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PubMed2000

Predicting extinction risk in declining species.

What biological attributes predispose species to the risk of extinction? There are many hypotheses but so far there has been no systematic analysis for discriminating between them. Using complete phylogenies of contemporary carnivores and primates, we present, to our knowledge, the first comparative test showing that high trophic level, low population density slow life history and, in particular, small geographical range size are all significantly and independently associated with a high extinction risk in declining species. These traits together explain nearly 50% of the total between-species variation in extinction risk. Much of the remaining variation can be accounted for by external anthropogenic factors that affect species irrespective of their biology.

Animals↗
PubMed1984

Determination of copper in biological materials by atomic absorption spectroscopy: a reevaluation of the extinction coefficients for azurin and stellacyanin.

A new method for the determination of copper in biological materials by graphite furnace atomic absorption spectroscopy is presented. This new procedure is an extension of the classic method of standard additions, where the analyte concentration is determined in a series of identical samples to which various amounts of metal standard have been added. The concentration of metal in the original sample is determined from an extrapolation of a plot of absorbance versus added analyte. In the new method, the amount of copper is determined by the method of standard additions for different concentrations of the sample under investigation as well. From an extrapolation of the data, the concentration of copper in the absence of interfering matrix is obtained. Studies with fetal bovine serum demonstrate that the new extrapolation technique is precise. Furthermore, considerably more copper is detected than by the classic method of standard additions applied to a nitric acid treated sample. The matrix effects of phosphate, nitrate, albumin, and serum were also examined. Both phosphate and serum, at physiological pH, decrease the detectability of added copper, while nitrate and albumin were without effect. The accuracy of this method has been verified by determining the extinction coefficients of stellacyanin and azurin. The values obtained, 4.33 X 10(3) and 3.75 X 10(3) M-1 cm-1, respectively, are considerably different from those determined by the method of standard additions on nitric acid digests of these proteins, but were close to values previously reported and determined colorimetrically.

Animals↗
PubMed1989

Stochastic models for subpopulation emergence in heterogeneous tumors.

A stochastic analog to a deterministic model describing subpopulation emergence in heterogeneous tumors is developed. The resulting system is described by the Fokker-Planck or forward Kolmogorov equation. A finite element approach for the numerical solution to this equation is described. Four biological and clinical scenarios are simulated (emergence of heterogeneity, exclusion of a subpopulation, and induction of drug resistance in both pure and heterogeneous tumors). The results of the simulations show that the stochastic model describes the same basic dynamics as its deterministic counterpart via a convective component, but that for each simulation a distribution of tumor sizes and mixes can also be derived from a diffusive component in the model. These distributions yield estimates for subpopulation extinction probabilities. The biological and clinical relevance of these results are discussed.

Drug Resistance↗
PubMed2000

Life and death near a windy oasis.

We propose a simple experiment to study delocalization and extinction in inhomogeneous biological systems. The nonlinear steady state for, say, a bacteria colony living on and near a patch of nutrient or favorable illumination ("oasis") in the presence of a drift term ("wind") is computed. The bacteria, described by a simple generalization of the Fisher equation, diffuse, divide A --> A + A, die A --> 0, and annihilate A + A --> 0. At high wind velocities all bacteria are blown into an unfavorable region ("desert"), and the colony dies out. At low velocity a steady state concentration survives near the oasis. In between these two regimes there is a critical velocity at which bacteria first survive. If the "desert" supports a small nonzero population, this extinction transition is replaced by a delocalization transition with increasing velocity. Predictions for the behavior as a function of wind velocity are made for one and two dimensions.

Bacteria↗
PubMed2000

Predictive accuracy of population viability analysis in conservation biology.

Population viability analysis (PVA) is widely applied in conservation biology to predict extinction risks for threatened species and to compare alternative options for their management. It can also be used as a basis for listing species as endangered under World Conservation Union criteria. However, there is considerable scepticism regarding the predictive accuracy of PVA, mainly because of a lack of validation in real systems. Here we conducted a retrospective test of PVA based on 21 long-term ecological studies--the first comprehensive and replicated evaluation of the predictive powers of PVA. Parameters were estimated from the first half of each data set and the second half was used to evaluate the performance of the model. Contrary to recent criticisms, we found that PVA predictions were surprisingly accurate. The risk of population decline closely matched observed outcomes, there was no significant bias, and population size projections did not differ significantly from reality. Furthermore, the predictions of the five PVA software packages were highly concordant. We conclude that PVA is a valid and sufficiently accurate tool for categorizing and managing endangered species.

