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PubMed1997

Impact of migration and fitness on the stability of lethal t-haplotype polymorphism in Mus musculus: a computer study.

The t-haplotype is a chromosomal region in Mus musculus characterized by meiotic drive such that heterozygous males transmit t-bearing chromosomes to roughly 90% of their offspring. Most naturally occurring t-haplotypes express a recessive embryonic lethality, preventing fixation of the t-haplotype. Surprisingly, the t-haplotype occurs in nature as a persistent, low-frequency polymorphism. Early modeling studies led LEWONTIN to hypothesize that this low level polymorphism results from a balance between genetic drift in small demes and interdemic migration. Here, we show that while combination of deme size and migration rate that predict natural t-haplotype frequencies exist, the range of such values is too narrow to be biologically plausible, suggesting that small deme size and interdemic migration alone do not explain the observed t-haplotype frequencies. In response, we tested other factors that might explain the observed t-polymorphism. Two led to biologically plausible models: substantially reduced heterozygous fitness and reduced meiotic drive. This raises the question whether these phenomena occur in nature. Our data suggest an alternative explanation: there is no stable, low-level t-polymorphism. Rather wild populations are in one of two stable states characterized by extinction of the t-haplotype and a high t-haplotype frequency, respectively, or in transition between the two.

Alleles↗

PubMed2006

Harvesting in a random environment: Itô or Stratonovich calculus?

We extend to harvesting stochastic differential equation (SDE) models in a random environment our previous work on models without harvesting concerning the resolution of the Itô-Stratonovich controversy. The resolution is obtained for the very general class of models dN/dt=N (r(N)-h(N)+sigmaepsilon(t)), where N=N(t) is the population size at time t, r(N) is the (density-dependent) "mean" per capita growth rate, h(N) is the (density-dependent) harvesting effort, epsilon(t) is a standard white noise (representing environmental random fluctuations), and sigma is a noise intensity parameter. Itô and Stratonovich calculus in the resolution of SDEs apparently give different qualitative and quantitative results, leading to controversy on which calculus is more appropriate and creating an obstacle on the use of this modeling approach. We show that the apparent difference between the two calculi is due to a semantic confusion based on the fallacious assumption that we are working with the same type of mean rates. After clearing the confusion, the two calculi yield exactly the same results and we obtain important common conditions for extinction and for existence of a stationary density. The resolution of the controversy is intertwined with and sheds light on the estimation issues.

Animals↗

PubMed2000

Qualitative behavior of a variable-yield simple food chain with an inhibiting nutrient.

A simple food chain which consists of nutrient, prey and predator in which nutrient is growth limiting at low concentrations but growth inhibiting at high concentrations is investigated in this study. It is assumed that the nutrient concentration is separated into internal and external nutrient concentration and only the internal nutrient level is capable of catalyzing cell growth. It is shown that the dynamics of the system depend on thresholds R(0) and R(1). With inhibition, there exist initial conditions for which the predator becomes extinct but not the prey when R(0)<1. If R(0),R(1)1, the system is uniformly persistent even in the inhibited environment.

Food Chain↗

PubMed2002

Anatomical and ecological constraints on Phanerozoic animal diversity in the marine realm.

We grouped the fossil records of marine animal genera into suites defined by function and physiology. The stratigraphic coherence of the resulting diversity history indicates the importance of ecological structure in constraining taxonomic richness through time. The proportional representation of major functional groups was stably maintained for intervals as long as 200 million years, despite evolutionary turnover and changes in total diversity. Early Paleozoic radiations established stable ecosystem relationships, and thereafter only the great era-bounding mass extinctions were able to break patterns of incumbency, permitting the emergence of new community structures with distinct proportional diversity relationships.

Animals↗

PubMed2006

Rate of lineage origin explains the diversity anomaly in the world's mangrove vegetation.

The contribution of nonecological factors to global patterns in diversity is evident when species richness differs between regions with similar habitats and geographic area. Mangrove environments in the Eastern Hemisphere harbor six times as many species of trees and shrubs as similar environments in the New World. Genetic divergence of mangrove lineages from terrestrial relatives, in combination with fossil evidence, suggests that mangrove diversity is limited by evolutionary transition into the stressful marine environment, the number of mangrove lineages has increased steadily over the Tertiary with little global extinction, and the diversity anomaly in mangrove vegetation reflects regional differences in the rate of origin of new mangrove lineages.

Bayes Theorem↗

PubMed2002

Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography.

