PCBs), and 16 elements were measured in American alligator (Alligator mississippiensis) eggs collected in 1984 from Lakes Apopka, Griffin, and Okeechobee in central and south Florida. Organochlorine pesticides were highest in eggs from Lake Apopka. None of the elements appeared to be present at harmful concentrations in eggs from any of the lakes. A larger sample of eggs was collected in 1985, but only from Lakes Griffin, a lake where eggs were relatively clean, and Apopka, where eggs were most contaminated. In 1985, hatching success of artificially incubated eggs was lower for Lake Apopka, and several organochlorine pesticides were higher than in eggs from Lake Griffin. However, within Lake Apopka, higher levels of pesticides in chemically analyzed eggs were not associated with reduced hatching success of the remaining eggs in the clutch. Therefore, it did not appear that any of the pesticides we measured were responsible for the reduced hatching of Lake Apopka eggs.

  12. Big lake records preserved in a little lake's sediment: An example from Silver Lake, Michigan, USA

    USGS Publications Warehouse

    Fisher, T.G.; Loope, W.L.; Pierce, W.; Jol, H.M.

    2007-01-01

    We reconstruct postglacial lake-level history within the Lake Michigan basin using soil stratigraphy, ground-penetrating radar (GPR), sedimentology and 14C data from the Silver Lake basin, which lies adjacent to Lake Michigan. Stratigraphy in nine vibracores recovered from the floor of Silver Lake appears to reflect fluctuation of water levels in the Lake Michigan basin. Aeolian activity within the study area from 3,000 years (cal yr. B.P.) to the present was inferred from analysis of buried soils, an aerial photograph sequence, and GPR. Sediments in and around Silver Lake appear to contain a paleoenvironmental record that spans the entire post-glacial history of the Lake Michigan basin. We suggest that (1) a pre-Nipissing rather than a Nipissing barrier separated Silver Lake basin from the Lake Michigan basin, (2) that the Nipissing transgression elevated the water table in the Silver Lake basin about 6,500 cal yr. B.P., resulting in reestablishment of a lake within the basin, and (3) that recent dune migration into Silver Lake is associated with levels of Lake Michigan.

  13. Evidence of Lake Trout reproduction at Lake Michigan's mid-lake reef complex

    USGS Publications Warehouse

    Janssen, J.; Jude, D.J.; Edsall, T.A.; Paddock, R.W.; Wattrus, N.; Toneys, M.; McKee, P.

    2006-01-01

    The Mid-Lake Reef Complex (MLRC), a large area of deep (> 40 m) reefs, was a major site where indigenous lake trout (Salvelinus namaycush) in Lake Michigan aggregated during spawning. As part of an effort to restore Lake Michigan's lake trout, which were extirpated in the 1950s, yearling lake trout have been released over the MLRC since the mid-1980s and fall gill net censuses began to show large numbers of lake trout in spawning condition beginning about 1999. We report the first evidence of viable egg deposition and successful lake trout fry production at these deep reefs. Because the area's existing bathymetry and habitat were too poorly known for a priori selection of sampling sites, we used hydroacoustics to locate concentrations of large fish in the fall; fish were congregating around slopes and ridges. Subsequent observations via unmanned submersible confirmed the large fish to be lake trout. Our technological objectives were driven by biological objectives of locating where lake trout spawn, where lake trout fry were produced, and what fishes ate lake trout eggs and fry. The unmanned submersibles were equipped with a suction sampler and electroshocker to sample eggs deposited on the reef, draw out and occasionally catch emergent fry, and collect egg predators (slimy sculpin Cottus cognatus). We observed slimy sculpin to eat unusually high numbers of lake trout eggs. Our qualitative approaches are a first step toward quantitative assessments of the importance of lake trout spawning on the MLRC.

  14. Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

    PubMed

    Near, Thomas J; Bossu, Christen M; Bradburd, Gideon S; Carlson, Rose L; Harrington, Richard C; Hollingsworth, Phillip R; Keck, Benjamin P; Etnier, David A

    2011-10-01

    Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of

  15. Winter Lake Breezes near the Great Salt Lake

    NASA Astrophysics Data System (ADS)

    Crosman, Erik T.; Horel, John D.

    2016-05-01

    Case studies of lake breezes during wintertime cold air pools in Utah's Salt Lake Valley are examined. While summer breezes originating from the Great Salt Lake are typically deeper, of longer duration, and have higher wind speeds than winter breezes, the rate of inland penetration and cross-frontal temperature differences can be higher during the winter. The characteristics of winter breezes and the forcing mechanisms controlling them (e.g., snow cover, background flow, vertical stability profile, clouds, lake temperature, lake sheltering, and drainage pooling) are more complex and variable than those evident in summer. During the afternoon in the Salt Lake Valley, these lake breezes can lead to elevated pollution levels due to the transport of fine particle pollutants from over the Great Salt Lake, decreased vertical mixing depth, and increased vertical stability.

  16. Crater Lake revealed

    USGS Publications Warehouse

    Ramsey, David W.; Dartnell, Peter; Bacon, Charles R.; Robinson, Joel E.; Gardner, James V.

    2003-01-01

    Around 500,000 people each year visit Crater Lake National Park in the Cascade Range of southern Oregon. Volcanic peaks, evergreen forests, and Crater Lake’s incredibly blue water are the park’s main attractions. Crater Lake partially fills the caldera that formed approximately 7,700 years ago by the eruption and subsequent collapse of a 12,000-foot volcano called Mount Mazama. The caldera-forming or climactic eruption of Mount Mazama drastically changed the landscape all around the volcano and spread a blanket of volcanic ash at least as far away as southern Canada. Prior to the climactic event, Mount Mazama had a 400,000 year history of cone building activity like that of other Cascade volcanoes such as Mount Shasta. Since the climactic eruption, there have been several less violent, smaller postcaldera eruptions within the caldera itself. However, relatively little was known about the specifics of these eruptions because their products were obscured beneath Crater Lake’s surface. As the Crater Lake region is still potentially volcanically active, understanding past eruptive events is important to understanding future eruptions, which could threaten facilities and people at Crater Lake National Park and the major transportation corridor east of the Cascades. Recently, the lake bottom was mapped with a high-resolution multibeam echo sounder. The new bathymetric survey provides a 2m/pixel view of the lake floor from its deepest basins virtually to the shoreline. Using Geographic Information Systems (GIS) applications, the bathymetry data can be visualized and analyzed to shed light on the geology, geomorphology, and geologic history of Crater Lake.

  17. The Wandering Lake

    NASA Technical Reports Server (NTRS)

    2002-01-01

    In the area at the very far eastern corner of China's Taklimakan Desert, Lop Nor Lake was located up until some years ago. Lop Nor, also called the 'the heart of the heart' of Asia, was the place where the waters of the largest inner basin (i.e., not flowing into the sea) of the world-including the Tarim and Kum-daria Rivers-were collected. Depending on the balance between rainfall water yield and evaporation, both position and size of the lake were strongly variable, thus giving rise to the legend of the Wandering Lake. 'Lop City' was the place where Marco Polo took his last rest before facing the one-year long crossing of the Gobi Desert. Starting from the end of the 19th century, several explorers tried to find the legendary place. One such explorer was Sven Hedin, who was commissioned by the Governor of Nanjing to lead an expedition to find the lake. In 1937, the Swedish explorer published his book entitled The Wandering Lake. Comparing this very precise map from Sven Hedin's book with the above Moderate-resolution Imaging Spectroradiometer (MODIS) false-color image (acquired on October 28, 2001), one can find a faint sign on the soil where the Lop Nor was located. This image, derived using a combination of MODIS' near-infrared and red channels (vegetation in red), shows where the Tarim River waters currently end their flow. The Wandering Lake does not exist anymore. The combination of climate change and human exploitation of water resources for agriculture caused the disappearance of the lake. This image was processed by Telespazio, Earth Observation division, new products development facility in Rome, Italy. The MODIS sensor flies aboard NASA's Terra spacecraft, launched in December 1999. Caption and image courtesy Luca Pietranera, Telespazio, Rome, Italy, based on data from the MODIS Science Team

  18. Lake Sarez, Tajikistan

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Lake Sarez (top), deep in the Pamir mountains of Tajikistan, was created 90 years ago when a strong earthquake triggered a massive landslide that, in turn, became a huge dam along the Murghob River, now called the Usoi Dam. The resulting lake is perched above surrounding drainages at an elevation greater than 3000m, and is part of the watershed that drains the towering Akademi Nauk Range (see the regional image, lower). The lake is 61 km long and as deep as 500 m, and holds an estimated 17 cubic km of water. The area experiences considerable seismic activity, and scientists fear that part of the right bank may slump into the lake, creating a huge wave that will top over and possibly breach the natural dam. Such a wave would create a catastrophic flood downstream along the Bartang, Panj and Amu Darya Rivers, perhaps reaching all the way to the Aral Sea. Currently, central Asian governments, as well as the World Bank and the UN are monitoring the dam closely, and have proposed gradually lowering the lake level as a preventive measure. More information about the lake is available at the following web sites: Lake Sarez Study group, UN Report, Reliefweb Digital photograph numbers ISS002-E-7771 and ISS002-E-7479 were taken in the spring of 2001 from Space Station Alpha and are provided by the Earth Sciences and Image Analysis Laboratory at Johnson Space Center. Additional images taken by astronauts and cosmonauts can be viewed at the NASA-JSC Gateway to Astronaut Photography of Earth.

  19. Examining indirect effects of lake trout recovery

    EPA Science Inventory

    With the recovery of lake trout populations in Lake Superior, there are indications of decreased forage fish abundance and density-dependence in lake trout. In Lake Superior, lean lake trout historically occupied depths < 60 m, and siscowet lake trout occupied depths > 60 m...

  20. Hydrogeologic Controls on Lake Level at Mountain Lake, Virginia

    NASA Astrophysics Data System (ADS)

    Roningen, J. M.; Burbey, T. J.

    2011-12-01

    Mountain Lake in Giles County, Virginia has a documented history of severe natural lake-level changes involving groundwater seepage that extend over the past 4200 years. Featured in the 1986 movie Dirty Dancing, the natural lake dried up completely in September 2008 and levels have not yet recovered. A hydrogeologic investigation was undertaken in an effort to determine the factors influencing lake level changes. A daily water balance, dipole-dipole electrical resistivity surveying, well logging and chemical sampling have shed light on: 1) the influence of a fault not previously discussed in literature regarding the lake, 2) the seasonal response to precipitation of a forested first-order drainage system in fractured rock, and 3) the possibility of flow pathways related to karst features. Geologic controls on lake level were investigated using several techniques. Geophysical surveys using dipole-dipole resistivity located possible subsurface flowpaths both to and from the lake. Well logs, lineament analysis, and joint sampling were used to assess structural controls on lake hydrology. Major ions were sampled at wells, springs, streams, and the lake to evaluate possible mixing of different sources of water in the lake. Groundwater levels were monitored for correlation to lake levels, rainfall events, and possible seismic effects. The hydrology of the lake was quantified with a water balance on a daily time step. Results from the water balance indicate steady net drainage and significant recharge when vegetation is dormant, particularly during rain-on-snow melt events. The resistivity survey reveals discrete areas that represent flow pathways from the lake, as well as flowpaths to springs upgradient of the lake located in the vicinity of the fault. The survey also suggests that some flowpaths may originate outside of the topographic watershed of the lake. Chemical evidence indicates karst may underlie the lakebed. Historical data suggest that artificial intervention

  1. 42. Peaks of Otter, Abbott Lake. View across lake to ...

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

    42. Peaks of Otter, Abbott Lake. View across lake to peaks of Outter Lodge, completed in 1964. Construction of the lake got underway in 1964. Looking east-northeast. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  2. Lake Michigan lake trout PCB model forecast post audit

    EPA Science Inventory

    Scenario forecasts for total PCBs in Lake Michigan (LM) lake trout were conducted using the linked LM2-Toxics and LM Food Chain models, supported by a suite of additional LM models. Efforts were conducted under the Lake Michigan Mass Balance Study and the post audit represents th...

  3. View of Lake Sabrina Dam and dry Lake Sabrina Basin ...

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

    View of Lake Sabrina Dam and dry Lake Sabrina Basin with the upstream side of the outlet structure visible at photo center, view to north-northwest - Bishop Creek Hydroelectric System, Plant 2, Lake Sabrina Dam, Bishop Creek, Bishop, Inyo County, CA

  4. National Lakes Assessment: A Collaborative Survey of the Nation's Lakes

    EPA Science Inventory

    The National Lakes Assessment A Collaborative Survey of the Nation's Lakes presents the results of an unprecedented assessment of the nation’s lakes. This report is part of the National Aquatic Resource Surveys, a series of statistically based surveys designed to provide the pub...

  5. Chemours Pompton Lakes Works Site, Pompton Lakes, NJ

    EPA Pesticide Factsheets

    E.I. DuPont De Nemours & Company is located at 2000 Cannonball Road, Pompton Lakes, New Jersey. The DuPont Pompton Lakes Works site (DuPont) occupies approximately 570 acres of land in Pompton Lakes and Wanaque.

  6. YeastIP: a database for identification and phylogeny of Saccharomycotina yeasts.

    PubMed

    Weiss, Stéphanie; Samson, Franck; Navarro, David; Casaregola, Serge

    2013-02-01

    With the advances in sequencing techniques, identification of ascomycetous yeasts to the species level and phylogeny reconstruction increasingly require curated and updated taxonomic information. A specific database with nucleotide sequences of the most common markers used for yeast taxonomy and phylogeny and a user-friendly interface allowing identification, taxonomy and phylogeny of yeasts species was developed. By 1 September 2012, the YeastIP database contained all the described Saccharomycotina species for which sequences used for taxonomy and phylogeny, such as D1/D2 rDNA and ITS, are available. The database interface was developed to provide a maximum of relevant information and data mining tools, including the following features: (1) the blast n program for the sequences of the YeastIP database; (2) easy retrieval of selected sequences; (3) display of the available markers for each selected group of species; and (4) a tool to concatenate marker sequences, including those provided by the user. The concatenation tool allows phylogeny reconstruction through a direct link to the Phylogeny.fr platform. YeastIP is thus a unique database in that it provides taxonomic information and guides users in their taxonomic analyses. YeastIP facilitates multigenic analysis to encourage good practice in ascomycetous yeast phylogeny (URL: http://genome.jouy.inra.fr/yeastip.).

  7. National Lakes Assessment 2007 Results

    EPA Pesticide Factsheets

    The National Lakes Assessment samples over 1,000 lakes, ponds and reservoirs across the country. Key findings from this assessment in 2007 include the biological condition and most widespread stressors of these waterbodies.

