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

Lightness Constancy in Surface Visualization

PubMed Central

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

2016-01-01

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

Determinants of Colour Constancy and the Blue Bias

PubMed Central

Gegenfurtner, Karl

2017-01-01

We investigated several sensory and cognitive determinants of colour constancy across 40 illumination hues. In the first experiment, we measured colour naming for the illumination and for the colour induced by the illumination on the colorimetric grey. Results confirmed that the induced colours are approximately complementary to the colour of the illumination. In the second experiment, we measured colour constancy using achromatic adjustments. Average colour constancy was perfect under the blue daylight illumination and decreased in colour directions away from the blue daylight illumination due to undershooting and a strong blue bias. Apart from this blue bias, colour constancy was not related to illumination discrimination and to chromatic detection measured previously with the same setup and stimuli. We also observed a strong negative relationship between the degree of colour constancy and the consensus of naming the illumination colour. Constancy coincided with a low naming consensus, in particular because bluish illumination colours were sometimes seen as achromatic. Blue bias and category consensus alone explained >68%, and all determinants together explained >94% of the variance of achromatic adjustments. These findings suggest that colour constancy is optimised for blue daylight. PMID:29348910

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

Uncertainty of sensory signal explains variation of color constancy.

PubMed

Witzel, Christoph; van Alphen, Carlijn; Godau, Christoph; O'Regan, J Kevin

2016-12-01

Color constancy is the ability to recognize the color of an object (or more generally of a surface) under different illuminations. Without color constancy, surface color as a perceptual attribute would not be meaningful in the visual environment, where illumination changes all the time. Nevertheless, it is not obvious how color constancy is possible in the light of metamer mismatching. Surfaces that produce exactly the same sensory color signal under one illumination (metamerism) may produce utterly different sensory signals under another illumination (metamer mismatching). Here we show that this phenomenon explains to a large extent the variation of color constancy across different colors. For this purpose, color constancy was measured for different colors in an asymmetric matching task with photorealistic images. Color constancy performance was strongly correlated to the size of metamer mismatch volumes, which describe the uncertainty of the sensory signal due to metamer mismatching for a given color. The higher the uncertainty of the sensory signal, the lower the observers' color constancy. At the same time, sensory singularities, color categories, and cone ratios did not affect color constancy. The present findings do not only provide considerable insight into the determinants of color constancy, they also show that metamer mismatch volumes must be taken into account when investigating color as a perceptual property of objects and surfaces.

The nature of instructional effects in color constancy.

PubMed

Radonjić, Ana; Brainard, David H

2016-06-01

The instructions subjects receive can have a large effect on experimentally measured color constancy, but the nature of these effects and how their existence should inform our understanding of color perception remains unclear. We used a factorial design to measure how instructional effects on constancy vary with experimental task and stimulus set. In each of 2 experiments, we employed both a classic adjustment-based asymmetric matching task and a novel color selection task. Four groups of naive subjects were instructed to make adjustments/selections based on (a) color (neutral instructions); (b) the light reaching the eye (physical spectrum instructions); (c) the actual surface reflectance of an object (objective reflectance instructions); or (d) the apparent surface reflectance of an object (apparent reflectance instructions). Across the 2 experiments we varied the naturalness of the stimuli. We find clear interactions between instructions, task, and stimuli. With simplified stimuli (Experiment 1), instructional effects were large and the data revealed 2 instruction-dependent patterns. In 1 (neutral and physical spectrum instructions) constancy was low, intersubject variability was also low, and adjustment-based and selection-based constancy were in agreement. In the other (reflectance instructions) constancy was high, intersubject variability was large, adjustment-based constancy deviated from selection-based constancy and for some subjects selection-based constancy increased across sessions. Similar patterns held for naturalistic stimuli (Experiment 2), although instructional effects were smaller. We interpret these 2 patterns as signatures of distinct task strategies-1 is perceptual, with judgments based primarily on the perceptual representation of color; the other involves explicit instruction-driven reasoning. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

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

Role of color memory in successive color constancy.

PubMed

Ling, Yazhu; Hurlbert, Anya

2008-06-01

We investigate color constancy for real 2D paper samples using a successive matching paradigm in which the observer memorizes a reference surface color under neutral illumination and after a temporal interval selects a matching test surface under the same or different illumination. We find significant effects of the illumination, reference surface, and their interaction on the matching error. We characterize the matching error in the absence of illumination change as the "pure color memory shift" and introduce a new index for successive color constancy that compares this shift against the matching error under changing illumination. The index also incorporates the vector direction of the matching errors in chromaticity space, unlike the traditional constancy index. With this index, we find that color constancy is nearly perfect.

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

PubMed

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

2016-08-01

Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

Individual differences in simultaneous color constancy are related to working memory.

PubMed

Allen, Elizabeth C; Beilock, Sian L; Shevell, Steven K

2012-02-01

Few studies have investigated the possible role of higher-level cognitive mechanisms in color constancy. Following up on previous work with successive color constancy [J. Exper. Psychol. Learn. Mem. Cogn. 37, 1014 (2011)], the current study examined the relation between simultaneous color constancy and working memory-the ability to maintain a desired representation while suppressing irrelevant information. Higher working memory was associated with poorer simultaneous color constancy of a chromatically complex stimulus. Ways in which the executive attention mechanism of working memory may account for this are discussed. This finding supports a role for higher-level cognitive mechanisms in color constancy and is the first to demonstrate a relation between simultaneous color constancy and a complex cognitive ability. © 2012 Optical Society of America

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

PubMed

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

2009-12-01

This study provides an experimental test of the hypothesis that level of gender constancy understanding affects children's sex typing. Preschool-age children (N=62, mean age=47 months) were randomly assigned to experimental lessons that taught that biological traits (including gender) are either fixed (pro-constancy condition) or mutable (anti-constancy condition). Posttests revealed that the lessons were effective; children in the pro-constancy condition showed higher gender constancy and appearance-reality distinction scores than did children in the anti-constancy condition. Sex typing did not, however, differ between treatment conditions at immediate and 3-month posttesting.

Color constancy: phenomenal or projective?

PubMed

Reeves, Adam J; Amano, Kinjiro; Foster, David H

2008-02-01

Naive observers viewed a sequence of colored Mondrian patterns, simulated on a color monitor. Each pattern was presented twice in succession, first under one daylight illuminant with a correlated color temperature of either 16,000 or 4000 K and then under the other, to test for color constancy. The observers compared the central square of the pattern across illuminants, either rating it for sameness of material appearance or sameness of hue and saturation or judging an objective property-that is, whether its change of color originated from a change in material or only from a change in illumination. Average color constancy indices were high for material appearance ratings and binary judgments of origin and low for hue-saturation ratings. Individuals' performance varied, but judgments of material and of hue and saturation remained demarcated. Observers seem able to separate phenomenal percepts from their ontological projections of mental appearance onto physical phenomena; thus, even when a chromatic change alters perceived hue and saturation, observers can reliably infer the cause, the constancy of the underlying surface spectral reflectance.

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

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.

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

PubMed Central

2016-01-01

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

Color constancy by characterization of illumination chromaticity

NASA Astrophysics Data System (ADS)

Nikkanen, Jarno T.

2011-05-01

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

Color constancy influenced by unnatural spatial structure.

PubMed

Mizokami, Yoko; Yaguchi, Hirohisa

2014-04-01

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

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.

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…

Color Constancy of Red-Green Dichromats and Anomalous Trichromats

PubMed Central

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

2010-01-01

Purpose. Color-vision deficiency is associated with abnormalities in color matching and color discrimination, but its impact on the ability of people to judge the constancy of surface colors under different lights (color constancy) is less clear. This work had two aims: first, to quantify the degree of color constancy in subjects with congenital red-green color deficiency; second, to test whether the degree of color constancy in anomalous trichromats can be predicted from their Rayleigh anomaloscope matches. Methods. Color constancy of red-green color-deficient subjects was tested in a task requiring the discrimination of illuminant changes from surface-reflectance changes. Mondrian-like colored patterns, generated on the screen of a computer monitor, were used as stimuli to avoid the spatial cues provided by natural objects and scenes. Spectral reflectances were taken from the Munsell Book of Color and from natural scenes. Illuminants were taken from the daylight locus. Results. Protanopes and deuteranopes performed more poorly than normal trichromats with Munsell spectral reflectances but were less impaired with natural spectral reflectances. Protanomalous and deuteranomalous trichromats performed as well as, or almost as well as, normal trichromats, independent of the type of reflectance. Individual differences were not correlated with Rayleigh anomaloscope matches. Conclusions. Despite the evidence of clinical color-vision tests, red-green color-deficient persons are less disadvantaged than might be expected in their judgments of surface colors under different lights. PMID:19892868

Categorical color constancy for simulated surfaces.

PubMed

Olkkonen, Maria; Hansen, Thorsten; Gegenfurtner, Karl R

2009-11-12

Color constancy is the ability to perceive constant surface colors under varying lighting conditions. Color constancy has traditionally been investigated with asymmetric matching, where stimuli are matched over two different contexts, or with achromatic settings, where a stimulus is made to appear gray. These methods deliver accurate information on the transformations of single points of color space under illuminant changes, but can be cumbersome and unintuitive for observers. Color naming is a fast and intuitive alternative to matching, allowing data collection from a large portion of color space. We asked observers to name the colors of 469 Munsell surfaces with known reflectance spectra simulated under five different illuminants. Observers were generally as consistent in naming the colors of surfaces under different illuminants as they were naming the colors of the same surfaces over time. The transformations in category boundaries caused by illuminant changes were generally small and could be explained well with simple linear models. Finally, an analysis of the pattern of naming consistency across color space revealed that largely the same hues were named consistently across illuminants and across observers even after correcting for category size effects. This indicates a possible relationship between perceptual color constancy and the ability to consistently communicate colors.

Synaesthesia and colour constancy.

PubMed

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

2013-04-01

Grapheme-colour synaesthesia is an atypical condition characterized by the perception of colours when reading achromatic text. We investigated the level of colour processing responsible for these experiences. To do so, we tapped a central characteristic of colour perception. In different lighting conditions the same wavelength of light can prompt the perception of different colours. This helps humans recognize distinctive coloured objects despite changes in illumination. We wanted to see if synaesthetic colours were generated at a neural locus that was susceptible to colour constancy analyses. We used colour matching and naming tasks to examine interactions between simulated coloured illuminants and synaesthetic colours. Neither synaesthetic colour matching or naming was impacted. This contrasted with non-synaesthetic control participants, who performed the colour-matching task with graphemes physically coloured to mimic synaesthesia. Our data suggest that synaesthetic colour signals are not generated at lower-levels of colour processing, but are introduced at higher levels of analysis and are therefore not impacted by the processes responsible for perceptual constancy. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

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.

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

PubMed

Granzier, Jeroen J M; Gegenfurtner, Karl R

2012-01-01

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

Experience-Dependent Color Constancy in Guppies (Poecilia reticulata)

PubMed Central

Intskirveli, I. E.; Roinishvili, M. O.; Kezeli, A. R.

2002-01-01

We investigated the ability to recognize the color of surfaces in fish (Poecilia reticulata), bred from birth in conditions of artificial light with constant spectral content. The capacity for color constancy significantly deteriorated when compared that to the control group. Further alteration of lighting conditions and transfer into natural daylight conditions restored the suppressed function to its normal level. We suggest that the color constancy function belongs in the visual system-response functions, the full development of which requires the accumulation of individual visual experience. PMID:12757371

Experience-dependent color constancy in guppies (Poecilia reticulata).

PubMed

Intskirveli, I E; Roinishvili, M O; Kezeli, A R

2002-01-01

We investigated the ability to recognize the color of surfaces in fish (Poecilia reticulata), bred from birth in conditions of artificial light with constant spectral content. The capacity for color constancy significantly deteriorated when compared that to the control group. Further alteration of lighting conditions and transfer into natural daylight conditions restored the suppressed function to its normal level. We suggest that the color constancy function belongs in the visual system-response functions, the full development of which requires the accumulation of individual visual experience.

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

Effects of memory colour on colour constancy for unknown coloured objects

PubMed Central

Granzier, Jeroen J M; Gegenfurtner, Karl R

2012-01-01

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

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.

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…

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

PubMed

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

2002-01-01

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

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

PubMed

Kanematsu, Erika; Brainard, David H

2014-08-01

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

No Measured Effect of a Familiar Contextual Object on Color Constancy

PubMed Central

Kanematsu, Erika; Brainard, David H.

2013-01-01

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

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.

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…

HDR imaging and color constancy: two sides of the same coin?

NASA Astrophysics Data System (ADS)

McCann, John J.

2011-01-01

At first, we think that High Dynamic Range (HDR) imaging is a technique for improved recordings of scene radiances. Many of us think that human color constancy is a variation of a camera's automatic white balance algorithm. However, on closer inspection, glare limits the range of light we can detect in cameras and on retinas. All scene regions below middle gray are influenced, more or less, by the glare from the bright scene segments. Instead of accurate radiance reproduction, HDR imaging works well because it preserves the details in the scene's spatial contrast. Similarly, on closer inspection, human color constancy depends on spatial comparisons that synthesize appearances from all the scene segments. Can spatial image processing play similar principle roles in both HDR imaging and color constancy?

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

USGS Publications Warehouse

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

1983-01-01

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

Color Constancy in Two-Dimensional and Three-Dimensional Scenes: Effects of Viewing Methods and Surface Texture.

PubMed

Morimoto, Takuma; Mizokami, Yoko; Yaguchi, Hirohisa; Buck, Steven L

2017-01-01

There has been debate about how and why color constancy may be better in three-dimensional (3-D) scenes than in two-dimensional (2-D) scenes. Although some studies have shown better color constancy for 3-D conditions, the role of specific cues remains unclear. In this study, we compared color constancy for a 3-D miniature room (a real scene consisting of actual objects) and 2-D still images of that room presented on a monitor using three viewing methods: binocular viewing, monocular viewing, and head movement. We found that color constancy was better for the 3-D room; however, color constancy for the 2-D image improved when the viewing method caused the scene to be perceived more like a 3-D scene. Separate measurements of the perceptual 3-D effect of each viewing method also supported these results. An additional experiment comparing a miniature room and its image with and without texture suggested that surface texture of scene objects contributes to color constancy.

Bromine species fluxes from Lake Constance’s catchment, and a preliminary lake mass balance

NASA Astrophysics Data System (ADS)

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

2011-06-01

Bromine was historically termed a cyclic salt in terrestrial freshwater environments due to its perceived conservative cycling between the oceans and the continents. This basic assumption has been challenged recently, with evidence that bromine is involved in dynamic chemical cycles in soils and freshwaters. We present here a study on dissolved bromine species (bromide, organically bound bromine, DOBr) concentrations and fluxes as well as sediment trap bromine levels and fluxes in Lake Constance, a large lake in southern Germany. Water samples were obtained from all major and some minor inflows and outflows over one year, where-after dissolved bromine species were measured by a combination of ICP-MS and ion chromatography coupled to an ICP-MS (IC-ICP-MS). Sediment traps were deployed at two locations for two years with Br, Ti and Zr levels being measured by μ-XRF. 190 t yr -1 of total dissolved bromine (TDBr) was delivered to the lake via 14 rivers and precipitation, with the rivers Alpenrhein (84 t TDBr yr -1) and the Schussen (50 t TDBr yr -1) providing the largest sources. The estimated particulate bromine flux contributed an extra 24-26 t Br yr -1. In comparison, only 40 t TDBr yr -1 was deposited to the lake's catchment by precipitation, and thus ˜80% of the riverine TDBr flux came from soils and rocks. Bromide was the dominant species accounting for, on average, 78% of TDBr concentrations and 93% of TDBr flux to the lake. Despite some high concentrations in the smaller lowland rivers, DOBr was only a minor component of the total riverine bromine flux (˜12 t yr -1, 7%), most of which came from the rivers Schussen, Bregenzer Ach and Argen. In contrast, most of the bromine in the sediment traps was bound to organic matter, and showed a clear seasonal pattern in concentrations, with a maximum in winter and minimum in summer. The summer minimum is thought to be due to dilution of a high Br autochthonous component by low bromine mineral and organic material from

Color constancy: enhancing von Kries adaption via sensor transformations

NASA Astrophysics Data System (ADS)

Finlayson, Graham D.; Drew, Mark S.; Funt, Brian V.

1993-09-01

Von Kries adaptation has long been considered a reasonable vehicle for color constancy. Since the color constancy performance attainable via the von Kries rule strongly depends on the spectral response characteristics of the human cones, we consider the possibility of enhancing von Kries performance by constructing new `sensors' as linear combinations of the fixed cone sensitivity functions. We show that if surface reflectances are well-modeled by 3 basis functions and illuminants by 2 basis functions then there exists a set of new sensors for which von Kries adaptation can yield perfect color constancy. These new sensors can (like the cones) be described as long-, medium-, and short-wave sensitive; however, both the new long- and medium-wave sensors have sharpened sensitivities -- their support is more concentrated. The new short-wave sensor remains relatively unchanged. A similar sharpening of cone sensitivities has previously been observed in test and field spectral sensitivities measured for the human eye. We present simulation results demonstrating improved von Kries performance using the new sensors even when the restrictions on the illumination and reflectance are relaxed.

Size constancy in bat biosonar? Perceptual interaction of object aperture and distance.

PubMed

Heinrich, Melina; Wiegrebe, Lutz

2013-01-01

Perception and encoding of object size is an important feature of sensory systems. In the visual system object size is encoded by the visual angle (visual aperture) on the retina, but the aperture depends on the distance of the object. As object distance is not unambiguously encoded in the visual system, higher computational mechanisms are needed. This phenomenon is termed "size constancy". It is assumed to reflect an automatic re-scaling of visual aperture with perceived object distance. Recently, it was found that in echolocating bats, the 'sonar aperture', i.e., the range of angles from which sound is reflected from an object back to the bat, is unambiguously perceived and neurally encoded. Moreover, it is well known that object distance is accurately perceived and explicitly encoded in bat sonar. Here, we addressed size constancy in bat biosonar, recruiting virtual-object techniques. Bats of the species Phyllostomus discolor learned to discriminate two simple virtual objects that only differed in sonar aperture. Upon successful discrimination, test trials were randomly interspersed using virtual objects that differed in both aperture and distance. It was tested whether the bats spontaneously assigned absolute width information to these objects by combining distance and aperture. The results showed that while the isolated perceptual cues encoding object width, aperture, and distance were all perceptually well resolved by the bats, the animals did not assign absolute width information to the test objects. This lack of sonar size constancy may result from the bats relying on different modalities to extract size information at different distances. Alternatively, it is conceivable that familiarity with a behaviorally relevant, conspicuous object is required for sonar size constancy, as it has been argued for visual size constancy. Based on the current data, it appears that size constancy is not necessarily an essential feature of sonar perception in bats.

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.

Color Constancy in Two-Dimensional and Three-Dimensional Scenes: Effects of Viewing Methods and Surface Texture

PubMed Central

Morimoto, Takuma; Mizokami, Yoko; Yaguchi, Hirohisa; Buck, Steven L.

2017-01-01

There has been debate about how and why color constancy may be better in three-dimensional (3-D) scenes than in two-dimensional (2-D) scenes. Although some studies have shown better color constancy for 3-D conditions, the role of specific cues remains unclear. In this study, we compared color constancy for a 3-D miniature room (a real scene consisting of actual objects) and 2-D still images of that room presented on a monitor using three viewing methods: binocular viewing, monocular viewing, and head movement. We found that color constancy was better for the 3-D room; however, color constancy for the 2-D image improved when the viewing method caused the scene to be perceived more like a 3-D scene. Separate measurements of the perceptual 3-D effect of each viewing method also supported these results. An additional experiment comparing a miniature room and its image with and without texture suggested that surface texture of scene objects contributes to color constancy. PMID:29238513

BRDF invariant stereo using light transport constancy.

PubMed

Wang, Liang; Yang, Ruigang; Davis, James E

2007-09-01

Nearly all existing methods for stereo reconstruction assume that scene reflectance is Lambertian and make use of brightness constancy as a matching invariant. We introduce a new invariant for stereo reconstruction called light transport constancy (LTC), which allows completely arbitrary scene reflectance (bidirectional reflectance distribution functions (BRDFs)). This invariant can be used to formulate a rank constraint on multiview stereo matching when the scene is observed by several lighting configurations in which only the lighting intensity varies. In addition, we show that this multiview constraint can be used with as few as two cameras and two lighting configurations. Unlike previous methods for BRDF invariant stereo, LTC does not require precisely configured or calibrated light sources or calibration objects in the scene. Importantly, the new constraint can be used to provide BRDF invariance to any existing stereo method whenever appropriate lighting variation is available.

Possible influences on color constancy by motion of color targets and by attention-controlled gaze.

PubMed

Wan, Lifang; Shinomori, Keizo

2018-04-01

We investigated the influence of motion on color constancy using a chromatic stimulus presented in various conditions (static, motion, and rotation). Attention to the stimulus and background was also controlled in different gaze modes, constant fixation of the stimulus, and random viewing of the stimulus. Color constancy was examined in six young observers using a haploscopic view of a computer monitor. The target and background were illuminated in simulation by red, green, blue, and yellow, shifted from daylight (D65) by specific color differences along L - M or S - (L + M) axes on the equiluminance plane. The standard pattern (under D65) and test pattern (under the color illuminant) of a 5-deg square were presented side by side, consisting of 1.2-deg square targets with one of 12 colors at each center, surrounded by 230 background ellipses consisting of eight other colors. The central color targets in both patterns flipped between top and bottom locations at the rate of 3 deg/s in the motion condition. The results indicated an average reduction of color constancy over the 12 test colors by motion. The random viewing parameter indicated better color constancy by more attention to the background, although the difference was not significant. Color constancy of the four color illuminations was better to worse in green, red, yellow, and blue, respectively. The reduction of color constancy by motion could be explained by less contribution of the illumination estimation effect on color constancy. In the motion with constant fixation condition, the retina strongly adapted to the mean chromaticity of the background. However, motion resulted in less attention to the color of the background, causing a weaker effect of the illumination estimation. Conversely, in the static state with a random viewing condition, more attention to the background colors caused a stronger illumination estimation effect, and color constancy was improved overall.

Disparity, motion, and color information improve gloss constancy performance.

PubMed

Wendt, Gunnar; Faul, Franz; Ekroll, Vebjørn; Mausfeld, Rainer

2010-09-01

S. Nishida and M. Shinya (1998) found that observers have only a limited ability to recover surface-reflectance properties under changes in surface shape. Our aim in the present study was to investigate how the degree of surface-reflectance constancy depends on the availability of information that may help to infer the reflectance and shape properties of surfaces. To this end, we manipulated the availability of (i) motion-induced information (static vs. dynamic presentation), (ii) disparity information (with the levels "monocular," "surface disparity," and "surface + highlight disparity"), and (iii) color information (grayscale stimuli vs. hue differences between diffuse and specular reflections). The task of the subjects was to match the perceived lightness and glossiness between two surfaces with different spatial frequency and amplitude by manipulating the diffuse component and the exponent of the Phong lighting model in one of the surfaces. Our results indicate that all three types of information improve the constancy of glossiness matches--both in isolation and in combination. The lightness matching data only revealed an influence of motion and color information. Our results indicate, somewhat counterintuitively, that motion information has a detrimental effect on lightness constancy.

Robust colour constancy in red-green dichromats

PubMed Central

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

2017-01-01

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

Robust colour constancy in red-green dichromats.

PubMed

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

2017-01-01

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

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.

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

PubMed

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

2017-01-01

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

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…

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.

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.

Detecting and accounting for violations of the constancy assumption in non-inferiority clinical trials.

PubMed

Koopmeiners, Joseph S; Hobbs, Brian P

2018-05-01

Randomized, placebo-controlled clinical trials are the gold standard for evaluating a novel therapeutic agent. In some instances, it may not be considered ethical or desirable to complete a placebo-controlled clinical trial and, instead, the placebo is replaced by an active comparator with the objective of showing either superiority or non-inferiority to the active comparator. In a non-inferiority trial, the experimental treatment is considered non-inferior if it retains a pre-specified proportion of the effect of the active comparator as represented by the non-inferiority margin. A key assumption required for valid inference in the non-inferiority setting is the constancy assumption, which requires that the effect of the active comparator in the non-inferiority trial is consistent with the effect that was observed in previous trials. It has been shown that violations of the constancy assumption can result in a dramatic increase in the rate of incorrectly concluding non-inferiority in the presence of ineffective or even harmful treatment. In this paper, we illustrate how Bayesian hierarchical modeling can be used to facilitate multi-source smoothing of the data from the current trial with the data from historical studies, enabling direct probabilistic evaluation of the constancy assumption. We then show how this result can be used to adapt the non-inferiority margin when the constancy assumption is violated and present simulation results illustrating that our method controls the type-I error rate when the constancy assumption is violated, while retaining the power of the standard approach when the constancy assumption holds. We illustrate our adaptive procedure using a non-inferiority trial of raltegravir, an antiretroviral drug for the treatment of HIV.

Detecting and Accounting for Violations of the Constancy Assumption in Non-Inferiority Clinical Trials

PubMed Central

Koopmeiners, Joseph S.; Hobbs, Brian P.

2016-01-01

Randomized, placebo-controlled clinical trials are the gold standard for evaluating a novel therapeutic agent. In some instances, it may not be considered ethical or desirable to complete a placebo-controlled clinical trial and, instead, the placebo is replaced by an active comparator (AC) with the objective of showing either superiority or non-inferiority to the AC. In a non-inferiority trial, the experimental treatment is considered non-inferior if it retains a pre-specified proportion of the effect of the AC as represented by the non-inferiority margin. A key assumption required for valid inference in the non-inferiority setting is the constancy assumption, which requires that the effect of the AC in the non-inferiority trial is consistent with the effect that was observed in previous trials. It has been shown that violations of the constancy assumption can result in a dramatic increase in the rate of incorrectly concluding non-inferiority in the presence of ineffective or even harmful treatment. In this paper, we illustrate how Bayesian hierarchical modeling can be used to facilitate multi-source smoothing of the data from the current trial with the data from historical studies, enabling direct probabilistic evaluation of the constancy assumption. We then show how this result can be used to adapt the non-inferiority margin when the constancy assumption is violated and present simulation results illustrating that our method controls the type-I error rate when the constancy assumption is violated, while retaining the power of the standard approach when the constancy assumption holds. We illustrate our adaptive procedure using a non-inferiority trial of raltegravir, an antiretroviral drug for the treatment of HIV. PMID:27587591

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.

Color constancy in dermatoscopy with smartphone

NASA Astrophysics Data System (ADS)

Cugmas, Blaž; Pernuš, Franjo; Likar, Boštjan

2017-12-01

The recent spread of cheap dermatoscopes for smartphones can empower patients to acquire images of skin lesions on their own and send them to dermatologists. Since images are acquired by different smartphone cameras under unique illumination conditions, the variability in colors is expected. Therefore, the mobile dermatoscopic systems should be calibrated in order to ensure the color constancy in skin images. In this study, we have tested a dermatoscope DermLite DL1 basic, attached to Samsung Galaxy S4 smartphone. Under the controlled conditions, jpeg images of standard color patches were acquired and a model between an unknown device-dependent RGB and a deviceindependent Lab color space has been built. Results showed that median and the best color error was 7.77 and 3.94, respectively. Results are in the range of a human eye detection capability (color error ≈ 4) and video and printing industry standards (color error is expected to be between 5 and 6). It can be concluded that a calibrated smartphone dermatoscope can provide sufficient color constancy and can serve as an interesting opportunity to bring dermatologists closer to the patients.

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

PubMed

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

2013-08-20

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

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

Size Constancy in Bat Biosonar? Perceptual Interaction of Object Aperture and Distance

PubMed Central

Heinrich, Melina; Wiegrebe, Lutz

2013-01-01

Perception and encoding of object size is an important feature of sensory systems. In the visual system object size is encoded by the visual angle (visual aperture) on the retina, but the aperture depends on the distance of the object. As object distance is not unambiguously encoded in the visual system, higher computational mechanisms are needed. This phenomenon is termed “size constancy”. It is assumed to reflect an automatic re-scaling of visual aperture with perceived object distance. Recently, it was found that in echolocating bats, the ‘sonar aperture’, i.e., the range of angles from which sound is reflected from an object back to the bat, is unambiguously perceived and neurally encoded. Moreover, it is well known that object distance is accurately perceived and explicitly encoded in bat sonar. Here, we addressed size constancy in bat biosonar, recruiting virtual-object techniques. Bats of the species Phyllostomus discolor learned to discriminate two simple virtual objects that only differed in sonar aperture. Upon successful discrimination, test trials were randomly interspersed using virtual objects that differed in both aperture and distance. It was tested whether the bats spontaneously assigned absolute width information to these objects by combining distance and aperture. The results showed that while the isolated perceptual cues encoding object width, aperture, and distance were all perceptually well resolved by the bats, the animals did not assign absolute width information to the test objects. This lack of sonar size constancy may result from the bats relying on different modalities to extract size information at different distances. Alternatively, it is conceivable that familiarity with a behaviorally relevant, conspicuous object is required for sonar size constancy, as it has been argued for visual size constancy. Based on the current data, it appears that size constancy is not necessarily an essential feature of sonar perception in bats

A blind human expert echolocator shows size constancy for objects perceived by echoes.

PubMed

Milne, Jennifer L; Anello, Mimma; Goodale, Melvyn A; Thaler, Lore

2015-01-01

Some blind humans make clicking noises with their mouth and use the reflected echoes to perceive objects and surfaces. This technique can operate as a crude substitute for vision, allowing human echolocators to perceive silent, distal objects. Here, we tested if echolocation would, like vision, show size constancy. To investigate this, we asked a blind expert echolocator (EE) to echolocate objects of different physical sizes presented at different distances. The EE consistently identified the true physical size of the objects independent of distance. In contrast, blind and blindfolded sighted controls did not show size constancy, even when encouraged to use mouth clicks, claps, or other signals. These findings suggest that size constancy is not a purely visual phenomenon, but that it can operate via an auditory-based substitute for vision, such as human echolocation.

Constance D'Arcy Mackay: A Historiographical Perspective.

ERIC Educational Resources Information Center

van de Water, Manon

1995-01-01

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

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)

Cues to viewing distance for stereoscopic depth constancy.

PubMed

Glennerster, A; Rogers, B J; Bradshaw, M F

1998-01-01

A veridical estimate of viewing distance is required in order to determine the metric structure of objects from binocular stereopsis. One example of a judgment of metric structure, which we used in our experiment, is the apparently circular cylinder task (E B Johnston, 1991 Vision Research 31 1351-1360). Most studies report underconstancy in this task when the stimulus is defined purely by binocular disparities. We examined the effect of two factors on performance: (i) the richness of the cues to viewing distance (using either a naturalistic setting with many cues to viewing distance or a condition in which the room and the monitors were obscured from view), and (ii) the range of stimulus disparities (cylinder depths) presented during an experimental run. We tested both experienced subjects (who had performed the task many times before under full-cue conditions) and naïve subjects. Depth constancy was reduced for the naïve subjects (from 62% to 46%) when the position of the monitors was obscured. Under similar conditions, the experienced subjects showed no reduction in constancy. In a second experiment, using a forced-choice method of constant stimuli, we found that depth constancy was reduced from 64% to 23% in naïve subjects and from 77% to 55% in experienced subjects when the same set of images was presented at all viewing distances rather than using a set of stimulus disparities proportional to the correct setting. One possible explanation of these results is that, under reduced-cue conditions, the range of disparities presented is used by the visual system as a cue to viewing distance.

Flux of the biogenic volatiles isoprene and dimethyl sulfide from an oligotrophic lake.

PubMed

Steinke, Michael; Hodapp, Bettina; Subhan, Rameez; Bell, Thomas G; Martin-Creuzburg, Dominik

2018-01-12

Biogenic volatile organic compounds (BVOCs) affect atmospheric chemistry, climate and regional air quality in terrestrial and marine atmospheres. Although isoprene is a major BVOC produced in vascular plants, and marine phototrophs release dimethyl sulfide (DMS), lakes have been widely ignored for their production. Here we demonstrate that oligotrophic Lake Constance, a model for north temperate deep lakes, emits both volatiles to the atmosphere. Depth profiles indicated that highest concentrations of isoprene and DMS were associated with the chlorophyll maximum, suggesting that their production is closely linked to phototrophic processes. Significant correlations of the concentration patterns with taxon-specific fluorescence data, and measurements from algal cultures confirmed the phototrophic production of isoprene and DMS. Diurnal fluctuations in lake isoprene suggested an unrecognised physiological role in environmental acclimation similar to the antioxidant function of isoprene that has been suggested for marine biota. Flux estimations demonstrated that lakes are a currently undocumented source of DMS and isoprene to the atmosphere. Lakes may be of increasing importance for their contribution of isoprene and DMS to the atmosphere in the arctic zone where lake area coverage is high but terrestrial sources of BVOCs are small.

Proprioceptive Distance Cues Restore Perfect Size Constancy in Grasping, but Not Perception, When Vision Is Limited.

PubMed

Chen, Juan; Sperandio, Irene; Goodale, Melvyn Alan

2018-03-19

Our brain integrates information from multiple modalities in the control of behavior. When information from one sensory source is compromised, information from another source can compensate for the loss. What is not clear is whether the nature of this multisensory integration and the re-weighting of different sources of sensory information are the same across different control systems. Here, we investigated whether proprioceptive distance information (position sense of body parts) can compensate for the loss of visual distance cues that support size constancy in perception (mediated by the ventral visual stream) [1, 2] versus size constancy in grasping (mediated by the dorsal visual stream) [3-6], in which the real-world size of an object is computed despite changes in viewing distance. We found that there was perfect size constancy in both perception and grasping in a full-viewing condition (lights on, binocular viewing) and that size constancy in both tasks was dramatically disrupted in the restricted-viewing condition (lights off; monocular viewing of the same but luminescent object through a 1-mm pinhole). Importantly, in the restricted-viewing condition, proprioceptive cues about viewing distance originating from the non-grasping limb (experiment 1) or the inclination of the torso and/or the elbow angle of the grasping limb (experiment 2) compensated for the loss of visual distance cues to enable a complete restoration of size constancy in grasping but only a modest improvement of size constancy in perception. This suggests that the weighting of different sources of sensory information varies as a function of the control system being used. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2012-01-01

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

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

PubMed

Werner, Annette

2014-11-01

Illumination in natural scenes changes at multiple temporal and spatial scales: slow changes in global illumination occur in the course of a day, and we encounter fast and localised illumination changes when visually exploring the non-uniform light field of three-dimensional scenes; in addition, very long-term chromatic variations may come from the environment, like for example seasonal changes. In this context, I consider the temporal and spatial properties of chromatic adaptation and discuss their functional significance for colour constancy in three-dimensional scenes. A process of fast spatial tuning in chromatic adaptation is proposed as a possible sensory mechanism for linking colour constancy to the spatial structure of a scene. The observed middlewavelength selectivity of this process is particularly suitable for adaptation to the mean chromaticity and the compensation of interreflections in natural scenes. Two types of sensory colour constancy are distinguished, based on the functional differences of their temporal and spatial scales: a slow type, operating at a global scale for the compensation of the ambient illumination; and a fast colour constancy, which is locally restricted and well suited to compensate region-specific variations in the light field of three dimensional scenes. Copyright © 2014 Elsevier B.V. All rights reserved.

