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PubMed2003

The amplification of environmental noise in population models: causes and consequences.

Environmental variability is a ubiquitous feature of every organism's habitat. However, the interaction between density dependence and those density-independent factors that are manifested as environmental noise is poorly understood. We are interested in the conditions under which noise interacts with the density dependence to cause amplification of that noise when filtered by the system. For a broad family of structured population models, we show that amplification occurs near the threshold from stable to unstable dynamics by deriving an analytic formula for the amplification under weak noise. We confirm that the effect of noise is to sustain oscillations that would otherwise decay, and we show that it is the amplitude and not the phase that is affected. This is a feature noted in several recent studies. We study this phenomenon in detail for the lurchin and LPA models of population dynamics. We find that the degree of amplification is sensitive to both the noise input and life-history stage through which it acts, that the results hold for surprisingly high levels of noise, and that stochastic chaos (as measured by local Lyapunov exponents) is a concomitant feature of amplification. Further, it is shown that the temporal autocorrelation, or "color," of the noise has a major impact on the system response. We discuss the conditions under which color increases population variance and hence the risk of extinction, and we show that periodicity is sharpened when the color of the noise and dynamics coincide. Otherwise, there is interference, which shows how difficult it is in practice to separate the effects of nonlinearity and noise in short time series. The sensitivity of the population dynamics to noise when close to a bifurcation has wide-ranging consequences for the evolution and ecology of population dynamics.

Animals↗

PubMed2003

Extinction and permanence of a two-prey one-predator system with impulsive effect.

In this paper, we investigate a two-prey one-predator system with impulsive effect on the predator of fixed moment. By using Floquet's theorem and small-amplitude perturbation skills, we show that there exists a globally asymptotically stable two-pest eradication periodic solution when the impulsive period is less than some critical value. Further, we prove that the system is permanent if the impulsive period is larger than some critical value, and meanwhile the conditions for the extinction of one of the two prey and permanence of the remaining two species are given. Finally, numerical simulation shows that there exists a stable positive periodic solution with a maximum value no larger than a given level. Therefore, we can use the stability of the positive periodic solution and its period to control insect pests at acceptably low levels.

Animals↗

PubMed2005

The interplay of positive and negative species interactions across an environmental gradient: insights from an individual-based simulation model.

Positive interspecific interactions are commonplace, and in recent years ecologists have begun to realize how important they can be in determining community and ecosystem dynamics. It has been predicted that net positive interactions are likely to occur in environments characterized by high abiotic stress. Although empirical field studies have started to support these predictions, little theoretical work has been carried out on the dynamic nature of these effects and their consequences for community structure. We use a simple patch-occupancy model to simulate the dynamics of a pair of species living on an environmental gradient. Each of the species can exist as either a mutualist or a cheater. The results confirm the prediction: a band of mutualists tends to occur in environmental conditions beyond the limits of the cheaters. The region between mutualists and cheaters is interesting: population density here is low. Mutualists periodically occupy this area, but are displaced by cheaters, who themselves go extinct in the absence of the mutualists. Furthermore, the existence of mutualists extends the area occupied by the cheaters, essentially increasing their realized niche. Our approach has considerable potential for improving our understanding of the balance between positive and negative interspecific interactions and for predicting the probable impacts of habitat loss and climate change on communities dominated by positive interspecific interactions.

Computer Simulation↗

PubMed1978

Problems associated with analysis and interpretation of small molecule/macromolecule binding data.

In the analysis of binding data, arbitrary transformations such as the Scatchard plot, may give misleading estimates of the binding parameters. The statistically correct approach is to determine values of K and n by non-linear regression of the actual dependent variable against the actual independent variable. In the case of the spectrophotometric titration method the dependent variable is the absorbance and the independent variable is the composition of the drug/macromolecule mixture. The method relies on an accurate estimate of the extinction coefficient of the bound drug and this is best treated as a parameter to be estimated in the regression analysis. In testing models by data fits alone it is emphasized that whilst a model may be rejected if it does not fit the data, a good fit does not ensure uniquieness and confirmatory, independent evidence must be sought.

DNA↗

PubMed1986

In vitro aggregation of normal platelets: a hypothetical first-approximation model for light extinction in platelet-rich plasma.

Aggregometer tracings of light transmission through platelet-rich-plasma are routinely used for the clinical evaluation of platelet function. The analytical relation between the changing aggregometer curve tracings of the light extinction and the aggregation process remains unknown. A first-approximation equation for this relation is proposed, based upon a highly simplified view of the in vitro aggregation process for normal platelets. The model described is capable of generating curves which show strong resemblance to those predicted by light scattering theory as well as those observed experimentally, including biphasic structures.