  8. Microplastic pollution in lakes and lake shoreline sediments - A case study on Lake Bolsena and Lake Chiusi (central Italy).

    PubMed

    Fischer, Elke Kerstin; Paglialonga, Lisa; Czech, Elisa; Tamminga, Matthias

    2016-06-01

    Rivers and effluents have been identified as major pathways for microplastics of terrestrial sources. Moreover, lakes of different dimensions and even in remote locations contain microplastics in striking abundances. This study investigates concentrations of microplastic particles at two lakes in central Italy (Lake Bolsena, Lake Chiusi). A total number of six Manta Trawls have been carried out, two of them one day after heavy winds occurred on Lake Bolsena showing effects on particle distribution of fragments and fibers of varying size categories. Additionally, 36 sediment samples from lakeshores were analyzed for microplastic content. In the surface waters 2.68 to 3.36 particles/m(3) (Lake Chiusi) and 0.82 to 4.42 particles/m(3) (Lake Bolsena) were detected, respectively. Main differences between the lakes are attributed to lake characteristics such as surface and catchment area, depth and the presence of local wind patterns and tide range at Lake Bolsena. An event of heavy winds and moderate rainfall prior to one sampling led to an increase of concentrations at Lake Bolsena which is most probable related to lateral land-based and sewage effluent inputs. The abundances of microplastic particles in sediments vary from mean values of 112 (Lake Bolsena) to 234 particles/kg dry weight (Lake Chiusi). Lake Chiusi results reveal elevated fiber concentrations compared to those of Lake Bolsena what might be a result of higher organic content and a shift in grain size distribution towards the silt and clay fraction at the shallow and highly eutrophic Lake Chiusi. The distribution of particles along different beach levels revealed no significant differences.

  9. Sanctuaries for lake trout in the Great Lakes

    USGS Publications Warehouse

    Stanley, Jon G.; Eshenroder, Randy L.; Hartman, Wilbur L.

    1987-01-01

    Populations of lake trout, severely depleted in Lake Superior and virtually extirpated from the other Great Lakes because of sea lamprey predation and intense fishing, are now maintained by annual plantings of hatchery-reared fish in Lakes Michigan, Huron, and Ontario and parts of Lake Superior. The extensive coastal areas of the Great Lakes and proximity to large populations resulted in fishing pressure on planted lake trout heavy enough to push annual mortality associated with sport and commercial fisheries well above the critical level needed to reestablish self-sustaining stocks. The interagency, international program for rehabilitating lake trout includes controlling sea lamprey abundance, stocking hatchery-reared lake trout, managing the catch, and establishing sanctuaries where harvest is prohibited. Three lake trout sanctuaries have been established in Lake Michigan: the Fox Island Sanctuary of 121, 500 ha, in the Chippewa-Ottawa Treaty fishing zone in the northern region of the lake; the Milwaukee Reef Sanctuary of 160, 000 ha in midlake, in boundary waters of Michigan and Wisconsin; and Julian's Reef Sanctuary of 6, 500 ha, in Illinois waters. In northern Lake Huron, Drummond Island Sanctuary of 55, 000 ha is two thirds in Indian treaty-ceded waters in Michigan and one third in Ontario waters of Canada. A second sanctuary, Six Fathom Bank-Yankee Reef Sanctuary, in central Lake Huron contains 168, 000 ha. Sanctuary status for the Canadian areas remains to be approved by the Provincial government. In Lake Superior, sanctuaries protect the spawning grounds of Gull Island Shoal (70, 000 ha) and Devils Island Shoal (44, 000 ha) in Wisconsin's Apostle Island area. These seven sanctuaries, established by the several States and agreed upon by the States, Indian tribes, the U.S. Department of the Interior, and the Province of Ontario, contribute toward solving an interjurisdictional fishery problem.

  10. Phylogeny mandalas of birds using the lithographs of John Gould's folio bird books.

    PubMed

    Hasegawa, Masami; Kuroda, Sayako

    2016-12-09

    The phylogeny mandala, which is a circular phylogeny with photos or drawings of species, is a suitable way to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. In this article, in order to demonstrate the recent progress of avian molecular phylogenetics, six phylogeny mandalas of various taxonomic groups of birds are presented with the lithographs of John Gould's folio bird books; i.e., (1) whole Aves, (2) Passeriformes, (3) Paradisaeidae in Corvoidea (Passeriformes), (4) Meliphagoidea (Passeriformes), (5) Trochili in Apodiformes, and (6) Galliformes.

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

    PubMed Central

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-07-01

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

  13. Eumalacostracan phylogeny and total evidence: limitations of the usual suspects

    PubMed Central

    Jenner, Ronald A; Dhubhghaill, Ciara Ní; Ferla, Matteo P; Wills, Matthew A

    2009-01-01

    Background The phylogeny of Eumalacostraca (Crustacea) remains elusive, despite over a century of interest. Recent morphological and molecular phylogenies appear highly incongruent, but this has not been assessed quantitatively. Moreover, 18S rRNA trees show striking branch length differences between species, accompanied by a conspicuous clustering of taxa with similar branch lengths. Surprisingly, previous research found no rate heterogeneity. Hitherto, no phylogenetic analysis of all major eumalacostracan taxa (orders) has either combined evidence from multiple loci, or combined molecular and morphological evidence. Results We combined evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I) with a newly synthesized morphological dataset. We tested the homogeneity of data partitions, both in terms of character congruence and the topological congruence of inferred trees. We also performed Bayesian and parsimony analyses on separate and combined partitions, and tested the contribution of each partition. We tested for potential long-branch attraction (LBA) using taxon deletion experiments, and with relative rate tests. Additionally we searched for molecular polytomies (spurious clades). Lastly, we investigated the phylogenetic stability of taxa, and assessed their impact on inferred relationships over the whole tree. We detected significant conflict between data partitions, especially between morphology and molecules. We found significant rate heterogeneity between species for both the 18S rRNA and combined datasets, introducing the possibility of LBA. As a test case, we showed that LBA probably affected the position of Spelaeogriphacea in the combined molecular evidence analysis. We also demonstrated that several clades, including the previously reported and surprising clade of Amphipoda plus Spelaeogriphacea, are 'supported' by zero length branches. Furthermore we showed that different sets of

  14. Michigan: The Great Lakes State

    ERIC Educational Resources Information Center

    McKay, Sandra Lee; La Luzerne-Oi, Sally

    2009-01-01

    Although Michigan is often called the "Wolverine State," its more common nickname is the "Great Lakes State." This name comes from the fact that Michigan is the only state in the United States that borders four of the five Great Lakes. Also referred to as the "Water Wonderland," Michigan has 11,000 additional lakes,…

  15. Viruses in Antarctic lakes

    NASA Technical Reports Server (NTRS)

    Kepner, R. L. Jr; Wharton, R. A. Jr; Suttle, C. A.; Wharton RA, J. r. (Principal Investigator)

    1998-01-01

    Water samples collected from four perennially ice-covered Antarctic lakes during the austral summer of 1996-1997 contained high densities of extracellular viruses. Many of these viruses were found to be morphologically similar to double-stranded DNA viruses that are known to infect algae and protozoa. These constitute the first observations of viruses in perennially ice-covered polar lakes. The abundance of planktonic viruses and data suggesting substantial production potential (relative to bacteria] secondary and photosynthetic primary production) indicate that viral lysis may be a major factor in the regulation of microbial populations in these extreme environments. Furthermore, we suggest that Antarctic lakes may be a reservoir of previously undescribed viruses that possess novel biological and biochemical characteristics.

  16. Lake-level frequency analysis for Devils Lake, North Dakota

    USGS Publications Warehouse

    Wiche, Gregg J.; Vecchia, Aldo V.

    1996-01-01

    An annual lake-volume model and a statistical water mass-balance model were used to estimate future lake-level probabilities for Devils Lake. Comparison of the models indicates upper exceedance levels of the water mass-balance model increase much more rapidly than those of the annual lake-volume model. For simulation year 5, the 99-percent exceedance is 1,417.6 feet above sea level for the annual lake-volume model and 1,423.2 feet above sea level for the water mass-balance model.

  17. Transient Tsunamis in Lakes

    NASA Astrophysics Data System (ADS)

    Couston, L.; Mei, C.; Alam, M.

    2013-12-01

    A large number of lakes are surrounded by steep and unstable mountains with slopes prone to failure. As a result, landslides are likely to occur and impact water sitting in closed reservoirs. These rare geological phenomena pose serious threats to dam reservoirs and nearshore facilities because they can generate unexpectedly large tsunami waves. In fact, the tallest wave experienced by contemporary humans occurred because of a landslide in the narrow bay of Lituya in 1958, and five years later, a deadly landslide tsunami overtopped Lake Vajont's dam, flooding and damaging villages along the lakefront and in the Piave valley. If unstable slopes and potential slides are detected ahead of time, inundation maps can be drawn to help people know the risks, and mitigate the destructive power of the ensuing waves. These maps give the maximum wave runup height along the lake's vertical and sloping boundaries, and can be obtained by numerical simulations. Keeping track of the moving shorelines along beaches is challenging in classical Eulerian formulations because the horizontal extent of the fluid domain can change over time. As a result, assuming a solid slide and nonbreaking waves, here we develop a nonlinear shallow-water model equation in the Lagrangian framework to address the problem of transient landslide-tsunamis. In this manner, the shorelines' three-dimensional motion is part of the solution. The model equation is hyperbolic and can be solved numerically by finite differences. Here, a 4th order Runge-Kutta method and a compact finite-difference scheme are implemented to integrate in time and spatially discretize the forced shallow-water equation in Lagrangian coordinates. The formulation is applied to different lake and slide geometries to better understand the effects of the lake's finite lengths and slide's forcing mechanism on the generated wavefield. Specifically, for a slide moving down a plane beach, we show that edge-waves trapped by the shoreline and free

  18. Megasplash at Lake Tahoe

    NASA Astrophysics Data System (ADS)

    Moore, J. G.; Schweickert, R. A.

    2013-12-01

    Backwash from a major ~10 km3 landslide in Lake Tahoe washed away Tioga age (21 ka) moraines (Schweickert, et al 2000; Howle, 2012). Coring in the lake demonstrates a 7700-8000 yr Mt. Mazama ash is widely distributed in lake sediments that overlie the landslide blocks. Moreover, core stratigraphy and radiocarbon ages indicate that all of the sediments cored (to about 3 m depth reaching back 12 ka) were deposited after the landslide (Smith et al., 2013). The age of the landslide is hence constrained at 12-21 ka. Fifteen major subaqueous sand wave channels 2.5 to 10.2 km in length originate from subaqueous delta-terraces at depths of 5-28 m on the margins of the lake. The channels, apparently formed by turbidity currents, are distinctly erosional in their upper part, and transform to deposition aprons in their lower part as they approach the flat lake floor at 500 m depth. The channels contain wave forms (giant ripple marks) convex upstream with maximum wavelengths of 450 m. The lower depositional aprons are surfaced by sand waves convex downstream with maximum wavelengths of 100-300 m. Sand wave convexity mimics the contour of the substrate. The sand wave channel systems are mantled by the post-slide 12 ka sediments and hence have been inactive since that time. These channel-fan structures were apparently produced by backwash from the giant Tahoe landslide, which splashed ~5 km3 of water onto the surrounding countryside thereby lowering lake level by ~10 m. The sediment-charged backwash first deposited the delta-terraces at the lowered lake level and then partly eroded them to generate the sand wave channels, within minutes or hours, while seiche activity resurfaced the delta-terraces. A remarkably similar, though smaller, presently-forming system of turbidity sand wave channels has been imaged at the mouth of the Squamish River in British Columbia (Hughes Clark et al., 2012). The Tahoe splash-induced backwash was briefly equivalent to more than fifteen Squamish

  19. The Great Lakes whitefish

    USGS Publications Warehouse

    Van Oosten, John; Elliot, Charles

    1942-01-01

    In every one of the Great Lakes- Ontario, Erie, Huron, Michigan, and Superior- the most valuable fishes are declining, and there is no evidence that this trend will be reversed. Under existing conditions of a diversity of regulations that vary between states and between the two countries, and with the present methods of fishing, the Great Lakes fisheries are doomed. This chapter deals with the common whitefish, a valuable species which many believe to be the next that will go unless positive action is forthcoming soon.

  20. Reevaluation of lake trout and lake whitefish bioenergetics models

    USGS Publications Warehouse

    Madenjian, Charles P.; Pothoven, Steve A.; Kao, Yu-Chun

    2013-01-01

    Using a corrected algorithm for balancing the energy budget, we reevaluated the Wisconsin bioenergetics model for lake trout (Salvelinus namaycush) in the laboratory and for lake whitefish (Coregonus clupeaformis) in the laboratory and in the field. For lake trout, results showed that the bioenergetics model slightly overestimated food consumption by the lake trout when they were fed low and intermediate rations, whereas the model predicted food consumption by lake trout fed ad libitum without any detectable bias. The slight bias in model predictions for lake trout on restricted rations may have been an artifact of the feeding schedule for these fish, and we would therefore recommend application of the Wisconsin lake trout bioenergetics model to lake trout populations in the field without any revisions to the model. Use of the Wisconsin bioenergetics model for coregonids resulted in overestimation of food consumption by lake whitefish both in the laboratory and in the field by between 20 and 30%, on average. This overestimation of food consumption was most likely due to overestimation of respiration rate. We therefore adjusted the respiration component of the bioenergetics model to obtain a good fit to the observed consumption in our laboratory tanks. The adjusted model predicted the consumption in the laboratory and the field without any detectable bias. Until a detailed lake whitefish respiration study can be conducted, we recommend application of our adjusted version of the Wisconsin generalized coregonid bioenergetics model to lake whitefish populations in the field.

  1. Gas exchange on Mono Lake and Crowley Lake, California

    NASA Technical Reports Server (NTRS)

    Wanninkhof, Rik; Ledwell, James R.; Broecker, Wallace S.

    1987-01-01

    Gas exchange coefficients (k) have been determined for freshwater Crowley Lake and saline Mono Lake through the use of a man-made purposefully injected gas, SF6. The concentration decreased from an initial value of 40 to 4 pmol/L for Mono Lake and from 20 to 1 pmol/L for Crowley lake over a period of 6 wks. Wind-speed (u) records from anemometers on the shore of each lake made it possible to determine the relationship between k and u. The average u and k values for the experiment were identical for the two lakes, despite the large chemical differences. It is estimated that, for the u values observed over Mono Lake from July to December 1984, the exchange of CO2 occurred 2.5 times faster than without chemical enhancement. This is a factor of 4 lower than needed to explain the high invasion rate of C-14 produced by nuclear bomb tests.

