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Results for “Extinction, Biological”

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PubMed1978

Direct measurement of pure absorbance spectra of living phototrophic microorganisms.

The pure absorbance of turbid cell suspensions of various phototrophic microorganisms were determined by collecting the scattered light. A conventional spectrophotometer was used, equipped with an intergrating sphere as receiver unit, which allowed precise measurements of the absorbance in the range from zero to 0.1. In the wavelength range 300--1100 nm, where photosynthesis occurs, light scattered only once by a bacterial cell retains predominantly the forward direction. This allows measurements of pure absorption, when the concentration of cells which the light has to pass through is small. For example, by comparison of measurements of pigmented and nonpigmented cell suspensions of Rhodopseudomonas acidophila, it was shown that the total sum of scattered light can be collected. The best results were obtained using cuvettes with a light path of 0.1 cm or 0.2 cm to measure cell suspensions of about 0.2 mg dry weight per ml. For R. acidophila this corresponds to 1--3 cell layers. Extinction-, absorbance- and scattering spectra for R. acidophila are presented, in addition to the absorbance spectra for Rhodospirillum rubrum, Aphanocapsa and Scenedesmus.

Cell Count↗

PubMed2006

A diffusive SI model with Allee effect and application to FIV.

A minimal reaction-diffusion model for the spatiotemporal spread of an infectious disease is considered. The model is motivated by the Feline Immunodeficiency Virus (FIV) which causes AIDS in cat populations. Because the infected period is long compared with the lifespan, the model incorporates the host population growth. Two different types are considered: logistic growth and growth with a strong Allee effect. In the model with logistic growth, the introduced disease propagates in form of a travelling infection wave with a constant asymptotic rate of spread. In the model with Allee effect the spatiotemporal dynamics are more complicated and the disease has considerable impact on the host population spread. Most importantly, there are waves of extinction, which arise when the disease is introduced in the wake of the invading host population. These waves of extinction destabilize locally stable endemic coexistence states. Moreover, spatially restricted epidemics are possible as well as travelling infection pulses that correspond either to fatal epidemics with succeeding host population extinction or to epidemics with recovery of the host population. Generally, the Allee effect induces minimum viable population sizes and critical spatial lengths of the initial distribution. The local stability analysis yields bistability and the phenomenon of transient epidemics within the regime of disease-induced extinction. Sustained oscillations do not exist.

Algorithms↗

PubMed1998

Some perspectives on modeling leukemia.

A diffusion model of leukemia is presented. The space-occupying effects of leukemic cells during leukemic expansion is investigated. The analyses and simulations of the model suggest that acute leukemia is a state in which positions inhabited by colonies of normal cells are invaded by emerging colonies of abnormal cells. Normal cells are then driven to a state of extinction as leukemic cells evolve toward high and dominant steady state levels.

Cell Division↗

PubMed2003

A complex microbiota from snowball Earth times: microfossils from the Neoproterozoic Kingston Peak Formation, Death Valley, USA.

A thin carbonate unit associated with a Sturtian-age ( approximately 750-700 million years ago) glaciogenic diamictite of the Neoproterozoic Kingston Peak Formation, eastern California, contains microfossil evidence of a once-thriving prokaryotic and eukaryotic microbial community (preserved in chert and carbonate). Stratiform stromatolites, oncoids, and rare columnar stromatolites also occur. The microbial fossils, which include putative autotrophic and heterotrophic eukaryotes, are similar to those found in chert in the underlying preglacial units. They indicate that microbial life adapted to shallow-water carbonate environments did not suffer the significant extinction postulated for this phase of low-latitude glaciation and that trophic complexity survived through snowball Earth times.

Biological Evolution↗

PubMed1997

Centaurea corymbosa, a cliff-dwelling species tottering on the brink of extinction: a demographic and genetic study.

Centaurea corymbosa (Asteraceae) is endemic to a small area (< or = 3 km2), and < 500 individuals reproduce in any given year. Nevertheless, enzyme polymorphism was found within and among the six local extant populations, the most distant at 2.3 km. Levels of gene flow among populations and seed and pollen dispersal data indicated very low dispersal capacity. Rarity of long distance dispersal events coupled with traits such as prolonged juvenile period, monocarpy, and self-incompatibility precludes the establishment of new populations and thus the evolution toward colonization ability through increased dispersal rate, polycarpy, or self-compatibility. The species thus appears to be trapped on an evolutionary dead-end toward extinction, even though, from a preliminary introduction experiment, we conclude that several nearby unoccupied sites would be suitable for the species.