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

PubMed

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

2008-08-05

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.

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

PubMed

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

2017-07-18

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

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

PubMed

Burmeister, K H

1999-01-01

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

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…

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

Color constancy in 3D-2D face recognition

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

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

Mystery #2 Answer

Atmospheric Science Data Center

2013-04-22

... D.   A lakeside town hosts an annual celebration of Celtic music. Answer: B is false Lake Constance provides drinking water for ... lakeside town of   Konstanz, Germany. An annual Celtic music festival is hosted on the Swiss shores of Lake Constance at the town of ...

Universal Trade-Off between Power, Efficiency, and Constancy in Steady-State Heat Engines

NASA Astrophysics Data System (ADS)

Pietzonka, Patrick; Seifert, Udo

2018-05-01

Heat engines should ideally have large power output, operate close to Carnot efficiency and show constancy, i.e., exhibit only small fluctuations in this output. For steady-state heat engines, driven by a constant temperature difference between the two heat baths, we prove that out of these three requirements only two are compatible. Constancy enters quantitatively the conventional trade-off between power and efficiency. Thus, we rationalize and unify recent suggestions for overcoming this simple trade-off. Our universal bound is illustrated for a paradigmatic model of a quantum dot solar cell and for a Brownian gyrator delivering mechanical work against an external force.

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

PubMed Central

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

2017-01-01

The genera of stingless bees play an important role as pollinators of plants. These bees are actively involved in the pollination of agricultural crops and known to have preferences in selecting flowers to pollinate. The aims of this study were to analyse the pollen load and flower constancy in Tetragonula laeviceps, Lepidotrigona terminata, and Heterotrigona itama. Each individual of species stingless bees collected and was put in a 1.5 mL micro-tube contain 0.5 mL 70% ethanol:glycerol (4:1). Pollen loads on each individual of stingless bees was counted by hemocytometer. Flower constancy of stingless bees was measured based on percentage of pollen type loaded on the body. Results showed that the pollen loads of H. itama was the highest (31392 pollen grains) followed by L. terminata (23017 pollen grains) and T. laeviceps (8015 pollen grains). These species also demonstrated different flower constancy, T. laeviceps on Poaceae flowers (76.49%), L. terminata on Euphorbiaceae flowers (80.46%), and H. itama on Solanaceae flowers (83.33%). PMID:28890769

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.

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)

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

PubMed

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

2013-01-01

By 12 months, children grasp that a phonetic change to a word can change its identity (phonological distinctiveness). However, they must also grasp that some phonetic changes do not (phonological constancy). To test development of phonological constancy, sixteen 15-month-olds and sixteen 19-month-olds completed an eye-tracking task that tracked their gaze to named versus unnamed images for familiar words spoken in their native (Australian) and an unfamiliar non-native (Jamaican) regional accent of English. Both groups looked longer at named than unnamed images for Australian pronunciations, but only 19-month-olds did so for Jamaican pronunciations, indicating that phonological constancy emerges by 19 months. Vocabulary size predicted 15-month-olds' identifications for the Jamaican pronunciations, suggesting vocabulary growth is a viable predictor for phonological constancy development. © 2013 The Authors. Child Development © 2013 Society for Research in Child Development, Inc.

The Relationship among Localization Skill, Existence Constancy and Object Permanence.

ERIC Educational Resources Information Center

Townes-Rosenwein, Linda

Two component skills of object permanence were studied: existence constancy -- the infants' ability to expect that an object continues to exist after it is hidden, and localization skill -- infants' ability to search in the correct place for a hidden object. Contradictions within the literature may occur because of task lability caused by failure…

Constancy and diversity in the flavivirus fusion peptide.

PubMed

Seligman, Stephen J

2008-02-14

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

A simple method for electron energy constancy measurement

PubMed Central

King, R. Paul; Anderson, R. Scott

2001-01-01

A device is described for use in confirming the energy constancy of clinical electron beams. A wedge shaped absorber is placed over an ionization chamber leading to an energy dependent response. A measurement under the energy filter is divided by a measurement in air to correct for the inherent energy dependence of the chamber. A nearly linear response is demonstrated. PACS number(s): 87.52.–g, 87.53.–j, 87.66.–a PMID:11674838

Color constancy in natural scenes explained by global image statistics

PubMed Central

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

2007-01-01

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. PMID:16961965

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

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…

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…

Loss of 3-D shape constancy in interior spaces: the basis of the Ames-room illusion.

PubMed

Dorward, F M; Day, R H

1997-01-01

The apparently rectangular form of the irregularly shaped Ames room is explained in terms of a loss of interior 3-D shape constancy consequent on viewing the room with one eye through a small specifically positioned aperture. In the absence of retinal disparity and motion parallax the appearance of the room is held to shift markedly toward the rectangular dimensions of its retinal image. Three experiments designed to test this explanation with a miniature (one-tenth size) version of the Ames room No 1 with the matched 2-D shape of the back wall and as an index of interior 3-D shape are reported. The experiments showed that interior constancy was almost fully restored with binocular viewing of the room (experiment 1). The effect with a 'skeletal' version of the room was about the same as that with the conventional version and was clearly evident when the back wall or its frame version was presented alone (experiment 2), and it varied according to whether the interior perspective corresponded with that of the Ames or a rectangular room (experiment 3). Experiment 3 also showed that a rectangular room is significantly distorted when the interior perspective accords with that of the Ames room. These outcomes are construed as supporting the loss-of-constancy explanation and as showing that the Ames-room effect is one of a class of illusions attributable to the absence of stimulus correlates that normally sustain visual shape constancy.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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,more » 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.« less

Color constancy using bright-neutral pixels

NASA Astrophysics Data System (ADS)

Wang, Yanfang; Luo, Yupin

2014-03-01

An effective illuminant-estimation approach for color constancy is proposed. Bright and near-neutral pixels are selected to jointly represent the illuminant color and utilized for illuminant estimation. To assess the representing capability of pixels, bright-neutral strength (BNS) is proposed by combining pixel chroma and brightness. Accordingly, a certain percentage of pixels with the largest BNS is selected to be the representative set. For every input image, a proper percentage value is determined via an iterative strategy by seeking the optimal color-corrected image. To compare various color-corrected images of an input image, image color-cast degree (ICCD) is devised using means and standard deviations of RGB channels. Experimental evaluation on standard real-world datasets validates the effectiveness of the proposed approach.

Colour Constancy Beyond the Classical Receptive Field.

PubMed

Akbarinia, Arash; Parraga, C Alejandro

2017-09-18

The problem of removing illuminant variations to preserve the colours of objects (colour constancy) has already been solved by the human brain using mechanisms that rely largely on centre-surround computations of local contrast. In this paper we adopt some of these biological solutions described by long known physiological findings into a simple, fully automatic, functional model (termed Adaptive Surround Modulation or ASM). In ASM, the size of a visual neuron's receptive field (RF) as well as the relationship with its surround varies according to the local contrast within the stimulus, which in turn determines the nature of the centre-surround normalisation of cortical neurons higher up in the processing chain. We modelled colour constancy by means of two overlapping asymmetric Gaussian kernels whose sizes are adapted based on the contrast of the surround pixels, resembling the change of RF size. We simulated the contrast-dependent surround modulation by weighting the contribution of each Gaussian according to the centre-surround contrast. In the end, we obtained an estimation of the illuminant from the set of the most activated RFs' outputs. Our results on three single-illuminant and one multi-illuminant benchmark datasets show that ASM is highly competitive against the state-of-the-art and it even outperforms learning-based algorithms in one case. Moreover, the robustness of our model is more tangible if we consider that our results were obtained using the same parameters for all datasets, that is, mimicking how the human visual system operates. These results might provide an insight on how dynamical adaptation mechanisms contribute to make object's colours appear constant to us.

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.…

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…

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

PubMed

Housworth, E A; Martins, E P

2001-01-01

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

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

PubMed

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

2016-03-01

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

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…

Baculovirus phylogeny and evolution.

PubMed

Herniou, Elisabeth A; Jehle, Johannes A

2007-10-01

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

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

PubMed

Dixon, Erica L; Shapiro, Arthur G

2017-03-01

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

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...

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

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

PubMed

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

2011-12-15

This research first focuses on the spatial and temporal patterns of heavy metals from contrasting environments (highly polluted to deepwater sites) of Lake Geneva. The mercury (Hg) and lead (Pb) records from two deepwater sites show that the heavy metal variations before the industrial period are primarily linked to natural weathering input of trace elements. By opposition, the discharge of industrial treated wastewaters into Vidy Bay of Lake Geneva during the second part of the 20th century, involved the sedimentation of highly metal-contaminated sediments in the area surrounding the WWTP outlet pipe discharge. Eventually, a new Pb isotope record of sediments from Lake Lucerne identifies the long-term increasing anthropogenic lead pollution after ca. 1500, probably due to the development of metallurgical activities during the High Middle Ages. These data furthermore allows to compare the recent anthropogenic sources of water pollution from three of the largest freshwater lakes of Western Europe (lakes Geneva, Lucerne, and Constance). High increases in Pb and Hg highlight the regional impact of industrial pollution after ca. 1750-1850, and the decrease of metal pollution in the 1980s due to the effects of remediation strategies such as the implementation of wastewater treatment plants (WWTPs). However, at all the studied sites, the recent metal concentrations remain higher than pre-industrial levels. Moreover, the local scale pollution data reveal two highly contaminated sites (>100 μg Pb/g dry weight sediment) by industrial activities, during the late-19th and early-20th centuries (Lake Lucerne) and during the second part of the 20th century (Vidy Bay of Lake Geneva). Overall, the regional scale pollution history inferred from the three large and deep perialpine lakes points out at the pollution of water systems by heavy metals during the last two centuries due to the discharge of industrial effluents. Copyright © 2011 Elsevier B.V. All rights reserved.

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

PubMed

Bussey, K; Bandura, A

1984-12-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

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

PubMed

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

2002-07-01

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

The Hyalella (Crustacea: Amphipoda) species cloud of the ancient Lake Titicaca originated from multiple colonizations.

PubMed

Adamowicz, Sarah J; Marinone, María Cristina; Menu-Marque, Silvina; Martin, Jeffrey W; Allen, Daniel C; Pyle, Michelle N; De Los Ríos, Patricio; Sobel, Crystal N; Ibañez, Carla; Pinto, Julio; Witt, Jonathan D S

2018-08-01

Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalella (Crustacea: Amphipoda) species complex of Lake Titicaca, using COI and 28S DNA sequences, including samples from the connected Small and Large Lakes that comprise Lake Titicaca as well as from a broader survey of southern South American sites. At least five evolutionarily distant lineages are present within Lake Titicaca, which were estimated to have diverged from one another 12-20 MYA. These major lineages are dispersed throughout the broader South American Hyalella phylogeny, with each lineage representing at least one independent colonization of the lake. Moreover, complex genetic relationships are revealed between Lake Titicaca individuals and those from surrounding water bodies, which may be explained by repeated dispersal into and out of the lake, combined with parallel intralacustrine diversification within two separate clades. Although further work in deeper waters will be required to determine the number of species present and modes of diversification, our results strongly indicate that this amphipod species cloud is polyphyletic with a complex geographic history. Copyright © 2018 Elsevier Inc. All rights reserved.

A simulation study on the constancy of cardiac energy metabolites during workload transition.

PubMed

Saito, Ryuta; Takeuchi, Ayako; Himeno, Yukiko; Inagaki, Nobuya; Matsuoka, Satoshi

2016-12-01

The cardiac energy metabolites such as ATP, phosphocreatine, ADP and NADH are kept relatively constant during physiological cardiac workload transition. How this is accomplished is not yet clarified, though Ca 2+ has been suggested to be one of the possible mechanisms. We constructed a detailed mathematical model of cardiac mitochondria based on experimental data and studied whether known Ca 2+ -dependent regulation mechanisms play roles in the metabolite constancy. Model simulations revealed that the Ca 2+ -dependent regulation mechanisms have important roles under the in vitro condition of isolated mitochondria where malate and glutamate were mitochondrial substrates, while they have only a minor role and the composition of substrates has marked influence on the metabolite constancy during workload transition under the simulated in vivo condition where many substrates exist. These results help us understand the regulation mechanisms of cardiac energy metabolism during physiological cardiac workload transition. The cardiac energy metabolites such as ATP, phosphocreatine, ADP and NADH are kept relatively constant over a wide range of cardiac workload, though the mechanisms are not yet clarified. One possible regulator of mitochondrial metabolism is Ca 2+ , because it activates several mitochondrial enzymes and transporters. Here we constructed a mathematical model of cardiac mitochondria, including oxidative phosphorylation, substrate metabolism and ion/substrate transporters, based on experimental data, and studied whether the Ca 2+ -dependent activation mechanisms play roles in metabolite constancy. Under the in vitro condition of isolated mitochondria, where malate and glutamate were used as mitochondrial substrates, the model well reproduced the Ca 2+ and inorganic phosphate (P i ) dependences of oxygen consumption, NADH level and mitochondrial membrane potential. The Ca 2+ -dependent activations of the aspartate/glutamate carrier and the F 1 F o -ATPase, and

Parallel detection of violations of color constancy

PubMed Central

Foster, David H.; Nascimento, Sérgio M. C.; Amano, Kinjiro; Arend, Larry; Linnell, Karina J.; Nieves, Juan Luis; Plet, Sabrina; Foster, Jeffrey S.

2001-01-01

The perceived colors of reflecting surfaces generally remain stable despite changes in the spectrum of the illuminating light. This color constancy can be measured operationally by asking observers to distinguish illuminant changes on a scene from changes in the reflecting properties of the surfaces comprising it. It is shown here that during fast illuminant changes, simultaneous changes in spectral reflectance of one or more surfaces in an array of other surfaces can be readily detected almost independent of the numbers of surfaces, suggesting a preattentive, spatially parallel process. This process, which is perfect over a spatial window delimited by the anatomical fovea, may form an early input to a multistage analysis of surface color, providing the visual system with information about a rapidly changing world in advance of the generation of a more elaborate and stable perceptual representation. PMID:11438751

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.

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. Copyright © 2015 Elsevier Inc. All rights reserved.

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

PubMed Central

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

2015-01-01

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

Simultaneous phylogeny reconstruction and multiple sequence alignment

PubMed Central

Yue, Feng; Shi, Jian; Tang, Jijun

2009-01-01

Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments. PMID:19208110

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

PubMed

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

2010-02-01

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Rong-Gen; Guo, Zong-Kuan; Yang, Tao, E-mail: cairg@itp.ac.cn, E-mail: guozk@itp.ac.cn, E-mail: yangtao@itp.ac.cn

We develop a new model-independent method to probe the constancy of the speed of light c . In our method, the degeneracy between the cosmic curvature and the speed of light can be eliminated, which makes the test more natural and general. Combining the independent observations of Hubble parameter H ( z ) and luminosity distance d {sub L} ( z ), we use the model-independent smoothing technique, Gaussian processes, to reconstruct them and then detect variation of the speed of light. We find no signal of deviation from the present value of the speed of light c {sub 0}.more » Moreover, to demonstrate the improvement in probing the constancy of the speed of light from future experiments, we produce a series of simulated data. The Dark Energy Survey will be able to detect Δ c / c {sub 0} ∼ 1% at ∼ 1.5σ confidence level and Δ c / c {sub 0} ∼ 2% at ∼ 3σ confidence level. If the errors are reduced to one-tenth of the expected DES ones, it can detect a Δ c / c {sub 0} ∼ 0.1% variation at ∼ 2σ confidence level.« less

What #theDress reveals about the role of illumination priors in color perception and color constancy

PubMed Central

Aston, Stacey; Hurlbert, Anya

2018-01-01

The disagreement between people who named #theDress (the Internet phenomenon of 2015) “blue and black” versus “white and gold” is thought to be caused by individual differences in color constancy. It is hypothesized that observers infer different incident illuminations, relying on illumination “priors” to overcome the ambiguity of the image. Different experiences may drive the formation of different illumination priors, and these may be indicated by differences in chronotype. We assess this hypothesis, asking whether matches to perceived illumination in the image and/or perceived dress colors relate to scores on the morningness-eveningness questionnaire (a measure of chronotype). We find moderate correlations between chronotype and illumination matches (morning types giving bluer illumination matches than evening types) and chronotype and dress body matches, but these are significant only at the 10% level. Further, although inferred illumination chromaticity in the image explains variation in the color matches to the dress (confirming the color constancy hypothesis), color constancy thresholds obtained using an established illumination discrimination task are not related to dress color perception. We also find achromatic settings depend on luminance, suggesting that subjective white point differences may explain the variation in dress color perception only if settings are made at individually tailored luminance levels. The results of such achromatic settings are inconsistent with their assumed correspondence to perceived illumination. Finally, our results suggest that perception and naming are disconnected, with observers reporting different color names for the dress photograph and their isolated color matches, the latter best capturing the variation in the matches. PMID:28793353

Gender Constancy and the "Cost" of Sex-Typed Behavior: A Test of the Conflict Hypothesis.

ERIC Educational Resources Information Center

Frey, Karin S.; Ruble, Diane N.

1992-01-01

Children between 5 and 10 years of age watched boys and girls endorse toys of varying attractiveness and then play with the toys. Boys with gender constancy spent more time than other boys in playing with unattractive sex-typed toys. Among girls, toy play was related to the toy's attractiveness. (BC)

Phylogeny mandalas for illustrating the Tree of Life.

PubMed

Hasegawa, Masami

2017-12-01

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. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

On simulated annealing phase transitions in phylogeny reconstruction.

PubMed

Strobl, Maximilian A R; Barker, Daniel

2016-08-01

Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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

PubMed

Cornils, Astrid; Blanco-Bercial, Leocadio

2013-12-01

The Paracalanidae are ecologically-important marine planktonic copepods that occur in the epipelagic zone in temperate and tropical waters. They are often the dominant taxon - in terms of biomass and abundance - in continental shelf regions. As primary consumers, they form a vital link in the pelagic food web between primary producers and higher trophic levels. Despite the ecological importance of the taxon, evolutionary and systematic relationships within the family remain largely unknown. A multigene phylogeny including 24 species, including representatives for all seven genera, was determined based on two nuclear genes, small-subunit (18S) ribosomal RNA and Histone 3 (H3) and one mitochondrial gene, cytochrome c oxidase subunit I (COI). The molecular phylogeny was well supported by Maximum likelihood and Bayesian inference analysis; all genera were found to be monophyletic, except for Paracalanus, which was separated into two distinct clades: the Paracalanus aculeatus group and Paracalanus parvus group. The molecular phylogeny also confirmed previous findings that Mecynocera and Calocalanus are genera of the family Paracalanidae. For comparison, a morphological phylogeny was created for 35 paracalanid species based on 54 morphological characters derived from published descriptions. The morphological phylogeny did not resolve all genera as monophyletic and bootstrap support was not strong. Molecular and morphological phylogenies were not congruent in the positioning of Bestiolina and the Paracalanus species groups, possibly due to the lack of sufficient phylogenetically-informative morphological characters. Copyright © 2013 Elsevier Inc. All rights reserved.

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…

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.

Primate diversification inferred from phylogenies and fossils.

PubMed

Herrera, James P

2017-12-01

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

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…

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

PubMed

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

2016-01-01

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

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.

Molecular taxonomy and phylogeny

USDA-ARS?s Scientific Manuscript database

The cyst nematodes comprise a group of sedentary endoparasitic nematodes that impact a wide range of crops in both tropical and temperate regions of the world. This chapter updates the taxonomy and phylogeny of this group and describes the nuclear protein coding, ribosomal, and mitochondrial sequenc...

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

PubMed

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

2014-08-01

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

Plastome phylogeny and early diversification of Brassicaceae.

PubMed

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

2017-02-16

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

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…

Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies.

PubMed

Min, Xiaoping; Zhang, Mouzhao; Yuan, Sisi; Ge, Shengxiang; Liu, Xiangrong; Zeng, Xiangxiang; Xia, Ningshao

2017-12-26

In recent years, to infer phylogenies, which are NP-hard problems, more and more research has focused on using metaheuristics. Maximum Parsimony and Maximum Likelihood are two effective ways to conduct inference. Based on these methods, which can also be considered as the optimal criteria for phylogenies, various kinds of multi-objective metaheuristics have been used to reconstruct phylogenies. However, combining these two time-consuming methods results in those multi-objective metaheuristics being slower than a single objective. Therefore, we propose a novel, multi-objective optimization algorithm, MOEA-RC, to accelerate the processes of rebuilding phylogenies using structural information of elites in current populations. We compare MOEA-RC with two representative multi-objective algorithms, MOEA/D and NAGA-II, and a non-consensus version of MOEA-RC on three real-world datasets. The result is, within a given number of iterations, MOEA-RC achieves better solutions than the other algorithms.

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. Copyright 2009 Elsevier Inc. All rights reserved.

Phylogeny predicts future habitat shifts due to climate change.

PubMed

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

2014-01-01

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

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

Phylogeny and adaptation shape the teeth of insular mice.

PubMed

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

2016-02-10

By accompanying human travels since prehistorical times, the house mouse dispersed widely throughout the world, and colonized many islands. The origin of the travellers determined the phylogenetic source of the insular mice, which encountered diverse ecological and environmental conditions on the various islands. Insular mice are thus an exceptional model to disentangle the relative role of phylogeny, ecology and climate in evolution. Molar shape is known to vary according to phylogeny and to respond to adaptation. Using for the first time a three-dimensional geometric morphometric approach, compared with a classical two-dimensional quantification, the relative effects of size variation, phylogeny, climate and ecology were investigated on molar shape diversity across a variety of islands. Phylogeny emerged as the factor of prime importance in shaping the molar. Changes in competition level, mostly driven by the presence or absence of the wood mouse on the different islands, appeared as the second most important effect. Climate and size differences accounted for slight shape variation. This evidences a balanced role of random differentiation related to history of colonization, and of adaptation possibly related to resource exploitation. © 2016 The Author(s).

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

PubMed

O'Malley, Maureen A

2013-12-01

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

Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae).

PubMed

Leduc-Robert, Geneviève; Maddison, Wayne P

2018-02-22

Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson's D statistics and D FOIL . We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti

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

PubMed

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

2016-01-01

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

Timing and Order of Transmission Events Is Not Directly Reflected in a Pathogen Phylogeny

PubMed Central

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

2014-01-01

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. PMID:24874208

A six-gene phylogeny provides new insights into choanoflagellate evolution.

PubMed

Carr, Martin; Richter, Daniel J; Fozouni, Parinaz; Smith, Timothy J; Jeuck, Alexandra; Leadbeater, Barry S C; Nitsche, Frank

2017-02-01

Recent studies have shown that molecular phylogenies of the choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the choanoflagellates. We examine the distribution within choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the choanoflagellates. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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…

Color constancy for an unseen surface.

PubMed

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

2014-12-01

The illumination of a scene strongly affects our perception of objects in that scene, e.g., the pages of a book illuminated by candlelight will appear quite yellow relative to other types of artificial illuminants. Yet at the same time, the reader still judges the pages as white, their surface color unaffected by the interplay of paper and illuminant. It has been shown empirically that we can indeed report two quite different interpretations of "color": one is dependent on the constant surface spectral reflectance of an object (surface color) and the other on the power of light of different wavelengths reflected from that object (reflected color). How then are these two representations related? The common view, dating from Aristotle, is that our experience of surface color is derived from reflected color or, in more familiar terms, that color perception follows from color sensation. By definition, color constancy requires that vision "discounts the illuminant"; thus, it seems reasonable that vision begins with the color of objects as they naively appear and that we infer from their appearances their surface color. Here, we question this classic view. We use metacontrast-masked priming and, by presenting the unseen prime and the visible mask under different illuminants, dissociate two ways in which the prime matched the mask: in surface color or in reflected color. We find that priming of the mask occurs when it matches the prime in surface color, not reflected color. It follows that color perception can arise without prior color sensation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes

PubMed Central

McCarthy, Charley G. P.

2017-01-01

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

On analyzing colour constancy approach for improving SURF detector performance

NASA Astrophysics Data System (ADS)

Zulkiey, Mohd Asyraf; Zaki, Wan Mimi Diyana Wan; Hussain, Aini; Mustafa, Mohd. Marzuki

2012-04-01

Robust key point detector plays a crucial role in obtaining a good tracking feature. The main challenge in outdoor tracking is the illumination change due to various reasons such as weather fluctuation and occlusion. This paper approaches the illumination change problem by transforming the input image through colour constancy algorithm before applying the SURF detector. Masked grey world approach is chosen because of its ability to perform well under local as well as global illumination change. Every image is transformed to imitate the canonical illuminant and Gaussian distribution is used to model the global change. The simulation results show that the average number of detected key points have increased by 69.92%. Moreover, the average of improved performance cases far out weight the degradation case where the former is improved by 215.23%. The approach is suitable for tracking implementation where sudden illumination occurs frequently and robust key point detection is needed.

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

PubMed

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

2017-01-01

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

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

PubMed

Gordon, Felicia

2015-03-01

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

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

Explaining evolution via constrained persistent perfect phylogeny

PubMed Central

2014-01-01

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

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

ERIC Educational Resources Information Center

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

2005-01-01

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

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

PubMed

Huang, Zuhao; Tu, Feiyun

2017-07-01

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

A Molecular Phylogeny of Living Primates

PubMed Central

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

2011-01-01

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

Molecular phylogeny and morphological change in the Psittacula parakeets.

PubMed

Groombridge, Jim J; Jones, Carl G; Nichols, Richard A; Carlton, Mark; Bruford, Michael W

2004-04-01

We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that extends from the chin to the cheek. We examine the extent of sexual dimorphism in tail length across the phylogeny and reveal large differences between closely related forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. An ancestral Psittacula form appears to have evolved during the late Miocene-early Pliocene (3.4-9.7MYA), a time when regional geological processes on the Asian continent may have promoted subsequent diversity at the species level, and many forms diverged relatively early on in the evolutionary history of Psittacula (between 2.5 and 7.7MYA). However, others, such as the derbyan and moustached parakeets, diverged as recently as 0.2MYA. Our phylogeny also suggests that the echo parakeet from Mauritius diverged from the Indian ringneck parakeet as opposed to the African ringneck, and may have done so relatively recently. The molecular results indicate support for a southwards radiation from India across the Indian Ocean to Mauritius, where the arrival-date of the echo parakeet appears consistent with the island's volcanic formation.

A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.

PubMed

Muscarella, Robert; Uriarte, María; Erickson, David L; Swenson, Nathan G; Zimmerman, Jess K; Kress, W John

2014-01-01

The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean

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

PubMed

Hasegawa, Masami; Kuroda, Sayako

2017-12-01

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. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

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.

Ciliate diversity, community structure, and novel taxa in lakes of the McMurdo Dry Valleys, Antarctica.

PubMed

Xu, Yuan; Vick-Majors, Trista; Morgan-Kiss, Rachael; Priscu, John C; Amaral-Zettler, Linda

2014-10-01

We report an in-depth survey of next-generation DNA sequencing of ciliate diversity and community structure in two permanently ice-covered McMurdo Dry Valley lakes during the austral summer and autumn (November 2007 and March 2008). We tested hypotheses on the relationship between species richness and environmental conditions including environmental extremes, nutrient status, and day length. On the basis of the unique environment that exists in these high-latitude lakes, we expected that novel taxa would be present. Alpha diversity analyses showed that extreme conditions-that is, high salinity, low oxygen, and extreme changes in day length-did not impact ciliate richness; however, ciliate richness was 30% higher in samples with higher dissolved organic matter. Beta diversity analyses revealed that ciliate communities clustered by dissolved oxygen, depth, and salinity, but not by season (i.e., day length). The permutational analysis of variance test indicated that depth, dissolved oxygen, and salinity had significant influences on the ciliate community for the abundance matrices of resampled data, while lake and season were not significant. This result suggests that the vertical trends in dissolved oxygen concentration and salinity may play a critical role in structuring ciliate communities. A PCR-based strategy capitalizing on divergent eukaryotic V9 hypervariable region ribosomal RNA gene targets unveiled two new genera in these lakes. A novel taxon belonging to an unknown class most closely related to Cryptocaryon irritans was also inferred from separate gene phylogenies. © 2014 Marine Biological Laboratory.

Ecosystem Alterations and Species Range Shifts: An Atlantic-Mediterranean Cephalaspidean Gastropod in an Inland Egyptian Lake

PubMed Central

Malaquias, Manuel António E.

2016-01-01

The eastern Atlantic and Mediterranean marine Cephalaspidea gastropod Haminoea orbignyana was collected from Lake Qarun (Fayoum, Egypt), a landlocked lake that has undergone a shift from freshwater to estuarine conditions in the past 100 years. Species identity was confirmed by both morphological (anatomical dissection and scanning electron microscopy) and molecular methods (COI gene phylogeny). Observations suggested a robust population of H. orbignyana in the lake with a density of ca. 64 individuals/m2 and ca. 105 egg masses/m2 during surveys conducted in the summer of 2013. The vast majority of snails and egg masses were found under rocks. Observations of egg masses in the lab showed a gradual change from whitish to yellow-green as the eggs matured and the release of veliger larvae alone after about a week. Although adult cephalaspideans readily consumed filamentous red and green algae, and cyanobacteria, laboratory trials showed that they consumed significantly more of the red alga Ceramium sp., than of the green alga Cladophora glomerata, with consumption of Oscillatoria margaritifera being similar to those on the two algae. When grown on these resources for 16 days, H. orbignyana maintained their mass on the rhodophyte and cyanobacterium, but not in starvation controls. No cephalaspideans grew over the course of this experiment. Lake Qarun has been periodically restocked with Mediterranean fishes and prawns since the 1920s to maintain local fisheries, which represents a possible route of colonization for H. orbignyana. Yet, based on literature records, it seems more likely that invasion of the lake by this gastropod species has occurred only within the last 20 years. As human activities redistribute species through direct and indirect means, the structure of the community of this inland lake has become unpredictable and the long-term effects of these recent introductions are unknown. PMID:27248835

Ecosystem Alterations and Species Range Shifts: An Atlantic-Mediterranean Cephalaspidean Gastropod in an Inland Egyptian Lake.

PubMed

Cruz-Rivera, Edwin; Malaquias, Manuel António E

2016-01-01

The eastern Atlantic and Mediterranean marine Cephalaspidea gastropod Haminoea orbignyana was collected from Lake Qarun (Fayoum, Egypt), a landlocked lake that has undergone a shift from freshwater to estuarine conditions in the past 100 years. Species identity was confirmed by both morphological (anatomical dissection and scanning electron microscopy) and molecular methods (COI gene phylogeny). Observations suggested a robust population of H. orbignyana in the lake with a density of ca. 64 individuals/m2 and ca. 105 egg masses/m2 during surveys conducted in the summer of 2013. The vast majority of snails and egg masses were found under rocks. Observations of egg masses in the lab showed a gradual change from whitish to yellow-green as the eggs matured and the release of veliger larvae alone after about a week. Although adult cephalaspideans readily consumed filamentous red and green algae, and cyanobacteria, laboratory trials showed that they consumed significantly more of the red alga Ceramium sp., than of the green alga Cladophora glomerata, with consumption of Oscillatoria margaritifera being similar to those on the two algae. When grown on these resources for 16 days, H. orbignyana maintained their mass on the rhodophyte and cyanobacterium, but not in starvation controls. No cephalaspideans grew over the course of this experiment. Lake Qarun has been periodically restocked with Mediterranean fishes and prawns since the 1920s to maintain local fisheries, which represents a possible route of colonization for H. orbignyana. Yet, based on literature records, it seems more likely that invasion of the lake by this gastropod species has occurred only within the last 20 years. As human activities redistribute species through direct and indirect means, the structure of the community of this inland lake has become unpredictable and the long-term effects of these recent introductions are unknown.

77 FR 41686 - Safety Zone; Sheffield Lake Fireworks, Lake Erie, Sheffield Lake, OH

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-16

...-AA00 Safety Zone; Sheffield Lake Fireworks, Lake Erie, Sheffield Lake, OH AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is establishing a temporary safety zone on Lake Erie, Sheffield Lake, OH. This safety zone is intended to restrict vessels from a portion of Lake Erie...

Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae-Opuntioideae).

PubMed

Ritz, C M; Reiker, J; Charles, G; Hoxey, P; Hunt, D; Lowry, M; Stuppy, W; Taylor, N

2012-11-01

The cacti of tribe Tephrocacteae (Cactaceae-Opuntioideae) are adapted to diverse climatic conditions over a wide area of the southern Andes and adjacent lowlands. They exhibit a range of life forms from geophytes and cushion-plants to dwarf shrubs, shrubs or small trees. To confirm or challenge previous morphology-based classifications and molecular phylogenies, we sampled DNA sequences from the chloroplast trnK/matK region and the nuclear low copy gene phyC and compared the resulting phylogenies with previous data gathered from nuclear ribosomal DNA sequences. The here presented chloroplast and nuclear low copy gene phylogenies were mutually congruent and broadly coincident with the classification based on gross morphology and seed micro-morphology and anatomy. Reconstruction of hypothetical ancestral character states suggested that geophytes and cushion-forming species probably evolved several times from dwarf shrubby precursors. We also traced an increase of embryo size at the expense of the nucellus-derived storage tissue during the evolution of the Tephrocacteae, which is thought to be an evolutionary advantage because nutrients are then more rapidly accessible for the germinating embryo. In contrast to these highly concordant phylogenies, nuclear ribosomal DNA data sampled by a previous study yielded conflicting phylogenetic signals. Secondary structure predictions of ribosomal transcribed spacers suggested that this phylogeny is strongly influenced by the inclusion of paralogous sequence probably arisen by genome duplication during the evolution of this plant group. Copyright © 2012 Elsevier Inc. All rights reserved.