  2. Pericentric satellite DNA and molecular phylogeny in Acomys (Rodentia).

    PubMed

    Kunze, B; Traut, W; Garagna, S; Weichenhan, D; Redi, C A; Winking, H

    1999-01-01

    Satellite DNAs (stDNAs) of four Acomys species (spiny-mice), A. cahirinus, A. cineraceus, A. dimidiatus and A. russatus, belong to closely related sequence families. Monomer sizes range from 338 to 364 bp. Between-species sequence identity was from 81.0% to 97.2%. The molecular phylogeny of the sequences helps to clarify the taxonomy of this 'difficult' group. The A. dimidiatus genome contains about 60000 repeats. According to the restriction patterns, repeats are arranged in tandem. The stDNA maps to the centromeric heterochromatin of most autosomes, both acrocentric and metacentric, but appears to be absent in the centromeric region of Y chromosomes. A well-conserved centromere protein B (CENP-B) box is present in the stDNA of A. russatus while it is degenerated in the other species.

  3. Phylogeny and comparative genome analysis of a Basidiomycete fungi

    SciTech Connect

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

    2011-03-14

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

  4. Molecular phylogeny analysis using correlation distance and spectral distance.

    PubMed

    Sabarish, R Anu; Thomas, Tessamma

    2014-01-01

    A wide range of methods with or without sequence alignment have been used to study molecular phylogeny for information on the evolution of species. Two approaches to construct the phylogenetic tree using (a) direct correlation of protein sequences and (b) difference between the Discrete Fourier Transform coefficients are described. The proposed methods use a transformation where each amino acid is represented by its Electron-Ion Interaction Potential (EIIP) value. Phylogenetic tree of two mammalian orders, primates and cetacea, is generated based on Fitch-Margoliash, Neighbour-Joining and UPGMA methods and compared. The phylogenetic tree of evolutionary relationships thus obtained can be used for comparison of species and gene sequences. The information thus gathered provide meaningful insights into the pattern and process of evolution which will help researchers in developing new breeds of animals and plants.

  5. Re-evaluating the phylogeny of allopolyploid Gossypium L.

    PubMed

    Grover, Corrinne E; Gallagher, Joseph P; Jareczek, Josef J; Page, Justin T; Udall, Joshua A; Gore, Michael A; Wendel, Jonathan F

    2015-11-01

    The formation of allopolyploid cotton precipitated a rapid diversification and colonization of dry coastal American tropical and subtropical regions. Previous phylogenetic analyses, combined with molecular divergence analyses, have offered a temporal framework for this radiation, but provide only weak support for some of the resolved branches. Moreover, these earlier analyses did not include the recently recognized sixth polyploid species, G. ekmanianum Wittmack. Here we use targeted sequence capture of multiple loci in conjunction with both concatenated and Bayesian concordance analyses to reevaluate the phylogeny of allopolyploid cotton species. Although phylogenetic resolution afforded by individual genes is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here.

  6. Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny.

    PubMed

    Egan, Ashley N; Vatanparast, Mohammad; Cagle, William

    2016-11-01

    Several taxonomic and phylogenetic studies have hypothesized polyphyly within Pueraria DC., a genus comprising 19 species (24 with varieties) including the highly invasive Pueraria montana var. lobata (Kudzu) introduced to the U.S.A. about 150years ago. Previous efforts to investigate monophyly of the genus have been hampered by limited taxon sampling or a lack of comprehensive evolutionary context that would enable definitive taxonomic associations. This work presents a comprehensive phylogenetic investigation of Pueraria within the context of tribe Phaseoleae (Leguminosae). Polyphyly was found to be more extensive than previously thought, with five distinct lineages spread across the tribe and spanning over 25mya of divergence strongly supported by two chloroplast and one nuclear marker, AS2, presented here as a phylogenetic marker for the first time. Our phylogenies support taxonomic revisions to rectify polyphyly within Pueraria, including the resurrection of Neustanthus, moving one species to Teyleria, and the creation of two new genera, Haymondia and Toxicopueraria (taxonomic revisions published elsewhere).

  7. Linguistic phylogenies support back-migration from Beringia to Asia.

    PubMed

    Sicoli, Mark A; Holton, Gary

    2014-01-01

    Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America.

  8. Quantifying Age-dependent Extinction from Species Phylogenies

    PubMed Central

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

    2016-01-01

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

  9. Comparing nodal versus bony metastatic spread using tumour phylogenies

    PubMed Central

    Mangiola, Stefano; Hong, Matthew K. H.; Cmero, Marek; Kurganovs, Natalie; Ryan, Andrew; Costello, Anthony J.; Corcoran, Niall M.; Macintyre, Geoff; Hovens, Christopher M.

    2016-01-01

    The role of lymph node metastases in distant prostate cancer dissemination and lethality is ill defined. Patients with metastases restricted to lymph nodes have a better prognosis than those with distant metastatic spread, suggesting the possibility of distinct aetiologies. To explore this, we traced patterns of cancer dissemination using tumour phylogenies inferred from genome-wide copy-number profiling of 48 samples across 3 patients with lymph node metastatic disease and 3 patients with osseous metastatic disease. Our results show that metastatic cells in regional lymph nodes originate from evolutionary advanced extraprostatic tumour cells rather than less advanced central tumour cell populations. In contrast, osseous metastases do not exhibit such a constrained developmental lineage, arising from either intra or extraprostatic tumour cell populations, at early and late stages in the evolution of the primary. Collectively, this comparison suggests that lymph node metastases may not be an intermediate developmental step for distant osseous metastases, but rather represent a distinct metastatic lineage. PMID:27653089

  10. Phylogeny- and Parsimony-Based Haplotype Inference with Constraints

    NASA Astrophysics Data System (ADS)

    Elberfeld, Michael; Tantau, Till

    Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. In their CPM 2009 paper, Fellows et al. studied an extension of this approach that incorporates prior knowledge in the form of a set of candidate haplotypes from which the right haplotypes must be chosen. While this approach may help to increase the accuracy of haplotyping methods, it was conjectured that the resulting formal problem constrained perfect phylogeny haplotyping might be NP-complete. In the present paper we present a polynomial-time algorithm for it. Our algorithmic ideas also yield new fixed-parameter algorithms for related haplotyping problems based on the maximum parsimony assumption.

  11. Hemiplasy and homoplasy in the karyotypic phylogenies of mammals

    PubMed Central

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

    2008-01-01

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

  12. Evolution of consciousness: phylogeny, ontogeny, and emergence from general anesthesia.

    PubMed

    Mashour, George A; Alkire, Michael T

    2013-06-18

    Are animals conscious? If so, when did consciousness evolve? We address these long-standing and essential questions using a modern neuroscientific approach that draws on diverse fields such as consciousness studies, evolutionary neurobiology, animal psychology, and anesthesiology. We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution. Thus, in agreement with Darwin's insight and the recent "Cambridge Declaration on Consciousness in Non-Human Animals," a review of modern scientific data suggests that the differences between species in terms of the ability to experience the world is one of degree and not kind.

  13. Linguistic Phylogenies Support Back-Migration from Beringia to Asia

    PubMed Central

    Sicoli, Mark A.; Holton, Gary

    2014-01-01

    Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America. PMID:24621925

  14. Ectocranial suture fusion in primates: pattern and phylogeny.

    PubMed

    Cray, James; Cooper, Gregory M; Mooney, Mark P; Siegel, Michael I

    2014-03-01

    Patterns of ectocranial suture fusion among Primates are subject to species-specific variation. In this study, we used Guttman Scaling to compare modal progression of ectocranial suture fusion among Hominidae (Homo, Pan, Gorilla, and Pongo), Hylobates, and Cercopithecidae (Macaca and Papio) groups. Our hypothesis is that suture fusion patterns should reflect their evolutionary relationship. For the lateral-anterior suture sites there appear to be three major patterns of fusion, one shared by Homo-Pan-Gorilla, anterior to posterior; one shared by Pongo and Hylobates, superior to inferior; and one shared by Cercopithecidae, posterior to anterior. For the vault suture pattern, the Hominidae groups reflect the known phylogeny. The data for Hylobates and Cercopithecidae groups is less clear. The vault suture site termination pattern of Papio is similar to that reported for Gorilla and Pongo. Thus, it may be that some suture sites are under larger genetic influence for patterns of fusion, while others are influenced by environmental/biomechanic influences.

  15. Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites.

    PubMed

    Vanhove, Maarten P M; Pariselle, Antoine; Van Steenberge, Maarten; Raeymaekers, Joost A M; Hablützel, Pascal I; Gillardin, Céline; Hellemans, Bart; Breman, Floris C; Koblmüller, Stephan; Sturmbauer, Christian; Snoeks, Jos; Volckaert, Filip A M; Huyse, Tine

    2015-09-03

    The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebrate radiation, we study monogenean parasites infecting tropheine cichlids from Lake Tanganyika. Monogeneans are flatworms usually infecting the body surface and gills of fishes. In contrast to many other parasites, they depend only on a single host species to complete their lifecycle. Our spatially comprehensive combined nuclear-mitochondrial DNA dataset of the parasites covering almost all tropheine host species (N = 18), reveals species-rich parasite assemblages and shows consistent host-specificity. Statistical comparisons of host and parasite phylogenies based on distance and topology-based tests demonstrate significant congruence and suggest that host-switching is rare. Molecular rate evaluation indicates that species of Cichlidogyrus probably diverged synchronically with the initial radiation of the tropheines. They further diversified through within-host speciation into an overlooked species radiation. The unique life history and specialisation of certain parasite groups has profound evolutionary consequences. Hence, evolutionary parasitology adds a new dimension to the study of biodiversity hotspots like Lake Tanganyika.

  16. Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites

    PubMed Central

    Vanhove, Maarten P. M.; Pariselle, Antoine; Van Steenberge, Maarten; Raeymaekers, Joost A. M.; Hablützel, Pascal I.; Gillardin, Céline; Hellemans, Bart; Breman, Floris C.; Koblmüller, Stephan; Sturmbauer, Christian; Snoeks, Jos; Volckaert, Filip A. M.; Huyse, Tine

    2015-01-01

    The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebrate radiation, we study monogenean parasites infecting tropheine cichlids from Lake Tanganyika. Monogeneans are flatworms usually infecting the body surface and gills of fishes. In contrast to many other parasites, they depend only on a single host species to complete their lifecycle. Our spatially comprehensive combined nuclear-mitochondrial DNA dataset of the parasites covering almost all tropheine host species (N = 18), reveals species-rich parasite assemblages and shows consistent host-specificity. Statistical comparisons of host and parasite phylogenies based on distance and topology-based tests demonstrate significant congruence and suggest that host-switching is rare. Molecular rate evaluation indicates that species of Cichlidogyrus probably diverged synchronically with the initial radiation of the tropheines. They further diversified through within-host speciation into an overlooked species radiation. The unique life history and specialisation of certain parasite groups has profound evolutionary consequences. Hence, evolutionary parasitology adds a new dimension to the study of biodiversity hotspots like Lake Tanganyika. PMID:26335652

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

    PubMed

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

    2012-01-01

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

  18. Nuclear and mitochondrial genes for inferring Trichuris phylogeny.

    PubMed

    Callejón, Rocío; Cutillas, Cristina; Nadler, Steven A

    2015-12-01

    Nucleotide sequences of the triose phosphate isomerase (TPI) gene (624 bp) and mitochondrial cytochrome b (cob) gene (520 bp) were obtained by PCR and evaluated for utility in inferring the phylogenetic relationships among Trichuris species. Published sequences of one other nuclear gene (18S or SSU rRNA, 1816-1846 bp) and one additional mitochondrial (mtDNA) gene (cytochrome oxidase 1, cox1, 342 bp) were also analyzed. Maximum likelihood and Bayesian inference methods were used to infer phylogenies for each gene separately but also for the combined mitochondrial data (two genes), the combined nuclear data (two genes), and the total evidence (four gene) dataset. Few Trichuris clades were uniformly resolved across separate analyses of individual genes. For the mtDNA, the cob gene trees had greater phylogenetic resolution and tended to have higher support values than the cox1 analyses. For nuclear genes, the SSU gene trees had slightly greater resolution and support values than the TPI analyses, but TPI was the only gene with reliable support for the deepest nodes in the tree. Combined analyses of genes yielded strongly supported clades in most cases, with the exception of the relationship among Trichuris clades 1, 2, and 3, which showed conflicting results between nuclear and mitochondrial genes. Both the TPI and cob genes proved valuable for inferring Trichuris relationships, with greatest resolution and support values achieved through combined analysis of multiple genes. Based on the phylogeny of the combined analysis of nuclear and mitochondrial genes, parsimony mapping of definitive host utilization depicts artiodactyls as the ancestral hosts for these Trichuris, with host-shifts into primates, rodents, and Carnivora.