Biological Evolution↗

PubMed1998

Empirical determinants of measles metapopulation dynamics in England and Wales.

A key issue in metapopulation dynamics is the relative impact of internal patch dynamics and coupling between patches. This problem can be addressed by analysing large spatiotemporal data sets, recording the local and global dynamics of metapopulations. In this paper, we analyse the dynamics of measles meta-populations in a large spatiotemporal case notification data set, collected during the pre-vaccination era in England and Wales. Specifically, we use generalized linear statistical models to quantify the relative importance of local influences (birth rate and population size) and regional coupling on local epidemic dynamics. Apart from the proportional effect of local population size on case totals, the models indicate patterns of local and regional dynamic influences which depend on the current state of epidemics. Birth rate and geographic coupling are not associated with the size of major epidemics. By contrast, minor epidemics--and especially the incidence of local extinction of infection--are influenced both by birth rate and geographical coupling. Birth rate at a lag of four years provides the best fit, reflecting the delayed recruitment of susceptibles to school cohorts. A hierarchical index of spatial coupling to large centres provides the best spatial model. The model also indicates that minor epidemics and extinction patterns are more strongly influenced by this regional effect than the local impact of birth rate.

Disease Outbreaks↗

PubMed2006

Supertree analyses of the roles of viviparity and habitat in the evolution of atherinomorph fishes.

Using supertree phylogenetic reconstructions, we investigate how livebearing and freshwater adaptations may have shaped evolutionary patterns in the Atherinomorpha, a large clade (approximately 1500 extant species) of ray-finned fishes. Based on maximum parsimony reconstructions, livebearing appears to have evolved at least four times independently in this group, and no reversions to the ancestral state of oviparity were evident. With respect to habitat, at least five evolutionary transitions apparently occurred from freshwater to marine environments, at least two transitions in the opposite direction, and no clear ancestral state was identifiable. All viviparous clades exhibited more extant species than their oviparous sister taxa, suggesting that transitions to viviparity may be associated with cladogenetic diversification. Transitions to freshwater were usually, but not invariably associated with increased species richness, but the trend was, overall, not significant among sister clades. Additionally, we investigated whether livebearing and freshwater adaptations are currently associated with elevated risks of extinction as implied by species' presence on the 2004 IUCN Red List. Despite being correlated with decreased brood size, livebearing has not significantly increased extinction risk in the Atherinomorpha. However, freshwater species were significantly more likely than marine species to be listed as endangered.

Animals↗

PubMed2003

Risk management in biological evolution.

I present a framework to study the evolution of traits that allow an organism to survive life-threatening but rare risks. Specifically, I am concerned with risks so rare that any one individual in a population may not experience the risk-causing event in its lifetime. A theory of rare risk management is virtually absent in evolutionary biology, although it is well developed in economics. This is surprising because of the great influence economics had on evolutionary biology, and because biology is full of examples for evolved risk management traits. They include the ability of bacteria to sporulate, of pathogens to survive antibiotic treatment, of temperate bacteriophages to enter a lytic life cycle, as well as traits that allow higher organisms to survive rare environmental disasters, such as sporadic wildfires and irregular flooding. I make predictions about the sustenance of risk management traits under two scenarios, one where the catastrophic events cause individual deaths, and another one where catastrophic events cause population extinction. A well-developed theory of risk management will not only predict the distribution of risk management traits, but may also serve other purposes, such as to reconstruct the spectrum of environments that an organism encountered in its evolutionary history from the record stored in its genome's memory.

Adaptation, Physiological↗

PubMed1992

A continuous spectrophotometric assay for inorganic phosphate and for measuring phosphate release kinetics in biological systems.

A spectrophotometric method for the measurement of inorganic phosphate (P(i)) has been developed by using 2-amino-6-mercapto-7-methylpurine ribonucleoside and purine-nucleoside phosphorylase (purine-nucleoside:orthophosphate ribosyltransferase, EC 2.4.2.1). This substrate gives an absorbance increase at 360 nm on phosphorolysis at pH 6.5-8.5, and at pH 7.6 the change in extinction coefficient is 11,000 M-1.cm-1. The Michaelis-Menten constants of the two substrates with the enzyme are 70 microM for the nucleoside and 26 microM for P(i); the kcat is 40 s-1 (25 degrees C). The assay was shown to quantitate P(i) in solution at concentrations at least down to 2 microM. It can be used to measure the kinetics of P(i) release from phosphatases, such as GTPases and ATPases, by coupling the two enzymic reactions. The utility of this assay was shown by three test systems: glycerol kinase plus D-glyceraldehyde acting as an ATPase and actin-activated myosin ATPase, and myosin subfragment 1, hydrolyzing a single turnover of ATP, releasing P(i) with a rate constant the same as the steady-state ATPase activity.

