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PubMed1997

A model of mass extinction.

In the last few years a number of authors have suggested that evolution may be a so-called self-organized critical phenomenon, and that critical processes might have a significant effect on the dynamics of ecosystems. In particular it has been suggested that mass extinction may arise through a purely biotic mechanism as the result of "coevolutionary avalanches". In this paper we first explore the empirical evidence which has been put forward in favor of this conclusion. The data center principally around the existence of power-law functional forms in the distribution of the sizes of extinction events and other quantities. We then propose a new mathematical model of mass extinction which does not rely on coevolutionary effects and in which extinction is caused entirely by the action of environmental stress on species. In combination with a simple model of species adaption we show that this process can account for all the observed data without the need to invoke coevolution and critical processes. The model also makes some independent predictions, such as the existence of "aftershock" extinctions in the aftermath of large mass extinction events, which should in theory be testable against the fossil record.

Animals↗
PubMed2000

Predicting the time to quasi-extinction for populations far below their carrying capacity.

Populations threatened by extinction are often far below their carrying capacity. A population collapse or quasi-extinction is defined to occur when the population size reaches some given lower density. If this density is chosen to be large enough for the demographic stochasticity to be ignored compared to environmental stochasticity, then the logarithm of the population size may be modelled by a Brownian motion until quasi-extinction occurs. The normal-gamma mixture of inverse Gaussian distributions can then be applied to define prediction intervals for the time to quasi-extinction in such processes. A similar mixture is used to predict the population size at a finite time for the same process provided that quasi-extinction has not occurred before that time. Stochastic simulations indicate that the coverage of the prediction interval is very close to the probability calculated theoretically. As an illustration, the method is applied to predict the time to extinction of a declining population of white stork in southwestern Germany.

Animals↗
PubMed1999

Extinction risk and the 1/f family of noise models.

In order to predict extinction risk in the presence of reddened, or correlated, environmental variability, fluctuating parameters may be represented by the family of 1/f noises, a series of stochastic models with different levels of variation acting on different timescales. We compare the process of parameter estimation for three 1/f models (white, pink and brown noise) with each other, and with autoregressive noise models (which are not 1/f noises), using data from a model time-series (length, T) of population. We then calculate the expected increase in variance and the expected extinction risk for each model, and we use these to explore the implication of assuming an incorrect noise model. When parameterising these models, it is necessary to do so in terms of the measured ("sample") parameters rather than fundamental ("population") parameters. This is because these models are non-stationary: their parameters need not stabilize on measurement over long periods of time and are uniquely defined only over a specified "window" of timescales defined by a measurement process. We find that extinction forecasts can differ greatly between models, depending on the length, T, and the coefficient of variability, CV, of the time series used to parameterise the models, and on the length of time into the future which is to be projected. For the simplest possible models, ones with population itself the 1/f noise process, it is possible to predict the extinction risk based on CV of the observed time series. Our predictions, based on explicit formulae and on simulations, indicate that (a) for very short projection times relative to T, brown and pink noise models are usually optimistic relative to equivalent white noise model; (b) for projection timescales equal to and substantially greater than T, an equivalent brown or pink noise model usually predicts a greater extinction risk, unless CV is very large; and (c) except for very small values of CV, for timescales very much greater than T, the brown and pink models present a more optimistic picture than the white noise model. In most cases, a pink noise is intermediate between white and brown models. Thus, while reddening of environmental noise may increase the long-term extinction probability for stationary processes, this is not generally true for non-stationary processes, such as pink or brown noises.

Animals↗
PubMed2003

Deterministic extinction effect of parasites on host populations.

Experimental studies have shown that parasites can reduce host density and even drive host population to extinction. Conventional mathematical models for parasite-host interactions, while can address the host density reduction scenario, fail to explain such deterministic extinction phenomena. In order to understand the parasite induced host extinction, Ebert et al. (2000) formulated a plausible but ad hoc epidemiological microparasite model and its stochastic variation. The deterministic model, resembles a simple SI type model, predicts the existence of a globally attractive positive steady state. Their simulation of the stochastic model indicates that extinction of host is a likely outcome in some parameter regions. A careful examination of their ad hoc model suggests an alternative and plausible model assumption. With this modification, we show that the revised parasite-host model can exhibit the observed parasite induced host extinction. This finding strengthens and complements that of Ebert et al. (2000), since all continuous models are likely break down when all population densities are small. This extinction dynamics resembles that of ratio-dependent predator-prey models. We report here a complete global study of the revised parasite-host model. Biological implications and limitations of our findings are also presented.