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

    PubMed Central

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

    2012-01-01

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

  20. Phylogeny and biogeography of South Chinese brown frogs (Ranidae, Anura)

    PubMed Central

    Wang, Sirui; Zhu, Hedan; Li, Pipeng; Yang, Baotian; Ma, Jianzhang

    2017-01-01

    Few studies have explored the role of Cenozoic tectonic evolution in shaping the patterns and processes of extant animal distributions in and around East Asia. In this study, we selected South Chinese brown frogs as a model to examine the phylogenetic and biogeographical consequences of Miocene tectonic events within South China and its margins. We used mitochondrial and nuclear molecular data to reconstruct phylogenetic interrelationships among Chinese brown frogs using Bayesian and maximum likelihood analyses. The phylogeny results show that there are four main clades of Chinese brown frogs. Excepting the three commonly known Chinese brown frog species groups, R. maoershanensis forms an independent clade nearest to the R. japonica group. Phylogeny and P-distance analyses confirmed R. maoershanensis as a valid species. Among South Chinese brown frogs, there are four subclades associated with four geographical areas: (I) R. maoershanensis; (II) R. japonica; (III) R. chaochiaoensis; and (IV) other species of the R. longicrus species group. Divergence times, estimated using mitochondrial sequences, place the vicariance events among the four subclades in the middle to late Miocene epoch. Our results suggest that (1) South Chinese brown frogs originated due to a vicariance event separating them from the R. chensinensis species group at the time of the Geological movement (~18 million years ago, Ma) in southern Tibet and the Himalayan region; (2) the separation and speciation of R. maoershanensis from the R. japonica group occurred due to the dry climate at approximately 16 Ma; (3) South Chinese brown frogs migrated from South China to Japan at the time (~10.8 Ma) that the global sea-level fell and the East China Sea Shelf Basin was swamp facies, when a land gallery may have formed across the sea to connect the two areas; and (4) R. chaochiaoensis separated from other species of the R. longicrus species group during the uplift of the Tibetan Plateau at approximately 9

  1. Phylogeny and biogeography of South Chinese brown frogs (Ranidae, Anura).

    PubMed

    Zhou, Yu; Wang, Sirui; Zhu, Hedan; Li, Pipeng; Yang, Baotian; Ma, Jianzhang

    2017-01-01

    Few studies have explored the role of Cenozoic tectonic evolution in shaping the patterns and processes of extant animal distributions in and around East Asia. In this study, we selected South Chinese brown frogs as a model to examine the phylogenetic and biogeographical consequences of Miocene tectonic events within South China and its margins. We used mitochondrial and nuclear molecular data to reconstruct phylogenetic interrelationships among Chinese brown frogs using Bayesian and maximum likelihood analyses. The phylogeny results show that there are four main clades of Chinese brown frogs. Excepting the three commonly known Chinese brown frog species groups, R. maoershanensis forms an independent clade nearest to the R. japonica group. Phylogeny and P-distance analyses confirmed R. maoershanensis as a valid species. Among South Chinese brown frogs, there are four subclades associated with four geographical areas: (I) R. maoershanensis; (II) R. japonica; (III) R. chaochiaoensis; and (IV) other species of the R. longicrus species group. Divergence times, estimated using mitochondrial sequences, place the vicariance events among the four subclades in the middle to late Miocene epoch. Our results suggest that (1) South Chinese brown frogs originated due to a vicariance event separating them from the R. chensinensis species group at the time of the Geological movement (~18 million years ago, Ma) in southern Tibet and the Himalayan region; (2) the separation and speciation of R. maoershanensis from the R. japonica group occurred due to the dry climate at approximately 16 Ma; (3) South Chinese brown frogs migrated from South China to Japan at the time (~10.8 Ma) that the global sea-level fell and the East China Sea Shelf Basin was swamp facies, when a land gallery may have formed across the sea to connect the two areas; and (4) R. chaochiaoensis separated from other species of the R. longicrus species group during the uplift of the Tibetan Plateau at approximately 9

  2. A Radical Solution: The Phylogeny of the Nudibranch Family Fionidae

    PubMed Central

    Cella, Kristen; Ekimova, Irina; Chichvarkhin, Anton; Schepetov, Dimitry; Gosliner, Terrence M.

    2016-01-01

    Tergipedidae represents a diverse and successful group of aeolid nudibranchs, with approximately 200 species distributed throughout most marine ecosystems and spanning all biogeographical regions of the oceans. However, the systematics of this family remains poorly understood since no modern phylogenetic study has been undertaken to support any of the proposed classifications. The present study is the first molecular phylogeny of Tergipedidae based on partial sequences of two mitochondrial (COI and 16S) genes and one nuclear gene (H3). Maximum likelihood, maximum parsimony and Bayesian analysis were conducted in order to elucidate the systematics of this family. Our results do not recover the traditional Tergipedidae as monophyletic, since it belongs to a larger clade that includes the families Eubranchidae, Fionidae and Calmidae. This newly recovered clade is here referred to as Fionidae, the oldest name for this taxon. In addition, the present molecular phylogeny does not recover the traditional systematic relationships at a generic level, and therefore, systematic changes are required. We recognize the following clades within Fionidae: Calma, Cuthona, Cuthonella, Eubranchus, Fiona, Murmania, Tenellia, Tergipes, Tergiposacca gen. nov., Rubramoena gen. nov. and Abronica gen. nov. The type species of Tergiposacca, T. longicerata nov. sp. is described. The other two new genera have a previously described species as their type species. Most of these taxa, with the exceptions of Eubranchus, Tergipes and Fiona are composed of radically different constituent species from their traditional membership, but appear to be supported by morphological synapomorphies as well as molecular data. Aenigmastyletus, Catriona, Phestilla, Tenellia and Trinchesia are nested within other clades and, thus are here considered as synonyms of the larger clades. The phylogenetic position and validity of Myja, Guyvalvoria, Leostyletus and Subcuthona still need to be tested in future studies

  3. Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae

    PubMed Central

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

    2012-01-01

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

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

    PubMed

    Khan, Haseeb Ahmad; Arif, Ibrahim Abdulwahid

    2013-12-01

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

  5. A molecular phylogeny of the cotingas (Aves: Cotingidae).

    PubMed

    Ohlson, Jan I; Prum, Richard O; Ericson, Per G P

    2007-01-01

    The phylogenetic relationships of members of Cotingidae were investigated using >2100 bp of sequence data from two nuclear introns (myoglobin intron 2 and G3PDH intron 11) and one protein-coding mitochondrial gene (cytochrome b). Strong support was found for a monophyletic clade including 23 traditional cotingid genera, corresponding to the Cotingidae sensu [Remsen, J.V. Jr., Jaramillo, A., Nores, M., Pacheco, J.F., Robbins, M.B., Schulenberg, T.S., Stiles, F.G., da Silva, J.M.C., Stotz, D.F., Zimmer, K.J., 2005. Version 2005-11-15. A classification of the bird species of South America. American Ornithologists' Union. ]. Neither Oxyruncus nor any of the genera in Tityrinae sensu [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] are members of Cotingidae. Within Cotingidae a polytomy of four well-supported clades was recovered: (1) the fruiteaters Pipreola and Ampelioides; (2) the Ampelion group, including Phytotoma; (3) Rupicola and Phoenicircus; and (4) the 'core cotingas' consisting of the remainder of the Cotingas (e.g. fruitcrows, Cotinga, Procnias, Lipaugus, and Carpodectes), with Snowornis in a basal position. The separation of Snowornis from Lipaugus [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] was strongly supported, as were the close relationships between Gymnoderus and Conioptilon, and between Tijuca and Lipaugus. However, basal relationships among 'core cotinga' clades were not resolved.

  6. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    USGS Publications Warehouse

    Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

    2017-01-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  7. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake.

    PubMed

    Soldánová, Miroslava; Georgieva, Simona; Roháčová, Jana; Knudsen, Rune; Kuhn, Jesper A; Henriksen, Eirik H; Siwertsson, Anna; Shaw, Jenny C; Kuris, Armand M; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D; Kostadinova, Aneta

    2017-03-14

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  8. Old fossils–young species: evolutionary history of an endemic gastropod assemblage in Lake Malawi

    PubMed Central

    Schultheiß, Roland; Van Bocxlaer, Bert; Wilke, Thomas; Albrecht, Christian

    2009-01-01

    Studies on environmental changes provide important insights into modes of speciation, into the (adaptive) reoccupation of ecological niches and into species turnover. Against this background, we here examine the history of the gastropod genus Lanistes in the African Rift Lake Malawi, guided by four general evolutionary scenarios, and compare it with patterns reported from other endemic Malawian rift taxa. Based on an integrated approach using a mitochondrial DNA phylogeny and a trait-specific molecular clock in combination with insights from the fossil record and palaeoenvironmental data, we demonstrate that the accumulation of extant molecular diversity in the endemic group did not start before approximately 600 000 years ago from a single lineage. Fossils of the genus from the Malawi Rift, however, are over one million years older. We argue that severe drops in the lake level of Lake Malawi in the Pleistocene offer a potential explanation for this pattern. Our results also challenge previously established phylogenetic relationships within the genus by revealing parallel evolution and providing evidence that the endemic Lanistes species are not restricted to the lake proper but are present throughout the Malawi Rift. PMID:19439440

  9. Lake whitefish diet, condition, and energy density in Lake Champlain and the lower four Great Lakes following dreissenid invasions

    USGS Publications Warehouse

    Herbst, Seth J.; Marsden, J. Ellen; Lantry, Brian F.

    2013-01-01

    Lake Whitefish Coregonus clupeaformis support some of the most valuable commercial freshwater fisheries in North America. Recent growth and condition decreases in Lake Whitefish populations in the Great Lakes have been attributed to the invasion of the dreissenid mussels, zebra mussels Dreissena polymorpha and quagga mussels D. bugensis, and the subsequent collapse of the amphipod, Diporeia, a once-abundant high energy prey source. Since 1993, Lake Champlain has also experienced the invasion and proliferation of zebra mussels, but in contrast to the Great Lakes, Diporeia were not historically abundant. We compared the diet, condition, and energy density of Lake Whitefish from Lake Champlain after the dreissenid mussel invasion to values for those of Lake Whitefish from Lakes Michigan, Huron, Erie, and Ontario. Lake Whitefish were collected using gill nets and bottom trawls, and their diets were quantified seasonally. Condition was estimated using Fulton's condition factor (K) and by determining energy density. In contrast to Lake Whitefish from some of the Great Lakes, those from Lake Champlain Lake Whitefish did not show a dietary shift towards dreissenid mussels, but instead fed primarily on fish eggs in spring, Mysis diluviana in summer, and gastropods and sphaeriids in fall and winter. Along with these dietary differences, the condition and energy density of Lake Whitefish from Lake Champlain were high compared with those of Lake Whitefish from Lakes Michigan, Huron, and Ontario after the dreissenid invasion, and were similar to Lake Whitefish from Lake Erie; fish from Lakes Michigan, Huron, and Ontario consumed dreissenids, whereas fish from Lake Erie did not. Our comparisons of Lake Whitefish populations in Lake Champlain to those in the Great Lakes indicate that diet and condition of Lake Champlain Lake Whitefish were not negatively affected by the dreissenid mussel invasion.

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

    PubMed Central

    Kambhampati, S

    1995-01-01

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

  11. Temperature Trends in Montane Lakes

    NASA Astrophysics Data System (ADS)

    Melack, J. M.; Sadro, S.; Jellison, R.

    2014-12-01

    Long-term temperature trends in lakes integrate hydrological and meteorological factors. We examine temperature trends in a small montane lake with prolonged ice-cover and large seasonal snowfall and in a large saline lake. Emerald Lake, located in the Sierra Nevada (California), is representative of high-elevation lakes throughout the region. No significant trend in outflow temperature was apparent from 1991to 2012. Snowfall in the watershed accounted for 93% of the variability in average summer lake temperatures. Mono Lake (California) lies in a closed, montane basin and is hypersaline and monomictic or meromictic. Temperature profiles have been collected from 1982 to 2010. In the upper water column, the July-August-September water temperatures increased 0.8-1.0°C over the 29 years. This rate of warming is less than published estimates based on satellite-derived skin temperatures and will discussed in the context of general limnological interpretation of temperature trends.

  12. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach.

    PubMed

    Erickson, David L; Jones, Frank A; Swenson, Nathan G; Pei, Nancai; Bourg, Norman A; Chen, Wenna; Davies, Stuart J; Ge, Xue-Jun; Hao, Zhanqing; Howe, Robert W; Huang, Chun-Lin; Larson, Andrew J; Lum, Shawn K Y; Lutz, James A; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D; Fang-Sun, I; Wright, S Joseph; Wolf, Amy T; Ye, W; Xing, Dingliang; Zimmerman, Jess K; Kress, W John

    2014-01-01

    Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

  13. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

    PubMed Central

    Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

    2014-01-01

    Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

  14. Utah: Salt Lake City

    Atmospheric Science Data Center

    2014-05-15

    ... mountains surrounding Salt Lake City are renowned for the dry, powdery snow that results from the arid climate and location at the ... should be used with the red filter placed over your left eye. The canyons and peaks of the Uinta and Wasatch Mountains are ...

  15. The People's Lake

    ERIC Educational Resources Information Center

    Carlson, Karen Townsend

    1975-01-01

    Citizen action to stop the disposal of taconite tailings into Lake Superior was unsuccessful when the courts settled in the favor of industry. Although citizen research revealed a form of asbestos, as well as other toxic chemicals in the discharged wastes, company representatives stated that there were no health hazards. (MA)

  16. Lake Ontario: Nearshore Variability

    EPA Science Inventory

    We conducted a high-resolution survey with towed electronic instrumentation along the Lake Ontario nearshore (720 km) at a 20 meter contour. The survey was conducted September 6-10, 2008 with a shorter 300 km survey conducted August 14-15 for comparing of temporal variability. ...

  17. Lake Michigan: Nearshore Variability

    EPA Science Inventory

    We conducted a high-resolution survey in the nearshore of Lake Michigan at a 20 meter contour using towed electronic instrumentation. The nearly 1200 km survey was conducted Sep 8-15, 2010. We also conducted six cross-contour tows. Along the survey tracks we sampled fixed stat...

  18. Poet Lake Crystal Approval

    EPA Pesticide Factsheets

    This September 19, 2016 letter from EPA approves the petition from Poet Biorefining-Lake Crystal, regarding non-grandfathered ethanol produced through a dry mill process, qualifying under the Clean Air Act for renewable fuel (D-code 6) RINs under the RFS

  19. Quebec: Lake Manicouagan

    Atmospheric Science Data Center

    2013-04-17

    ... kilometers in diameter and is composed of impact-brecciated rock. Glaciation and other erosional processes have reduced the extent of the ... about 5 kilometers. The lake is bounded by erosion-resistant metamorphic and igneous rocks, and shock metamorphic effects are abundant in ...

  20. Great Minds? Great Lakes!

    ERIC Educational Resources Information Center

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

    This booklet introduces an environmental curriculum for use in a variety of elementary subjects. The lesson plans provide an integrated approach to incorporating Great Lakes environmental issues into the subjects of history, social studies, and environmental sciences. Each of these sections contains background information, discussion points, and a…

  1. Timing and order of transmission events is not directly reflected in a pathogen phylogeny.

    PubMed

    Romero-Severson, Ethan; Skar, Helena; Bulla, Ingo; Albert, Jan; Leitner, Thomas

    2014-09-01

    Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and the host transmission history. Here, we examine in detail the limitations of this relationship. First, all splits in a pathogen phylogeny of more than 1 host occur within hosts, not at the moment of transmission, predating the transmission events as described by the pretransmission interval. Second, the order in which nodes in a phylogeny occur may be reflective of the within-host dynamics rather than epidemiologic relationships. To investigate these phenomena, motivated by within-host diversity patterns, we developed a two-phase coalescent model that includes a transmission bottleneck followed by linear outgrowth to a maximum population size followed by either stabilization or decline of the population. The model predicts that the pretransmission interval shrinks compared with predictions based on constant population size or a simple transmission bottleneck. Because lineages coalesce faster in a small population, the probability of a pathogen phylogeny to resemble the transmission history depends on when after infection a donor transmits to a new host. We also show that the probability of inferring the incorrect order of multiple transmissions from the same host is high. Finally, we compare time of HIV-1 infection informed by genetic distances in phylogenies to independent biomarker data, and show that, indeed, the pretransmission interval biases phylogeny-based estimates of when transmissions occurred. We describe situations where caution is needed not to misinterpret which parts of a phylogeny that may indicate outbreaks and tight transmission clusters.

