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At least 649 records · Page 36Linked to original sources
PubMed2000

Extinction risk of a density-dependent population estimated from a time series of population size.

Environmental threats, such as habitat size reduction or environmental pollution, may not cause immediate extinction of a population but shorten the expected time to extinction. We develop a method to estimate the mean time to extinction for a density-dependent population with environmental fluctuation. We first derive a formula for a stochastic differential equation model (canonical model) of a population with logistic growth with environmental and demographic stochasticities. We then study an approximate maximum likelihood (AML) estimate of three parameters (intrinsic growth rate r, carrying capacity K, and environmental stochasticity sigma(2)(e)) from a time series of population size. The AML estimate of r has a significant bias, but by adopting the Monte Carlo method, we can remove the bias very effectively (bias-corrected estimate). We can also determine the confidence interval of the parameter based on the Monte Carlo method. If the length of the time series is moderately long (with 40-50 data points), parameter estimation with the Monte Carlo sampling bias correction has a relatively small variance. However, if the time series is short (less than or equal to 10 data points), the estimate has a large variance and is not reliable. If we know the intrinsic growth rate r, however, the estimate of K and sigma(2)(e)and the mean extinction time T are reliable even if only a short time series is available. We illustrate the method using data for a freshwater fish, Japanese crucian carp (Carassius auratus subsp.) in Lake Biwa, in which the growth rate and environmental noise of crucian carp are estimated using fishery records.

Animals↗
PubMed2001

Extinction and quasi-stationarity in the Verhulst logistic model.

We formulate and analyse a stochastic version of the Verhulst deterministic model for density-dependent growth of a single population. Three parameter regions with qualitatively different behaviours are identified. Explicit approximations of the quasi-stationary distribution and of the expected time to extinction are presented in each of these regions. The quasi-stationary distribution is approximately normal, and the time to extinction is long, in one of these regions. Another region has a short time to extinction and a quasi-stationary distribution that is approximately truncated geometric. A third region is a transition region between these two. Here the time to extinction is moderately long and the quasi-stationary distribution has a more complicated behaviour. Numerical illustrations are given.

Animals↗
PubMed2002

Species positions and extinction dynamics in simple food webs.

Recent investigations on the structure of complex networks have provided interesting results for ecologists. Being inspired by these studies, we analyse a well-defined set of small model food webs. The extinction probability caused by internal Lotka-Volterra dynamics is compared to the position of species. Simulations have revealed that some global properties of these food webs (e.g. the homogeneity of connectedness) and the positions of species therein (e.g. interaction pattern) make them prone to modelled biotic extinction caused by population dynamical effects. We found that: (a) homogeneity in the connectedness structure increases the probability of extinction events; (b) in addition to the number of interactions, their orientations also influence the future of species in a web. Since species in characteristic network positions are prone to extinction, results could also be interpreted as describing the properties of preferred states of food webs during community assembly. Our results may contribute to understanding the intimate relationship between pattern and process in ecology.

Animals↗
PubMed2002

Habitat destruction, environmental catastrophes, and metapopulation extinction.

The extinction process of fragmented populations, characterized by a small number of conspecifics inhabiting each patch, is heavily affected by natural and human disturbance. To evaluate the risk of extinction we consider a network of identical patches connected by passive or active dispersal and hosting a finite, discrete number of individuals. We discuss three types of disturbance affecting the metapopulation: permanent loss of habitat patches, erosion of existing patches, and random catastrophes that wipe out the entire population of a patch. Starting from an infinite-dimensional Markov model that fully accounts for demographic stochasticity, we reduce it to finite dimension via moment closure with negative-binomial approximation. The compact models obtained in this way account for the dynamics of the fraction of empty patches, the average number of individuals in occupied patches, and the variance of their distribution. After comparing the performance of these compact models with that of the infinite-dimensional model in the case of no disturbances, we then proceed to computing persistence-extinction boundaries as bifurcation lines of the compact models in the space of demographic and disturbance parameters. We consider bifurcations with respect to demographic and environmental parameters and contrast our results with those of previous theories. We find out that environmental catastrophes increase the risk of extinction for both frequent and infrequent dispersers, while the random loss of patches has a much larger influence on frequent dispersers. This influence can be counterbalanced by active dispersal. Local erosion of habitat fragments has a larger influence on infrequent than on frequent dispersers. We finally discuss the important synergistic effects of disturbances acting simultaneously.

