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PubMed1997

A unified theory of impact crises and mass extinctions: quantitative tests.

Several quantitative tests of a general hypothesis linking impacts of large asteroids and comets with mass extinctions of life are possible based on astronomical data, impact dynamics, and geological information. The waiting times of large-body impacts on the Earth derived from the flux of Earth-crossing asteroids and comets, and the estimated size of impacts capable of causing, large-scale environmental disasters, predict the impacts of objects > or = 5 km in diameter (> or = 10(7) Mt TNT equivalent) could be sufficient to explain the record of approximately 25 extinction pulses in the last 540 Myr, with the 5 recorded major mass extinctions related to impacts of the largest objects of > or = 10 km in diameter (> or = 10(8) Mt events). Smaller impacts (approximately 10(6) Mt), with significant regional environmental effects, could be responsible for the lesser boundaries in the geologic record. Tests of the "kill curve" relationship for impact-induced extinctions based on new data on extinction intensities, and several well-dated large impact craters, also suggest that major mass extinctions require large impacts, and that a step in the kill curve may exist at impacts that produce craters of approximately 100 km diameter, smaller impacts being capable of only relatively weak extinction pulses. Single impact craters less than approximately 60 km in diameter should not be associated with detectable global extinction pulses (although they may explain stage and zone boundaries marked by lesser faunal turnover), but multiple impacts in that size range may produce significant stepped extinction pulses. Statistical tests of the last occurrences of species at mass-extinction boundaries are generally consistent with predictions for abrupt or stepped extinctions, and several boundaries are known to show "catastrophic" signatures of environmental disasters and biomass crash, impoverished postextinction fauna and flora dominated by stress-tolerant and opportunistic species, and gradual ecological recovery and radiation of new taxa. Isotopic and other geochemical signatures are also generally consistent with the expected after-effects of catastrophic impacts. Seven of the recognized extinction pulses seem to be associated with concurrent (in some cases multiple) stratigraphic impact markers (e.g., layers with high iridium, shocked minerals, microtektites), and/or large, dated impact craters. Other less well-studied crisis intervals show elevated iridium, but well below that of the K/T spike, which might be explained by low-Ir impactors, ejecta blowoff, or sedimentary reworking and dilution of impact signatures. The best explanation for a possible periodic component of approximately 30 Myr in mass extinctions and clusters of impacts is the pulselike modulation of the comet flux associated with the solar system's periodic passage through the plane of the Milky Way Galaxy. The quantitative agreement between paleontologic and astronomical data suggests an important underlying unification of the processes involved.

Biological Evolution↗

PubMed2006

Developing an agenda for translational studies of resilience and vulnerability following trauma exposure.

Here we outline a translational research agenda for studies of resilience, defined as the process of adapting well in the face of adversity or trauma. We argue that an individual differences approach to the study of resilience, in which the full range of behavioral and biological responses to stress exposure is examined can be applied across human samples (e.g., people who have developed psychopathology versus those who have not; people who have been exposed to trauma versus those who have not) and even, in some cases, across species. We delineate important psychological resilience-related factors including positive affectivity and optimism, cognitive flexibility, coping, social support, emotion regulation, and mastery. Key brain regions associated with stress-related psychopathology have been identified with animal models of fear (e.g., extinction and fear conditioning; memory reconsolidation) and we describe how these regions can be studied in humans using neuroimaging technology. Finally, we cite recent research identifying neuroendocrine markers of resilience and recovery in humans (e.g., neuropeptide Y [NPY], dehydroepiandrosterone [DHEA]) that can also be measured, in some cases, in other species. That exposure to adversity or trauma does not necessarily lead to impairment and the development of psychopathology in all people is an important observation. Understanding why this is so will provide clues for the development of therapeutic interventions for those people who do develop stress-related psychopathology, or even for the prevention of adverse outcomes.

Brain Chemistry↗

PubMed2003

Time and space issues in ecotoxicology: population models, landscape pattern analysis, and long-range environmental chemistry.