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.

Lake level variability in Silver Lake, Michigan: a response to fluctuations in lake levels of Lake Michigan

USGS Publications Warehouse

Fisher, Timothy G.; Loope, Walter L.

2004-01-01

Sediment from Silver Lake, Michigan, can be used to constrain the timing and elevation of Lake Michigan during the Nipissing transgression. Silver Lake is separated from Lake Michigan by a barrier/dune complex and the Nipissing, Calumet, and Glenwood shorelines of Lake Michigan are expressed landward of this barrier. Two Vibracores were taken from the lake in February 2000 and contain pebbly sand, sand, buried soils, marl, peat, and sandy muck. It is suggested here that fluctuations in the level of Lake Michigan are reflected in Silver Lake since the Chippewa low phase, and possibly at the end of the Algonquin phase. An age of 12,490 B.P. (10,460±50 14C yrs B.P.) on wood from a buried Entisol may record the falling Algonquin phase as the North Bay outlet opened. A local perched water table is indicated by marl deposited before 7,800 B.P. and peat between 7,760-7,000 B.P. when Lake Michigan was at the low elevation Chippewa phase. Continued deepening of the lake is recorded by the transition from peat to sandy muck at 7,000 B.P. in the deeper core, and with the drowning of an Inceptisol nearly 3 m higher at 6,410 B.P. in the shallower core. A rising groundwater table responding to a rising Lake Michigan base level during the Nipissing transgression, rather than a response to mid-Holocene climate change, explains deepening of Silver Lake. Sandy muck was deposited continually in Silver Lake between Nipissing and modern time. Sand lenses within the muck are presumed to be eolian in origin, derived from sand dunes advancing into the lake on the western side of the basin.

Resolution of ray-finned fish phylogeny and timing of diversification.

PubMed

Near, Thomas J; Eytan, Ron I; Dornburg, Alex; Kuhn, Kristen L; Moore, Jon A; Davis, Matthew P; Wainwright, Peter C; Friedman, Matt; Smith, W Leo

2012-08-21

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.

PubMed

Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-02-01

Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. © The Authors 2017. Published by Oxford University Press.

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

PubMed Central

Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-01-01

Abstract Background Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. PMID:29186447

The discovery of Halictivirus resolves the Sinaivirus phylogeny.

PubMed

Bigot, Diane; Dalmon, Anne; Roy, Bronwen; Hou, Chunsheng; Germain, Michèle; Romary, Manon; Deng, Shuai; Diao, Qingyun; Weinert, Lucy A; Cook, James M; Herniou, Elisabeth A; Gayral, Philippe

2017-11-01

By providing pollination services, bees are among the most important insects, both in ecological and economical terms. Combined next-generation and classical sequencing approaches were applied to discover and study new insect viruses potentially harmful to bees. A bioinformatics virus discovery pipeline was used on individual Illumina transcriptomes of 13 wild bees from three species from the genus Halictus and 30 ants from six species of the genera Messor and Aphaenogaster. This allowed the discovery and description of three sequences of a new virus termed Halictus scabiosae Adlikon virus (HsAV). Phylogenetic analyses of ORF1, RNA-dependent RNA-polymerase (RdRp) and capsid genes showed that HsAV is closely related to (+)ssRNA viruses of the unassigned Sinaivirus genus but distant enough to belong to a different new genus we called Halictivirus. In addition, our study of ant transcriptomes revealed the first four sinaivirus sequences from ants (Messor barbarus, M. capitatus and M. concolor). Maximum likelihood phylogenetic analyses were performed on a 594 nt fragment of the ORF1/RdRp region from 84 sinaivirus sequences, including 31 new Lake Sinai viruses (LSVs) from honey bees collected in five countries across the globe and the four ant viral sequences. The phylogeny revealed four main clades potentially representing different viral species infecting honey bees. Moreover, the ant viruses belonged to the LSV4 clade, suggesting a possible cross-species transmission between bees and ants. Lastly, wide honey bee screening showed that all four LSV clades have worldwide distributions with no obvious geographical segregation.

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. Copyright © 2014 Kuhner and McGill.

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. Copyright © 2012 Elsevier Inc. All rights reserved.

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.

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. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Well-Resolved Phylogeny of the Trees of Puerto Rico Based on DNA Barcode Sequence Data

PubMed Central

Muscarella, Robert; Uriarte, María; Erickson, David L.; Swenson, Nathan G.; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Background The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. Methodology/principal findings We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. Conclusions/significance With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and

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

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

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.

Carbonate deposition, Pyramid Lake subbasin, Nevada: 1. Sequence of formation and elevational distribution of carbonate deposits (Tufas)

USGS Publications Warehouse

Benson, L.

1994-01-01

During the late Quarternary, the elevation of terrace cutting and carbonate deposition in the Pyramid Lake subbasin were controlled by constancy of lake level imposed by spill to adjoining subbasins. Sill elevations are 1177-1183 m (Mud Lake Slough Sill), 1207 m (Emerson Pass Sill), and 1265 m (Darwin Pass Sill). Carbonate deposition was favored by: (1) hydrologic closure, (2) proximity to a source of calcium, (3) elevated water temperature, and (4) a solid substrate. The thickness and aspect of tufa are a function oflake-level dynamics. Relatively thin sheets and pendant sheets were deposited during a rising or falling lake. The upper parts of thick reef-form tufas have a horizontal aspect and were deposited in a lake which was stabilized by spill to the Carson Desert subbasin. The lower parts of the reef-form tufas are thinner and their outer surface has a vertical aspect, indicating that the lower part formed in a receding lake. The thickest and most complete sequences of tufa are mounds that border the Pyramid Lake shore. The tops of the tallest mounds reach the elevation of the Darwin Pass Sill and many mounds have been eroded to the elevations of the Mud Lake Slough Sill of the Emerson Pass Sill. The sequence of tufa formation (from oldest to youngest) displayed in these mounds is: (1) a beachrock containing carbonate-cemented volcanic cobbles, (2) broken and eroded old spheroids that contain thinolitic tufa and an outer rind of dense laminated tufa, (3) large cylindrical (tubular) tufas capped by (4) coatings of old dense tufas, and (5) several generations of old branching tufa commonly associated with thin, platy tufas and coatings of thinolitic tufa, (6) young spheroids that contain poorly oriented young thinolitic tufa in the center and several generations of radially oriented young thinolitic tufas near the outer edge, (7) a transitional thinolite-to-branching tufa, (8) two or more layers of young branching tufa, (9) a 0.5-cm-thick layer of fine

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

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

Resolution of ray-finned fish phylogeny and timing of diversification

PubMed Central

Near, Thomas J.; Eytan, Ron I.; Dornburg, Alex; Kuhn, Kristen L.; Moore, Jon A.; Davis, Matthew P.; Wainwright, Peter C.; Friedman, Matt; Smith, W. Leo

2012-01-01

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the “bush at the top of the tree” that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the “Second Age of Fishes.” PMID:22869754

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.

Molecular phylogeny and morphological evolution of the Acantharia (Radiolaria).

PubMed

Decelle, Johan; Suzuki, Noritoshi; Mahé, Fredéric; de Vargas, Colomban; Not, Fabrice

2012-05-01

Acantharia are ubiquitous and abundant rhizarian protists in the world ocean. The skeleton made of strontium sulphate and the fact that certain harbour microalgal endosymbionts make them key planktonic players for the ecology of marine ecosystems. Based on morphological criteria, the current taxonomy of Acantharia was established by W.T. Schewiakoff in 1926, since when no major revision has been undertaken. Here, we established the first comprehensive molecular phylogeny from single morphologically-identified acantharian cells, isolated from various oceans. Our phylogenetic analyses based on 78 18S rDNA and 107 partial 28S rDNA revealed the existence of 6 main clades, sub-divided into 13 sub-clades. The polyphyletic nature of acantharian families and genera demonstrates the need for revision of the current taxonomy. This molecular phylogeny, which highlights the taxonomic relevance of specific morphological criteria, such as the presence of a shell and the organisation of the central junction, provides a robust phylogenetic framework for future taxonomic emendation. Finally, mapping all the existing environmental sequences available to date from different marine ecosystems onto our reference phylogeny unveiled another 3 clades and improved the understanding of the biogeography and ecology of Acantharia. Copyright © 2011 Elsevier GmbH. All rights reserved.

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.

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.

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.

[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

2016 Lake Michigan Lake Trout Working Group Report

USGS Publications Warehouse

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

2017-01-01

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

Asian horses deepen the MSY phylogeny.

PubMed

Felkel, S; Vogl, C; Rigler, D; Jagannathan, V; Leeb, T; Fries, R; Neuditschko, M; Rieder, S; Velie, B; Lindgren, G; Rubin, C-J; Schlötterer, C; Rattei, T; Brem, G; Wallner, B

2018-02-01

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages. © 2018 Stichting International Foundation for Animal Genetics.

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

PubMed Central

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

1994-01-01

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

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

USGS Publications Warehouse

Heinz, Gary H.; Percival, H. Franklin; 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 success of Lake Apopka eggs.

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.

Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).

PubMed

Vélez-Zuazo, Ximena; Agnarsson, Ingi

2011-02-01

Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively

Character analysis and the integration of molecular and morphological data in an understanding of sand dollar phylogeny.

PubMed

Marshall, C R

1992-03-01

Reconciling discordant morphological and molecular phylogenies remains a problem in modern systematics. By examining conflicting DNA-hybridization and morphological phylogenies of sand dollars, I show that morphological criteria may be used to help evaluate the reliability of molecular phylogenies where they differ from morphological trees. All available criteria for assessing the reliability of DNA-hybridization phylogenies suggest that the sand dollar DNA-hybridization phylogeny is robust. Standard homology-recognition criteria are used to assess the a priori reliabilities of the morphological attributes associated with the node drawn into question by the DNA data, and it is shown that these attributes are among the least phylogenetically informative of all the morphological characters. Moreover, the questioned node has the smallest number of supporting characters, and most of these characters are associated with the food grooves, which suggests that they may be functionally correlated. Thus, on the basis of the analysis of the morphological data and given the robustness of the DNA tree, the DNA phylogeny is preferred. Further, paleobiogeographic data support the DNA tree rather than the morphological tree, and a plausible heterochronic mechanism has been proposed that may account for the homoplasious morphological evolution that must have occurred if the DNA tree is correct.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andrews, F.L.; Wells, F.C.; Shelby, W.J.

1988-01-01

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

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.

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. © 2015 John Wiley & Sons Ltd/CNRS.

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

A novel molecular marker for the study of Neotropical cichlid phylogeny.

PubMed

Fabrin, T M C; Gasques, L S; Prioli, S M A P; Prioli, A J

2015-12-22

The use of molecular markers has contributed to phylogeny and to the reconstruction of species' evolutionary history. Each region of the genome has different evolution rates, which may or may not identify phylogenetic signal at different levels. Therefore, it is important to assess new molecular markers that can be used for phylogenetic reconstruction. Regions that may be associated with species characteristics and are subject to selective pressure, such as opsin genes, which encode proteins related to the visual system and are widely expressed by Cichlidae family members, are interesting. Our aim was to identify a new nuclear molecular marker that could establish the phylogeny of Neotropical cichlids and is potentially correlated with the visual system. We used Bayesian inference and maximum likelihood analysis to support the use of the nuclear opsin LWS gene in the phylogeny of eight Neotropical cichlid species. Their use concatenated to the mitochondrial gene COI was also tested. The LWS gene fragment comprised the exon 2-4 region, including the introns. The LWS gene provided good support for both analyses up to the genus level, distinguishing the studied species, and when concatenated to the COI gene, there was a good support up to the species level. Another benefit of utilizing this region, is that some polymorphisms are associated with changes in spectral properties of the LWS opsin protein, which constitutes the visual pigment that absorbs red light. Thus, utilization of this gene as a molecular marker to study the phylogeny of Neotropical cichlids is promising.

A molecular phylogeny of anseriformes based on mitochondrial DNA analysis.

PubMed

Donne-Goussé, Carole; Laudet, Vincent; Hänni, Catherine

2002-06-01

To study the phylogenetic relationships among Anseriformes, sequences for the complete mitochondrial control region (CR) were determined from 45 waterfowl representing 24 genera, i.e., half of the existing genera. To confirm the results based on CR analysis we also analyzed representative species based on two mitochondrial protein-coding genes, cytochrome b (cytb) and NADH dehydrogenase subunit 2 (ND2). These data allowed us to construct a robust phylogeny of the Anseriformes and to compare it with existing phylogenies based on morphological or molecular data. Chauna and Dendrocygna were identified as early offshoots of the Anseriformes. All the remaining taxa fell into two clades that correspond to the two subfamilies Anatinae and Anserinae. Within Anserinae Branta and Anser cluster together, whereas Coscoroba, Cygnus, and Cereopsis form a relatively weak clade with Cygnus diverging first. Five clades are clearly recognizable among Anatinae: (i) the Anatini with Anas and Lophonetta; (ii) the Aythyini with Aythya and Netta; (iii) the Cairinini with Cairina and Aix; (iv) the Mergini with Mergus, Bucephala, Melanitta, Callonetta, Somateria, and Clangula, and (v) the Tadornini with Tadorna, Chloephaga, and Alopochen. The Tadornini diverged early on from the Anatinae; then the Mergini and a large group that comprises the Anatini, Aythyini, Cairinini, and two isolated genera, Chenonetta and Marmaronetta, diverged. The phylogeny obtained with the control region appears more robust than the one obtained with mitochondrial protein-coding genes such as ND2 and cytb. This suggests that the CR is a powerful tool for bird phylogeny, not only at a small scale (i.e., relationships between species) but also at the family level. Whereas morphological analysis effectively resolved the split between Anatinae and Anserinae and the existence of some of the clades, the precise composition of the clades are different when morphological and molecular data are compared. (c) 2002 Elsevier

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.

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

PubMed Central

Kenah, Eben; Britton, Tom; Halloran, M. Elizabeth; Longini, Ira M.

2016-01-01

Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

Spatial patterns in PCB concentrations of Lake Michigan lake trout

USGS Publications Warehouse

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

1999-01-01

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

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

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

2017-08-15

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. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular and phenetic characterization of the bacterial assemblage of Hot Lake, WA, an environment with high concentrations of magnesium sulphate, and its relevance to Mars

NASA Astrophysics Data System (ADS)

Kilmer, Brian R.; Eberl, Timothy C.; Cunderla, Brent; Chen, Fei; Clark, Benton C.; Schneegurt, Mark A.

2014-01-01

Hot Lake (Oroville, WA) is an athalassohaline epsomite lake that can have precipitating concentrations of MgSO4 salts, mainly epsomite. Little biotic study has been done on epsomite lakes and it was unclear whether microbes isolated from epsomite lakes and their margins would fall within recognized halotolerant genera, common soil genera or novel phyla. Our initial study cultivated and characterized epsotolerant bacteria from the lake and its margins. Approximately 100 aerobic heterotrophic microbial isolates were obtained by repetitive streak-plating in high-salt media including either 10% NaCl or 2 M MgSO4. The collected isolates were all bacteria, nearly evenly divided between Gram-positive and Gram-negative clades, the most abundant genera being Halomonas, Idiomarina, Marinobacter, Marinococcus, Nesterenkonia, Nocardiopsis and Planococcus. Bacillus, Corynebacterium, Exiguobacterium, Kocuria and Staphylococcus also were cultured. This initial study included culture-independent community analysis of direct DNA extracts of lake margin soil using PCR-based clone libraries and 16S rRNA gene phylogeny. Clones assigned to Gram-positive bacterial clades (70% of total clones) were dominated by sequences related to uncultured actinobacteria. There were abundant Deltaproteobacteria clones related to bacterial sulphur metabolisms and clones of Legionella and Coxiella. These epsomite lake microbial communities seem to be divided between bacteria primarily associated with hyperhaline environments rich in NaCl and salinotolerant relatives of common soil organisms. Archaea appear to be in low abundance and none were isolated, despite near-saturated salinities. Growth of microbes at very high concentrations of magnesium and other sulphates has relevance to planetary protection and life-detection missions to Mars, where scant liquid water may form as deliquescent brines and appear as eutectic liquids.

Why do morphological phylogenies vary in quality? An investigation based on the comparative history of lizard clades.

PubMed

Arnold, E N

1990-05-22

Phylogenies based on morphology vary considerably in their quality: some are robust and explicit with little conflict in the data set, whereas others are far more tenuous, with much conflict and many possible alternatives. The main primary reasons for untrue or inexplicit morphological phylogenies are: not enough characters developed between branching points, uncertain character polarity, poorly differentiated character states, homoplasy caused by parallelism or reversal, and extinction, which may remove species entirely from consideration and can make originally conflicting data sets misleadingly compatible, increasing congruence at the expense of truth. Extinction differs from other confounding factors in not being apparent either in the data set or in subsequent analysis. One possibility is that variation in the quality of morphological phylogenies has resulted from exposure to different ecological situations. To investigate this, it is necessary to compare the histories of the clades concerned. In the case of explicit morphological phylogenies, ecological and behavioural data can be integrated with them and it may then be possible to decide whether morphological characters are likely to have been elicited by the environments through which the clade has passed. The credibility of such results depends not only on the phylogeny being robust but also on its detailed topology: a pectinate phylogeny will often allow more certain and more explicit statements to be made about historical events. In the case of poor phylogenies, it is not possible to produce detailed histories, but they can be compared with robust phylogenies in the range of ecological situations occupied, and whether they occupy novel situations in comparison with their outgroups. LeQuesne testing can give information about niche homoplasy, and it may also be possible to see if morphological features are functionally associated with ecological parameters, even if the direction of change is unknown

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

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.

Phylogeny of the túngara frog genus Engystomops (= Physalaemus pustulosus species group; Anura: Leptodactylidae).

PubMed

Ron, Santiago R; Santos, Juan C; Cannatella, David C

2006-05-01

We present a phylogeny of the Neotropical genus Engystomops (= Physalaemus pustulosus species group) based on sequences of approximately 2.4 kb of mtDNA, (12S rRNA, valine-tRNA, and 16S rRNA) and propose a phylogenetic nomenclature. The phylogeny includes all described taxa and two unnamed species. All analyses indicate that Engystomops is monophyletic and contains two basal allopatric clades. Clade I (Edentulus) includes E. pustulosus and the Amazonian E. petersi + E. cf. freibergi. Clade II (Duovox) includes all species distributed in W Ecuador and NW Peru. Brevivox, a clade of small-sized species is strongly supported within Duovox. Populations of Engystomops pustulosus fall into two well-supported clades, each of which occupies two disjunct portions of the species range. Overall, our phylogeny is congruent with most previous hypotheses. This study is among the few published species-level phylogenies of Neotropical amphibians derived from molecular datasets. A review of the proportion of new species detected by similar studies suggests that the increasing use of molecular techniques will lead to the discovery of a vast number of species of Neotropical amphibians.

Evolution of alkaline lakes - Lake Van case study

NASA Astrophysics Data System (ADS)

Tillman Meyer, Felix; Viehberg, Finn; Bahroun, Sonya; Wolf, Annabel; Immenhauser, Adrian; Kwiecien, Ola

2017-04-01

Lake Van in Eastern Anatolia (Turkey) is the largest terminal soda lake on Earth. The lake sedimentary profile covers ca. 600 ka (Stockhecke et al. 2014) Based on lithological changes, the presence of freshwater microfossils and close-to-freshwater pH value in the pore water, members of ICDP PALEOVAN concluded that Lake Van might have started as an open lake. Here we show paleontological and geochemical evidence in favour of this idea and constrain the time, when Lake Van likely transformed into a closed lake. Additionally we provide the first conceptual model of how this closure may have happened. Our archives of choice are inorganic and biogenic carbonates, separated by wet sieving. We identified microfossil assemblages (fraction > 125 µm) and performed high-resolution oxygen isotope (delta18O) and elemental (Mg/Ca, Sr/Ca) analyses of the fraction < 63 µm assuming that it represents only carbonates precipitating in the water column. Microfossil assemblage consists of three different species of ostracods (Candona spp, Loxoconcha sp, Amnicythere spp.), diatoms, gastropods and bivalves. Brakish-water ostracods, Loxoconcha sp and Amnicythere sp occur more often after 530 ka. Additionaly, Loxoconcha sp is a shallow-water species relaying on plants growing in the photic zone as food supply. These two aspects point to an increasing salinity in a shallowing lake. The delta18O values of inorganic carbonates are relatively low during the initial phase of Lake Van and increase abruptly (ca. 7‰) after 530 ka BP. At approximately the same time combination of Sr/Ca and Mg/Ca data suggest first occurrence of aragonite. Again, these findings suggest geochemical changes of the lake water concurrent with transition documented by microfossils. Comparison between Lake Van and Lake Ohrid (Lacey et al. 2016) delta18O data, precludes regional climate change (e.g.: increased evaporation) as the main driver of observed changes. With no evidence for increased volcanic or tectonic

Embryotoxicity of an extract from Great Lakes lake trout to rainbow trout and lake trout

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, P.J.; Tillitt, D.E.

1995-12-31

Aquatic ecosystems such as the Great Lakes are known to be contaminated with chemicals that are toxic to fish. However, the role of these contaminants in reproductive failures of fishes, such as lake trout recruitment, has remained controvertible. It was the objective to evaluate dioxin-like embryotoxicity of a complex mixture of chemicals and predict their potential to cause the lack of recruitment in Great Lakes lake trout. Graded doses of a complex environmental extract were injected into eggs of both rainbow trout and lake trout. The extract was obtained from whole adult lake trout collected from Lake Michigan in 1988.more » The extract was embryotoxic in rainbow trout, with LD50 values for Arlee strain and Erwin strain of 33 eggEQ and 14 eggEQ respectively. The LOAEL for hemorrhaging, yolk-sac edema, and craniofacial deformities in rainbow trout were 2, 2, and 4 eggEQ, respectively. Subsequent injections of the extract into lake trout eggs were likewise embryotoxic, with an LD50 value of 7 eggEQ. The LOAEL values for the extract in lake trout for hemorrhaging, yolk-sac edema, and craniofacial deformities were 0.1, 1, and 2 eggEQ, respectively. The current levels of contaminants in lake trout eggs are above the threshold for hemorrhaging and yolk-sac edema. The results also support the use of an additive model of toxicity to quantify PCDDs, PCDFs, Non-o-PCBs, and Mono-o-PCBs in relation to early life stage mortality in Lake Michigan lake trout.« less

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

Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence.

PubMed

Kropáčková, Lucie; Těšický, Martin; Albrecht, Tomáš; Kubovčiak, Jan; Čížková, Dagmar; Tomášek, Oldřich; Martin, Jean-François; Bobek, Lukáš; Králová, Tereza; Procházka, Petr; Kreisinger, Jakub

2017-10-01

Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%-30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by-product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans-generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM. © 2017 John Wiley & Sons Ltd.

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

PubMed

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

2013-03-01

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

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

Lake-level frequency analysis for Devils Lake, North Dakota

USGS Publications Warehouse

Wiche, Gregg J.; Vecchia, Aldo V.

1996-01-01

Two approaches were used to estimate future lake-level probabilities for Devils Lake. The first approach is based on an annual lake-volume model, and the second approach is based on a statistical water mass-balance model that generates seasonal lake volumes on the basis of seasonal precipitation, evaporation, and inflow. Autoregressive moving average models were used to model the annual mean lake volume and the difference between the annual maximum lake volume and the annual mean lake volume. Residuals from both models were determined to be uncorrelated with zero mean and constant variance. However, a nonlinear relation between the residuals of the two models was included in the final annual lakevolume model.Because of high autocorrelation in the annual lake levels of Devils Lake, the annual lake-volume model was verified using annual lake-level changes. The annual lake-volume model closely reproduced the statistics of the recorded lake-level changes for 1901-93 except for the skewness coefficient. However, the model output is less skewed than the data indicate because of some unrealistically large lake-level declines. The statistical water mass-balance model requires as inputs seasonal precipitation, evaporation, and inflow data for Devils Lake. Analysis of annual precipitation, evaporation, and inflow data for 1950-93 revealed no significant trends or long-range dependence so the input time series were assumed to be stationary and short-range dependent.Normality transformations were used to approximately maintain the marginal probability distributions; and a multivariate, periodic autoregressive model was used to reproduce the correlation structure. Each of the coefficients in the model is significantly different from zero at the 5-percent significance level. Coefficients relating spring inflow from one year to spring and fall inflows from the previous year had the largest effect on the lake-level frequency analysis.Inclusion of parameter uncertainty in the model

Lake-level frequency analysis for Devils Lake, North Dakota

USGS Publications Warehouse

Wiche, Gregg J.; Vecchia, Aldo V.

1995-01-01

Two approaches were used to estimate future lake-level probabilities for Devils Lake. The first approach is based on an annual lake-volume model, and the second approach is based on a statistical water mass-balance model that generates seasonal lake volumes on the basis of seasonal precipitation, evaporation, and inflow.Autoregressive moving average models were used to model the annual mean lake volume and the difference between the annual maximum lake volume and the annual mean lake volume. Residuals from both models were determined to be uncorrelated with zero mean and constant variance. However, a nonlinear relation between the residuals of the two models was included in the final annual lake-volume model.Because of high autocorrelation in the annual lake levels of Devils Lake, the annual lakevolume model was verified using annual lake-level changes. The annual lake-volume model closely reproduced the statistics of the recorded lake-level changes for 1901-93 except for the skewness coefficient However, the model output is less skewed than the data indicate because of some unrealistically large lake-level declines.The statistical water mass-balance model requires as inputs seasonal precipitation, evaporation, and inflow data for Devils Lake. Analysis of annual precipitation, evaporation, and inflow data for 1950-93 revealed no significant trends or long-range dependence so the input time series were assumed to be stationary and short-range dependent.Normality transformations were used to approximately maintain the marginal probability distributions; and a multivariate, periodic autoregressive model was used to reproduce the correlation structure. Each of the coefficients in the model is significantly different from zero at the 5-percent significance level. Coefficients relating spring inflow from one year to spring and fall inflows from the previous year had the largest effect on the lake-level frequency analysis.Inclusion of parameter uncertainty in the model

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.

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.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

PubMed

Hinchliff, Cody E; Smith, Stephen A; Allman, James F; Burleigh, J Gordon; Chaudhary, Ruchi; Coghill, Lyndon M; Crandall, Keith A; Deng, Jiabin; Drew, Bryan T; Gazis, Romina; Gude, Karl; Hibbett, David S; Katz, Laura A; Laughinghouse, H Dail; McTavish, Emily Jane; Midford, Peter E; Owen, Christopher L; Ree, Richard H; Rees, Jonathan A; Soltis, Douglas E; Williams, Tiffani; Cranston, Karen A

2015-10-13

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences

PubMed Central

Li, Hu; Shao, Renfu; Song, Nan; Song, Fan; Jiang, Pei; Li, Zhihong; Cai, Wanzhi

2015-01-01

Mitochondrial (mt) genome data have been proven to be informative for animal phylogenetic studies but may also suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity. We analyzed the mt genomes of 25 insect species from the four paraneopteran orders, aiming to better understand how accelerated substitution rate and compositional heterogeneity affect the inferences of the higher-level phylogeny of this diverse group of hemimetabolous insects. We found substantial heterogeneity in base composition and contrasting rates in nucleotide substitution among these paraneopteran insects, which complicate the inference of higher-level phylogeny. The phylogenies inferred with concatenated sequences of mt genes using maximum likelihood and Bayesian methods and homogeneous models failed to recover Psocodea and Hemiptera as monophyletic groups but grouped, instead, the taxa that had accelerated substitution rates together, including Sternorrhyncha (a suborder of Hemiptera), Thysanoptera, Phthiraptera and Liposcelididae (a family of Psocoptera). Bayesian inference with nucleotide sequences and heterogeneous models (CAT and CAT + GTR), however, recovered Psocodea, Thysanoptera and Hemiptera each as a monophyletic group. Within Psocodea, Liposcelididae is more closely related to Phthiraptera than to other species of Psocoptera. Furthermore, Thysanoptera was recovered as the sister group to Hemiptera. PMID:25704094

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

PubMed Central

Fitzpatrick, David A; Logue, Mary E; Stajich, Jason E; Butler, Geraldine

2006-01-01

Background To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to reconstruct evolutionary events using entire genomes. As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available. Results A dataset of 345,829 genes was extracted from 42 publicly available fungal genomes. Supertree methods were employed to derive phylogenies from 4,805 single gene families. We found that the average consensus supertree method may suffer from long-branch attraction artifacts, while matrix representation with parsimony (MRP) appears to be immune from these. A genome phylogeny was also reconstructed from a concatenated alignment of 153 universally distributed orthologs. Our MRP supertree and concatenated phylogeny are highly congruent. Within the Ascomycota, the sub-phyla Pezizomycotina and Saccharomycotina were resolved. Both phylogenies infer that the Leotiomycetes are the closest sister group to the Sordariomycetes. There is some ambiguity regarding the placement of Stagonospora nodurum, the sole member of the class Dothideomycetes present in the dataset. Within the Saccharomycotina, a monophyletic clade containing organisms that translate CTG as serine instead of leucine is evident. There is also strong support for two groups within the CTG clade, one containing the fully sexual species Candida lusitaniae, Candida guilliermondii and Debaryomyces hansenii, and the second group containing Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis and Lodderomyces elongisporus. The second major clade within the Saccharomycotina contains species whose genomes have undergone a whole genome duplication (WGD), and their close relatives. We could not

[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.

Lake Level Variation in Small Lakes: Not a Clear Picture

NASA Astrophysics Data System (ADS)

Starratt, S.

2017-12-01

Lake level is a useful tool for identifying regional changes in precipitation and evaporation. Due to the volume of water in large lakes, they may only record large-scale changes in water balance, while smaller lakes may record more subtle variations. However, the record of water level in small lakes is affected by a number of factors including elevation, bathymetry, nutrient load, and aquatic macrophyte abundance. The latest Quaternary diatom records from three small lakes with areas of <10 ha (Hobart Lake, OR, 1458 masl; Swamp Lake, CA, 1554 masl; Favre Lake, NV, 2899 masl) and a larger lake (Medicine Lake, CA, 2036 masl, 154 ha) were compared in this study. All the lakes have a deep central basin (>10 m) surrounded by a shallow (1-2 m) shelf. Changes in the abundance of diatoms representing different life habits (benthic, tychoplanktic, planktic) were used to identify lake level variation. Benthic taxa dominate the assemblage when only the central basin is occupied. As the shallow shelf is flooded, the abundance of tychoplanktic taxa increases. Planktic taxa increase with the establishment of stratification. Favre Lake presents the clearest indication of initial lake level rise (7600-5750 cal yr BP) and intermittent flooding of the shelf for the remainder of the record. Stratification appears to become established only in the last few hundred years. Higher nutrient levels in the early part of the Hobart Lake record lead to a nearly monotypic planktic assemblage which is replaced by a tychoplanktic-dominated assemblage as the lake floods the shelf at about 3500 cal yr BP. The last 500 years is dominated by benthic taxa associated with aquatic macrophytes. The consistent presence of planktic taxa in the Swamp Lake record suggests that the lake was stratified during most of its history, although slight variations in the relative abundances of planktic and tychoplanktic groups occur. The Medicine Lake record shows a gradual increase in planktic species between 11

78 FR 53675 - Safety Zone; Lake Erie Heritage Foundation, Battle of Lake Erie Reenactment; Lake Erie, Put-in...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-30

...-AA00 Safety Zone; Lake Erie Heritage Foundation, Battle of Lake Erie Reenactment; Lake Erie, Put-in-Bay... temporary safety zone in the waters of Lake Erie in the vicinity of Put-In-Bay, OH. This safety zone is intended to restrict vessels from a portion of Lake Erie during Battle of Lake Erie Reenactment near Put-In...

Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

PubMed Central

Zhang, Yan-Cong; Lin, Kui

2015-01-01

Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy.

PubMed

Xia, Rong; Durand, Jean-Dominique; Fu, Cuizhang

2016-03-01

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera. Copyright © 2015 Elsevier Inc. All rights reserved.

Lake trout spawning habitat in the Six Fathom Bank-Yankee Reef lake trout sanctuary, Lake Huron

USGS Publications Warehouse

Edsall, Thomas A.; Brown, Charles L.; Kennedy, Gregory W.; Poe, Thomas P.

1992-01-01

Attempts to reestablish self-sustaining stocks of lake trout (Salvelinus namaycush) in the lower four Great Lakes, where the species was extinguished in the 1950s and 1960s, have been largely unsuccessful. To avoid many of the problems believed to be contributing to this failure, the fishery management community recently established several sanctuaries in the offshore waters of the Great Lakes where the development and protection of self-sustaining stocks of lake trout would be a primary management objective. One of these, the Six Fathom Bank-Yankee Reef sanctuary, was created in the south-central portion of Lake Huron. This sanctuary covers 168,000 ha and includes the shallower portions of the Six Fathom and Ipperwash scarps, which are major bathymetric features in the southern half of the lake. Historical accounts describe Six Fathom Bank as the most important lake trout spawning ground in the lake. Here we present the results of lake bed surveys conducted in the sanctuary with side-scan sonar, underwater videocamera systems, and a small research submarine. Our observations of the lake bed are consistent with what is known of the bedrock stratigraphy, glacial history, and karst geomorphology of the Lake Huron basin. Most of the loose rock we found seemed to be derived from local carbonate bedrock formations, although non-carbonate rock probably from Precambrian sources to the north was also present in some areas. Much of the bedrock and loose rock displayed karst solution features described for the Bruce Peninsula on the Ontario shoreline. Our surveys revealed substantial areas of lake bed at water depths of 20–36 m that resembled suitable spawning and fry production habitat for the shallow-water strains of lake trout that are the focus of the rehabilitation effort. Low mid-lake nutrient levels documented recently by others and the extremely high abundance of Mysis relicta (an important item in the diet of young lake trout) that we documented on Yankee Reef

Lake-level variability and water availability in the Great Lakes

USGS Publications Warehouse

Wilcox, Douglas A.; Thompson, Todd A.; Booth, Robert K.; Nicholas, J.R.