Disasters↗
PubMed2005

Foot-and-mouth disease virus evolution: exploring pathways towards virus extinction.

Foot-and-mouth disease virus (FMDV) is genetically and phenotypically variable. As a typical RNA virus, FMDV follows a quasispecies dynamics, with the many biological implications of such a dynamics. Mutant spectra provide a reservoir of FMDV variants, and minority subpopulations may become dominant in response to environmental demands or as a result of statistical fluctuations in population size. Accumulation of mutations in the FMDV genome occurs upon subjecting viral populations to repeated bottleneck events and upon viral replication in the presence of mutagenic base or nucleoside analogs. During serial bottleneck passages, FMDV survive during extended rounds of replication maintaining low average relative fitness, despite linear accumulation of mutations in the consensus genomic sequence. The critical event is the occurrence of a low frequency of compensatory mutations. In contrast, upon replication in the presence of mutagens, the complexity of mutant spectra increases, apparently no compensatory mutations can express their fitness-enhancing potential, and the virus can cross an error threshold for maintenance of genetic information, resulting in virus extinction. Low relative fitness and low viral load favor FMDV extinction in cell culture. The comparison of the molecular basis of resistance to extinction upon bottleneck passage and extinction by enhanced mutagenesis is providing new insights in the understanding of quasispecies dynamics. Such a comparison is contributing to the development of new antiviral strategies based on the transition of viral replication into error catastrophe.

Biological Evolution↗
PubMed1989

The role of subicular outputs in the development of the partial reinforcement extinction effect.

Rats were trained to run in an alley for food reward given on every trial (Continuous Reinforcement, CR) or on a random fifty percent of trials (Partial Reinforcement, PR) and the running response was then extinguished. Sham Operated controls showed the normal partial reinforcement extinction effect (PREE) in that PR-trained animals were significantly more resistant to extinction than CR-trained animals. The PREE was abolished by a knife cut placed at the base of the lateral septum to interrupt ventral subicular fibres destined for the ventral striatum. This outcome stemmed purely from a decrease in resistance to extinction in the lesion PR group. A large lesion that also sectioned the dorsal subicular pathway in the descending columns of the fornix left the PREE intact, though there were some signs of a reduction in its size primarily due to increased resistance to extinction in the lesion CR group. We conclude that previous reports demonstrating reduction or abolition of the PREE following conventional total septal or lateral septal lesions, may have achieved their results through damage to subicular fibres en passage through the septum.

Animals↗
PubMed1987

On density and extinction in continuous population models.

Survival analyses, investigations of extinction and persistence, are executed for populations represented by a nonautonomous differential equation model. The population is assumed governed by density dependent and time varying density independent demographic parameters. While traditional approaches to extinction postulate extinction on an infinite time horizon and at zero abundance level, survival analysis is developed not only for this traditional setting but also on a finite time horizon and at a nonzero threshold level. A main conclusion is that extinction of a temporally stressed population is determined by a totality of density independent and density dependent factors.

Animals↗
PubMed1995

Extinction coefficient of polymerized diaminobenzidine complexed with cobalt as final reaction product of histochemical oxidase reactions.

The extinction coefficient is essential for the conversion of cytophotometric (mean integrated) absorbance values into absolute units of enzyme activity, for instance expressed in terms of moles of substrate converted per unit time and per unit wet weight of tissue. The extinction coefficient of polymerized diaminobenzidine (polyDAB) complexed with cobalt as the final reaction product of oxidase reactions was estimated at 575 nm by comparison of the amounts of final reaction products formed after incubation of serial unfixed cryostat sections of rat kidney to demonstrate D-amino acid oxidase activity with either the tetrazolium salt method or the cerium-DAB-cobalt-hydrogen peroxide method. Both procedures resulted in similar localization patterns of final reaction product in a granular form in epithelial cells of proximal tubules in rat kidney. The granules were peroxisomes. Linear relationships were found for both methods between the specific amounts of final reaction product generated by D-amino acid oxidase activity and incubation time. The cerium salt method gave rise to 7.4 times higher absorbance values of final reaction product generated per unit time and per unit wet weight of tissue than the tetrazolium salt procedure. The extinction coefficient of tetranitro BT-formazan is 19,000 at 557 nm. Therefore, the cytophotometric extinction coefficient of the polyDAB-cobalt complex as final reaction product of oxidase reactions was established to be 140,000.