Advances in ecotoxicology addressing problems of time and spatial scales are presented and interpreted in the frame of concepts on population/community dynamics and landscape pattern analysis. Example deterministic/probabilistic modeling experiments are used to illustrate key concepts. Space and time scales analyzed are single and multigenerations of local populations, metapopulations, community, and ecosystem/landscape. Most population models used in recent ecotoxicology studies are deterministic and do not include a formal treatment of spatial processes, like migration or local random extinction. Some metapopulation models have been applied with success. Upscaling of ecotoxicological results at the community level is less developed, probably because of the inherent complexity of indirect and direct coactions among organisms. Community and ecosystem toxicity end points that could find a broad use in regulatory applications have not yet been identified. Some practical issues like the estimation of the potential for the natural attenuation of toxicity and the transport of contaminants along food chains must be addressed at these scales/levels of biological complexity. The estimation of ecotoxicological effects has been increasingly evolving to integrate modeling and monitoring contaminant transport and fate, landscape pattern analysis, and spatially explicit population dynamics (including direct and indirect communal interactions).

Agriculture↗

PubMed1994

Assembly and molecular organization of self-assembled lipid bilayers on solid substrates monitored by surface plasmon resonance spectroscopy.

The structural properties of lipid films, made from a squalene/butanol solution containing varying amounts (0-15 mg/ml) of egg phosphatidylcholine and deposited on a thin metallic silver layer, were investigated using surface plasmon resonance (SPR) spectroscopy. Optical parameters (thickness, refractive index and extinction coefficient) of such supported self-assembled lipid membranes were obtained from a theoretical analysis of the experimental SPR curves. The mass of the lipid membrane and the area and volume occupied by one lipid molecule were also calculated. The results were consistent with the formation of durable and homogeneous lipid bilayers on the solid substrate, and indicated similarities in structural properties between the present lipid bilayers and freely suspended and Langmuir-Blodgett bilayer membranes. Such bilayers represent a simple model for biological membranes, as well as providing a means of immobilizing proteins for various practical applications, including receptor-based sensors and molecular devices. The results confirm the value of the SPR technique for investigating the properties of thin biomolecular dielectric films deposited on a metal surface.

Lipid Bilayers↗

PubMed2002

Fidelity and spatio-temporal control in MAP kinase (ERKs) signalling.

Extracellular signals transduced via receptor tyrosine kinases, G-protein-coupled receptors or integrins activate Ras, a key switch in cellular signalling. Although Ras can activate multiple downstream effectors (PI3K, Ral em leader ) one of the major activated pathway is a conserved sequential protein kinase cascade referred to as the mitogen activated protein (MAP) kinase module: Raf>MEK>ERK. The fidelity of signalling among protein kinases and the spatio-temporal activation are certainly key determinants for generating precise biological responses. The fidelity is ensured by scaffold proteins, a sort of protein kinase "insulators" and/or specific docking sites among the members of the signalling cascade. These docking sites are found in upstream and downstream regulators and MAPK substrates [Nat Cell Biol 2 2000 110]. The duration and the intensity of the response are in part controlled by the compartmentalisation of the signalling molecules. Growth factors promote nuclear accumulation and persistent activation of ERK (p42/p44 MAP kinases) during the entire G1 period with an extinction during S-phase. These features are exquisitely well controlled by (i) the temporal induction of the MAP kinase phosphatases, MKP1-3, and (ii) the compartmentalisation of the signalling molecules. We have shown that MKP1-2 induction is strictly controlled by the activation of the MAP kinase module providing evidence for an autoregulatory mechanism. This negative regulatory loop was further enhanced by the capacity of ERK to phosphorylate MKP1 and 2. This action reduced the degradation rate of these MKPs through the ubiquitin-proteasomal system [Science 286 1999 2514]. Whereas the two upstream kinases of the module, Raf and MEK remained cytoplasmic, ERK anchored to MEK in the cytoplasm of resting cells, rapidly translocated to the nucleus upon mitogenic stimulation. This process was rapid, reversible, and controlled by the strict activation of the MAPK cascade. Prevention of this nuclear translocation, by overexpression of a cytoplasmic ERK-docking molecule (inactive MKP3) prevented growth factor-stimulated DNA replication [EMBO J 18 1999 664]. Following long term stimulation, ERK progressively accumulated in the nucleus in an inactive form. This nuclear retention relied on the neosynthesis of short-lived nuclear anchoring proteins. Nuclear inactivation and sequestration was likely to be controlled by MAP kinase phosphatases 1 and 2. Therefore we propose that the nucleus represents a site for ERK action, sequestration and signal termination [J Cell Sci 114 2001 3433]. In addition, with the generation of mice invalidated for each of the ERK isoforms, we will illustrate that besides controlling cell proliferation the ERK cascade also controls cell differentiation and cell behaviour [Science 286 1999 1374].