2007-01-01

In this report, we present recorded and reconstructed (pre-historical) changes in water levels in the Great Lakes, relate them to climate changes of the past, and highlight major water-availability implications for storage, coastal ecosystems, and human activities. 'Water availability,' as conceptualized herein, includes a recognition that water must be available for human and natural uses, but the balancing of how much should be set aside for which use is not discussed. The Great Lakes Basin covers a large area of North America. The lakes capture and store great volumes of water that are critical in maintaining human activities and natural ecosystems. Water enters the lakes mostly in the form of precipitation and streamflow. Although flow through the connecting channels is a primary output from the lakes, evaporation is also a major output. Water levels in the lakes vary naturally on timescales that range from hours to millennia; storage of water in the lakes changes at the seasonal to millennial scales in response to lake-level changes. Short-term changes result from storm surges and seiches and do not affect storage. Seasonal changes are driven by differences in net basin supply during the year related to snowmelt, precipitation, and evaporation. Annual to millennial changes are driven by subtle to major climatic changes affecting both precipitation (and resulting streamflow) and evaporation. Rebounding of the Earth's surface in response to loss of the weight of melted glaciers has differentially affected water levels. Rebound rates have not been uniform across the basin, causing the hydrologic outlet of each lake to rise in elevation more rapidly than some parts of the coastlines. The result is a long-term change in lake level with respect to shoreline features that differs from site to site. The reconstructed water-level history of Lake Michigan-Huron over the past 4,700 years shows three major high phases from 2,300 to 3,300, 1,100 to 2,000, and 0 to 800

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)…

Increased piscivory by lake whitefish in Lake Huron

USGS Publications Warehouse

Pothoven, Steven A.; Madenjian, Charles P.

2013-01-01

We evaluated the diet of Lake Whitefish Coregonus clupeaformis in Lake Huron during 2002–2011 to determine the importance of Round Goby Neogobius melanostomus and other fish as prey items. Lake Whitefish that had reached approximately 400 mm in length incorporated fish into their diets. The overall percentage of adult Lake Whitefish in Lake Huron that had eaten fish increased from 10% in 2002–2006 to 20% in 2007–2011, with a corresponding decrease in the frequency of Lake Whitefish that ate Dreissena spp. from 52% to 33%. During 2002–2006, Round Goby (wet mass, 38%), sculpins (Cottidae) (34%), and Ninespine Stickleback Pungitius pungitius (18%) were the primary fish eaten, whereas Round Goby accounted for 92% of the fish eaten in 2007–2011. Overall, Round Goby were found in the fewest Lake Whitefish stomachs in the north region of Lake Huron (6%) and in the most in the central (23%) and south (19%) regions of the lake. In the central region, Round Goby were eaten during all seasons that were sampled (spring through fall). In the south region, Round Goby were eaten only in the winter and spring but not in the summer when Dreissena spp. and spiny water flea Bythotrephes longimanus dominated the diet. Based on the 2007–2011 diet composition, an individual Lake Whitefish would need to have increased their consumption relative to that in 1983–1994 by 6% in the north region, 12% in the central region, and 41% in the southern region in order to achieve the same growth that was observed before dreissenid mussels arrived. However, Lake Whitefish weight adjusted for length only increased by 2% between 2002–2006 and 2007–2011 in the central region, decreased by 4% in the northern region, and remained constant in the southern region. This suggests that a shift toward more frequent piscivory does not necessarily improve the condition of a generalist feeder like Lake Whitefish.

SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP.

PubMed

van Rens, Karen E; Mäkinen, Veli; Tomescu, Alexandru I

2015-04-01

Recent studies sequenced tumor samples from the same progenitor at different development stages and showed that by taking into account the phylogeny of this development, single-nucleotide variant (SNV) calling can be improved. Accurate SNV calls can better reveal early-stage tumors, identify mechanisms of cancer progression or help in drug targeting. We present SNV-PPILP, a fast and easy to use tool for refining GATK's Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny. We tested SNV-PPILP on simulated data, with a varying number of samples, SNVs, read coverage and violations of the perfect phylogeny assumption. We always match or improve the accuracy of GATK, with a significant improvement on low read coverage. SNV-PPILP, available at cs.helsinki.fi/gsa/snv-ppilp/, is written in Python and requires the free ILP solver lp_solve. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Host phylogeny determines viral persistence and replication in novel hosts.

PubMed

Longdon, Ben; Hadfield, Jarrod D; Webster, Claire L; Obbard, Darren J; Jiggins, Francis M

2011-09-01

Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts.

Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts

PubMed Central

Longdon, Ben; Hadfield, Jarrod D.; Webster, Claire L.

2011-01-01

Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts. PMID:21966271

Holocene lake-level fluctuations of Lake Aricota, Southern Peru

USGS Publications Warehouse

Placzek, C.; Quade, Jay; Betancourt, J.L.

2001-01-01

Lacustrine deposits exposed around Lake Aricota, Peru (17?? 22???S), a 7.5-km2 lake dammed by debris flows, provide a middle to late Holocene record of lake-level fluctuations. Chronological context for shoreline deposits was obtained from radiocarbon dating of vascular plant remains and other datable material with minimal 14C reservoir effects (<350 yr). Diatomites associated with highstands several meters above the modern lake level indicate wet episodes. Maximum Holocene lake level was attained before 6100 14C yr B.P. and ended ???2700 14C yr B.P. Moderately high lake levels occurred at 1700 and 1300 14C yr B.P. The highstand at Lake Aricota during the middle Holocene is coeval with a major lowstand at Lake Titicaca (16?? S), which is only 130 km to the northeast and shares a similar climatology. Comparisons with other marine and terrestrial records highlight emerging contradictions over the nature of mid-Holocene climate in the central Andes. ?? 2001 University of Washington.

Holocene Lake-Level Fluctuations of Lake Aricota, Southern Peru

NASA Astrophysics Data System (ADS)

Placzek, Christa; Quade, Jay; Betancourt, Julio L.

2001-09-01

Lacustrine deposits exposed around Lake Aricota, Peru (17° 22‧S), a 7.5-km2 lake dammed by debris flows, provide a middle to late Holocene record of lake-level fluctuations. Chronological context for shoreline deposits was obtained from radiocarbon dating of vascular plant remains and other datable material with minimal 14C reservoir effects (<350 yr). Diatomites associated with highstands several meters above the modern lake level indicate wet episodes. Maximum Holocene lake level was attained before 6100 14C yr B.P. and ended ∼2700 14C yr B.P. Moderately high lake levels occurred at 1700 and 1300 14C yr B.P. The highstand at Lake Aricota during the middle Holocene is coeval with a major lowstand at Lake Titicaca (16°S), which is only 130 km to the northeast and shares a similar climatology. Comparisons with other marine and terrestrial records highlight emerging contradictions over the nature of mid-Holocene climate in the central Andes.

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.

Late Holocene lake-level fluctuations in Walker Lake, Nevada, USA

USGS Publications Warehouse

Yuan, F.; Linsley, B.K.; Howe, S.S.; Lund, S.P.; McGeehin, J.P.

2006-01-01

Walker Lake, a hydrologically closed, saline, and alkaline lake, is situated along the western margin of the Great Basin in Nevada of the western United States. Analyses of the magnetic susceptibility (??), total inorganic carbon (TIC), and oxygen isotopic composition (??18O) of carbonate sediments including ostracode shells (Limnocythere ceriotuberosa) from Walker Lake allow us to extend the sediment record of lake-level fluctuations back to 2700??years B.P. There are approximately five major stages over the course of the late Holocene hydrologic evolution in Walker Lake: an early lowstand (> 2400??years B.P.), a lake-filling period (??? 2400 to ??? 1000??years B.P.), a lake-level lowering period during the Medieval Warm Period (MWP) (??? 1000 to ??? 600??years B.P.), a relatively wet period (??? 600 to ??? 100??years B.P.), and the anthropogenically induced lake-level lowering period (< 100??years B.P.). The most pronounced lowstand of Walker Lake occurred at ??? 2400??years B.P., as indicated by the relatively high values of ??18O. This is generally in agreement with the previous lower resolution paleoclimate results from Walker Lake, but contrasts with the sediment records from adjacent Pyramid Lake and Siesta Lake. The pronounced lowstand suggests that the Walker River that fills Walker Lake may have partially diverted into the Carson Sink through the Adrian paleochannel between 2700 to 1400??years B.P. ?? 2006 Elsevier B.V. All rights reserved.

Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study

PubMed Central

Gascuel, Olivier

2017-01-01

Inferring epidemiological parameters such as the R0 from time-scaled phylogenies is a timely challenge. Most current approaches rely on likelihood functions, which raise specific issues that range from computing these functions to finding their maxima numerically. Here, we present a new regression-based Approximate Bayesian Computation (ABC) approach, which we base on a large variety of summary statistics intended to capture the information contained in the phylogeny and its corresponding lineage-through-time plot. The regression step involves the Least Absolute Shrinkage and Selection Operator (LASSO) method, which is a robust machine learning technique. It allows us to readily deal with the large number of summary statistics, while avoiding resorting to Markov Chain Monte Carlo (MCMC) techniques. To compare our approach to existing ones, we simulated target trees under a variety of epidemiological models and settings, and inferred parameters of interest using the same priors. We found that, for large phylogenies, the accuracy of our regression-ABC is comparable to that of likelihood-based approaches involving birth-death processes implemented in BEAST2. Our approach even outperformed these when inferring the host population size with a Susceptible-Infected-Removed epidemiological model. It also clearly outperformed a recent kernel-ABC approach when assuming a Susceptible-Infected epidemiological model with two host types. Lastly, by re-analyzing data from the early stages of the recent Ebola epidemic in Sierra Leone, we showed that regression-ABC provides more realistic estimates for the duration parameters (latency and infectiousness) than the likelihood-based method. Overall, ABC based on a large variety of summary statistics and a regression method able to perform variable selection and avoid overfitting is a promising approach to analyze large phylogenies. PMID:28263987

Bathythermal habitat use by strains of Great Lakes- and Finger Lakes-origin lake trout in Lake Huron after a change in prey fish abundance and composition

USGS Publications Warehouse

Bergstedt, Roger A.; Argyle, Ray L.; Krueger, Charles C.; Taylor, William W.

2012-01-01

A study conducted in Lake Huron during October 1998–June 2001 found that strains of Great Lakes-origin (GLO) lake trout Salvelinus namaycush occupied significantly higher temperatures than did Finger Lakes-origin (FLO; New York) lake trout based on data from archival (or data storage) telemetry tags that recorded only temperature. During 2002 and 2003, we implanted archival tags that recorded depth as well as temperature in GLO and FLO lake trout in Lake Huron. Data subsequently recorded by those tags spanned 2002–2005. Based on those data, we examined whether temperatures and depths occupied by GLO and FLO lake trout differed during 2002–2005. Temperatures occupied during those years were also compared with occupied temperatures reported for 1998–2001, before a substantial decline in prey fish biomass. Temperatures occupied by GLO lake trout were again significantly higher than those occupied by FLO lake trout. This result supports the conclusion of the previous study. The GLO lake trout also occupied significantly shallower depths than FLO lake trout. In 2002–2005, both GLO and FLO lake trout occupied significantly lower temperatures than they did in 1998–2001. Aside from the sharp decline in prey fish biomass between study periods, the formerly abundant pelagic alewife Alosa pseudoharengus virtually disappeared and the demersal round goby Neogobius melanostomus invaded the lake and became locally abundant. The lower temperatures occupied by lake trout in Lake Huron during 2002–2005 may be attributable to changes in the composition of the prey fish community, food scarcity (i.e., a retreat to cooler water could increase conversion efficiency), or both.

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.

Porewater salinity reveals past lake-level changes in Lake Van, the Earth's largest soda lake.

PubMed

Tomonaga, Yama; Brennwald, Matthias S; Livingstone, David M; Kwiecien, Olga; Randlett, Marie-Ève; Stockhecke, Mona; Unwin, Katie; Anselmetti, Flavio S; Beer, Jürg; Haug, Gerald H; Schubert, Carsten J; Sturm, Mike; Kipfer, Rolf

2017-03-22

In closed-basin lakes, sediment porewater salinity can potentially be used as a conservative tracer to reconstruct past fluctuations in lake level. However, until now, porewater salinity profiles did not allow quantitative estimates of past lake-level changes because, in contrast to the oceans, significant salinity changes (e.g., local concentration minima and maxima) had never been observed in lacustrine sediments. Here we show that the salinity measured in the sediment pore water of Lake Van (Turkey) allows straightforward reconstruction of two major transgressions and a major regression that occurred during the last 250 ka. We observed strong changes in the vertical salinity profiles of the pore water of the uppermost 100 m of the sediments in Lake Van. As the salinity balance of Lake Van is almost at steady-state, these salinity changes indicate major lake-level changes in the past. In line with previous studies on lake terraces and with seismic and sedimentological surveys, we identify two major transgressions of up to +105 m with respect to the current lake level at about 135 ka BP and 248 ka BP starting at the onset of the two previous interglacials (MIS5e and MIS7), and a major regression of about -200 m at about 30 ka BP during the last ice age.

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

Spatial and temporal genetic diversity of lake whitefish (Coregonus clupeaformis (Mitchill)) from Lake Huron and Lake Erie

USGS Publications Warehouse

Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Hartman, Travis; Johnson, Jim; Roseman, Edward F.

2013-01-01

Lake whitefish (Coregonus clupeaformis (Mitchill)) are important commercially, culturally, and ecologically in the Laurentian Great Lakes. Stocks of lake whitefish in the Great Lakes have recovered from low levels of abundance in the 1960s. Reductions in abundance, loss of habitat and environmental degradation can be accompanied by losses of genetic diversity and overall fitness that may persist even as populations recover demographically. Therefore, it is important to be able to identify stocks that have reduced levels of genetic diversity. In this study, we investigated patterns of genetic diversity at microsatellite DNA loci in lake whitefish collected between 1927 and 1929 (historical period) and between 1997 and 2005 (contemporary period) from Lake Huron and Lake Erie. Genetic analysis of lake whitefish from Lakes Huron and Erie shows that the amount of population structuring varies from lake to lake. Greater genetic divergences among collections from Lake Huron may be the result of sampling scale, migration patterns and demographic processes. Fluctuations in abundance of lake whitefish populations may have resulted in periods of increased genetic drift that have resulted in changes in allele frequencies over time, but periodic genetic drift was not severe enough to result in a significant loss of genetic diversity. Migration among stocks may have decreased levels of genetic differentiation while not completely obscuring stock boundaries. Recent changes in spatial boundaries to stocks, the number of stocks and life history characteristics of stocks further demonstrate the potential of coregonids for a swift and varied response to environmental change and emphasise the importance of incorporating both spatial and temporal considerations into management plans to ensure that diversity is preserved.

Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny

NASA Astrophysics Data System (ADS)

Misra, Navodit; Blelloch, Guy; Ravi, R.; Schwartz, Russell

Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from optimal. Practical exact methods, which yield exponential worst-case running times but generally much better times in practice, provide an important alternative. We report progress in this direction by introducing a provably optimal method for the weighted multi-state maximum parsimony phylogeny problem. The method is based on generalizing the notion of the Buneman graph, a construction key to efficient exact methods for binary sequences, so as to apply to sequences with arbitrary finite numbers of states with arbitrary state transition weights. We implement an integer linear programming (ILP) method for the multi-state problem using this generalized Buneman graph and demonstrate that the resulting method is able to solve data sets that are intractable by prior exact methods in run times comparable with popular heuristics. Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

PubMed Central

Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Laughinghouse, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, Douglas E.; Williams, Tiffani; Cranston, Karen A.

2015-01-01

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. PMID:26385966

Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes).

PubMed

Marki, Petter Z; Jønsson, Knud A; Irestedt, Martin; Nguyen, Jacqueline M T; Rahbek, Carsten; Fjeldså, Jon

2017-02-01

With nearly 300 species, the infraorder Meliphagides represents one of the largest and most conspicuous Australasian bird radiations. Although the group has been the focus of a number of recent phylogenetic studies, a comprehensive species-level phylogenetic hypothesis is still lacking. This has impeded the assessment of broad-scale evolutionary, biogeographic and ecological hypotheses. In the present study, we use a supermatrix approach including five mitochondrial and four nuclear markers to infer a time-calibrated phylogeny of the Meliphagides. Our phylogeny, which includes 286 of the 289 (99%) currently recognized species, is largely congruent with previous estimates. However, the addition of 60 newly sequenced species reveals some novel relationships. Our biogeographic analyses suggest an Australian origin for the group in the early Oligocene (31.3Mya, 95% HPD 25.2-38.2Mya). In addition, we find that dispersal events out of Australia have been numerous and frequent, particularly to New Guinea, which has also been the source of multiple back-colonizations to the Australian mainland. The phylogeny provides an important framework for studying a wide variety of macroecological and macroevolutionary themes, including character evolution, origin and timing of diversification, biogeographic patterns and species responses to climate change. Copyright © 2016 Elsevier Inc. All rights reserved.

Movements of hatchery-reared lake trout in Lake Superior

USGS Publications Warehouse

Pycha, Richard L.; Dryer, William R.; King, George R.

1965-01-01

The history of stocking of lake trout (Salvelinus namaycush) in the Great Lakes is reviewed. The study of movements is based on capture of 24,275 fin-clipped lake trout taken in experimental gill nets and trawls and commercial gill nets. Yearling lake trout planted from shore dispersed to 15-fath (27-m) depths in 3A? hr. Most fish remained within 2 miles (3.2 km) of the planting site 2 months, but within 4 months some fish had moved as much as 17 miles (27 km). The highest abundance of planted lake trout was in areas 2-4 miles (3.2-6.4 km) from the planting site even 3 years after release. Distance moved and size of fish were not correlated. Dispersal of lake trout begins at planting and probably continues until the fish are mature. Most movement was eastward in southern Lake Superior and followed the counterclockwise surface currents. Movement is most rapid in areas of strong currents and slowest in areas of weak currents or eddies. Movement to areas west of the Keweenaw Peninsula was insignificant from plantings in Keweenaw Bay and nil from other plantings farther east. Lake trout planted in the eastern third of the lake dispersed more randomly than those planted farther west. Few fish moved farther offshore than the 50-fath (91-m) contour. Lake trout planted in Canadian waters made insignificant contributions to populations in US waters.

A new theory of phylogeny inference through construction of multidimensional vector space.

PubMed

Kitazoe, Y; Kurihara, Y; Narita, Y; Okuhara, Y; Tominaga, A; Suzuki, T

2001-05-01

Here, a new theory of molecular phylogeny is developed in a multidimensional vector space (MVS). The molecular evolution is represented as a successive splitting of branch vectors in the MVS. The end points of these vectors are the extant species and indicate the specific directions reflected by their individual histories of evolution in the past. This representation makes it possible to infer the phylogeny (evolutionary histories) from the spatial positions of the end points. Search vectors are introduced to draw out the groups of species distributed around them. These groups are classified according to the nearby order of branches with them. A law of physics is applied to determine the species positions in the MVS. The species are regarded as the particles moving in time according to the equation of motion, finally falling into the lowest-energy state in spite of their randomly distributed initial condition. This falling into the ground state results in the construction of an MVS in which the relative distances between two particles are equal to the substitution distances. The species positions are obtained prior to the phylogeny inference. Therefore, as the number of species increases, the species vectors can be more specific in an MVS of a larger size, such that the vector analysis gives a more stable and reliable topology. The efficacy of the present method was examined by using computer simulations of molecular evolution in which all the branch- and end-point sequences of the trees are known in advance. In the phylogeny inference from the end points with 100 multiple data sets, the present method consistently reconstructed the correct topologies, in contrast to standard methods. In applications to 185 vertebrates in the alpha-hemoglobin, the vector analysis drew out the two lineage groups of birds and mammals. A core member of the mammalian radiation appeared at the base of the mammalian lineage. Squamates were isolated from the bird lineage to compose the

Energy density of lake whitefish Coregonus clupeaformis in Lakes Huron and Michigan

USGS Publications Warehouse

Pothoven, S.A.; Nalepa, T.F.; Madenjian, C.P.; Rediske, R.R.; Schneeberger, P.J.; He, J.X.

2006-01-01

We collected lake whitefish Coregonus clupeaformis off Alpena and Tawas City, Michigan, USA in Lake Huron and off Muskegon, Michigan USA in Lake Michigan during 2002–2004. We determined energy density and percent dry weight for lake whitefish from both lakes and lipid content for Lake Michigan fish. Energy density increased with increasing fish weight up to 800 g, and then remained relatively constant with further increases in fish weight. Energy density, adjusted for weight, was lower in Lake Huron than in Lake Michigan for both small (≤800 g) and large fish (>800 g). Energy density did not differ seasonally for small or large lake whitefish or between adult male and female fish. Energy density was strongly correlated with percent dry weight and percent lipid content. Based on data from commercially caught lake whitefish, body condition was lower in Lake Huron than Lake Michigan during 1981–2003, indicating that the dissimilarity in body condition between the lakes could be long standing. Energy density and lipid content in 2002–2004 in Lake Michigan were lower than data for comparable sized fish collected in 1969–1971. Differences in energy density between lakes were attributed to variation in diet and prey energy content as well as factors that affect feeding rates such as lake whitefish density and prey abundance.

Effects of lake trout refuges on lake whitefish and cisco in the Apostle Islands Region of Lake Superior

USGS Publications Warehouse

Zuccarino-Crowe , Chiara M.; Taylor, William W.; Hansen, Michael J.; Seider, Michael J.; Krueger, Charles C.

2016-01-01

Lake trout refuges in the Apostle Islands region of Lake Superior are analogous to the concept of marine protected areas. These refuges, established specifically for lake trout (Salvelinus namaycush) and closed to most forms of recreational and commercial fishing, were implicated as one of several management actions leading to successful rehabilitation of Lake Superior lake trout. To investigate the potential significance of Gull Island Shoal and Devils Island Shoal refuges for populations of not only lake trout but also other fish species, relative abundances of lake trout, lake whitefish (Coregonus clupeaformis), and cisco (Coregonus artedi) were compared between areas sampled inside versus outside of refuge boundaries. During 1982–2010, lake trout relative abundance was higher and increased faster inside the refuges, where lake trout fishing was prohibited, than outside the refuges. Over the same period, lake whitefish relative abundance increased faster inside than outside the refuges. Both evaluations provided clear evidence that refuges protected these species. In contrast, trends in relative abundance of cisco, a prey item of lake trout, did not differ significantly between areas inside and outside the refuges. This result did not suggest indirect or cascading refuge effects due to changes in predator levels. Overall, this study highlights the potential of species-specific refuges to benefit other fish species beyond those that were the refuges' original target. Improved understanding of refuge effects on multiple species of Great Lakes fishes can be valuable for developing rationales for refuge establishment and predicting associated fish community-level effects.

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.

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.

Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom.

PubMed

Bourlat, Sarah J; Nielsen, Claus; Economou, Andrew D; Telford, Maximilian J

2008-10-01

The new animal phylogeny inferred from ribosomal genes some years ago has prompted a number of radical rearrangements of the traditional, morphology based metazoan tree. The two main bilaterian clades, Deuterostomia and Protostomia, find strong support, but the protostomes consist of two sister groups, Ecdysozoa and Lophotrochozoa, not seen in morphology based trees. Although widely accepted, not all recent molecular phylogenetic analyses have supported the tripartite structure of the new animal phylogeny. Furthermore, even if the small ribosomal subunit (SSU) based phylogeny is correct, there is a frustrating lack of resolution of relationships between the phyla that make up the three clades of this tree. To address this issue, we have assembled a dataset including a large number of aligned sequence positions as well as a broad sampling of metazoan phyla. Our dataset consists of sequence data from ribosomal and mitochondrial genes combined with new data from protein coding genes (5139 amino acid and 3524 nucleotide positions in total) from 37 representative taxa sampled across the Metazoa. Our data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda. We also provide some resolution within the Lophotrochozoa, where we confirm support for a monophyletic clade of Echiura, Sipuncula and Annelida and surprising evidence of a close relationship between Brachiopoda and Nemertea.

Radiographic film dosimetry of proton beams for depth‐dose constancy check and beam profile measurement

PubMed Central

Teran, Anthony; Ghebremedhin, Abiel; Johnson, Matt; Patyal, Baldev

2015-01-01

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 5 mm; the distal edge was reproducible within 1 mm. At 5 cm depth, the

Spatial Updating and the Maintenance of Visual Constancy

PubMed Central

Klier, Eliana M.; Angelaki, Dora E.

2008-01-01

Spatial updating is the means by which we keep track of the locations of objects in space even as we move. Four decades of research have shown that humans and non-human primates can take the amplitude and direction of intervening movements into account, including saccades (both head-fixed and head-free), pursuit, whole-body rotations and translations. At the neuronal level, spatial updating is thought to be maintained by receptive field locations that shift with changes in gaze and evidence for such shifts have been shown in several cortical areas. These regions receive information about the intervening movement from several sources including motor efference copies when a voluntary movement is made and vestibular/somatosensory signals when the body is in motion. Many of these updating signals arise from brainstem regions that monitor our ongoing movements and subsequently transmit this information to the cortex via pathways that likely include the thalamus. Several issues of debate include (1) the relative contribution of extra-retinal sensory and efference copy signals to spatial updating, (2) the source of an updating signal for real life, three-dimensional motion that cannot arise from brain areas encoding only two-dimensional commands, and (3) the reference frames used by the brain to integrate updating signals from various sources. This review highlights the relevant spatial updating studies and provides a summary of the field today. We find that spatial constancy is maintained by a highly evolved neural mechanism that keeps track of our movements, transmits this information to relevant brain regions, and then uses this information to change the way in which single neurons respond. In this way, we are able to keep track of relevant objects in the outside world and interact with them in meaningful ways. PMID:18786618

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…

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.

Reconnaissance data on lakes in the Alpine Lakes Wilderness Area, Washington

USGS Publications Warehouse

Dethier, David P.; Heller, Paul L.; Safioles, Sally A.

1979-01-01

Sixty lakes in the Alpine Lakes Wilderness Area have been sampled from rubber rafts or helicopter to obtain information on their physical setting and on present water-quality conditions. The lakes are located near the crest of the Cascade Range in Chelan and King Counties, Washington. Basic data from these lakes will be useful for planners concerned with lake and wilderness management, and of interest to hikers and other recreationists who use the lakes.

Phylogeny and species traits predict bird detectability

USGS Publications Warehouse

Solymos, Peter; Matsuoka, Steven M.; Stralberg, Diana; Barker, Nicole K. S.; Bayne, Erin M.

2018-01-01

Avian acoustic communication has resulted from evolutionary pressures and ecological constraints. We therefore expect that auditory detectability in birds might be predictable by species traits and phylogenetic relatedness. We evaluated the relationship between phylogeny, species traits, and field‐based estimates of the two processes that determine species detectability (singing rate and detection distance) for 141 bird species breeding in boreal North America. We used phylogenetic mixed models and cross‐validation to compare the relative merits of using trait data only, phylogeny only, or the combination of both to predict detectability. We found a strong phylogenetic signal in both singing rates and detection distances; however the strength of phylogenetic effects was less than expected under Brownian motion evolution. The evolution of behavioural traits that determine singing rates was found to be more labile, leaving more room for species to evolve independently, whereas detection distance was mostly determined by anatomy (i.e. body size) and thus the laws of physics. Our findings can help in disentangling how complex ecological and evolutionary mechanisms have shaped different aspects of detectability in boreal birds. Such information can greatly inform single‐ and multi‐species models but more work is required to better understand how to best correct possible biases in phylogenetic diversity and other community metrics.

The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes).

PubMed

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

2017-09-20

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

75 FR 20920 - Safety Zone; Lake Havasu Grand Prix, Lake Havasu, AZ

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-22

...-AA00 Safety Zone; Lake Havasu Grand Prix, Lake Havasu, AZ AGENCY: Coast Guard, DHS. ACTION: Temporary... of Lake Havasu on the Colorado River in Lake Havasu City, Arizona for the Lake Havasu Grand Prix... established in support of the Lake Havasu Grand Prix, a marine event that includes participating vessels...

Water-Balance Model to Simulate Historical Lake Levels for Lake Merced, California

NASA Astrophysics Data System (ADS)

Maley, M. P.; Onsoy, S.; Debroux, J.; Eagon, B.

2009-12-01

Lake Merced is a freshwater lake located in southwestern San Francisco, California. In the late 1980s and early 1990s, an extended, severe drought impacted the area that resulted in significant declines in Lake Merced lake levels that raised concerns about the long-term health of the lake. In response to these concerns, the Lake Merced Water Level Restoration Project was developed to evaluate an engineered solution to increase and maintain Lake Merced lake levels. The Lake Merced Lake-Level Model was developed to support the conceptual engineering design to restore lake levels. It is a spreadsheet-based water-balance model that performs monthly water-balance calculations based on the hydrological conceptual model. The model independently calculates each water-balance component based on available climate and hydrological data. The model objective was to develop a practical, rule-based approach for the water balance and to calibrate the model results to measured lake levels. The advantage of a rule-based approach is that once the rules are defined, they enhance the ability to then adapt the model for use in future-case simulations. The model was calibrated to historical lake levels over a 70-year period from 1939 to 2009. Calibrating the model over this long historical range tested the model over a variety of hydrological conditions including wet, normal and dry precipitation years, flood events, and periods of high and low lake levels. The historical lake level range was over 16 feet. The model calibration of historical to simulated lake levels had a residual mean of 0.02 feet and an absolute residual mean of 0.42 feet. More importantly, the model demonstrated the ability to simulate both long-term and short-term trends with a strong correlation of the magnitude for both annual and seasonal fluctuations in lake levels. The calibration results demonstrate an improved conceptual understanding of the key hydrological factors that control lake levels, reduce uncertainty

Genome-Scale Phylogeny of the Alphavirus Genus Suggests a Marine Origin

PubMed Central

Palacios, G.; Tesh, R. B.; Savji, N.; Guzman, H.; Sherman, M.; Weaver, S. C.; Lipkin, W. I.

2012-01-01

The genus Alphavirus comprises a diverse group of viruses, including some that cause severe disease. Using full-length sequences of all known alphaviruses, we produced a robust and comprehensive phylogeny of the Alphavirus genus, presenting a more complete evolutionary history of these viruses compared to previous studies based on partial sequences. Our phylogeny suggests the origin of the alphaviruses occurred in the southern oceans and spread equally through the Old and New World. Since lice appear to be involved in aquatic alphavirus transmission, it is possible that we are missing a louse-borne branch of the alphaviruses. Complete genome sequencing of all members of the genus also revealed conserved residues forming the structural basis of the E1 and E2 protein dimers. PMID:22190718

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.

`Inter-Arrival Time' Inspired Algorithm and its Application in Clustering and Molecular Phylogeny

NASA Astrophysics Data System (ADS)

Kolekar, Pandurang S.; Kale, Mohan M.; Kulkarni-Kale, Urmila

2010-10-01

Bioinformatics, being multidisciplinary field, involves applications of various methods from allied areas of Science for data mining using computational approaches. Clustering and molecular phylogeny is one of the key areas in Bioinformatics, which help in study of classification and evolution of organisms. Molecular phylogeny algorithms can be divided into distance based and character based methods. But most of these methods are dependent on pre-alignment of sequences and become computationally intensive with increase in size of data and hence demand alternative efficient approaches. `Inter arrival time distribution' (IATD) is a popular concept in the theory of stochastic system modeling but its potential in molecular data analysis has not been fully explored. The present study reports application of IATD in Bioinformatics for clustering and molecular phylogeny. The proposed method provides IATDs of nucleotides in genomic sequences. The distance function based on statistical parameters of IATDs is proposed and distance matrix thus obtained is used for the purpose of clustering and molecular phylogeny. The method is applied on a dataset of 3' non-coding region sequences (NCR) of Dengue virus type 3 (DENV-3), subtype III, reported in 2008. The phylogram thus obtained revealed the geographical distribution of DENV-3 isolates. Sri Lankan DENV-3 isolates were further observed to be clustered in two sub-clades corresponding to pre and post Dengue hemorrhagic fever emergence groups. These results are consistent with those reported earlier, which are obtained using pre-aligned sequence data as an input. These findings encourage applications of the IATD based method in molecular phylogenetic analysis in particular and data mining in general.

Relationships of Reproductive Traits With the Phylogeny of the African Noctuid Stem Borers

PubMed Central

Calatayud, Paul-André; Dupas, Stéphane; Frérot, Brigitte; Genestier, Gilles; Ahuya, Peter; Capdevielle-Dulac, Claire; Le Ru, Bruno

2016-01-01

The display of the reproductive behavior in most noctuid Lepidoptera follows a diel periodicity and is limited to a precise period of either the day or the night. These behavioral traits and the sex pheromone chemistry can be species specific and thus might be linked to the phylogeny. The objective of this study was to test the relationship of these reproductive traits with phylogeny. The study was undertaken using eight closely related species of noctuid stem borers, which are easy to rear under artificial conditions, namely, Busseola fusca, B. nairobica, B. sp. nr. segeta, Manga melanodonta, M. sp. nr. nubifera, Pirateolea piscator, Sesamia calamistis, and S. nonagrioides. For each species, the adult emergence period, the mating time, and the oviposition period were estimated, referred as biological traits. The components of the sex pheromones emitted by the females of each species were also analyzed by gas chromatography–mass spectrometry. Among the biological traits measured, only those linked to the oviposition pattern (timing and egg loads per night) were significantly correlated with the phylogeny of these species. For the sex pheromone components, among the 13 components identified in all species, only four, namely, Z9-tetradecenyl acetate (Z9-TDA), Z11-TDA, E11-TDA, and Z11-hexadecenyl acetate (Z11-HDA), showed the highest significant correlations with the phylogeny. These results suggest that among the different reproductive traits evaluated, only few are phylogenetically constrained. Their involvement in the reinforcement of ecological speciation in noctuid stem borers is discussed. PMID:27867304

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group.

PubMed

Singh, Reema; Schilde, Christina; Schaap, Pauline

2016-11-17

Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum

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)

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)

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.