Adenosine Diphosphate↗

PubMed1992

Spontaneous regression of residual tumour burden: prediction by Monte Carlo simulation.

Current cancer treatment protocols are designed to release the tumour burden down to a small number of cells. In this study, we use Monte Carlo simulations to show that small populations of cells with intrinsic cell loss rates comparable to the cell loss rates observed clinically in human tumours, may regress spontaneously. Large populations of cells tend to grow under the same conditions of cell loss that result in extinction of small clones. Furthermore, minor variations in the intrinsic cell death probability near 0.50 result in large differences in the number of surviving cells calculated at the 100th generation. When Monte Carlo simulations of clonal growth resulted in clones with large populations (> 50 cells), the population as a whole behaved in a deterministic fashion (logarithmic growth) similar to those observed in clinically observed neoplasms and consistent with other published models of tumour growth. These findings provide a plausible explanation for the clinically observed failure of tumours to recur in instances where tumour burden remains following cancer therapy. The findings also demonstrate the usefulness of the Monte Carlo method to simulate biologic events in populations where the fate of each member of a population can be modeled probabilistically.

Cell Death↗

PubMed2026

Building phenotypic character matrices for phylogenetic inference: exploration of 35 years of practice.

Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.

Phylogeny↗

PubMed1997

Extinction and the loss of evolutionary history.

Extinction episodes, such as the anthropogenic one currently under way, result in a pruned tree of life. But what fraction of the underlying evolutionary history survives when k of n species in a taxon are lost? This is relevant both to how species loss has translated into a loss of evolutionary history and to assigning conservation priorities. Here it is shown that approximately 80 percent of the underlying tree of life can survive even when approximately 95 percent of species are lost, and that algorithms that maximize the amount of evolutionary history preserved are not much better than choosing the survivors at random. Given the political, economic, and social realities constraining conservation biology, these findings may be helpful.

Animals↗

PubMed2003

Maintenance of aphid clonal lineages: images of immortality?

Artificial cloning and ancient asexuals have impacted upon both scientific and lay thinking in applied and theoretical fields as diverse as medicine and evolution. Hence, this is an opportune time to promote debate and discussion on what maintains a clonal lineage. The genetic fidelity of a clone has been discussed in detail elsewhere [Genet. Res. 79 (2002) 1; Biol. J. Linnean Soc. 79 (2003) 3]. In this paper, we focus on the lineage integrity (=longevity), or physiological lifespan of a clone with respect to senesce in relation to factors controlling telomere functioning. Aspects of cell line research pertinent to eukaryotic clonal lineages are discussed and, in particular, we try to extrapolate aspects of this research and apply it to apomictic (=mitotic) aphid lineages to suggest how they may be maintained. Analogies are made between single cells and individual aphids that senescence through a generation, whilst the respective lineages persist for finite periods, unless that is, compensatory mechanisms have evolved allowing immortality in the one and ancient asexuality in the other. Such comparison may allow fresh insights into the mechanisms of clonal lineage maintenance and evolution. We hypothesise that: (1). the cause of extinction in eukaryotic clonal lineages is due to deleterious effects on key regions of the genome, the chromosomal telomere being one such site; (2). recombination acts as a common mechanism to reset telomere functioning, perhaps more fundamental than its utility to reduce genetic load and maintain adaptability; and (3). ancient lineages persist through time as a function of group-specific compensatory mechanisms that maintain telomere integrity.

Aging↗

PubMed2003

The last dicynodont: an Australian Cretaceous relict.

Some long-forgotten fossil evidence reveals that a dicynodont (mammal-like reptile of the infraorder Dicynodontia) inhabited Australia as recently as the Early Cretaceous, ca. 110 Myr after the supposed extinction of dicynodonts in the Late Triassic. This remarkably late occurrence more than doubles the known duration of dicynodont history (from ca. 63 Myr to ca. 170 Myr) and betrays the profound impact of geographical isolation on Australian terrestrial faunas through the Mesozoic. Australia's late-surviving dicynodont may be envisaged as a counterpart of the ceratopians (horned dinosaurs) in Cretaceous tetrapod faunas of Asia and North America.

Animals↗

PubMedDate not supplied

Vectorial capacity of North American Ixodes ticks.