Animals↗

PubMed2003

Epidemiological modeling in a branching population. Particular case of a general SIS model with two age classes.

This paper covers the elaboration of a general class of multitype branching processes for modeling in a branching population, the evolution of a disease with horizontal and vertical transmissions. When the size of the population may tend to infinity, normalization must be carried out. As the initial size tends to infinity, the normalized model converges a.s. to a dynamical system the solution of which is the probability law of the state of health for an individual ancestors line. The focal point of this study concerns the transient and asymptotical behaviors of a SIS model with two age classes in a branching population. We will compare the asymptotical probability of extinction on the scale of a finite population and on the scale of an individual in an infinite population: when the rates of transmission are small compared to the rate of renewing the population of susceptibles, the two models lead to a.s. extinction, giving consistent results, which no longer applies to the opposite situation of important transmissions. In that case the size of the population plays a crucial role in the spreading of the disease.

Age Factors↗

PubMed1999

Modeling insight into spontaneous regression of tumors.

The phenomenon of spontaneous regression of benign and malignant tumors is well documented in the literature and is commonly attributed to the induction of apoptosis or activation of the immune system. We attempt at evaluating the role of random effects in this phenomenon. To this end, we consider a stochastic model of tumor growth which is descriptive of the fact that tumors are inherently prone to spontaneous regression due to the random nature of their development. The model describes a population of actively proliferating cells which may give rise to differentiated cells. The process of cell differentiation is irreversible and terminates in cell death. We formulate the model in terms of temporally inhomogeneous Markov branching processes with two types of cells so that the expected total number of neoplastic cells is consistent with the observed mean growth kinetics. Within the framework of this model, the extinction probability for proliferating cells tends to one as time tends to infinity. Given the event of nonextinction, the distribution of tumor size is asymptotically exponential. The limiting conditional distribution of tumor size is in good agreement with epidemiologic data on advanced lung cancer.

Humans↗

PubMed2003

Introduced species and their missing parasites.

Damage caused by introduced species results from the high population densities and large body sizes that they attain in their new location. Escape from the effects of natural enemies is a frequent explanation given for the success of introduced species. Because some parasites can reduce host density and decrease body size, an invader that leaves parasites behind and encounters few new parasites can experience a demographic release and become a pest. To test whether introduced species are less parasitized, we have compared the parasites of exotic species in their native and introduced ranges, using 26 host species of molluscs, crustaceans, fishes, birds, mammals, amphibians and reptiles. Here we report that the number of parasite species found in native populations is twice that found in exotic populations. In addition, introduced populations are less heavily parasitized (in terms of percentage infected) than are native populations. Reduced parasitization of introduced species has several causes, including reduced probability of the introduction of parasites with exotic species (or early extinction after host establishment), absence of other required hosts in the new location, and the host-specific limitations of native parasites adapting to new hosts.

Adaptation, Physiological↗

PubMed2006

Applications of emerging technologies to the study and conservation of threatened and endangered species.

