bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minority rule supertrees? MRP, Compatibility, and Minimum Flip may display the least frequent groups
Authors: Goloboff Pablo A. 
Published: July 2005

AbstractNew examples are presented, showing that supertree methods such as matrix representation with parsimony, minimum flip trees, and compatibility analysis of the matrix representing the input trees, produce supertrees that cannot be interpreted as displaying the groups present in the majority of the input trees. These methods may produce a supertree displaying some groups present in the minority of the trees, and contradicted by the majority. Of the three methods, compatibility analysis is the least used, but it seems to be the one that differs the least from majority rule consensus. The three methods are similar in that they choose the supertree(s) that best fit the set of input trees (quantified as some measure of the fit to the matrix representation of the input trees); in the case of complete trees, it is argued that, for a supertree method to be equivalent to majority rule or frequency difference consensus, two necessary (but not sufficient) conditions must be met. First, the measure of fit between a supertree and an input tree must be symmetrical. Second, the fit for a character representing a group must be measured as absolute: either it fits or it does not fit. In the restricted case of complete and equally resolved input trees, compatibility analysis (unlike MRP and minimum flipping) fulfils these two conditions: it is symmetrical (i.e., as long as the trees have the same taxon sets and are equally resolved, the number of characters in the matrix representation of tree A that require homoplasy in tree B is always the same as the number of characters in the matrix representation of tree B that require homoplasy in tree A) and it measures fit as all‐or‐none. In the case of just two complete and equally resolved input trees, the two conditions (symmetry and absolute fit) are necessary and sufficient, which explains why the compatibility analysis of such trees behaves as majority consensus. With more than two such trees, these conditions are still necessary but no longer sufficient for the equivalence; in such cases, the compatibility supertree may differ significantly from the majority rule consensus, even when these conditions apply (as shown by example). MRP and minimum flipping are asymmetric and measure various degrees of fit for each character, which explains why they often behave very differently from majority rule procedures, and why they are very likely to have groups contradicted by each of the input trees, or groups supported by a minority of the input trees.© The Willi Hennig Society 2005.
Phylogenetic analysis of Themira (Sepsidae: Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study
Authors: Laamanen Torsten R. , Meier Rudolf , Miller Michael A. , Hille Axel , Wiegmann Brian M. 
Published: July 2005

AbstractIn this study we use sensitivity analysis sensuWheeler (1995) for a matrix entirely composed of DNA sequences. We propose that not only congruence but also phylogenetic structure, as measured by character resampling, should be used to choose among competing weighting regimes. An extensive analysis of a five‐gene data set for Themira (Sepsidae: Diptera) reveals that even with different ways of partitioning the data, measures of topological congruence, character incongruence, and phylogenetic structure favor similar weighting regimes involving the down‐weighting of transitions. We furthermore use sensitivity analysis for obtaining empirical evidence that allows us to select weights for third positions, deciding between treating indels as fifth character states or missing values, and choosing between manual and computational alignments. For our data, sensitivity analysis favors manual alignment over a Clustal‐generated numerical alignment, the treatment of indels as fifth character states over considering them missing values, and equal weights for all positions in protein‐encoding genes over the down‐weighting of third positions. Among the topological congruence measures compared, symmetric tree distance performed best. Partitioned Bremer Support analysis reveals that COI contributes the largest amount of support for our phylogenetic tree for Themira.© The Willi Hennig Society 2005.
Water‐repellent soil and its relationship to granularity, surface roughness and hydrophobicity: a materials science view
Authors: McHale G. , Newton M. I. , Shirtcliffe N. J. 
Published: July 2005