  2. Temperate Lakes Discovered on Titan

    NASA Astrophysics Data System (ADS)

    Vixie, Graham; Barnes, Jason W.; Jackson, Brian; Wilson, Paul

    2012-04-01

    We have discovered two temperate lakes on Titan using Cassini's Visual and Infrared Mapping Spectrometer (VIMS). Three key features help to identify these surface features as lakes: morphology, albedo, and specular reflection. The presence of lakes at the mid-latitudes mean liquid can accumulate and remain stable outside of the poles. We first identify a lake surface by looking for possible shorelines with a lacustrine morphology. Then, we apply a simple atmospheric correction that produces an approximate surface albedo. Next, we prepare cylindrical projection maps of the brightness of the sky as seen from any points on the surface to identify specular reflections. Our techniques can then be applied to other areas, such as Arrakis Planitia, to test for liquid. Currently, all the known lakes on Titan are concentrated at the poles. Lakes have been suggested in the tropic zone by Griffith et al. Our discovery of non-transient, temperate lakes has important implications for Titan's hydrologic cycle. Clouds have been recorded accumulating in the mid-latitudes and areas have been darkened by rainfall but later brightened after evaporation (Turtle et al. 2011). Stable temperate lakes would affect total rainfall, liquid accumulation, evaporation rates, and infiltration. Polaznik Macula (Figure 1) is a great candidate for lake filling, evaporation rates, and stability. References: Griffith, C., et al.: "Evidence for Lakes on Titan's Tropical Surface". AAS/Division for Planetary Sciences Meeting Abstracts #42, Vol. 42, pp. 1077, 2010. Turtle, E. P., et al.: "Rapid and Extensive Surface Changes Near Titan's Equator: Evidence of April Showers". Science, Vol. 331, pp. 1414-, 2011. Figure 1: Polaznik Macula is the large, dark area central to the figure. The encircled dark blue areas represent positively identified lake regions in the T66 flyby. The light blue areas represent lake candidates still under analysis. The green circle marks a non-lake surface feature enclosed by a

  3. Microbiology of Lonar Lake and other soda lakes.

    PubMed

    Antony, Chakkiath Paul; Kumaresan, Deepak; Hunger, Sindy; Drake, Harold L; Murrell, J Colin; Shouche, Yogesh S

    2013-03-01

    Soda lakes are saline and alkaline ecosystems that are believed to have existed throughout the geological record of Earth. They are widely distributed across the globe, but are highly abundant in terrestrial biomes such as deserts and steppes and in geologically interesting regions such as the East African Rift valley. The unusual geochemistry of these lakes supports the growth of an impressive array of microorganisms that are of ecological and economic importance. Haloalkaliphilic Bacteria and Archaea belonging to all major trophic groups have been described from many soda lakes, including lakes with exceptionally high levels of heavy metals. Lonar Lake is a soda lake that is centered at an unusual meteorite impact structure in the Deccan basalts in India and its key physicochemical and microbiological characteristics are highlighted in this article. The occurrence of diverse functional groups of microbes, such as methanogens, methanotrophs, phototrophs, denitrifiers, sulfur oxidizers, sulfate reducers and syntrophs in soda lakes, suggests that these habitats harbor complex microbial food webs that (a) interconnect various biological cycles via redox coupling and (b) impact on the production and consumption of greenhouse gases. Soda lake microorganisms harbor several biotechnologically relevant enzymes and biomolecules (for example, cellulases, amylases, ectoine) and there is the need to augment bioprospecting efforts in soda lake environments with new integrated approaches. Importantly, some saline and alkaline lake ecosystems around the world need to be protected from anthropogenic pressures that threaten their long-term existence.

  4. Lake trout rehabilitation in Lake Erie: a case history

    USGS Publications Warehouse

    Cornelius, Floyd C.; Muth, Kenneth M.; Kenyon, Roger

    1995-01-01

    Native lake trout (Salvelinus namaycush) once thrived in the deep waters of eastern Lake Erie. The impact of nearly 70 years of unregulated exploitation and over 100 years of progressively severe cultural eutrophication resulted in the elimination of lake trout stocks by 1950. Early attempts to restore lake trout by stocking were unsuccessful in establishing a self-sustaining population. In the early 1980s, New York's Department of Environmental Conservation, Pennsylvania's Fish and Boat Commission, and the U.S. Fish and Wildlife Service entered into a cooperative program to rehabilitate lake trout in the eastern basin of Lake Erie. After 11 years of stocking selected strains of lake trout in U.S. waters, followed by effective sea lamprey control, lake trout appear to be successfully recolonizing their native habitat. Adult stocks have built up significantly and are expanding their range in the lake. Preliminary investigations suggest that lake trout reproductive habitat is still adequate for natural reproduction, but natural recruitment has not been documented. Future assessments will be directed toward evaluation of spawning success and tracking age-class cohorts as they move through the fishery.

  5. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama.

    PubMed

    Kress, W John; Erickson, David L; Jones, F Andrew; Swenson, Nathan G; Perez, Rolando; Sanjur, Oris; Bermingham, Eldredge

    2009-11-03

    The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.

  6. Potential strategies for recovery of lake whitefish and lake herring stocks in eastern Lake Erie

    USGS Publications Warehouse

    Oldenburg, K.; Stapanian, M.A.; Ryan, P.A.; Holm, E.

    2007-01-01

    Lake Erie sustained large populations of ciscoes (Salmonidae: Coregoninae) 120 years ago. By the end of the 19th century, abundance of lake whitefish (Coregonus clupeaformis) had declined drastically. By 1925, the lake herring (a cisco) population (Coregonus artedii) had collapsed, although a limited lake herring fishery persisted in the eastern basin until the 1950s. In the latter part of the 20th century, the composition of the fish community changed as oligotrophication proceeded. Since 1984, a limited recovery of lake whitefish has occurred, however no recovery was evident for lake herring. Current ecological conditions in Lake Erie probably will not inhibit recovery of the coregonine species. Recovery of walleye (Sander vitreus) and efforts to rehabilitate the native lake trout (Salvelinus namaycush) in Lake Erie will probably assist recovery because these piscivores reduce populations of alewife (Alosa psuedoharengus) and rainbow smelt (Osmerus mordax), which inhibit reproductive success of coregonines. Although there are considerable spawning substrates available to coregonine species in eastern Lake Erie, eggs and fry would probably be displaced by storm surge from most shoals. Site selection for stocking or seeding of eggs should consider the reproductive life cycle of the stocked fish and suitable protection from storm events. Two potential sites in the eastern basin have been identified. Recommended management procedures, including commercial fisheries, are suggested to assist in recovery. Stocking in the eastern basin of Lake Erie is recommended for both species, as conditions are adequate and the native spawning population in the eastern basin is low. For lake herring, consideration should be given to match ecophenotypes as much as possible. Egg seeding is recommended. Egg seeding of lake whitefish should be considered initially, with fingerling or yearling stocking suggested if unsuccessful. Spawning stocks of whitefish in the western basin of Lake

  7. Lake Mead--clear and vital

    USGS Publications Warehouse

    Wessells, Stephen M.; Rosen, Michael

    2013-01-01

    Lake Mead – Clear and Vital” is a 13 minute documentary relating the crucial role of science in maintaining high water quality in Lake Mead. The program was produced coincident with release of the Lakes Mead and Mohave Circular a USGS publication covering past and on-going research in the lakes and tributaries of the Lake Mead National Recreation Area.

  8. Lake Erie...Take a Bow.

    ERIC Educational Resources Information Center

    Canning, Maureen; Dunlevy, Margie

    This elementary school teaching unit was developed as a part of a series of teaching units that deal with Lake Erie. This unit was developed to enable children to: (1) identify the Great Lakes and pick out Lake Erie on a map; (2) demonstrate knowledge of Lake Erie's origin and geography; (3) list some uses of Lake Erie; and (4) give examples of…

  9. Predicting Maximum Lake Depth from Surrounding Topography

    EPA Science Inventory

    Lake volume aids understanding of the physical and ecological dynamics of lakes, yet is often not readily available. The data needed to calculate lake volume (i.e. bathymetry) are usually only collected on a lake by lake basis and are difficult to obtain across broad regions. ...

  10. Lake Garda, Italy

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This ASTER image was acquired on July 29, 2000 and covers an area of 30 by 57 km in northern Italy. Lake Garda was formed by glaciers during the last Ice Age, and is Italy's largest lake. Lago di Garda lies in the provinces of Verona, Brescia, and Trento, and is 51 kilometers (32 miles) long and from 3 to 18 kilometers (2 to 11 miles) wide. The Sarca is its chief affluent, and the lake is drained southward by the Mincio, which discharges into the Po River. Many villas are situated on its shores. On the peninsula of Sirmione, at the southern end of the lake, are the ruins of a Roman villa and a castle of the Scaligers, an Italian family of the 16th century. The RIGHT image has the land area masked out, and a harsh stretch was applied to the lake values to display variations in sediment load. Also visible are hundreds of boats and their wakes, criss-crossing the lake.

    The image is centered at 45.6 degrees north latitude, 10.6 degrees east longitude.

    Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of International Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products. Dr. Anne Kahle at NASA's Jet Propulsion Laboratory, Pasadena, Calif., is the U.S. Science team leader; Moshe Pniel of JPL is the project manager. ASTER is the only high resolution imaging sensor on Terra. The primary goal of the ASTER mission is to obtain high-resolution image data in 14 channels over the entire land surface, as well as black and white stereo images. With revisit time of between 4 and 16 days, ASTER will provide the capability for repeat coverage of changing areas on Earth's surface.

    The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for

  11. Future volcanic lake research: revealing secrets from poorly studied lakes

    NASA Astrophysics Data System (ADS)

    Rouwet, D.; Tassi, F.; Mora-Amador, R. A.

    2012-04-01

    Volcanic lake research boosted after the 1986 Lake Nyos lethal gas burst, a limnic rather than volcanic event. This led to the formation of the IAVCEI-Commission on Volcanic Lakes, which grew out into a multi-disciplinary scientific community since the 1990's. At Lake Nyos, a degassing pipe is functional since 2001, and two additional pipes were added in 2011, aimed to prevent further limnic eruption events. There are between 150 and 200 volcanic lakes on Earth. Some acidic crater lakes topping active magmatic-hydrothermal systems are monitored continuously or discontinuously. Such detailed studies have shown their usefulness in volcanic surveillance (e.g. Ruapehu, Yugama-Kusatsu-Shiran, Poás). Others are "Nyos-type" lakes, with possible gas accumulation in bottom waters and thus potentially hazardous. "Nyos-type" lakes tend to remain stably stratified in tropical and sub-tropical climates (meromictic), leading to long-term gas build-up and thus higher potential risk. In temperate climates, such lakes tend to turn over in winter (monomictic), and thus liberating its gas charge yearly. We line out research strategies for the different types of lakes. We believe a complementary, multi-disciplinary approach (geochemistry, geophysics, limnology, biology, statistics, etc.) will lead to new insights and ideas, which can be the base for future following-up and monitoring. After 25 years of pioneering studies on rather few lakes, the scientific community should be challenged to study the many poorly studied volcanic lakes, in order to better constrain the related hazard, based on probabilistic approaches.

  12. Effect of wave exposure dynamics on gut content mass and growth of young-of-the-year fishes in the littoral zone of lakes.

    PubMed

    Stoll, S; Hofmann, H; Fischer, P

    2010-05-01

    Total length, body mass and gut content mass of young-of-the-year (YOY) perch Perca fluviatilis, dace Leuciscus leuciscus and bleak Alburnus alburnus were recorded over the summer of 2006 at three littoral sites at Upper Lake Constance. In P. fluviatilis and L. leuciscus, gut content mass correlated positively with wave-induced energy flux (E(F)) of the respective site and sampling day, while no correlation of gut content mass with E(F) was found in A. alburnus. It was assumed that benthivorous P. fluviatilis and L. leuciscus profited from suspended or uncovered benthic food items generated by wave action at sites and periods with high E(F). Alburnus alburnus, in contrast, feeding mainly on zooplankton in upper parts of the water column, could not profit from increased E(F). In P. fluviatilis, increased gut content mass during periods of high E(F) resulted in higher growth rates. For L. leuciscus, no real growth rates in local fish populations could be determined, as individuals were less sedentary, and when increased growth occurred at sites during the periods of high E(F), migration of fish levelled out the resulting size differences within few days. The results of this study show that dynamic habitat variables affect site profitability in the littoral zone of lakes, especially in benthivorous fishes. Therefore, dynamic habitat variables should be considered in addition to fixed habitat properties in analyses of habitat choice of fishes in the littoral zone of lakes.

  13. Molecular Phylogeny and Biogeography of Percocypris (Cyprinidae, Teleostei)

    PubMed Central

    Wang, Mo; Yang, Jun-Xing; Chen, Xiao-Yong

    2013-01-01

    Fierce predatory freshwater fishes, the species of Percocypris (Cyprinidae, Teleostei) inhabit large rivers or lakes, and have a specific distribution pattern. Only a single species or subspecies occurs in each large-scale drainage basin of the Southeastern Tibetan Plateau. In this study, the molecular phylogenetic relationships for all but one of the described subspecies/species of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results of Maximum Likelihood and Bayesian Inference analyses show that Percocypris is a strongly supported monophyletic group and that it is the sister group of Schizothorax. Combined with analyses of morphological characters, our results suggest that Percocypris needs to be reclassified, and we propose that six species be recognized, with corresponding distributions in five main drainages (including one lake). In addition, based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance (due to the uplift of the Tibetan Plateau modifying the large-scale morphologies of drainage basins in the Southeastern Tibetan Plateau) has played an important role in the speciation of the genus. Furthermore, external morphological characters (such as the length of the fins) and an internal trait (the position of pterygiophore) appear to be correlated with different habitats in rivers and the lake. PMID:23750199

  14. Genetic diversity of Diporeia in the Great Lakes: comparison of Lake Superior to the other Great Lakes

    EPA Science Inventory

    Abundances of Diporeia have dropped drastically in the Great Lakes, except in Lake Superior, where data suggest that population counts actually have risen. Various ecological, environmental, or geographic hypotheses have been proposed to explain the greater abundance of Lake Supe...