Ixodes dammini, the vector of Lyme disease and babesiosis, is distributed in various locations in the northeastern quadrant of the United States and nearby Canada. The life cycle of this tick, which includes larval, nymphal, and adult stages, spans at least two years. The tick over-winters between larval and nymphal feeding. Horizontal transmission of pathogens is facilitated by a feeding pattern in which both the larval and nymphal stages feed on the white-footed mouse, Peromyscus leucopus, and by a seasonal pattern of activity in which nymphs precede larvae. The species range appears to have expanded from a single island location, and has invaded new sites since the 1940s, some as recently as 1980. This increased abundance appears to be related to the increased abundance of deer, the preferred host of the adult stage. I. muris predominated in coastal Massachusetts before I. dammini became abundant, but is probably now extinct. I. scapularis, which is present in the southern U.S., is a poor vector of mouse parasites because about 90 percent of these immature ticks feed on lizards. To the extent that horizontal transmission occurs, we suggest that mice serve as the principal reservoir for the Lyme spirochete as well as Babesia microti.

Animals↗

PubMed2005

Aquatic Resource Conservation. The first Yangtze finless porpoise successfully born in captivity.

BACKGROUND: As the sole freshwater subspecies of finless porpoise (Neophocaena phocaenoides), the Yangtze finless porpoise (N. p. asiaeorientalis) lives only in the middle and lower reaches of the Yangtze River and its appended Poyang and Dongting Lakes. As a result of human activity on the river, including over and illegal fishing, pollution, transportation and dam construction, the population of Yangtze finless porpoises has been steadily and rapidly decreasing during the past several decades, which leads the animal to be endangered. METHODS: For saving this unique animal from extinction, three corresponding measures, in situ conservation, ex situ conservation, and intensifying breeding research in captivity, were proposed and have been implemented since the 1980s. RESULTS: After successfully rearing the animals in captivity for almost nine years, the first Yangtze finless porpoise was successfully born in captivity on July 5, 2005. The calf is male, with a body length of 69 cm. This is the first freshwater cetacean ever born in captivity. CONCLUSION: The successful birth of this calf confirms that it is possible to breed the Yangtze finless porpoise in captivity. Furthermore, this will greatly benefit the conservation efforts, and also greatly bolster our on-going efforts to study the reproductive biology of these animals. RECOMMENDATION: More studies and efforts are expected to establish a sustainable, captive colony of the Yangtze finless porpoise, which will not only greatly expand our knowledge about the reproduction biology of this animal, but also help to redeem the wild population through a careful yearly 'soft releasing' process.

Animal Husbandry↗

PubMed2005

Impact seeding and reseeding in the inner solar system.

Assuming that asteroidal and cometary impacts onto Earth can liberate material containing viable microorganisms, we studied the subsequent distribution of the escaping impact ejecta throughout the inner Solar System on time scales of 30,000 years. Our calculations of the delivery rates of this terrestrial material to Mars and Venus, as well as back to Earth, indicate that transport to great heliocentric distances may occur in just a few years and that the departure speed is significant. This material would have been efficiently and quickly dispersed throughout the Solar System. Our study considers the fate of all the ejected mass (not just the slowly moving material), and tabulates impact rates onto Venus and Mars in addition to Earth itself. Expressed as a fraction of the ejected particles, roughly 0.1% and 0.001% of the ejecta particles would have reached Venus and Mars, respectively, in 30,000 years, making the biological seeding of those planets viable if the target planet supported a receptive environment at the time. In terms of possibly safeguarding terrestrial life by allowing its survival in space while our planet cools after a major killing thermal pulse, we show via our 30,000- year integrations that efficient return to Earth continues for this duration. Our calculations indicate that roughly 1% of the launched mass returns to Earth after a major impact regardless of the impactor speed; although a larger mass is ejected following impacts at higher speeds, a smaller fraction of these ejecta is returned. Early bacterial life on Earth could have been safeguarded from any purported impact-induced extinction by temporary refuge in space.

Earth, Planet↗

PubMed2003

A technique for estimating maximum harvesting effort in a stochastic fishery model.

Exploitation of biological resources and the harvest of population species are commonly practiced in fisheries, forestry and wild life management. Estimation of maximum harvesting effort has a great impact on the economics of fisheries and other bio-resources. The present paper deals with the problem of a bioeconomic fishery model under environmental variability. A technique for finding the maximum harvesting effort in fluctuating environment has been developed in a two-species competitive system, which shows that under realistic environmental variability the maximum harvesting effort is less than what is estimated in the deterministic model. This method also enables us to find out the safe regions in the parametric space for which the chance of extinction of the species is minimized. A real life fishery problem has been considered to obtain the inaccessible parameters of the system in a systematic way. Such studies may help resource managers to get an idea for controlling the system.