Animals↗
PubMed2006

Dynamical evolution of ecosystems.

The assembly of an ecosystem such as a tropical forest depends crucially on the species interaction network, and the deduction of its rules is a formidably complex problem. In spite of this, many recent studies using Hubbell's neutral theory of biodiversity and biogeography have demonstrated that the resulting emergent macroscopic behaviour of the ecosystem at or near a stationary state shows a surprising simplicity reminiscent of many physical systems. Indeed the symmetry postulate, that the effective birth and death rates are species-independent within a single trophic level, allows one to make analytical predictions for various static distributions such as the relative species abundance, beta-diversity and the species-area relationship. In contrast, there have only been a few studies of the dynamics and stability of tropical rain forests. Here we consider the dynamical behaviour of a community, and benchmark it against the exact predictions of a neutral model near or at stationarity. In addition to providing a description of the relative species abundance, our analysis leads to a quantitative understanding of the species turnover distribution and extinction times, and a measure of the temporal scales of neutral evolution. Our model gives a very good description of the large quantity of data collected in Barro Colorado Island in Panama in the period 1990-2000 with just three ecologically relevant parameters and predicts the dynamics of extinction of the existing species.

Animals↗
PubMed1996

Evaluation of the concentration and bioactivity of adenovirus vectors for gene therapy.

Development of adenovirus vectors as potential therapeutic agents for multiple applications of in vivo human gene therapy has resulted in numerous preclinical and clinical studies. However, lack of standardization of the methods for quantifying the physical concentration and functionally active fraction of virions in these studies has often made comparison between various studies difficult or impossible. This study was therefore carried out to define the variables for quantification of the concentration of adenovirus vectors. The methods for evaluation of total virion concentration included electron microscopy and optical absorbance. The methods for evaluation of the concentration of functional virions included detection of gene transfer (transgene transfer and expression) and the plaque assay on 293 cells. Enumeration of total virion concentration by optical absorbance was found to be a precise procedure, but accuracy was dependent on physical disruption of the virion to eliminate artifacts from light scattering and also on a correct value for the extinction coefficient. Both biological assays for enumerating functional virions were highly dependent on the assay conditions and in particular the time of virion adsorption and adsorption volume. Under optimal conditions, the bioactivity of the vector, defined as the fraction of total virions which leads to detected target cell infection, was determined to be 0.10 in the plaque assay and 0.29 in the gene transfer assay. This difference is most likely due to the fact that detection by gene transfer requires only measurement of levels of transgene expression in the infected cell whereas plaque formation is dependent on a series of biological events of much greater complexity. These results show that the exact conditions for determination of infectious virion concentration and bioactivity of recombinant adenovirus vectors are critical and must be standardized for comparability. These observations may be very useful in comparison of data from different preclinical and clinical studies and may also have important implications for how adenovirus vectors can optimally be used in human gene therapy.

Adenoviridae↗
PubMed2005

An epizootic of avian pox in endemic short-toed larks (Calandrella rufescens) and Berthelot's pipits (Anthus berthelotti) in the Canary Islands, Spain.

Between January 2002 and November 2003, 50% (n = 395) of short-toed larks (Calandrella rufescens) and 28% (n = 139) of Berthelot's pipits (Anthus berthelotti) examined on the islands of Fuerteventura and Lanzarote, Canary Islands, had gross lesions compatible with avian pox. However, Spanish sparrows (Passer hispaniolensis, n = 128) and trumpeter finches (Bucanetes githagineus, n = 228), which inhabit the same steppe habitats associated with goat husbandry, did not have poxlike lesions. Histopathology and electron microscopy confirmed poxvirus in the lesions, whereas serology using standard, fowl poxvirus-and pigeon poxvirus-based diagnostic agar gel immunodiffusion techniques was negative, likely because of the limited (74.6% pipit; 74.9% lark) similarity between the viruses in our species and fowlpox virus on which the serologic tests rely. On the basis of polymerase chain reaction analyses, the virus isolated from dried lesions of C. rufescens has 80.5% similarity with the virus isolated from A. berthelotti and 91.3% similarity with canarypox, whereas A. berthelotti poxvirus has only 80% similarity with canarypox. We have two distinct and possibly new avian poxviruses. Both poultry and the wild birds on the farms were heavily infested by fleas, which may have acted as vectors in transmission of poxvirus. Disease prevalence in these Canary Island passerines is higher than that described in song birds in Hawaii that are now threatened, endangered, or extinct. Environmental and biological factors contributing to increased disease susceptibility of these isolated populations must be investigated.