Host and parasite morphology influence congruence between host and parasite phylogenies.

PubMed

Sweet, Andrew D; Bush, Sarah E; Gustafsson, Daniel R; Allen, Julie M; DiBlasi, Emily; Skeen, Heather R; Weckstein, Jason D; Johnson, Kevin P

2018-03-23

Comparisons of host and parasite phylogenies often show varying degrees of phylogenetic congruence. However, few studies have rigorously explored the factors driving this variation. Multiple factors such as host or parasite morphology may govern the degree of phylogenetic congruence. An ideal analysis for understanding the factors correlated with congruence would focus on a diverse host-parasite system for increased variation and statistical power. In this study, we focused on the Brueelia-complex, a diverse and widespread group of feather lice that primarily parasitise songbirds. We generated a molecular phylogeny of the lice and compared this tree with a phylogeny of their avian hosts. We also tested for the contribution of each host-parasite association to the overall congruence. The two trees overall were significantly congruent, but the contribution of individual associations to this congruence varied. To understand this variation, we developed a novel approach to test whether host, parasite or biogeographic factors were statistically associated with patterns of congruence. Both host plumage dimorphism and parasite ecomorphology were associated with patterns of congruence, whereas host body size, other plumage traits and biogeography were not. Our results lay the framework for future studies to further elucidate how these factors influence the process of host-parasite coevolution. Copyright © 2018 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Bathymetry of Bonnie Doone Lake, Kornbow Lake, Mintz Pond, and Glenville Lake, Cumberland County, North Carolina, 1996-98

USGS Publications Warehouse

Giorgino, M.J.; Strain, R.E.

1999-01-01

Bathymetric surveys were conducted at four water-supply impoundments of Little Cross Creek in Cumberland County, North Carolina. The surveys were conducted in April 1996 at Mintz Pond and Glenville Lake, and in January 1998 at Bonnie Doone Lake and Kornbow Lake. The resulting bathymetric maps are the first to cover the entire range in depth for these reservoirs and provide a framework for future evaluations of bathymetry and storage capacity. Bathymetric maps were constructed from depth and position data collected at each reservoir. A boat-mounted, research-grade fathometer was used to record water depths with a vertical accuracy of 0.1 foot. At Mintz Pond and Glenville Lake, position was measured by using a wide-band laser tracking system interfaced with a total station survey instrument. This positioning method required multiple land-based control points to be established and was hampered by line-of-sight restrictions between the control points and the boat. At Bonnie Doone Lake and Kornbow Lake, a global positioning system was used to collect differentially corrected location data. This positioning method enabled more rapid data collection, eliminated the need for land-based control points, and provided improved data coverage. Spillway elevations range from 172.8 feet above mean sea level at Bonnie Doone Lake to 113.1 feet at Glenville Lake. Surface area and storage volume were computed for each reservoir and were related to water-surface elevations at 1-foot intervals. The combined surface acreage of the four Little Cross Creek reservoirs at their full-pool elevations is 120.97 acres, consisting of 21.20 acres at Bonnie Doone Lake, 47.09 acres at Kornbow Lake, 15.56 acres at Mintz Pond, and 37.12 acres at Glenville Lake. The four reservoirs have a combined usable storage capacity of 674.91 acre-feet, which is the sum of 127.93 acre-feet in Bonnie Doone Lake, 320.62 acre-feet in Kornbow Lake, 53.25 acre-feet in Mintz Pond, and 173.11 acre-feet in Glenville Lake.

Lake trout in the Great Lakes: Basin-wide stock collapse and binational restoration

USGS Publications Warehouse

Hansen, Michael J.; Taylor, William W.; Ferreri, C. Paola

1999-01-01

The lake trout (Salvelinus namaycush) was important to the human settlement of each of the Great Lakes, and underwent catastrophic collapses in each lake in the nineteenth and twentieth centuries. The timing of lake trout stock collapses were different in each lake, as were the causes of the collapses, and have been the subject of much scientific inquiry and debate. The purpose of this chapter is to summarize and review pertinent information relating historical changes in Great Lakes lake trout stocks, binational efforts to restore those stocks, and progress toward stock restoration. This presentation attempts to generalize patterns across the Great Lakes, rather than to focus within each lake. Lake specific analyses have been used to understand lake specific causes and effects, but there is continuing debate about some of these causes and effects. A basinwide review may suggest mechanisms for observed changes that are not evident by lake specific analysis.

Evolutionary history of freshwater sculpins, genus Cottus (Teleostei; Cottidae) and related taxa, as inferred from mitochondrial DNA phylogeny.

PubMed

Yokoyama, Ryota; Goto, Akira

2005-09-01

The freshwater sculpins, genus Cottus (Teleostei; Cottidae), comprise bottom-dwelling fishes that exhibit various life-history styles, having radiated throughout Northern Hemisphere freshwater habitats. The phylogenetic relationships among Cottus and related taxa were estimated from mitochondrial DNA 12S rRNA and control region (CR) sequences, the freshwater sculpins examined falling into five lineages (A-E). Lineage A consisted of Trachidermus fasciatus and C. kazika, both having a catadromous life-history. The remaining species (lineages B-E) spawn in freshwater habitats regardless of life-history (amphidromous, lacustrine or fluvial), suggesting that the various life-history types post-dated a common ancestor of lineages B-E. Molecular clock estimates suggested a Pliocene-Pleistocene radiation (or Miocene-Pliocene from the alternative clock) of lineages B-E. In eastern Eurasia, speciation with life-history changes to amphidromous or fluvial styles has apparently occurred independently in some lineages, as a general pattern. Mitochondrial DNA CR phylogeny showed the monophyletic Baikalian cottoids (Cottoidei) to be nested within Cottus and Trachidermus, suggesting that the former ecologically and morphologically divergent cottoids may have originated from a single lineage which invaded the ancient lake.

GloboLakes: A global observatory of lake responses to environmental change.

NASA Astrophysics Data System (ADS)

Groom, Steve; Tyler, Andrew; Hunter, Peter; Spyrakos, Evangelos; Martinez-Vicente, Victor; Merchant, Chris; Cutler, Mark; Rowan, John; Dawson, Terry; Maberly, Stephen; Cavalho, Laurence; Elliot, Alex; Thackery, Stephen; Miller, Claire; Scott, Marian

2014-05-01

The world's freshwater ecosystems are vital components of the global biosphere, yet are vulnerable to climate and other human-induced change. There is increasing recognition that lakes play an important role in global biogeochemical cycling and provide key ecosystem services. However, our understanding of how lakes respond to environmental change at a global scale, and how this impacts on their status and function, is hampered by limited information on their chemical, physical and ecological condition. There are estimated to be over 300 million lakes globally, of which over 17,000 are greater than 10 km2 in surface area. These numbers have limited the systematic study of lake ecosystems. GloboLakes is a five-year UK research programme investigating the state of lakes and their response to climatic and other environmental drivers of change. It will establish a satellite-based observatory with archive and near-real time data processing to produce a time series of observed biogeochemical parameters and lake temperature for over 1000 lakes globally. This will be supported by linked ancillary data on climate and catchment land-use. The ability to monitor a large number of lakes consistently at high frequency and globally will facilitate a paradigm shift in our understanding of how lakes respond to environmental change at different spatial and temporal scales. A key requirement is to validate satellite retrieval algorithms and test the time-series of resulting lake properties such as chlorophyll-a by comparison with in situ data. To support the former extensive bio-optical and constituent data were taken in year 1 of the project in a number of UK lakes with a variety of trophic states. Furthermore, for wider validation activities GloboLakes has established the LIMNADES initiative to create a centralised database of ground bio-optical measurements of worldwide lakes through voluntary cooperation across the international scientific community. This presentation will

Live phylogeny with polytomies: Finding the most compact parsimonious trees.

PubMed

Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G

2017-08-01

Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Three-dimensional reconstruction and the phylogeny of extinct chelicerate orders

PubMed Central

Dunlop, Jason

2014-01-01

Arachnids are an important group of arthropods. They are: diverse and abundant; a major constituent of many terrestrial ecosystems; and possess a deep and extensive fossil record. In recent years a number of exceptionally preserved arachnid fossils have been investigated using tomography and associated techniques, providing valuable insights into their morphology. Here we use X-ray microtomography to reconstruct members of two extinct arachnid orders. In the Haptopoda, we demonstrate the presence of ‘clasp-knife’ chelicerae, and our novel redescription of a member of the Phalangiotarbida highlights leg details, but fails to resolve chelicerae in the group due to their small size. As a result of these reconstructions, tomographic studies of three-dimensionally preserved fossils now exist for three of the four extinct orders, and for fossil representatives of several extant ones. Such studies constitute a valuable source of high fidelity data for constructing phylogenies. To illustrate this, here we present a cladistic analysis of the chelicerates to accompany these reconstructions. This is based on a previously published matrix, expanded to include fossil taxa and relevant characters, and allows us to: cladistically place the extinct arachnid orders; explicitly test some earlier hypotheses from the literature; and demonstrate that the addition of fossils to phylogenetic analyses can have broad implications. Phylogenies based on chelicerate morphology—in contrast to molecular studies—have achieved elements of consensus in recent years. Our work suggests that these results are not robust to the addition of novel characters or fossil taxa. Hypotheses surrounding chelicerate phylogeny remain in a state of flux. PMID:25405073

Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae).

PubMed

Weng, Mao-Lun; Ruhlman, Tracey A; Gibby, Mary; Jansen, Robert K

2012-09-01

The phylogeny of 58 Pelargonium species was estimated using five plastid markers (rbcL, matK, ndhF, rpoC1, trnL-F) and one mitochondrial gene (nad5). The results confirmed the monophyly of three major clades and four subclades within Pelargonium but also indicate the need to revise some sectional classifications. This phylogeny was used to examine karyotype evolution in the genus: plotting chromosome sizes, numbers and 2C-values indicates that genome size is significantly correlated with chromosome size but not number. Accelerated rates of nucleotide substitution have been previously detected in both plastid and mitochondrial genes in Pelargonium, but sparse taxon sampling did not enable identification of the phylogenetic distribution of these elevated rates. Using the multigene phylogeny as a constraint, we investigated lineage- and locus-specific heterogeneity of substitution rates in Pelargonium for an expanded number of taxa and demonstrated that both plastid and mitochondrial genes have had accelerated substitution rates but with markedly disparate patterns. In the plastid, the exons of rpoC1 have significantly accelerated substitution rates compared to its intron and the acceleration was mainly due to nonsynonymous substitutions. In contrast, the mitochondrial gene, nad5, experienced substantial acceleration of synonymous substitution rates in three internal branches of Pelargonium, but this acceleration ceased in all terminal branches. Several lineages also have dN/dS ratios significantly greater than one for rpoC1, indicating that positive selection is acting on this gene, whereas the accelerated synonymous substitutions in the mitochondrial gene are the result of elevated mutation rates. Published by Elsevier Inc.

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae.

PubMed

Bernhardt, Nadine; Brassac, Jonathan; Kilian, Benjamin; Blattner, Frank R

2017-06-16

Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago. The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.

Watershed vs. within-lake drivers of nitrogen: phosphorus dynamics in shallow lakes.

PubMed

Ginger, Luke J; Zimmer, Kyle D; Herwig, Brian R; Hanson, Mark A; Hobbs, William O; Small, Gaston E; Cotner, James B

2017-10-01

Research on lake eutrophication often identifies variables affecting amounts of phosphorus (P) and nitrogen (N) in lakes, but understanding factors influencing N:P ratios is important given its influence on species composition and toxin production by cyanobacteria. We sampled 80 shallow lakes in Minnesota (USA) for three years to assess effects of watershed size, proportion of watershed as both row crop and natural area, fish biomass, and lake alternative state (turbid vs. clear) on total N : total P (TN : TP), ammonium, total dissolved phosphorus (TDP), and seston stoichiometry. We also examined N:P stoichiometry in 20 additional lakes that shifted states during the study. Last, we assessed the importance of denitrification by measuring denitrification rates in sediment cores from a subset of 34 lakes, and by measuring seston δ 15 N in four additional experimental lakes before and after they were experimentally manipulated from turbid to clear states. Results showed alternative state had the largest influence on overall N:P stoichiometry in these systems, as it had the strongest relationship with TN : TP, seston C:N:P, ammonium, and TDP. Turbid lakes had higher N at given levels of P than clear lakes, with TN and ammonium 2-fold and 1.4-fold higher in turbid lakes, respectively. In lakes that shifted states, TN was 3-fold higher in turbid lakes, while TP was only 2-fold higher, supporting the notion N is more responsive to state shifts than is P. Seston δ 15 N increased after lakes shifted to clear states, suggesting higher denitrification rates may be important for reducing N levels in clear states, and potential denitrification rates in sediment cores were among the highest recorded in the literature. Overall, our results indicate lake state was a primary driver of N:P dynamics in shallow lakes, and lakes in clear states had much lower N at a given level of P relative to turbid lakes, likely due to higher denitrification rates. Shallow lakes are often

Changes in Rongbuk lake and Imja lake in the Everest region of Himalaya

NASA Astrophysics Data System (ADS)

Chen, W.; Doko, T.; Liu, C.; Ichinose, T.; Fukui, H.; Feng, Q.; Gou, P.

2014-12-01

The Himalaya holds the world record in terms of range and elevation. It is one of the most extensively glacierized regions in the world except the Polar Regions. The Himalaya is a region sensitive to climate change. Changes in the glacial regime are indicators of global climate changes. Since the second half of the last century, most Himalayan glaciers have melted due to climate change. These changes directly affected the changes of glacial lakes in the Himalayan region due to the glacier retreat. New glacial lakes are formed, and a number of them have expanded in the Everest region of the Himalayas. This paper focuses on the two glacial lakes which are Imja Lake, located at the southern slope, and Rongbuk Lake, located at the northern slope in the Mt. Everest region, Himalaya to present the spatio-temporal changes from 1976 to 2008. Topographical conditions between two lakes were different (Kruskal-Wallis test, p < 0.05). Rongbuk Lake was located at 623 m higher than Imja Lake, and radiation of Rongbuk Lake was higher than the Imja Lake. Although size of Imja Lake was larger than the Rongbuk Lake in 2008, the growth speed of Rongbuk Lake was accelerating since 2000 and exceeds Imja Lake in 2000-2008. This trend of expansion of Rongbuk Lake is anticipated to be continued in the 21st century. Rongbuk Lake would be the biggest potential risk of glacial lake outburst flood (GLOF) at the Everest region of Himalaya in the future.

78 FR 17097 - Safety Zone; Lake Havasu Triathlon; Lake Havasu City, AZ

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-20

...-AA00 Safety Zone; Lake Havasu Triathlon; Lake Havasu City, AZ AGENCY: Coast Guard, DHS. ACTION... waters of Lake Havasu and the London Bridge Channel for the Lake Havasu Triathlon. This temporary safety... participants. The waterside swim course consists of 1500 meters in Lake Havasu and the London Bridge Channel...

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

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

PubMed

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.

Competition between larval lake herring (Coregonus artedi) and lake whitefish (Coregonus clupeaformis) for zooplankton

USGS Publications Warehouse

Davis, Bruce M.; Todd, Thomas N.

1998-01-01

Diet and growth of larval lake herring (Coregonus artedi) and lake whitefish (Coregonus clupeaformis) were compared in mesocosm experiments in a small mesotrophic lake in southeastern Michigan. Fish were sampled from single-species and mixed assemblages in 2-m3 cages for 8 weeks during April and May. Both species initially ate mostly cyclopoid copepodites and small cladocerans (Bosmia spp.). Schoener's index of diet overlap showed considerable overlap (70-90%). Lake whitefish ate Daphnia spp. and adult copepods about 2 weeks earlier than did lake herring, perhaps related to their larger mean mouth gape. Lake whitefish were consistently larger than lake herring until the eighth week, especially in the sympatric treatments. Lake whitefish appeared to have a negative effect on the growth of lake herring, as lake herring in mixed-species treatments were smaller and weighed less than lake herring reared in single-species treatments. The diet similarities of lake whitefish and lake herring larvae could make them competitors for food in the Great Lakes. The greater initial size of lake whitefish could allow them to eat larger prey earlier and thereby limit availability of these prey to lake herring at a crucial period of development.

The Morphometry of Lake Palmas, a Deep Natural Lake in Brazil

PubMed Central

Barroso, Gilberto F.; Gonçalves, Monica A.; Garcia, Fábio da C.

2014-01-01

Lake Palmas (A = 10.3km2) is located in the Lower Doce River Valley (LDRV), on the southeastern coast of Brazil. The Lake District of the LDRV includes 90 lakes, whose basic geomorphology is associated with the alluvial valleys of the Barreiras Formation (Cenozoic, Neogene) and with the Holocene coastal plain. This study aimed to investigate the relationship of morphometry and thermal pattern of a LDRV deep lake, Lake Palmas. A bathymetric survey carried out in 2011 and the analysis of hydrographic and wind data with a geographic information system allowed the calculation of several metrics of lake morphometry. The vertical profiling of physical and chemical variables in the water column during the wet/warm and dry/mild cold seasons of 2011 to 2013 has furnished a better understanding of the influence of the lake morphometry on its structure and function. The overdeepened basin has a subrectangular elongated shape and is aligned in a NW-SE direction in an alluvial valley with a maximum depth (Zmax) of 50.7m, a volume of 2.2×108 m3 (0.22km3) and a mean depth (Zmv) of 21.4m. These metrics suggest Lake Palmas as the deepest natural lake in Brazil. Water column profiling has indicated strong physical and chemical stratification during the wet/warm season, with a hypoxic/anoxic layer occupying one-half of the lake volume. The warm monomictic pattern of Lake Palmas, which is in an accordance to deep tropical lakes, is determined by water column mixing during the dry and mild cold season, especially under the influence of a high effective fetch associated with the incidence of cold fronts. Lake Palmas has a very long theoretical retention time, with a mean of 19.4 years. The changes observed in the hydrological flows of the tributary rivers may disturb the ecological resilience of Lake Palmas. PMID:25406062

Embryotoxicity of Great Lakes lake trout extracts to developing rainbow trout

USGS Publications Warehouse

Wright, Peggy J.; Tillitt, Donald E.

1999-01-01

Planar halogenated hydrocarbons (PHHs), such as polychlorinated dibenzo-p-dioxins, dibenzofurans, and biphenyls are present in aquatic systems, and are known to produce adverse effects in fish. This study investigated the embryotoxicity of PHH mixtures through the nanoinjection of environmental extracts into newly fertilized eggs from two strains of rainbow trout. Organic extracts were obtained from whole adult lake trout collected from Lake Michigan in 1988 and Lake Superior in 1994. The graded doses of the final extracts used for injection were quantified as 2,3,7,8-tetrachlorodibenzo-p-dioxin toxic-equivalents (TEQs) based on the concentrations of dioxins, furans and non-o-PCBs in each, and as equivalent amounts found in the eggs of the original lake trout (eggEQ). Total TEQs in the lake trout were 14.7 pg TEQ/g in the Lake Michigan sample and 7.3 pg TEQ/g in the Lake Superior sample. The extract of the Lake Michigan lake trout was embryotoxic to rainbow trout; LD50 values were 35 eggEQ (15–90, 95% F.L.) in the Arlee strain and 14 eggEQ (5–99, 95% F.L.) in the Erwin strain of rainbow trout. The LD50 values of the Lake Michigan extract in either of these strains of rainbow trout fall within the actual range of TCDD LD50values based on TEQs. This indicates that an additive model of toxicity is appropriate to quantify PHHs in relation to early life stage mortality in fish. Gross lesions characteristic of exposure to PHHs (i.e. yolk-sac edema, craniofacial deformities, and hemorrhaging) increased in a dose-related manner. The lowest observable adverse effect concentrations (LOAEC) for these gross lesions and cumulative mortalities suggests that current concentrations of PHHs in lake trout from Lake Michigan are above a threshold for adverse effects and these compounds may have implications on the lack of recruitment in certain Great Lakes lake trout populations.

Great Lakes

NASA Image and Video Library

2017-12-08

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

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...

Molecular phylogeny of choanoflagellates, the sister group to Metazoa

PubMed Central

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

2008-01-01

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

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

2017-04-01

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. Copyright © 2016 Elsevier GmbH. All rights reserved.

Water-quality and lake-stage data for Wisconsin lakes, water year 2005

USGS Publications Warehouse

Rose, W.J.; Garn, H.S.; Goddard, G.L.; Marsh, S.B.; Olson, D.L.; Robertson, Dale M.

2006-01-01

The U.S. Geological Survey (USGS), in cooperation with local and other agencies, collects data at selected lakes throughout Wisconsin. These data, accumulated over many years, provide a data base for developing an improved understanding of the water quality of lakes. The purpose of this report is to provide information about the chemical and physical charac-teristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected include measure-ments of in-lake water quality and lake stage. Time series graphs of Secchi depths, surface total phosphorus and chlorophyll a concentrations collected during non-frozen periods are included for all lakes. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive infor-mation for each lake includes: location of the lake, area of the lake's watershed, period for which data are available, revisions to previously published records, and pertinent remarks.

Using Satellite Imagery to Monitor the Major Lakes; Case Study Lake Hamun

NASA Astrophysics Data System (ADS)

Norouzi, H.; Islam, R.; Bah, A.; AghaKouchak, A.

2015-12-01

Proper lakes function can ease the impact of floods and drought especially in arid and semi-arid regions. They are important environmentally and can directly affect human lives. Better understanding of the effect of climate change and human-driven changes on lakes would provide invaluable information for policy-makers and local people. As part of a comprehensive study, we aim to monitor the land-cover/ land-use changes in the world's major lakes using satellite observations. As a case study, Hamun Lake which is a pluvial Lake, also known as shallow Lake, located on the south-east of Iran and adjacent to Afghanistan, and Pakistan borders is investigated. The Lake is the main source of resources (agriculture, fishing and hunting) for the people around it and politically important in the region since it is shared among three different countries. The purpose of the research is to find the Lake's area from 1972 to 2015 and to see if any drought or water resources management has affected the lake. Analyzing satellites imagery from Landsat shows that the area of the Lake changes seasonally and intra-annually. Significant seasonal effects are found in 1975,1977, 1987, 1993, 1996, 1998, 2000, 2009 and 2011, as well as, substantial amount of shallow water is found throughout the years. The precipitation records as well as drought historical records are studied for the lake's basin. Meteorological studies suggest that the drought, decrease of rainfalls in the province and the improper management of the Lake have caused environmental, economic and geographical consequences. The results reveal that lake has experienced at least two prolong dryings since 1972 which drought cannot solely be blamed as main forcing factor.Proper lakes function can ease the impact of floods and drought especially in arid and semi-arid regions. They are important environmentally and can directly affect human lives. Better understanding of the effect of climate change and human-driven changes on lakes

A coupled lake-atmosphere model (CLAM) and its application to Lake Kinneret

NASA Astrophysics Data System (ADS)

Pan, Hai

1999-08-01

Kinneret is a 166-km2 lake located in Northern Israel, in the central part of the Jordan Valley, a corridor running from north to south, between the Galilee hills in the west and the Golan Heights in the east. Both the Galilee hills and the Golan Heights reach an elevation of about 400 m above mean sea level (MSL), and the lake is about -210 m (MSL). North of the lake is the mountainous area of the Hermon, culminating at about 2800 m (MSL). About 120 km south of it is the Dead Sea, which is about -410 m (MSL), and about 45 km west of it is the Mediterranean Sea. The complexity of the terrain, combined with relatively arid soil and various ground covers surrounding the lake, results in a very complicated system of atmospheric and lake processes. To understand this system, especially the processes affecting the atmosphere and lake dynamics and thermodynamics, and their effects on Lake Kinneret evaporation, a coupled lake-atmosphere model (CLAM) was developed and applied to the lake region. The CLAM is based on the Regional Atmospheric Modeling System (RAMS) and the oceanic S-coordinate Rutgers University Model (SCRUM). Energy, mass, and momentum are conserved at the interface between the atmosphere and the lake, and appropriate balance equations are applied there. In the atmospheric module, two nested grids are employed to simulate Northern Israel at a resolution of 4 x 4 km2, and the near-lake region at a resolution of 1 x 1 km 2. Synoptic conditions obtained from the National Meteorological Center (NMC) reanalysis are assimilated by the model. Soil moisture, which appears to have a significant impact on atmospheric circulation in this region, was transformed from the normalized difference vegetation index (NDVI). Observations collected during two summers above and inside the lake emphasize the good capability of CLAM to simulate surface fluxes and other microclimatic conditions, as well as lake temperature and currents. Although the lake is small (about 12-km wide

Bathymetric Surveys of Lake Arthur and Raccoon Lake, Pennsylvania, June 2007

USGS Publications Warehouse

Hittle, Clinton D.; Ruby, A. Thomas

2008-01-01

In spring of 2007, bathymetric surveys of two Pennsylvania State Park lakes were performed to collect accurate data sets of lake-bed elevations and to develop methods and techniques to conduct similar surveys across the state. The lake-bed elevations and associated geographical position data can be merged with land-surface elevations acquired through Light Detection and Ranging (LIDAR) techniques. Lake Arthur in Butler County and Raccoon Lake in Beaver County were selected for this initial data-collection activity. In order to establish accurate water-surface elevations during the surveys, benchmarks referenced to NAVD 88 were established on land at each lake by use of differential global positioning system (DGPS) surveys. Bathymetric data were collected using a single beam, 210 kilohertz (kHz) echo sounder and were coupled with the DGPS position data utilizing a computer software package. Transects of depth data were acquired at predetermined intervals on each lake, and the shoreline was delineated using a laser range finder and compass module. Final X, Y, Z coordinates of the geographic positions and lake-bed elevations were referenced to NAD 83 and NAVD 88 and are available to create bathymetric maps of the lakes.

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.

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.

Comparison of catch and lake trout bycatch in commercial trap nets and gill nets targeting lake whitefish in northern Lake Huron

USGS Publications Warehouse

Johnson, James E.; Ebener, Mark P.; Gebhardt, Kenneth; Bergstedt, Roger

2004-01-01

We compared seasonal lake whitefish catch rates, lake trout bycatch, and gearinduced lake trout mortality between commercial trap nets and gill nets in north-central Lake Huron. Onboard monitors recorded catches from 260 gill net and 96 trap net lifts from October 1998 through December 1999. Catch rates for lake whitefish were highest in fall for both gear types, reflecting proximity of spawning sites to the study area. Lake whitefish catch rates were also relatively high in spring but low in both gear types in summer. Lake trout were the principal bycatch species in both gears. The lake trout bycatch was lowest in both gear types in fall, highest in gill nets in spring, and highest in trap nets in summer. The ratio of lake trout to legal whitefish (the target species) was highest in summer and lowest in fall in both gear types. The high lake trout ratio in summer was due principally to low catch rates of lake whitefish. All but 3 of 186 live lake trout removed from trap net pots survived for at least two days of observation in laboratory tanks. Therefore, we estimated that post-release survival of trap netted lake trout that had not been entangled in the mesh was 98.4%. In addition, we accounted for stress-induced mortality for lake trout that were live at capture but entangled in the mesh of either gear type. Resulting estimates of lake trout survival were higher in trap nets (87.8%) than in gill nets (39.6%). The number of lake trout killed per lift was highest during summer in trap nets and during spring in gill nets. In trap nets, 85% of dead lake trout were observed to be entangled in the mesh of the pot or tunnels. Survival rates of lake trout in gill nets were higher in our study than reported by others, probably because our nets were hand lifted in a small boat. Our trap net-induced mortality estimates on lake trout were higher than those reported by others because we adjusted our estimates to account for post-release mortality caused by handling and

Lake levels, streamflow, and surface-water quality in the Devils Lake area, North Dakota

USGS Publications Warehouse

Wiche, Gregg J.

1996-01-01

The Devils Lake Basin is a 3,810-square-mile (mi2) closed basin (fig. 1) in the Red River of the North Basin. About 3,320 mi2 of the total 3,810 mi2 is tributary to Devils Lake; the remainder is tributary to Stump Lake.Since glaciation, the lake level of Devils Lake has fluctuated from about 1,457 feet (ft) above sea level (asl), the natural spill elevation of the lake to the Sheyenne River, to 1,400 ft asl (Aronow, 1957). Although no documented records of lake levels are available before 1867, Upham (1895, p. 595), on the basis of tree-ring chronology, indicated that the lake level was 1,441 ft asl in 1830. Lake levels were recorded sporadically from 1867 to 1901 when the U.S. Geological Survey established a gaging station on Devils Lake. From 1867 to the present (1996), the lake level has fluctuated between a maximum of 1,438.4 ft asl in 1867 and a minimum of 1,400.9 ft asl in 1940 (fig. 2). On July 31, 1996, the lake level was 1,437.8 ft asl, about 15.2 ft higher than the level recorded in February 1993 and the highest level in about 120 years.Since 1993, the lake level of Devils Lake (fig. 2) has risen rapidly in response to above-normal precipitation from the summer of 1993 to the present, and 30,000 acres of land around the lake have been flooded. The above-normal precipitation also has caused flooding elsewhere in the Devils Lake Basin. State highways near Devils Lake are being raised, and some local roads have been closed because of flooding.In response to the flooding, the Devils Lake Basin Interagency Task Force, comprised of many State and Federal agencies, was formed in 1995 to find and propose intermediate (5 years or less) solutions to reduce the effects of high lake levels. In addition to various planning studies being conducted by Federal agencies, the North Dakota State Water Commission has implemented a project to store water on small tracts of land and in the chain of lakes (Sweetwater Lake, Morrison Lake, Dry Lake, Mikes Lake, Chain Lake

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...

Water-quality and lake-stage data for Wisconsin lakes, water year 1996

USGS Publications Warehouse

,

1997-01-01

The purpose of this report is to provide information about the physical and chemical characteristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected includes measurements of lake stage and in-lake water quality. Graphs of Secchi depths, surface totalphosphorus and chlorophyll-a concentrations versus time are included for lakes with two or more years of data. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive information for each lake includes: location of the lake, drainage area of the lake's watershed, period for which data are available, revisions to previously published records, and pertinent remarks. Additional data, such as streamflow and water quality in tributary and outlet streams of some of the lakes, are published in another volume: "Water Resources Data-Wisconsin, 1996."

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.

PubMed

Kress, W John; Erickson, David L; Swenson, Nathan G; Thompson, Jill; Uriarte, Maria; Zimmerman, Jess K

2010-11-09

Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny. Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history. As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.

Phylogeny-guided (meta)genome mining approach for the targeted discovery of new microbial natural products.

PubMed

Kang, Hahk-Soo

2017-02-01

Genomics-based methods are now commonplace in natural products research. A phylogeny-guided mining approach provides a means to quickly screen a large number of microbial genomes or metagenomes in search of new biosynthetic gene clusters of interest. In this approach, biosynthetic genes serve as molecular markers, and phylogenetic trees built with known and unknown marker gene sequences are used to quickly prioritize biosynthetic gene clusters for their metabolites characterization. An increase in the use of this approach has been observed for the last couple of years along with the emergence of low cost sequencing technologies. The aim of this review is to discuss the basic concept of a phylogeny-guided mining approach, and also to provide examples in which this approach was successfully applied to discover new natural products from microbial genomes and metagenomes. I believe that the phylogeny-guided mining approach will continue to play an important role in genomics-based natural products research.

Delineation of sympatric morphotypes of lake trout in Lake Superior

USGS Publications Warehouse

Moore, Seth A.; Bronte, Charles R.

2001-01-01

Three morphotypes of lake trout Salvelinus namaycush are recognized in Lake Superior: lean, siscowet, and humper. Absolute morphotype assignment can be difficult. We used a size-free, whole-body morphometric analysis (truss protocol) to determine whether differences in body shape existed among lake trout morphotypes. Our results showed discrimination where traditional morphometric characters and meristic measurements failed to detect differences. Principal components analysis revealed some separation of all three morphotypes based on head and caudal peduncle shape, but it also indicated considerable overlap in score values. Humper lake trout have smaller caudal peduncle widths to head length and depth characters than do lean or siscowet lake trout. Lean lake trout had larger head measures to caudal widths, whereas siscowet had higher caudal peduncle to head measures. Backward stepwise discriminant function analysis retained two head measures, three midbody measures, and four caudal peduncle measures; correct classification rates when using these variables were 83% for leans, 80% for siscowets, and 83% for humpers, which suggests the measures we used for initial classification were consistent. Although clear ecological reasons for these differences are not readily apparent, patterns in misclassification rates may be consistent with evolutionary hypotheses for lake trout within the Laurentian Great Lakes.