A major tenet of African Tertiary biogeography posits that lowland rainforest dominated much of Africa in the late Cretaceous and was replaced by xeric vegetation as a response to continental uplift and consequent widespread aridification beginning in the late Paleogene. The aridification of Africa is thought to have been a major factor in the extinction of many African humid-tropical lineages, and in the present-day disparity of species diversity between Africa and other tropical regions. This primarily geologically based model can be tested with independent phylogenetic evidence from widespread African plant groups containing both humid- and xeric-adapted species. We estimated the phylogeny and lineage divergence times within one such angiosperm group, the acridocarpoid clade (Malpighiaceae), with combined ITS, ndhF, and trnL-F data from 15 species that encompass the range of morphological and geographic variation within the group. Dispersal-vicariance analysis and divergence-time estimates suggest that the basal acridocarpoid divergence occurred between African and Southeast Asian lineages approximately 50 million years ago (mya), perhaps after a southward ancestral retreat from high-latitude tropical forests in response to intermittent Eocene cooling. Dispersion of Aeridocarpus from Africa to Madagascar is inferred between approximately 50 and 35 mya, when lowland humid tropical forest was nearly continuous between these landmasses. A single dispersal event within Acridocarpus is inferred from western Africa to eastern Africa between approximately 23 and 17 mya, coincident with the widespread replacement of humid forests by savannas in eastern Africa. Although the spread of xeric environments resulted in the extinction of many African plant groups, our data suggest that for others it provided an opportunity for further diversification.

Africa↗

PubMed2004

Allee effect and self-fertilization in hermaphrodites: reproductive assurance in demographically stable populations.

The fact that selfing increases seed set (reproductive assurance) has often been put forward as an important selective force for the evolution of selfing. However, the role of reproductive assurance in hermaphroditic populations is far from being clear because of a lack of theoretical work. Here, I propose a theoretical model that analyzes self-fertilization in the presence of reproductive assurance. Because reproductive assurance directly influences the per capita growth rate, I developed an explicit demographic model for partial selfers in the presence of reproductive assurance, specifically when outcrossing is limited by the possibility of pollen transfer (Allee effect). Mating system parameters are derived as a function of the underlying demographical parameters. The functional link between population demography and mating system parameters (reproductive assurance, selfing rate) can be characterized. The demographic model permits the analysis of the evolution of self-fertilization in stable populations when reproductive assurance occurs. The model reveals some counterintuitive results such as the fact that increasing the fraction of selfed ovules can, in certain circumstances, increase the fraction of outcrossed ovules. Moreover, I demonstrate that reproductive assurance per se cannot account for the evolution of stable mixed selfing rates. Also, the model reveals that the extinction of outcrossing populations depends on small changes in population density (ecological perturbations), while the transition from outcrossing to selfing can, in certain cases, lead the population to extinction (evolutionary suicide). More generally, this paper highlights the fact that self-fertilization affects both the dynamics of individuals and the dynamics of selfing genes in hermaphroditic populations.

Biological Evolution↗

PubMed2000

Nonrandom extinction and the loss of evolutionary history.

The hierarchical nature of phylogenies means that random extinction of species affects a smaller fraction of higher taxa, and so the total amount of evolutionary history lost may be comparatively slight. However, current extinction risk is not phylogenetically random. We show the potentially severe implications of the clumped nature of threat for the loss of biodiversity. An additional 120 avian and mammalian genera are at risk compared with the number predicted under random extinction. We estimate that the prospective extra loss of mammalian evolutionary history alone would be equivalent to losing a monotypic phylum.

Animals↗

PubMed1988

The brain of Thylacosmilus atrox. Extinct South American saber-tooth carnivore marsupial.

Two endocasts of the extinct marsupial Thylacosmilus atrox are studied. The specimens were found in outcrops at present considered of Pliocene Age. The followings are the conclusions arrived in the study: 1) The encephalon of Thylacosmilus atrox shows a well developed neocortex, with a deep rhinal fissure and the major marsupial neocortical sulci well observable. The homologies of the sulci was certainly easy in the major part of them, and consequently, functional inferencies were possible. 2) The somatic neocortical area shows certain distinctive characteristics. It appears that the size proportions between the mandibular and maxillary areas is reversed in T. atrox, which appears congruent with the infered function of its peculiar cranial anatomy. 3) The relative brain size of T. atrox is very heigh for a Polyprotodont marsupial being its encephalization quotients and progression indexes at the level of the living Diprotodonta. 4) Thylacosmilus atrox was a very peculiar extinct carnivore marsupial, which at the Late Tertiary in South America reached higher levels of encephalization than the posterior or living representatives of its same Order.