  15. Incised bifurcations and uneven radial distribution of channel incision in the Wax Lake Delta, USA

    NASA Astrophysics Data System (ADS)

    Shaw, J. B.; Mohrig, D. C.

    2009-12-01

    The Wax Lake Delta, southern Louisiana, has been found to possess distributary channels whose beds range from non-depositional to strongly erosional, cut into pre-delta muds. This discovery was unexpected given that the overall depositional setting has created greater than 100 square km of subareal land in less than 40 years. Furthermore, while map views of the system reveal an approximately radial symmetric depositional pattern and delta shape, the pattern of channel incision is unevenly distributed across the distributary network. The apex of Wax Lake delta is defined by an adverse ramp with a bed slope of 0.006 that connects the deep feeder channel (18m) to the shallower, first set of bifurcations. We find two distinct zones of channel bottom character within the distributary network. The first zone consists of substantially incised channels stemming from the bifurcation directly downstream of the Wax Lake Outlet and ramp described above. The maximum depth of incision into pre-delta mud decreases from roughly 3m to 1.5m nearer the delta front. This incision can make up greater than 1/3 of the total flow depth in these channels. The second zone is characterized by non-depositional channel bottoms that are located off to either side of the swath of incisional channels. These channels sit on top of the pre-delta substrate, showing no significant erosion or deposition. The occurrence of bed erosion and non-deposition throughout the observed channel network raises the previously unasked questions of whether these regimes extend to the very front of the delta located 10km from the delta apex, and whether incision plays an important role in the original development of bifurcations on this delta. The development of channel bifurcations under conditions with significant bed incision has yet to be discussed in the river bifurcation literature, and may play an important role in the observed constancy of channel network patterns. Using USACE bathymetry surveys as well as

  16. Mass and environment as drivers of galaxy evolution. III. The constancy of the faint-end slope and the merging of galaxies

    SciTech Connect

    Peng, Ying-jie; Lilly, Simon J.; Carollo, Marcella; Renzini, Alvio

    2014-08-01

    Using our continuity approach, we explore the underlying connections between the evolution of the faint-end slope α{sub s} of the stellar mass function of star-forming galaxies, the logarithmic slope β of the specific star formation rate (sSFR)-mass relation, and the merging of galaxies. We derive analytically the consequences of the observed constancy of α{sub s} since redshifts of at least z ∼ 2. If the logarithmic slope β of the sSFR-mass relation is negative, then the faint-end slope α{sub s} should quickly diverge due to the differential mass increase of galaxies on the star-forming main sequence, and this will also quickly destroy the Schechter form of the mass function. This problem can be solved by removing low-mass galaxies by merging them into more massive galaxies. We quantify this process by introducing the specific merger mass rate (sMMR) as the specific rate of mass added to a given galaxy through mergers. For a modest negative value of β ∼ –0.1, an average sMMR ∼ 0.1 sSFR across the population is required to keep α{sub s} constant with epoch, as observed. This in turn implies a merger rate of ∼0.2 sSFR for major mergers, which is consistent with the available observational estimates. More negative values of β require higher sMMR and higher merger rates, and the steepening of the mass function becomes impossible to control for β < –(α{sub s} + 2). The close link that is required between the in situ sSFR and the sMMR probably arises because both are closely linked to the buildup of dark matter halos. These new findings further develop the formalism for the evolving galaxy population that we introduced earlier and show how striking symmetries in the galaxy population can emerge as the result of deep links between the physical processes involved.

  17. Evidence of spring spawning lake trout in Lake Superior

    USGS Publications Warehouse

    Bronte, Charles R.

    1993-01-01

    In 1992, the U. S. Fish and Wildlife Service began research on the life history, population dynamics, and stock delineation of siscowet lake trout Salvelinus namaycush siscowet in Lake Superior. Siscowet were captured with gill nets in 80-150 m of water on 23-26 April 1992 north of the Apostle Islands in western Lake Superior. Of 91 captured siscowets, one male had fully developed testes in nearly ripe condition and one female had eggs running from the vent. This observation represents the earliest dates that lake trout of any morphotype have been found in spawning or near-spawning condition.

  18. Method for lake restoration

    DOEpatents

    Dawson, Gaynor W.; Mercer, Basil W.

    1979-01-01

    A process for removing pollutants or minerals from lake, river or ocean sediments or from mine tailings is disclosed. Magnetically attractable collection units containing an ion exchange or sorbent media with an affinity for a chosen target substance are distributed in the sediments or tailings. After a period of time has passed sufficient for the particles to bind up the target substances, a magnet drawn through the sediments or across the tailings retrieves the units along with the target substance.

  19. THOUSAND LAKES WILDERNESS, CALIFORNIA.

    USGS Publications Warehouse

    Till, Alison B.; McHugh, Edward L.

    1984-01-01

    A mineral survey of the Thousand Lakes Wilderness in northern California indicated little promise for the occurrence of mineral resources. Volcanic stone and cinders occur, but similar materials are found in abundance outside the wilderness. The wilderness is in the Cascade Volcanic Province, a setting locally favorable for geothermal resource potential. No geothermal potential was identified in the wilderness; subsurface potential cannot be evaluated without regional studies and drilling.

  20. Great Lakes Demonstration 2

    DTIC Science & Technology

    2012-06-01

    Representatives from CG Districts 1, 5 , 13, and 17  Enbridge Pipeline, Co.  EPA  National Oceanic and Atmospheric Administration (NOAA)  Observers (CG...distances from the vessel‟s hull. (Figure 5 ) In that configuration, the recovery hose and hydraulic lines dragged across the surface of the nearby...No. CG-D-08-12 2. Government Accession Number 3. Recipient’s Catalog No. 4. Title and Subtitle Great Lakes Demonstration 2 Final Report 5

  1. Not so Great Lakes?

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    In 1965, Frank Sinatra won the Grammy Award for his album, “September of My Years” “Early Bird,” the first commercial communications satellite, was launched; and Dr. Martin Luther King, Jr. was arrested in Selma, Alabama, during demonstrations against voter-registration rules.The year 1965 was also the last time water levels in the U.S. Great Lakes were as low as they are now.

  2. Not so Great Lakes?

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    In 1965, Frank Sinatra won the Grammy Award for his album, "September of My Years;" "Early Bird," the first commercial communications satellite, was launched; and Dr. Martin Luther King, Jr. was arrested in Selma, Alabama, during demonstrations against voter-registration rules.The year 1965 was also the last time water levels in the U.S. Great Lakes were as low as they are now.

  3. Archaea in Yellowstone Lake.

    PubMed

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

    2011-11-01

    The Yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the Archaea. This study continues on this theme, examining Yellowstone Lake and its lake floor hydrothermal vents. Significant Archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. Phylogenetic diversity was assessed using 454-FLX sequencing (~51,000 pyrosequencing reads; V1 and V2 regions) and Sanger sequencing of 200 near-full-length polymerase chain reaction (PCR) clones. Automated classifiers (Ribosomal Database Project (RDP) and Greengenes) were problematic for the 454-FLX reads (wrong domain or phylum), although BLAST analysis of the 454-FLX reads against the phylogenetically placed full-length Sanger sequenced PCR clones proved reliable. Most of the archaeal diversity was associated with vents, and as expected there were differences between the vents and the near-surface photic zone samples. Thaumarchaeota dominated all samples: vent-associated organisms corresponded to the largely uncharacterized Marine Group I, and in surface waters, ~69-84% of the 454-FLX reads matched archaeal clones representing organisms that are Nitrosopumilus maritimus-like (96-97% identity). Importance of the lake nitrogen cycling was also suggested by >5% of the alkaline vent phylotypes being closely related to the nitrifier Candidatus Nitrosocaldus yellowstonii. The Euryarchaeota were primarily related to the uncharacterized environmental clones that make up the Deep Sea Euryarchaeal Group or Deep Sea Hydrothermal Vent Group-6. The phylogenetic parallels of Yellowstone Lake archaea to marine microorganisms provide opportunities to examine interesting evolutionary tracks between freshwater and marine lineages.

  4. Angora Fire, Lake Tahoe

    NASA Technical Reports Server (NTRS)

    2007-01-01

    On the weekend of June 23, 2007, a wildfire broke out south of Lake Tahoe, which stretches across the California-Nevada border. By June 28, the Angora Fire had burned more than 200 homes and forced some 2,000 residents to evacuate, according to The Seattle Times and the Central Valley Business Times. On June 27, the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite captured this image of the burn scar left by the Angora fire. The burn scar is dark gray, or charcoal. Water bodies, including the southern tip of Lake Tahoe and Fallen Leaf Lake, are pale silvery blue, the silver color a result of sunlight reflecting off the surface of the water. Vegetation ranges in color from dark to bright green. Streets are light gray, and the customary pattern of meandering residential streets and cul-de-sacs appears throughout the image, including the area that burned. The burn scar shows where the fire obliterated some of the residential areas just east of Fallen Leaf Lake. According to news reports, the U.S. Forest Service had expressed optimism about containing the fire within a week of the outbreak, but a few days after the fire started, it jumped a defense, forcing the evacuation of hundreds more residents. Strong winds that had been forecast for June 27, however, did not materialize, allowing firefighters to regain ground in controlling the blaze. On June 27, authorities hoped that the fire would be completely contained by July 3. According to estimates provided in the daily report from the National Interagency Fire Center, the fire had burned 3,100 acres (about 12.5 square kilometers) and was about 55 percent contained as of June 28. Some mandatory evacuations remained in effect. NASA image by Jesse Allen, using data provided courtesy of the NASA/GSFC/MITI/ERSDAC/JAROS, and U.S./Japan ASTER Science Team.

  5. Great Lakes Energy Institute

    SciTech Connect

    Alexander, J. Iwan

    2012-11-18

    The vision of the Great Lakes Energy Institute is to enable the transition to advanced, sustainable energy generation, storage, distribution and utilization through coordinated research, development, and education. The Institute will place emphasis on translating leading edge research into next generation energy technology. The Institute’s research thrusts focus on coordinated research in decentralized power generation devices (e.g. fuel cells, wind turbines, solar photovoltaic devices), management of electrical power transmission and distribution, energy storage, and energy efficiency.

  6. Where This Occurs: Lakes and Rivers

    EPA Pesticide Factsheets

    Nutrient pollution builds up in our nation's lakes, ponds, and streams. EPA's 2010 National Lakes Assessment found that almost 20 percent of the 50,000 lakes surveyed had been impacted by nitrogen and phosphorus pollution.

  7. Gender Constancy and Sibling Status.

    ERIC Educational Resources Information Center

    Katz, Phyllis A.; Rank, Sara Anne

    To test effects of family constellation on children's acquisition of sex-role, the sex-role behavior of 175 children between the ages of 3 and one half and 6 years from one-child and two-child families was compared. Included in the design were five categories: only children, and four additional categories based on sex and relative age of siblings…

  8. Person Constancy within Developmental Change.

    ERIC Educational Resources Information Center

    Maccoby, Eleanor E.

    Using findings on the unstability of previously stable physical activity levels of young children as a kind of case study to aid thought about the trait-dimensional approach to developmental continuity and discontinuity, this discussion explores the applicability of a dual theory of concept formation to the problem of personal stability and…

  9. Progress toward lake trout restoration in Lake Michigan

    USGS Publications Warehouse

    Holey, Mark E.; Rybicki, Ronald W.; Eck, Gary W.; Brown, Edward H.; Marsden, J. Ellen; Lavis, Dennis S.; Toneys, Michael L.; Trudeau, Tom N.; Horrall, Ross M.

    1995-01-01

    Progress toward lake trout restoration in Lake Michigan is described through 1993. Extinction of the native lake trout fishery by sea lamprey predation, augmented by exploitation and habitat destruction, resulted in an extensive stocking program of hatchery-reared lake trout that began in 1965. Sea lamprey abundance was effectively controlled using selective chemical toxicants. The initial stocking produced a measurable wild year class of lake trout by 1976 in Grand Traverse Bay, but failed to continue probably due to excessive exploitation. The overall lack of successful reproduction lakewide by the late 1970s led to the development and implementation in 1985 of a focused inter-agency lakewide restoration plan by a technical committee created through the Lake Committee structure of the Great Lakes Fishery Commission. Strategies implemented in 1985 by the plan included setting a 40% total mortality goal lakewide, creating two large refuges designed to encompass historically the most productive spawning habitat and protect trout stocked over their home range, evaluating several lake trout strains, and setting stocking priorities throughout the lake. Target levels for stocking in the 1985 Plan have never been reached, and are much less than the estimated lakewide recruitment of yearlings by the native lake trout stocks. Since 1985, over 90% of the available lake trout have been stocked over the best spawning habitat, and colonization of the historically productive offshore reefs has occurred. Concentrations of spawning lake trout large enough for successful reproduction, based on observations of successful hatchery and wild stocks, have developed at specific reefs. Continued lack of recruitment at these specific sites suggests that something other than stotk abundance has limited success. Poor survival of lake trout eggs, assumed to be related to contaminant burden, occurred in the late 1970s and early 1980s, but survival has since increased to equal survival in the

  10. Neotropical mutualism between Acacia and Pseudomyrmex: phylogeny and divergence times.

    PubMed

    Gómez-Acevedo, Sandra; Rico-Arce, Lourdes; Delgado-Salinas, Alfonso; Magallón, Susana; Eguiarte, Luis E

    2010-07-01

    The interaction between Acacia and Pseudomyrmex is a textbook example of mutualism between ants and plants, nevertheless aspects of its evolutionary biology have not been formally explored. In this paper we analyze primarily the phylogenies of both New World Acacia and of their associated species of ants, and the geographic origin of this mutualism. Until now, there has been no molecular analysis of this relationship in terms of its origin and age. We analyzed three chloroplast markers (matK, psaB-rps14, and trnL-trnF) on a total of 70 taxa of legumes from the subfamily Mimosoideae, and two nuclear regions (long-wavelength rhodopsine and wingless) on a total of 43 taxa of ants from subfamily Pseudomyrmecinae. The monophyly of subgenus Acacia and within the New World lineages that of the myrmecophilous Acacia group was established. In addition, our results supported the monophyly of the genus Pseudomyrmex and of the associated acacia-ants P. ferrugineus group. Using Bayesian methods and calibration data, the estimated divergence times for the groups involved in the mutualism are: 5.44+/-1.93 My for the myrmecophilous acacias and 4.58+/-0.82 My for their associated ant species, implying that their relationship originated in Mesoamerica between the late Miocene to the middle Pliocene, with eventual diversification of both groups in Mexico.