SummaryConsiderable soil water repellency has been observed at a wide range of locations worldwide. The soil exhibiting water repellency is found within the upper part of the soil profile. The reduced rate of water infiltration into these soils leads to severe runoff erosion, and reduction of plant growth. Soil water repellency is promoted by drying of soil, and can be induced by fire or intense heating of soil containing hydrophobic organic matter. Recent studies outside soil science have shown how enhancement of the natural water repellency of materials, both porous and granular, by surface texture (i.e. surface roughness, pattern and morphology) into super‐hydrophobicity is possible. The similarities between these super‐hydrophobic materials and observed properties of water‐repellent soil are discussed from a non‐soil scientist, materials‐based perspective. A simple model is developed for a hydrophobic granular surface and it is shown that this can provide a mechanism for enhancement of soil water repellency through the relative size and spacing of grains and pores. The model provides a possible explanation for why soil water repellency should be more prevalent under dry conditions than wet. Consequences for water runoff, raindrop splash and soil erosion are discussed.
Redox reactions and phosphorus release in re‐flooded soils of an altered wetland
Authors: Shenker M. , Seitelbach S. , Brand S. , Haim A. , Litaor M. I. 
Published: July 2005

SummaryPhosphorus loss from land can be a major factor affecting surface water quality. We studied P‐release mechanisms in wetland soils that had been drained and cultivated for four decades and then re‐flooded. We measured redox, pH and solution composition in two sites in the field and in four peat and calcareous soils incubated in biogeochemical microcosms. The redox and pH measurements during the 120 days of incubation and the resulting soil solution composition indicated that the main process leading to P release is reductive dissolution of ferric hydroxides on which P was adsorbed and in which P was occluded. The molar Fe:P ratio increased with period of reduction from below 1 in the first week of re‐flooding to 15–60 after 120 days. This suggests an increased P‐retention capacity upon reoxidation of the soil solution, whether within the soil profile or in the drainage canals. Prolonged flooding of the calcite‐poor, gypsum‐rich peat soils increased the oversaturation of soil solutions with respect to hydroxyapatite and occasionally β‐Ca3(PO4)2(c), indicating that in spite of the large Ca concentration, the rate of Ca‐P precipitation was insufficient to maintain the saturation status of the Ca‐P system. In the calcareous soils the Ca‐P system effectively controlled the P activity in soil solution throughout the incubation period. In both cases the precipitation of Ca‐P minerals could be an important P‐retention mechanism.
Virus and microbial loop dynamics over an annual cycle in three contrasting Antarctic lakes
Authors: MADAN NANETTE J. , MARSHALL WILLIAM A. , LAYBOURN‐PARRY JOHANNA 
Published: July 2005

Summary1. Viral and microbial loop dynamics were investigated over an annual cycle in three contrasting saline Antarctic lakes – Highway Lake (salinity 4‰), Pendant Lake (salinity 19‰) and Ace Lake, a meromictic system (with a mixolimnion salinity of 18‰) in order to assess the importance of viruses in extreme, microbially dominated systems.2. Virus like particles (VLP) showed no clear seasonal pattern, with high concentrations occurring in both winter and summer (range 0.89 × 107 ± 0.038 to 12.017 × 107 ± 1.28 mL−1). VLP abundances reflected lake productivity based on chlorophyll a concentrations. Bacterial abundances and biomass did not correlate with VLP numbers except in Pendant Lake, the most productive of the three lakes studied.3. Pendant Lake supported the highest bacterial biomass (range Highway: 18.44 ± 1.35 to 59.43 ± 2.80 ng C mL−1; Ace: 14.42 ± 2.69 to 68.39 ± 2.95 ng C mL−1; Pendant: 31.36 ± 3.94 to 115.95 ± 4.49 ng C mL−1) so that virus to bacteria ratios (VBR) (range 30.48 ± 7.96 to 96.67 ± 8.21) were higher in Ace Lake (range 30.58 ± 3.98 to 80.037 ± 1.60) and Highway Lake (range 18.63 ± 3.12 to 126.74 ± 6.50).4. Negative correlations occurred between VLP and cryptophytes (dominant phototrophic nanoflagellates), suggesting that they were not hosts to lytic viruses. Among the other protists only the heterotrophic nanoflagellates of Highway Lake (dominated by the marine choanoflagellate Diaphanoeca grandis) showed a positive correlation with VLP.5. The VLP was negatively correlated with photosynthetically active radiation (PAR) and temperature, both of which increased with ice thinning and breakout, increasing viral decay. In winter VLP probably persisted in cold, dark water.6. High VLP concentrations and high VBR (values at the upper end of those reported for marine and lacustrine systems) indicated that viruses, most of which were probably bacteriophage, are a major element within the microbial communities in extreme, saline lakes.
Is there competition among ciliates and nematodes?
Authors: BERGTOLD MATTHIAS , GÜNTER VIKTOR , TRAUNSPURGER WALTER 
Published: July 2005