Animals↗

PubMed2002

Disease, habitat fragmentation and conservation.

Habitat loss and the resultant fragmentation of remaining habitat is the primary cause of loss of biological diversity. How do these processes affect the dynamics of parasites and pathogens? Hess has provided some important insights into this problem using metapopulation models for pathogens that exhibit 'S-I' dynamics; for example, pathogens such as rabies in which the host population may be divided into susceptible and infected individuals. A major assumption of Hess's models is that infected patches become extinct, rather than recovering and becoming resistant to future infections. In this paper, we build upon this framework in two different ways: first, we examine the consequences of including patches that are resistant to infection; second, we examine the consequences of including a second species of host that can act as a reservoir for the pathogen. Both of these effects are likely to be important from a conservation perspective. The results of both sets of analysis indicate that the benefits of corridors and other connections that allow species to disperse through the landscape far outweigh the possible risks of increased pathogen transmission. Even in the commonest case, where harmful pathogens are maintained by a common reservoir host, increased landscape connectance still allows greater coexistence and persistence of a threatened or endangered host.

Animal Diseases↗

PubMed1996

HIV-1 infection kinetics in tissue cultures.

Despite intensive experimental work on HIV-1, very little theoretical work has focused on HIV-1 spread in tissue culture. This article uses two systems of ordinary differential equations to model two modes of viral spread, cell-free virus and cell-to-cell contact. The two models produce remarkably similar qualitative results. Simulations using realistic parameter regimes showed that starting with a small fraction of cells infected, both cell-free viral spread and direct cell-to-cell transmission give an initial exponential phase of viral growth, followed by either a crash or a gradual decline, extinguishing the culture. Under some conditions, an oscillatory phase may precede the extinction. Some previous models of in vivo HIV-1 infection oscillate, but only in unrealistic parameter regimes. Experimental tissue infections sometimes display several sequential cycles of oscillation, however, so our models can at least mimic them qualitatively. Significantly, the models show that infective oscillations can be explained by infection dynamics; biological heterogeneity is not required. The models also display proportionality between infected cells and cell-free virus, which is reassuringly consistent with assumptions about the equivalence of several measures of viral load, except that the proportionality requires a relatively constant total cell concentration. Tissue culture parameter values can be determined from accurate, controlled experiments. Therefore, if verified, our models should make interpreting experimental data and extrapolating it to in vivo conditions sharper and more reliable.

CD4-Positive T-Lymphocytes↗

PubMed2002

Marine biodiversity hotspots and conservation priorities for tropical reefs.

Coral reefs are the most biologically diverse of shallow water marine ecosystems but are being degraded worldwide by human activities and climate warming. Analyses of the geographic ranges of 3235 species of reef fish, corals, snails, and lobsters revealed that between 7.2% and 53.6% of each taxon have highly restricted ranges, rendering them vulnerable to extinction. Restricted-range species are clustered into centers of endemism, like those described for terrestrial taxa. The 10 richest centers of endemism cover 15.8% of the world's coral reefs (0.012% of the oceans) but include between 44.8 and 54.2% of the restricted-range species. Many occur in regions where reefs are being severely affected by people, potentially leading to numerous extinctions. Threatened centers of endemism are major biodiversity hotspots, and conservation efforts targeted toward them could help avert the loss of tropical reef biodiversity.

Animals↗

PubMed2003

Detection, identification, and estimation of biological aerosols and vapors with a Fourier-transform infrared spectrometer.

Two experiments were conducted with a Fourier-transform infrared (FTIR) spectrometer. The purpose of the first experiment was to detect and identify Bacillus subtilis subsp. niger (BG) bioaerosol spores and kaolin dust in an open-air release for which the thermal contrast between the aerosol temperature and background brightness temperature is small. The second experiment estimated the concentration of a small amount of triethyl phosphate (TEP) vapor in a closed chamber in which an external blackbody radiation source was used and where the thermal contrast was large. The deduced BG (TEP) extinction spectrum (identification) showed an excellent match to the library BG (TEP) extinction spectrum. Analysis of the time sequence of the measurements coincided well with the presence (detection) of the BG during the measurements, and the estimated concentration of time-dependent TEP vapor was excellent. The data were analyzed with hyperspectral detection, identification, and estimation algorithms. The algorithms were based on radiative transfer theory and statistical signal-processing methods. A subspace orthogonal projection operator was used to statistically subtract the large thermal background contribution to the measurements, and a robust maximum-likelihood solution was used to deduce the target (aerosol or vapor cloud) spectrum and estimate its mass-column concentration. A Gaussian-mixture probability model for the deduced mass-column concentration was computed with an expectation-maximization algorithm to produce the detection threshold, the probability of detection, and the probability of false alarm. The results of this study are encouraging, as they suggest for the first time to the authors' knowledge the feasibility of detecting biological aerosols with passive FTIR sensors.