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

PubMed

Dias, Zanoni; Goldenstein, Siome; Rocha, Anderson

2013-09-10

In the past few years, several near-duplicate detection methods appeared in the literature to identify the cohabiting versions of a given document online. Following this trend, there are some initial attempts to go beyond the detection task, and look into the structure of evolution within a set of related images overtime. In this paper, we aim at automatically identify the structure of relationships underlying the images, correctly reconstruct their past history and ancestry information, and group them in distinct trees of processing history. We introduce a new algorithm that automatically handles sets of images comprising different related images, and outputs the phylogeny trees (also known as a forest) associated with them. Image phylogeny algorithms have many applications such as finding the first image within a set posted online (useful for tracking copyright infringement perpetrators), hint at child pornography content creators, and narrowing down a list of suspects for online harassment using photographs. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

LakeMIP Kivu: Evaluating the representation of a large, deep tropical lake by a set of 1-dimensional lake models

NASA Astrophysics Data System (ADS)

Thiery, Wim; Stepanenko, Viktor; Darchambeau, François; Joehnk, Klaus; Martynov, Andrey; Mironov, Dmitrii; Perroud, Marjorie; van Lipzig, Nicole

2013-04-01

The African great lakes are of utmost importance for the local economy (fishing), as well as being essential to the survival of the local people. During the last decades, these lakes experienced fast changes in ecosystem structure and functioning and their future evolution is a major concern. In this study, for the first time a set of one-dimensional lake models are evaluated over East-Africa, in particular over Lake Kivu (2.28 °S; 28.98 °E). The unique limnology of meromictic Lake Kivu, with the importance of salinity and geothermal springs in a tropical high-altitude climate, presents a worthy challenge to the 1D-lake models currently involved in the Lake Model Intercomparison Project (LakeMIP). Furthermore, this experiment will serve as the basis for a future, more complex intercomparison, coupling lake models with atmospheric circulation models to analyse climate change effects on the lake. Meteorological observations from two automatic weather stations, one at Kamembe airport (Rwanda, 2003-2008), the other at ISP Bukavu (DRC, 2003-2011), are used to drive each of these models. For the evaluation, a unique dataset is used which contains over 150 temperature profiles recorded since 2002. The standard LakeMIP protocol is adapted to mirror the limnological conditions in Lake Kivu and to unify model parameters as far as possible. Since some lake models do not account for salinity and its effect upon lake stratification, two sets of simulations are performed with each model: one for the freshwater layer only (60 m) and one for the average lake depth (240 m) including salinity. Therewith, on the one hand it is investigated whether each model is able to reproduce the correct mixing regime in Lake Kivu and captures the controlling of this seasonality by the relative humidity, which constrains evaporation except during summer (JJA). On the other hand, the ability of different models to simulate salinity- and geothermal-induced effects upon deep water stratification is

Planetary Lake Lander - A Robotic Sentinel to Monitor a Remote Lake

NASA Technical Reports Server (NTRS)

Pedersen, Liam; Smith, Trey; Lee, Susan; Cabrol, Nathalie; Rose, Kevin

2012-01-01

The Planetary Lake Lander Project is studying the impact of rapid deglaciation at a high altitude alpine lake in the Andes, where disrupted environmental, physical, chemical, and biological cycles result in newly emerging natural patterns. The solar powered Lake Lander robot is designed to monitor the lake system and characterize both baseline characteristics and impacts of disturbance events such as storms and landslides. Lake Lander must use an onboard adaptive science-on-the-fly approach to return relevant data about these events to mission control without exceeding limited energy and bandwidth resources. Lake Lander carries weather sensors, cameras and a sonde that is winched up and down the water column to monitor temperature, dissolved oxygen, turbidity and other water quality parameters. Data from Lake Lander is returned via satellite and distributed to an international team of scientists via web-based ground data systems. Here, we describe the Lake Lander Project scientific goals, hardware design, ground data systems, and preliminary data from 2011. The adaptive science-on-the-fly system will be described in future papers.

Patterns of organochlorine contamination in lake trout from Wisconsin waters of the Great Lakes

USGS Publications Warehouse

Miller, Michael A.; Madenjian, Charles P.; Masnado, Robert G.

1992-01-01

To investigate spatial and temporal patterns of organochlorine contamination in lake trout from Wisconsin waters of the Great Lakes, we examined laboratory contaminant analysis data of muscle tissue samples from Lake Michigan (n=317) and Lake Superior (n=53) fish. Concentrations of polychlorinated biphenyls (PCBs), chlordane, and dieldrin, reported as mg/kg wet weight in 620 mm to 640 mm mean length Lake Michigan lake trout, decreased over time. Mean total PCB concentration declined exponentially from 9.7 in 1975 to 1.9 in 1990. Total chlordane concentration declined 63 percent from 0.48 in 1983 to 0.18 in 1990, and dieldrin declined 52 percent during this same period, from 0.21 to 0.10. The bioaccumulation rate of PCBs is significantly lower for lake trout inhabiting Lake Michigan's midlake reef complex, compared to lake trout from the nearshore waters of western Lake Michigan. Organochlorine compound concentrations were greater in Lake Michigan lake trout than Lake Superior fish. Lake Superior lean lake trout and siscowet exhibited similar rates of PCB bioaccumulation despite major differneces in muscle tissue lipid content between the two subspecies. The lack of a significant difference in the PCB bioaccumulation rates of lean trout and siscowet suggests that lipid content may not be an important factor influencing PCB bioaccumulation in lake trout, within the range of lipid concentrations observed. Relative concentrations of the various organochlorine contaminants found in lake trout were highly correlated, suggesting similar mass balance processes for these compounds. Evidence presented revealing spatial and temporal patterns of organochlorine contamination may be of value in reestablishing self-sustaining populations of lake trout in Lake Michigan.

Winter diet of lake herring (Coregonus artedi) in western Lake Superior

USGS Publications Warehouse

Link, Jason; Selgeby, James H.; Hoff, Michael H.; Haskell, Craig

1995-01-01

Lake herring (Coregonus artedi) and zooplankton samples were simultaneously collected through the ice in the Apostle Islands region of western Lake Superior to provide information on the winter feeding ecology of lake herring. Zooplankton constituted the entire diet of the 38 lake herring collected for this study. We found no evidence of piscivory, although it has been reported by anglers. Diet selectivities were calculated using a Wilcoxon signed-ranks test and showed a preference of lake herring for larger zooplankton, especially Diaptomus sicilis, whereas the smaller copepod,Cyclops bicuspidatus thomasi, and immature copepod stages were selected against. These data document that overwintering copepods are food for a broad size range of lake herring in winter.

Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China.

PubMed

Feng, Shang-Guo; Lu, Jiang-Jie; Gao, Ling; Liu, Jun-Jun; Wang, Hui-Zhong

2014-04-01

Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

PubMed Central

2013-01-01

Background The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. PMID:23627680

Mono Lake, California

NASA Image and Video Library

2017-03-24

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

Synthetic Musk Fragrances in Lake Erie and Lake Ontario Sediment Cores

PubMed Central

Peck, Aaron M.; Linebaugh, Emily K.; Hornbuckle, Keri C.

2009-01-01

Two sediment cores collected from Lake Ontario and Lake Erie were sectioned, dated, and analyzed for five polycyclic musk fragrances and two nitro musk fragrances. The polycyclic musk fragrances were HHCB (Galaxolide), AHTN (Tonalide), ATII (Traseolide), ADBI (Celestolide), and AHMI (Phantolide). The nitro musk fragrances were musk ketone and musk xylene. Chemical analysis was performed by gas chromatography/mass spectrometry (GC/MS) and results from Lake Erie were confirmed using gas chromatography/triple-quadrupole mass spectrometry (GC/MS/MS). The chemical signals observed at the two sampling locations were different from each other due primarily to large differences in the sedimentation rates at the two sampling locations. HHCB was detected in the Lake Erie core while six compounds were detected in the Lake Ontario core. Using measured fragrance and 210Pb activity, the burden of synthetic musk fragrances estimated from these sediment cores is 1900 kg in Lake Erie and 18000 kg in Lake Ontario. The input of these compounds to the lakes is increasing. The HHCB accumulation rates in Lake Erie for 1979-2003 and 1990-2003 correspond to doubling times of 16 ± 4 yr and 8 ± 2 yr, respectively. The results reflect current U.S. production trends for the sum of all fragrance compounds. PMID:17007119

Status of lake trout rehabilitation in the Northern Refuge of Lake Michigan

USGS Publications Warehouse

Madenjian, Charles P.; DeSorcie, Timothy J.

1999-01-01

The Northern Refuge in Lake Michigan was established in 1985 as part of a rehabilitation program to stock yearling lake trout Salvelinus namaycush in areas with the best potential for success. Stocking of hatchery-reared lake trout within the refuge began in 1986 at three reefs: Boulder Reef, Gull Island Reef, and Richards Reef. On each reef from 1991 to 1997 we conducted gill-net surveys during the fall spawning season to evaluate performance of adult lake trout, and we conducted beam trawl surveys for naturally reproduced age-0 lake trout in the spring. Criteria to evaluate performance included spawner density, growth, maturity, and mortality. We found no evidence of natural reproduction by lake trout from our surveys. Nevertheless, density of spawning lake trout on Boulder Reef (69 fish/305 m of gill net/night) and Gull Island Reef (34 fish/305 m of gill net/night) appeared to be sufficiently high to initiate a self-sustaining population. Growth and maturity rates of lake trout in the Northern Refuge were similar to those for lake trout stocked in the nearshore region of Lake Michigan. In the Northern Refuge, growth rate for the Marquette strain of lake trout was slightly higher than for the Lewis Lake strain. Annual mortality estimates from catch curve analyses ranged from 0.46 to 0.41, and therefore, these estimates approached a level that was considered to be sufficiently low to allow for a self-sustaining population. Thus, it appeared that the lack of evidence for natural reproduction by lake trout in the Northern Refuge should not be attributed to inability of the population to attain a sufficiently large stock of spawners.

Water-Quality and Lake-Stage Data for Wisconsin Lakes, Water Year 2007

USGS Publications Warehouse

Wisconsin Water Science Center Lake-Studies Team: Rose, W. J.; Garn, H.S.; Goddard, G.L.; Marsh, S.B.; Olson, D.L.; Robertson, Dale M.

2008-01-01

The U.S. Geological Survey (USGS), in cooperation with local and other agencies, collects data at selected lakes throughout Wisconsin. These data, accumulated over many years, provide a data base for developing an improved understanding of the water quality of lakes. To make these data available to interested parties outside the USGS, the data are published annually in this report series. The locations of water-quality and lake-stage stations in Wisconsin for water year 2007 are shown in figure 1. A water year is the 12-month period from October 1 through September 30. It is designated by the calendar year in which it ends. Thus, the period October 1, 2005 through September 30, 2007 is called 'water year 2007.' The purpose of this report is to provide information about the chemical and physical characteristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected include measurements of in-lake water quality and lake stage. Time series of Secchi depths, surface total phosphorus and chlorophyll a concentrations collected during non-frozen periods are included for all lakes. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive information for each lake includes: location of the lake, area of the lake?s watershed, period for which data are available, revisions to previously published records, and pertinent remarks. Additional data, such as streamflow and water quality in tributary and outlet streams of some of the lakes, are published in another volume: 'Water Resources Data-Wisconsin, 2007.'

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

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.

PubMed

Ahrenfeldt, Johanne; Skaarup, Carina; Hasman, Henrik; Pedersen, Anders Gorm; Aarestrup, Frank Møller; Lund, Ole

2017-01-05

Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods. Our aim was to create a benchmark data set that mimics sequencing data of the sort that might be collected during an outbreak of an infectious disease. This was achieved by letting an E. coli hypermutator strain grow in the lab for 8 consecutive days, each day splitting the culture in two while also collecting samples for sequencing. The result is a data set consisting of 101 whole genome sequences with known phylogenetic relationship. Among the sequenced samples 51 correspond to internal nodes in the phylogeny because they are ancestral, while the remaining 50 correspond to leaves. We also used the newly created data set to compare three different online available methods that infer phylogenies from whole-genome sequencing reads: NDtree, CSI Phylogeny and REALPHY. One complication when comparing the output of these methods with the known phylogeny is that phylogenetic methods typically build trees where all observed sequences are placed as leafs, even though some of them are in fact ancestral. We therefore devised a method for post processing the inferred trees by collapsing short branches (thus relocating some leafs to internal nodes), and also present two new measures of tree similarity that takes into account the identity of both internal and leaf nodes. Based on this analysis we find that, among the investigated methods, CSI Phylogeny had the best performance, correctly identifying 73% of all branches in the

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.

Phylogeny of Selaginellaceae: There is value in morphology after all!

PubMed

Weststrand, Stina; Korall, Petra

2016-12-01

The cosmopolitan lycophyte family Selaginellaceae, dating back to the Late Devonian-Early Carboniferous, is notorious for its many species with a seemingly undifferentiated gross morphology. This morphological stasis has for a long time hampered our understanding of the evolutionary history of the single genus Selaginella. Here we present a large-scale phylogenetic analysis of Selaginella, and based on the resulting phylogeny, we discuss morphological evolution in the group. We sampled about one-third of the approximately 750 recognized Selaginella species. Evolutionary relationships were inferred from both chloroplast (rbcL) and single-copy nuclear gene data (pgiC and SQD1) using a Bayesian inference approach. The morphology of the group was studied and important features mapped onto the phylogeny. We present an overall well-supported phylogeny of Selaginella, and the phylogenetic positions of some previously problematic taxa (i.e., S. sinensis and allies) are now resolved with strong support. We show that even though the evolution of most morphological characters involves reversals and/or parallelisms, several characters are phylogenetically informative. Seven major clades are identified, which each can be uniquely diagnosed by a suite of morphological features. There is value in morphology after all! Our hypothesis of the evolutionary relationships of Selaginella is well founded based on DNA sequence data, as well as morphology, and is in line with previous findings. It will serve as a firm basis for further studies on Selaginella with respect to, e.g., the poorly known alpha taxonomy, as well as evolutionary questions such as historical biogeographic reconstructions. © 2016 Weststrand and Korall. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY 4.0).

Patterns of egg deposition by lake trout and lake whitefish at Tawas artificial Reef, Lake Huron, 1990-1993

USGS Publications Warehouse

Foster, N.R.; Kennedy, G.W.; Munawar, M.; Edsall, T.; Leach, J.

1995-01-01

In August 1987, the Michigan Department of Natural Resources (MDNR), with the help and co-sponsorship of Walleyes for Iosco County, constructed Tawas artificial reef to improve recreational fishing in Tawas Bay. Post-construction assessment in October, 1987, by the MDNR found twice as many adult lake trout in a gill net set on the reef as in a similar net set off the reef, indicating that lake trout already had begun to investigate this new habitat. Similar netting efforts in October 1989 caught three times as many adults on the reef as off it, even though the on-reef net was set for less than one third as long a period. Using a remotely operated vehicle (ROV), we detected prespawning aggregations of lake trout on the reef in fall 1989, and MDNR biologists set emergent fly traps on the reef in April-May 1990-1991. These fry traps captured several newly emerged lake trout and lake whitefish fry, demonstrating that eggs of both species has hatched successfully. Gill netting in 1992-1993 by U.S. Fish and Wildlife Service biologists netted large numbers of ripe lake trout in late October and ripe lake whitefish in early to mid-November. The purpose of this paper is to describe the relative quantities of eggs deposited and the spatial patterns of egg deposition by lake trout and lake whitefish at Tawas artificial reef during 1990-1993.

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

Lake Powell

NASA Image and Video Library

2007-09-20

The white ring around Lake Powell tells the story. The surface is down 98 feet. This is critical, because Powell, Lake Mead, and other lakes along the Colorado River provide water for millions of people in five states. We are in the eighth year of a drought on the Colorado River. This year was the driest year ever reported in Southern California, and there is a severe drought in Northern California, down to less than 30-percent of snow pack. This ASTER image of part of Lake Powell was acquired in 2001. The gray area depicts the shrunken, reduced 2007 lake extent compared to the extended, larger black area in 2001. The image covers an area of 24 x 30 km, and is centered near 37.1 degrees north latitude, 111.3 degrees west longitude. This image from NASA Terra satellite. http://photojournal.jpl.nasa.gov/catalog/PIA10614

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...

Hydrology of the Lake Deaton and Lake Okahumpka area, Northeast Sumter County, Florida

USGS Publications Warehouse

Simonds, Edward P.; German, E.R.

1980-01-01

The Floridan aquifer in the Lake Deaton and Lake Okahumpka area is 50 to 130 feet below land surface. During the 16-year period 1963-78 lake evaporation exceeded rainfall by 0.4 inches. Drainage from Lake Deaton and its surrounding area goes into Chitty Chatty Creek and on the Hogeye Sink when the altitude of the potentiometric surface of the Floridan aquifer is low. During a higher altitude of the Floridan potentiometric surface, Hogeye Sink may discharge water; this water, along with the normal runoff, goes into Lake Okahumpka. Average lake fluctuation is 1.5 to 2.0 feet per year. Lake Deaton supports a large population of blue-green algae and Lake Okahumpka is choked with aquatic plants. The water quality of the two lakes differ, with Lake Deaton having a sodium chloride water and Lake Okahumpka having a calcium bicarbonate water. Analysis of water and bottom material samples showed that only cadmium and mercury exceeded the Florida Department of Environmental Regulation 's criteria for Class III waters; however, the amounts detected were at or slightly above the limits of the analytical method. (USGS)

Strand-plain evidence for late Holocene lake-level variations in Lake Michigan

USGS Publications Warehouse

Thompson, T.A.; Baedke, S.J.

1997-01-01

Lake level is a primary control on shoreline behavior in Lake Michigan. The historical record from lake-level gauges is the most accurate source of information on past lake levels, but the short duration of the record does not permit the recognition of long-term patterns of lake-level change (longer than a decade or two). To extend the record of lake-level change, the internal architecture and timing of development of five strand plains of late Holocene beach ridges along the Lake Michigan coastline were studied. Relative lake-level curves for each site were constructed by determining the elevation of foreshore (swash zone) sediments in the beach ridges and by dating basal wetland sediments in the swales between ridges. These curves detect long-term (30+ yr) lake-level variations and differential isostatic adjustments over the past 4700 yr at a greater resolution than achieved by other studies. The average timing of beach-ridge development for all sites is between 29 and 38 yr/ridge. This correspondence occurs in spite of the embayments containing the strand plains being different in size, orientation, hydrographic regime, and available sediment type and caliber. If not coincidental, all sites responded to a lake-level fluctuation of a little more than three decades in duration and a range of 0.5 to 0.6 m. Most pronounced in the relative lake-level curves is a fluctuation of 120-180 yr in duration. This ???150 yr variation is defined by groups of four to six ridges that show a rise and fall in foreshore elevations of 0.5 to 1.5 m within the group. The 150 yr variation can be correlated between sites in the Lake Michigan basin. The ???30 and 150 yr fluctuations are superimposed on a long-term loss of water to the Lake Michigan basin and differential rates of isostatic adjustment.

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

Treesearch

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

2013-01-01

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

Water-Quality and Lake-Stage Data for Wisconsin Lakes, Water Year 2006

USGS Publications Warehouse

Rose, W.J.; Garn, H.S.; Goddard, G.L.; Marsh, S.B.; Olson, D.L.; Robertson, Dale M.

2007-01-01

The U.S. Geological Survey (USGS), in cooperation with local and other agencies, collects data at selected lakes throughout Wisconsin. These data, accumulated over many years, provide a data base for developing an improved understanding of the water quality of lakes. To make these data available to interested parties outside the USGS, the data are published annually in this report series. The locations of water-quality and lake-stage stations in Wisconsin for water year 2006 are shown in figure 1. A water year is the 12-month period from October 1 through September 30. It is designated by the calendar year in which it ends. Thus, the period October 1, 2005 through September 30, 2006 is called 'water year 2006.' The purpose of this report is to provide information about the chemical and physical characteristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected include measurements of in-lake water quality and lake stage. Time series of Secchi depths, surface total phosphorus and chlorophyll a concentrations collected during non-frozen periods are included for all lakes. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive information for each lake includes: location of the lake, area of the lake's watershed, period for which data are available, revisions to previously published records, and pertinent remarks. Additional data, such as streamflow and water quality in tributary and outlet streams of some of the lakes, are published in another volume: 'Water Resources Data-Wisconsin, 2006.' Water-resources data, including stage and discharge data at most streamflow-gaging stations, are available through the World Wide Web on the Internet. The Wisconsin Water Science Center's home page is at http://wi.water.usgs.gov/. Information on the

Diet and prey selection by Lake Superior lake trout during springs 1986-2001

USGS Publications Warehouse

Ray, B.A.; Hrabik, T.R.; Ebener, M.P.; Gorman, O.T.; Schreiner, D.R.; Schram, S.T.; Sitar, S.P.; Mattes, W.P.; Bronte, C.R.

2007-01-01

We describe the diet and prey selectivity of lean (Salvelinus namaycush namaycush) and siscowet lake trout (S. n. siscowet) collected during spring (April–June) from Lake Superior during 1986–2001. We estimated prey selectivity by comparing prey numerical abundance estimates from spring bottom trawl surveys and lake trout diet information in similar areas from spring gill net surveys conducted annually in Lake Superior. Rainbow smelt (Osmerus mordax) was the most common prey and was positively selected by both lean and siscowet lake trout throughout the study. Selection by lean lake trout for coregonine (Coregonus spp.) prey increased after 1991 and corresponded with a slight decrease in selection for rainbow smelt. Siscowet positively selected for rainbow smelt after 1998, a change that was coincident with the decrease in selection for this prey item by lean lake trout. However, diet overlap between lean and siscowet lake trout was not strong and did not change significantly over the study period. Rainbow smelt remains an important prey species for lake trout in Lake Superior despite declines in abundance.

Biology, population structure, and estimated forage requirements of lake trout in Lake Michigan

USGS Publications Warehouse

Eck, Gary W.; Wells, LaRue

1983-01-01

Data collected during successive years (1971-79) of sampling lake trout (Salvelinus namaycush) in Lake Michigan were used to develop statistics on lake trout growth, maturity, and mortality, and to quantify seasonal lake trout food and food availability. These statistics were then combined with data on lake trout year-class strengths and age-specific food conversion efficiencies to compute production and forage fish consumption by lake trout in Lake Michigan during the 1979 growing season (i.e., 15 May-1 December). An estimated standing stock of 1,486 metric tons (t) at the beginning of the growing season produced an estimated 1,129 t of fish flesh during the period. The lake trout consumed an estimated 3,037 t of forage fish, to which alewives (Alosa pseudoharengus) contributed about 71%, rainbow smelt (Osmerus mordax) 18%, and slimy sculpins (Cottus cognatus) 11%. Seasonal changes in bathymetric distributions of lake trout with respect to those of forage fish of a suitable size for prey were major determinants of the size and species compositions of fish in the seasonal diet of lake trout.

Lakes and lake-like waters of the Hawaiian Archipelago

USGS Publications Warehouse

Maciolek, J.A.

1982-01-01

This summary of Hawaiian lacustrine limnology is based on 12 years of field and literature surveys of archipelagic inland waters. Lakes here are distinguished from other standing waters by limits on surface oceanic area (> 0.1 ha) and depth (> 2 m), and by the absence of flatural surface oceanic connection. A variety of extinct and existing water bodies, sometimes referred to as lakes, are noted. Six lakes are described. Five of them are in crater basins, 3 are freshwater, and 2 are elevated (highest = 3969 m). The scarcity of elevated lakes results from general permeability of the substrata. Among the 6 lakes, surface areas range from 0.22 to 88 ha and maximum depths from 3 to 248 m. Naturally occurring aquatic biota generally is low in species diversity except for phytoplankton; fishes and submersed vascular plants are absent. Two lowland lakes, freshwater Green (Wai a Pele) and saline Kauhak6, are described for the first time. Profundal Kauhak6, 248 m deep, has a surface area of only 0.35 ha, which results in an extraordinary relative depth of 370%. It is permanently stratified, a condition apparently due primarily to the unique morphometry of its basin. 

Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference.

PubMed

Swain, Timothy D

2018-01-01

The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Relationship of Individual and Group Change: Ontogeny and Phylogeny in Biology.

ERIC Educational Resources Information Center

Gould, Steven Jay

1984-01-01

Considers the issue of parallels between ontogeny and phylogeny from an historical perspective. Discusses such parallels in relationship to two ontogenetic principles concerning recapitulation and sequence of stages. Differentiates between Piaget's use of the idea of recapitulation and Haeckel's biogenetic law. (Author/RH)

Ciscoes (Coregonus, subgenus Leucichthys) of the Laurentian Great Lakes and Lake Nipigon

USGS Publications Warehouse

Eshenroder, Randy L.; Vecsei, Paul; Gorman, Owen T.; Yule, Daniel; Pratt, Thomas C.; Mandrak, Nicholas E.; Bunnell, David B.; Muir, Andrew M.

2016-01-01

This study of the ciscoes (Coregonus, subgenus Leucichthys) of the Great Lakes and Lake Nipigon represents a furtherance through 2015 of field research initiated by Walter Koelz in 1917 and continued by Stanford Smith in the mid-1900s—a period spanning nearly a century. Like Koelz’s study, this work contains information on taxonomy, geographical distribution, ecology, and status of species (here considered forms). Of the seven currently recognized forms (C. artedi, C. hoyi, C. johannae, C. kiyi, C. nigripinnis, C. reighardi, and C. zenithicus) described by Koelz as major in his 1929 monograph, two (C. johannae and C. reighardi) are extinct. In addition, C. alpenae, described by Koelz but subsequently synonymized with C. zenithicus, although extinct, is recognized as valid making a total of eight major forms. Six of these forms, all but C. artedi and C. hoyi, have been lost from Lake Michigan, and seven have been lost from Lake Huron, leaving in Lake Huron only C. artedi and an introgressed deepwater form that we term a hybrid swarm. C. artedi appears, like its sister form C. alpenae, to have been lost from Lake Erie. Only C. artedi remains extant in Lake Ontario, its three sister forms (C. hoyi, C. kiyi, and C. reighardi) having disappeared long ago.Lakes Superior and Nipigon have retained their original species flocks consisting of four forms each: C. artedi, C. hoyi, and C. zenithicus in both lakes; C. kiyi in Lake Superior; and C. nigripinnis in Lake Nipigon. Morphological deviations from the morphotypes described by Koelz have been modest in contemporary samples. Overall, C. kiyi and C. artedi were the most morphologically stable forms while C. hoyi, C. nigripinnis, and C. zenithicus were the least stable. Although contemporary populations of C. artedi from Lakes Michigan and Huron are highly diverged from the morphotypes described by Koelz, the contemporary samples were of undescribed deep-bodied forms unlikely to have been sampled by Koelz because of

Phylogeny and biogeography of Hydra (Cnidaria: Hydridae) using mitochondrial and nuclear DNA sequences.

PubMed

Martínez, D E; Iñiguez, A R; Percell, K M; Willner, J B; Signorovitch, J; Campbell, R D

2010-10-01

The polyp hydra is ubiquitous in freshwater and is highly variable, with many species names assigned to different strains. Types of hydra do fall into four morphologically recognizable groups but many of the species determinations are confusing. To assess the diversity of hydra we collected 101 strains from six continents and built a phylogeny using three genetic markers. Each of the four well-defined groups of species represents a clade in our phylogeny. The green hydra group diverged first, followed by the braueri group and finally the sister groups vulgaris and oligactis. Each of eight species easily definable by morphological criteria represents a distinct clade in our phylogeny. Hydra of two clades, the green and the vulgaris hydra, are found on all continents (except Antarctica) and many islands, whereas hydra of the other two groups (braueri and oligactis) are restricted to the Northern Hemisphere. Our best estimate of the time of origin of hydra is about 60 Ma, long after the breakage of Pangea into northern and southern landmasses. Hydra appear to have diversified in the Northern Hemisphere, and their current diversity is greatest here. Two species were then able to disperse to the Southern Hemisphere, perhaps due to their thermal tolerance. Copyright 2010 Elsevier Inc. All rights reserved.

Sedimentary constraints on late Quaternary lake-level fluctuations at Bear Lake, Utah and Idaho

USGS Publications Warehouse

Smoot, J.P.; Rosenbaum, J.G.

2009-01-01

A variety of sedimentological evidence was used to construct the lake-level history for Bear Lake, Utah and Idaho, for the past ???25,000 years. Shorelines provide evidence of precise lake levels, but they are infrequently preserved and are poorly dated. For cored sediment similar to that in the modern lake, grain-size distributions provide estimates of past lake depths. Sedimentary textures provide a highly sensitive, continuous record of lake-level changes, but the modern distribution of fabrics is poorly constrained, and many ancient features have no modern analog. Combining the three types of data yields a more robust lake-level history than can be obtained from any one type alone. When smooth age-depth models are used, lake-level curves from multiple cores contain inconsistent intervals (i.e., one record indicates a rising lake level while another record indicates a falling lake level). These discrepancies were removed and the multiple records were combined into a single lake-level curve by developing age-depth relations that contain changes in deposition rate (i.e., gaps) where indicated by sedimentological evidence. The resultant curve shows that, prior to 18 ka, lake level was stable near the modern level, probably because the lake was overflowing. Between ca. 17.5 and 15.5 ka, lake level was ???40 m below the modern level, then fluctuated rapidly throughout the post-glacial interval. Following a brief rise centered ca. 15 ka ( = Raspberry Square phase), lake level lowered again to 15-20 m below modern from ca. 14.8-11.8 ka. This regression culminated in a lowstand to 40 m below modern ca. 12.5 ka, before a rapid rise to levels above modern ca. 11.5 ka. Lake level was typically lower than present throughout the Holocene, with pronounced lowstands 15-20 m below the modern level ca. 10-9, 7.0, 6.5-4.5, 3.5, 3.0-2.5, 2.0, and 1.5 ka. High lake levels near or above the modern lake occurred ca. 8.5-8.0, 7.0-6.5, 4.5-3.5, 2.5, and 0.7 ka. This lake-level history

Fat content of the flesh of siscowets and lake trout from Lake Superior

USGS Publications Warehouse

Eschmeyer, Paul H.; Phillips, Arthur M.

1965-01-01

Samples of flesh were excised from the middorsal region of 67 siscowets (Salvelinus namaycush siscowet) and 46 lake trout (Salvelinus n. namaycush) collected from Lake Superior. Chemical analysis of the samples revealed a range in fat content (dry weight) of 32.5 to 88.8 per cent in siscowets and 6.6 to 52.3 per cent in lake trout. Percentage fat increased progressively with increase in length of fish in both forms, but the average rate of increase was far greater for siscowets than for lake trout at lengths between 12 and 20 inches. Despite substantial individual variation, the percentage fat in the two forms was widely different and without overlap at all comparable lengths. The range in iodine number of the fat was 100 to 160 for siscowets and 103 to 161 for lake trout; average values were generally lower for siscowets than for lake trout among fish of comparable length. Percentage fat and relative weight were not correlated significantly in either subspecies. The fat content of flesh samples from a distinctive subpopulation of Lake Superior lake trout known as 'humpers' was more closely similar to that of typical lean lake trout than to siscowets, but the rate of increase in fat with increasing length was greater than for lean lake trout. Flesh samples from hatchery-reared stocks of lake trout, hybrid lake trout X siscowets, and siscowets tended to support the view that the wide difference in fat content between siscowets and lake trout is genetically determined.

Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis.

PubMed

Thirugnanasambantham, Krishnaraj; Saravanan, Subramanian; Karikalan, Kulandaivelu; Bharanidharan, Rajaraman; Lalitha, Perumal; Ilango, S; HairulIslam, Villianur Ibrahim

2015-10-01

Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-coding RNA with ability to regulate gene expression by bind the 3' UTR region of target mRNA and are evolved at different rates in different plant species. In this study we have utilized homology based computational approach and identified 27 mature miRNAs for the first time from this bio-medically important plant. The phylogenetic tree developed from binary data derived from the data on presence/absence of the identified miRNAs were noticed to be uncertain and biased. Most of the identified miRNAs were highly conserved among the plant species and sequence based phylogeny analysis of miRNAs resolved the above difficulties in phylogeny approach using miRNA. Predicted gene targets of the identified miRNAs revealed their importance in regulation of plant developmental process. Reported miRNAs held sequence conservation in mature miRNAs and the detailed phylogeny analysis of pre-miRNA sequences revealed genus specific segregation of clusters. Copyright © 2015 Elsevier Ltd. All rights reserved.

77 FR 9652 - Proposed CERCLA Administrative Cost Recovery Settlement; Lake Linden Superfund Site in Lake...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-17

... Settlement; Lake Linden Superfund Site in Lake Linden, Houghton County, MI AGENCY: Environmental Protection... concerning the Lake Linden Superfund Site in Lake Linden, Houghton County, Michigan with Honeywell Specialty...-6609. Comments should reference the Lake Linden Superfund Site in Lake Linden, Houghton County...

Quantifying Transmission Heterogeneity Using Both Pathogen Phylogenies and Incidence Time Series

PubMed Central

Li, Lucy M.; Grassly, Nicholas C.; Fraser, Christophe

2017-01-01

Abstract Heterogeneity in individual-level transmissibility can be quantified by the dispersion parameter k of the offspring distribution. Quantifying heterogeneity is important as it affects other parameter estimates, it modulates the degree of unpredictability of an epidemic, and it needs to be accounted for in models of infection control. Aggregated data such as incidence time series are often not sufficiently informative to estimate k. Incorporating phylogenetic analysis can help to estimate k concurrently with other epidemiological parameters. We have developed an inference framework that uses particle Markov Chain Monte Carlo to estimate k and other epidemiological parameters using both incidence time series and the pathogen phylogeny. Using the framework to fit a modified compartmental transmission model that includes the parameter k to simulated data, we found that more accurate and less biased estimates of the reproductive number were obtained by combining epidemiological and phylogenetic analyses. However, k was most accurately estimated using pathogen phylogeny alone. Accurately estimating k was necessary for unbiased estimates of the reproductive number, but it did not affect the accuracy of reporting probability and epidemic start date estimates. We further demonstrated that inference was possible in the presence of phylogenetic uncertainty by sampling from the posterior distribution of phylogenies. Finally, we used the inference framework to estimate transmission parameters from epidemiological and genetic data collected during a poliovirus outbreak. Despite the large degree of phylogenetic uncertainty, we demonstrated that incorporating phylogenetic data in parameter inference improved the accuracy and precision of estimates. PMID:28981709

Long-term simulations of dissolved oxygen concentrations in Lake Trout lakes

NASA Astrophysics Data System (ADS)

Jabbari, A.; Boegman, L.; MacKay, M.; Hadley, K.; Paterson, A.; Jeziorski, A.; Nelligan, C.; Smol, J. P.

2016-02-01

Lake Trout are a rare and valuable natural resource that are threatened by multiple environmental stressors. With the added threat of climate warming, there is growing concern among resource managers that increased thermal stratification will reduce the habitat quality of deep-water Lake Trout lakes through enhanced oxygen depletion. To address this issue, a three-part study is underway, which aims to: analyze sediment cores to understand the past, develop empirical formulae to model the present and apply computational models to forecast the future. This presentation reports on the computational modeling efforts. To this end, a simple dissolved oxygen sub-model has been embedded in the one-dimensional bulk mixed-layer thermodynamic Canadian Small Lake Model (CSLM). This model is currently being incorporated into the Canadian Land Surface Scheme (CLASS), the primary land surface component of Environment Canada's global and regional climate modelling systems. The oxygen model was calibrated and validated by hind-casting temperature and dissolved oxygen profiles from two Lake Trout lakes on the Canadian Shield. These data sets include 5 years of high-frequency (10 s to 10 min) data from Eagle Lake and 30 years of bi-weekly data from Harp Lake. Initial results show temperature and dissolved oxygen was predicted with root mean square error <1.5 °C and <3 mgL-1, respectively. Ongoing work is validating the model, over climate-change relevant timescales, against dissolved oxygen reconstructions from the sediment cores and predicting future deep-water temperature and dissolved oxygen concentrations in Canadian Lake Trout lakes under future climate change scenarios. This model will provide a useful tool for managers to ensure sustainable fishery resources for future generations.

