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PubMed2006

Forecasting extinction risk with nonstationary matrix models.

Matrix population growth models are standard tools for forecasting population change and for managing rare species, but they are less useful for predicting extinction risk in the face of changing environmental conditions. Deterministic models provide point estimates of lambda, the finite rate of increase, as well as measures of matrix sensitivity and elasticity. Stationary matrix models can be used to estimate extinction risk in a variable environment, but they assume that the matrix elements are randomly sampled from a stationary (i.e., non-changing) distribution. Here we outline a method for using nonstationary matrix models to construct realistic forecasts of population fluctuation in changing environments. Our method requires three pieces of data: (1) field estimates of transition matrix elements, (2) experimental data on the demographic responses of populations to altered environmental conditions, and (3) forecasting data on environmental drivers. These three pieces of data are combined to generate a series of sequential transition matrices that emulate a pattern of long-term change in environmental drivers. Realistic estimates of population persistence and extinction risk can be derived from stochastic permutations of such a model. We illustrate the steps of this analysis with data from two populations of Sarracenia purpurea growing in northern New England. Sarracenia purpurea is a perennial carnivorous plant that is potentially at risk of local extinction because of increased nitrogen deposition. Long-term monitoring records or models of environmental change can be used to generate time series of driver variables under different scenarios of changing environments. Both manipulative and natural experiments can be used to construct a linking function that describes how matrix parameters change as a function of the environmental driver. This synthetic modeling approach provides quantitative estimates of extinction probability that have an explicit mechanistic basis.

Adaptation, Physiological↗
PubMedDate not supplied

[Correction of light refraction and reflection in medical transmission optical tomography].

The effects of light refraction and reflection on the quality of image reconstruction in medical transmission optical tomography of high-scattering media are considered. It has been first noted that light refraction not only distorts the geometric scheme of measurements, but may lead to the appearance of object areas that cannot be scanned. Some ways of decreasing the effect of refraction on the reconstruction of spatial distribution of the extinction coefficient are stated.

Biophysical Phenomena↗
PubMed1981

Quantitative microspectrometrical determination of the total protein and total protein-SH content of the nuclei of Ehrlich ascites tumor cells without prior isolation.

The total protein and total protein-SH content of both the cytoplasmic fraction and the nuclei of Ehrlich ascites tumor cells (EATC) were determined macroscopically and microspectrometrically. The separation into cytoplasmic and nuclear fraction was performed by a modification of the method of Mamaril et al. [4]. The macroscopical determination of the total protein and the total protein-SH content were performed with the Folin method of Lowry et al. [2] and the DTNB method of Ellman [1], respectively. The quantitative microspectrometrical determinations of total protein content and of total protein-SH content were performed using the tetrazonium staining method of Nöhammer [5] and Nöhammer et al. [6] and the mercurochromcyanide (MCN) method of Nöhammer et al. [7], respectively. Within the intact cells, fixed and stained histochemically, the total protein and the total protein-SH content of the nuclei were determined microspectrometrically. The so called "nuclear extinctions", measured as the sum of the extinctions of the nucleus and of the parts of the cytoplasm above and below the nucleus, were calculated into the true nuclear extinctions, which then show a good correspondence to the values measured both microspectrometrically and macroscopically on isolated nuclei. The calculation for the true nuclear extinctions is based on a special preparation of spherically shaped cells and nuclei.

Animals↗
PubMed1993

Is humanity suicidal?

The world's fauna and flora has entered a crisis unparalleled since the end of the Mesozoic Era, with the extinction rate of species now elevated to more than a thousand times that existing before the coming of humanity. Scientists and policy makers are ill-prepared to moderate this hemorrhaging, because so little is known of the biology of the Earth's millions of species and because so little effort has been directed toward conservation thus far. With the vanished species will go great potential wealth in scientific knowledge, new products, ecosystems services, and part of the natural world in which the human species originated. The need for new research and improved management is thus urgent. If it is not met, humanity will likely survive, but in a world biologically impoverished for all time.

Animals↗
PubMed2003

A whole blood immunoassay using gold nanoshells.

A rapid immunoassay capable of detecting analyte within complex biological media without any sample preparation is described. This was accomplished using gold nanoshells, layered dielectric-metal nanoparticles whose optical resonance is a function of the relative size of its constituent layers. Aggregation of antibody/nanoshell conjugates with extinction spectra in the near-infrared was monitored spectroscopically in the presence of analyte. Successful detection of immunoglobulins was achieved in saline, serum, and whole blood. This system constitutes a simple immunoassay capable of detecting sub-nanogram-per-milliliter quantities of various analytes in different media within 10-30 min.

Animals↗
PubMed2006

Pleistocene rewilding: an optimistic agenda for twenty-first century conservation.