Animals↗

PubMed2006

A juvenile-adult model with periodic vital rates.

A global branch of positive cycles is shown to exist for a general discrete time, juvenile-adult model with periodically varying coefficients. The branch bifurcates from the extinction state at a critical value of the mean, inherent fertility rate. In comparison to the autonomous system with the same mean fertility rate, the critical bifurcation value can either increase or decrease with the introduction of periodicities. Thus, periodic oscillations in vital parameter can be either advantageous or deleterious. A determining factor is the phase relationship among the oscillations in the inherent fertility and survival rates.

Algorithms↗

PubMed1998

Vesicular amine transporter expression and isoform selection in developing brain, peripheral nervous system and gut.

The vesicular monoamine transporters VMAT1 and VMAT2 are essential components of monoaminergic neurons and endocrine cells whose expression in development may provide insight into lineage pathways for chemical coding in the diffuse neuroendocrine system. Thus, the brain is a compartment in which only monoaminergic neurons are generated, the gut epithelium generates only endocrine monoamine-containing cells, and the neural crest produces both autonomic monoaminergic neurons and endocrine/paracrine monoaminergic cells. Selection of either the VMAT1 or VMAT2 isoform was examined in these three compartments during development. In the central nervous system VMAT2, but not VMAT1, was expressed in neuroepithelial cells by embryonic day 12 (E12), and all major monoaminergic cell groups by E14. Thalamocortical and hypothalamic neurons that do not express VMAT2 in adulthood were transiently VMAT2-positive from E16 to postnatal day 6 (P6). EC cells of the gut expressed exclusively VMAT1 from E19 on, while histamine-containing enterochromaffin-like (ECL) cells of the stomach expressed only VMAT2 by E19 and throughout postnatal development. VMAT2 and the vesicular acetylcholine transporter VAChT were co-expressed in early development of the primary sympathetic chain as well as in the cranial parasympathetic ganglia. VAChT was progressively restricted to a small population of VMAT2-negative post-ganglionic neurons in the adult sympathetic chain, while VMAT2 expression persisted in sympathetic principal ganglion and SIF cells but was eventually extinguished in cranial parasympathetic ganglia. VMAT1 was co-expressed with VAChT and VMAT2 mRNA in the primary sympathetic chain on E12, but progressively restricted to small intensely fluorescent (SIF) and chromaffin cells thereafter. Thus, expression of the vesicular amine transporters appropriate for chemical coding of brain neurons and gut endocrine cells are pre-determined developmentally. In contrast, the neural crest-derived sympathoadrenal and neural crest-derived parasympathetic cell groups examined here initially co-express two or more vesicular amine transporters, followed by extinction of the inappropriate transporter(s) later in development. Some neural crest-derived neuroendocrine cell populations continue to express both isoforms of VMAT even in adulthood. Lineage distinctions in ontogeny of vesicular amine transporter expression in brain, gut and autonomic nervous system make it likely that the same genes are regulated differently in the autonomic nervous system compared to brain and gut.

Animals↗

PubMed2003

Population dynamics of HTLV-I infection: a discrete-time mathematical epidemic model approach.

Human T-cell Leukaemia Virus Type I (HTLV-I) is a retrovirus that causes Adult T-cell Leukaemia (ATL). The transmission routes of HTLV-I are (i) from infected mothers to their newborn babies, (ii) from infected males (husbands) to females (their wives) by long-term sexual intercourse, and (iii) from infected females (wives) to males (their husbands). Eshima et al. (2001) analysed a continuous-time HTLV-I model with no age structure in the population. In this paper, we consider the population dynamics of HTLV-I infection in a discrete-time mathematical model incorporating an age structure. The necessary and sufficient condition for the extinction of HTLV-I is derived from the mathematical model. A simulation of the HTLV-I infection based on the model demonstrates a rapid reduction of the HTLV-I infection proportion in Japan.

Adolescent↗

PubMed2005

Multiple causes of high extinction risk in large mammal species.

Many large animal species have a high risk of extinction. This is usually thought to result simply from the way that species traits associated with vulnerability, such as low reproductive rates, scale with body size. In a broad-scale analysis of extinction risk in mammals, we find two additional patterns in the size selectivity of extinction risk. First, impacts of both intrinsic and environmental factors increase sharply above a threshold body mass around 3 kilograms. Second, whereas extinction risk in smaller species is driven by environmental factors, in larger species it is driven by a combination of environmental factors and intrinsic traits. Thus, the disadvantages of large size are greater than generally recognized, and future loss of large mammal biodiversity could be far more rapid than expected.

Animals↗