A Dynamical Downscaling study over the Great Lakes Region Using WRF-Lake: Historical Simulation

NASA Astrophysics Data System (ADS)

Xiao, C.; Lofgren, B. M.

2014-12-01

As the largest group of fresh water bodies on Earth, the Laurentian Great Lakes have significant influence on local and regional weather and climate through their unique physical features compared with the surrounding land. Due to the limited spatial resolution and computational efficiency of general circulation models (GCMs), the Great Lakes are geometrically ignored or idealized into several grid cells in GCMs. Thus, the nested regional climate modeling (RCM) technique, known as dynamical downscaling, serves as a feasible solution to fill the gap. The latest Weather Research and Forecasting model (WRF) is employed to dynamically downscale the historical simulation produced by the Geophysical Fluid Dynamics Laboratory-Coupled Model (GFDL-CM3) from 1970-2005. An updated lake scheme originated from the Community Land Model is implemented in the latest WRF version 3.6. It is a one-dimensional mass and energy balance scheme with 20-25 model layers, including up to 5 snow layers on the lake ice, 10 water layers, and 10 soil layers on the lake bottom. The lake scheme is used with actual lake points and lake depth. The preliminary results show that WRF-Lake model, with a fine horizontal resolution and realistic lake representation, provides significantly improved hydroclimates, in terms of lake surface temperature, annual cycle of precipitation, ice content, and lake-effect snowfall. Those improvements suggest that better resolution of the lakes and the mesoscale process of lake-atmosphere interaction are crucial to understanding the climate and climate change in the Great Lakes region.

Survival of lake trout eggs and fry reared in water from the upper Great Lakes

USGS Publications Warehouse

Mac, Michael J.; Edsall, Carol Cotant; Seelye, James G.

1985-01-01

As part of continuing studies of the reproductive failure of lake trout (Salvelinus namaycush) in Lake Michigan, we measured the survival of lake trout eggs and fry of different origins and reared in different environments. Eggs and milt were stripped from spawning lake trout collected in the fall of 1980 from southeastern Lake Michigan, northwestern Lake Huron, south central Lake Superior, and from hatchery brood stock. Eggs from all sources were incubated, and the newly hatched fry were reared for 139 days in lake water from each of the three upper Great Lakes and in well water. Survival of eggs to hatching at all sites was lowest for those from Lake Michigan (70% of fertilized eggs) and highest for eggs from Lake Superior (96%). Comparisons of incubation water from the different lakes indicated that hatching success of eggs from all sources was highest in Lake Huron water, and lowest in Lake Michigan water. The most notable finding was the nearly total mortality of fry from eggs of southeastern Lake Michigan lake trout. At all sites, the mean survival of Lake Michigan fry through 139 days after hatching was only 4% compared to near 50% for fry from the other three sources. In a comparison of the rearing sites, little influence of water quality on fry survival was found. Thus, the poor survival was associated with the source of eggs and sperm, not the water in which the fry were reared.

The most acidified Austrian lake in comparison to a neutralized mining lake

PubMed Central

Moser, Michael; Weisse, Thomas

2011-01-01

This study investigated two mining lakes located in the north of Lower Austria. These lakes arose 45 years ago when open cast lignite mining ceased. The lakes are separated by a 7-m wide dam. Due to the oxidation of pyrite, both lakes have been acidified and exhibit iron, sulphate, and heavy metal concentrations several orders of magnitude higher than in circumneutral lakes. The water column of both lakes is divided into two layers by a pronounced chemocline. The smaller mining lake (AML), with pH close to of 2.6, is the most acidic lake in Austria, whereas flooding with stream water and by drainage from the surrounding fields neutralized the adjacent larger pit lake. The goal of our study was to investigate the effect of flooding on its physical, chemical and biological properties, in comparison to the pristine AML. Even relative to other extremely acidic lakes, the flora and fauna in the AML was reduced and composed of only two flagellate, one ciliate, and one rotifer species. The simplified pelagic food web in the mixolimnion consisted of heterotrophic bacteria, the mixotrophic flagellates Chlamydomonas acidophila and Ochromonas sp., the ciliate Oxytricha sp., and the rotifer Cephalodella sp. The latter two are as yet undescribed new species. The heliozoan Actinophrys sp. that may act as top predator occurred only in low abundance. The euglenid Lepocinclis buetschlii formed a stable deep chlorophyll maximum (DCM) at 7 m depth. Highest cell numbers of L. buetschlii in the DCM exceeded 108 L−1. The neutralized mining lake harboured higher plankton diversity similar to that of natural circumneutral lakes. A peak of at least 16 different phytoplankton taxa was observed during summer. The zooplankton consisted of several copepod species, daphnids and other cladocerans, and at least six different rotifer species. Several fish species occurred in the neutralized lake. Although the effect of non-permanent flooding was largely sustainable, interannual fluctuations of

Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional chromosome painting.

PubMed

Gomes, Anderson José Baia; Nagamachi, Cleusa Yoshiko; Rodrigues, Luis Reginaldo Ribeiro; Ferguson-Smith, Malcolm Andrew; Yang, Fengtang; O'Brien, Patricia Caroline Mary; Pieczarka, Julio Cesar

2018-04-25

The family Phyllostomidae (Chiroptera) shows wide morphological, molecular and cytogenetic variation; many disagreements regarding its phylogeny and taxonomy remains to be resolved. In this study, we use chromosome painting with whole chromosome probes from the Phyllostomidae Phyllostomus hastatus and Carollia brevicauda to determine the rearrangements among several genera of the Nullicauda group (subfamilies Gliphonycterinae, Carolliinae, Rhinophyllinae and Stenodermatinae). These data, when compared with previously published chromosome homology maps, allow the construction of a phylogeny comparable to those previously obtained by morphological and molecular analysis. Our phylogeny is largely in agreement with that proposed with molecular data, both on relationships between the subfamilies and among genera; it confirms, for instance, that Carollia and Rhinophylla, previously considered as part of the same subfamily are, in fact, distant genera. The occurrence of the karyotype considered ancestral for this family in several different branches suggests that the diversification of Phyllostomidae into many subfamilies has occurred in a short period of time. Finally, the comparison with published maps using human whole chromosome probes allows us to track some syntenic associations prior to the emergence of this family.

Seismic Data Reveal Lake-Level Changes in Lake Issyk-Kul, Kyrgyzstan

NASA Astrophysics Data System (ADS)

Gebhardt, C.; Spiess, V.; Keil, H.; Sauermilch, I.; Oberhänsli, H.; Abdrakhmatov, K.; De Batist, M. A.; Naudts, L.; De Mol, L.

2013-12-01

Lake Issyk-Kul is located in an intramontane basin of the Tien Shan, Kyrgyzstan, Central Asia, at 1607 m above sea level. It has formed in a tectonically active region with W-E striking major thrust zones both N and S of the lake. The lake is elongated with 180 km in W-E and 60 km in S-N direction and a water depth of roughly 670 m at its central plain. With a surface area of 6232 km2 and a total water colume of around 1736 km3, Lake Issyk-Kul is the second largest lake in the higher altitudes (De Batist et al., 2002). Two large delta areas have formed at the E and W end. Steep slopes at both the N and S shore separate rather narrow, shallow shelf areas from the central deeper plain. First seismic data of lake Issyk-Kul were acquired in 1982 by the Moscow University with a total of 31 profiles across the lake. In 1997 and 2001, a second and third seismic survey of the lake were carried out by the group of Marc De Batist (Ghent, Belgium) in cooperation with the Royal Museum of Central Africa (Tervuren, Belgium) and the SBRAS (Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia) using a sparker system with a single-channel streamer. These surveys were recently completed by a fourth expedition carried out by the University of Bremen in April 2013. During this expedition, 33 additional profiles were acquired with an airgun and a multi-channel streamer. The sparker surveys mostly cover the delta and shelf areas in high detail, while the airgun survey covers the deeper parts of the lake with penetration beyond the first multiple. Bathymetry data reveal that at the delta areas, the shelf is divided into two parts. The shallower comprises the part down to 110 m water depth with an average inclination of 0.5°, while the deeper part reaches from 110 m to 300 m water depth with an average slope inclination of 1°. Incised paleo-river channels of up to 2-3 km width and 50 m depth are visible both on the eastern and western shelf, but are limited to the

Phylogeny and species delineation in European species of the genus Steganacarus (Acari, Oribatida) using mitochondrial and nuclear markers.

PubMed

Kreipe, Victoria; Corral-Hernández, Elena; Scheu, Stefan; Schaefer, Ina; Maraun, Mark

2015-06-01

Species of the genus Steganacarus are soil-living oribatid mites (Acari, Phthiracaridae) with a ptychoid body. The phylogeny and species status of the species of Steganacarus are not resolved, some authors group all ten German species of Steganacarus within the genus Steganacarus whereas others split them into three subgenera, Steganacarus, Tropacarus and Atropacarus. Additionally, two species, S. magnus and T. carinatus, comprise morphotypes of questionable species status. We investigated the phylogeny and species status of ten European Steganacarus species, i.e. S. applicatus, S. herculeanus, S. magnus forma magna, S. magnus forma anomala, S. spinosus, Tropacarus brevipilus, T. carinatus forma carinata, T. carinatus forma pulcherrima, Atropacarus striculus and Rhacaplacarus ortizi. We used two molecular markers, a 251 bp fragment of the nuclear gene 28S rDNA (D3) and a 477 bp fragment of the mitochondrial COI region. The phylogeny based on a combined analysis of D3 and COI separated four subgenera (Steganacarus, Tropacarus and Atropacarus, Rhacaplacarus) indicating that they form monophyletic groups. The COI region separated all ten species of the genus Steganacarus and showed variation within some species often correlating with the geographic origin of the species. Resolution of the more conserved D3 region was limited, indicating that radiation events are rather recent. Overall, our results indicate that both genes alone cannot be used for phylogeny and barcoding since variation is too low in D3 and too high in COI. However, when used in combination these genes provide reliable insight into the phylogeny, radiation and species status of taxa of the genus Steganacarus.

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

2017-04-25

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.

Morphometry and mixing regime of a tropical lake: Lake Nova (Southeastern Brazil).

PubMed

Gonçalves, Monica A; Garcia, Fábio C; Barroso, Gilberto F

2016-09-01

Lake Nova (15.5 km2) is the second largest lake in the Lower Doce River Valley (Southeastern Brazil). A better understanding of ecosystem structure and functioning requires knowledge about lake morphometry, given that lake basin form influences water column stratification. The present study aims to contribute to the understanding of relationship between morphometry and mixing patterns of deep tropical lakes in Brazil. Water column profiles of temperature and dissolved oxygen were taken on four sampling sites along the lake major axis during 2011, 2012 and 2013. The bathymetric survey was carried out in July 2011, along 131.7 km of hydrographic tracks yield 51,692 depth points. Morphometric features of lake size and form factors describe the relative deep subrectangular elongated basin with maximum length of 15.7 km, shoreline development index 5.0, volume of 0.23 km3, volume development of 1.3, and maximum, mean and relative depths of 33.9 m, 14.7 m and 0.7 %, respectively. The deep basin induces a monomictic pattern, with thermal stratification during the wet/warm season associated with anoxic bottom waters (1/3 of lake volume), and mixing during dry and cool season. Based on in situ measurements of tributary river discharges, theoretical retention time (RT) has been estimated in 13.4 years. The morphometry of Lake Nova promote long water RT and the warm monomictic mixing pattern, which is in accordance to the deep tropical lakes in Brazil.

Characterization of Lake Michigan coastal lakes using zooplankton assemblages

USGS Publications Warehouse

Whitman, Richard L.; Nevers, Meredith B.; Goodrich, Maria L.; Murphy, Paul C.; Davis, Bruce M.

2004-01-01

Zooplankton assemblages and water quality were examined bi-weekly from 17 April to 19 October 1998 in 11 northeastern Lake Michigan coastal lakes of similar origin but varied in trophic status and limnological condition. All lakes were within or adjacent to Sleeping Bear Dunes National Lakeshore, Michigan. Zooplankton (principally microcrustaceans and rotifers) from triplicate Wisconsin net (80 I?m) vertical tows taken at each lake's deepest location were analyzed. Oxygen-temperature-pH-specific conductivity profiles and surface water quality were concurrently measured. Bray-Curtis similarity analysis showed small variations among sample replicates but large temporal differences. The potential use of zooplankton communities for environmental lake comparisons was evaluated by means of BIOENV (Primer 5.1) and principal component analyses. Zooplankton analyzed at the lowest identified taxonomic level yielded greatest sensitivity to limnological variation. Taxonomic and ecological aggregations of zooplankton data performed comparably, but less well than the finest taxonomic analysis. Secchi depth, chlorophyll a, and sulfate concentrations combined to give the best correlation with patterns of variation in the zooplankton data set. Principal component analysis of these variables revealed trophic status as the most influential major limnological gradient among the study lakes. Overall, zooplankton abundance was an excellent indicator of variation in trophic status.

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.

Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation

PubMed Central

2016-01-01

Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in

Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation.

PubMed

Andriananjamanantsoa, Herinandrianina N; Engberg, Shannon; Louis, Edward E; Brouillet, Luc

Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in

Molecular phylogeny and evolutionary history of Moricandia DC (Brassicaceae).

PubMed

Perfectti, Francisco; Gómez, José M; González-Megías, Adela; Abdelaziz, Mohamed; Lorite, Juan

2017-01-01

The phylogeny of tribe Brassiceae (Brassicaceae) has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genus Moricandia DC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species of Moricandia have been used in several phylogenetic studies, the phylogeny of this genus is not well established. Here we present a phylogenetic analysis of the genus Moricandia using a nuclear (the internal transcribed spacers of the ribosomal DNA) and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and the trn T- trn F region). We also included in the analyses members of their sister genus Rytidocarpus and from the close genus Eruca . The phylogenetic analyses showed a clear and robust phylogeny of the genus Moricandia . The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genus Moricandia appears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plus M. arvensis . We dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed to Rytidocarpus moricandioides is indeed a Moricandia species, and we propose to name it as M. rytidocarpoides sp. nov. In addition, in all the phylogenetic analyses, M. foleyi appeared outside the Moricandia

Geographical distributions of lake trout strains stocked in Lake Ontario

USGS Publications Warehouse

Elrod, Joseph H.; O'Gorman, Robert; Schneider, Clifford P.; Schaner, Ted

1996-01-01

Geographical distributions of lake trout (Salvelinus namaycush) stocked at seven locations in U.S. waters and at four locations in Canadian waters of Lake Ontario were determined from fish caught with gill nets in September in 17 areas of U.S. waters and at 10 fixed locations in Canadian waters in 1986-95. For fish of a given strain stocked at a given location, geographical distributions were not different for immature males and immature females or for mature males and mature females. The proportion of total catch at the three locations nearest the stocking location was higher for mature fish than for immature fish in all 24 available comparisons (sexes combined) and was greater for fish stocked as yearlings than for those stocked as fingerlings in all eight comparisons. Mature fish were relatively widely dispersed from stocking locations indicating that their tendency to return to stocking locations for spawning was weak, and there was no appreciable difference in this tendency among strains. Mature lake trout were uniformly distributed among sampling locations, and the strain composition at stocking locations generally reflected the stocking history 5 to 6 years earlier. Few lake trout moved across Lake Ontario between the north and south shores or between the eastern outlet basin and the main lake basin. Limited dispersal from stocking sites supports the concept of stocking different genetic strains in various parts of the lake with the attributes of each strain selected to match environmental conditions in the portion of the lake where it is stocked.

Deglaciation, lake levels, and meltwater discharge in the Lake Michigan basin

USGS Publications Warehouse

Colman, Steven M.; Clark, J.A.; Clayton, L.; Hansel, A.K.; Larsen, C.E.

1994-01-01

The deglacial history of the Lake Michigan basin, including discharge and routing of meltwater, is complex because of the interaction among (1) glacial retreats and re-advances in the basin (2) the timing of occupation and the isostatic adjustment of lake outlets and (3) the depositional and erosional processes that left evidence of past lake levels. In the southern part of the basin, a restricted area little affected by differential isostasy, new studies of onshore and offshore areas allow refinement of a lake-level history that has evolved over 100 years. Important new data include the recognition of two periods of influx of meltwater from Lake Agassiz into the basin and details of the highstands gleaned from sedimentological evidence. Major disagreements still persist concerning the exact timing and lake-level changes associated with the Algonquin phase, approximately 11,000 BP. A wide variety of independent data suggests that the Lake Michigan Lobe was thin, unstable, and subject to rapid advances and retreats. Consequently, lake-level changes were commonly abrupt and stable shorelines were short-lived. The long-held beliefs that the southern part of the basin was stable and separated from deformed northern areas by a hinge-line discontinuity are becoming difficult to maintain. Numerical modeling of the ice-earth system and empirical modeling of shoreline deformation are both consistent with observed shoreline tilting in the north and with the amount and pattern of modern deformation shown by lake-level gauges. New studies of subaerial lacustrine features suggest the presence of deformed shorelines higher than those originally ascribed to the supposed horizontal Glenwood level. Finally, the Lake Michigan region as a whole appears to behave in a similar manner to other areas, both local (other Great Lakes) and regional (U.S. east coast), that have experienced major isostatic changes. Detailed sedimentological and dating studies of field sites and additional

77 FR 39638 - Safety Zone; Barbara Harder Wedding Fireworks, Lake Erie, Lake View, NY

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-05

...-AA00 Safety Zone; Barbara Harder Wedding Fireworks, Lake Erie, Lake View, NY AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is establishing a temporary safety zone on Lake Erie, Lake View, NY. This safety zone is intended to restrict vessels from a portion of Lake Erie...

Genetic diversity of lake whitefish in lakes Michigan and Huron: sampling, standardization, and research priorities

USGS Publications Warehouse

Stott, Wendylee; VanDeHey, Justin A.; Sloss, Brian L.

2010-01-01

We combined data from two laboratories to increase the spatial extent of a genetic data set for lake whitefish Coregonus clupeaformis from lakes Huron and Michigan and saw that genetic diversity was greatest between lakes, but that there was also structuring within lakes. Low diversity among stocks may be a reflection of relatively recent colonization of the Great Lakes, but other factors such as recent population fluctuation and localized stresses such as lamprey predation or heavy exploitation may also have a homogenizing effect. Our data suggested that there is asymmetrical movement of lake whitefish between Lake Huron and Lake Michigan; more genotypes associated with Lake Michigan were observed in Lake Huron. Adding additional collections to the calibrated set will allow further examination of diversity in other Great Lakes, answer questions regarding movement among lakes, and estimate contributions of stocks to commercial yields. As the picture of genetic diversity and population structure of lake whitefish in the Great Lakes region emerges, we need to develop methods to combine data types to help identify important areas for biodiversity and thus conservation. Adding genetic data to existing models will increase the precision of predictions of the impacts of new stresses and changes in existing pressures on an ecologically and commercially important species.

[Characterizing chromophoric dissolved organic matter (CDOM) in Lake Honghu, Lake Donghu and Lake Liangzihu using excitation-emission matrices (EEMs) fluorescence and parallel factor analysis (PARAFAC)].

PubMed

Zhou, Yong-Qiang; Zhang, Yun-Lin; Niu, Cheng; Wang, Ming-Zhu

2013-12-01

Little is known about DOM characteristics in medium to large sized lakes located in the middle and lower reaches of Yangtze River, like Lake Honghu, Lake Donghu and Lake Liangzihu. Absorption, fluorescence and composition characteristics of chromophoric dissolved organic matter (CDOM) are presented using the absorption spectroscopy, the excitation-emission ma trices (EEMs) fluorescence and parallel factor analysis (PARAFAC) model based on the data collected in Sep-Oct. 2007 including 15, 9 and 10 samplings in Lake Honghu, Lake Donghu and Lake Liangzihu, respectively. CDOM absorption coefficient at 350 nm a(350) coefficient in Lake Honghu was significantly higher than those in Lake Donghu and Lake Liangzihu (t-test, p< 0. 001). A significant negative correlation was found between CDOM spectral slope in the wavelength range of 280-500 nm (S280-500) and a(350) (R2 =0. 781, p<0. 001). The mean value of S280-500 in Lake Honghu was significantly lower than those in Lake Donghu (t-test, pLake Liangzihu (t-test, p<0. 001). The mean value of spectral slope ratio SR in Lake Honghu was also significantly lower than those in Lake Donghu and Lake Liangzihu (t-test, p<0. 05). Two humic-like (C1, C2) and two protein-like fluorescent components (C3, C4) were identified by PARAFAC model, among which significant positive correlations were found between C1 and C2 (R2 =0. 884, p<0. 001), C3 and C4 (R2 =0. 677, p<0.001), respectively, suggesting that the sources of the two humic-like components as well as the two protein-like components were similar. However, no significant correlation has been found between those 4 fluorescent components and DOC concentration. Th e fluorescenceindices of FI255 (HIX), Fl265, FI310 (BIX) and Fl370 in Lake Donghu were all significantly higher than those in Lake Liangzihu (t-test, p <0.05) and Lake Honghu (t-test, p<0. 01), indicating that the eutrophication status in Lake Donghu was higher than Lake Honghu and Lake Liangzihu.

Exploring trends, causes, and consequences of declining lipids in Lake Superior lake trout

EPA Science Inventory

The ability of lake trout to forage in deepwater habitats is facilitated by high lipid content, which affords buoyancy. In Lake Superior, lean lake trout historically occupied depths < 80 m, and siscowet lake trout occupied depths > 80 m. Siscowets have been known f...

Great Lakes

USGS Publications Warehouse

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

1998-01-01

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

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

Suspended-sediment budget, flow distribution, and lake circulation for the Fox Chain of Lakes in Lake and McHenry Counties, Illinois, 1997-99

USGS Publications Warehouse

Schrader, David L.; Holmes, Robert R.

2000-01-01

The Fox Chain of Lakes is a glacial lake system in McHenry and Lake Counties in northern Illinois and southern Wisconsin. Sedimentation and nutrient overloading have occurred in the lake system since the first dam was built (1907) in McHenry to raise water levels in the lake system. Using data collected from December 1, 1997, to June 1, 1999, suspended-sediment budgets were constructed for the most upstream lake in the system, Grass Lake, and for the lakes downstream from Grass Lake. A total of 64,900 tons of suspended sediment entered Grass Lake during the study, whereas a total of 70,600 tons of suspended sediment exited the lake, indicating a net scour of 5,700 tons of sediment. A total of 44,100 tons of suspended sediment was measured exiting the Fox Chain of Lakes at Johnsburg, whereas 85,600 tons entered the system downstream from Grass Lake. These suspended-sediment loads indicate a net deposition of 41,500 tons downstream from Grass Lake, which represents a trapping efficiency of 48.5 percent. A large amount of recreational boating takes place on the Fox Chain of Lakes during summer months, and suspended-sediment load was observed to rise from 110 tons per day to 339 tons per day during the 1999 Memorial Day weekend (May 26 ?31, 1999). Presumably, this rise was the result of the boating traffic because no other hydrologic event is known to have occurred that might have caused the rise. This study covers a relatively short period and may not represent the long-term processes of the Fox Chain of Lakes system, although the sediment transport was probably higher than an average year. The bed sediments found on the bottom of the lakes are composed of mainly fine particles in the silt-clay range. The Grass Lake sediments were characterized as black peat with an organic content of between 9 and 18 percent, and the median particle size ranged from 0.000811 to 0.0013976 inches. Other bed material samples were collected at streamflow-gaging stations on the

Changing abundance of Hexagenia mayfly nymphs in western Lake Erie of the Laurentian Great Lakes: Impediments to assessment of lake recovery?

USGS Publications Warehouse

Schloesser, D.W.; Nalepa, T.F.

2001-01-01

After an absence of 40 years, mayfly nymphs of the genus Hexagenia were found in sediments of western Lake Erie of the Laurentian Great Lakes in 1993 and, by 1997, were abundant enough to meet a mayfly-density management goal (ca. 350 nymphs m—2) based on pollution-abatement programs. We sampled nymphs in western Lake Erie and Lake St. Clair, located upstream of western Lake Erie, to determine the importance of seasonal abundance and life-history characteristics of nymphs (e.g., emergence and recruitment) on density estimates relative to the mayfly-density management goal. Two types of density patterns were observed: (1) densities were relatively high in spring and gradually decreased through late summer (observed in Lake Erie and Lake St. Clair in 1997 and Lake St. Clair in 1999) and (2) densities were relatively high in spring, gradually decreased to mid summer, abruptly decreased in mid summer, and then increased between summer and late fall (Lake Erie and Lake St. Clair in 1998 and Lake Erie in 1999). Length-frequency distributions of nymphs and observations of adults indicate that the primary cause for the two density patterns was attributed to failed (first pattern) and successful (second pattern) reproduction and emergence of nymphs into adults in mid summer. Gradual declines in densities were attributed to mortality of nymphs. Our results indicate that caution should be used when evaluating progress of pollution-abatement programs based on mayfly densities because recruitment success is variable both between and within years. Additionally, the interpretation of progress toward management goals, relative to the restoration of Hexagenia populations in the Great Lakes and possibly other water bodies throughout the world, is influenced by the number of years in which consequtive collections are made.

33 CFR 162.220 - Hoover Dam, Lake Mead, and Lake Mohave (Colorado River), Ariz.-Nev.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Hoover Dam, Lake Mead, and Lake... REGULATIONS § 162.220 Hoover Dam, Lake Mead, and Lake Mohave (Colorado River), Ariz.-Nev. (a) Lake Mead and... the axis of Hoover Dam and that portion of Lake Mohave (Colorado River) extending 4,500 feet...

33 CFR 162.220 - Hoover Dam, Lake Mead, and Lake Mohave (Colorado River), Ariz.-Nev.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Hoover Dam, Lake Mead, and Lake... REGULATIONS § 162.220 Hoover Dam, Lake Mead, and Lake Mohave (Colorado River), Ariz.-Nev. (a) Lake Mead and... the axis of Hoover Dam and that portion of Lake Mohave (Colorado River) extending 4,500 feet...

33 CFR 162.220 - Hoover Dam, Lake Mead, and Lake Mohave (Colorado River), Ariz.-Nev.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Hoover Dam, Lake Mead, and Lake... REGULATIONS § 162.220 Hoover Dam, Lake Mead, and Lake Mohave (Colorado River), Ariz.-Nev. (a) Lake Mead and... the axis of Hoover Dam and that portion of Lake Mohave (Colorado River) extending 4,500 feet...

33 CFR 162.220 - Hoover Dam, Lake Mead, and Lake Mohave (Colorado River), Ariz.-Nev.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Hoover Dam, Lake Mead, and Lake... REGULATIONS § 162.220 Hoover Dam, Lake Mead, and Lake Mohave (Colorado River), Ariz.-Nev. (a) Lake Mead and... the axis of Hoover Dam and that portion of Lake Mohave (Colorado River) extending 4,500 feet...

Lake Characteristics Influencing Spawning Success of Muskellunge in Northern Wisconsin Lakes

Treesearch

Ashley J. Rust; James S. Diana; Terry L. Margenau; Clayton J. Edwards

2002-01-01

We determined the physical, chemical, biological, and land use characteristics that distinguish northern Wisconsin lakes with self-sustaining populations of muskellunge Esox masquinongy from lakes where stocking is required to maintain populations. Lakes that supported self-sustaining muskellunge populations were characterized by fewer shoreline...

Evaluating COSMO's lake module (FLake) for an East-African lake using a comprehensive set of lake temperature profiles

NASA Astrophysics Data System (ADS)

Thiery, W.; Martynov, A.; Darchambeau, F.; Demuzere, M.; van Lipzig, N.

2012-04-01

The African great lakes are of utmost importance for the local economy (fishing), as well as being essential to the survival of the local people. During last decades, these lakes have been changing rapidly and their evolution is a major concern. Hence, it is important to correctly represent them in regional climate models for simulations over tropical Africa. However, so far lake models have been developed and tested primarily for boreal conditions. In this study, for the first time the freshwater lake model FLake is evaluated over East-Africa, more specifically over lake Kivu. Meteorological observations from January 2003 to December 2008 from an automatic weather station in Bukavu, DRC, are used to drive the standalone version of FLake. For the evaluation, a unique dataset is used which contains over 200 temperature profiles recorded since 2002. Results show that FLake in its default configuration is very successful at reproducing both the timing and magnitude of the seasonal cycle at 5 m depth. Flake captures that this seasonality is regulated by the water vapour pressure, which constrains evaporation except during summer (JJA). A positive bias of ~1 K is attributed to the driving data, which are collected in the city and are therefore expected to mirror higher temperatures and lower wind speeds compared to the lake surface. The evaluation also showed that driving FLake with Era-Interim from the nearest pixel does only slightly deteriorate the model performance. Using forcing fields from the Canadian Regional Climate Model, version 5 (CRCM5) simulation output gives similar performance as Era-Interim. Furthermore, a drawback of FLake is that it does not account for salinity and its effect upon lake stratification, and therefore requires artificial initial conditions for both lake depth and bottom temperature in order to reproduce the correct mixing regime in lake Kivu. Further research will therefore aim at improving FLake's representation of tropical lakes.

Phylogeny and biogeography of North-American wild rice (Zizania L.Poaceae)

USDA-ARS?s Scientific Manuscript database

The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z. latifolia) in eastern Asia. The phylogeny and biogeography of Zizania were explored using sequences o...

Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China.

PubMed

Wang, Xuewei; Liu, Xingzhong; Groenewald, Johannes Z

2017-01-01

The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.

Seasonal thermal ecology of adult walleye (Sander vitreus) in Lake Huron and Lake Erie.

PubMed

Peat, Tyler B; Hayden, Todd A; Gutowsky, Lee F G; Vandergoot, Christopher S; Fielder, David G; Madenjian, Charles P; Murchie, Karen J; Dettmers, John M; Krueger, Charles C; Cooke, Steven J

2015-10-01

The purpose of this study was to characterize thermal patterns and generate occupancy models for adult walleye from lakes Erie and Huron with internally implanted biologgers coupled with a telemetry study to assess the effects of sex, fish size, diel periods, and lake. Sex, size, and diel periods had no effect on thermal occupancy of adult walleye in either lake. Thermal occupancy differed between lakes and seasons. Walleye from Lake Erie generally experienced higher temperatures throughout the spring and summer months than did walleye in Lake Huron, due to limnological differences between the lakes. Tagged walleye that remained in Saginaw Bay, Lake Huron (i.e., adjacent to the release location), as opposed to those migrating to the main basin of Lake Huron, experienced higher temperatures, and thus accumulated more thermal units (the amount of temperature units amassed over time) throughout the year. Walleye that migrated toward the southern end of Lake Huron occupied higher temperatures than those that moved toward the north. Consequently, walleye that emigrated from Saginaw Bay experienced thermal environments that were more favorable for growth as they spent more time within their thermal optimas than those that remained in Saginaw Bay. Results presented in this paper provide information on the thermal experience of wild fish in a large lake, and could be used to refine sex- and lake-specific bioenergetics models of walleye in the Great Lakes to enable the testing of ecological hypotheses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Seasonal thermal ecology of adult walleye (Sander vitreus) in Lake Huron and Lake Erie

USGS Publications Warehouse

Peat, Tyler B; Hayden, Todd A.; Gutowsky, Lee F G; Vandergoot, Christopher S.; Fielder, David G.; Madenjian, Charles P.; Murchie, Karen J; Dettmers, John M.; Krueger, Charles C.; Cooke, Steven J.

2015-01-01

The purpose of this study was to characterize thermal patterns and generate occupancy models for adult walleye from lakes Erie and Huron with internally implanted biologgers coupled with a telemetry study to assess the effects of sex, fish size, diel periods, and lake. Sex, size, and diel periods had no effect on thermal occupancy of adult walleye in either lake. Thermal occupancy differed between lakes and seasons. Walleye from Lake Erie generally experienced higher temperatures throughout the spring and summer months than did walleye in Lake Huron, due to limnological differences between the lakes. Tagged walleye that remained in Saginaw Bay, Lake Huron (i.e., adjacent to the release location), as opposed to those migrating to the main basin of Lake Huron, experienced higher temperatures, and thus accumulated more thermal units (the amount of temperature units amassed over time) throughout the year. Walleye that migrated toward the southern end of Lake Huron occupied higher temperatures than those that moved toward the north. Consequently, walleye that emigrated from Saginaw Bay experienced thermal environments that were more favorable for growth as they spent more time within their thermal optimas than those that remained in Saginaw Bay. Results presented in this paper provide information on the thermal experience of wild fish in a large lake, and could be used to refine sex- and lake-specific bioenergetics models of walleye in the Great Lakes to enable the testing of ecological hypotheses.

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.

First evidence of successful natural reproduction by planted lake trout in Lake Huron

USGS Publications Warehouse

Nester, Robert T.; Poe, Thomas P.

1984-01-01

Twenty-two lake trout (Salvelinus namaycush) swim-up fry, 24-27 mm long, were captured with emergent fry traps and a tow net in northwestern Lake Huron on a small nearshore reef off Alpena, Michigan, between May 10 and June 1, 1982. These catches represent the first evidence of successful production of swim-up fry by planted, hatchery-reared lake trout in Lake Huron since the lake trout rehabilitation program began in 1973.

Estimation of lake water - groundwater interactions in meromictic mining lakes by modelling isotope signatures of lake water.

PubMed

Seebach, Anne; Dietz, Severine; Lessmann, Dieter; Knoeller, Kay

2008-03-01

A method is presented to assess lake water-groundwater interactions by modelling isotope signatures of lake water using meteorological parameters and field data. The modelling of delta(18)O and deltaD variations offers information about the groundwater influx into a meromictic Lusatian mining lake. Therefore, a water balance model is combined with an isotope water balance model to estimate analogies between simulated and measured isotope signatures within the lake water body. The model is operated with different evaporation rates to predict delta(18)O and deltaD values in a lake that is only controlled by weather conditions with neither groundwater inflow nor outflow. Comparisons between modelled and measured isotope values show whether the lake is fed by the groundwater or not. Furthermore, our investigations show that an adaptation of the Craig and Gordon model [H. Craig, L.I. Gordon. Deuterium and oxygen-18 variations in the ocean and the marine atmosphere. In Stable Isotopes in Oceanographic Studies and Paleotemperature, Spoleto, E. Tongiorgi (Ed.), pp. 9-130, Consiglio Nazionale delle Ricerche, Laboratorio di Geologia Nucleare, Pisa (1965).] to specific conditions in temperate regions seems necessary.