Animals↗
PubMed1992

Statistical determination of the average values of the extinction coefficients of tryptophan and tyrosine in native proteins.

Spectroscopic measurement of protein concentration requires knowledge of the value of the relevant extinction coefficient. If the amino acid composition of a protein is known, however, extinction coefficients can be calculated approximately, provided that the values of the molar absorptivities for tryptophan and tyrosine residues in the protein are known. We have applied a matrix linear regression procedure and a mapping of average absolute deviations between experimental and calculated values to find molar extinction coefficients (epsilon M, 1 cm, 280 nm) of 5540 M-1 cm-1 for tryptophan and 1480 M-1 cm-1 for tyrosine residues in an "average" protein, as defined by a set of experimentally determined extinction coefficients for more than 30 proteins. Use of these values provides a significant improvement in extinction coefficient estimation over that obtained with the commonly used values obtained from solutions of model compounds in guanidine-HCl. The consistency of these results when compared to the large deviations often observed between experimentally determined extinction coefficients suggest that this method may offer acceptable accuracy in the initial estimation of molar absorptivities of globular proteins.

Animals↗
PubMed1984

Extinction of muscle-specific properties in somatic cell heterokaryons.

In studies of gene regulation using somatic cell fusion techniques, the analysis of heterokaryons circumvents several problematic aspects of the more traditional approach utilizing proliferating hybrid cells. We have analyzed the expression of muscle specific properties in heterokaryons between muscle and nonmuscle cells in order to investigate whether differentiating cells contain regulatory factors that repress the expression of alternative developmental pathways. Heterokaryons and cybrids were derived from polyethylene glycol-mediated fusion of differentiated mononucleate chicken myocytes with mouse melanoma cells, mouse melanoma cytoplasts, chicken fibroblasts, or other chicken myocytes. Our results demonstrate that fusion of a myocyte with a nonmyogenic cell generally results in extinction of muscle-specific properties in the immediate fusion product. Myocyte X melanoma heterokaryons ceased to express the skeletal muscle forms of myosin, desmin and creatine kinase, reinitiated DNA synthesis, and showed a loss of spontaneous fusion competence within 96 hr after their formation. Although chicken myocyte X mouse melanoma heterokaryons showed extinction of muscle specific properties, they continued to synthesize protein and to incorporate [3H]hypoxanthine, presumably due to the continued production of constitutive chicken HPRT. That presence of the melanoma nucleus was required for extinction to be observed was demonstrated by the continued expression of muscle proteins in cybrids between chicken myocytes and melanoma cytoplasts. Significantly, heterokaryons between chicken myocytes and chicken fibroblasts also exhibited extinction of muscle proteins, demonstrating for the first time that extinction is not restricted to fusions in which at least one parental cell type was derived from an established cell line. Our results strongly support the notion that extinction reflects cell-type specific gene regulatory mechanisms operative during development.

Animals↗
PubMed1988

Interocular transfer of extinction of visual pattern discriminations in split-chiasm and split-brain cats.

The interocular transfer of the extinction of visual pattern discrimination was studied in cats with either section of optic chiasm (split-chiasm cats) or combined sections of chiasm and forebrain commissures (split-brain cats). Visual pattern discriminations were monocularly learned and their interocular transfer was assessed through the opposite eye. Then, learning was unilaterally extinguished and interocular transfer of extinction was tested on the other side. In split-chiasm cats, the total number of trials to extinction criterion (EC) was significantly lower with the second eye than with the first eye, indicating a successful interocular transfer. In split-brain cats, EC with the second eye was attained faster than with the first in some performances; it was similar with both eyes in other tasks, and with the second eye was higher than with the first in still other tasks. Statistical analysis applied to this group of split-brain cats pointed out that extinction performances with the two eyes were not significantly different. These findings suggest that interocular transfer of extinction was abolished in split-brain cats and that memory for extinction was unilaterally established in the absence of forebrain commissures.

Animals↗
PubMed1988

Peripheral noradrenaline depletion does not impair extinction of food-rewarded running in the rat.