3,3'-Diaminobenzidine↗
PubMed2003

Extinction and re-evolution of similar adaptive types (ecomorphs) in Cenozoic North American ungulates and carnivores reflect van der Hammen's cycles.

Numerous patterns in periodicity (e.g., climate, extinction, and sedimentary cycles) and evolutionary change (e.g., chronofaunas and coordinated stasis) have been described based on aspects of the geologic record. Recently, convergent occurrences of faunal types or "repeating faunas" have received attention, but a highly specific, iterative pattern was first reported over 40 years ago. In the late 1950s, van der Hammen described climatic/floral cycles on the order of six million years based on a succession of A, B, and C pollen community types in South America. These A-B-C cycles are also seen in the replacement pattern of particular carnivore and ungulate adaptive types in Cenozoic North America as reported by Martin in the 1980s. For example, in the last 36 million years, there were four iterations of a sabertooth cat ecomorph independently evolving, dominating the niche through an A-B-C cycle, and then going extinct. Here we show further support for the existence of these cycles in the dominance turnover in hippo and dog ecomorphs in the North American Cenozoic. Shared patterns of extinction and re-evolution of adaptive types among plants and mammals across two continents suggest a global mechanism, which appears to be climatic change. Iterative climatic cycles of various scales may form a predictive framework for understanding fundamental patterns in the geologic record, such as radiations, extinction, rates of change, convergence, and sedimentary cycles.

Acclimatization↗
PubMed2000

Problems in Extinction Model Selection and Parameter Estimation.

It is a vexing problem to achieve a consensus about the proper scientific way to assess population viability for habitat conservation plans. Rather than a hypothesis-testing approach, here it is proposed to select population models, estimate extinction parameters, and assess prediction uncertainty using a pragmatic, empirical Bayesian approach. The simplest usable models include the effects of population growth, r; carrying capacity, K; Allee threshold, N(A); and environmental stochasticity, v(r). Analytic predictions of expected extinction times are available for such models. Models that are more complex can be elaborated from this basis. Selection from a hierarchy of nesting population models can often be done through the evaluation of parameters. The estimation of the most important extinction parameters can be undertaken in a variety of ways. Time series can be analyzed to estimate r(d), v(r), rho, and K. Habitat models and individualistic population models may help estimate N(A) and K and demographic stochasticity. Fine-scale biogeography and climatological data may be useful in the estimation of a variety of parameters. Because it takes many years to estimate extinction parameters accurately for a given population of interest, the most efficient estimation procedures are desirable. I propose the use of prior information from an (as yet nonexistent) population biology database. The accumulation of local information through monitoring will improve our estimates allowing adaptive management. Uncertainty in the estimates will always remain, but it may be quantified by the posterior distributions. A crude example is discussed using treefrog population data. Although the motivations, beliefs, and biases of competing stakeholders will differ, a habitat conservation plan could accommodate this variation in the prior distributions. Field experience from monitoring will increasingly clear up any discrepancies between the opposing beliefs and the real ecosystem. As the world is an uncertain place and because there is no universal scientific method, there will always be controversy and surprises. The best we can do is (1) agree about our prior information, (2) agree about the strategy of model selection and parameter estimation, and (3) agree about our strategy for adaptive management. Perhaps the greatest impediment to such prior agreements for HCPs is the likely paranoia inspired by the use of unfamiliar statistical methodology. We need to train students of ecology in a more flexible and deeper understanding of statistics and philosophy of science.

Journal Article↗
PubMed2000

Stochastic epidemics in dynamic populations: quasi-stationarity and extinction.