75 FR 13232 - Safety Zone; Lake Mead Intake Construction, Lake Mead, Boulder City, NV

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-19

...-AA00 Safety Zone; Lake Mead Intake Construction, Lake Mead, Boulder City, NV AGENCY: Coast Guard, DHS... waters of Lake Mead in support of the construction project for Lake Mead's Intake 3. This safety zone is... for the placement of an Intake Pipe from Lake Mead throughout 2010. This safety zone is necessary to...

78 FR 17869 - Safety Zone; Desert Storm Shootout; Lake Havasu, Lake Havasu City, AZ

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-25

...-AA00 Safety Zone; Desert Storm Shootout; Lake Havasu, Lake Havasu City, AZ AGENCY: Coast Guard, DHS... navigable waters of the Colorado River in Lake Havasu, Lake Havasu City, Arizona in support of the Desert... Coast Guard to establish safety zones (33 U.S.C 1221 et seq.). Lake Racer LLC is sponsoring the Desert...

Bioturbation enhances the aerobic respiration of lake sediments in warming lakes.

PubMed

Baranov, Viktor; Lewandowski, Jörg; Krause, Stefan

2016-08-01

While lakes occupy less than 2% of the total surface of the Earth, they play a substantial role in global biogeochemical cycles. For instance, shallow lakes are important sites of carbon metabolism. Aerobic respiration is one of the important drivers of the carbon metabolism in lakes. In this context, bioturbation impacts of benthic animals (biological reworking of sediment matrix and ventilation of the sediment) on sediment aerobic respiration have previously been underestimated. Biological activity is likely to change over the course of a year due to seasonal changes of water temperatures. This study uses microcosm experiments to investigate how the impact of bioturbation (by Diptera, Chironomidae larvae) on lake sediment respiration changes when temperatures increase. While at 5°C, respiration in sediments with and without chironomids did not differ, at 30°C sediment respiration in microcosms with 2000 chironomids per m(2) was 4.9 times higher than in uninhabited sediments. Our results indicate that lake water temperature increases could significantly enhance lake sediment respiration, which allows us to better understand seasonal changes in lake respiration and carbon metabolism as well as the potential impacts of global warming. © 2016 The Authors.

Bioturbation enhances the aerobic respiration of lake sediments in warming lakes

PubMed Central

Krause, Stefan

2016-01-01

While lakes occupy less than 2% of the total surface of the Earth, they play a substantial role in global biogeochemical cycles. For instance, shallow lakes are important sites of carbon metabolism. Aerobic respiration is one of the important drivers of the carbon metabolism in lakes. In this context, bioturbation impacts of benthic animals (biological reworking of sediment matrix and ventilation of the sediment) on sediment aerobic respiration have previously been underestimated. Biological activity is likely to change over the course of a year due to seasonal changes of water temperatures. This study uses microcosm experiments to investigate how the impact of bioturbation (by Diptera, Chironomidae larvae) on lake sediment respiration changes when temperatures increase. While at 5°C, respiration in sediments with and without chironomids did not differ, at 30°C sediment respiration in microcosms with 2000 chironomids per m2 was 4.9 times higher than in uninhabited sediments. Our results indicate that lake water temperature increases could significantly enhance lake sediment respiration, which allows us to better understand seasonal changes in lake respiration and carbon metabolism as well as the potential impacts of global warming. PMID:27484649

Lake Sturgeon, Acipenser fulvescens, movements in Rainy Lake, Minnesota and Ontario

USGS Publications Warehouse

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

2006-01-01

Rainy Lake, Minnesota-Ontario, contains a native population of Lake Sturgeon (Acipenser fulvescens) that has gone largely unstudied. The objective of this descriptive study was to summarize generalized Lake Sturgeon movement patterns through the use of biotelemetry. Telemetry data reinforced the high utilization of the Squirrel Falls geographic location by Lake Sturgeon, with 37% of the re-locations occurring in that area. Other spring aggregations occurred in areas associated with Kettle Falls, the Pipestone River, and the Rat River, which could indicate spawning activity. Movement of Lake Sturgeon between the Seine River and the South Arm of Rainy Lake indicates the likelihood of one integrated population on the east end of the South Arm. The lack of re-locations in the Seine River during the months of September and October may have been due to Lake Sturgeon moving into deeper water areas of the Seine River and out of the range of radio telemetry gear or simply moving back into the South Arm. Due to the movements between Minnesota and Ontario, coordination of management efforts among provincial, state, and federal agencies will be important.

Stratigraphic framework and lake level history of Lake Kivu, East African Rift

NASA Astrophysics Data System (ADS)

Wood, Douglas A.; Scholz, Christopher A.

2017-10-01

Sediment cores and seismic reflection data acquired from the eastern basin of Lake Kivu, Rwanda reveal extensive limnologic variations due to changes in regional climate and basin structure. The eastern basin of the lake contains a sedimentary wedge which is > 1.5 km in thickness on its western side, and basal sediments are estimated to be at least 1.5 million years old. Sediments are likely to be thicker and older than this in the northern, Congolese basin of the lake. Above the ∼300 m iosbath only a thin layer of Holocene sediments are observed indication that this may have been the lake's high stand prior to that time. There are at least three erosional unconformities interpreted as desiccation or near-desiccation events which are estimated to have occurred at ∼475 ka, ∼100 ka, and ∼20 ka; the two most recent of these low stages likely developed during the African Megadrought and Last Glacial Maximum (LGM) periods. Following the LGM, the water levels rose to form a ∼100 m deep lake with its surface ∼370 m below the current lake level. The lake remained near that level for several thousand years and during this time the Virunga Volcanic Province expanded. At ∼12.2 ka a change to wetter climate conditions rapidly filled the lake to spill out of the Bukavu Bay basin southward toward Lake Tanganyika. Tephra sampled from the cores show that there have been at least 24 large local volcanic events since the early Holocene lake transgression.

Unhealthy behaviours and risk of visual impairment: The CONSTANCES population-based cohort.

PubMed

Merle, Bénédicte M J; Moreau, Gwendoline; Ozguler, Anna; Srour, Bernard; Cougnard-Grégoire, Audrey; Goldberg, Marcel; Zins, Marie; Delcourt, Cécile

2018-04-26

Unhealthy behaviours are linked to a higher risk of eye diseases, but their combined effect on visual function is unknown. We aimed to examine the individual and combined associations of diet, physical activity, smoking and alcohol consumption with visual impairment among French adults. 38 903 participants aged 18-73 years from the CONSTANCES nationwide cohort (2012-2016) with visual acuity measured and who completed, lifestyle, medical and food frequency questionnaires were included. Visual impairment was defined as a presenting visual acuity <20/40 in the better eye. After full multivariate adjustment, the odds for visual impairment increased with decreasing diet quality (p for trend = 0.04), decreasing physical activity (p for trend = 0.02) and increasing smoking pack-years (p for trend = 0.03), whereas no statistically significant association with alcohol consumption was found. Combination of several unhealthy behaviours was associated with increasing odds for visual impairment (p for trend = 0.0002), with a fully-adjusted odds ratio of 1.81 (95% CI 1.18 to 2.79) for participants reporting 2 unhealthy behaviours and 2.92 (95% CI 1.60 to 5.32) for those reporting 3 unhealthy behaviours. An unhealthy lifestyle including low/intermediate diet quality, low physical activity and heavy smoking was associated with visual impairment in this large population-based study.

Hydrology of Crater, East and Davis Lakes, Oregon; with section on Chemistry of the Lakes

USGS Publications Warehouse

Phillips, Kenneth N.; Van Denburgh, A.S.

1968-01-01

Crater, East, and Davis Lakes are small bodies of fresh water that occupy topographically closed basins in Holocene volcanic terrane. Because the annual water supply exceeds annual evaporation, water must be lost by seepage from each lake. The seepage rates vary widely both in volume and in percentage of the total water supply. Crater Lake loses about 89 cfs (cubic feet per second), equivalent to about 72 percent of its average annual supply. East Lake loses about 2.3 cfs, or about 44 percent of its estimated supply. Davis Lake seepage varies greatly with lake level, but the average loss is about 150 cfs, more than 90 percent of its total supply. The destination of the seepage loss is not definitely known for any of the lakes. An approximate water budget was computed for stationary level for each lake, by using estimates 'by the writer to supplement the hydrologic data available. The three lake waters are dilute. Crater Lake contains about 80 ppm, (parts per million) of dissolved solids---mostly silica, sodium, and bicarbonate, and lesser amounts of calcium, sulfate, and chloride. Much of the dissolved-solids content of Crater Lake---especially the sulfate and chloride---may be related to fumarole and thermal-spring activity that presumably followed the collapse of Mount Mazama. Although Grater Lake loses an estimated 7,000 tons of its 1.5million-ton salt content each year by leakage, the chemical character of the lake did not change appreciably between 1912 and 1964. East Lake contains 200 ppm of dissolved solids, which includes major proportions of calcium, sodium, bicarbonate, and sulfate, but almost no chloride. The lake apparently receives much of its dissolved solids from subsurface thermal springs. Annual solute loss from East Lake by leakage is about 450 tons, or 3 percent of the lake's 15,000-ton estimated solute content. Davis Lake contains only 48 ppm of dissolved solids, much of which is silica and bicarbonate; chloride is almost completely absent

76 FR 2579 - Safety Zone; Lake Mead Intake Construction, Lake Mead, Boulder City, NV

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-14

...-AA00 Safety Zone; Lake Mead Intake Construction, Lake Mead, Boulder City, NV AGENCY: Coast Guard, DHS... waters of Lake Mead in support of the construction project for Lake Mead's Intake 3 during the first 6... blasting operations for the placement of a water intake pipe in Lake Mead during the first 6 months of 2011...

Evaluation of methods to estimate lake herring spawner abundance in Lake Superior

USGS Publications Warehouse

Yule, D.L.; Stockwell, J.D.; Cholwek, G.A.; Evrard, L.M.; Schram, S.; Seider, M.; Symbal, M.

2006-01-01

Historically, commercial fishers harvested Lake Superior lake herring Coregonus artedi for their flesh, but recently operators have targeted lake herring for roe. Because no surveys have estimated spawning female abundance, direct estimates of fishing mortality are lacking. The primary objective of this study was to determine the feasibility of using acoustic techniques in combination with midwater trawling to estimate spawning female lake herring densities in a Lake Superior statistical grid (i.e., a 10′ latitude × 10′ longitude area over which annual commercial harvest statistics are compiled). Midwater trawling showed that mature female lake herring were largely pelagic during the night in late November, accounting for 94.5% of all fish caught exceeding 250 mm total length. When calculating acoustic estimates of mature female lake herring, we excluded backscattering from smaller pelagic fishes like immature lake herring and rainbow smelt Osmerus mordax by applying an empirically derived threshold of −35.6 dB. We estimated the average density of mature females in statistical grid 1409 at 13.3 fish/ha and the total number of spawning females at 227,600 (95% confidence interval = 172,500–282,700). Using information on mature female densities, size structure, and fecundity, we estimate that females deposited 3.027 billion (109) eggs in grid 1409 (95% confidence interval = 2.356–3.778 billion). The relative estimation error of the mature female density estimate derived using a geostatistical model—based approach was low (12.3%), suggesting that the employed method was robust. Fishing mortality rates of all mature females and their eggs were estimated at 2.3% and 3.8%, respectively. The techniques described for enumerating spawning female lake herring could be used to develop a more accurate stock–recruitment model for Lake Superior lake herring.

Lake Chad, Chad, Africa

NASA Image and Video Library

1990-04-29

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

Water-quality and lake-stage data for Wisconsin lakes, water year 2014

USGS Publications Warehouse

Manteufel, S. Bridgett; Robertson, Dale M.

2017-05-25

IntroductionThe U.S. Geological Survey (USGS), in cooperation with local and other agencies, collects data at selected lakes throughout Wisconsin. These data, accumulated over many years, provide a database for developing an improved understanding of the water quality of lakes. To make these data available to interested parties outside the USGS, the data are published annually in this report series. The locations of water-quality and lake-stage stations in Wisconsin for water year 2014 are shown in figure 1. A water year is the 12-month period from October 1 through September 30. It is designated by the calendar year in which it ends. Thus, the periodOctober 1, 2013, through September 30, 2014, is called “water year 2014.”The purpose of this report is to provide information about the chemical and physical characteristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected include measurements of in-lake water quality and lake stage. Time series of Secchi depths, surface total phosphorus, and chlorophyll a concentrations collected during nonfrozen periods are included for many lakes. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive information for each lake includes the location of the lake, area of the lake’s watershed, period for which data are available, revisions to previously published records, and pertinent remarks. Additional data, such as streamflow and water quality in tributary and outlet streams of some of the lakes, are published online at http://nwis.waterdata.usgs.gov/wi/nwis.Water-resources data, including stage and discharge data at most streamflow-gaging stations, are available online. The Wisconsin Water Science Center’s home page is at https://www.usgs.gov/centers/wisconsin-water-science-center. Information

Barcoding of ancient lake ostracods (crustacea) reveals cryptic speciation with extremely low distances.

PubMed

Karanovic, Ivana

2015-01-01

Ostracods are drastically reduced crustaceans, with never more than eight appendages enclosed between two valves, leaving only a limited number of morphological characters for species delineation. Conservative morphology of characters used to define genera, along with high variability of characters used to define species are creating problems in applying a morphospecies concept. A high intraspecific variability in a Lake Biwa (Japan) endemic, Physocypria biwaensis (Okubo, 1990), has been observed previously but was never studied in detail. Two sympatric forms, differing in pigmentation and size, suggest a presence of reproductive isolation. The aim of this study is to employ molecular and morphometric tools to aid in species delineation within P. biwaensis complex and reconstruct their phylogenetic relationships. A fragment of the mtCOI gene was amplified from 30 specimens, and an additional 37 specimens were studied for morphological characters. Resulting phylogenies showed that each morphologically distinct form is associated with a distinct phylogenetic group based on mtDNA. The average pairwise distance is very low (5%), indicating a recent divergence time. I speculate that there is a possibility that one of them originated in the lake, while the other probably colonized it afterwards. This seems to be supported with an apparent niche partitioning at different depths. In spite of the fact that traditionally used sexual characters are highly variable in these two species, the morphometric analysis of shell and soft part related characters clearly delineates them and suggests that such characters may be useful for future detection of seemingly cryptic ostracod species.

Helminths in an intensively stocked population of lake trout, Salvelinus namaycush, from Lake Huron

USGS Publications Warehouse

Muzzall, Patrick M.; Bowen, Charles A.

2000-01-01

Eighty stocked lake trout Salvelinus namaycush (Salmonidae), collected from 2 locations in Lake Huron in May 1995, were examined for parasites. The parasite fauna of this top predator in Lake Huron was characterized by only 6 helminth species. Echinorhynchus salmonis infected all lake trout with a mean intensity of 163.9. The intensity of this acanthocephalan species significantly increased with host length and weight. Eubothrium salvelini infected 78 lake trout with a maximum number of 81 scoleces counted. Diplostomum sp., Cyathocephalus truncatus, Capillaria salvelini, and Neoechinorhynchus sp. infrequently infected lake trout. The low parasite species richness in these lake trout is believed to be due to their large size at stocking and to the loss of historical enzootic host-parasite relationships that followed the absence of this fish species in Lake Huron for 26 yr.

Glaciers, Glacial lakes and Glacial Lake Outburst Floods in the Koshi Basin

NASA Astrophysics Data System (ADS)

Shrestha, F.; Gao, X.; Khanal, N. R.; Maharjan, S. B.; Bajracharya, S. R.; Shrestha, R. B.; Lizong, W.; Mool, P. K.

2016-12-01

Glacier is a vital water resources for mountain communities. Recession in glacier area either increased the glacial lake size or develop a new lake. The consequences of these changes in lake has become one of the major issue in the management of GLOF risk. This paper presents the distribution of, and changes in, glaciers, glacial lakes in the Koshi basin and also looks at past GLOF events that have occurred in the basin and their distance of impact. Data on the number of glaciers and glacial lakes and their areas were generated for the years 1977, 1990, 2000, and 2010 using Landsat images. The study revealed that there were a total of 845 glaciers (Nepal side) and 2,168 glacial lakes (Nepal and China side) with a total area of 1,103 km2 and 127.608 km2 in 2010. The number of glacier increased by 15% (109) and area decreased by 26% (396 km2) over 33 years. In case of glacier lakes, the number and area increased from 1,160 to 2,168 and from 94.444 km2 to 127.608 km2 during 33 years with an overall growth rates of 86.9% and 35.1%. A large number of glacial lakes are small in size (≤ 0.1 km2). End moraine dammed lakes with area ≥ 0.1 km2 were selected to analyse the change characteristics of glacial lakes. The results show that there were 134 lakes ≥ 0.1 km2 in 2010; these lakes had a total area of 43.06 km2 in 1997, increased to 64.35 km2 in 2010. The distribution of lakes on the north side of the Himalayas (in China) was three times higher than on the south side of the Himalayas (in Nepal). Comparing the mean growth rate in area and length for the 33 years, the growth rate on the north side was found to be a little slower than that on the south side. This relationship did not hold true for length change in the different periods. The study identified 42 rapidly growing large lakes that are dangerous in terms of GLOF risk. In the past, 18 GLOF events have been reported. The downstream distance impacted by those events was up to 90 km. Among them, 13 GLOF events

Lake Michigan lake trout PCB model forecast post audit (oral presentation)

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 an...

Simulating Lake-Groundwater Interactions During Decadal Climate Cycles: Accounting For Variable Lake Area In The Watershed

NASA Astrophysics Data System (ADS)

Virdi, M. L.; Lee, T. M.

2009-12-01

The volume and extent of a lake within the topo-bathymetry of a watershed can change substantially during wetter and drier climate cycles, altering the interaction of the lake with the groundwater flow system. Lake Starr and other seepage lakes in the permeable sandhills of central Florida are vulnerable to climate changes as they rely exclusively on rainfall and groundwater for inflows in a setting where annual rainfall and recharge vary widely. The groundwater inflow typically arrives from a small catchment area bordering the lake. The sinkhole origin of these lakes combined with groundwater pumping from underlying aquifers further complicate groundwater interactions. Understanding the lake-groundwater interactions and their effects on lake stage over multi-decadal climate cycles is needed to manage groundwater pumping and public expectation about future lake levels. The interdependence between climate, recharge, changing lake area and the groundwater catchment pose unique challenges to simulating lake-groundwater interactions. During the 10-year study period, Lake Starr stage fluctuated more than 13 feet and the lake surface area receded and expanded from 96 acres to 148 acres over drier and wetter years that included hurricanes, two El Nino events and a La Nina event. The recently developed Unsaturated Zone Flow (UZF1) and Lake (LAK7) packages for MODFLOW-2005 were used to simulate the changing lake sizes and the extent of the groundwater catchment contributing flow to the lake. The lake area was discretized to occupy the largest surface area at the highest observed stage and then allowed to change size. Lake cells convert to land cells and receive infiltration as receding lake area exposes the underlying unsaturated zone to rainfall and recharge. The unique model conceptualization also made it possible to capture the dynamic size of the groundwater catchment contributing to lake inflows, as the surface area and volume of the lake changed during the study

Lake Granbury and Lake Whitney Assessment Initiative Final Scientific/Technical Report Summary

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, B. L.; Roelke, Daniel; Brooks, Bryan

A team of Texas AgriLife Research, Baylor University and University of Texas at Arlington researchers studied the biology and ecology of Prymnesium parvum (golden algae) in Texas lakes using a three-fold approach that involved system-wide monitoring, experimentation at the microcosm and mesocosm scales, and mathematical modeling. The following are conclusions, to date, regarding this organism's ecology and potential strategies for mitigation of blooms by this organism. In-lake monitoring revealed that golden algae are present throughout the year, even in lakes where blooms do not occur. Compilation of our field monitoring data with data collected by Texas Parks and Wildlife andmore » Brazos River Authority (a period spanning a decade) revealed that inflow and salinity variables affect bloom formations. Thresholds for algae populations vary per lake, likely due to adaptations to local conditions, and also to variations in lake-basin morphometry, especially the presence of coves that may serve as hydraulic storage zones for P. parvum populations. More specifically, our in-lake monitoring showed that the highly toxic bloom that occurred in Lake Granbury in the winter of 2006/2007 was eliminated by increased river inflow events. The bloom was flushed from the system. The lower salinities that resulted contributed to golden algae not blooming in the following years. However, flushing is not an absolute requirement for bloom termination. Laboratory experiments have shown that growth of golden algae can occur at salinities ~1-2 psu but only when temperatures are also low. This helps to explain why blooms are possible during winter months in Texas lakes. Our in-lake experiments in Lake Whitney and Lake Waco, as well as our laboratory experiments, revealed that cyanobacteria, or some other bacteria capable of producing algicides, were able to prevent golden algae from blooming. Identification of this organism is a high priority as it may be a key to managing golden algae

Water balance of a lake with floodplain buffering: Lake Tana, Blue Nile Basin, Ethiopia

NASA Astrophysics Data System (ADS)

Dessie, Mekete; Verhoest, Niko E. C.; Pauwels, Valentijn R. N.; Adgo, Enyew; Deckers, Jozef; Poesen, Jean; Nyssen, Jan

2015-03-01

Lakes are very important components of the earth's hydrological cycle, providing a variety of services for humans and ecosystem functioning. For a sustainable use of lakes, a substantial body of knowledge on their water balance is vital. We present here a detailed daily water balance analysis for Lake Tana, the largest lake in Ethiopia and the source of the Blue Nile. Rainfall on the lake is determined by Thiessen polygon procedure, open water evaporation is estimated by the Penman-combination equation and observed inflows for the gauged catchments as well as outflow data at the two lake outlets are directly used. Runoff from ungauged catchments is estimated using a simple rainfall-runoff model and runoff coefficients. Hillslope catchments and floodplains are treated separately, which makes this study unique compared to previous water balance studies. Impact of the floodplain on the lake water balance is analyzed by conducting scenario-based studies. We found an average yearly abstraction of 420 × 106 m3 or 6% of river inflows to the lake by the floodplain in 2012 and 2013. Nearly 60% of the inflow to the lake is from the Gilgel Abay River. Simulated lake levels compare well with the observed lake levels (R2 = 0.95) and the water balance can be closed with a closure error of 82 mm/year (3.5% of the total lake inflow). This study demonstrates the importance of floodplains and their influence on the water balance of the lake and the need of incorporating the effects of floodplains and water abstraction for irrigation to improve predictions.

Molecular phylogeny of extant Holothuroidea (Echinodermata).

PubMed

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

2017-06-01

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

Morphological variation of siscowet lake trout in Lake Superior

USGS Publications Warehouse

Bronte, C.R.; Moore, S.A.

2007-01-01

Historically, Lake Superior has contained many morphologically distinct forms of the lake trout Salvelinus namaycush that have occupied specific depths and locations and spawned at specific times of the year. Today, as was probably the case historically, the siscowet morphotype is the most abundant. Recent interest in harvesting siscowets to extract oil containing omega-3 fatty acids will require additional knowledge of the biology and stock structure of these lightly exploited populations. The objective of this study was to determine whether shape differences exist among siscowet populations across Lake Superior and whether these shape differences can be used to infer stock structure. Morphometric analysis (truss protocol) was used to differentiate among siscowets sampled from 23 locations in Lake Superior. We analyzed 31 distance measurements among 14 anatomical landmarks taken from digital images of fish recorded in the field. Cluster analysis of size-corrected data separated fish into three geographic groups: The Isle Royale, eastern (Michigan), and western regions (Michigan). Finer scales of stock structure were also suggested. Discriminant function analysis demonstrated that head measurements contributed to most of the observed variation. Cross-validation classification rates indicated that 67–71% of individual fish were correctly classified to their region of capture. This is the first study to present shape differences associated with location within a lake trout morphotype in Lake Superior.

Geophysical investigation of sentinel lakes in Lake, Seminole, Orange, and Volusia Counties, Florida

USGS Publications Warehouse

Reich, Christopher; Flocks, James; Davis, Jeffrey

2012-01-01

This study was initiated in cooperation with the St. Johns River Water Management District (SJRWMD) to investigate groundwater and surface-water interaction in designated sentinel lakes in central Florida. Sentinel lakes are a SJRWMD established set of priority water bodies (lakes) for which minimum flows and levels (MFLs) are determined. Understanding both the structure and lithology beneath these lakes can ultimately lead to a better understanding of the MFLs and why water levels fluctuate in certain lakes more so than in other lakes. These sentinel lakes have become important water bodies to use as water-fluctuation indicators in the SJRWMD Minimum Flows and Levels program and will be used to define long-term hydrologic and ecologic performance measures. Geologic control on lake hydrology remains poorly understood in this study area. Therefore, the U.S. Geological Survey investigated 16 of the 21 water bodies on the SJRWMD priority list. Geologic information was obtained by the tandem use of high-resolution seismic profiling (HRSP) and direct-current (DC) resistivity profiling to isolate both the geologic framework (structure) and composition (lithology). Previous HRSP surveys from various lakes in the study area have been successful in identifying karst features, such as subsidence sinkholes. However, by using this method only, it is difficult to image highly irregular or chaotic surfaces, such as collapse sinkholes. Resistivity profiling was used to complement HRSP by detecting porosity change within fractured or collapsed structures and increase the ability to fully characterize the subsurface. Lake Saunders (Lake County) is an example of a lake composed of a series of north-south-trending sinkholes that have joined to form one lake body. HRSP shows surface depressions and deformation in the substrate. Resistivity data likewise show areas in the southern part of the lake where resistivity shifts abruptly from approximately 400 ohm meters (ohm-m) along the

Mercury accumulation in yellow perch in Wisconsin seepage lakes: Relation to lake characteristics

USGS Publications Warehouse

Cope, W.G.; Wiener, J.G.; Rada, R.G.

1990-01-01

We studied relations between lacustrine characteristics and the total mercury (Hg) content of calendar age-2 yellow perch (Perca flavescens) in 10 seepage lakes in north-central Wisconsin. Mean concentrations and burdens (masses) of Hg in whole perch varied widely among lakes, were negatively correlated with lake pH and were positively correlated with total Hg concentration in surficial profundal sediment. Approximately 80 to 90% of the variation in Hg concentration and burden in whole perch was explained with multiple regressions containing two independent variables: either lake pH or alkalinity, and Hg concentration in surficial sediment. Variation among lakes in the Hg concentration in yellow perch was unrelated to their relative rates of growth. The mean concentration of Hg in axial muscle tissue of age-5 walleyes (Stizostedion vitreum vitreum) from five of the study lakes was highly correlated with the mean concentration in whole age-2 perch in the same lakes. We hypothesized that the high Hg concentrations often seen in piscivorous fish in low-alkalinity lakes (relative to high-alkalinity lakes) is at least partly due to a greater dietary intake of Hg in such waters. Furthermore, the analysis of small yellow perch—the preferred prey of adult walleyes and an important forage species for many predatory fishes in the north-central United States—may be an effective approach to assessing Hg bioavailability in the region's lakes.

Using Pseudozoids to Teach Classification and Phylogeny to Middle School Students

ERIC Educational Resources Information Center

Freidenberg, Rolfe Jr.; Kelly, Martin G.

2004-01-01

This research compared the outcomes of teaching middle school students two different methods of classification and phylogeny. Two classes were randomly selected and taught using traditional methods of instruction. Three classes were taught using the "Pseudozoid" approach, where students learned to classify, develop and read dichotomous keys, and…

Estimate of net trophic transfer efficiency of PCBs to Lake Michigan lake trout from their prey

USGS Publications Warehouse

Madenjian, Charles P.; Hesselberg, Robert J.; DeSorcie, Timothy J.; Schmidt, Larry J.; Stedman, Ralph M.; Quintal, Richard T.; Begnoche, Linda J.; Passino-Reader, Dora R.

1998-01-01

Most of the polychlorinated biphenyl (PCB) body burden accumulated by lake trout (Salvelinus namaycush) from the Laurentian Great Lakes is from their food. We used diet information, PCB determinations in both lake trout and their prey, and bioenergetics modeling to estimate the efficiency with which Lake Michigan lake trout retain PCBs from their food. Our estimates were the most reliable estimates to date because (a) the lake trout and prey fish sampled during our study were all from the same vicinity of the lake, (b) detailed measurements were made on the PCB concentrations of both lake trout and prey fish over wide ranges in fish size, and (c) lake trout diet was analyzed in detail over a wide range of lake trout size. Our estimates of net trophic transfer efficiency of PCBs to lake trout from their prey averaged from 0.73 to 0.89 for lake trout between the ages of 5 and 10 years old. There was no evidence of an upward or downward trend in our estimates of net trophic transfer efficiency for lake trout between the ages of 5 and 10 years old, and therefore this efficiency appeared to be constant over the duration of the lake trout's adult life in the lake. On the basis of our estimtes, lake trout retained 80% of the PCBs that are contained within their food.

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.

Climate-driven changes in grassland vegetation, snow cover, and lake water of the Qinghai Lake basin

NASA Astrophysics Data System (ADS)

Wang, Xuelu; Liang, Tiangang; Xie, Hongjie; Huang, Xiaodong; Lin, Huilong

2016-07-01

Qinghai Lake basin and the lake have undergone significant changes in recent decades. We examine MODIS-derived grassland vegetation and snow cover of the Qinghai Lake basin and their relations with climate parameters during 2001 to 2010. Results show: (1) temperature and precipitation of the Qinghai Lake basin increased while evaporation decreased; (2) most of the grassland areas improved due to increased temperature and growing season precipitation; (3) weak relations between snow cover and precipitation/vegetation; (4) a significantly negative correlation between lake area and temperature (r=-0.9, p<0.05) and (5) a positive relation between lake level (lake-level difference) and temperature (precipitation). Compared with Namco Lake (located in the inner Tibetan Plateau) where the primary water source of lake level increases was the accelerated melt of glacier/perennial snow cover in the lake basin, for the Qinghai Lake, however, it was the increased precipitation. Increased precipitation explained the improvement of vegetation cover in the Qinghai Lake basin, while accelerated melt of glacier/perennial snow cover was responsible for the degradation of vegetation cover in Namco Lake basin. These results suggest different responses to the similar warming climate: improved (degraded) ecological condition and productive capacity of the Qinghai Lake basin (Namco Lake basin).

Lake whitefish and Diporeia spp. in the Great lakes: an overview

USGS Publications Warehouse

Nalepa, Thomas F.; Mohr, Lloyd C.; Henderson, Bryan A.; Madenjian, Charles P.; Schneeberger, Philip J.

2005-01-01

Because of growing concern in the Great Lakes over declines in abundance and growth of lake whitefish (Coregonus clupeaformis) and declines in abundance of the benthic amphipod Diporeia spp., a workshop was held to examine past and current trends, to explore trophic links, and to discuss the latest research results and needs. The workshop was divided into sessions on the status of populations in each of the lakes, bioenergetics and trophic dynamics, and exploitation and management. Abundance, growth, and condition of whitefish populations in Lakes Superior and Erie are stable and within the range of historical means, but these variables are declining in Lakes Michigan and Ontario and parts of Lake Huron. The loss of Diporeia spp., a major food item of whitefish, has been a factor in observed declines, particularly in Lake Ontario, but density-dependent factors also likely played a role in Lakes Michigan and Huron. The loss of Diporeia spp. is temporally linked to the introduction and proliferation of dreissenid mussels, but a direct cause for the negative response of Diporeia spp. has not been established. Given changes in whitefish populations, age-structured models need to be re-evaluated. Other whitefish research needs to include a better understanding of what environmental conditions lead to strong year-classes, improved aging techniques, and better information on individual population (stock) structure. Further collaborations between assessment biologists and researchers studying the lower food web would enhance an understanding of links between trophic levels.

Lake trout (Salvelinus namaycush) populations in Lake Superior and their restoration in 1959-1993

USGS Publications Warehouse

Hansen, Michael J.; Peck, James W.; Schorfhaar, Richard G.; Selgeby, James H.; Schreiner, Donald R.; Schram, Stephen T.; Swanson, Bruce L.; MacCallum, Wayne R.; Burnham-Curtis, Mary K.; Curtis, Gary L.; Heinrich, John W.; Young, Robert J.

1995-01-01

Naturally-reproducing populations of lake trout (Salvelinus namaycush) have been reestablished in most of Lake Superior, but have not been restored to 1929-1943 average abundance. Progress toward lake trout restoration in Lake Superior is described, management actions are reviewed, and the effectiveness of those actions is evaluated; especially stocking lake trout as a tool for building spawning stocks, and subsequently, populations of wild recruits. Widespread destruction of lake trout stocks in the 1950s due to an intense fishery and sea lamprey (Petromyzon marinus) predation resulted in lower overall phenotypic diversity than was previously present. Stocking of yearling lake trout, begun in the 1950s, produced high densities of spawners that reproduced wherever inshore spawning habitat was widespread. Sea lampreys were greatly reduced, beginning in 1961, using selective chemical toxicants and barrier dams, but continue to exert substantial mortality. Fishery regulation was least effective in Wisconsin, where excessive gillnet effort caused high by-catch of lake trout until 1991, and in eastern Michigan, where lake trout restoration was deferred in favor of a tribal fishery for lake whitefish (Coregonus clupeaformis) in 1985. Restoration of stocks was quicker in offshore areas where remnant wild lake trout survived and fishing intensity was low, and was slower in inshore areas where stocked lake trout reproduced successfully and fishing intensity was high. Inshore stocks of wild lake trout are currently about 61 % of historic abundance in Michigan and 53% in Wisconsin. Direct comparison of modern and historic abundances of inshore lake trout stocks in Minnesota and Ontario is impossible due to lack of historic stock assessment data. Stocks in Minnesota are less abundant at present than in Michigan or Wisconsin, and stocks in Ontario are similar to those in Michigan. Further progress in stock recovery can only be achieved if sea lampreys are depressed and if

Three-gene based phylogeny of the Urostyloidea (Protista, Ciliophora, Hypotricha), with notes on classification of some core taxa☆