Summary1. Biotic interaction between the ciliate Cyclidium glaucoma and the nematode Caenorhabditis elegans was investigated by manipulating the densities of the organisms in microcosms with and without sediment.2. After 11 days the abundance of ciliates, nematodes and bacteria as well as extracellular enzyme activity were determined. Ciliates had a negative effect on nematode abundance in microcosms without sediment and in microcosms with sandy sediment, whereas in muddy sediment the effect was less distinctive. An effect of nematodes on ciliates was not observed.3. The common resource bacteria were not affected negatively by the activity of the grazers. Overall grazer biomass increased with the addition of sediment to the microcosms, suggesting a rise of the carrying capacity in the experimental system. Especially in muddy sediment the abundance of bacteria and extracellular enzyme activity was higher compared to the microcosms without sediment.4. The results of the experiment suggest a strong interspecific competition between nematodes and ciliates, where nematodes are, at least temporary, strongly affected.
Combining a regional climate model with a phytoplankton community model to predict future changes in phytoplankton in lakes
Authors: ALEX ELLIOTT J. , THACKERAY STEPHEN J. , HUNTINGFORD CHRIS , JONES RICHARD G. 
Published: July 2005

Summary1. Linking a regional climate model (RCM) configured for contemporary atmospheric greenhouse gas concentrations, with a phytoplankton community model (PROTECH) produced realistic simulations of 20 years of recent phytoplankton data from Bassenthwaite Lake, in the North‐West of England.2. Meteorological drivers were derived from the RCM to represent a future climate scenario involving a 1% per annum compound increase in atmospheric CO2 concentrations until 2100. Using these drivers, PROTECH was run for another 20 year period representing the last two decades of the 21st century.3. Comparison of these present and future simulations revealed likely impacts on the current seasonal phytoplankton development. Under future climate conditions, the simulated spring bloom showed an increase in cyanobacteria dominance caused by greater success of Planktothrix. Also, the summer cyanobacteria bloom declined earlier because of nutrient limitation caused by the increased spring growth. Overall productivity in the lake did not change.4. Analysis showed that these predicted changes were driven by changes in water temperature, which were in turn triggered by the higher air temperatures predicted by the RCM.
A demographic model explains life‐history variation in Arabis fecunda
Authors: LESICA P. , YOUNG T. P. 
Published: July 2005

Summary

The distinction between semelparity and iteroparity is one of the most fundamental in life‐history biology. Despite an abundance of theory proposed to explain the evolution of this dichotomy, few quantitative empirical tests exist.
We report here on life‐history variation in the perennial herb Arabis fecunda (Brassicaceae), in which differences in the frequency of iteroparity and terminal flowering (facultative semelparity) are expressed among populations. These differences are consistent over time, and a common garden experiment suggested that they may be at least partly genetically based.
An analysis of demographic data over a 5‐year period from three populations indicated that a simple demographic model of life‐history evolution is consistent with life‐history variation in this species. Individuals in populations with greater mean adult survival were more likely to express iteroparity than individuals in populations with lower adult survival.
How are animals with ornaments predicted to compensate for a bad start in life? A dynamic optimization model approach
Authors: LINDSTRÖM J. , METCALFE N. B. , ROYLE N. J. 
Published: July 2005