Empirical evidence shows that childhood diseases persist in large communities whereas in smaller communities the epidemic goes extinct (and is later reintroduced by immigration). The present paper treats a stochastic model describing the spread of an infectious disease giving life-long immunity, in a community where individuals die and new individuals are born. The time to extinction of the disease starting in quasi-stationarity (conditional on non-extinction) is exponentially distributed. As the population size grows the epidemic process converges to a diffusion process. Properties of the limiting diffusion are used to obtain an approximate expression for tau, the mean-parameter in the exponential distribution of the time to extinction for the finite population. The expression is used to study how tau depends on the community size but also on certain properties of the disease/community: the basic reproduction number and the means and variances of the latency period, infectious period and life-length. Effects of introducing a vaccination program are also discussed as is the notion of the critical community size, defined as the size which distinguishes between the two qualitatively different behaviours.

Child↗
PubMed1981

Relative blue-light extinction in lens nucleus related to age and cataract.

The extent of visual function loss from nuclear cataractous change can be estimated by observing the extinction of blue light compared to white light as a function of sagittal lens depth in standard slit lamps. Apparent extinction (loss of transmissivity) of 50% or more of the depth of the lens in blue light of maximal intensity compared to white light at minimal intensity is associated with marked visual loss. However, this transmissivity ratio of 0.5 or less also applies if light intensity remains constant and the blue filter is simply moved in and out of the light beam. Therefore, if 50% or more of the lens appears dark to blue-filtered light, nuclear changes have significantly decreased effective visual acuity. Relative blue-light extinction associated with nuclear change that may be amenable to surgical correction can thus be distinguished from the extinction effect caused by age alone.

Adolescent↗
PubMed1993

Developmental extinction of liver lipoprotein lipase mRNA expression might be regulated by an NF-1-like site.

The molecular mechanism underlying the extinction of lipoprotein lipase (LPL) expression in rat liver during development was investigated. A mouse (BWTG3) and a rat (7777) hepatoma, both of which exhibit characteristics of fetal hepatocytes, were found to contain LPL mRNA, whereas the more differentiated human (Hep G2 and Hep 3B) or rat (Fa32) hepatoma cell lines did not. Somatic cell hybrids between LPL-producing hepatoma cells and non-LPL-producing cells, such as adult rat hepatocytes or fibroblasts, exhibited extinction of LPL gene expression. Assay of expression of nested deletions in the 5' regulatory sequences of the LPL gene in the Hep G2 cell line and in BWTG3 cells localized sequences involved in the suppression of LPL production to a region between -591 and -288 relative to the transcription initiation site. A site with sequence homology to a glucocorticoid responsive element (GRE) was shown not to play an important role in the extinction process. A novel transcription factor, termed RF-1-LPL, was shown to bind to an NF-1-like site in this region. In contrast to neonatal animals, in adult animals an additional protein complex (RF-2-LPL), was formed on the NF-1-like site, suggesting that this sequence might recruit a trans-acting factor involved in the extinction of LPL gene expression in adult rat liver.

Animals↗
PubMed1988

Extinction of growth hormone expression in somatic cell hybrids involves repression of the specific trans-activator GHF-1.

Growth hormone (GH) expression in pituitary-derived cells has been attributed to the presence of a positive trans-activator, GHF-1, which binds to two sites on the GH promoter. Somatic cell hybridization of non-GH-expressing L cells with pituitary-derived GH3 cells usually results in extinction of GH production. While previous studies showed that extinction occurs at the level of GH transcription, the exact mechanism remained elusive. We therefore characterized two parental cell lines and three hybrids, two of which extinguish GH expression and one in which GH is reexpressed after loss of mouse chromosomal material. Using in vivo transfections, in vitro transcription, DNAase I footprints, and immunoblotting experiments, no evidence for a direct repressor of GH transcription was found. Rather, extinction of GH expression in fibroblast x pituitary hybrids was accompanied by loss of GHF-1 protein and mRNA expression, suggesting that extinction occurs by repression of this trans-activator.

Animals↗
PubMed2005

Inactivation of the brachium conjunctivum prevents extinction of classically conditioned eyeblinks.