Journal Article↗

PubMed2002

A new model using liposomes that allow to distinguish between absorption and oxidative properties of sunscreens.

We have developed a new model using liposome-encapsulated fluorescent probes, aiming at assessing both the physical and the biological protection provided by filter molecules such as those incorporated in sunscreens. The fluorescent indicator Indo-1 or 2',7'-dichlorofluorescin (DCFH) was inside the liposomes, in the aqueous inner compartment, whereas the filter molecules octyl methoxycinnamate (OMC), benzophenone-3 (BP3) or avobenzone, widely used in sunscreens, were incorporated into liposome membranes. When liposome suspensions were placed in a fluorometer cuvette exposed to an incident UV beam, the decrease of Indo-1 fluorescence as a function of filter concentration was related to the extinction coefficient of the filters. On the other hand, when liposome suspensions were exposed to moderate UVB doses allowing Indo-1 photobleaching, the remaining intact Indo-1 was linked to the protection provided by filter-containing liposome membranes. Finally, when liposome-encapsulated DCFH was exposed to UVB, the degree of photo-oxidation of the fluorescent probe into 2',7'-dichlorofluorescein accounted for the photoprotection provided by the filter contained in liposome membranes. BP3 was more potent and slightly less efficient than the other two filters in preventing Indo-1 fluorescence; all three filters provided a similar concentration-dependent protection of Indo-1 photobleaching, whereas only OMC was able to prevent the photooxidation of DCFH. The liposome model presented here has the advantage of combining both physical and biological parameters to assess the photoprotection provided by filter molecules, and the lack of photoprotection by two sunscreen molecules having a good filter capacity highlights the need for such a biological parameter when talking about the safety of sunscreens.

Absorption↗

PubMedDate not supplied

[The parasite capacity of the host population].

The estimation of parasitic pressure on the host populations is frequently required in parasitological investigations. The empirical values of prevalence of infection are used for this, however the latter one as an estimation of parasitic pressure on the host population is insufficient. For example, the same prevalence of infection can be insignificant for the population with high reproductive potential and excessive for the population with the low reproductive potential. Therefore the development of methods of an estimation of the parasitic pressure on the population, which take into account the features the host population, is necessary. Appropriate parameters are to be independent on view of the researcher, have a clear biological sense and be based on easily available characteristics. The methods of estimation of parasitic pressure on the host at the organism level are based on various individual viability parameters: longevity, resistance to difficult environment etc. The natural development of this approach for population level is the analysis of viability parameters of groups, namely, the changing of extinction probability of host population under the influence of parasites. Obviously, some critical values of prevalence of infection should exist; above theme the host population dies out. Therefore the heaviest prevalence of infection, at which the probability of host population size decreases during the some period is less than probability of that increases or preserves, can serve as an indicator of permissible parasitic pressure on the host population. For its designation the term "parasite capacity of the host population" is proposed. The real parasitic pressure on the host population should be estimated on the comparison with its parasite capacity. Parasite capacity of the host population is the heaviest possible prevalence of infection, at which, with the generation number T approaching infinity, there exists at least one initial population size ni(0) for which the probability of size decrease through T generations is less than the probability of its increase. [formula: see text] The estimation of the probabilities of host population size changes is necessary for the parasite capacity determination. The classical methods for the estimation of extinction probability of population are unsuitable in this case, as these methods require the knowledge of population growth rates and their variances for all possible population sizes. Thus, the development methods of estimate of extinction probability of population, based on the using of available parameters (sex ratio, fecundity, mortality, prevalence of infection PI) is necessary. The population size change can be considered as the Markov process. The probabilities of all changes of population size for a generation in this case are described by a matrix of transition probabilities of Markov process (pi) with dimensions Nmax x Nmax (maximum population size). The probabilities of all possible size changes for T generations can be calculated as pi T. Analyzing the behaviour matrix of transition at various prevalence of infection, it is possible to determine the parasite capacity of the host population. In constructing of the matrix of transition probabilities, should to be taken into account the features the host population and the influence of parasites on its reproductive potential. The set of the possible population size at a generation corresponds to each initial population size. The transition probabilities for the possible population sizes at a generation can be approximated to the binomial distribution. The possible population sizes at a generation nj(t + 1) can be calculated as sums of the number of survived parents N1 and posterities N2; their probabilities--as P(N1) x P(N2). The probabilities of equal sums N1 + N2 and nj(t + 1) > or = Nmax are added. The number of survived parents N1 may range from 0 to (1-PI) x ni(t). The survival probabilities can be estimated for each N1 as [formula: see text] The number of survived posterities N2 may range from 0 to N2max (the maximum number of posterities). N2max is [formula: see text] and the survival probabilities for each N2, is defined as [formula: see text] where [formula: see text], ni(t) is the initial population size (including of males and infected specimens of host), PI is the prevalence of infection, Q1 is the survival probabilities of parents, Pfemales is the frequency of females in the host population, K is the number of posterities per a female, and Q2 is the survival probabilities of posterities. When constructing matrix of transition probabilities of Markov process (pi), the procedure outlined above should be repeated for all possible initial population size. Matrix of transition probabilities for T generations is defined as pi T. This matrix (pi T) embodies all possible transition probabilities from the initial population sizes to the final population sizes and contains a wealth of information by itself. From the practical point of view, however, the plots of the probability of population size decrease are more suitable for analysis. They can be received by summing the probabilities within of lines of matrix from 0 to ni--1 (ni--the population size, which corresponds to the line of the matrix). Offered parameter has the number of advantages. Firstly, it is independent on a view of researcher. Secondly, it has a clear biological sense--this is a limit of prevalence, which is safe for host population. Thirdly, only available parameters are used in the calculation of parasite capacity: population size, sex ratio, fecundity, mortality. Lastly, with the availability of modern computers calculations do not make large labour. Drawbacks of this parameter: 1. The assumption that prevalence of infection, mortality, fecundity and sex ratio are constant in time (the situations are possible when the variability of this parameters can not be neglected); 2. The term "maximum population size" has no clear biological sense; 3. Objective restrictions exist for applications of this mathematical approach for populations with size, which exceeds 1000 specimens (huge quantity of computing operations--order Nmax 3*(T-1), work with very low probabilities). The further evolution of the proposed approach will allow to transfer from the probabilities of size changes of individual populations to be probabilities of size changes of population systems under the influence of parasites. This approach can be used at the epidemiology and in the conservation biology.