Large vertebrates are strong interactors in food webs, yet they were lost from most ecosystems after the dispersal of modern humans from Africa and Eurasia. We call for restoration of missing ecological functions and evolutionary potential of lost North American megafauna using extant conspecifics and related taxa. We refer to this restoration as Pleistocene rewilding; it is conceived as carefully managed ecosystem manipulations whereby costs and benefits are objectively addressed on a case-by-case and locality-by-locality basis. Pleistocene rewilding would deliberately promote large, long-lived species over pest and weed assemblages, facilitate the persistence and ecological effectiveness of megafauna on a global scale, and broaden the underlying premise of conservation from managing extinction to encompass restoring ecological and evolutionary processes. Pleistocene rewilding can begin immediately with species such as Bolson tortoises and feral horses and continue through the coming decades with elephants and Holarctic lions. Our exemplar taxa would contribute biological, economic, and cultural benefits to North America. Owners of large tracts of private land in the central and western United States could be the first to implement this restoration. Risks of Pleistocene rewilding include the possibility of altered disease ecology and associated human health implications, as well as unexpected ecological and sociopolitical consequences of reintroductions. Establishment of programs to monitor suites of species interactions and their consequences for biodiversity and ecosystem health will be a significant challenge. Secure fencing would be a major economic cost, and social challenges will include acceptance of predation as an overriding natural process and the incorporation of pre-Columbian ecological frameworks into conservation strategies.

Animals↗
PubMed2004

Resistance to extinction is associated with impaired immediate early gene induction in medial prefrontal cortex and amygdala.

Extinction of classical fear conditioning is thought to involve activity-dependent potentiation of synaptic transmission in the medial prefrontal cortex (mPFC), resulting in the inhibition of amygdala-dependent fear responses. While many studies have addressed the mechanisms underlying extinction learning, it is unclear what determines whether extinction memory is consolidated or whether spontaneous recovery of the fear response occurs. Here we show, using a combined electrophysiological and immunocytochemical approach, that spontaneous recovery of conditioned fear in mice is associated with a prolonged expression of long-term depression of synaptic transmission in the mPFC and the failure of induction of the immediate-early genesc-Fos and zif268 in the mPFC and the basolateral nucleus of the amygdala. This suggests that coordinated activity-dependent changes in gene expression in the mPFC and the amygdala may underlie the formation of long-term fear extinction memory.

Amygdala↗
PubMed1999

Analysis of parasite host-switching: limitations on the use of phylogenies.

Even the most generalist parasites usually occur in only a subset of potential host species, a tendency which reflects overriding environmental constraints on their distributions in nature. The periodic shifting of these limitations represented by host-switches may have been an important process in the evolution of many host-parasite assemblages. To study such events, however, it must first be established where and when they have occurred. Past host-switches within a group of parasites are usually inferred from a comparison of the parasite phylogeny with that of the hosts. Congruence between the phylogenies is often attributed to a history of association by descent with cospeciation, and incongruence to host-switching or extinction in 'duplicated' parasite lineages (which diverged without a corresponding branching of the host tree). The inference of host-switching from incongruent patterns is discussed. Difficulties arise because incongruence can frequently be explained by different combinations of biologically distinct events whose relative probabilities are uncertain. Also, the models of host-parasite relationships implicit in historical reconstructions may often not allow for plausible sources of incongruence other than host-switching or duplication/extinction, or for the possibility that colonization could, in some circumstances, be disguised by 'false' congruence.

Adaptation, Physiological↗
PubMedDate not supplied

Phylogenetic networks: modeling, reconstructibility, and accuracy.

Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.

Algorithms↗
PubMed1987

Scaling of biological community structure: a systems approach to community complexity.

Local community dynamics are determined by the interaction of environmental variation and the biotic properties of communities. This interaction occurs on many spatial and temporal scales, hence the expectation is that community dynamics will be complex. Previous theoretical approaches to communities have assumed linear, near equilibrium dynamics. An alternative approach suggests that community dynamics are the result of the balance between energy use by the community and its tendency to move towards thermodynamic equilibrium, in this case extinction of all species in the community. Because this balance will be imprecise, community dynamics should be oscillatory. Furthermore, because energy use by a community can be broken down into a hierarchical set of processes occurring on different time scales, community dynamics should reflect multiple periodicities. The above theoretical treatment suggests that since community dynamics are scaled, a hierarchical observational approach should help resolve important aspects of community structure. This approach of scaling community observations provides a technique for evaluation of community responses to environmental change, including human induced perturbations. A thermodynamic approach to community dynamics can also provide the basis for new theoretical and empricial discoveries about biological communities.

Animals↗
PubMed2002

Extinction dynamics in mainland-island metapopulations: an N-patch stochastic model.