To test whether the sympathetic nervous system influences the inhibition of non-rewarded running in the runway, we examined the effects of peripheral noradrenaline depletion, induced by 6-hydroxydopamine (6-OHDA HBr, 30 mg/kg, i.p.), on extinction of food-rewarded running in rats. This was done in two separate experiments. In the first, in which the inter-trial interval (ITI) was one day and rats were injected before acquisition, running times at the end of extinction did not differ. The 6-OHDA appeared to slow down running times at the end of acquisition and the start of extinction. In the second experiment (15 s ITI) therefore, rats were injected after stable running had been acquired; there was no effect on running in subsequent rewarded trials. In extinction, although the groups ran similarly at first, the 6-OHDA treated animals subsequently ran more slowly than the controls; that is they showed greater extinction. Taken together with other published evidence, the sympathetic nervous system does not appear to contribute to the extinction of continuously reinforced responses.

Animals↗
PubMed1993

Extinction and viruses.

The micropaleontological record of deep-sea sediments is demonstrably continuous through time and, therefore, it can be used to study in detail the evolutionary process. Several taxa, including Coccolithophorida, planktic Foraminifera, Radiolaria, and diatoms, are abundantly represented. Some species, apparently evolved in the marginal marine environment, appear suddenly in the record while other species grade into different ones at rates that range from 100,000 years to millions of years. The rates are usually different for different morphological characters within the same lineage. Every few million years a mass extinction occurs--the disappearance of a number of taxa apparently caused by an environmental upset of some kind. These events are used by stratigraphers to subdivide geologic time. Interspersed between mass extinctions are the background extinctions, the individual extinctions of well-established species while the sympatric species exhibit no sign of stress. It is hypothesized that background extinctions are caused by host-specific viral action. It is further hypothesized that background extinctions are a fundamental component of the process of evolution.

Animals↗
PubMed2004

Analysis of extinction in ultraviolet and visible spectra of water bodies of the Paraguay and Brazil wetlands.

The extinction spectra in ultraviolet and visible radiation were analyzed using filtered and unfiltered water samples obtained in 11 open water bodies in the Neembucù (Paraguay) and Pantanal (Brazil) wetlands. The role of dissolved and suspended matter in the total extinction was analyzed between 260 nm and 700 nm. The chromophoric dissolved organic matter (CDOM) was the major component in extinction of considered ultraviolet radiation (260-400 nm). The differences in CDOM concentrations explained the main pattern of extinction of the ultraviolet radiation in the samples. Nevertheless, differences between the studied water bodies were found also to depend on the rate of photodegradation and photobleaching. The methodology developed in the present study was to distinguish "humic optic waters" according to quantity and quality of dissolved and suspended matter present. In the "humic optic water", the penetration of 10% of incident UV radiation and the photoactive layer are estimated. The influence of particulate matter increases in the total extinction of the wavelengths higher than 400 nm. The integral of the extinction curve of suspended matter in the visible wavelengths (400-700 nm) was found to relate with the total suspended solids and chlorophyll concentrations.

Brazil↗
PubMed2005

Extinction risk of a meta-population: aggregation approach.

Aggregation of variables of a complex mathematical model with realistic structure gives a simplified model which is more suitable than the original one when the amount of data for parameter estimation is limited. Here we explore use of a formula derived for a single unstructured population (canonical model) in predicting the extinction time for a population living in multiple habitats. In particular we focus multiple populations each following logistic growth with demographic and environmental stochasticities, and examine how the mean extinction time depends on the migration and environmental correlation. When migration rate and/or environmental correlation are very large or very small, we may express the mean extinction time exactly using the formula with properly modified parameters. When parameters are of intermediate magnitude, we generate a Monte Carlo time series of the population size for the realistic structured model, estimate the "effective parameters" by fitting the time series to the canonical model, and then calculate the mean extinction time using the formula for a single population. The mean extinction time predicted by the formula was close to those obtained from direct computer simulation of structured models. We conclude that the formula for an unstructured single-population model has good approximation capability and can be applicable in estimating the extinction risk of the structured meta-population model for a limited data set.

Animals↗
PubMed2005

Extinction risk, coloured noise and the scaling of variance.