SummaryAnimals may compensate for a poor start in life by accelerated (‘catch up’) growth if conditions subsequently improve. Although this incurs costs, the occurrence of catch up growth across taxa suggests there are also considerable benefits to it.A state‐dependent, dynamic optimization model was constructed to explore how and under what circumstances individuals are predicted to vary their compensatory resource allocation to somavssexual ornaments.In the model, individuals of differing initial state either experienced a constant environment, or one in which initially poor resource availability subsequently improved. Individuals could allocate resources, at each time step, to body growth, somatic maintenance or a sexual ornament.The results showed that resource allocation strategies are sensitive to the fitness return functions used. Consequently, there is a wide range of potential optimal adult phenotypes.Four general patterns emerged. (i) Making specific predictions about compensatory resource allocation is difficult owing to the general lack of information about the shape of the fitness return functions. (ii) Complete compensation in expected fitness (such that a poor start does not reduce future fitness) is likely to occur rarely. (iii) If a sexual ornament is required for mating success, compensating individuals are likely to be smaller in body size than those experiencing a constant environment. (iv) Poor initial resource availability in life tends to delay sexual maturation.
Cichlid jaw mechanics: linking morphology to feeding specialization
Authors: HULSEY C. D. , GARCÍA DE LEÓN F. J. 
Published: July 2005

Summary

The utility of the anterior jaw four‐bar linkage model and the trophic consequences of jaw protrusion were investigated in Heroine cichlids by examining the evolutionary relationships among maxillary kinematic transmission (KT), maximum jaw protrusion and dietary specialization on evasive prey.
In 31 species of Heroine cichlids, a four‐bar linkage model was used to generate kinematic predictions of maxillary KT, the angular amount of maxilla rotation per unit lower jaw rotation, expected during mouth opening. Maxillary KT averaged 0·79 and ranged from 0·58 in Herichthys tamasopoensis to 1·06 in Petenia splendida.
Because the maxilla pushes the toothed premaxilla out during jaw protrusion, we predicted higher maxillary KT should characterize species with greater maximum jaw protrusion. Maximum jaw protrusion ranged from 1·5 to 14·2% of cichlid standard length and was highly correlated with greater maxillary KT.
The proportion of fish and crustaceans in the diet of these cichlids was correlated with maximum protrusion, suggesting jaw protrusion may aid in the capture of evasive prey.
Phylogenetic independent contrasts indicate changes in anterior jaw mechanics may be necessary for diversification of cichlid jaw protrusion abilities, and the labile evolution of jaw protrusion in Heroine cichlids likely facilitated the repeated specialization on evasive prey during their diversification.
Estimating adhesive seed‐dispersal distances: field experiments and correlated random walks
Authors: MOUISSIE A. M. , LENGKEEK W. , VAN DIGGELEN R. 
Published: July 2005

Summary

In this study we aimed to estimate distance distributions of adhesively dispersed seeds and the factors that determine them.
Seed attachment and detachment were studied using field experiments with a real sheep, a sheep dummy and a cattle dummy. Seed‐retention data were used in correlated random walk models to simulate adhesive seed dispersal.
Seed attachment to the sheep dummy was larger in quantity and in number of species, and stronger in relation to seed density in the vegetation, than was seed attachment to the cattle dummy. Species found on the real sheep were also found on the sheep dummy.
Detachment from sheep wool differed little between smooth, bristly, small or large seeds, but smooth seeds detached from cattle fur within a few metres. Seeds applied within reach of vegetation detached sooner than seeds applied higher on the dummy.
The simulations showed that sheep are long‐distance seed‐dispersal vectors for seeds of any morphology (99 percentile distance, 2·9 km). The virtual cattle and Fallow Deer dispersed bristly and hooked seeds over long distances (99 percentile distance, 435–840 m), but not smooth seeds. Wood Mouse simulations generated only short‐distance dispersal (99 percentile distance, 12 m).
Lactate and free glucose in supercooled hatchling Painted Turtles (Chrysemys picta) exposed to natural and semi‐natural thermal regimes
Authors: PACKARD M. J. , PACKARD G. C. 
Published: July 2005