Animals↗

PubMed2001

Rich dynamics of a ratio-dependent one-prey two-predators model.

The objective of this paper is to systematically study the qualitative properties of a ratio-dependent one-prey two-predator model. We show that the dynamics outcome of the interactions are very sensitive to parameter values and initial data. Specifically, we show the interactions can lead to all the following possible outcomes: 1). competitive exclusion; 2). total extinction, i.e., collapse of the whole system; 3). coexistence in the form of positive steady state; 4). coexistence in the form of oscillatory solutions; and 5). introducing a friendly and better competitor can save a otherwise doomed prey species. These results reveal far richer dynamics compared to similar prey dependent models. Biological implications of these results are discussed.

Animals↗

PubMed1989

Spectrophotometric and high-performance chromatographic assays of hydroperoxides by the iodometric technique.

Samples containing between 1 and 50 nmol of hydroperoxides in oxygen-free methanol-acetic acid containing I- were incubated at 50 degrees C. This ensured reduction of all hydroperoxides tested in 15 min. Addition of sufficient Cd acetate to combine with the remaining I- allowed reading of absorbance of the I3- produced in open cuvettes. The absorbance was stable for several hours. It had a maximum at 358 nm with molar extinction coefficient of 2.97 X 10(4) 1 mol-1 cm-1. Sensitivity of the assay could be improved by injecting the I3- into a C-18 HPLC column eluted with methanol-water-acetic acid solution. Both methods are potentially suitable for assay of hydroperoxides in a wide range of biological materials.

Acetates↗

PubMed1981

Self-sustaining multiplication and reproduction of microsystems in protobiogenesis.

The appearance of reproducing microsystems during stimulated protobiogenesis is investigated theoretically, based upon the observation that proteinoid microsystems, which are local aggregates of reacting chemicals, act as reaction nodes. Further splitting of such nodes follows if sufficient growth takes place. Parent-connected daughter nodes thus appear. A parent-connected daughter node rejuvenates itself while its parent node survives, although an extinction of the latter is inevitable in the presence of spontaneous disturbances. The degree of rejuvenation is measured in terms of the molecule intake and dissociation rates at the node. A daughter node grows and matures after the extinction of its parent, and gives rise to second-generation nodes when it grows sufficiently large. The parent node alternates with its parent-connected daughter nodes successively.

Mathematics↗