The impact of temporally correlated fluctuating environments (coloured noise) on the extinction risk of populations has become a main focus in theoretical population ecology. In this study we particularly focus on the extinction risk in strongly correlated environments. Here, we found that, in contrast to moderate auto-correlation, the extinction risk was highly dependent on the process of noise generation, in particular on the method of variance scaling. Such scaling is commonly applied to avoid variance-driven biases when comparing the extinction risk under white and coloured noise. We show that for strong auto-correlation often-used scaling techniques lead to a high variability in the variances of the resulting time series and thus to deviations in the subsequent extinction risk. Therefore, we present an alternative scaling method that always delivers the target variance, even in the case of strong auto-correlation. In contrast to earlier techniques, our very intuitive method is not bound to auto-regressive processes but can be applied to all types of coloured noises. We strongly recommend our method to generate time series when the target of interest is the effect of noise colour on extinction risk not obscured by any variance effects.

Animals↗
PubMed1997

Critical analysis of the extinction coefficient of chloroplast cytochrome f.

In oxygenic photosynthesis the cytochrome bf complex links electron transport between photosystem II and photosystem I. The largest subunit of the complex is cytochrome f, a 32-kDa polypeptide that is anchored in the membrane by a transmembrane alpha helix located near the carboxyl end. The three-dimensional structure of the soluble domain of cytochrome f isolated from turnip has been determined by X-ray crystallography to 1.96 A resolution. The structure revealed several novel features compared to previously solved soluble c-type cytochrome structures, including a predominant beta-strand motif, the N-terminal alpha-amino group of a tyrosyl residue as an orthogonal ligand, and a bound internal water chain. Here we report a novel and unprecedented extinction coefficient for cytochrome f. Using the pyridine hemochrome assay, the reduced minus oxidized extinction coefficient for the soluble domain of turnip cytochrome f was 26 +/- 1 mM-1 cm-1 for the alpha-band wavelength peak at 554 nm relative to the isosbestic wavelengths (534, 543.5 and 560.5 nm), and 25 +/- 1 mM-1 cm-1 for spinach cytochrome f relative to the isosbestic wavelengths (533.5, 543.3 and 560.2). The extinction coefficients reported here are significantly higher than previously published values for cytochrome f. We believe earlier determinations underestimated the cytochrome f extinction coefficient and that the same is likely true for commonly used extinction coefficients of cytochrome b6. The cytochrome f extinction coefficient is large compared to most other c-type cytochromes, which could be due to the unique axial ligand of the cytochrome f heme. Polarographic measurements show the midpoint potential of soluble turnip cytochrome f to be 362 +/- 5 mV at pH 7.5. The midpoint potential was pH-independent from 5.0 to 8.5, and pH-dependent from pH 8.5 to 10.5 (-58 mV/pH unit) with a pK on the oxidized from near 9. Storage of some samples of purified turnip and spinach cytochrome f at -20 degrees C modified the heme environment in a fraction of the protein, shifting the midpoint potential to near -165 mV (pH 7.5) and the peak of the alpha-band absorption spectrum from 554 nm to 552 nm.

Chloroplasts↗
PubMed1996

Input and response determinants of visual extinction: a case study.

We have studied a patient, CZ, with contralateral visual extinction due to a large ischaemic frontal-parietal-temporal lesion in the right hemisphere. We found that manipulation of intensity of the visual stimulus had little effect while an increase in eccentricity substantially increased extinction rate. An important factor was represented by the hemifield of stimulus presentation: when double stimuli were presented to the contralesional (left) hemifield, the leftmost stimulus was consistently extinguished while when stimuli were presented to the ipsilesional (right) hemifield, extinction was absent. Such effect was specific to hemifield rather than to head- and trunk-defined hemispace. Manipulation of response-related variables affected extinction to a large extent: In particular, the use of nonverbal responses diminished extinction considerably. This suggests that an important component of extinction may be represented by an impaired access of visual information to the left hemisphere. Finally, the RT results confirmed previous evidence of an ipsilesional attentional bias favouring the rightmost stimuli both in the contralesional and in the ipsilesional hemifield.

Brain Ischemia↗
PubMed1997

Corticosterone levels during extinction of runway response in rats.