  11. The phylogeny and evolutionary history of tyrannosauroid dinosaurs.

    PubMed

    Brusatte, Stephen L; Carr, Thomas D

    2016-02-02

    Tyrannosauroids--the group of carnivores including Tyrannosaurs rex--are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work.

  12. The phylogeny and evolutionary history of tyrannosauroid dinosaurs

    NASA Astrophysics Data System (ADS)

    Brusatte, Stephen L.; Carr, Thomas D.

    2016-02-01

    Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work.

  13. Molecular phylogeny of the forensically important genus Cochliomyia (Diptera: Calliphoridae)

    PubMed Central

    Yusseff-Vanegas, Sohath; Agnarsson, Ingi

    2016-01-01

    Abstract Cochliomyia Townsend includes several abundant and one of the most broadly distributed, blow flies in the Americas, and is of significant economic and forensic importance. For decades, Cochliomyia hominivorax (Coquerel) and Cochliomyia macellaria (Fabricius) have received attention as livestock parasites and primary indicator species in forensic entomology. However, Cochliomyia minima Shannon and Cochliomyia aldrichi Del Ponte have only been subject to basic taxonomy and faunistic studies. Here we present the first complete phylogeny of Cochliomyia including numerous specimens per species, collected from 13 localities in the Caribbean. Four genes, the mitochondrial COI and the nuclear EF-1α, 28S rRNA, and ITS2, were analyzed. While we found some differences among gene trees, a concatenated gene matrix recovered a robustly supported monophyletic Cochliomyia with Compsomyiops Townsend as its sister group and recovered the monophyly of Cochliomyia hominivorax, Cochliomyia macellaria and Cochliomyia minima. Our results support a close relationship between Cochliomyia minima and Cochliomyia aldrichi. However, we found Cochliomyia aldrichi containing Cochliomyia minima, indicating recent speciation, or issues with the taxonomy of the group. We provide basic information on habitat preference, distribution and feeding habits of Cochliomyia minima and Cochliomyia aldrichi that will be useful for future forensic studies in the Caribbean. PMID:27563274

  14. Big cat phylogenies, consensus trees, and computational thinking.

    PubMed

    Sul, Seung-Jin; Williams, Tiffani L

    2011-07-01

    Phylogenetics seeks to deduce the pattern of relatedness between organisms by using a phylogeny or evolutionary tree. For a given set of organisms or taxa, there may be many evolutionary trees depicting how these organisms evolved from a common ancestor. As a result, consensus trees are a popular approach for summarizing the shared evolutionary relationships in a group of trees. We examine these consensus techniques by studying how the pantherine lineage of cats (clouded leopard, jaguar, leopard, lion, snow leopard, and tiger) evolved, which is hotly debated. While there are many phylogenetic resources that describe consensus trees, there is very little information, written for biologists, regarding the underlying computational techniques for building them. The pantherine cats provide us with a small, relevant example to explore the computational techniques (such as sorting numbers, hashing functions, and traversing trees) for constructing consensus trees. Our hope is that life scientists enjoy peeking under the computational hood of consensus tree construction and share their positive experiences with others in their community.

  15. Evolution of consciousness: Phylogeny, ontogeny, and emergence from general anesthesia

    PubMed Central

    Mashour, George A.; Alkire, Michael T.

    2013-01-01

    Are animals conscious? If so, when did consciousness evolve? We address these long-standing and essential questions using a modern neuroscientific approach that draws on diverse fields such as consciousness studies, evolutionary neurobiology, animal psychology, and anesthesiology. We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution. Thus, in agreement with Darwin’s insight and the recent “Cambridge Declaration on Consciousness in Non-Human Animals,” a review of modern scientific data suggests that the differences between species in terms of the ability to experience the world is one of degree and not kind. PMID:23754370

  16. Family level phylogenies reveal modes of macroevolution in RNA viruses

    PubMed Central

    Kitchen, Andrew; Shackelton, Laura A.; Holmes, Edward C.

    2011-01-01

    Despite advances in understanding the patterns and processes of microevolution in RNA viruses, little is known about the determinants of viral diversification at the macroevolutionary scale. In particular, the processes by which viral lineages assigned as different “species” are generated remain largely uncharacterized. To address this issue, we use a robust phylogenetic approach to analyze patterns of lineage diversification in five representative families of RNA viruses. We ask whether the process of lineage diversification primarily occurs when viruses infect new host species, either through cross-species transmission or codivergence, and which are defined here as analogous to allopatric speciation in animals, or by acquiring new niches within the same host species, analogous to sympatric speciation. By mapping probable primary host species onto family level viral phylogenies, we reveal a strong clustering among viral lineages that infect groups of closely related host species. Although this is consistent with lineage diversification within individual hosts, we argue that this pattern more likely represents strong biases in our knowledge of viral biodiversity, because we also find that better-sampled human viruses rarely cluster together. Hence, although closely related viruses tend to infect related host species, it is unlikely that they often infect the same host species, such that evolutionary constraints hinder lineage diversification within individual host species. We conclude that the colonization of new but related host species may represent the principle mode of macroevolution in RNA viruses. PMID:21173251

  17. Phylogeny of marine Bacillus isolates from the Gulf of Mexico

    NASA Technical Reports Server (NTRS)

    Siefert, J. L.; Larios-Sanz, M.; Nakamura, L. K.; Slepecky, R. A.; Paul, J. H.; Moore, E. R.; Fox, G. E.; Jurtshuk, P. Jr

    2000-01-01

    The phylogeny of 11 pigmented, aerobic, spore-forming isolates from marine sources was studied. Forty-two biochemical characteristics were examined, and a 16S rDNA sequence was obtained for each isolate. In a phylogenetic tree based on 16S sequencing, four isolates (NRRL B-14850, NRRL B-14904, NRRL B-14907, and NRRL B-14908) clustered with B. subtilis and related organisms; NRRL B-14907 was closely related to B. amyloliquefaciens. NRRL B-14907 and NRRL B-14908 were phenotypically similar to B. amyloliquefaciens and B. pumilus, respectively. Three strains (NRRL B-14906, NRRL B-14910, and NRRL B-14911) clustered in a clade that included B. firmus, B. lentus, and B. megaterium. NRRL B-14910 was closely related phenotypically and phylogenetically to B. megaterium. NRRL B-14905 clustered with the mesophilic round spore-producing species, B. fusiformis and B. sphaericus; the isolate was more closely related to B. fusiformis. NRRL B-14905 displayed characteristics typical of the B. sphaericus-like organisms. NRRL B-14909 and NRRL B-14912 clustered with the Paenibacillus species and displayed characteristics typical of the genus. Only NRRL B-14851, an unusually thin rod that forms very small spores, may represent a new Bacillus species.

  18. The phylogeny and evolutionary history of tyrannosauroid dinosaurs

    PubMed Central

    Brusatte, Stephen L.; Carr, Thomas D.

    2016-01-01

    Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work. PMID:26830019

  19. Phylogeny, biogeography, and ecology of Ficus section Malvanthera (Moraceae).

    PubMed

    Rønsted, Nina; Weiblen, George D; Savolainen, V; Cook, James M

    2008-07-01

    We conducted the first molecular phylogenetic study of Ficus section Malvanthera (Moraceae; subgenus Urostigma) based on 32 Malvanthera accessions and seven outgroups representing other sections of Ficus subgenus Urostigma. We used DNA sequences from the nuclear ribosomal internal and external transcribed spacers (ITS and ETS), and the glyceraldehyde-3-phosphate dehydrogenase (G3pdh) region. Phylogenetic analysis using maximum parsimony, maximum likelihood and Bayesian methods recovered a monophyletic section Malvanthera to the exclusion of the rubber fig, Ficus elastica. The results of the phylogenetic analyses do not conform to any previously proposed taxonomic subdivision of the section and characters used for previous classification are homoplasious. Geographic distribution, however, is highly conserved and Melanesian Malvanthera are monophyletic. A new subdivision of section Malvanthera reflecting phylogenetic relationships is presented. Section Malvanthera likely diversified during a period of isolation in Australia and subsequently colonized New Guinea. Two Australian series are consistent with a pattern of dispersal out of rainforest habitat into drier habitats accompanied by a reduction in plant height during the transition from hemi-epiphytic trees to lithophytic trees and shrubs. In contradiction with a previous study of Pleistodontes phylogeny suggesting multiple changes in pollination behaviour, reconstruction of changes in pollination behaviour on Malvanthera, suggests only one or a few gains of active pollination within the section.

  20. The rRNA evolution and procaryotic phylogeny

    NASA Technical Reports Server (NTRS)

    Fox, G. E.

    1986-01-01

    Studies of ribosomal RNA primary structure allow reconstruction of phylogenetic trees for prokaryotic organisms. Such studies reveal major dichotomy among the bacteria that separates them into eubacteria and archaebacteria. Both groupings are further segmented into several major divisions. The results obtained from 5S rRNA sequences are essentially the same as those obtained with the 16S rRNA data. In the case of Gram negative bacteria the ribosomal RNA sequencing results can also be directly compared with hybridization studies and cytochrome c sequencing studies. There is again excellent agreement among the several methods. It seems likely then that the overall picture of microbial phylogeny that is emerging from the RNA sequence studies is a good approximation of the true history of these organisms. The RNA data allow examination of the evolutionary process in a semi-quantitative way. The secondary structures of these RNAs are largely established. As a result it is possible to recognize examples of local structural evolution. Evolutionary pathways accounting for these events can be proposed and their probability can be assessed.

  1. Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

    PubMed Central

    Moreira, Cristiana; Vasconcelos, Vitor; Antunes, Agostinho

    2013-01-01

    Phylogeny is an evolutionary reconstruction of the past relationships of DNA or protein sequences and it can further be used as a tool to assess population structuring, genetic diversity and biogeographic patterns. In the microbial world, the concept that everything is everywhere is widely accepted. However, it is much debated whether microbes are easily dispersed globally or whether they, like many macro-organisms, have historical biogeographies. Biogeography can be defined as the science that documents the spatial and temporal distribution of a given taxa in the environment at local, regional and continental scales. Speciation, extinction and dispersal are proposed to explain the generation of biogeographic patterns. Cyanobacteria are a diverse group of microorganisms that inhabit a wide range of ecological niches and are well known for their toxic secondary metabolite production. Knowledge of the evolution and dispersal of these microorganisms is still limited, and further research to understand such topics is imperative. Here, we provide a compilation of the most relevant information regarding these issues to better understand the present state of the art as a platform for future studies, and we highlight examples of both phylogenetic and biogeographic studies in non-symbiotic cyanobacteria and cyanotoxins. PMID:24189276

  2. Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited

    PubMed Central

    Hess, Sebastian; Sausen, Nicole; Melkonian, Michael

    2012-01-01

    With the advent of molecular phylogenetic techniques the polyphyly of naked filose amoebae has been proven. They are interspersed in several supergroups of eukaryotes and most of them already found their place within the tree of life. Although the ‘vampire amoebae’ have attracted interest since the middle of the 19th century, the phylogenetic position and even the monophyly of this traditional group are still uncertain. In this study clonal co-cultures of eight algivorous vampyrellid amoebae and the respective food algae were established. Culture material was characterized morphologically and a molecular phylogeny was inferred using SSU rDNA sequence comparisons. We found that the limnetic, algivorous vampyrellid amoebae investigated in this study belong to a major clade within the Endomyxa Cavalier-Smith, 2002 (Cercozoa), grouping together with a few soil-dwelling taxa. They split into two robust clades, one containing species of the genus Vampyrella Cienkowski, 1865, the other containing the genus Leptophrys Hertwig & Lesser, 1874, together with terrestrial members. Supported by morphological data these clades are designated as the two families Vampyrellidae Zopf, 1885, and Leptophryidae fam. nov. Furthermore the order Vampyrellida West, 1901 was revised and now corresponds to the major vampyrellid clade within the Endomyxa, comprising the Vampyrellidae and Leptophryidae as well as several environmental sequences. In the light of the presented phylogenetic analyses morphological and ecological aspects, the feeding strategy and nutritional specialization within the vampyrellid amoebae are discussed. PMID:22355342

  3. Phylogeny-aware identification and correction of taxonomically mislabeled sequences

    PubMed Central

    Kozlov, Alexey M.; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros

    2016-01-01

    Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences (‘mislabels’) using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa. PMID:27166378

  4. Deep phylogeny, ancestral groups and the four ages of life.

    PubMed

    Cavalier-Smith, Thomas

    2010-01-12

    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution.

  5. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials.

    PubMed

    Mitchell, Kieren J; Pratt, Renae C; Watson, Laura N; Gibb, Gillian C; Llamas, Bastien; Kasper, Marta; Edson, Janette; Hopwood, Blair; Male, Dean; Armstrong, Kyle N; Meyer, Matthias; Hofreiter, Michael; Austin, Jeremy; Donnellan, Stephen C; Lee, Michael S Y; Phillips, Matthew J; Cooper, Alan

    2014-09-01

    Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

  6. Molecular phylogeny of the Homoptera: a paraphyletic taxon.

    PubMed

    von Dohlen, C D; Moran, N A

    1995-08-01

    Homoptera and Heteroptera comprise a large insect assemblage, the Hemiptera. Many of the plant sap-sucking Homoptera possess unusual and complex life histories and depend on maternally inherited, intracellular bacteria to supplement their nutritionally deficient diets. Presumably in connection with their diet and lifestyles, the morphology of many Homoptera has become greatly reduced, leading to major controversies regarding the phylogenetic affiliations of homopteran superfamilies. The most fundamental question concerns whether the Homoptera as a whole are monophyletic. Recent studies based on morphology have argued that the Homoptera Sternorrhyncha (Aphidoidea, Coccoidea, Psylloidea, Aleyrodoidea) is a sister group to a group comprising the Homoptera Auchenorrhyncha (Fulgoroidea, Cicadoidea, Cercopoidea, Cicadelloidea) and the Heteroptera, making the Homoptera paraphyletic. We sequenced the 5' 580-680 base pairs of small-subunit (18S) ribosomal DNA from a selection of Homoptera, Hemiptera, and their putative outgroups, the Thysanoptera and Psocoptera, to apply molecular characters to the problem of Homoptera phylogeny. Parsimony, distance, maximum-likelihood, and bootstrap methods were used to construct trees from sequence data and assess support for the topologies produced. Molecular data corroborate current views of relationships within the Sternorrhyncha and Auchenorrhyncha based on morphology and strongly support the hypothesis of homopteran paraphyly as stated above. In addition, it was found that Homoptera Sternorrhyncha have extra, GC-rich sequence concentrated in a variable region of the 18S rDNA, which indicates that some unique evolutionary processes are occurring in this lineage.