Sustaining viable populations of all wildlife species requires the maintenance of habitat, as well as an understanding of the behaviour and physiology of individual species. Despite substantial efforts, there are thousands of species threatened by extinction, often because of complex factors related to politics, social and environmental conditions and economic needs. When species become critically endangered, ex situ recovery programmes that include reproductive scientists are the usual first line of defence. Despite the potential of reproductive technologies for rapidly increasing numbers in such small populations, there are few examples of success. This is not the result of a failure on the part of the technologies per se, but rather is due to a lack of knowledge about the fundamental biology of the species in question, information essential for allowing reproductive technologies to be effective in the production of offspring. In addition, modern conservation concepts correctly emphasise the importance of maintaining heterozygosity to sustain genetic vigour, thereby limiting the practical usefulness of some procedures (such as nuclear transfer). However, because of the goal of maintaining all extant gene diversity and because, inevitably, many species are (or will become) 'critically endangered', it is necessary to explore every avenue for a potential contributory role. There are many 'emerging technologies' emanating from the study of livestock and laboratory animals. We predict that a subset of these may have application to the rescue of valuable genes from individual endangered species and eventually to the genetic management of entire populations or species. The present paper reviews the potential candidate techniques and their potential value (and limitations) to the study and conservation of rare wildlife species.

Animals↗

PubMed2001

Golden eagles, feral pigs, and insular carnivores: how exotic species turn native predators into prey.

Island ecosystems are particularly vulnerable to exotic species. Here we show how an introduced prey has led to the wholesale restructuring of an island food web, including the near extinction of an endemic carnivore. Introduced pigs, by providing abundant food, enabled golden eagles to colonize the California Channel Islands. Eagles preyed heavily on the island fox, whose resulting decline toward extinction released populations of the competitively inferior island skunk. The presence of exotic pigs led to major ecosystem shifts by indirectly causing predation to replace competition as the dominant force shaping these island communities.

Animals↗

PubMed1999

Walter Rudolf Hess (1881-1973) and his contribution to neuroscience.

The present account includes a brief life history of Walter Rudolf Hess (1881-1973) and a review of his major neurophysiological contributions. Hess belonged to the nearly extinct generation of great universalists among students of human physiology. He began his scientific work in hemodynamics and ophthalmology, then studied the functional organization and regulation of circulation and respiration and developed a number of highly sophisticated instruments which fostered his international reputation. By electrically stimulating the brain of the unanesthetized, freely moving animal he explored the functional organization and localization of the cat diencephalon in terms of autonomic, extrapyramidal motor functions, and instinctive behavior, e.g. hunger, thirst, fear, and rage. His thoughts on biological order led him to consider the problems of psychic forces. He was convinced of the close correlation of behavioral research and neurophysiology and believed that neuronal patterns determine the content of consciousness without providing clues concerning the transformation of such patterns into subjective experience.

History, 20th Century↗

PubMed2003

Early hominin speciation at the Plio/Pleistocene transition.

Over the last half-decade or so, there has been an explosion in the recognition of hominin genera and species. We now have the late Miocene genera Orrorin and Sahelanthropus, the mid Pliocene genus Kenyanthropus, three new Pliocene species of Australopithecus (A. anamensis, A. garhi and A. bahrelghazali) and a sub species of Ardipithecus (Ar. r. kadabba) to contend with. Excepting also the more traditional species allocated to Paranthropus, Australopithecus and early Homo we are approaching around 15 species over 5 million years (excluding hominin evolution over the last one million years). Can such a large number of hominin species be justified? An examination of extant hominid (Gorilla gorilla, Pan troglodytes, and Pan paniscus) anatomical variability indicates that the range of fossil hominin variability supports the recognition of this large number of fossil species. It is also shown that not all hominins are directly related to the emergence of early Homo and as such have become extinct. Indeed the traditional australopithecine species 'A'. anamensis, 'A'. afarensis and 'A'. garhi are considered here to belong to a distinct genus Praeanthropus. They are also argued not be hominins, but rather an as yet undefined hominid group from which the more derived hominins evolved. The first hominin is represented by A. africanus or a hominin very much like it. The Paranthropus clade is defined by a derived heterochronic condition of peramorphosis, associated with sequential progenesis (contraction of successive growth stages) in brain and dental development, but a mixture of peramorphic and paedomorphic features in its craniofacial anatomy. Conversely, Kenyanthropus and Homo both share a pattern of peramorphosis, associated with sequential hypermorphosis (prolongation of successive growth stages) in brain development, and paedomorphosis processes in cranial, facial and dental development. This suggests, that these two clades share an important synapomorphy not recognised in the parsimony analyses, suggesting that they may form a sister group relationship to the exclusion of Paranthropus. This highlights the need to re-interpret phylogenetic results in terms of function and development. The rapid speciation and extinction as argued here is in keeping with other fossil groups in Africa at the Plio/Pleistocene transition. This emphasises that we must approach the pre-australopithecines and hominins as part of the endemic African fauna, and not in isolation to the evolutionary and climatic processes that were operating all around them.