This investigation examined whether the hypothalamic-pituitary-adrenocortical axis would activate during extinction of a straight runway response. Four groups of rats were trained to run in a straight runway for 3 (for 3S and 3L groups) or 10 (for 10S and 10L groups) food pellets as a reward for either 15 (for 3S and 10S groups) or 25 (for 3L and 10L groups) acquisition days followed by 3 extinction days. Blood samples for determination of serum corticosterone concentration were taken from all animals under 5 different situations: 10 min after entering the experimental room, after the 24th acquisition day, after the first and third extinction days and under the deprivation control. Running speed of 10S and 10L groups in extinction days were reduced more quickly than that of 3S and 3L groups. After the third extinction day, serum corticosterone concentrations were significantly elevated in 10S and 10L, but not in 3S and 3L groups. These results indicate that the amount of reward in the acquisition phase influences not only the running speed, but also the corticosterone concentration in the extinction phase.

Adrenal Cortex↗
PubMed1997

Attentional competition between modalities: extinction between touch and vision after right hemisphere damage.

The phenomenon of extinction, which occurs frequently after unilateral brain damage, involves a failure to detect the more contralesional of two simultaneously presented stimuli, but with preserved detection of single ipsilesional or contralesional stimuli. Current accounts suggest that the disorder reflects a bias of selective attention, in which ipsilesional stimuli have a competitive advantage. Extinction may be manifested within any one of the major sensory modalities (vision, audition, touch), or it may occur within several modalities in a given individual. Given recent evidence in normals for attentional links between separate sensory modalities, we examined whether extinction can also occur cross-modally, i.e. for double-simultaneous stimuli in separate sensory modalities. We tested whether an ipsilesional event sufficient to extinguish a contralesional stimulus within the same modality may also extinguish a contralesional stimulus in a different modality. Our three patients had right hemisphere damage, and reliable within-modality extinction for visual and tactile stimuli. They also showed significant cross-modal extinction, such that an ipsilesional tactile (or visual) event extinguished awareness of a simultaneous visual (or tactile) event on the contralesional side. These results, which provide the first quantitative evidence for cross-modal extinction, were replicated in a second experiment in which visual and tactile stimuli in the cross-modal conditions were presented at non-homologous elevations within each hemispace. We conclude that after unilateral damage, ipsilesional stimuli have a competitive advantage over contralesional stimuli, and that this affects competition between stimuli from different modalities as well as stimuli within the same modality. These findings are consistent with recent evidence for competitive interactions between tactile and visual events in the control of spatial attention in normals.

Adult↗
PubMed2003

Allee effects, extinctions, and chaotic transients in simple population models.

Discrete time single species models with overcompensating density dependence and an Allee effect due to predator satiation and mating limitation are investigated. The models exhibit four behaviors: persistence for all initial population densities, bistability in which a population persists for intermediate initial densities and otherwise goes extinct, extinction for all initial densities, and essential extinction in which "almost every" initial density leads to extinction. For fast-growing populations, these models show populations can persist at high levels of predation even though lower levels of predation lead to essential extinction. Alternatively, increasing the predator's handling time, the population's carrying capacity, or the likelihood of mating success may lead to essential extinction. In each of these cases, the mechanism behind these disappearances are chaotic dynamics driving populations below a critical threshold determined by the Allee effect. These disappearances are proceeded by chaotic transients that are proven to be approximately exponentially distributed in length and highly sensitive to initial population densities.

Alleles↗
PubMed1997

State-dependency of conditioning and extinction of an appetitive response with amphetamine and midazolam.

Rats received a single conditioning session in which unsignaled food pellets were delivered to the food magazine of a training box, followed by a single extinction session without pellet presentations. Groups of rats differed in the drug state induced prior to conditioning and extinction according to a 2 x 2 design using d-amphetamine sulphate (AMP, 0.5 mg/kg, S.C.) and midazolam (MID, 0.1 mg/kg, S.C.). Subsequently, all rats received nonreinforced test sessions under AMP and MID. The dependent measure was the frequency of magazine visits during selected portions of each session. Rats that received extinction in the same drug state as had been present during conditioning did not respond significantly more during the extinction session than rats extinguished in a different drug state. This implies that conditioning was not state dependent. However, during the AMP tests, the rats extinguished under MID responded more under AMP than under MID, whereas the rats extinguished under AMP did not respond differentially during the tests under AMP vs. MID. These results were interpreted as reflecting the joint operation of state-dependent extinction and unconditioned drug effects. As in studies manipulating external contextual stimuli, extinction proved to be more vulnerable to becoming context dependent than conditioning.

Amphetamine↗