Summary

Hatchlings of the North American Painted Turtle, Chrysemys picta (Schneider 1783) typically spend their first winter of life inside a shallow, terrestrial hibernaculum (the natal nest) where they commonly are exposed for extended periods to ice and cold. Current evidence indicates that turtles withstand such exposure by resisting freezing and becoming supercooled.
Supercooled hatchlings held at constant temperatures in the laboratory experience circulatory impairment and stagnant hypoxia, and consequently rely on anaerobic metabolism to meet a portion of their energy needs. As a result, lactate accumulates in bodies of supercooled animals.
The first experiment in the current investigation demonstrated that unfrozen hatchlings exposed to subzero temperatures like those recorded in a natural hibernaculum contained elevated quantities of lactic acid (and free glucose). This finding validates the widespread reliance on laboratory studies to gain insights regarding the physiology of animals overwintering in the field.
In a second study, hatchling Painted Turtles held for 20 days at −6 °C contained nearly twice as much lactate as turtles sampled after 10 days at that temperature. Hatchlings held for 10 days at −6 °C and then for another 10 days at −3 °C also contained more lactate than turtles sampled after 10 days at −6 °C, but not as much as the hatchlings that spent 20 days at −6 °C. Thus, animals held for part of the time at the higher subzero temperature still relied on anaerobic metabolism, but not to the same extent as turtles held continuously at the lower temperature. In contrast, hatchlings held for 10 days at −6 °C and then for another 10 days at either 0 °C or +3 °C contained no more lactate than control animals that never were exposed to subzero temperatures. Hatchlings exposed for the second 10 days to either 0 °C or +3 °C apparently were able to catabolize or otherwise process all the lactate that was accumulated during the first 10 days of their treatment.
Free glucose in bodies of hatchlings was elevated in all animals exposed to subzero temperatures, even when the initial exposure was followed by 10 days at temperatures as high as +3 °C. This finding has important implications with regard to the substrate that is used to support intermediary metabolism in supercooled turtles as well as to the metabolic pathways that are used to remove accumulated lactate once body temperature of the turtles rises at least to 0 °C.
Heat shocking of Philippine green mussels, Perna viridis
Authors: Azanza Ma. Patricia V. , Azanza Rhodora V. , Ventura Sharon R. 
Published: July 2005

SummaryThe use of different methods of heat shocking for green mussels was evaluated. These methods were heat treatment at 60 and 100 °C either in a hot water bath, in water‐saturated air or in dry heat. It was established that relaxation of the adductor muscles, which facilitates shucking, was quickest for the hot water bath treatment at both test temperatures. This treatment caused 100% of the mussels to be open at either 60 or 100 °C in 3–5 and 0.33–1 min exposure times respectively. The sensory acceptability of all the heat‐shocked mussel meats ranged from dislike slightly to like slightly. Generally, the increase in pH and water activity of the heat‐treated mussels, relative to the untreated mussels, was not statistically significant at the 5% level of significance.
Validation and cross‐comparison of MRI temperature mapping against fibre optic thermometry for microwave heating of foods
Authors: Nott Kevin P. , Hall Laurance D. 
Published: July 2005

SummaryThe heating of a 5% starch gel in a standard domestic microwave oven has been measured using a combination of magnetic resonance imaging (MRI) ‘offline’, and fibre optic thermometry ‘online’. MRI was used to locate potential hot and cold spots for optimal placement of the fibre optic probes used to measure temperatures both during microwave heating and for the subsequent 100 s which is the time required for transfer of the sample to the magnet (38–48 s) and the acquisition of the 32 × 32 × 128 pixel MRI temperature map (52 s). The MRI data have a systematic offset because of the finite transferral time and duration of the MRI scan, but not to the detriment of high spatial resolution which is necessary to resolve the high temperature gradients induced. It is believed that 3D MRI temperature mapping will be invaluable to further studies of microwave heating as optimized placement of fibre optic thermometry probes is difficult, and the spatial distribution of microwave absorption is highly variable.