It is well established that the intermediate cerebellum is involved in the acquisition of classically conditioned eyeblink responses (CRs). Recent studies that inactivated the interposed nuclei (IN) demonstrated that blocking the intermediate cerebellum also interrupts CR extinction. Is this extinction deficit related to interrupting the information flow to efferent targets of the IN? To address this question, we inactivated axons of IN neurons in the brachium conjunctivum (BC). This treatment blocked the output of the intermediate cerebellum without directly affecting neurons in the deep cerebellar nuclei. Rabbits were trained in a delay classical conditioning paradigm, using a tone as the conditioned stimulus (CS) and a corneal air puff as the unconditioned stimulus (US). Then, the BC was microinjected with a sodium channel blocker, tetrodotoxin, during 4 extinction sessions in which rabbits were presented only with the CS. Tests performed after the 4-day injection period revealed that CRs did not extinguish in BC inactivation sessions but extinguished at a normal rate in the absence of the drug. CRs were then re-acquired. These data show that the normal flow of information along axons of cerebellar nuclear cells is required for CR extinction.

Animals↗
PubMed2005

Light extinction at agglomerates of spheres--a practical test on the submicroscale.

Today's theories applied to the inversion of measurement data from optical measurement devices are restricted to single spherical particles. However, particles formed in industrial processes such as precipitation and crystallization are often nonspherical or agglomerates. Theoretical approaches to describe the optical behavior of such particle systems have already been proposed. The verification of these theories has mostly been done using microwave scattering experiments with agglomerates in the millimeter range. This paper provides a first but surely not all-embracing practical test for a general extension of the Mie theory to agglomerates of submicroscale spheres. For the sake of simplicity and from practical viewpoints of online-sensor development only light extinction of an agglomerated suspension has been examined. The required rigid agglomerates have been produced using a spray-drying method that generates particles with a much higher mechanical stability than can be obtained by the usual procedures. Subsequent fractionation of the suspension delivers systems with only a limited number of agglomerate configurations. Extinction measurements at multiple wavelengths using dynamic extinction spectroscopy have been conducted to determine the extinction cross section of the agglomerated dispersions. These data are compared with computations of agglomerates scattering.

Journal Article↗
PubMed2005

Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection.

Between 1996 and 1998, two clades (B and C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000, a third clade (A; genotype III) of DENV-1, which had been circulating at that locality for at least 25 years, became extinct. These changes preceded the largest outbreak of dengue recorded in Myanmar, in 2001, in which more than 95% of viruses recovered from patients were DENV-1, but where the incidence of severe disease was much less than in previous years. Phylogenetic analyses of viral genomes indicated that the two new clades of DENV-1 did not arise from the, now extinct, clade A viruses nor was the extinction of this clade due to differences in the fitness of the viral populations. Since the extinction occurred during an inter-epidemic period, we suggest that it was due to a stochastic event attributable to the low rate of virus transmission in this interval.

Aedes↗
PubMed2004

Retrovirus silencing, variegation, extinction, and memory are controlled by a dynamic interplay of multiple epigenetic modifications.

Retrovirus silencing in stem cells produces silent or variegated provirus. Additional memory and extinction mechanisms act during differentiation. Here we show that retrovirus is silent or variegated in mouse embryonic stem (ES) cells that are de novo methyltransferase (dnmt3a and dnmt3b) null. Memory is maintained during differentiation, and extinction occurs on variegated retrovirus, indicating that DNA methylation is dispensable for all forms of retrovirus silencing. Silent and variegated provirus are marked by hypoacetylated histone H3 and bound H1. In wild-type ES cells, silent and variegated proviruses are methylated and bound by hypoacetylated H3, MeCP2, and less H1. Silencing, variegation, and extinction are partially reactivated by 5-AzaC in this context. Lentivirus vectors are also silent or variegated, marked by silent chromatin, and exhibit memory and extinction. We conclude that the universal epigenetic mark of retrovirus silencing is silent chromatin established via the dynamic interplay of multiple epigenetic modifications that include but do not require DNA methylation. A molecular mechanism of competitive H1 and MeCP2 binding may account for this epigenetic interplay, and a model for variegation is discussed.

Animals↗