Animals↗
PubMed2000

Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions.

If we are to plan conservation strategies that minimize the loss of evolutionary history through human-caused extinctions, we must understand how this loss is related to phylogenetic patterns in current extinction risks and past speciation rates. Nee & May (1997, Science 278, 692-694) showed that for a randomly evolving clade (i) a single round of random extinction removed relatively little evolutionary history, and (ii) extinction management (choosing which taxa to sacrifice) offered only marginal improvement. However, both speciation rates and extinction risks vary across lineages within real clades. We simulated evolutionary trees with phylogenetically patterned speciation rates and extinction risks (closely related lineages having similar rates and risks) and then subjected them to several biologically informed models of extinction. Increasing speciation rate variation increases the extinction-management pay-off. When extinction risks vary among lineages but are uncorrelated with speciation rates, extinction removes more history (compared with random trees), but the difference is small. When extinction risks vary and are correlated with speciation rates, history loss can dramatically increase (negative correlation) or decrease (positive correlation) with speciation rate variation. The loss of evolutionary history via human-caused extinctions may therefore be more severe, yet more manageable, than first suggested.

Biological Evolution↗
PubMed2003

Competitive fates of bacterial social parasites: persistence and self-induced extinction of Myxococcus xanthus cheaters.

Cooperative biological systems are susceptible to disruption by cheating. Using the social bacterium Myxococcus xanthus, we have tested the short-term competitive fates of mixed cheater and wild-type strains over multiple cycles of cooperative development. Cheater/wild-type mixes underwent several cycles of starvation-induced multicellular development followed by spore germination and vegetative population growth. The population sizes of cheater and wild-type strains in each pairwise mixture were measured at the end of each developmental phase and each growth phase. Cheater genotypes showed several distinct competitive fates, including cheater persistence at high frequencies with little effect on total population dynamics, cheater persistence after major disruption of total population dynamics, self-extinction of cheaters with wild-type survival, and total population extinction. Our results empirically demonstrate that social exploitation can destabilize a cooperative biological system and increase the risk of local extinction events.

Biological Evolution↗
PubMed2026

Skull morphology of the extinct Tasmanian tiger suggests unique biting style.

The recently extinct thylacine (Tasmanian tiger) was the largest modern marsupial predator. It is considered a classic example of evolutionary convergence due to striking similarities with placental canids (e.g., foxes and wolves), particularly in the skull, despite ~160 million years of evolutionary separation. However, we here present geometric and linear morphometric evidence that the thylacine's cranial form arises from a mosaic of traits not represented among canids or other living mammalian carnivores. Thylacines had disproportionately large heads, tall and gracile snouts with a flared canine region, and conspicuously large infraorbital foramina. Many of these traits suggest adaptations to fast, high-impact snapping behaviour in prey capture, as proposed for several living and extinct predatorial vertebrates with similar trait combinations. The thylacine's cranial function may therefore not be inferable from observation of living mammals. However, genomic progress presents new opportunities for future insights into the evolution and development of thylacine cranial adaptation.

Animals↗
PubMed2006

Larval ecology, geographic range, and species survivorship in Cretaceous mollusks: organismic versus species-level explanations.

The observation that geographic range size in Cretaceous mollusks is correlated with species survivorship and is heritable at the species level has figured repeatedly in discussions of species selection over the past two decades. However, some authors have suggested that the relationship between mode of larval development and geographic range supports the reduction of this example to selection on organismic properties. Our reanalysis of Jablonski's work on heritability at the species level finds that geographic range is significantly heritable (using a randomization test) in both bivalves and gastropods, even within a single larval mode. Further, generalized linear models show that geographic range size is more important than larval mode in predicting extinction probability in both gastropods and bivalves. These results reaffirm the role and heritability of geographic range as a species-level property that can promote species selection; the model-based approach applied here may help to operationalize "screening off " and related approaches to evaluating hierarchical explanations in evolution.

Animals↗
PubMed2005

Palaeoanatomy and biological affinities of a Cambrian deuterostome (Stylophora).