Guanosine↗

PubMed2001

The influence of predator--prey population dynamics on the long-term evolution of food web structure.

We develop a set of equations to describe the population dynamics of many interacting species in food webs. Predator-prey interactions are nonlinear, and are based on ratio-dependent functional responses. The equations account for competition for resources between members of the same species, and between members of different species. Predators divide their total hunting/foraging effort between the available prey species according to an evolutionarily stable strategy (ESS). The ESS foraging behaviour does not correspond to the predictions of optimal foraging theory. We use the population dynamics equations in simulations of the Webworld model of evolving ecosystems. New species are added to an existing food web due to speciation events, whilst species become extinct due to coevolution and competition. We study the dynamics of species-diversity in Webworld on a macro-evolutionary time-scale. Coevolutionary interactions are strong enough to cause continuous overturn of species, in contrast to our previous Webworld simulations with simpler population dynamics. Although there are significant fluctuations in species diversity because of speciation and extinction, very large-scale extinction avalanches appear to be absent from the dynamics, and we find no evidence for self-organized criticality.

Animals↗

PubMed2005

Dynamical systems basis of metamorphosis: diversity and plasticity of cellular states in reaction diffusion network.

Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relation to the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics and considering the division and death of cells, the development of cells is studied. Cell differentiation process is found to occur through instability in transient dynamics and cell-cell interaction. In long-term behavior, extinction of multiple cells is repeated, which leads to itinerancy over successive quasi-stable multi-cellular states consisting of different types of cells. By defining the plasticity of a cellular state, it is shown that the plasticity of cells decreases before the extinction of most cell types, from which diversity and plasticity are later recovered. In the following, a decrease of plasticity occurs again, leading to the next extinction. This cycle of diversification and extinction is repeated. Relevance of our results to development and evolution is briefly discussed.

Animals↗

PubMed2007

Loss or gain? Invasive aliens and biodiversity in the Mediterranean Sea.

More than 500 alien species were listed from the Mediterranean Sea. Though no extinction of a native species is known, sudden decline in abundance, and even local extirpations, concurrent with proliferation of aliens, had been recorded. Examination of the profound ecological impacts of some of the most conspicuous invasive alien species underscores their role, among multiple anthropogenic stressors, in altering the infralittoral communities. Local population losses and niche contraction of native species may not induce immediate extirpation, but they augur reduction of genetic diversity, loss of functions, processes, and habitat structure, increase the risk of decline and extinction, and lead to biotic homogenization. The relevant environmental policy and management framework is discussed.

Animals↗

PubMed2004

Allee-like effects in metapopulation dynamics.

The existences of the Allee effect at the local population level and of the Allee-like effect at the metapopulation level are important for both ecology and conservation. Although there have been a great many papers on the Allee effect, they have mainly referred to only local populations and have not dealt with the relationship between the two. In this paper, we begin with local population dynamics and then construct a model including both local population and metapopulation dynamics. Then we simulate with computer at these two levels. The results indicate that the Allee-like effect in a metapopulation may emerge from the imposed Allee effect at the local population level. This threshold fraction of occupied patches below which the metapopulation goes extinct is seriously affected by the per capita migration rate, the survival rate during migration and the initial population size on the occupied patches. We also find that severe demographic stochasticity may compound the metapopulation extinction risk posed by the Allee effect. These conclusions are helpful for nature conservation, especially for the preservation of rare species.

Adaptation, Biological↗

PubMed2006

High-level similarity of dentitions in carnivorans and rodents.