  7. Phylogeny and radiation of pollination systems in DISA (Orchidaceae).

    PubMed

    Johnson, S; Linder, H; Steiner, K

    1998-03-01

    We studied the patterns of adaptive radiation in Disa, a large orchid genus in southern Africa. A cladogram for 27 species was constructed using 44 morphological characters. Pollination systems were then mapped onto the phylogeny in order to analyze pathways of floral evolution. Shifts from one pollination system to another have been a major feature of the evolutionary diversification of Disa. Unlike many plant genera that are pollinated mainly by a single group of insects, radiation in Disa has encompassed nearly all major groups of pollinating insects; in all, 19 different specialized pollination systems have been found in the 27 species included in this analysis. Another striking pattern is the repeated evolution of broadly similar pollination systems in unrelated clades. For example, butterfly-pollinated flowers have evolved twice; showy deceptive flowers pollinated by carpenter bees, twice; long-spurred flowers pollinated by long-tongued flies, four times; night-scented flowers pollinated by moths, three times; and self-pollination, three times. This suggests that a few dominant pollinator species in a region may be sufficient to generate diversification in plants through repeated floral shifts that never retrace the same pathways.

  8. Angiosperm phylogeny based on matK sequence information.

    PubMed

    Hilu, Khidir W; Borsch, Thomas; Müller, Kai; Soltis, Douglas E; Soltis, Pamela S; Savolainen, Vincent; Chase, Mark W; Powell, Martyn P; Alice, Lawrence A; Evans, Rodger; Sauquet, Hervé; Neinhuis, Christoph; Slotta, Tracey A B; Rohwer, Jens G; Campbell, Christopher S; Chatrou, Lars W

    2003-12-01

    Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all individual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79% are supported by high jackknife values, averaging 88%. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The matK gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of matK and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution.

  9. Deep phylogeny, ancestral groups and the four ages of life

    PubMed Central

    Cavalier-Smith, Thomas

    2010-01-01

    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria—the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution. PMID:20008390

  10. Molecular phylogeny of wild hops, Humulus lupulus L.

    PubMed

    Murakami, A; Darby, P; Javornik, B; Pais, M S S; Seigner, E; Lutz, A; Svoboda, P

    2006-07-01

    We have analysed wild hops collected widely from the Northern Hemisphere, assessing the genetic diversity and the geographical distribution of haplotypes, to investigate the evolution and phylogeny of hops, Humulus lupulus. The haplotypes were characterized by the nuclear ribosomal DNA spacer region (length and DNA sequence) and chloroplast DNA noncoding regions (DNA sequences). The results indicated that primary divergence into European (including Caucasus and Altai hops), and Asian-North American types, was 1.05+/-0.28 to 1.27+/-0.30 million years ago. Although an Eastern boundary for European nuclear haplotype distribution was unclear due to the ambiguous origin of Northern Chinese samples, the European hop group showed a wide geographical distribution across Eurasia from the Altai region to Portugal. The low genetic variation in this group suggested rapid and recent expansion. The North American hop group showed high diversity, and is considered to include hops that have migrated from Asia. Japanese and Chinese hops were identified as genetically distinct. This study has shown that wild hops in each growing region are genetically differentiated with considerable genetic diversity. It gives insights into the evolution and domestication of hops that are discussed.

  11. Complete, accurate, mammalian phylogenies aid conservation planning, but not much.

    PubMed

    Rodrigues, Ana S L; Grenyer, Richard; Baillie, Jonathan E M; Bininda-Emonds, Olaf R P; Gittlemann, John L; Hoffmann, Michael; Safi, Kamran; Schipper, Jan; Stuart, Simon N; Brooks, Thomas

    2011-09-27

    In the face of unprecedented global biodiversity loss, conservation planning must balance between refining and deepening knowledge versus acting on current information to preserve species and communities. Phylogenetic diversity (PD), a biodiversity measure that takes into account the evolutionary relationships between species, is arguably a more meaningful measure of biodiversity than species diversity, but cannot yet be applied to conservation planning for the majority of taxa for which phylogenetic trees have not yet been developed. Here, we investigate how the quality of data on the taxonomy and/or phylogeny of species affects the results of spatial conservation planning in terms of the representation of overall mammalian PD. The results show that the better the quality of the biodiversity data the better they can serve as a basis for conservation planning. However, decisions based on incomplete data are remarkably robust across different levels of degrading quality concerning the description of new species and the availability of phylogenetic information. Thus, given the level of urgency and the need for action, conservation planning can safely make use of the best available systematic data, limited as these data may be.

  12. Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets

    PubMed Central

    Blanco-Míguez, Aitor; Sánchez, Borja

    2016-01-01

    Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future. PMID:28033346

  13. Phylogeny and disjunct distribution: evolution of Saintpaulia (Gesneriaceae).

    PubMed Central

    Möller, M; Cronk, Q C

    1997-01-01

    The molecular phylogeny of African violets (Saintpaulia H. Wendl.), based on ribosomal DNA internal transcribed spacer (ITS) sequences, follows the disjunct biogeography of the genus. Sequence analysis by parsimony of 19 accessions, representing 17 currently recognized Saintpaulia species, resulted in four trees of 182 steps. The first major division is between S. goetzeana, from the Uluguru Mts, Tanzania, and the rest of the genus. The basal position of S. goetzeana, and its putative primitive characters, may indicate an Uluguru origin for Saintpaulia and subsequent colonization of the more northerly mountains. Of the remainder, S. teitensis, from the Teita Hills of Kenya, is sister taxon to the other species (which occur mainly in the Usambara Mts of north-east Tanzania). A group of nine Usambaran species that we call the 'ionantha complex' show minimal ITS genetic differentiation and are also taxonomically critical. Species diversity in the Usambara Mts appears to be the result of rapid, recent (possibly Pleistocene) radiation. This study reveals the limitations of ITS sequences for elucidating the radiation of poorly differentiated species (the ionantha complex). However, the molecular data strongly suggest that conservation of the Uluguru and Teita populations is essential for the protection of the full range of diversity within the genus. PMID:9447739

  14. Phylogeny of genetic codes and punctuation codes within genetic codes.

    PubMed

    Seligmann, Hervé

    2015-03-01

    Punctuation codons (starts, stops) delimit genes, reflect translation apparatus properties. Most codon reassignments involve punctuation. Here two complementary approaches classify natural genetic codes: (A) properties of amino acids assigned to codons (classical phylogeny), coding stops as X (A1, antitermination/suppressor tRNAs insert unknown residues), or as gaps (A2, no translation, classical stop); and (B) considering only punctuation status (start, stop and other codons coded as -1, 0 and 1 (B1); 0, -1 and 1 (B2, reflects ribosomal translational dynamics); and 1, -1, and 0 (B3, starts/stops as opposites)). All methods separate most mitochondrial codes from most nuclear codes; Gracilibacteria consistently cluster with metazoan mitochondria; mitochondria co-hosted with chloroplasts cluster with nuclear codes. Method A1 clusters the euplotid nuclear code with metazoan mitochondria; A2 separates euplotids from mitochondria. Firmicute bacteria Mycoplasma/Spiroplasma and Protozoan (and lower metazoan) mitochondria share codon-amino acid assignments. A1 clusters them with mitochondria, they cluster with the standard genetic code under A2: constraints on amino acid ambiguity versus punctuation-signaling produced the mitochondrial versus bacterial versions of this genetic code. Punctuation analysis B2 converges best with classical phylogenetic analyses, stressing the need for a unified theory of genetic code punctuation accounting for ribosomal constraints.

  15. A phylogeny of the land snails (Gastropoda: Pulmonata).

    PubMed Central

    Wade, C. M.; Mordan, P. B.; Clarke, B.

    2001-01-01

    We have undertaken the first large-scale molecular phylogenetic analysis of the Stylommatophora. Sequences of the ribosomal RNA gene-cluster were examined in 104 species of snails and slugs from 50 families, encompassing all the currently recognized major groups. It allows an independent test of the present classification based on morphology. At the level of families our molecular phylogeny closely supports the current taxonomy, but the deep branches within the tree do not. Surprisingly, a single assemblage including the families Achatinidae, Subulinidae and Streptaxidae lies near the base of the tree, forming a sister group to all remaining stylommatophorans. This primary division into 'achatinoid' and 'non-achatinoid' taxa is unexpected, and demands a radical reinterpretation of early stylommatophoran evolution. In particular, the Orthurethra appear to be relatively advanced within the 'non-achatinoid clade', and broadly equivalent to other super-familial clusters. This indicates that supposedly primitive features such as the orthurethran kidney are derived. The molecular tree also suggests that the origin of the Stylommatophora is much earlier than the main period of their diversification. PMID:11270439

  16. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana

    PubMed Central

    Beilstein, Mark A.; Nagalingum, Nathalie S.; Clements, Mark D.; Manchester, Steven R.; Mathews, Sarah

    2010-01-01

    Dated molecular phylogenies are the basis for understanding species diversity and for linking changes in rates of diversification with historical events such as restructuring in developmental pathways, genome doubling, or dispersal onto a new continent. Valid fossil calibration points are essential to the accurate estimation of divergence dates, but for many groups of flowering plants fossil evidence is unavailable or limited. Arabidopsis thaliana, the primary genetic model in plant biology and the first plant to have its entire genome sequenced, belongs to one such group, the plant family Brassicaceae. Thus, the timing of A. thaliana evolution and the history of its genome have been controversial. We bring previously overlooked fossil evidence to bear on these questions and find the split between A. thaliana and Arabidopsis lyrata occurred about 13 Mya, and that the split between Arabidopsis and the Brassica complex (broccoli, cabbage, canola) occurred about 43 Mya. These estimates, which are two- to threefold older than previous estimates, indicate that gene, genomic, and developmental evolution occurred much more slowly than previously hypothesized and that Arabidopsis evolved during a period of warming rather than of cooling. We detected a 2- to 10-fold shift in species diversification rates on the branch uniting Brassicaceae with its sister families. The timing of this shift suggests a possible impact of the Cretaceous–Paleogene mass extinction on their radiation and that Brassicales codiversified with pierid butterflies that specialize on mustard-oil–producing plants. PMID:20921408

  17. Shedding light on vampires: the phylogeny of vampyrellid amoebae revisited.

    PubMed

    Hess, Sebastian; Sausen, Nicole; Melkonian, Michael

    2012-01-01

    With the advent of molecular phylogenetic techniques the polyphyly of naked filose amoebae has been proven. They are interspersed in several supergroups of eukaryotes and most of them already found their place within the tree of life. Although the 'vampire amoebae' have attracted interest since the middle of the 19th century, the phylogenetic position and even the monophyly of this traditional group are still uncertain. In this study clonal co-cultures of eight algivorous vampyrellid amoebae and the respective food algae were established. Culture material was characterized morphologically and a molecular phylogeny was inferred using SSU rDNA sequence comparisons. We found that the limnetic, algivorous vampyrellid amoebae investigated in this study belong to a major clade within the Endomyxa Cavalier-Smith, 2002 (Cercozoa), grouping together with a few soil-dwelling taxa. They split into two robust clades, one containing species of the genus Vampyrella Cienkowski, 1865, the other containing the genus Leptophrys Hertwig & Lesser, 1874, together with terrestrial members. Supported by morphological data these clades are designated as the two families Vampyrellidae Zopf, 1885, and Leptophryidae fam. nov. Furthermore the order Vampyrellida West, 1901 was revised and now corresponds to the major vampyrellid clade within the Endomyxa, comprising the Vampyrellidae and Leptophryidae as well as several environmental sequences. In the light of the presented phylogenetic analyses morphological and ecological aspects, the feeding strategy and nutritional specialization within the vampyrellid amoebae are discussed.

  18. Arthropod phylogeny based on eight molecular loci and morphology

    NASA Technical Reports Server (NTRS)

    Giribet, G.; Edgecombe, G. D.; Wheeler, W. C.

    2001-01-01

    The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

  19. Ribosomal DNA evolution and phylogeny in Aloe (Asphodelaceae).

    PubMed

    Adams, S P; Leitch, I J; Bennett, M D; Chase, M W; Leitch, A R

    2000-11-01

    All Aloe taxa (∼400 species) share a conserved bimodal karyotype with a basic genome of four large and three small submetacentric/acrocentric chromosomes. We investigated the physical organization of 18S-5.8S-26S and 5S ribosomal DNA (rDNA) using fluorescent in situ hybridization (FISH) to 13 Aloe species. The organization was compared with a phylogenetic tree of 28 species (including the 13 used for FISH) constructed by sequence analysis of the internal transcribed spacer (ITS) of 18S-5.8S-26S rDNA. The phylogeny showed little divergence within Aloe, although distinct, well-supported clades were found. FISH analysis of 5S rDNA distribution showed a similar interstitial location on a large chromosome in all species examined. In contrast, the distribution of 18S-5.8S-26S rDNA was variable, with differences in number, location, and size of loci found between species. Nevertheless, within well-supported clades, all species had the same organizational patterns. Thus, despite the striking stability of karyotype structure and location of 5S rDNA, the distribution of 18S-5.8S-26S rDNA is not so constrained and has clearly changed during Aloe speciation.

  20. New insights into Paleozoic charophyte morphology and phylogeny.

    PubMed

    Feist, Monique; Liu, Junying; Tafforeau, Paul

    2005-07-01

    Examination of Paleozoic charophyte fructifications using microscopy and high-resolution x-ray synchrotron microtomography has revealed that most of them have a utricle that forms a supplementary calcified cover around the gyrogonite. All Paleozoic families with utricles have been assigned to the Sycidiales. We consider the Moellerinaceae to occupy a central position in the phylogeny of the Charophyta. From these, one group of descendants constitutes the gyrogonites inside the utricles of the Sycidiales; a second descendant goup is thought to be the utricle-free ancestors of the Charales prior to inversion of spiralization and reduction in cell number. The Sycidiales have a multilayered wall and an internal vesicle, but their families are distinguished by diversity in orientation of external cells, complexity of the utricle wall, and in presence or absence of antheridia. The solidly packed structure of the utricle is believed to be an organ protecting the zygote against dessication. We interpret the morphological similarities between Paleozoic Sycidiales and Mesozoic Clavatoraceae, both with a utricle, as homoplasous rather than expressing a true phylogenetic relationship. We confirm that some umbellids might correspond to utricles of charophytes.