Stylophora are a peculiar extinct group of asymmetrical deuterostomes whose biological affinity has been fiercely debated. Disarticulated skeletal elements of a ceratocystid stylophoran recovered from the earliest Middle Cambrian of Morocco are not only the oldest stylophorans in the fossil record, but their exceptional preservation provides crucial data on the microstructure of its skeleton. Stylophoran plates are constructed of a three-dimensional mesh, termed 'stereom', identical to that of living echinoderms in which stereom microstructure provides a reliable guide to the nature of the investing soft tissues. Using modern echinoderm anatomy to interpret stereom microstructure of stylophoran elements, here we show that the large proximal lumen of their appendage was filled with muscle and that ligamentary tissues bound distal elements firmly together. We find no evidence for a mouth in the proximal lumen and no evidence that the covering plates of the appendage were articulated. Thus, although skeletal structure suggests that stylophorans are echinoderms, their appendage was not a feeding arm but a muscular locomotory organ.

Animals↗
PubMed2001

Parametric analysis of the ratio-dependent predator-prey model.

We present a complete parametric analysis of stability properties and dynamic regimes of an ODE model in which the functional response is a function of the ratio of prey and predator abundances. We show the existence of eight qualitatively different types of system behaviors realized for various parameter values. In particular, there exist areas of coexistence (which may be steady or oscillating), areas in which both populations become extinct, and areas of "conditional coexistence" depending on the initial values. One of the main mathematical features of ratio-dependent models, distinguishing this class from other predator-prey models, is that the Origin is a complicated equilibrium point, whose characteristics crucially determine the main properties of the model. This is the first demonstration of this phenomenon in an ecological model. The model is investigated with methods of the qualitative theory of ODEs and the theory of bifurcations. The biological relevance of the mathematical results is discussed both regarding conservation issues (for which coexistence is desired) and biological control (for which extinction is desired).

Animals↗
PubMed2006

A model describing the effect of sex-reversed YY fish in an established wild population: The use of a Trojan Y chromosome to cause extinction of an introduced exotic species.

A novel means of inducing extinction of an exotic fish population is proposed using a genetic approach to shift the ratio of male to females within a population. In the proposed strategy, sex-reversed fish containing two Y chromosomes are introduced into a normal fish population. These YY fish result in the production of a disproportionate number of male fish in subsequent generations. Mathematical modeling of the system following introduction of YY fish at a constant rate reveals that female fish decline in numbers over time, leading to eventual extinction of the population.

Animals↗
PubMed2004

Measured infrared optical cross sections for a variety of chemical and biological aerosol simulants.

We conducted a series of spectral extinction measurements on a variety of aerosolized chemical and biological simulants over the spectral range 3-13 microm using conventional Fourier-transform IR (FTIR) aerosol spectroscopy. Samples consist of both aerosolized particulates and atomized liquids. Materials considered include Bacillus subtilis endospores, lyophilized ovalbumin, polyethylene glycol, dimethicone (SF-96), and three common background materials: kaolin clay (hydrated aluminum silicate), Arizona road dust (primarily SiO2), and diesel soot. Aerosol size distributions and mass density were measured simultaneously with the FTIR spectra. As a result, all optical parameters presented here are mass normalized, i.e., in square meters per gram. In an effort to establish the utility of using Mie theory to predict such parameters, we conducted a series of calculations. For materials in which the complex indices of refraction are known, e.g., silicone oil (SF-96) and kaolin, measured size distributions were convolved with Mie theory and the resultant spectral extinction calculated. Where there was good agreement between measured and calculated extinction spectra, absorption, total scattering, and backscatter were also calculated.

Aerosols↗
PubMed2004

Human population density and extinction risk in the world's carnivores.

Understanding why some species are at high risk of extinction, while others remain relatively safe, is central to the development of a predictive conservation science. Recent studies have shown that a species' extinction risk may be determined by two types of factors: intrinsic biological traits and exposure to external anthropogenic threats. However, little is known about the relative and interacting effects of intrinsic and external variables on extinction risk. Using phylogenetic comparative methods, we show that extinction risk in the mammal order Carnivora is predicted more strongly by biology than exposure to high-density human populations. However, biology interacts with human population density to determine extinction risk: biological traits explain 80% of variation in risk for carnivore species with high levels of exposure to human populations, compared to 45% for carnivores generally. The results suggest that biology will become a more critical determinant of risk as human populations expand. We demonstrate how a model predicting extinction risk from biology can be combined with projected human population density to identify species likely to move most rapidly towards extinction by the year 2030. African viverrid species are particularly likely to become threatened, even though most are currently considered relatively safe. We suggest that a preemptive approach to species conservation is needed to identify and protect species that may not be threatened at present but may become so in the near future.

Animals↗