The study of mammalian evolution depends greatly on understanding the evolution of teeth and the relationship of tooth shape to diet. Links between gross tooth shape, function and diet have been proposed since antiquity, stretching from Aristotle to Cuvier, Owen and Osborn. So far, however, the possibilities for exhaustive, quantitative comparisons between greatly different tooth shapes have been limited. Cat teeth and mouse teeth, for example, are fundamentally distinct in shape and structure as a result of independent evolutionary change over tens of millions of years. There is difficulty in establishing homology between their tooth components or in summarizing their tooth shapes, yet both carnivorans and rodents possess a comparable spectrum of dietary specializations from animals to plants. Here we introduce homology-free techniques to measure the phenotypic complexity of the three-dimensional shape of tooth crowns. In our geographic information systems (GIS) analysis of 441 teeth from 81 species of carnivorans and rodents, we show that the surface complexity of tooth crowns directly reflects the foods they consume. Moreover, the absolute values of dental complexity for individual dietary classes correspond between carnivorans and rodents, illustrating a high-level similarity between overall tooth shapes despite a lack of low-level similarity of specific tooth components. These results suggest that scale-independent forces have determined the high-level dental shape in lineages that are widely divergent in size, ecology and life history. This link between diet and phenotype will be useful for inferring the ecology of extinct species and illustrates the potential of fast-throughput, high-level analysis of the phenotype.

Animals↗

PubMed2001

Life in the end-Permian dead zone.

The fossil record of land plants is an obvious source of information on the dynamics of mass extinctions in the geological past. In conjunction with the end-Permian ecological crisis, approximately 250 million years ago, palynological data from East Greenland reveal some unanticipated patterns. We document the significant time lag between terrestrial ecosystem collapse and selective extinction among characteristic Late Permian plants. Furthermore, ecological crisis resulted in an initial increase in plant diversity, instead of a decrease. Paradoxically, these floral patterns correspond to a "dead zone" in the end-Permian faunal record, characterized by a paucity of marine invertebrate megafossils. The time-delayed, end-Permian plant extinctions resemble modeled "extinction debt" responses of multispecies metapopulations to progressive habitat destruction.

Biological Evolution↗

PubMed1990

Opal phytoliths found on the teeth of the extinct ape Gigantopithecus blacki: implications for paleodietary studies.

Identification of opal phytoliths bonded to the enamel surface of the teeth of Gigantopithecus blacki indicates that this extinct ape had a varied diet of grasses and fruits. By using the scanning electron microscope at magnifications of 2000-6000x specific opal phytoliths were observed and photographed on the fossilized teeth of an extinct species. Since opal phytoliths represent the inorganic remains of once-living plant cells, their documentation on the teeth of Gigantopithecus introduces a promising technique for the determination of diet in extinct mammalian species which should find numerous applications in the field of paleoanthropology as well as vertebrate paleontology.

Animals↗

PubMed2003

Local extinction and the evolution of dispersal rates: causes and correlations.

We present the results of individual-based simulation experiments on the evolution of dispersal rates of organisms living in metapopulations. We find conflicting results regarding the relationship between local extinction rate and evolutionarily stable (ES) dispersal rate depending on which principal mechanism causes extinction: if extinction is caused by environmental catastrophes eradicating local populations, we observe a positive correlation between extinction and ES dispersal rate; if extinction is a consequence of stochastic local dynamics and environmental fluctuations, the correlation becomes ambiguous; and in cases where extinction is caused by dispersal mortality, a negative correlation between local extinction rate and ES dispersal rate emerges. We conclude that extinction rate, which both affects and is affected by dispersal rates, is not an ideal predictor for optimal dispersal rates.

Animals↗

PubMed2004

Large species shifts triggered by small forces.

Changes in species composition of communities seem to proceed gradually at first sight, but remarkably rapid shifts are known to occur. Although disrupting disturbances seem an obvious explanation for such shifts, evidence for large disturbances is not always apparent. Here we show that complex communities tend to move through occasional catastrophic shifts in response to gradual environmental change or evolution. This tendency is caused by multiple attractors that may exist in such systems. We show that alternative attractors arise robustly in randomly generated multispecies models, especially if competition is symmetrical and if interspecific competition is allowed to exceed intraspecific competition. Inclusion of predators as a second trophic level did not alter the results greatly, although it reduced the probability of alternative attractors somewhat. These results suggest that alternative attractors may commonly arise from interactions between large numbers of species. Consequently, the response of complex communities to environmental change is expected to be characterized by hysteresis and sudden shifts. Some unexplained regime shifts observed in ecosystems could be related to alternative attractors arising from complex species interactions. Additionally, our results support the idea that ancient mass extinctions may partly be due to an intrinsic loss of stability of species configurations.

Animals↗