Africa↗

PubMed2006

Stochastic predation events and population persistence in bighorn sheep.

Many studies have reported temporal changes in the relative importance of density-dependence and environmental stochasticity in affecting population growth rates, but they typically assume that the predominant factor limiting growth remains constant over long periods of time. Stochastic switches in limiting factors that persist for multiple time-steps have received little attention, but most wild populations may periodically experience such switches. Here, we consider the dynamics of three populations of individually marked bighorn sheep (Ovis canadensis) monitored for 24-28 years. Each population experienced one or two distinct cougar (Puma concolor) predation events leading to population declines. The onset and duration of predation events were stochastic and consistent with predation by specialist individuals. A realistic Markov chain model confirms that predation by specialist cougars can cause extinction of isolated populations. We suggest that such processes may be common. In such cases, predator-prey equilibria may only occur at large geographical and temporal scales, and are unlikely with increasing habitat fragmentation.

Alberta↗

PubMed1998

Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators.

The constitutive DNase I hypersensitive site at the 5' end of the chicken beta-globin locus marks the boundary of the active chromatin domain in erythroid cells. The DNA sequence containing this site has the properties of an insulator, as shown by its ability in stable transformation experiments to block enhancer-promoter interaction when it lies between the two, but not when it lies outside, and to protect against position effects in Drosophila. We now show that the chicken insulator can protect a stably integrated gene, which is otherwise subject to great variability of expression, from chromatin-mediated repression in cell culture. When the integrated reporter gene is surrounded by insulator elements, stably transformed cell lines display consistent enhancer-dependent expression levels, in accord with the strength of the enhancer. In the absence of insulators, long-term nonselective propagation of cells carrying the integrated reporter gene results in gradual extinction of the reporter's expression, with expression patterns from tandemly repeated inserted genes suggesting that the extinction of adjacent genes is coupled. We show that the uninsulated reporter genes, in addition to becoming transcriptionally inactive, lose several epigenetic hallmarks of active chromatin, including nuclease accessibility, DNA hypomethylation, and histone hyperacetylation during time in culture. Treatment with inhibitors of histone deacetylase or DNA methylation reverses the extinction of the uninsulated genes. Extinction is completely prevented by flanking the reporter construct with insulators. Furthermore, in contrast to the uninsulated reporter genes, chromatin over the insulated genes retains nuclease accessibility and histone hyperacetylation. However, there is no clear correlation between the presence of the insulators and the level of DNA methylation. This leads us to propose a model for the insulator's ability to protect against extinction in the transformed cell lines and to function as a chromatin boundary for the chicken beta-globin locus in normal erythroid cells.

Acetylation↗

PubMed1995

Ancient DNA.

The investigation of molecular traits for evolutionary studies is a valuable alternative to the classic morphological approach. Since the mid-1980s molecular evolution has extended its field of investigation into the past. This has become possible with development of the polymerase chain reaction, which allows amplification of, and hence the study of, DNA from individuals long since dead. Many ancient, mostly extinct, animals and plants have been studied in order to determine their phylogenetic relationships with extant species. The biochemical properties of ancient DNA are also under investigation. The modifications that this molecule undergoes over long periods of time are of great interest as attempts are made to retrieve DNA from increasingly older remains.

Animals↗

PubMed1987

Adaptation, plant evolution, and the fossil record.