A generalization of the well-known Levins' model of metapopulations is studied. The generalization consists of (i) the introduction of immigration from a mainland, and (ii) assuming the dynamics is stochastic, rather than deterministic. A master equation, for the probability that n of the patches are occupied, is derived and the stationary probability Ps(n), together with the mean and higher moments in the stationary state, determined. The time-dependence of the probability distribution is also studied: through a Gaussian approximation for general n when the boundary at n = 0 has little effect, and by calculating P(0, t), the probability that no patches are occupied at time t, by using a linearization procedure. These analytic calculations are supplemented by carrying out numerical solutions of the master equation and simulations of the stochastic process. The various approaches are in very good agreement with each other. This allows us to use the forms for Ps(0) and P(0,t) in the linearization approximation as a basis for calculating the mean time for a metapopulation to become extinct. We give an analytical expression for the mean time to extinction derived within a mean field approach. We devise a simple method to apply our mean field approach even to complex patch networks in realistic model metapopulations. After studying two spatially extended versions of this nonspatial metapopulation model--a lattice metapopulation model and a spatially realistic model--we conclude that our analytical formula for the mean extinction time is generally applicable to those metapopulations which are really endangered, where extinction dynamics dominates over local colonization processes. The time evolution and, in particular, the scope of our analytical results, are studied by comparing these different models with the analytical approach for various values of the parameters: the rates of immigration from the mainland, the rates of colonization and extinction, and the number of patches making up the metapopulation.

Animals↗
PubMed1984

Stochastic models of tumor growth and the probability of elimination by cytotoxic cells.

The probability of tumor extinction due to the action of cytotoxic cell populations is investigated by several one dimensional stochastic models of the population growth and elimination processes of a tumor. The several models are made necessary by the nonlinearity of the processes and the different parameter ranges explored. The deterministic form of the model is T' = gamma 0T - k'6T/(K1 + T) where gamma 0, k'6 and K1 are positive constants. The parameter of most import is lambda 0 = gamma 0 - k'6/K1 which determines the stability of the T = 0 equilibrium. With an initial tumor size of one, a (linear) branching process is used to estimate the extinction probability. However, in the case lambda = 0 when the linearization of the deterministic model gives no information (T = 0 is actually unstable) the branching model is unsatisfactory. This makes necessary the utilization of a density-dependent branching process to approximate the population. Through scaling a diffusion limit is reached which enables one to again compute the probability of extinction. For populations away from one a sequence of density-dependent jump Markov processes are approximated by a sequence of diffusion processes. In limiting cases, the estimates of extinction correspond to that computed from the original branching process. Table 1 summarizes the results.

Cell Survival↗
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↗
PubMed2005

Density-dependence as a size-independent regulatory mechanism.

The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population.

Animals↗
PubMed2006

On linear perturbations of the Ricker model.

A class of linearly perturbed discrete-time single species scramble competition models, like the Ricker map, is considered. Perturbations can be of both recruitment and harvesting types. Stability (bistability) is considered for models, where parameters of the map do not depend on time. For models with recruitment, the result is in accordance with Levin and May conjecture [S.A. Levin, R.M. May, A note on difference delay equations, Theor. Pop. Biol. 9 (1976) 178]: the local stability of the positive equilibrium implies its global stability. For intrinsic growth rate r-->infinity the way to chaos is broken down to get extinction of population for the depletion case and to establish a stable two-cycle period for models with immigration. The latter behaviour is also studied for models with random discrete constant perturbations of recruitment type. Extinction, persistence and existence of periodic solutions are studied for the perturbed Ricker model with time-dependent parameters.

Animals↗
PubMed2000

Effect of aggregating behavior on population recovery on a set of habitat islands.

We consider a single-species model which is composed of several patches connected by linear migration rates and having logistic growth with a threshold. We show the existence of an aggregating mechanism that allows the survival of a species which is in danger of extinction due to its low population density. Numerical experiments illustrate these results.

Animals↗
PubMed2003

How much does an individual habitat fragment contribute to metapopulation dynamics and persistence?

We derive measures for assessing the value of an individual habitat fragment for the dynamics and persistence of a metapopulation living in a network of many fragments. We demonstrate that the most appropriate measure of fragment value depends on the question asked. Specifically, we analyse four alternative measures: the contribution of a fragment to the metapopulation capacity of the network, to the equilibrium metapopulation size, to the expected time to metapopulation extinction and the long-term contribution of a fragment to colonization events in the network. The latter measure is comparable to density-dependent measures in general matrix population theory, though some differences are introduced by the fact that "density dependence" is spatially localized in the metapopulation context. We show that the value of a fragment depends not only on the properties of the landscape but also on the properties of the species. Most importantly, variation in fragment values between the habitat fragments is greatest in the case of rare species that occur close to the extinction threshold, as these species are likely to be restricted to the most favorable parts of the landscape. We expect that the measures of habitat fragment value described and analysed here have applications in landscape ecology and in conservation biology.

Animals↗