The importance of adaptation in determining patterns of evolution has become an important focus of debate in evolutionary biology. As it pertains to paleobotany, the issue is whether or not adaptive evolution mediated by natural selection is sufficient to explain the stratigraphic distributions of taxa and character states observed in the plant fossil record. One means of addressing this question is the functional evaluation of stratigraphic series of plant organs set in the context of paleoenvironmental change and temporal patterns of floral composition within environments. For certain organ systems, quantitative estimates of biophysical performance can be made on the basis of structures preserved in the fossil record. Performance estimates for plants separated in time or space can be compared directly. Implicit in different hypotheses of the forces that shape the evolutionary record (e.g. adaptation, mass extinction, rapid environmental change, chance) are predictions about stratigraphic and paleoenvironmental trends in the efficacy of functional performance. Existing data suggest that following the evolution of a significant structural innovation, adaptation for improved functional performance can be a major determinant of evolutionary changes in plants; however, there are structural and development limits to functional improvement, and once these are reached, the structure in question may no longer figure strongly in selection until and unless a new innovation evolves. The Silurian-Devonian paleobotanical record is consistent with the hypothesis that the succession of lowland floodplain dominants preserved in the fossil record of this interval was determined principally by the repeated evolution of new taxa that rose to ecological importance because of competitive advantages conferred by improved biophysical performance. This does not seem to be equally true for Carboniferous-Jurassic dominants of swamp and lowland floodplain environments. In these cases, environmental disruption appears to have been a major factor in shaping the fossil record. This does not mean that continuing adaptation was not important during this interval, but it may indicate that adaptive evolution was strongest in environments other than those best represented in the paleobotanical record.

Adaptation, Biological↗

PubMed2000

Stochastic modelling of environmental variation for biological populations.

We examine stochastic effects, in particular environmental variability, in population models of biological systems. Some simple models of environmental stochasticity are suggested, and we demonstrate a number of analytic approximations and simulation-based approaches that can usefully be applied to them. Initially, these techniques, including moment-closure approximations and local linearization, are explored in the context of a simple and relatively tractable process. Our presentation seeks to introduce these techniques to a broad-based audience of applied modellers. Therefore, as a test case, we study a natural stochastic formulation of a non-linear deterministic model for nematode infections in ruminants, proposed by Roberts and Grenfell (1991). This system is particularly suitable for our purposes, since it captures the essence of more complicated formulations of parasite demography and herd immunity found in the literature. We explore two modes of behaviour. In the endemic regime the stochastic dynamic fluctuates widely around the non-zero fixed points of the deterministic model. Enhancement of these fluctuations in the presence of environmental stochasticity can lead to extinction events. Using a simple model of environmental fluctuations we show that the magnitude of this system response reflects not only the variance of environmental noise, but also its autocorrelation structure. In the managed regime host-replacement is modelled via periodic perturbation of the population variables. In the absence of environmental variation stochastic effects are negligible, and we examine the system response to a realistic environmental perturbation based on the effect of micro-climatic fluctuations on the contact rate. The resultant stochastic effects and the relevance of analytic approximations based on simple models of environmental stochasticity are discussed.

Animals↗

PubMed2003

Interactions in a tritrophic acarine predator-prey metapopulation system V: within-plant dynamics of Phytoseiulus persimilis and Tetranychus urticae (Acari: Phytoseiidae, Tetranychidae).

To investigate the relative contributions of bottom-up (plant condition) and top-down (predatory mites) factors on the dynamics of the two-spotted spider mite (Tetranychus urticae), a series of experiments were conducted in which spider mites and predatory mites were released on bean plants. Plants inoculated with 2, 4, 8, 16, and 32 adult female T. urticae were either left untreated or were inoculated with 3 or 5 adult female predators (Phytoseiulus persimilis) one week after the introduction of spider mites. Plant area, densities of T. urticae and P. persimilis, and plant injury were assessed by weekly sampling. Data were analysed by a combination of statistical methods and a tri-trophic mechanistic simulation model partly parameterised from the current experiments and partly from previous data. The results showed a clear effect of predators on the density of spider mites and on the plant injury they cause. Plant injury increased with the initial number of spider mites and decreased with the initial number of predators. Extinction of T. urticae, followed by extinction of P. persimilis, was the most likely outcome for most initial combinations of prey and predators. Eggs constituted a relatively smaller part of the prey population as plant injury increased and of the predator population as prey density decreased. We did not find statistical evidence of P. persimilis having preference for feeding on T. urticae eggs. The simulation model demonstrated that bottom-up and top-down factors interact synergistically to reduce the density of spider mites. This may have important implications for biological control of spider mites by means of predatory mites.

Animals↗